Academic literature on the topic 'No mutation identified'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'No mutation identified.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Journal articles on the topic "No mutation identified"
1
Hutton, Michael. "?Missing? tau mutation identified." Annals of Neurology 47, no. 4 (April 2000): 417–18. http://dx.doi.org/10.1002/1531-8249(200004)47:4<417::aid-ana1>3.0.co;2-b.
Full text
2
Pawlik, Timothy M., Darrell R. Borger, Yuhree Kim, David Cosgrove, Sorin Alexandrescu, Ryan Thomas Groeschl, Vikram Deshpande, et al. "Genomic profiling of intrahepatic cholangiocarcinoma: Refining prognostic determinants and identifying therapeutic targets." Journal of Clinical Oncology 32, no. 3_suppl (January 20, 2014): 210. http://dx.doi.org/10.1200/jco.2014.32.3_suppl.210.
Full textAbstract:
210 Background: The molecular alterations that drive tumorigenesis in intrahepatic cholangiocarcinoma (ICC) remain poorly defined. We sought to define the incidence and prognostic significance of mutations associated with ICC among patients undergoing surgical resection. Methods: 138 patients who underwent resection at 6 centers in the United States and Europe were included in the cohort. Mutational profiling was performed using nucleic acids that were extracted from resected ICC tumor specimens; mutations were identified using a multiplexed mutational profiling platform. The frequency of mutations was ascertained and the impact on outcome determined. Results: Most patients had a solitary tumor (82%) and median tumor size was 6.0cm. Most patients had R0 resection (89%); 19% patients had N1 disease, while 15% had microscopic vascular invasion. A minority received adjuvant therapy (30%). The majority (55%) of patients had no genetic mutation identified. Among the 62 (45%) patients with a genetic mutation, only a small number of gene mutations were identified with a frequency of >5%: IDH1 (17.4%), KRAS (8.7%), BRAF (5.8%), PIK3CA (5.1%). In contrast, other genetic mutations were identified in very low frequency: IDH2 (3.6%), NRAS (3.6%), TP53 (2.2%), MAP2K1 (1.5%), CTNNB1 (0.7%), and PTEN (0.7%). Approximately 7% of IDH1-mutant tumors were associated with a concurrent PIK3CA gene mutation, and to a much lower extent, a mutation in MAP2K1 (2%). No concurrent mutations in IDH1 and KRAS were noted. Compared with ICC tumors that had no identified mutation, IDH1-mutant tumors were more often bilateral (OR 3.46), while KRAS-mutant tumors were more likely to be associated with perineural invasion (OR 5.72)(both P<0.05). While clinicopathological features such as tumor number and nodal status were associated with survival, no specific mutation was associated with prognosis. Conclusions: Most patients with resected ICC had no somatic mutation identified on multiplexed mutational profiling. IDH1 and KRAS were the most common mutations noted. While certain mutations were associated with ICC clinicopathological features, mutational status did not seemingly impact long-term prognosis.
3
Dutta, Ravi Kumar, Thomas Arnesen, Anette Heie, Martin Walz, Piero Alesina, Peter Söderkvist, and Oliver Gimm. "A somatic mutation in CLCN2 identified in a sporadic aldosterone-producing adenoma." European Journal of Endocrinology 181, no. 5 (November 2019): K37—K41. http://dx.doi.org/10.1530/eje-19-0377.
Full textAbstract:
Objective To screen for CLCN2 mutations in apparently sporadic cases of aldosterone-producing adenomas (APAs). Description Recently, CLCN2, encoding for the voltage-gated chloride channel protein 2 (ClC-2), was identified to be mutated in familial hyperaldosteronism II (FH II). So far, somatic mutations in CLCN2 have not been reported in sporadic cases of APAs. We screened 80 apparently sporadic APAs for mutations in CLCN2. One somatic mutation was identified at p.Gly24Asp in CLCN2. The male patient had a small adenoma in size but high aldosterone levels preoperatively. Postoperatively, the patient had normal aldosterone levels and was clinically cured. Conclusion In this study, we identified a CLCN2 mutation in a sporadic APA comprising about 1% of all APAs investigated. This mutation was complementary to mutations in other susceptibility genes for sporadic APAs and may thus be a driving mutation in APA formation.
4
Lowstuter, Katrina, Carin R. Espenschied, Duveen Sturgeon, Charité Ricker, Rachid Karam, Holly LaDuca, Julie O. Culver, et al. "Unexpected CDH1 Mutations Identified on Multigene Panels Pose Clinical Management Challenges." JCO Precision Oncology, no. 1 (November 2017): 1–12. http://dx.doi.org/10.1200/po.16.00021.
Full textAbstract:
Purpose Mutations in the CDH1 gene confer up to an 80% lifetime risk of diffuse gastric cancer and up to a 60% lifetime risk of lobular breast cancer. Testing for CDH1 mutations is recommended for individuals who meet the International Gastric Cancer Linkage Consortium (IGCLC) guidelines. However, the interpretation of unexpected CDH1 mutations identified in patients who do not meet IGCLC criteria or do not have phenotypes suggestive of hereditary diffuse gastric cancer is clinically challenging. This study aims to describe phenotypes of CDH1 mutation carriers identified through multigene panel testing (MGPT) and to offer informed recommendations for medical management. Patients and Methods This cross-sectional prevalence study included all patients who underwent MGPT between March 2012 and September 2014 from a commercial laboratory (n = 26,936) and an academic medical center cancer genetics clinic (n = 318) to estimate CDH1 mutation prevalence and associated clinical phenotypes. CDH1 mutation carriers were classified as IGCLC positive (met criteria), IGCLC partial phenotype, and IGCLC negative. Results In the laboratory cohort, 16 (0.06%) of 26,936 patients were identified as having a pathogenic CDH1 mutation. In the clinic cohort, four (1.26%) of 318 had a pathogenic CDH1 mutation. Overall, 65% of mutation carriers did not meet the revised testing criteria published in 2015. All three CDH1 mutation carriers who had risk-reducing gastrectomy had pathologic evidence of diffuse gastric cancer despite not having met IGCLC criteria. Conclusion The majority of CDH1 mutations identified on MGPT are unexpected and found in individuals who do not fit the accepted diagnostic testing criteria. These test results alter the medical management of CDH1-positive patients and families and provide opportunities for early detection and risk reduction.
5
Zhu, Xiaoqiong, Xingnong Ye, Chen DAN, and Jian Huang. "Uncommon Hpgd Mutation Identified in Familial Erythrocytosis." Blood 138, Supplement 1 (November 5, 2021): 4627. http://dx.doi.org/10.1182/blood-2021-145881.
Full textAbstract:
Abstract Familial erythrocytosis (congenital erythrocytosis, FE), is a rare congenital disorder defined by elevated hemoglobin and hematocrit, with different genetic background. Clinically, FE is difficult to distinguish from polycythemia vera（PV）. A 53-years-old male was diagnosed with polycythemia vera without discovery of the JAK2 mutation when he was 31-years-old. The patient's family history revealed his father， a 86-years-old male， also suffered polycythemia for more than 20 years. The pedigree of the Chinese family with erythrocytosis is shown in Figure 1a. The index patient was a 53-years-old male (patient Ⅱ-1, Fig.1), who was hospitalized in our department in 2019 with a 22-year history of elevated red cell mass (RCM). When he was 31-years-old, he initially diagnosed with polycythemia vera without discovery of the JAK2 mutation. Over the last two decades he had irregular phlebotomy almost every two years and seldom prescribed any cytoreductive treatment. At our department he accepted 2 venesections because of Hct level of 64%. Upon medical history taking he reported that his father had suffered by polycythemia with more than 20 years, and were undergoing occasional phlebotomies.The father of the index patient was a 86-years-old male (patient Ⅰ-1, Fig.1), who was diagnosed with polycythemia for more than 20 years and suffered from diabetes. Similar to his son, he did not use any cytoreductive agent, and he had been phlebotomized occasionally. He was chronically treated with low-dose of aspirin . In our department he was treated with erythrocyte separation because of Hct level of 58.9%. He did not report any thrombembolic event. For the last one year of follow-up, the patient continued taking aspirin and her Hct level fluctuated between 54% and 57% while rejected to receive erythrocyte separation again.The elder sister (subject Ⅱ-2 Fig.1) of the index patient did not have any clinical and laboratory signs of elevated RCM as of January 2019, she was a 57-years-old female, who suffered from hypertension and diabetes.The daughter (subject Ⅲ-1 Fig.1) and the nephew (subject Ⅲ-2 Fig.1) of the index patient also did not have any clinical and laboratory signs of elevated RCM as of January 2019. They were subjected to whole exome sequencing (WES), the results revealed four mutations in all three of them, among, a frameshift mutation in the 15-hydroxyprostaglandin dehydrogenase（HPGD） gene is contained in both father and son, which at position c.310_311 ,translating into c.310_311delCT nucleotide mutation and p.L104Afs*3 amino acid mutation. In order to verify the mutation, we adopt the method of Sanger sequencing, then confirmed the presence of the same HPGD frameshift mutation in the index patient and his father. However, The mutation was absent in the elder sister of the index patient, when she was examined by WES and Sanger sequence. The ARHGAP26 mutation is contained in all three of them, but is a type of somatic mutation. The two mutations of VHL and FANCD2 are inexistent in the index patient, but are contained in his father and his elder sister. In conclusion, here we reported the first extensive genetic and clinical study of a family with two members carrying the HPGD gene frameshift mutation. Although functional studies were not made to confirm the pathogenic role of this mutation, the type and location of the mutation suggest that it can be the cause of the erythrocytosis observed in two patients. This study demonstrated the utility of the WES/NGS as the tool for identification of mutations in congenital erythrocytosis as well as helps to discovery these rare erythrocytosis-associated genes. The role and pathogenesis in haematopathy of HPGD mutation has been seriously underestimated, which is deserved to be explored in depth. Acknowledgment:The research was supported by the Public Technology Application Research Program of Zhejiang, China (LGF21H080003), the Key Project of Jinhua Science and Technology Plan, China (2020XG-29 and 2020-3-011), the Academician Workstation of the Fourth Affiliated Hospital of the Zhejiang University School of Medicine (2019-2024), the Key Medical Discipline of Yiwu, China (Hematology, 2018-2020) and the Key Medical Discipline of Jinhua, China (Hematology, 2019-2021). Correspondence to: Dr Jian Huang, Department of Hematology, The Fourth Affiliated Hospital of Zhejiang University School of Medicine. N1 Shangcheng Road. Yiwu, Zhejiang, Peoples R China. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.
6
Bradbury, Jane. "Canine epilepsy gene mutation identified." Lancet Neurology 4, no. 3 (March 2005): 143. http://dx.doi.org/10.1016/s1474-4422(05)01004-5.
Full text
7
BRADBURY, J. "Canine epilepsy gene mutation identified." Lancet Neurology 4, no. 3 (March 2005): 143. http://dx.doi.org/10.1016/s1474-4422(05)70010-7.
Full text
8
Shi, Zhongxun, Bing Li, Tiejun Qin, Zefeng Xu, Lijuan Pan, Shiqiang Qu, Gang Huang, and Zhijian Xiao. "Clonal Architecture Analysis of TET2 Identified Distinct Origins in Myelodysplastic Syndromes." Blood 136, Supplement 1 (November 5, 2020): 18. http://dx.doi.org/10.1182/blood-2020-139329.
Full textAbstract:
Next-generation sequencing (NGS) has deepened our understanding of myelodysplastic syndromes (MDS). Genetic mutations of TET2 were common in MDS and were also detected in asymptomatic elder persons, which were defined as aged related clonal haematopoiesis (ARCH) and considered as a myelodysplastic syndrome precursor state. In this study, we analyzed the mutation profiles of TET2 in 770 newly-diagnosed MDS subjects. 73 mutations were found in 67 of 770(8.7%) subjects. 14.9% were frame shifts, 29.9% were nonsense, 44.8% were missense and 10.7% harbored 2 TET2 mutations. TET2MT subjects were older than TET2WT subjects (P=0.024) and the variant allele frequency (VAF) of TET2 was positively correlated with age (r=0.318, P=0.009). Clonal architecture was determined using a copy number-adjusted VAF difference between 2 mutation events in 49 TET2MT subjects with 2 or more mutations. 19 (38.3%) were TET2ancestral and 30(61.2%) were TET2subclonal. TET2ancestral subjects were significantly older than TET2WT subjects (P=0.013) while no difference was found between TET2subclonal subjects and TET2WT subjects (P=0.509). The frequency of cytosine-to-thymine (C→T) transition was significantly higher in TET2ancestralsubjects compared with TET2subclonal subjects (P=0.029), which was considered to be a somatic mutational signature of aging, indicating that MDS driven by TET2ancestral was likely derived from TET2MT ARCH. The most common upstream mutations in TET2subclonal subjects were U2AF1 (16.7%) and ASXL1 (13.3%), and the most common downstream mutations in TET2ancestral subjects were ASXL1 (21.1%) and RUNX1 (15.8%). TET2 mutations rarely existed alone in TET2ancestral subjects (14.3%) and were always accompanied by another mutations like U2AF1, SF3B1 and ASXL1, suggesting that the acquisition of another mutation led to the progress of ARCH to MDS in TET2ancestral subjects. TET2MT had no impact on survivals in overall cohort (P=0.218) while predicted poorer survivals in IPSS-R lower risk group (P=0.004). Additional ASXL1, U2AF1 and RUNX1 mutations in TET2MT subjects indicated poorer prognosis compared with TET2WT subjects (P=0.005; P=0.04; P<0.001) .There was no significant difference in OS of TET2MT subjects with different clonal architecture (P=0.76). Subjects with TET2 VAF≥30% had poorer survivals compared with TET2WT subjects (P=0.057). In conclusion, TET2MT MDS subjects with different clonal architectures may have different origins. TET2ancestral subjects may be derived from ARCH and progressed to MDS after secondary hits. The effects of TET2 mutation on the prognosis depended on the accompanying mutations and clonal burdens. Disclosures No relevant conflicts of interest to declare.
9
Claes, Kathleen, Eva Machackova, Michel De Vos, Bruce Poppe, Anne De Paepe, and Ludwine Messiaen. "Mutation Analysis of the BRCA1 and BRCA2 Genes in the Belgian Patient Population and Identification of a Belgian Founder Mutation BRCA1 IVS5+3A>G." Disease Markers 15, no. 1-3 (1999): 69–73. http://dx.doi.org/10.1155/1999/241046.
Full textAbstract:
Since the identification of the BRCA1 and BRCA2 genes, several hundred different germline mutations in both genes have been reported. Recurrent mutations are rare and mainly due to founder effects. As the mutational spectrum of the BRCA1 and BRCA2 genes in the Belgian patient population is largely unknown, we initiated mutation analysis for the complete coding sequence of both genes in Belgian families with multiple breast and/or ovarian cancer patients and in “sporadic” patients with early onset disease. We completed the analysis in 49 families and in 19 “sporadic” female patients with early onset breast and/or ovarian cancer. In 15 families we identified a mutation (12 mutations in BRCA1 and 3 mutations in BRCA2). In 5 apparently unrelated families the same splice site mutation was identified (BRCA1 IVS5+3A>G). Haplotype analysis revealed a common haplotype immediately flanking the mutation in all families suggesting that disease alleles are identical by descent. In none of the 19 sporadic patients was a mutation found.
10
Percy, Melanie J., F. G. C. Jones, T. R. J. Lappin, and M. F. McMullin. "Mutations in the VHL Gene Are the Major Identified Cause of Inherited Erythrocytosis." Blood 106, no. 11 (November 16, 2005): 569. http://dx.doi.org/10.1182/blood.v106.11.569.569.
Full textAbstract:
Abstract The molecular basis of inherited erythrocytosis in most patients remains to be defined. Although all such patients have an absolute increase in red cell mass, their erythropoietin (EPO) levels differ widely, so they constitute a heterogeneous group of disorders known collectively as idiopathic erythrocytosis (IE). A proportion of individuals with IE progress to polycythemia vera (PV), a clonal disorder arising from a multipotent progenitor. Recently a gain-of-function mutation in Janus kinase 2 (JAK2), V617F, has been described in myeloproliferative disorders (MPD) and a stream of publications has confirmed its presence in the majority of patients with PV. Screening IE patients for this mutation will provide a useful additional means for delineating inherited and clonal disorders of erythrocytosis. Over the last decade we have maintained a registry of British and Irish erythrocytosis patients, consisting of clinical information and DNA samples obtained following full ethical approval. Screening the EPO receptor (EPO-R) in 120 patients identified one patient with a G6002A mutation, which leads to truncation of the receptor by 70 amino acids, increased sensitivity to EPO, and erythrocytosis. Screening the same patients for mutations in the von Hippel Lindau (VHL) gene has revealed individuals from 8 families of Asian origin who are homozygous for the Chuvash (R200W) mutation causing erythrocytosis. In addition, one Caucasian individual of English descent is compound heterozygous for R200W and the recently described G144R VHL mutation. A further individual, D1 (Percy et al, 2003Blood102:1097), of the same ethnicity is heterozygous for the Chuvash mutation and has been found to express the wild type allele. Both his mother and son, who are heterozygous for the Chuvash mutation, do not have IE, suggesting that the patient harbors a second unidentified genetic defect. Several such individuals have already been described (reviewed by Randi et al, 2005 Haematologica 90:689). In order to estimate the proportion of IE patients likely to progress to PV, 65 individuals from the registry with EPO levels in the low to normal range were screened by amplification refractory mutation system (ARMS) PCR for the MPD-associated V617F JAK2 mutation. Two individuals were positive, one of whom subsequently proceeded rapidly to PV, while the other has remained stable without any disease progression. In addition 9 families with VHL mutations were also screened and all were found to be negative for the JAK2 mutation, suggesting that the occurrence of these mutations tends to be mutually exclusive. Also the V617F JAK2 mutation does not constitute the second genetic defect in patient D1 who is heterozygous for the Chuvash VHL mutation. Although VHL mutations are the most frequent cause of inherited erythrocytosis in our registry they are present in only ~10% of patients, while the gain-of-function of JAK2 mutation is rare, leaving ~90% of the IE cases unexplained. Further study of this group may reveal additional regulatory mechanisms involved in red cell homeostasis.
Dissertations / Theses on the topic "No mutation identified"
1
Kozusko, Kristina. "Molecular mechanisms of Perilipin-1 action : characterisation of a novel PLIN1 mutation identified in patients with familial partial lipodystrophy." Thesis, University of Cambridge, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.709005.
Full text
2
Chen, Tao [Verfasser]. "Identification and functional characterization of a de novo point mutation identified in a patient with non-syndromal microcephaly and intellectual disability / Tao Chen." Berlin : Freie Universität Berlin, 2016. http://d-nb.info/1108270913/34.
Full text
3
PERON, ANGELA. "TUBEROUS SCLEROSIS COMPLEX: IDENTIFICATION OF THE GENETIC CAUSE IN PATIENTS WITH NO MUTATION DETECTED, AND ANALYSIS OF MOSAICISM." Doctoral thesis, Università degli Studi di Milano, 2021. http://hdl.handle.net/2434/885842.
Full textAbstract:
Tuberous sclerosis complex (TSC) is an autosomal dominant multisystem disorder characterized by development of hamartomas, intellectual disability, seizures and autism. TSC is caused by inactivating mutations in either the TSC1 or the TSC2 genes. A pathogenic variant is not identified in up to 10% of the patients with a clinical diagnosis of TSC despite full molecular assessment. These individuals are referred to as NMI (No Mutation Identified), and it is not clear if they should be monitored and/or treated in similar fashion to those with known etiology of TSC.
To identify the genetic cause of TSC in these patients, we selected ten individuals with a definite clinical diagnosis of TSC and NMI and performed a pilot study. Three different technologies were used and their results were compared: chromosomal microarray, trio whole genome sequencing, and targeted deep-coverage next generation sequencing of TSC1 and TSC2. We identified mosaic variants in TSC1/TSC2 in six patients. No variants in other genes were detected in the remaining individuals.
Based on the results of the pilot study and on recent literature, we then performed targeted deep-coverage TSC1/TSC2 sequencing on 200 affected individuals using peripheral blood DNA and saliva or other tissue samples where available. We identified 24 patients with mosaic pathogenic variants in TSC1 (n=2) or TSC2 (n=22), defining a rate of mosaicism of 12%. Mosaic variant allele frequency (VAF) ranged from 2% to 32% in blood and from 2% to 35% in saliva. Most affected individuals had low-level mosaicism (VAF ≤10%). We performed an extensive analysis of the phenotype, and show that individuals with a mosaic variant in TSC1/TSC2 often display normal cognitive functioning, although other TSC-associated neuropsychiatric disorders (TAND) are seen in 62% of the patients. Cortical tubers are invariably present and seizures are diagnosed in 54% of the cohort, but infantile spasms are rare. The number of cutaneous manifestations in these patients is often insufficient to meet diagnostic criteria, except for facial angiofibromas. We observed a high frequency of pulmonary and renal manifestations in our mosaic cohort, which are as severe as those seen in the general TSC population. None of the patients who have reproduced transmitted the variant to their offspring.
In conclusion, our study shows that genome sequencing fails to identify rare variants in new genes related to TSC, and a third gene is therefore unlikely to exist. We demonstrated that at least one out of 10 patients with a clinical diagnosis of TSC carries a mosaic pathogenic variant in TSC1 or TSC2. We also showed that individuals with mosaic variants have a distinctive phenotypic severity, with important implications for surveillance.
4
Li, Jia. "Identifier les variations conduisant au cancer dans le génome non codant et du transcriptome." Thesis, Université Paris-Saclay (ComUE), 2015. http://www.theses.fr/2015SACLS161/document.
Full textAbstract:
L'annotation fonctionnelle de mutations somatiques est un point focal des études de génomique du cancer. Jusque récemment, la recherche s'est concentré sur des mutations dans la fraction codante du génome, pour lesquelles de puissants outils bioinformatiques ont été développés afin de distinguer des mutations délétères des mutations neutres. On identifie un nombre croissant de variants associés à des maladies dans le génome non-codant. L'interprétation des mutations non-codantes dans le cancer est donc devenue une tâche urgente. Des projets de grande envergure tels que ENCODE ont rendu possible l'interprétation fonctionnelle de variants dans les cancers. Plusieurs programmes ont été produits sur la base de ces informations fonctionnelles. Ces outilssont encore limités, notamment, une bas précision de la prédiction, le manque d'information de la mutation de cancer et biais de constatation importante. Dans le chapitre 2 de cette thèse, pour interpréter fonctionnellement les mutations non-codantes dans les cancers, nous avons développé deux modèles de forêts aléatoires indépendants, appelées SNP et SOM. Compte tenu de la combinaison de caractéristiques fonctionnelles à une position donnée du génome, le modèle SNP prédit la fraction de SNP rares (une mesure de la sélection négative), et le modèle SOM prédit la densité de mutations somatiques attendue à cette position. Nous avons appliqué nos deux modèles pour évaluer des clinvariant and HGMD variants asociés à des maladies, et un ensemble de SNP-contrôle aléatoires. Les résultats ont montré que les variants associés à des maladies ont des scores plus élevés que les SNP-contrôle avec le modèle SNP et inférieures avec le modèle SOM, confortant notre hypothèse selon laquelle la sélection négative, telle que mesurée par fraction de SNP rares et de densité de mutation somatiques, nous informe sur l'impact fonctionnel des mutations tumorales dans le génome non-codant. Jusqu'à présent, les chercheurs ont surtout considéré les gènes protéiques comme critiques dans l'initiation et la progression des cancers. Toutefois, des preuves récentes ont montré que les ARN non-codants, en particulier les lncRNAs, sont activement impliqués dans divers processus de cancer. Un chapitre de cette thèse est consacré à cette classe de transcripts non codants. Comme pour les gènes codants, il pourrait exister un grand nombre de lncRNAs driver de cancer. Le développement d'outils bioinformatiques pour identifier et hiérarchiser les lncRNA et autres ARN non-codants est devenu un important objet de recherche en oncologie.La dernière partie de cette thèse est consacrée à la mise en œuvre de méthodes pour découvrir des éléments non-codants potentiellement driver de cancer. Nous avons d'abord appliqué trois outils tierces, CADD, funSeq2, GWAVA, ainsi que nos modèles SNP et SOM, pour évaluer l'impact des mutations non-codantes dans tout le génome. Pour chaque locus, nous calculons la moyenne des scores de tous les variants observés à l'aide de l'un des modèles, et nous prenons au hasard le même nombre de variants et calculons leur score moyen 1 million de fois pour former une distribution nulle et obtenir une P-valeur pour ce locus. Pour valider notre hypothèse et notre modèle de permutation, nous avons testé ce système sur 452 gènes codants et 61 lncRNA liés au cancer, en utilisant des données de mutation somatique de cancer du foie, cancer du poumon, CLL et mélanome. Nous avons constaté que les lncRNAs et gènes codants associés au cancer avaient des valeurs-P significativement plus faibles que l'ensemble de lncRNAs et gènes codant. Appliquer ce test de permutation à des lncRNAs avec cinq systèmes de notation différents nous a permis de prioriser les centaines de candidats potentiellement liés au cancer.Ces candidats peuvent maintenant être soumis à validation expérimentaleFunctional annotation of somatic mutations have been a consistent hotspot of cancer genomics studies. In the past, researchers preferentially focused on mutations in the coding fraction of the genome, for which ample bioinformatics tools were developed to distinguish cancer-driver mutations from neutral ones. In recent years, as an increasing number of variants were being identified as disease-associated in the non-coding genome, interpreting non-coding cancer mutations has become an urgent task. The completion of large scale projects such as ENCODE, has made functional interpretation of cancer variants achievable, and several programs were produced based on this functional information. However, there still exists some limitations as to these prediction tools, such as low prediction accuracy, lack of cancer mutation information and significant ascertainment bias. In chapter 2 of this thesis, in order to functionally interpret non-coding mutations in cancer, we developed two independent random forest models, referred to as SNP and SOM. Given a combination of features at a given genome positions, the SNP model predicts the expected fraction of rare SNPs (a measure of negative selection), and the SOM model predicts the expected mutation density at this position. We applied our two models to score these non-coding disease-associated clinvariant and HGMD variants and a set of random control SNPs. Results showed that disease-associated variants were scored higher than control SNPs with the SNP model and lower than control SNPs with the SOM model, supporting our hypothesis that purifying selection as measured by fraction of rare SNPs and mutation density is informative for the evaluation of the functional impact of cancer mutations in the non-coding genome. In the past, researchers have preferentially considered protein-coding genes as critical to the initiation and progression of cancers. However, recent evidences have shown that ncRNAs, in particular lncRNAs, are actively implicated in various cancer processes. A chapter of this thesis is devoted to this class of non-coding transcripts. Similar to protein coding genes, there might be a large number of lncRNAs with cancer-driving functions. The development of bioinformatics tools to prioritize them has become a new focus of research for computational oncologists.The last part of this thesis is devoted to the implementation of methods for discovering potential cancer-driving non-coding elements in lncRNA and protein-coding genes. We applied three scoring tools, CADD, funSeq2, GWAVA, together with our SNP and SOM scoring systems to prioritize cancer-associated elements using a permutation-based algorithm. For each locus, we compute the average score of all observed variants using one of the models, and we randomly take the same number of variants and compute their average score 1 million times to form a null distribution and obtain a P value for this locus. To validate our hypothesis and permutation model, we tested this system on 61 cancer-related lncRNA and 452 cancer genes using somatic mutation data from liver cancer, lung cancer, CLL and melanoma. We observed that both cancer lncRNAs and protein-coding genes had significantly lower average P values than total lncRNAs and protein-coding genes in all cases. Applying the permutation test to lncRNAs with five different scoring systems enabled us to prioritize hundreds to thousands of cancer-related lncRNA candidates. These candidates can be used for future experimental validation
5
Duff, Jennifer. "Characterisation of androgen receptor mutations identified from prostate cancer patients." Thesis, University of Aberdeen, 2005. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU200888.
Full textAbstract:
Mutations of the AR are implicated as one of the key components in the development of prostate cancer and its poor prognosis to treatment. As prostate cancer is the second leading cause of cancer related death in Caucasian men much interest is currently focused on understanding it mechanisms of development. At present around fifty AR prostate cancer mutations have been reported in the androgen receptor mutation database, most of which have been either incompletely or poorly characterised. This study aims to clarify some of the molecular consequences of specific prostate cancer mutations that have been mapped to the receptor ligand-binding domain (LBD). It was observed that certain mutations such as the T877A and H874Y mutations were altered in ligand responsiveness to non-androgen ligands as has been previously reported, and that the Q798E mutation was also activated to some extent with progesterone. Other mutations such as D879G and V757A appeared to have a reduced transactivation response when stimulated by androgens in cell culture experiments. Gross experimental analysis of the mutant protein structures revealed that there were no major changes in the conformation of any of the proteins compared to wildtype. While modelling analysis of the ligand binding domain DHT bound crystal structure using the Swissprot Deepview programme revealed that several of the mutations resulted in more minor structural alterations such as altered H bonding or steric clashes. Finally several mutant proteins were revealed to have an altered interaction with p160 co-activator proteins in vitro. Most significant of these were the H874Y and the K720E AR mutants, which were also shown to be enhanced to a greater extent by the presence of certain co-activators in in vivo cell culture experiments.
6
Dempsey, Nunez Laura. "Spectrum of mutations in MMAA identified by high resolution melting analysis." Thesis, McGill University, 2012. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=110535.
Full textAbstract:
The gene product of MMAA is required for the intracellular metabolism of cobalamin (Cbl). Mutations in this gene lead to the cblA class of disorders, characterized by isolated methylmalonic aciduria. We have been concerned that somatic cell methods of diagnosis may miss patients with mild cellular phenotypes. A high resolution melting (HRM) analysis assay was developed to rapidly scan the coding exons and flanking intronic regions of the MMAA genes for variants. DNA from 96 unaffected reference individuals, 72 patients with complementation confirmed cblA, and 181 patients with elevated isolated methylmalonic acid, who could not be diagnosed using complementation analysis, were scanned by HRM. Suspected variants were confirmed using Sanger sequencing. In the cblA cohort, HRM correctly identified all previously known mutations as well as an additional 22 variants, 10 of which had not been previously reported. Novel variants included one duplication (C.551dupG, p.C187LfsX3), one deletion (c.387delC, p.Y129YfsX13), one splice site mutation (c.440-2A>G, splice site), 4 missense mutations (c.748G>A, p.E520K; c.820G>A, p.G274S; c.627G>T, p.R209S; c.826A>G, p.K276E), and 3 nonsense mutations (c.960G>A, p.W320X; c.1075C>T, p.E359X; c.1084C>T, p.Q362X). All novel missense variants, listed above, affect highly conserved residues and are predicted to be damaging. Scanning of MMAA in the 181 undiagnosed samples revealed a single novel heterozygous missense change (c.821G>A, p.G274D).Le produit génique du MMAA est nécessaire pour le métabolisme de la cobalamine intracellulaire (Cbl). Des mutations dans ce gène conduisent à la classe de maladies cblA, caractérisé par l'acidurie méthylmalonique isolée. Nous avons été concernés que les méthodes de diagnostic de cellules somatiques peuvent manquer les patients atteints phénotypes cellulaires moins sévère. Une teste de fusion à haute résolution a été développé pour balayer rapidement les exons codantes et les régions introniques adjacentes du gène MMAA pour des variantes. Nous avons testé l'ADN à partir de 96 personnes de référence qui ne sont pas touchés, 72 patients atteints de cblA confirmé par complémentation et 181 patients présentant une élévation de l'acide méthylmalonique isolée, qui ne pouvaient pas être diagnostiquée à l'aide d'analyse de complémentation. Les variantes suspectes ont été confirmées à l'aide de séquençage Sanger. Dans la cohorte cblA, l'analyse de fusion à haute résolution a correctement identifié toutes les mutations connues antérieurement, ainsi que 22 autres variantes, dont 10 n'avaient pas été signalés précédemment. Nouveaux variantes inclus une duplication (C.551dupG, p.C187LfsX3), une délétion (c.387delC, p.Y129YfsX13), une mutation du site d'épissage (c.440-2A> G, site d'épissage), 4 mutations faux-sens (c. 748G> A, p.E520K; c.820G> A, p.G274S; c.627G> T, p.R209S; c.826A> G, p.K276E), et 3 mutations non-sens (c.960G> A, p.W320X; c.1075C> T, p.E359X; c.1084C> T, p.Q362X). Toutes les variantes faux-sens nouveaux, énumérés ci-dessus, affectent des résidus hautement conservés et sont prévus pour être endommageant. L'analyse de MMAA dans les 181 échantillons non diagnostiqués a révélé un seul changement faux-sens hétérozygote (c.821G> A, p.G274D).
7
Illson, Margaret. "Spectrum of mutations in MMAB identified by high resolution melting analysis." Thesis, McGill University, 2012. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=110564.
Full textAbstract:
Pathogenic variants in the MMAB gene (OMIM 607958) are responsible for the cblB class of cobalamin-responsive methylmalonic aciduria (MMA) (OMIM 251110). MMAB encodes cobalamin adenosyltransferase, a mitochondrial enzyme responsible for the formation of adenosylcobalamin (AdoCbl). AdoCbl subsequently functions as a cofactor for methylmalonyl-CoA mutase (MCM) during the isomerization of L-methylmalonyl-CoA to succinyl-CoA. Somatic cells studies have been used to evaluate patient samples for cobalamin related disorders. Due to high basal levels of propionate incorporation, some patients with mild MMA biochemical phenotypes cannot be diagnosed by complementation analysis. A high resolution melting analysis (HRMA) assay was developed to rapidly scan the coding exons and flanking intronic regions for variants in the MMAB gene.Three cohorts of samples were scanned by HRMA: an unaffected reference population, 42 samples assigned to the cblB by complementation analysis and 181 patients with unresolved isolated MMA. HRMA correctly identified all of the previously reported mutations in the cblB cohort as well as seven additional variants including a novel nonsense variant (c.12C>A, p.C4X). Scanning of the unresolved MMA cohort identified six samples containing MMAB variants. Two samples, WG3948 and WG4034, contained compound heterozygous variants. They shared a c.572 G>A (p.R191Q) mutation. WG3948, the index case for this study, was found to have c.398 C>T (p.S133F) as the second mutation, and WG4034, the second patient, contained a novel variant c.394 C>T (p.C132R). Samples from four other affected patients contained a single variant. The c.572 G>A (p. R191Q) was found in both WG3546 and WG4090. WG3759 contained a c.521C>T ( p.S174L) substitution, and WG4029 contained a novel c.185 C>T (p.T62M) substitution. The identification of two patients with compound heterozygous variants in the MMAB gene suggests the existence of an infrequent but distinct atypical cblB phenotype. This subclass is characterized by levels of propionate incorporation and of AdoCbl synthesis within reference ranges, preventing diagnosis by somatic cell studies.Des variantes pathogéniques dans le gène MMAB (OMIM 607958) sont responsables de la classe cblB d'acidurie méthylmalonique (AMM) respondant à la cobalamine (OMIM 251110). MMAB encode cobalamine adénosyltranférase, une enzyme mitochondriale responsable de la formation de l'adénosylcobalamine (AdoCbl). AdoCbl fonctionne par la suite en tant que cofacteur pour méthylmalonyl-CoA mutase (MCM) durant l'isomérisation de L-méthylmalonyl-CoA vers succinyl-CoA. Des analyses sur des cellules somatiques ont été utilisées pour évaluer des échantillons de patients pour des troubles reliés à la cobalamine. En raison de niveaux de base élevés d'incorporation de propionate, certains patients présentant des phénotypes biochimiques bénins d'AMM ne peuvent être diagnostiqués par analyse de complémentation. Une analyse de fusion à haute résolution (AFHR) a été développée pour balayer rapidement les exons codants et les régions introniques avoisinnantes pour des variantes dans le gène MMAB.Trois cohortes d'échantillons ont été balayées par AFHR : une population de référence non-affectée, 42 échantillons assignés au groupe cblB par analyse de complémentation et 181 patients avec une AMM isolée sans diagnostique. L'AFHR a correctement identifié toutes les mutations précédemment rapportées dans la cohorte cblB ainsi que sept variantes additionelles, incluant une nouvelle variante non-sens (c.12C>A, p.C4X). Le balayage de la cohorte avec de l'AMM isolée a identifié six échantillons contenant des variantes dans MMAB. Deux échantillons, WG3948 et WG4034, étaient des porteurs de variantes hétérozygotes composés. Ils partageaient la mutation c.572G>A (p.R191Q). WG3948, le cas index pour cette étude, était porteur du c.398C>T (p.S133F) pour la deuxième mutation et WG4034, le deuxième patient, contenait une nouvel variante c.394C>T (p.C132R). Les échantillons provenant de quatre autres patients atteints contenait une seule variante. Le c.572G>A (p.R191Q) a été trouvé dans WG3546 et WG4090. WG3759 contenait une substitution c.52C>T (p.S174L), et WG4029 contenait une nouvelle substitution c.185C>T (p.T62M).L'identification de deux patients avec des variantes hétérozygotes composées dans le gène MMAB suggère l'existence d'un phénotype rare mais distinct de cblB. Cette sous-classe est charactérisée par des niveaux d'incorporation de propionate et de synthèse d'AdoCbl dans les valeurs normales, empêchant le diagnostique par analyse des cellules somatiques.
8
Mori, Minako. "Pathogenic mutations identified by a multimodality approach in 117 Japanese Fanconi anemia patients." Kyoto University, 2019. http://hdl.handle.net/2433/243302.
Full text
9
Schröder, Michael, Rainer Winnenburg, and Conrad Plake. "Improved mutation tagging with gene identifiers applied to membrane protein stability prediction." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-177379.
Full textAbstract:
Background
The automated retrieval and integration of information about protein point mutations in combination with structure, domain and interaction data from literature and databases promises to be a valuable approach to study structure-function relationships in biomedical data sets.
Results
We developed a rule- and regular expression-based protein point mutation retrieval pipeline for PubMed abstracts, which shows an F-measure of 87% for the mutation retrieval task on a benchmark dataset. In order to link mutations to their proteins, we utilize a named entity recognition algorithm for the identification of gene names co-occurring in the abstract, and establish links based on sequence checks. Vice versa, we could show that gene recognition improved from 77% to 91% F-measure when considering mutation information given in the text. To demonstrate practical relevance, we utilize mutation information from text to evaluate a novel solvation energy based model for the prediction of stabilizing regions in membrane proteins. For five G protein-coupled receptors we identified 35 relevant single mutations and associated phenotypes, of which none had been annotated in the UniProt or PDB database. In 71% reported phenotypes were in compliance with the model predictions, supporting a relation between mutations and stability issues in membrane proteins.
Conclusion
We present a reliable approach for the retrieval of protein mutations from PubMed abstracts for any set of genes or proteins of interest. We further demonstrate how amino acid substitution information from text can be utilized for protein structure stability studies on the basis of a novel energy model.
10
Schröder, Michael, Rainer Winnenburg, and Conrad Plake. "Improved mutation tagging with gene identifiers applied to membrane protein stability prediction." BioMed Central, 2009. https://tud.qucosa.de/id/qucosa%3A28888.
Full textAbstract:
Background
The automated retrieval and integration of information about protein point mutations in combination with structure, domain and interaction data from literature and databases promises to be a valuable approach to study structure-function relationships in biomedical data sets.
Results
We developed a rule- and regular expression-based protein point mutation retrieval pipeline for PubMed abstracts, which shows an F-measure of 87% for the mutation retrieval task on a benchmark dataset. In order to link mutations to their proteins, we utilize a named entity recognition algorithm for the identification of gene names co-occurring in the abstract, and establish links based on sequence checks. Vice versa, we could show that gene recognition improved from 77% to 91% F-measure when considering mutation information given in the text. To demonstrate practical relevance, we utilize mutation information from text to evaluate a novel solvation energy based model for the prediction of stabilizing regions in membrane proteins. For five G protein-coupled receptors we identified 35 relevant single mutations and associated phenotypes, of which none had been annotated in the UniProt or PDB database. In 71% reported phenotypes were in compliance with the model predictions, supporting a relation between mutations and stability issues in membrane proteins.
Conclusion
We present a reliable approach for the retrieval of protein mutations from PubMed abstracts for any set of genes or proteins of interest. We further demonstrate how amino acid substitution information from text can be utilized for protein structure stability studies on the basis of a novel energy model.
Books on the topic "No mutation identified"
1
Miller-Hodges, Eve, and Christopher Mitchell. The patient with Wilms tumour. Edited by Giuseppe Remuzzi. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780199592548.003.0173_update_001.
Full textAbstract:
Wilms tumour is the most common renal tumour in childhood. It is most commonly identified as a large abdominal mass. Treatment by surgical removal and chemotherapy, and radiotherapy in more advanced stages, is curative in most patients. Five year survival is over 90%. Survivors may be at some risk from long term complications including the effects of radiotherapy on the remaining kidney.A small minority of Wilms tumours occur in individuals with an underlying mutation in the WT1 gene. WT1 mutations may also cause developmental abnormalities of the genitourinary system, and renal disease including steroid-resistant nephrotic syndrome / focal segmental glomerulosclerosis.
2
Mammoser, Aaron. Infiltrative Astrocytomas. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0126.
Full textAbstract:
Diffuse astrocytomas are WHO grade II astrocytomas that are distinguished from other WHO grade I and II astrocytomas because they are infiltrative, incurable, and have an intrinsic tendency to undergo malignant transformation to an anaplastic astrocytoma or a secondary glioblastoma. They are most often diagnosed in young adults in their 30s and 40s, and have a genetic profile that is different than primary glioblastoma. Anaplastic astrocytomas frequently arise from diffuse astroctyomas and share many of the same molecular abnormalities but tend to acquire more as they inevitably progress to glioblastoma. Recent studies identified mutations associated with WHO grade II and III tumors that predict a progression to a secondary glioblastoma with a better overall prognosis than primary glioblastoma. WHO grade II and III tumors that do not exhibit this typical mutation pattern often behave more aggressively than their counterparts, with a worse prognosis than higher grade tumors with a more favorable genotype.
3
Syrris, Petros, and Alexandros Protonotarios. Arrhythmogenic right ventricular cardiomyopathy: genetics. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198784906.003.0359.
Full textAbstract:
Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a disorder of the heart muscle which is typically inherited in an autosomal dominant manner. It is believed to be familial in over 50% of cases. A recessive mode of inheritance has also been reported in syndromic cases with cardiocutaneous features. The classic form of the disorder is considered to be ‘a disease of the desmosome’ as pathogenic variants have been identified in five genes encoding key desmosomal proteins: plakoglobin, desmoplakin, plakophilin-2, desmoglein-2, and desmocollin-2. Mutations in these genes account for 30–50% of ARVC cases. A further eight non-desmosomal genes have also been implicated in the pathogenesis of the disorder but only account for rare cases. Studies of patients with ARVC-associated gene mutations have revealed marked genetic heterogeneity and very limited genotype–phenotype correlation. Disease expression often varies significantly amongst individuals carrying the same mutation. It has been proposed that the presence of more than one sequence variant is required to determine overt clinical disease and patients with multiple variants have a more severe phenotype compared to single variant carriers. Identification of a potentially pathogenic variant comprises a major criterion in the diagnosis of ARVC but informative integration of genetic testing into clinical practice remains challenging. Gene testing should be used to identify asymptomatic family members at risk and only aids diagnosis in cases of high suspicion for ARVC, along with other evident features of the disease already present. However, genetic findings should be used with caution in clinical practice and their interpretation must be performed in expert centres.
4
Walsh, Richard A. Parkinson’s Disease or Essential Tremor? Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780190607555.003.0016.
Full textAbstract:
Fragile X-associated tremor ataxia syndrome is a heredodegenerative syndrome that presents in older men as a tremor syndrome with less prominent ataxia and cognitive impairment initially. The underlying genetic cause, a premutation in the FMR1 gene, results in a toxic accumulation of mRNA. The full mutation, a triple-repeat expansion of more than 200 CGG repeats, gives rise to a reduction in FMR1 protein expression and fragile X, a neurodevelopmental disorder that may be identified in successive male generations. The prevalence of carrier status is high in the general population, and it is likely that most movement disorders clinics will have one or more patients with this syndrome, potentially carrying a label of essential tremor.
5
Quain, Angela, and Anne M. Comi. Sturge-Weber Syndrome and Related Cerebrovascular Malformation Syndromes. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0112.
Full textAbstract:
Sturge-Weber syndrome is a rare disorder presenting with a capillary malformation, better known as a port-wine birthmark, on the upper face, glaucoma, and a leptomeningeal angioma. Most children develop seizures and strokes, with variable degrees of neurodevelopmental impairments including hemiparesis, visual field deficits, cognitive deficits, epilepsy, and migraines. In 2013, a somatic activating mutation in GNAQ was identified in the capillary malformations and leptomeningeal angiomas of Sturge-Weber patients. In the diagnosis of Sturge-Weber syndrome, contrast-enhanced imaging is essential to the diagnosis of brain involvement. Functional imaging has demonstrated impaired venous drainage and a role for seizures in exacerbating perfusion deficits. Aggressive seizure management is fundamental to treatment. Some data supports the use of low-dose aspirin to reduce the occurrence of strokelike episodes and seizures.
6
Mammoser, Aaron. Primary and Secondary Glioblastoma. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0127.
Full textAbstract:
Glioblastoma, formerly glioblastoma multiforme, is synonymous with WHO grade IV astrocytoma and is the most commonly diagnosed astrocytoma; it carries with it significant clinical, histologic, and molecular heterogeneity, with subtypes of the tumor and important new mutations associated with it characterized over the previous decade. Gene expression profiling has identified four tumor subgroups associated with specific mutational patterns, age of onset, and prognosis. The discovery of isocitrate dehydrogenase (IDH) mutations has led to further delineation between primary and secondary glioblastoma. Despite promising new investigational treatments, glioblastoma remains an incurable and fatal tumor.
7
Schwartz, Peter J., and Lia Crotti. Monogenic and oligogenic cardiovascular diseases: genetics of arrhythmias—catecholaminergic polymorphic ventricular tachycardia. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198784906.003.0152.
Full textAbstract:
Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a rare inherited disorder associated with syncope and sudden death manifesting in the young during sympathetic activation. The electrocardiogram is normal and the heart is structurally normal. The diagnosis is usually made with an exercise stress test that shows a typical pattern of onset and offset of adrenergically induced ventricular arrhythmias. Molecular screening of RyR2, the major CPVT gene, is recommended whenever the suspicion of CPVT is high. If a disease-causing mutation is identified, cascade screening allows pre-symptomatic diagnosis among family members. All affected subjects should be treated with beta blockers (nadolol or propranolol). Preliminary data support the association of beta blockers with flecainide. After a cardiac arrest, an implantable cardioverter defibrillator (ICD) should be implanted, but it is accompanied by a disquietingly high incidence of adverse effects. After syncope on beta blocker therapy, left cardiac sympathetic denervation is most effective, preserves quality of life, and does not preclude a subsequent ICD implantation.
8
Hall, Andrew, and Shamima Rahman. Mitochondrial diseases and the kidney. Edited by Neil Turner. Oxford University Press, 2015. http://dx.doi.org/10.1093/med/9780199592548.003.0340.
Full textAbstract:
Mitochondrial disease can affect any organ in the body including the kidney. As increasing numbers of patients with mitochondrial disease are either surviving beyond childhood or being diagnosed in adulthood, it is important for all nephrologists to have some understanding of the common renal complications that can occur in these individuals. Mitochondrial proteins are encoded by either mitochondrial or nuclear DNA (mtDNA and nDNA, respectively); therefore, disease causing mutations may be inherited maternally (mtDNA) or autosomally (nDNA), or can arise spontaneously. The commonest renal phenotype in mitochondrial disease is proximal tubulopathy (Fanconi syndrome in the severest cases); however, as all regions of the nephron can be affected, from the glomerulus to the collecting duct, patients may also present with proteinuria, decreased glomerular filtration rate, nephrotic syndrome, water and electrolyte disorders, and renal tubular acidosis. Understanding of the relationship between underlying genotype and clinical phenotype remains incomplete in mitochondrial disease. Proximal tubulopathy typically occurs in children with severe multisystem disease due to mtDNA deletion or mutations in nDNA affecting mitochondrial function. In contrast, glomerular disease (focal segmental glomerulosclerosis) has been reported more commonly in adults, mainly in association with the m.3243A<G point mutation. Co-enzyme Q10 (CoQ10) deficiency has been particularly associated with podocyte dysfunction and nephrotic syndrome in children. Underlying mitochondrial disease should be considered as a potential cause of unexplained renal dysfunction; clinical clues include lack of response to conventional therapy, abnormal mitochondrial morphology on kidney biopsy, involvement of other organs (e.g. diabetes, cardiomyopathy, and deafness) and a maternal family history, although none of these features are specific. The diagnostic approach involves acquiring tissue (typically skeletal muscle) for histological analysis, mtDNA screening and oxidative phosphorylation (OXPHOS) complex function tests. A number of nDNA mutations causing mitochondrial disease have now been identified and can also be screened for if clinically indicated. Management of mitochondrial disease requires a multidisciplinary approach, and treatment is largely supportive as there are currently very few evidence-based interventions. Electrolyte deficiencies should be corrected in patients with urinary wasting due to tubulopathy, and CoQ10 supplementation may be of benefit in individuals with CoQ10 deficiency. Nephrotic syndrome in mitochondrial disease is not typically responsive to steroid therapy. Transplantation has been performed in patients with end-stage kidney disease; however, immunosuppressive agents such as steroids and tacrolimus should be used with care given the high incidence of diabetes in mitochondrial disease.
9
Elliott, Perry, and Alexandros Protonotarios. Arrhythmogenic right ventricular cardiomyopathy: management of symptoms and prevention of sudden cardiac death. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198784906.003.0361.
Full textAbstract:
Patients with arrhythmogenic right ventricular cardiomyopathy (ARVC) have arrhythmia-related symptoms or are identified during screening of an affected family. Heart failure symptoms occur late in the disease’s natural history. As strenuous exercise has been associated with disease acceleration and worsening of ventricular arrhythmias, lifestyle modification with restricted athletic activities is recommended upon disease diagnosis or even identification of mutation carrier status. An episode of an haemodynamically unstable, sustained ventricular tachycardia or ventricular fibrillation as well as severe systolic ventricular dysfunction constitute definitive indications for implantable cardioverter defibrillator (ICD) implantation, which should also be considered following tolerated sustained or non-sustained ventricular tachycardia episodes, syncope, or in the presence of moderate ventricular dysfunction. Antiarrhythmic medications are used as an adjunct to device therapy. Catheter ablation is recommended for incessant ventricular tachycardia or frequent appropriate ICD interventions despite maximal pharmacological therapy. Amiodarone alone or in combination with beta blockers is most effective for symptomatic ventricular arrhythmias. Beta blockers are considered for use in all patients with a definite diagnosis but evidence for their prognostic benefit is sparse. Heart failure symptoms are managed using standard protocols and heart transplantation is considered for severe ventricular dysfunction or much less commonly uncontrollable ventricular arrhythmias.
10
Sadleir, Lynette G., Jozef Gecz, and Ingrid E. Scheffer. Epilepsies That Occur Predominantly in Girls. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0041.
Full textAbstract:
Availability of DNA sequencing has led to an increase in the number of children being identified with mutations in specific genes in specific epilepsy phenotypes. The presence of mutations that cause epilepsy only in females is one of the discoveries revealed in the sequencing era. Mutations in PCDH19 and CDKL5 are distinctive and identifiable forms of female-only epilepsy, and clinicians should consider PCDH19 in normal girls presenting with clusters of afebrile or febrile seizures in the first 3 years of life, and CDKL5 in girls or boys presenting with severe developmental delay within the first 6 months of life followed by intractable seizures including spasms within the first 2 years.
Book chapters on the topic "No mutation identified"
1
Nakagawa, Hitoshi. "History of mutation breeding and molecular research using induced mutations in Japan." In Mutation breeding, genetic diversity and crop adaptation to climate change, 24–39. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0003.
Full textAbstract:
Abstract Following the construction of the Gamma Field at the Institute of Radiation Breeding in 1960, mutation breeding was accelerated in Japan. The facility is used, with a radiation dose up to 2 Gy/day (ca. 300,000 times that of natural background), to induce mutations at a higher frequency than occurs in nature. There have been 318 direct- use mutant cultivars representing 79 species generated through irradiation of gamma-rays, X-rays, ion beams and chemicals and somaclonal variation. Approximately 79% of these direct-use cultivars were induced by radiation. There have been 375 indirect-use mutant cultivars, including 332 rice, of which 162 cultivars (48.8%) were derived from the semi-dwarf mutant cv. 'Reimei'. The economic impact of these mutant cultivars, primarily of rice and soybean, is very large. Some useful mutations are discussed for rice, such as low digestible protein content, low amylose content, giant embryo and non-shattering. Useful mutations in soybean such as radiosensitivity, fatty acid composition and super-nodulation have been identified. Japanese pear and apple resistant to Alternaria disease have also been identified. The achievements of biological research such as characterization and determination of deletion size generated by gamma-rays, the effect of deletion size and the location, and a mechanism of dominant mutation induction are identified. Similarly, genetic studies on mutations generated through the use of gamma-ray induced mutations, such as phytochrome response, aluminium tolerance, stay-green (Mendel's gene) and epicuticular wax have also been conducted. Mutation breeding is a very useful technology for isolating genes and for elucidating gene functions and metabolic pathways in various crops.
2
Lundqvist, Udda. "Scandinavian mutation research during the past 90 years - a historical review." In Mutation breeding, genetic diversity and crop adaptation to climate change, 10–23. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0002.
Full textAbstract:
Abstract In 1928, the Swedish geneticists Herman Nilsson-Ehle and Åke Gustafsson started to act on their own ideas with the first experiments with induced mutations using diploid barley. They started with X-rays and UV irradiation. Very soon the first chlorophyll mutations were obtained and followed by the first 'vital' mutations Erectoides (ert) (Franckowiak and Lundqvist, 2001). Several other valuable mutations were identified as early maturity, high yielding, lodging resistant and characters with altered plant architecture. The experiments expanded to include other different types of irradiation, followed by chemical mutagenesis starting with mustard gas and concluding with sodium azide. The research brought a wealth of observations of general biological importance, such as the physiological effects of radiation as well as the difference in the mutation spectrum with respect to mutagens. This research was non-commercial, even if some mutants have become of important agronomic value. It peaked in activity during the 1950s to 1980s and, throughout, barley was the main experimental crop. About 12,000 different morphological and physiological mutants with a very broad phenotypic diversity were brought together and are incorporated in the Nordic Genetic Resource Centre (NordGen), Sweden. Several important mutant groups have been analysed in more detail genetically, with regard to mutagen specificity and gene cloning. These are: (i) early maturity mutants (Praematurum); (ii) six-rowed and intermedium-spike mutants; (iii) mutants affecting surface wax coating (Eceriferum); and (iv) mutants affecting rachis spike density (Erectoides). Some of these groups are presented in more detail in this review. Once work with induction of mutations began, it was evident that mutations should regularly be included in breeding programmes of crop plants. In Sweden, direct X-ray induced macro-mutants have been successfully released as cultivars, some of them having been used in combination breeding. Their importance for breeding is discussed in more detail.
3
Kumar, Arun, Binay Kumar Agarwal, Rajesh Kumar, Sanjay J. Jambhulkar, Varsha Rani, and Zille Ali Haider. "Induction of variability for yield components in Indian mustard (Brassica juncea L. Czern & Coss) under acidic soil regime of Jharkhand." In Mutation breeding, genetic diversity and crop adaptation to climate change, 258–68. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0026.
Full textAbstract:
Abstract Indian mustard (Brassica juncea L.) is the most important oilseed crop of the state of Jharkhand in India, where 78% of the cultivable soil is acidic, causing a sizeable yield reduction. Potential seed yield from such soils cannot be realized within existing varieties and therefore a mutation breeding approach has been followed to isolate mutants tolerant to acidic soil. Three doses of gamma-rays (900 Gy, 1000 Gy and 1100 Gy) and a combined treatment of gamma irradiation and 0.3% EMS were used for induction of mutation in the varieties 'Shivani' and 'Pusa Bold'. A total of 139,720 M2 plants (75,760 of 'Shivani' and 63,960 of 'Pusa Bold') were screened under acidic soil conditions (pH 4.8). A wide spectrum of variability for tolerance to soil acidity, earliness, seed colour, seed yield and yield components, and morphological traits was observed in the M2 generation. True-breeding mutants for different traits were confirmed in the M3 generation. Mutations were recorded in 'Shivani' and 'Pusa Bold', respectively, for secondary branch number (38 and 24), siliquae per plant (1223 and 562) and single plant seed yield (45.49 g and 34.84 g). In addition, a large spectrum of variability for morphological characters was identified.
4
Jankowicz-Cieslak, Joanna, Florian Goessnitzer, Sneha Datta, Altus Viljoen, Ivan Ingelbrecht, and Bradley J. Till. "Induced mutations for generating bananas resistant to Fusarium wilt tropical race 4." In Mutation breeding, genetic diversity and crop adaptation to climate change, 366–78. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0038.
Full textAbstract:
Abstract Bananas are a staple for more than 400 million people. Additionally, more than 16.5 million tonnes are exported, making it both an important food security and a cash crop. Productivity of Cavendish-type bananas is threatened by both abiotic and biotic stresses. The fact that triploid bananas are sterile, parthenocarpic and obligate vegetatively propagated makes them particularly susceptible to diseases, including Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 (Foc TR4). This is because continual clonal propagation has led to loss of genetic diversity. Additionally, lack of meiosis limits methods for breeding. Foc TR4 has been devastating Cavendish bananas in South-east Asia but has recently also been reported from Queensland in Australia, the Middle East and Mozambique, thus threatening global banana production. To address this, we are performing mutagenesis of in vitro propagated bananas to broaden the genetic diversity in order to find new alleles conferring disease resistance. We have developed methods for efficient induction of mutations in isolated apical meristems from shoot tips using chemical mutagens and ionizing radiation. Mutation discovery methods have been adapted to recover mutations including single point mutations and large deletions spanning millions of base pairs. We have created approximately 5000 mutated lines for forward-genetic screens to identify TR4 resistance in greenhouse- evaluated material. A subset of ca. 500 in vitro plantlets was subjected to glasshouse-based screening using a virulent F. oxysporum isolate. To date, 23 lines showing altered resistance responses to Foc TR4 have been identified.
5
Sevanthi, Amitha Mithra V., Prashant Kale, Chandra Prakash, M. K. Ramkumar, Neera Yadav, V. Sureshkumar, Yugandhar Poli, et al. "National repository of EMS induced mutants of an upland rice cultivar Nagina 22: progress update on characterization and utilization." In Mutation breeding, genetic diversity and crop adaptation to climate change, 290–302. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0030.
Full textAbstract:
Abstract The Indian initiative for creating mutant resources in rice has generated 87,000 mutants in the background of a popular drought- and heat-tolerant upland cultivar, Nagina 22 (N22), through EMS mutagenesis. So far, 541 macro-mutants from this resource have been identified, maintained in the mutant garden and characterized in detail based on 44 descriptors pertaining to distinctness, uniformity and stability (DUS) of rice and other agronomic parameters. The similarity index of the mutants was more than 0.6 for nearly 90% of the mutants with respect to DUS descriptors, further establishing the validity of the mutants. The available high-quality sequence resource of N22 has been improved by reducing the gaps by 0.02% in the coding sequence (CDS) region. This was made possible using the newly synthesized whole-genome data of N22 which helped to remove 9006 'Ns' and replace 12,746 existing nucleotides with the accurate ones. These sequence and morphological details have been updated in the mutant database 'EMSgardeN22'. Further, 1058 mutants have been identified for low-P tolerance, tolerance to sheath blight, blast, drought, heat, higher photosynthetic efficiency and agronomic and root traits from this resource. A novel herbicide-tolerant (imazethapyr) mutant earlier identified and characterized from this resource is now being used in introgressing the herbicide-tolerant trait in eight major rice varieties in India. Further, robust and simpler screening systems have been tested for studying low-P tolerance of the mutants. A grain-size mutant, heat-tolerant mutant, drought-tolerant mutant, stay-green mutant and low-P tolerant and water-use efficient high-root-volume mutants have been characterized at morphological and molecular levels. A brief account of all these mutants, the entire mutant resource and the elaborate trait-based screenings is presented in this chapter.
6
Das, Priyanka, Rajeev N. Bahuguna, Rohit Joshi, Sneh Lata Singla-Pareek, and Ashwani Pareek. "In search of mutants for gene discovery and functional genomics for multiple stress tolerance in rice." In Mutation breeding, genetic diversity and crop adaptation to climate change, 444–50. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0045.
Full textAbstract:
Abstract Mutation breeding is a commanding tool, which has been adapted to generate altered genetic material to study functional genomics, including understanding the molecular basis of stress tolerance. Hitherto, several rice lines have been generated through mutagenesis and the mutated genes responsible for the 'gain of function' in terms of plant architecture, stress tolerance, disease resistance and grain quality have been characterized. Oryza sativa L. cv. IR64 is a high-yielding rice cultivar but sensitive to abiotic stresses such as acute temperatures, salinity and drought. In this study, a population of rice IR64 mutants was generated using gamma irradiation. The population was then subjected to a preliminary phenotypic screening under abiotic stresses such as heat and salinity at the seedling stage. On the basis of root length, shoot length, fresh weight, dry weight and chlorophyll measurements, we identified eight 'gain-of-function' mutant lines and used them for further biochemical and molecular characterization. Phenotyping results demonstrated that the identified mutant plants have gained the potential to thrive under heat and salinity conditions. This information would be of wide scientific interest and helpful for developing novel cultivars able to maintain yield in saline, hot and dry areas.
7
Morales, Yonis, and Rolando Grajeda. "Virulence genes of new population of coffee rust (Hemileia vastatrix) affecting coffee variety 'Lempira', in Honduras; resistant and susceptible varieties." In Mutation breeding, genetic diversity and crop adaptation to climate change, 338–43. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0035.
Full textAbstract:
Abstract The coffee variety 'Lempira', released in Honduras in 1998, was classified 100% resistant to races I and II of coffee rust identified by Portugal's Centre for Research into Coffee Rusts (Centro de Investigação das Ferrugens do Cafeeiro) (CIFC) in 1997. However, since 2007, the disease has been reported in seed foundation plots and producer farms, the most recent epidemic report being in April 2016 in Vegas de Jalan, Juticalpa Olancho, affecting 210 ha. Since this variety constitutes 45% of the cultivated area under coffee in the country, there is a need to identify the virulence genes of the new strain and to determine the resistance and susceptibility of other cultivated varieties. For these purposes, mass samples of rust were inoculated on leaf discs of the differential clones 1343/269, 110/5, 147/1, 152/3, 33/1, 419/20, 832/1 and 832/2, together with 87/1, 1006/10, 420/10 and 420/2 from the Federal University of Vicosa, as well as on the two main cultivated resistant varieties ('Parainema' and 'IHCAFE- 90'), and seven promising genotypes, under controlled temperature conditions and relative humidity. After 20-60 days of inoculation, seven virulence genes were identified (v1, v2, v4, v5, v6, v7, v9), of which v1, v4, v6, v7 and v9 had not been reported in Honduras previously. It is inferred that this rust population arose by recombination of race v5 with v6, v7 or v9. Races with 3, 4, 5, 6 or 7 virulence determinants were identified as the most complex and aggressive strains described but they lacked the v3 and v8 determinants. In addition, it was found that 'Parainema', 'H27', 'T5296-170', 'Central American', 'Pacamara yellow' and 'Anacafe-14' are resistant because they possess the SH8 gene, absent from 'Lempira'. 'IHCAFE-90' and 'Obatá' showed 20% susceptibility, and 'Ruiru 11' was susceptible. The results reveal the diversity of rust virulence genes in Honduras and emphasize the importance of the SH3 and SH8 genes as sources of resistance.
8
da Luz, Viviane Kopp, Vívian Ebeling Viana, Gabriela Magalhães da Fonseca, Camila Pegoraro, Luciano Carlos da Maia, and Antonio Costa de Oliveira. "Identification of rice mutants tolerant to cold stress at the germination stage by TILLING." In Mutation breeding, genetic diversity and crop adaptation to climate change, 111–19. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0011.
Full textAbstract:
Abstract Cold stress is a common factor affecting rice culture in temperate regions, which impairs seed germination, crop establishment and grain yield. This work aimed to identify, through a TILLING assay, rice mutant families displaying cold tolerance during the germination stage. The mutant analyses were performed in 4000 M3 plants obtained through chemical mutagenesis with ethyl methanesulfonate. We screened for mutations in the Os03g0103300 (qLTG3-1) gene, which is responsible for cold tolerance during germination. The TILLING assay identified a mutant (516 A3) which was tested for germination efficiency in cold stress (13°C). The mutant genotype showed a higher relative performance in germination and germination velocity index, which was more than 50% higher compared with wild-type. The mutation induction was efficient in creating genetic variability for cold stress tolerance during germination. Gene expression analyses demonstrate that Os03g0103300 was downregulated in stage S3 in the mutant and wild-type plants germinated under cold stress. However, downregulation in the Os03g0103300 gene was less severe in the mutant, which suggests that the expression related to germination ability under cold stress may be detected in the previous stages, embryo activation and weakening of the tissues that cover the embryo. Overall, the mutant 516 A3 presents a new genetic variant for cold tolerance during germination.
9
Liu, Lu-xiang, Yong-dun Xie, Hui-jun Guo, Lin-shu Zhao, Hong-chun Xiong, Jia-yu Gu, and Shi-rong Zhao. "New mutation techniques for crop improvement in China." In Mutation breeding, genetic diversity and crop adaptation to climate change, 47–52. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0005.
Full textAbstract:
Abstract There are at least 1 billion hungry people worldwide and the Asia and Pacific region harbours the biggest estimated regional distribution of hunger. Lifting a billion people out of poverty and feeding more than 9 billion by 2050 will require increasing cereal production by 70%. Accelerating the development of agriculture to continually increase productivity should be the final approach to end poverty. Mutation techniques have played very significant roles in ensuring food security by developing new mutant germplasm and mutant varieties in China, which have generated a tremendous socio-economic impact. New mutagenesis approaches were initiated in the late 1980s by Chinese scientists, including spaceflight and heavy-ion beam irradiation used as new effective and alternative ways for crop genetic improvement. Protocols for crop mutation induction by space radiation with high-energy heavy-ion beams have been established and applied for crop breeding. More than 1030 mutant varieties with high-yielding, fine-quality and multi-resistant traits have been developed and officially released mainly in cereals, oil and vegetable crops. They have been playing an important role in agricultural production. Hundreds of rare mutant germplasm accessions with a possible breakthrough effect on main economic traits such as grain yield and quality were also identified and applied in conventional breeding programmes. The development of new mutation techniques will be heavily based on, and associated with, not only effective use of nuclear and aerospace research platforms, but also advanced plant omics and molecular biology.
10
Jegadeesan, Souframanien, and Kandali Sreenivasulu Reddy. "Radiation-induced mutations in genetic enhancement and development of new crop varieties in black gram (Vigna mungo (L.) Hepper)." In Mutation breeding, genetic diversity and crop adaptation to climate change, 303–11. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0031.
Full textAbstract:
Abstract Black gram (Vigna mungo (L.) Hepper), popularly known as urdbean or mash or black gram, is a grain legume rich in protein (25-28%), widely cultivated in the Indian subcontinent and to a lesser extent in Thailand, Australia and other Asian and South Pacific countries. Genetic improvement in this crop is hindered due to the narrow genetic base. As genetic variability is a prerequisite for any crop improvement programme, induced mutations provide an important source for generating variability. Radiation (gamma, X-rays and neutron) induced mutants were identified for various morphological and biochemical traits, creating a pool of genetic variability. These mutants were used in a cross-breeding programme to develop high-yielding, disease-resistant varieties in black gram. The effective blend of mutation and recombination breeding at the Bhabha Atomic Research Centre has resulted in the release of five black gram varieties (TAU-1, TAU-2, TPU-4, TU94-2 and TU-40) by incorporating desirable traits like large seed, wider adaptability, resistance to disease and improved quality. These varieties have been developed from mutants directly or by using them in cross-breeding programmes. For example, a black gram variety, N0.55, was irradiated with gamma-rays and electron beams to obtain a large number of mutants. The large-seed mutants, UM-196 and UM-201, were used in cross-breeding with the elite cultivar T-9 for developing the high-yielding varieties TAU-1, TAU-2, TPU-4, TU94-2 and TU-40. TAU-1 has become the most popular variety in Maharashtra state, occupying the maximum area under black gram cultivation. Induced mutations will continue to play an increasing role in generating genetic variability for various traits as a major component of environmentally sustainable agriculture.
Conference papers on the topic "No mutation identified"
1
Birch, David G., Gabriel H. Travis, Kirsten G. Locke, and Donald C. Hood. "Rod Ergs in Mice and Humans with Putative Null Mutations in the RDS Gene." In Vision Science and its Applications. Washington, D.C.: Optica Publishing Group, 1997. http://dx.doi.org/10.1364/vsia.1997.ma.4.
Full textAbstract:
Mutations causing autosomal dominant retinitis pigmentosa (RP) have been identified in RDS, the human homologue of the gene that was first identified and isolated as the cause of mouse "retinal degeneration slow" or rds (1, 2). The rds gene encodes rds/peripherin, an integral membrane glycoprotein located in outer segment disks (1, 3, 4). More than 15 distinct disease-causing mutations in the RDS gene have been reported (5). The clinical phenotypes include adRP, dominant retinitis punctata albescens, dominant butterfly shaped pigment dystrophy of the fovea and autosomal dominant macular degeneration (6). That RDS mutation can cause either RP and/or macular degeneration is consistent with the observation that the protein is expressed in both rods and cones, though its exact functional role in each photoreceptor must be different. Finally, there is an additional form of retinitis pigmentosa, digenic RP (7) that results from a combination of one mutation in RDS and one in R0M1. Neither mutation alone in a heterozygote causes degeneration.
2
Mukhopadhyay, Asima, Nicola Curtin, and Richard Edmondson. "Evaluation of different methods to assess homologous recombination status and sensitivity to PARP inhibitors in ovarian cancer." In 16th Annual International Conference RGCON. Thieme Medical and Scientific Publishers Private Ltd., 2016. http://dx.doi.org/10.1055/s-0039-1685289.
Full textAbstract:
Methods: Matched samples of ascites and tumor tissue were taken from patients undergoing surgery for epithelial ovarian cancer. Tumor samples were formalin fixed and paraffin embedded (FFPE); ascites samples were used to generate primary cultures (PC). HR status was determined in PCs as previously described.[1] IC50 for the PARP inhibitor Rucaparib was estimated using SRB assays. DNA was extracted from the FFPE tissue. The following techniques were evaluated in PCs or paired FFPE samples: DR-GFP reporter assay, PARP activity assay, BRCA1 expression on immunohistochemistry, BRCA1 methylation status and BRCA1/2 mutation analysis. A next generation sequencing based assay was used to detect mutations and other genomic alterations in a large panel of cancer-associated genes, including BRCA1/2. Results: Paired samples were collected from 64 patients and characterized for HR function. 47/64 (76%) were high grade serous. 44% (28/64)) were HR defective (HRD) by Rad51 assay and correlated with Rucaparib sensitivity (PPV-92%, NPV-100%). Molecular analysis revealed that all mutations and other genomic alterations detected in ascites derived PCs were also found in matched FFPE tumor tissues. All tumors with serous histology contained p53 mutations, whilst the remaining tumors without p53 mutations were non-serous in histology. DR-GFP assay was unreliable in PC due to poor transfection. In a subset of 50 cancers there was reduced BRCA1 expression in the HRD vs. HRC tumours (34.8% vs. 22.7%, ns) whilst in a further subset of 30 cases there was no difference in endogenous or stimulated PARP activity between HRD and HRC tumours. Deleterious BRCA2 mutations were identified in 7 tumors, 6 of which were HRD. Only 1 deleterious BRCA1 mutation was detected but methylation of BRCA1 was identified in 13 of 64 (20%) tumors, 7 of which were HRD. Mutation of BRCA2 was mutually exclusive to methylation of BRCA1. HRD vs. HRC tumours showed BRCA1 methylation (25% vs. 17%) and BRCA1/2 mutation (21% vs. 0.3%). 14/28 (50%) HR defective tumors do not have BRCA1/2 mutations or BRCA1 methylation, suggesting other mechanisms can also result in a HR defective phenotype. 28/64 (43%) of samples demonstrated the HR defective phenotype. In all cases HR status correlated with sensitivity to Rucaparib. Conclusion: As expected, deleterious BRCA2 mutations conferred a HRD phenotype in cells but methylation of BRCA1 was not universally associated with HRD. This may be as a result of only partial silencing of the gene by methylation and further work is required to identify thresholds of methylation which may predict HR status. The use of BRCA1/2 mutation testing alone is unlikely to identify the majority of HR defective ovarian tumors. Assessment of functional status of HRD is the preferred option and further technologies should be developed to simplify the Rad51 assay.
3
Kant, Nimita, and Perumal Senthiappan Jayaraj. "Evaluation of Telomerase Reverse Transcriptase Expression in Squamous Cell Carcinoma of the Skin." In Annual Conference of Indian Society of Medical and Paediatric Oncology (ISMPO). Thieme Medical and Scientific Publishers Pvt. Ltd., 2021. http://dx.doi.org/10.1055/s-0041-1735375.
Full textAbstract:
Abstract Introduction Squamous cell carcinoma (SCC) is highly invasive malignant tumor showing keratinocytic differentiation and is often associated with chronic exposure to UV light. Telomerase is RNA dependent DNA polymerase that causes addition of telomeric repeat DNA sequences to chromosomal ends. Recently, UV signature mutations have been identified in core promoter region of TERT gene, which encodes the main catalytic subunit leading to overexpression in cutaneous melanoma. However, its role and expression pattern have not been studied in eyelid skin SCC. Objectives Present study aimed to analyze the presence of telomerase reverse transcriptase (TERT) in eyelid SCC, as its expression pattern and mutational status have not been studied in SCC. Materials and Methods Nineteen cases of eyelid SCC were evaluated for the presence of TERT protein using monoclonal antibody against TERT, and its mutational status was verified using PCR and DNA sequencing. Bioedit software was used for analyzes and primers were vindicated using NCBI Primer Blast. Results were correlated with clinicopathological features of SCC. Results A C to T mutation was observed in 6 of 19 SCC cases. Positive expression of TERT was found in 57% of the cases analyzed and it showed a significant association with keratinocytic differentiation (p = 0.04). Conclusion Relation between TERT promoter mutation and TERT immunohistochemistry is studied for the first time in eyelid skin SCC. Our results suggested that overexpression of TERT may contribute to the aggressive behavior associated with SCC and such patients may warrant aggressive treatment.
4
Youssoufiän, H., A. Patel, D. Phillips, H. H. Kazazian, and S. E. Antonarakis. "RECURRENT MUTATIONS AND AN UNUSUAL DELETION IN HEMOPHILIA A." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644014.
Full textAbstract:
We have identified 15 mutations of the factor VIII (F8) gene from a panel of 107 patients with hemophilia A and have characterized these gene defects byrestriction analysis, oligonucleotide hybridization, cloning and DNA sequencing. Recurrent point mutations that involve CG to TG transitions were identified in exon 18, exon 22, and exon 24; a single CG to TG transition was identified in exon 23; and a CG to CA transition was identified in exon 24. In addition, a Taq I site alteration in intron 4 was identified in a patient with mild hemophilia, which arose dg. S23&in a grandpaternal germ cell. Cloning and sequencing of this region suggests the generation of a newsplice donor site. These data suggest that CG to TG transition is a prominent mechanism of mutation in hemophilia A. Six different deletions were also characterized. In one family, the deletion involved exon 26. However, the deletion endpoints in the male proband were different from those in his carrier mother, suggesting either gonadal mosaicism or a second deletion event in maternal meiosis.Of the 15 mutations, 6 occurred de novo within 2 generations: 4 in males and 2 in females. In these djg.novo mutations paternal age at conception was 35 (range = 32-38) and maternal age was 24 and 27. The ability to discover a sizable number of mutations in the F8 gene producing hemophilia A enables us to determine the frequency and nature of de novo mutations in man.
5
Brooks, Joseph Bruno Bidin, Fábio César Prosdócimi, Lara Fenley Granzotto, and Matheus Garcez Jorge Mariani. "Camptocormia and genetic Parkinson’s disease caused by the mutation of the LRRK2 gene. Case report." In XIII Congresso Paulista de Neurologia. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1516-3180.183.
Full textAbstract:
Context: Parkinsonism is a clinical syndrome characterized by bradykinesia, tremor at rest, muscle stiffness and postural instability. Parkinson’s disease is the most common cause of parkinsonism. Pathogenic mutations in the leucine- rich repeat kinase 2 gene (LRRK2) have been identified in PARK8-linked autosomal dominant parkinsonism. This mutation is the most common and explains about 1–7% of family cases of parkinsonism of European and American origin and 1–3% of sporadic PD. This case report was approved by the Ethics Committee of Universidade Metropolitana de Santos. Case Report: The present case relates to a 40-year-old, white man, who presented insidious and progressive parkinsonism for 6 years, akinetic-rigid and asymmetric (Hoehn Yahr 2.5 scale) associated with early camptocormia and non-motor symptoms and partial response to levodopa. The classic phenotype of late-onset parkinsonism was found on the paternal side of the patient’s family, suggesting family inheritance. Exome sequencing showed heterozygous mutation PARK8 LRRK2 (Gly2019Ser). Conclusions: The presentation of this case was aimed at alerting to Parkinson’s genetic disease in adults with family inheritance associated with early camptocormia. The presentation of this case was aimed at alerting to Parkinson’s genetic disease in adults with family inheritance associated with early camptocormia.
6
Higuchi, M., L. Kochhan, R. Schwaab, H. H. Brackmann, H. Egli, and K. Olek. "DETECTION OF MUTATIONS IN HEMOPHILIA A." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644012.
Full textAbstract:
Hemophilia A (HA) is a x-linked bleeding disordercaused by lack or abnormality of factor VIII:C. Because of the heterogeneity of the clinical picture thedisease might result from many different molecular lesions.We examined 202 patients of HA from 160 families by restriction analysis with Taq I, Msp I and EcoR I using three subcloned cDNA fragments of factor VIII:C.We detected 13 mutations within the factor VI11:C gene. All of these patients suffer from the severe form of HA.Table I shows six deletions which we characterized. We also identified seven point mutations on four different exons using restriction enzyme Taq I. The results are shown in Table II.That means in approximately 3.8% of the patients we found deletions and in 4.4% we found point mutations.This confirms the results of Youssofian et al (1986):These authors consider the CpG-dimer as a mutation hotspot in the factor VI11:C gene.
7
Lee, Dae-Won, Yongjun Cha, Sae-Won Han, Si-Hyun Lee, Hwang-Phill Kim, Jaemyun Lyu, Hyojun Han, et al. "Abstract A72: Mutation signature associated with colorectal cancer prognosis identified by targeted next-generation sequencing." In Abstracts: AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; November 5-9, 2015; Boston, MA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1535-7163.targ-15-a72.
Full text
8
Burg, ED, and JX Yuan. "A Tetramerization Domain Mutation in KCNA5 Identified in Pulmonary Arterial Hypertension Patients Causes Abnormal Trafficking Patterns." In American Thoracic Society 2009 International Conference, May 15-20, 2009 • San Diego, California. American Thoracic Society, 2009. http://dx.doi.org/10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a6015.
Full text
9
Feijão, Maria Clara Tomaz, Fernanda Pimentel Arraes Maia, Mateus Coelho Gondim de Oliveira Lima, Vitória Moreira Soares, and Luiz Gonzaga Porto Pinheiro. "CONCERNING A FAMILY WITH BRCA2 MUTATION." In XXIV Congresso Brasileiro de Mastologia. Mastology, 2022. http://dx.doi.org/10.29289/259453942022v32s1019.
Full textAbstract:
Introduction: Breast cancer is the most common malignancy in women and represents a major obstacle to public health worldwide. The molecular diagnosis of this type of cancer is one of the main contemporary challenges in oncology, since it is hampered by a complex inheritance pattern, characterized by both genetic and environmental factors. Only a minority of breast cancers are explained by the presence of high penetrance gene mutations, such as those in the BRCA1 and BRCA2 genes, which together with mutations in intermediate penetrance genes explain only up to 25% of the risk. In fact, much of the genetic influence is elucidated by low penetrance variants. Mutations in the germline BRCA1 and BRCA2 are the most common alterations in cases of early onset or of family history of breast cancer. It is also important to acknowledge that BRCA2 mutations can increase the risk of developing other cancers. Some studies show a relation between BRCA2 mutations and the development of leukemia, especially acute myeloid leukemia (AML). Also, some of these mutations, when inherited from both parents, cause a rare form of Fanconi anemia, a syndrome associated with the development of AML. In addition, there are studies evaluating a higher risk of pancreatic and esophageal cancer in carriers of BRCA2 mutations. The risk of colorectal cancer is also increased in patients with BRCA1 mutations. However, there are also some authors who defend that BRCA2 mutations could also be related. The specific statistics are not well defined because of the lack of data focusing on the relationship with the aforecited types of cancers, demonstrating the need for further analysis. This study aims to report the case of a woman with breast cancer at an early age. Such malignancy is associated and was somehow induced by the rich family history, represented by the high prevalence of cancer in the ancestry. We report a 34-year-old woman with an extensive history of carcinoma in the family, who was diagnosed with breast cancer in July 2016. In order to confirm the diagnosis, it was required an ultrasound, which resulted in a 2.2×1.5 cm node on the right breast’s left superior quadrant, classified as BIRADS 4A. It also performed an ultrasound-guided biopsy that showed a tubular carcinoma on the right breast with the following characteristics: positive for estrogen and progesterone receptor, positive for KI 67 (5%), and negative for HER2, with staging of T1cN0M0. During anamnesis, the patient mentioned menarche at 12 years old, history of birth control pills use for 10 years, no pregnancy, and no breastfeeding. When it comes to family history, a great number of relatives were previously diagnosed with some type of cancer. Her paternal grandfather had rectum cancer at 42 years old and breast cancer at 62 years old. The paternal grandmother passed away because of a fast-progression leukemia at the age of 68. It is important to mention that her progenitors were first cousins. Furthermore, the patient’s dad was diagnosed with breast cancer at 62 years, alongside his three brothers who were also diagnosed with cancer: one with prostatic cancer at the age of 64 years and the other two with intestinal cancer at the ages of 64 and 68 years old. Considering such a family history, a genetic panel was performed, analyzing the genes related to hereditary cancer risk, and it identified mutations in the patient’s BRCA2 gene. Then, firstly, she performed a bilateral mastectomy in January 2017 with sentinel lymph node investigation, which was negative for neoplastic cells in the lymph nodes. Later, considering the BRCA2 mutation, in August 2017, the patient had to undergo prophylactic surgery: oophorectomy with salpingectomy.
10
Benslimane, Fatiha M., Hebah Al Khatib, Dana Albatesh, Ola Al-Jamal, Sonia Boughattas, Asmaa A. Althani, and Hadi M. Yassine. "Nanopore Sequencing SARS-CoV-2 Genome in Qatar." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0289.
Full textAbstract:
Background: The current pandemic, COVID-19, is cause by an RNA Coronavirus that was recently identified as SARS-CoV-2. RNA viruses tend to have a high mutation rate; the rate is around a million times greater than that of their hosts. The mutagenic potential of the virus depends on many factors, including the fidelity of nucleic acid-replicating viral enzymes, such as SARSCoV-2 RNA dependent RNA polymerase (RdRp). The rate of mutation drives viral evolution and genome variability, consequently allowing viruses to escape the immunity of the host and develop resistance to drugs. Therefore, the characterization of SARS-CoV-2 variants might lead to implement better therapeutics treatments, vaccines design and identify new diagnostics approaches. Aim: The aim of this study was to establish a fast sequencing method to identify SARS-CoV-2 mutations in Qatar. This will help to assess if there are new viral variants that are spreading in country. Methods: RNA was isolated from samples collected from Qatar COVID-19 positive patients. The Artic Network V3 primer scheme and Oxford Nanopore ligation sequencing kit were used to prepare the sequencing libraries. Libraries were loaded on to R9.4.1 flow cells and ran on a GridION. Bioinformatics analysis was done following the Artic Network SARA-CoV-2 bioinformatics tools. Results: Genome coverage of sequenced samples was >80% and the depth was average at 200x. The coverage was highly dependable on sample viral load; samples of CT value lower than 30 resulted in better sequence coverage. The sequenced genomes were deposited in GISAID and were mainly clustering with genomes deposited from the UK. Sequences were compared to Illumina and sanger sequences and they showed compatible results. Conclusion: The use of ONT to sequence SARA-CoV-2 is a quick, affordable, and reliable technique to determine viral mutation. Using this technique, the first sequences from Qatar were deposited in to GISAID. Up to date, 700 genomes have been sequenced from Qatari samples.
Reports on the topic "No mutation identified"
1
Ori, Naomi, and Mark Estelle. Specific mediators of auxin activity during tomato leaf and fruit development. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597921.bard.
Full textAbstract:
The plant hormone auxin is involved in numerous developmental processes, including leaf and fruit development. The tomato (Solanumlycopersicum) gene ENTIRE (E) encodes an auxin-response inhibitor from the Aux/IAA family. While most loss-offunction mutations in Aux/IAA genes are similar to the wild type due to genetic redundancy, entire (e) mutants show specific effects on leaf and fruit development. e mutants have simple leaves, in contrast to the compound leaves of wild type tomatoes. In addition, e plants produce parthenocarpic fruits, in which fruit set occurs independently of fertilization. The aim of this research program was to utilize the e mutation to identify and characterize genes that mediate the specific effect of auxin in leaf and fruit development. The specific objectives of the project were to: 1. Characterize and map modifiers of the e leaf phenotype. 2. Characterize and map suppressors of the e fruit phenotype. 3. Dissect the developmental specificity of the E gene. 4. Examine the effect of fruit-overexpression of identified genes on fruit set and seed production. To identify mediators of auxin in leaf development, we mainly focused on one mutant, crawling elephant (crel, previously called t282), which showed substantial suppression of the e phenotype and other auxin-relatedphenotypes. We have identified the CREL gene as a homolog of the Arabidopsis VRN5 gene, involved in recruiting polycomb silencing complexes to specific targets. We showed that CREL affects auxin sensitivity in tomato. Suppressors of the e fruit phenotype have been further characterized and selected for more profound effects. Expression profiling by RNAseq was used to analyze the effect of e as well as crel on gene expression in leaves and fruits. This analysis has identified putative E and CREL targets. We have initiated studies to assess the role of some of these targets in flower and fruit development. The research has identified potential mediators of auxin response in leaf, flower and fruit development.
2
Whitham, Steven A., Amit Gal-On, and Tzahi Arazi. Functional analysis of virus and host components that mediate potyvirus-induced diseases. United States Department of Agriculture, March 2008. http://dx.doi.org/10.32747/2008.7591732.bard.
Full textAbstract:
The mechanisms underlying the development of symptoms in response to virus infection remain to be discovered in plants. Insight into symptoms induced by potyviruses comes from evidence implicating the potyviral HC-Pro protein in symptom development. In particular, recent studies link the development of symptoms in infected plants to HC-Pro's ability to interfere with small RNA metabolism and function in plant hosts. Moreover, mutation of the highly conserved FRNK amino acid motif to FINK in the HC-Pro of Zucchini yellow mosaic virus (ZYMV) converts a severe strain into an asymptomatic strain, but does not affect virus accumulation in cucurbit hosts. The ability of this FINK mutation to uncouple symptoms from virus accumulation creates a unique opportunity to study symptom etiology, which is usually confounded by simultaneous attenuation of both symptoms and virus accumulation. Our goal was to determine how mutations in the conserved FRNK motif affect host responses to potyvirus infection in cucurbits and Arabidopsis thaliana. Our first objective was to define those amino acids in the FRNK motif that are required for symptoms by mutating the FRNK motif in ZYMV and Turnip mosaic virus (TuMV). Symptom expression and accumulation of resulting mutant viruses in cucurbits and Arabidopsis was determined. Our second objective was to identify plant genes associated with virus disease symptoms by profiling gene expression in cucurbits and Arabidopsis in response to mutant and wild type ZYMV and TuMV, respectively. Genes from the two host species that are differentially expressed led us to focus on a subset of genes that are expected to be involved in symptom expression. Our third objective was to determine the functions of small RNA species in response to mutant and wild type HC-Pro protein expression by monitoring the accumulation of small RNAs and their targets in Arabidopsis and cucurbit plants infected with wild type and mutant TuMV and ZYMV, respectively. We have found that the maintenance of the charge of the amino acids in the FRNK motif of HC-Pro is required for symptom expression. Reduced charge (FRNA, FRNL) lessen virus symptoms, and maintain the suppression of RNA silencing. The FRNK motif is involved in binding of small RNA species including microRNAs (miRNA) and short interfering RNAs (siRNA). This binding activity mediated by the FRNK motif has a role in protecting the viral genome from degradation by the host RNA silencing system. However, it also provides a mechanism by which the FRNK motif participates in inducing the symptoms of viral infection. Small RNA species, such as miRNA and siRNA, can regulate the functions of plant genes that affect plant growth and development. Thus, this binding activity suggests a mechanism by which ZYMVHC-Pro can interfere with plant development resulting in disease symptoms. Because the host genes regulated by small RNAs are known, we have identified candidate host genes that are expected to play a role in symptoms when their regulation is disrupted during viral infections. As a result of this work, we have a better understanding of the FRNK amino acid motif of HC-Pro and its contribution to the functions of HC-Pro, and we have identified plant genes that potentially contribute to symptoms of virus infected plants when their expression becomes misregulated during potyviral infections. The results set the stage to establish the roles of specific host genes in viral pathogenicity. The potential benefits include the development of novel strategies for controlling diseases caused by viruses, methods to ensure stable expression of transgenes in genetically improved crops, and improved potyvirus vectors for expression of proteins or peptides in plants.
3
Olszewski, Neil, and David Weiss. Role of Serine/Threonine O-GlcNAc Modifications in Signaling Networks. United States Department of Agriculture, September 2010. http://dx.doi.org/10.32747/2010.7696544.bard.
Full textAbstract:
Significant evidence suggests that serine/threonine-O-linked N-acetyl glucosamine0-(GlcNAc) modifications play a central role in the regulation of plant signaling networks. Forexample, mutations in SPINDLY,) SPY (an O-GlcNAc transferase,) OGT (promote gibberellin GA) (signal transduction and inhibit cytokinin responses. In addition, mutating both Arabidopsis OGTsSEC (and SPY) causes embryo lethality. The long-term goal of this research is to elucidate the mechanism by which Arabidopsis OGTs regulate signaling networks. This project investigated the mechanisms of O-GlcNAc regulation of cytokinin and gibberellin signaling, identified additional processes regulated by this modification and investigated the regulation of SEC activity. Although SPY is a nucleocytoplasmic protein, its site of action and targets were unknown. Severalstudies suggested that SPY acted in the nucleus where it modified nuclear components such as the DELLA proteins. Using chimeric GFP-SPY fused to a nuclear-export signal or to a nuclear-import signal, we showed that cytosolic, but not nuclear SPY, regulated cytokinin and GA signaling. We also obtained evidence suggesting that GA and SPY affect cytokinin signaling via a DELLA-independent pathway. Although SEC and SPY were believed to have overlapping functions, the role of SEC in cytokinin and GA signaling was unclear. The role of SEC in cytokinin and GA responses was investigated by partially suppressing SPY expression in secplants using a synthetic Spymicro RNA miR(SPY). The possible contribution of SEC to the regulation of GA and cytokinin signaling wastest by determining the resistance of the miR spy secplants to the GA biosynthesis inhibitor paclobutrazol and to cytokinin. We found that the transgenic plants were resistant to paclobutrazol and to cytokinin, butonlyata level similar to spy. Moreover, expressing SEC under the 35S promoter in spy mutant did not complement the spy mutation. Therefore, we believe that SEC does not act with SPY to regulate GA or cytokinin responses. The cellular targets of Spy are largely unknown. We identified the transcription factor TCP15 in a two-hybrid screen for SPY-interacting proteins and showed that both TCP15 and its closely homolog TCP14 were O-GlcNAc modified by bacterially-produced SEC. The significance of the interaction between SPY and these TCPs was examined by over-expressing the minwild-type and spy-4plants. Overexpression of TCP14 or TCP15 in wild-type background produced phenotypes typical of plants with increased cytokinin and reduced GA signaling. TCP14 overexpression phenotypes were strongly suppressed in the spy background, suggesting that TCP14 and TCP15 affect cytokinin and GA signaling and that SPY activates them. In agreement with this hypothesis, we created a tcp14tcp15 double mutant and found that it has defects similar to spyplants. In animals, O-GlcNAc modification is proposed to regulate the activity of the nuclear pore. Therefore, after discovering that SEC modified a nucleoporinNUP) (that also interacts with SPY, we performed genetic experiments exploring the relationship between NUPs and SPY nupspy double mutants exhibited phenotypes consistent with SPY and NUPs functioning in common processes and nupseeds were resistant to GA biosynthesis inhibitors. All eukaryotic OGTs have a TPR domain. Deletion studies with bacterially-expressed SEC demonstrated SEC'sTPR domain inhibits SEC enzymatic activity. Since the TPR domain interacts with other proteins, we propose that regulatory proteins regulate OGT activity by binding and modulating the inhibitory activity of the TPR domain.
4
Avni, Adi, and Gitta L. Coaker. Proteomic investigation of a tomato receptor like protein recognizing fungal pathogens. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600030.bard.
Full textAbstract:
Maximizing food production with minimal negative effects on the environment remains a long-term challenge for sustainable food production. Microbial pathogens cause devastating diseases, minimizing crop losses by controlling plant diseases can contribute significantly to this goal. All plants possess an innate immune system that is activated after recognition of microbial-derived molecules. The fungal protein Eix induces defense responses in tomato and tobacco. Plants recognize Eix through a leucine-rich-repeat receptor- like-protein (LRR-RLP) termed LeEix. Despite the knowledge obtained from studies on tomato, relatively little is known about signaling initiated by RLP-type immune receptors. The focus of this grant proposal is to generate a foundational understanding of how the tomato xylanase receptor LeEix2 signals to confer defense responses. LeEix2 recognition results in pattern triggered immunity (PTI). The grant has two main aims: (1) Isolate the LeEix2 protein complex in an active and resting state; (2) Examine the biological function of the identified proteins in relation to LeEix2 signaling upon perception of the xylanase elicitor Eix. We used two separate approaches to isolate receptor interacting proteins. Transgenic tomato plants expressing LeEix2 fused to the GFP tag were used to identify complex components at a resting and activated state. LeEix2 complexes were purified by mass spectrometry and associated proteins identified by mass spectrometry. We identified novel proteins that interact with LeEix receptor by proteomics analysis. We identified two dynamin related proteins (DRPs), a coiled coil – nucleotide binding site leucine rich repeat (SlNRC4a) protein. In the second approach we used the split ubiquitin yeast two hybrid (Y2H) screen system to identified receptor-like protein kinase At5g24010-like (SlRLK-like) (Solyc01g094920.2.1) as an interactor of LeEIX2. We examined the role of SlNRC4a in plant immunity. Co-immunoprecipitation demonstrates that SlNRC4a is able to associate with different PRRs. Physiological assays with specific elicitors revealed that SlNRC4a generally alters PRR-mediated responses. SlNRC4a overexpression enhances defense responses while silencing SlNRC4 reduces plant immunity. We propose that SlNRC4a acts as a non-canonical positive regulator of immunity mediated by diverse PRRs. Thus, SlNRC4a could link both intracellular and extracellular immune perception. SlDRP2A localizes at the plasma membrane. Overexpression of SlDRP2A increases the sub-population of LeEIX2 inVHAa1 endosomes, and enhances LeEIX2- and FLS2-mediated defense. The effect of SlDRP2A on induction of plant immunity highlights the importance of endomembrane components and endocytosis in signal propagation during plant immune . The interaction of LeEIX2 with SlRLK-like was verified using co- immunoprecipitation and a bimolecular fluorescence complementation assay. The defence responses induced by EIX were markedly reduced when SlRLK-like was over-expressed, and mutation of slrlk-likeusing CRISPR/Cas9 increased EIX- induced ethylene production and SlACSgene expression in tomato. Co-expression of SlRLK-like with different RLPs and RLKs led to their degradation, apparently through an endoplasmic reticulum-associated degradation process. We provided new knowledge and expertise relevant to expression of specific be exploited to enhance immunity in crops enabling the development of novel environmentally friendly disease control strategies.
5
McClure, Michael A., Yitzhak Spiegel, David M. Bird, R. Salomon, and R. H. C. Curtis. Functional Analysis of Root-Knot Nematode Surface Coat Proteins to Develop Rational Targets for Plantibodies. United States Department of Agriculture, October 2001. http://dx.doi.org/10.32747/2001.7575284.bard.
Full textAbstract:
The goal of this research was to provide a better understanding of the interface between root-knot nematodes, Meloidogyne spp., and their host in order to develop rational targets for plantibodies and other novel methods of nematode control directed against the nematode surface coat (SC). Specific objectives were: 1. To produce additional monoclonal SC antibodies for use in Objectives 2, 3, and 4 and as candidates for development of plantibodies. 2. To determine the production and distribution of SC proteins during the infection process. 3. To use biochemical and immunological methods to perturbate the root-knot nematode SC in order to identify SC components that will serve as targets for rationally designed plantibodies. 4. To develop SC-mutant nematodes as additional tools for defining the role of the SC during infection. The external cuticular layer of nematodes is the epicuticle. In many nematodes, it is covered by a fuzzy material termed "surface coat" (SC). Since the SC is the outermost layer, it may playa role in the interaction between the nematode and its surroundings during all life stages in soil and during pathogenesis. The SC is composed mainly of proteins, carbohydrates (which can be part of glycoproteins), and lipids. SC proteins and glycoproteins have been labeled and extracted from preparasitic second-stage juveniles and adult females of Meloidogyne and specific antibodies have been raised against surface antigens. Antibodies can be used to gain more information about surface function and to isolate genes encoding for surface antigens. Characterization of surface antigens and their roles in different life-stages may be an important step towards the development of alternative control. Nevertheless, the role of the plant- parasitic nematode's surface in plant-nematode interaction is still not understood. Carbohydrates or carbohydrate-recognition domains (CROs) on the nematode surface may interact with CROs or carbohydrate molecules, on root surfaces or exudates, or be active after the nematode has penetrated into the root. Surface antigens undoubtedly play an important role in interactions with microorganisms that adhere to the nematodes. Polyclonal (PC) and monoclonal (MC) antibodies raised against Meloidogyne javanica, M. incognita and other plant-parasitic nematodes, were used to characterize the surface coat and secreted-excreted products of M. javanica and M. incognita. Some of the MC and PC antibodies raised against M. incognita showed cross-reactivity with the surface coat of M. javanica. Further characterization, in planta, of the epitopes recognized by the antibodies, showed that they were present in the parasitic juvenile stages and that the surface coat is shed during root penetration by the nematode and its migration between root cells. At the molecular level, we have followed two lines of experimentation. The first has been to identify genes encoding surface coat (SC) molecules, and we have isolated and characterized a small family of mucin genes from M. incognita. Our second approach has been to study host genes that respond to the nematode, and in particular, to the SC. Our previous work has identified a large suite of genes expressed in Lycopersicon esculentum giant cells, including the partial cDNA clone DB#131, which encodes a serine/threonine protein kinase. Isolation and predicted translation of the mature cDNA revealed a frame shift mutation in the translated region of nematode sensitive plants. By using primers homologous to conserved region of DB#131 we have identified the orthologues from three (nematode-resistant) Lycopersicon peruvianum strains and found that these plants lacked the mutation.
6
Chen, Junping, Zach Adam, and Arie Admon. The Role of FtsH11 Protease in Chloroplast Biogenesis and Maintenance at Elevated Temperatures in Model and Crop Plants. United States Department of Agriculture, May 2013. http://dx.doi.org/10.32747/2013.7699845.bard.
Full textAbstract:
specific objectives of this proposal were to: 1) determine the location, topology, and oligomerization of FtsH11 protease; 2) identify the substrate/s of FtsH11 and the downstream components involved in maintaining thermostability of chloroplasts; 3) identify new elements involved in FtsH11 protease regulatory network related to HT adaptation processes in chloroplast; 4) Study the role of FtsH11 homologs from crop species in HT tolerance. Background to the topic: HT-tolerant varieties that maintain high photosynthetic efficiency at HT, and cope better with daily and seasonal temperature fluctuations are in great need to alleviate the effect of global warming on food production. Photosynthesis is a very complex process requiring accurate coordination of many complex systems and constant adjustments to the changing environments. Proteolytic activities mediated by various proteases in chloroplast are essential part of this process and critical for maintaining normal chloroplast functions under HT. However, little is known about mechanisms that contribute to adaptation of photosynthetic processes to HT. Our study has shown that a chloroplast-targeted Arabidopsis FtsH11 protease plays an essential and specific role in maintaining thermostability of thylakoids and normal photosynthesis at moderate HT. We hypothesized that FtsH11 homologs recently identified in other plant species might have roles similarly to that of AtFtsH1. Thus, dissecting the underlying mechanisms of FtsH11 in the adaptation mechanisms in chloroplasts to HT stress and other elements involved will aid our effort to produce more agricultural products in less favorable environments. Major conclusions, solutions, achievements - Identified the chloroplast inner envelope membrane localization of FtsH11. - Revealed a specific association of FtsH11 with the a and b subunits of CPN60. - Identified the involvement of ARC6, a protein coordinates chloroplast division machineries in plants, in FtsH11 mediated HT adaptation process in chloroplast. -Reveal possible association of a polyribonucleotide nucleotidyltransferase (cpPNPase), coded by At3G03710, with FtsH11 mediated HT adaptation process in chloroplast. - Mapped 4 additional loci in FtsH11 mediated HT adaptation network in chloroplast. - Demonstrated importance of the proteolytic activity of FtsH11 for thermotolerance, in addition to the ATPase activity. - Demonstrated a conserved role of plant FtsH11 proteases in chloroplast biogenesis and in maintaining structural and functional thermostability of chloroplast at elevated temperatures. Implications, both scientific and agricultural:Three different components interacting with FtsH11 were identified during the course of this study. At present, it is not known whether these proteins are directly involved in FtsH11mediated thermotolerance network in chloroplast and/or how these elements are interrelated. Studies aiming to connect the dot among biological functions of these networks are underway in both labs. Nevertheless, in bacteria where it was first studied, FtsH functions in heat shock response by regulating transcription level of σ32, a heat chock factor regulates HSPsexpression. FtsH also involves in control of biosynthesis of membrane components and quality control of membrane proteins etc. In plants, both Arc 6 and CPN60 identified in this study are essential in chloroplast division and developments as mutation of either one impairs chloroplast division in Arabidopsis. The facts that we have found the specific association of both α and β CPN60 with FtsH11 protein biochemically, the suppression/ enhancement of ftsh11 thermosensitive phenotype by arc6 /pnp allele genetically, implicate inter-connection of these networks via FtsH11 mediated network(s) in regulating the dynamic adaptation processes of chloroplast to temperature increases at transcriptional, translational and post-translational levels. The conserved role of FtsH11 proteases in maintaining thermostability of chloroplast at HT demonstrated here provides a foundation for improving crop photosynthetic performance at high temperatures.
7
Ohad, Itzhak, and Himadri Pakrasi. Role of Cytochrome B559 in Photoinhibition. United States Department of Agriculture, December 1995. http://dx.doi.org/10.32747/1995.7613031.bard.
Full textAbstract:
The aim of this research project was to obtain information on the role of the cytochrome b559 in the function of Photosystem-II (PSII) with special emphasis on the light induced photo inactivation of PSII and turnover of the photochemical reaction center II protein subunit RCII-D1. The major goals of this project were: 1) Isolation and sequencing of the Chlamydomonas chloroplast psbE and psbF genes encoding the cytochrome b559 a and b subunits respectively; 2) Generation of site directed mutants and testing the effect of such mutation on the function of PSII under various light conditions; 3) To obtain further information on the mechanism of the light induced degradation and replacement of the PSII core proteins. This information shall serve as a basis for the understanding of the role of the cytochrome b559 in the process of photoinhibition and recovery of photosynthetic activity as well as during low light induced turnover of the D1 protein. Unlike in other organisms in which the psbE and psbF genes encoding the a and b subunits of cytochrome b559, are part of an operon which also includes the psbL and psbJ genes, in Chlamydomonas these genes are transcribed from different regions of the chloroplast chromosome. The charge distribution of the derived amino-acid sequences of psbE and psbF gene products differs from that of the corresponding genes in other organisms as far as the rule of "positive charge in" is concerned relative to the process of the polypeptide insertion in the thylakoid membrane. However, the sum of the charges of both subunits corresponds to the above rule possibly indicating co-insertion of both subunits in the process of cytochrome b559 assembly. A plasmid designed for the introduction of site-specific mutations into the psbF gene of C. reinhardtii. was constructed. The vector consists of a DNA fragment from the chromosome of C. reinhardtii which spans the region of the psbF gene, upstream of which the spectinomycin-resistance-conferring aadA cassette was inserted. This vector was successfully used to transform wild type C. reinhardtii cells. The spectinomycin resistant strain thus obtained can grow autotrophically and does not show significant changes as compared to the wild-type strain in PSII activity. The following mutations have been introduced in the psbF gene: H23M; H23Y; W19L and W19. The replacement of H23 involved in the heme binding to M and Y was meant to permit heme binding but eventually alter some or all of the electron transport properties of the mutated cytochrome. Tryptophane W19, a strictly conserved residue, is proximal to the heme and may interact with the tetrapyrole ring. Therefore its replacement may effect the heme properties. A change to tyrosine may have a lesser affect on the potential or electron transfer rate while a replacement of W19 by leucine is meant to introduce a more prominent disturbance in these parameters. Two of the mutants, FW19L and FH23M have segregated already and are homoplasmic. The rest are still grown under selection conditions until complete segregation will be obtained. All mutants contain assembled and functional PSII exhibiting an increased sensitivity of PSII to the light. Work is still in progress for the detailed characterization of the mutants PSII properties. A tobacco mutant, S6, obtained by Maliga and coworkers harboring the F26S mutation in the b subunit was made available to us and was characterized. Measurements of PSII charge separation and recombination, polypeptide content and electron flow indicates that this mutation indeed results in light sensitivity. Presently further work is in progress in the detailed characterization of the properties of all the above mutants. Information was obtained demonstrating that photoinactivation of PSII in vivo initiates a series of progressive changes in the properties of RCII which result in an irreversible modification of the RCII-D1 protein leading to its degradation and replacement. The cleavage process of the modified RCII-D1 protein is regulated by the occupancy of the QB site of RCII by plastoquinone. Newly synthesized D1 protein is not accumulated in a stable form unless integrated in reassembled RCII. Thus the degradation of the irreversibly modified RCII-D1 protein is essential for the recovery process. The light induced degradation of the RCII-D1 protein is rapid in mutants lacking the pD1 processing protease such as in the LF-1 mutant of the unicellular alga Scenedesmus obliquus. In this case the Mn binding site of PSII is abolished, the water oxidation process is inhibited and harmful cation radicals are formed following light induced electron flow in PSII. In such mutants photo-inactivation of PSII is rapid, it is not protected by ligands binding at the QB site and the degradation of the inactivated RCII-D1 occurs rapidly also in the dark. Furthermore the degraded D1 protein can be replaced in the dark in absence of light driven redox controlled reactions. The replacement of the RCII-D1 protein involves the de novo synthesis of the precursor protein, pD1, and its processing at the C-terminus end by an unknown processing protease. In the frame of this work, a gene previously isolated and sequenced by Dr. Pakrasi's group has been identified as encoding the RCII-pD1 C-terminus processing protease in the cyanobacterium Synechocystis sp. PCC 6803. The deduced sequence of the ctpA protein shows significant similarity to the bovine, human and insect interphotoreceptor retinoid-binding proteins. Results obtained using C. reinhardtii cells exposes to low light or series of single turnover light flashes have been also obtained indicating that the process of RCII-D1 protein turnover under non-photoinactivating conditions (low light) may be related to charge recombination in RCII due to back electron flow from the semiquinone QB- to the oxidised S2,3 states of the Mn cluster involved in the water oxidation process.
8
Weller, Joel I., Harris A. Lewin, and Micha Ron. Determination of Allele Frequencies for Quantitative Trait Loci in Commercial Animal Populations. United States Department of Agriculture, February 2005. http://dx.doi.org/10.32747/2005.7586473.bard.
Full textAbstract:
Individual loci affecting economic traits in dairy cattle (ETL) have been detected via linkage to genetic markers by application of the granddaughter design in the US population and the daughter design in the Israeli population. From these analyses it is not possible to determine allelic frequencies in the population at large, or whether the same alleles are segregating in different families. We proposed to answer this question by application of the "modified granddaughter design", in which granddaughters with a common maternal grandsire are both genotyped and analyzed for the economic traits. The objectives of the proposal were: 1) to fine map three segregating ETL previously detected by a daughter design analysis of the Israeli dairy cattle population; 2) to determine the effects of ETL alleles in different families relative to the population mean; 3) for each ETL, to determine the number of alleles and allele frequencies. The ETL on Bostaurusautosome (BT A) 6 chiefly affecting protein concentration was localized to a 4 cM chromosomal segment centered on the microsatellite BM143 by the daughter design. The modified granddaughter design was applied to a single family. The frequency of the allele increasing protein percent was estimated at 0.63+0.06. The hypothesis of equal allelic frequencies was rejected at p<0.05. Segregation of this ETL in the Israeli population was confirmed. The genes IBSP, SPP1, and LAP3 located adjacent to BM143 in the whole genome cattle- human comparative map were used as anchors for the human genome sequence and bovine BAC clones. Fifteen genes within 2 cM upstream of BM143 were located in the orthologous syntenic groups on HSA4q22 and HSA4p15. Only a single gene, SLIT2, was located within 2 cM downstream of BM143 in the orthologous HSA4p15 region. The order of these genes, as derived from physical mapping of BAC end sequences, was identical to the order within the orthologous syntenic groups on HSA4: FAM13A1, HERC3. CEB1, FLJ20637, PP2C-like, ABCG2, PKD2. SPP, MEP, IBSP, LAP3, EG1. KIAA1276, HCAPG, MLR1, BM143, and SLIT2. Four hundred and twenty AI bulls with genetic evaluations were genotyped for 12 SNPs identified in 10 of these genes, and for BM143. Seven SNPs displayed highly significant linkage disequilibrium effects on protein percentage (P<0.000l) with the greatest effect for SPP1. None of SNP genotypes for two sires heterozygous for the ETL, and six sires homozygous for the ETL completely corresponded to the causative mutation. The expression of SPP 1 and ABCG2 in the mammary gland corresponded to the lactation curve, as determined by microarray and QPCR assays, but not in the liver. Anti-sense SPP1 transgenic mice displayed abnormal mammary gland differentiation and milk secretion. Thus SPP 1 is a prime candidate gene for this ETL. We confirmed that DGAT1 is the ETL segregating on BTA 14 that chiefly effects fat concentration, and that the polymorphism is due to a missense mutation in an exon. Four hundred Israeli Holstein bulls were genotyped for this polymorphism, and the change in allelic frequency over the last 20 years was monitored.
9
Gelb, Jr., Jack, Yoram Weisman, Brian Ladman, and Rosie Meir. Identification of Avian Infectious Brochitis Virus Variant Serotypes and Subtypes by PCR Product Cycle Sequencing for the Rational Selection of Effective Vaccines. United States Department of Agriculture, December 2003. http://dx.doi.org/10.32747/2003.7586470.bard.
Full textAbstract:
Objectives 1. Determine the serotypic identities of 40 recent IBV isolates from commercial chickens raised in the USA and Israel. 2. Sequence all IBV field isolates using PCR product cycle sequencing and analyze their S 1 sequence to detennine their homology to other strains in the Genbank and EMBL databases. 3. Select vaccinal strains with the highest S 1 sequence homology to the field isolates and perform challenge of immunity studies in chickens in laboratory trials to detennine level of protection afforded by the vaccines. Background Infectious bronchitis (IB) is a common, economically important disease of the chicken. IB occurs as a respiratory form, associated with airsacculitis, condemnation, and mortality of meat-type broilers, a reproductive form responsible for egg production losses in layers and breeders, and a renal form causing high mortality in broilers and pullets. The causative agent is avian coronavirus infectious bronchitis virus (IBV). Replication of the virus' RNA genome is error-prone and mutations commonly result. A major target for mutation is the gene encoding the spike (S) envelope protein used by the virus to attach and infect the host cell. Mutations in the S gene result in antigenic changes that can lead to the emergence of variant serotypes. The S gene is able to tolerate numerous mutations without compromising the virus' ability to replicate and cause disease. An end result of the virus' "flexibility" is that many strains of IBV are capable of existing in nature. Once formed, new mutant strains, often referred to as variants, are soon subjected to immunological selection so that only the most antigenically novel variants survive in poultry populations. Many novel antigenic variant serotypes and genotypes have been isolated from commercial poultry flocks. Identification of the field isolates of IBV responsible for outbreaks is critical for selecting the appropriate strain(s) for vaccination. Reverse transcriptase polymerase chain reaction (RT-PCR) of the Sl subunit of the envelope spike glycoprotein gene has been a common method used to identify field strains, replacing other time-consuming or less precise tests. Two PCR approaches have been used for identification, restriction fragment length polymorphism (RFLP) and direct automated cycle sequence analysis of a diagnostically relevant hypervariab1e region were compared in our BARD research. Vaccination for IB, although practiced routinely in commercial flocks, is often not protective. Field isolates responsible for outbreaks may be unrelated to the strain(s) used in the vaccination program. However, vaccines may provide varying degrees of cross- protection vs. unrelated field strains so vaccination studies should be performed. Conclusions RFLP and S1 sequence analysis methods were successfully performed using the field isolates from the USA and Israel. Importantly, the S1 sequence analysis method enabled a direct comparison of the genotypes of the field strains by aligning them to sequences in public databases e.g. GenBank. Novel S1 gene sequences were identified in both USA and Israel IBVs but greater diversity was observed in the field isolates from the USA. One novel genotype, characterized in this project, Israel/720/99, is currently being considered for development as an inactivated vaccine. Vaccination with IBV strains in the US (Massachusetts, Arkansas, Delaware 072) or in Israel (Massachusetts, Holland strain) provided higher degrees of cross-protection vs. homologous than heterologous strain challenge. In many cases however, vaccination with two strains (only studies with US strains) produced reasonable cross-protection against heterologous field isolate challenge. Implications S1 sequence analysis provides numerical similarity values and phylogenetic information that can be useful, although by no means conclusive, in developing vaccine control strategies. Identification of many novel S1 genotypes of IBV in the USA is evidence that commercial flocks will be challenged today and in the future with strains unrelated to vaccines. In Israel, monitoring flocks for novel IBV field isolates should continue given the identification of Israel/720/99, and perhaps others in the future. Strains selected for vaccination of commercial flocks should induce cross- protection against unrelated genotypes. Using diverse genotypes for vaccination may result in immunity against unrelated field strains.
10
Weller, Joel I., Derek M. Bickhart, Micha Ron, Eyal Seroussi, George Liu, and George R. Wiggans. Determination of actual polymorphisms responsible for economic trait variation in dairy cattle. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600017.bard.
Full textAbstract:
The project’s general objectives were to determine specific polymorphisms at the DNA level responsible for observed quantitative trait loci (QTLs) and to estimate their effects, frequencies, and selection potential in the Holstein dairy cattle breed. The specific objectives were to (1) localize the causative polymorphisms to small chromosomal segments based on analysis of 52 U.S. Holstein bulls each with at least 100 sons with high-reliability genetic evaluations using the a posteriori granddaughter design; (2) sequence the complete genomes of at least 40 of those bulls to 20 coverage; (3) determine causative polymorphisms based on concordance between the bulls’ genotypes for specific polymorphisms and their status for a QTL; (4) validate putative quantitative trait variants by genotyping a sample of Israeli Holstein cows; and (5) perform gene expression analysis using statistical methodologies, including determination of signatures of selection, based on somatic cells of cows that are homozygous for contrasting quantitative trait variants; and (6) analyze genes with putative quantitative trait variants using data mining techniques. Current methods for genomic evaluation are based on population-wide linkage disequilibrium between markers and actual alleles that affect traits of interest. Those methods have approximately doubled the rate of genetic gain for most traits in the U.S. Holstein population. With determination of causative polymorphisms, increasing the accuracy of genomic evaluations should be possible by including those genotypes as fixed effects in the analysis models. Determination of causative polymorphisms should also yield useful information on gene function and genetic architecture of complex traits. Concordance between QTL genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 30 trait-by-chromosomal segment effects that are segregating in the U.S. Holstein population; a probability of <10²⁰ was used to accept the null hypothesis that no segregating gene within the chromosomal segment was affecting the trait. Genotypes for 83 grandsires and 17,217 sons were determined by either complete sequence or imputation for 3,148,506 polymorphisms across the entire genome. Variant sites were identified from previous studies (such as the 1000 Bull Genomes Project) and from DNA sequencing of bulls unique to this project, which is one of the largest marker variant surveys conducted for the Holstein breed of cattle. Effects for stature on chromosome 11, daughter pregnancy rate on chromosome 18, and protein percentage on chromosome 20 met 3 criteria: (1) complete or nearly complete concordance, (2) nominal significance of the polymorphism effect after correction for all other polymorphisms, and (3) marker coefficient of determination >40% of total multiple-regression coefficient of determination for the 30 polymorphisms with highest concordance. The missense polymorphism Phe279Tyr in GHR at 31,909,478 base pairs on chromosome 20 was confirmed as the causative mutation for fat and protein concentration. For effect on fat percentage, 12 additional missensepolymorphisms on chromosome 14 were found that had nearly complete concordance with the suggested causative polymorphism (missense mutation Ala232Glu in DGAT1). The markers used in routine U.S. genomic evaluations were increased from 60,000 to 80,000 by adding markers for known QTLs and markers detected in BARD and other research projects. Objectives 1 and 2 were completely accomplished, and objective 3 was partially accomplished. Because no new clear-cut causative polymorphisms were discovered, objectives 4 through 6 were not completed.