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1
Hammad, Muhammad, Onder Babur, Hamid Abdul Basit e Mark Van Den Brand. "Clone-Seeker: Effective Code Clone Search Using Annotations". IEEE Access 10 (2022): 11696–713. http://dx.doi.org/10.1109/access.2022.3145686.
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Farhadi, Mohammad Reza, Benjamin C. M. Fung, Yin Bun Fung, Philippe Charland, Stere Preda e Mourad Debbabi. "Scalable code clone search for malware analysis". Digital Investigation 15 (dicembre 2015): 46–60. http://dx.doi.org/10.1016/j.diin.2015.06.001.
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ZHANG, YU, XUMING CHEN, LIHUA WU, ZIQIANG LUO e XIAOJIE LIU. "MHC-INSPIRED ANTIBODY CLONE ALGORITHM". International Journal of Computational Methods 07, n. 02 (giugno 2010): 299–318. http://dx.doi.org/10.1142/s0219876210002179.
Abstract (sommario):
For solving complex optimization problems in some engineering applications, intelligent optimization algorithms based on biological mechanisms have better performance than traditional optimization algorithms. Most of these intelligent algorithms, however, have disadvantages in population diversity and preservation of elitist antibody genes, which lead to the degenerative phenomenon, the zigzag phenomenon, poor global optimization, and low convergence speed. Drawing inspiration from the features of major histocompatibility complex (MHC) in the biological immune system, we propose a novel MHC-inspired antibody clone algorithm (ACAMHC) for solving the above problems. ACAMHC preserves elitist antibody genes through the MHC strings that emulate the MHC haplotype in order to improve its local search capability; it improves the antibody population diversity by gene mutation that mimick the MHC polymorphism to enhance its global search capability. To expand the antibody search space, ACAMHC will add some new random immigrant antibodies with a certain ratio. The convergence of ACAMHC is theoretically proven. The experiments of ACAMHC compared with the canonical clone selection algorithm (CLONALG) on 20 benchmark functions are carried out. The experimental results indicate that the performance of ACAMHC is better than that of CLONALG. The ACAMHC algorithm provides new opportunities for solving previously intractable optimization problems.
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Zhang, Yu, Li Hua Wu e Zi Qiang Luo. "Catastrophe-Based Antibody Clone Algorithm". Applied Mechanics and Materials 121-126 (ottobre 2011): 4415–20. http://dx.doi.org/10.4028/www.scientific.net/amm.121-126.4415.
Abstract (sommario):
In solving complex optimization problems, intelligent optimization algorithms such as immune algorithm show better advantages than traditional optimization algorithms. Most of these immune algorithms, however, have disadvantages in population diversity and preservation of elitist antibodies genes, which will lead to the degenerative phenomenon, the zigzag phenomenon, poor global optimization, and low convergence speed. By introducing the catastrophe factor into the ACAMHC algorithm, we propose a novel catastrophe-based antibody clone algorithm (CACA) to solve the above problems. CACA preserves elitist antibody genes through the vaccine library to improve its local search capability; it improves the antibody population diversity by gene mutation that mimics the catastrophe events to the natural world to enhance its global search capability. To expand the antibody search space, CACA will add some new random immigrant antibodies with a certain ratio. The convergence of CACA is theoretically proved. The experiments of CACA compared with the clone selection algorithm (ACAMHC) on some benchmark functions are carried out. The experimental results indicate that the performance of CACA is better than that of ACAMHC. The CACA algorithm provides new opportunities for solving previously intractable optimization problems.
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Keivanloo, Iman, Chanchal K. Roy e Juergen Rilling. "SeByte: Scalable clone and similarity search for bytecode". Science of Computer Programming 95 (dicembre 2014): 426–44. http://dx.doi.org/10.1016/j.scico.2013.10.006.
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Tan, Yan Song. "An Improved Immune Clone Algorithm Logistics Delivery Strategy". Journal of Advanced Computational Intelligence and Intelligent Informatics 23, n. 2 (20 marzo 2019): 309–12. http://dx.doi.org/10.20965/jaciii.2019.p0309.
Abstract (sommario):
Logistics routing problem is a typical NP hard problem, which is very difficult to solve accurately. On the basis of establishing logistics path optimization model, an immune clone algorithm is proposed. To improve the accuracy of search algorithms, the clonal selection and high frequency variations in the immune algorithm method are introduced. Then the antibody encoding virtual distribution point algorithm is designed to improve search efficiency. The benchmark problem of logistics delivery path optimization is simulated and analyzed. Experimental results show that the proposed immune cloning algorithm expands the range of population search and it have obvious advantages in solving large-scale complex physical distribution optimization problems. Also, the proposed algorithm can solve the optimal distribution of logistics effectively.
7
Park, Jin-woo, Mu-Woong Lee, Jong-Won Roh, Seung-won Hwang e Sunghun Kim. "Surfacing code in the dark: an instant clone search approach". Knowledge and Information Systems 41, n. 3 (3 agosto 2013): 727–59. http://dx.doi.org/10.1007/s10115-013-0677-z.
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Nishi, Manziba Akanda, e Kostadin Damevski. "Scalable code clone detection and search based on adaptive prefix filtering". Journal of Systems and Software 137 (marzo 2018): 130–42. http://dx.doi.org/10.1016/j.jss.2017.11.039.
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Ragkhitwetsagul, Chaiyong, e Jens Krinke. "Siamese: scalable and incremental code clone search via multiple code representations". Empirical Software Engineering 24, n. 4 (5 marzo 2019): 2236–84. http://dx.doi.org/10.1007/s10664-019-09697-7.
10
EL-MATBOULI, M., e H. SOLIMAN. "Construction and screening of a cDNA library from the triactinomyxon spores ofMyxobolus cerebralis, the causative agent of salmonid Whirling Diseases". Parasitology 132, n. 4 (3 gennaio 2006): 467–77. http://dx.doi.org/10.1017/s0031182005009522.
Abstract (sommario):
The ZAP Express cDNA library was constructed using mRNA extracted from the triactinomyxon spores ofMyxobolus cerebralis. First-strand cDNA was synthesized using Moloney Murine leukaemia virus reverse transcriptase. Following second-strand cDNA synthesis, the double-stranded cDNA was digested withXhoI restriction enzyme, cDNA fragments less than 400 bp were removed and the remaining cDNA was ligated with the lambda ZAP Express vector. The recombinants were packagedin vitrousing Gigapack III gold packaging extract. The primary cDNA library titre contained 0·5×106clones, with 97% recombinant and only 3% non-recombinant clones. The cDNA library was then screened using the anti-triactinomyxon antibodies. Positive clones were selected and re-screened twice more to give a final selection of 526 clones. One clone (46-5) was selected randomly and subjected toin vivo excision of the pBK-CMV phagemid from the ZAP express vector. The sequence of the entire clone was obtained using rapid amplification of the cDNA ends. A search of the clone sequence against GenBank revealed that it related to ribosomal protein L23 and it had a high percentage similarity to this protein from different species. A conserved domain for ribosomal protein L23 was also identified in the clone sequence.
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Han, F. P., G. Fedak, T. Ouellet, H. Dan e D. J. Somers. "Mapping of genes expressed in Fusarium graminearum-infected heads of wheat cultivar 'Frontana'". Genome 48, n. 1 (1 febbraio 2005): 88–96. http://dx.doi.org/10.1139/g04-098.
Abstract (sommario):
The isolation, physical, and genetic mapping of a group of wheat genes expressed in infected heads of Triticum aestivum 'Frontana' resistant to Fusarium head blight is reported. A cDNA library was built from heads of 'Frontana' through suppressive subtractive hybridization, to enrich for sequences induced by the pathogen Fusarium graminearum during infection. A group of 1794 clones was screened by dot blot hybridization for differential gene expression following infection. Twenty of these clones showed a strong difference in intensity of hybridization between infected and mock-inoculated wheat head samples, suggesting that they corresponded to genes induced during infection. The 20 clones were sequenced and used for mapping analysis. We determined a precise chromosomal location for 14 selected clones by using series of chromosome deletion stocks. It was shown that the 14 clones detected 90 fragments with the use of the restriction enzyme EcoRI; 52 bands were assigned to chromosome bins, whereas 38 fragments could not be assigned. The selected clones were also screened for polymorphisms on a 'Wuhan' × 'Maringa' wheat doubled haploid mapping population. One clone, Ta01_02b03, was related to a quantitative trait locus for type II resistance located on chromosome 2AL, as determined with simple sequence repeat markers on another mapping population, but did not map in the same location on our population. Another clone, Ta01_06f04, was identified by BLAST (basic local alignment search tool) search in public databases to code for a novel β-1,3-glucanase, homologous to a major pathogenesis-related protein. This clone mapped to chromosomal regions on chromosome 3, including 3BL and 3DL, where B glucanase gene clusters are known to exist. Seven other clones, including 1 coding for an ethylene-response element binding protein and 3 for ribosomal proteins, and 4 clones corresponding to proteins with unknown function, were also mapped.Key words: deletion stock, Fusarium head blight, physical mapping, expressed sequence tags, glucanase.
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ISHIO, Takashi, Naoto MAEDA, Kensuke SHIBUYA, Kenho IWAMOTO e Katsuro INOUE. "NCDSearch: Sliding Window-Based Code Clone Search Using Lempel-Ziv Jaccard Distance". IEICE Transactions on Information and Systems E105.D, n. 5 (1 maggio 2022): 973–81. http://dx.doi.org/10.1587/transinf.2021edp7222.
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Bonnicksen, Andrea L. "Creating a Clone in Ninety Days: In Search of a Cloning Policy". Politics and the Life Sciences 16, n. 2 (settembre 1997): 304–8. http://dx.doi.org/10.1017/s0730938400024874.
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Wei, Y. F., P. Robins, K. Carter, K. Caldecott, D. J. Pappin, G. L. Yu, R. P. Wang, B. K. Shell, R. A. Nash e P. Schär. "Molecular cloning and expression of human cDNAs encoding a novel DNA ligase IV and DNA ligase III, an enzyme active in DNA repair and recombination." Molecular and Cellular Biology 15, n. 6 (giugno 1995): 3206–16. http://dx.doi.org/10.1128/mcb.15.6.3206.
Abstract (sommario):
Three distinct DNA ligases, I to III, have been found previously in mammalian cells, but a cloned cDNA has been identified only for DNA ligase I, an essential enzyme active in DNA replication. A short peptide sequence conserved close to the C terminus of all known eukaryotic DNA ligases was used to search for additional homologous sequences in human cDNA libraries. Two different incomplete cDNA clones that showed partial homology to the conserved peptide were identified. Full-length cDNAs were obtained and expressed by in vitro transcription and translation. The 103-kDa product of one cDNA clone formed a characteristic complex with the XRCC1 DNA repair protein and was identical with the previously described DNA ligase III. DNA ligase III appears closely related to the smaller DNA ligase II. The 96-kDa in vitro translation product of the second cDNA clone was also shown to be an ATP-dependent DNA ligase. A fourth DNA ligase (DNA ligase IV) has been purified from human cells and shown to be identical to the 96-kDa DNA ligase by unique agreement between mass spectrometry data on tryptic peptides from the purified enzyme and the predicted open reading frame of the cloned cDNA. The amino acid sequences of DNA ligases III and IV share a related active-site motif and several short regions of homology with DNA ligase I, other DNA ligases, and RNA capping enzymes. DNA ligases III and IV are encoded by distinct genes located on human chromosomes 17q11.2-12 and 13q33-34, respectively.
15
Abu-Helu, Rasmi. "Cloning and Expression of SARS COV-2 Surface Protein and its Use in Detecting Corona Viral Infections". Al-Quds Journal for Academic Research 01, n. 3 (10 maggio 2023): 28–34. http://dx.doi.org/10.47874/2023:pp:28-34.
Abstract (sommario):
The main aim of this study was to develop indirect enzyme linked immune sorbent assay based on the use of bacterial cloned SARS CoV-2 spike protein as a cheap and continuously available source of antigen. This test was proved to be useful for a quantitative measurement and evaluation of antibody immune response among SARS-CoV-2 infected individuals. Standard cloning procedures had been used in cloning two different segments of the spike gene and its expression. The size of the two cloned segments were of 700 base pair and of 500 base pair, which were named clone 8 and clone 105, respectively. These DNA segments were cloned in pET28a plasmid and then expressed in Bl21 E. coli. Different serum samples were tested from: current, previous infection, vaccinated and non-vaccinated patients using the amplified expressed proteins in enzyme linked immune sorbent assay. The expressed proteins from each clone were responded with varying degrees of sensitivity against COVID-19 positive human sera, and we attempted to validate which of the two recombinant proteins is the best to be used in Corona IgG and IgM antibody detection. Based on the results of indirect enzyme linked immunoassay, most of the tested samples had greater antibody titers with clone 8, which was found to have a higher similarity (99% resemblance) to the severe acute respiratory syndrome coronavirus 2 surface protein using BLAST search. We recommend clone 8 with high potential to be used for large-scale screening for COVID-19 outbreak; nevertheless, it requires greater sensitivity and specificity validation
16
Sriramulu, Dinesh Diraviam. "Small Heat Shock Proteins Produced by Pseudomonas Aeruginosa Clonal Variants Isolated from Diverse Niches". Proteomics Insights 2 (gennaio 2009): PRI.S3760. http://dx.doi.org/10.4137/pri.s3760.
Abstract (sommario):
Genomic islands interspersed in the chromosome of P. aeruginosa led to inter- and intraclonal diversity. Recently, a particular clone of P. aeruginosa called clone C was isolated from cystic fibrosis (CF) patients, clinical and non-clinical habitats throughout Europe and in Canada. P. aeruginosa clone C strains harbour up to several hundred acquired genes involved in the adaptation of bacteria to diverse niches. Two genes ( hp25 and hp18) from one of the hypervariable regions in the chromosome of clone C strains were highly expressed under standard culture conditions as well as under conditions that mimicked CF sputum environment. Protein sequence analysis revealed that Hp25 and Hp18 belonged to small heat shock protein (sHSP) family. Hp25 protein possessed α-crystallin domain, which is a conserved region among heat shock proteins involved in diverse functions. Sequence homology search revealed that in the Methylobacillus flagellatus genome both genes were situated close to each other and the hp25 gene is found among a few other members of Proteobacteria. Expression of hp25 and hp18 by inter- and intraclonal strains of P. aeruginosa suggested that both genes were present in the stable part of the hypervariable region at the toxR locus and might play a role in their adaptation to diverse niches including the CF lung environment.
17
CHEN, JIANYONG, QIUZHEN LIN e LINLIN SHEN. "AN IMMUNE-INSPIRED EVOLUTION STRATEGY FOR CONSTRAINED OPTIMIZATION PROBLEMS". International Journal on Artificial Intelligence Tools 20, n. 03 (giugno 2011): 549–61. http://dx.doi.org/10.1142/s0218213011000279.
Abstract (sommario):
Based on clonal selection principle, this paper proposes an immune-inspired evolution strategy (IIES) for constrained optimization problems with two improvements. Firstly, in order to enhance global search capability, more clones are produced by individuals that have far-off nearest neighbors in the less-crowed regions. On the other hand, immune update mechanism is proposed to replace the worst individuals in clone population with the best individuals stored in immune memory in every generation. Therefore, search direction can always focus on the fittest individuals. These proposals are able to avoid being trapped in local optimal regions and remarkably enhance global search capability. In order to examine the optimization performance of IIES, 13 well-known benchmark test functions are used. When comparing with various state-of-the-arts and recently proposed competent algorithms, simulation results show that IIES performs better or comparably in most cases.
18
Giorda, R., e H. L. Ennis. "Structure of two developmentally regulated Dictyostelium discoideum ubiquitin genes". Molecular and Cellular Biology 7, n. 6 (giugno 1987): 2097–103. http://dx.doi.org/10.1128/mcb.7.6.2097-2103.1987.
Abstract (sommario):
A previously isolated cDNA clone, pLK229, that is specific for mRNA developmentally expressed during Dictyostelium discoideum spore germination and multicellular development, was used to screen two genomic libraries. Two genomic sequences homologous to pLK229 were isolated and sequenced. Genomic clone p229 is identical to the cDNA clone pLK229 and codes for a polypeptide of 381 amino acids. This polypeptide is composed of five tandem repeats of the same 76-amino-acid sequence. Clone lambda 229 codes for a protein of 229 amino acids, containing three tandem repeats of the identical 76-amino-acid sequence. A computer search for homology to known proteins revealed that the 76-amino-acid repeat was identical to human and bovine ubiquitin except for two amino acid differences.
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Giorda, R., e H. L. Ennis. "Structure of two developmentally regulated Dictyostelium discoideum ubiquitin genes." Molecular and Cellular Biology 7, n. 6 (giugno 1987): 2097–103. http://dx.doi.org/10.1128/mcb.7.6.2097.
Abstract (sommario):
A previously isolated cDNA clone, pLK229, that is specific for mRNA developmentally expressed during Dictyostelium discoideum spore germination and multicellular development, was used to screen two genomic libraries. Two genomic sequences homologous to pLK229 were isolated and sequenced. Genomic clone p229 is identical to the cDNA clone pLK229 and codes for a polypeptide of 381 amino acids. This polypeptide is composed of five tandem repeats of the same 76-amino-acid sequence. Clone lambda 229 codes for a protein of 229 amino acids, containing three tandem repeats of the identical 76-amino-acid sequence. A computer search for homology to known proteins revealed that the 76-amino-acid repeat was identical to human and bovine ubiquitin except for two amino acid differences.
20
Zhou, Xu, Yanheng Liu e Bin Li. "A multi-objective discrete cuckoo search algorithm with local search for community detection in complex networks". Modern Physics Letters B 30, n. 07 (20 marzo 2016): 1650080. http://dx.doi.org/10.1142/s0217984916500809.
Abstract (sommario):
Detecting community is a challenging task in analyzing networks. Solving community detection problem by evolutionary algorithm is a heated topic in recent years. In this paper, a multi-objective discrete cuckoo search algorithm with local search (MDCL) for community detection is proposed. To the best of our knowledge, it is first time to apply cuckoo search algorithm for community detection. Two objective functions termed as negative ratio association and ratio cut are to be minimized. These two functions can break through the modularity limitation. In the proposed algorithm, the nest location updating strategy and abandon operator of cuckoo are redefined in discrete form. A local search strategy and a clone operator are proposed to obtain the optimal initial population. The experimental results on synthetic and real-world networks show that the proposed algorithm has better performance than other algorithms and can discover the higher quality community structure without prior information.
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Pereira, Bárbara Luísa Corradi, Aylson Costa Oliveira, Ana Márcia Macedo Ladeira Carvalho, Angélica de Cássia Oliveira Carneiro, Larissa Carvalho Santos e Benedito Rocha Vital. "Quality of Wood and Charcoal fromEucalyptusClones for Ironmaster Use". International Journal of Forestry Research 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/523025.
Abstract (sommario):
Considering the wide variety of species and clones ofEucalyptuscultivated in Brazil, it is necessary to search for new information on wood properties, so that the selection of genetically superior material may be successful. The present study aimed to determine the properties of wood and charcoal from different clones ofEucalyptusspp. Six clones at the age of 7.5 years were evaluated and the samples were from a clonal, located in the city of Lassance, Minas Gerais, Brazil. Basic density, chemical composition, and higher heating value were determined. Carbonizations in a laboratory kiln were done and the levels of volatile matter, ash, and fixed carbon, higher heating value, and bulk density of the charcoal produced were determined. Evaluated genetic materials showed differences in their properties. According to research results, several properties of wood should be considered together for the selection of clones for charcoal production. However, basic density and chemical composition of wood, especially high contents of lignin and low contents of extractives, are the properties that had more influence on charcoal yield and its quality. Concerning charcoal production for steelmaking, clone 6 stood out and, conversely, clone 4 showed inferior properties to those of others.
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Lopez Rubio, Montserrat, Anna Gaya, Marta Morado, Vicente Carrasco, Ataulfo Gonzalez Fernandez e Ana Villegas. "Relationship Between Myelodysplastic Syndrome and Paroxysmal Nocturnal Hemoglobinuria: Spanish Erythropathology Group and Spanish Paroxysmal Nocturnal Hemoglobinuria Working Group Experience". Blood 126, n. 23 (3 dicembre 2015): 4546. http://dx.doi.org/10.1182/blood.v126.23.4546.4546.
Abstract (sommario):
Abstract INTRODUCTION PNH clones appear frequently in patients with myelodysplastic syndrome (MDS) and aplastic anemia (AA) which may even evolve into classic PNH. It has been described isolated cases of clonal evolution from AA, through classic PNH and MDS; and at the end, acute leukemia (AL) has rarely been described. These patients show a progressive replacement of the PNH clone by a dysplastic one carrying a monosomy of chromosome 7. OBJECTIVE We designed a retrospective study of patients included in the database of the Spanish PNH Registry in search of patients with a MDS and a PNH clone or those with a classic PNH who evolved into MDS. Our aim was to study the characteristics of patients who showed some of these entities and AA history. RESULTS Our search retrieved 6 patients, of whom 3 were MDS cases with a small PNH clone (Table 1). One of the patients had had a previous classic PNH followed by a MDS. The remaining two patients had been diagnosed with AA, developing classical PNH and MDS later; of these, one (patient 2) died with an acute leukemia. The median follow-up time was 83 (range 56-480) months, while the follow-up time from diagnosis of MDS was 68 (range 6-108) months. The patient characteristics are describe in Table 1. There are two remarkable features, diagnosis of a RAEB-1 in two cases and the frequency of trisomies of chromosome 8 and 21 and deletion of chromosome 7. These chromosomal abnormalities appeared sequentially as MDS evolved in 3 patients. The PNH clone disappeared in those patients who developed a MDS after an AA/classic PNH and persisted in those MDS cases who showed a PNH clone at diagnosis of MDS. Table 1. Patients Characteristics Previous diagnosis Follow-up time MDS type Karyotype Case 1 None 70 RARS + 8 Case 2 AA + PNH 56 RCMD -7 evolution to -7, + 21 Case 3 Classical PNH 83 RAEB-1 + 8 Case 4 None 83 RAEB-1 +21 evolution to +21, +8 Case 5 AA + classical PNH 480 RCMD + 8 evolution to +8, -7 Case 6 None 108 RCMD Normal CONCLUSIONS Patients with a diagnosis of AA, classic PNH or MDS with a PNH clone must be followed up for life, with bone marrow studies with karyotype and measurements of the PNH clone, to rule out the development of other hematological entities. Our series is a small one and only studies with a larger number of patients will allow us to establish definitive conclusions. The inclusion of these patients in the International PNH Registry is strongly advised. Disclosures No relevant conflicts of interest to declare.
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Sun, Ying, Yuelin Gao e Xudong Shi. "Chaotic Multi-Objective Particle Swarm Optimization Algorithm Incorporating Clone Immunity". Mathematics 7, n. 2 (3 febbraio 2019): 146. http://dx.doi.org/10.3390/math7020146.
Abstract (sommario):
It is generally known that the balance between convergence and diversity is a key issue for solving multi-objective optimization problems. Thus, a chaotic multi-objective particle swarm optimization approach incorporating clone immunity (CICMOPSO) is proposed in this paper. First, points in a non-dominated solution set are mapped to a parallel-cell coordinate system. Then, the status of the particles is evaluated by the Pareto entropy and difference entropy. At the same time, the algorithm parameters are adjusted by feedback information. At the late stage of the algorithm, the local-search ability of the particle swarm still needs to be improved. Logistic mapping and the neighboring immune operator are used to maintain and change the external archive. Experimental test results show that the convergence and diversity of the algorithm are improved.
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Ilnitskaya, Elena Tarasovna, Marina Victorovna Makarkina, Anna Aleksandrovna Marmorshtein, Anton Vladimirovich Prakh, Olga Nikolaevna Shelud'ko, Elena Georgievna Pyata, Ekaterina Aleksandrovna Mitrofanova e Tatiana Dmitrievna Kozina. "SEARCH FOR CLONE VARIATIONS OF SAPERAVI GRAPE VARIETY IN THE PLANTINGS OF THE TEMRYUK DISTRICT". Fruit growing and viticulture of South Russia 6, n. 78 (20 novembre 2022): 396–410. http://dx.doi.org/10.30679/2219-5335-2022-6-78-396-410.
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Gérard, C. M., C. Mollereau, G. Vassart e M. Parmentier. "Molecular cloning of a human cannabinoid receptor which is also expressed in testis". Biochemical Journal 279, n. 1 (1 ottobre 1991): 129–34. http://dx.doi.org/10.1042/bj2790129.
Abstract (sommario):
A cDNA clone encoding a receptor protein which presents all the characteristics of a guanine-nucleotide-binding protein (G-protein)-coupled receptor was isolated from a human brain stem cDNA library. The probe used (HGMP08) was a 600 bp DNA fragment amplified by a low-stringency PCR, using human genomic DNA as template and degenerate oligonucleotide primers corresponding to conserved sequences amongst the known G-protein-coupled receptors. The deduced amino acid sequence encodes a protein of 472 residues which shares 97.3% identity with the rat cannabinoid receptor cloned recently [Matsuda, Lolait, Brownstein, Young & Bronner (1990) Nature (London) 346, 561-564]. Abundant transcripts were detected in the brain, as expected, but lower amounts were also found in the testis. The same probe was used to screen a human testis cDNA library. The cDNA clones obtained were partially sequenced, demonstrating the identity of the cannabinoid receptors expressed in both tissues. Specific binding of the synthetic cannabinoid ligand [3H]CP55940 was observed on membranes from Cos-7 cells transfected with the recombinant receptor clone. In stably transfected CHO-K1 cell lines, cannabinoid agonists mediated a dose-dependent and stereoselective inhibition of forskolin-induced cyclic AMP accumulation. The ability to express the human cannabinoid receptor in mammalian cells should help in developing more selective drugs, and should facilitate the search for the endogenous cannabinoid ligand(s).
26
Ishii, Kotaro, Ryuji Sugiyama, Megumi Onuki, Yusuke Kazama, Sachihiro Matsunaga e Shigeyuki Kawano. "The Y chromosome-specific STS marker MS2 and its peripheral regions on the Y chromosome of the dioecious plant Silene latifolia". Genome 51, n. 4 (aprile 2008): 251–60. http://dx.doi.org/10.1139/g08-005.
Abstract (sommario):
Sex determination in Silene latifolia uses the XX/XY system. The recent evolution of dioecy in S. latifolia provides a unique opportunity to study the early stages of Y chromosome evolution. However, the current Y chromosome map still contains many large gaps with no available markers. In this study, a sequence tagged site (STS) marker, MS2, was isolated and mapped to the same locus as L8 on the Y chromosome. To investigate the peripheral regions of MS2, a bacterial artificial chromosome (BAC) library was constructed from a male plant, and the BAC clone containing MS2 (MS2-9d12F) was isolated from 32 640 clones with an average insert size of 115 kb. A 109-kb insert of the BAC clone was analyzed. BLASTX analysis showed 11 sequences similar to some known proteins, most of which are retrotransposon-like elements. The ORF Finder predicted 9 ORFs within MS2-9d12F. RT-PCR analyses revealed that only 4 of the 9 predicted ORFs are expressed in both male and female plants. These 4 ORFs are candidates for genes having counterparts on both the X and Y chromosomes. Dot-matrix plot analysis and a BLASTN search revealed LTR-like sequences close to the retrotransposon-like elements and high similarity to 3 known genomic sequences of S. latifolia. These results suggest an accumulation of retrotransposons and segmental duplications in peripheral regions of MS2 during the early stage of sex chromosome evolution.
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Griscelli-Bennaceur, A., E. Gluckman, ML Scrobohaci, P. Jonveaux, T. Vu, A. Bazarbachi, ED Carosella, F. Sigaux e G. Socie. "Aplastic anemia and paroxysmal nocturnal hemoglobinuria: search for a pathogenetic link". Blood 85, n. 5 (1 marzo 1995): 1354–63. http://dx.doi.org/10.1182/blood.v85.5.1354.bloodjournal8551354.
Abstract (sommario):
The association of paroxysmal nocturnal hemoglobinuria (PNH) and aplastic anemia (AA) raises the yet unresolved questions as to whether these two disorders are different forms of the same disease. We compared two groups of patients with respect to cytogenetic features, glycosylphosphatidylinositol (GPI)-linked protein expression, protein C/protein S/thrombomodulin/antithrombin III activity, and PIG-A gene expression. The first group consisted of eight patients with PNH (defined as positive Ham and sucrose tests at diagnosis), and the second, 37 patients with AA. Twelve patients with AA later developed a PNH clone. Monoclonal antibodies used to study GPI-linked protein expression (CD14 [on monocytes], CD16 [on neutrophils], CD48 [on lymphocytes and monocytes], CD67 [on neutrophils and eosinophils], and, more recently, CD55, CD58, and CD59 [on erythrocytes]) were also tested on a cohort of 20 normal subjects and five patients with constitutional AA. Ham and sucrose tests were performed on the same day as flow- cytometric analysis. Six of 12 patients with AA, who secondarily developed a PNH clone, had clinical symptoms, while all eight patients with PNH had pancytopenia and/or thrombosis and/or hemolytic anemia. Cytogenetic features were normal in all but two patients. Proteins C and S, thrombomodulin, and antithrombin III levels were within the normal range in patients with PNH and in those with AA (with or without a PNH clone). In patients with PNH, CD16 and CD67 expression were deficient in 78% to 98% of the cells and CD14 in 76% to 100%. By comparison, a GPI-linked defect was detected in 13 patients with AA, affecting a mean of 32% and 33% of CD16/CD67 and CD14 cell populations, respectively. Two of three tested patients with PNH and 1 of 12 patients with AA had a defect in the CD48 lymphocyte population. In a follow-up study of our patient cohort, we used the GPI-linked molecules on granulocytes and monocytes investigated earlier and added the study of CD55, CD58, and CD59 on erythrocytes. Two patients with PNH and 14 with AA were studied for 6 to 13 months after the initial study. Among patients with AA, four in whom no GPI-anchoring defect was detected in the first study had no defect in follow-up studies of all blood-cell subsets (including erythrocytes). Analysis of granulocytes, monocytes, and erythrocytes was performed in 7 of 13 AA patients in whom affected monocytes and granulocytes were previously detected. A GPI-anchoring defect was detected on erythrocytes in five of six.(ABSTRACT TRUNCATED AT 400 WORDS)
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Katsu, Yoshinao, Shin Oana, Xiaozhi Lin, Susumu Hyodo, Laurent Bianchetti e Michael E. Baker. "Cloning of nine glucocorticoid receptor isoforms from the slender African lungfish (Protopterus dolloi)". PLOS ONE 17, n. 8 (1 agosto 2022): e0272219. http://dx.doi.org/10.1371/journal.pone.0272219.
Abstract (sommario):
We wanted to clone the glucocorticoid receptor (GR) from slender African lungfish (Protopterus dolloi) for comparison to the P. dolloi mineralocorticoid receptor (MR), which we had cloned and were characterizing, as well as for comparison to the GRs from humans, elephant shark and zebrafish. However, although sequencing of the genome of the Australian lungfish (Neoceratodus forsteri), as well as, that of the West African lungfish (Protopterus annectens) were reported in the first three months of 2021, we could not retrieve a GR sequence with a BLAST search of GenBank, when we submitted our research for publication in July 2021. Moreover, we were unsuccessful in cloning the GR from slender African lungfish using a cDNA from the ovary of P. dolloi and PCR primers that had successfully cloned a GR from elephant shark, Xenopus and gar GRs. On October 21, 2021 the nucleotide sequence of West African lungfish (P. annectens) GR was deposited in GenBank. We used this GR sequence to construct PCR primers that successfully cloned the GR from the slender spotted lungfish. Here, we report the sequences of nine P. dolloi GR isoforms and explain the basis for the previous failure to clone a GR from slender African lungfish using PCR primers that cloned the GR from elephant shark, Xenopus and gar. Studies are underway to determine corticosteroid activation of these slender African lungfish GRs.
29
Pereira, Leonardo T., e Claudio F. M. Toledo. "Speeding up Search-Based Algorithms for Level Generation in Physics-Based Puzzle Games". International Journal on Artificial Intelligence Tools 26, n. 05 (ottobre 2017): 1760019. http://dx.doi.org/10.1142/s0218213017600193.
Abstract (sommario):
This research uses Machine Learning (ML) techniques in order to aid search-based (SB) algorithms to improve level generation for physics-based puzzle games. These algorithms’ performance are improved by reducing simulation time when the ML techniques are applied. Classification algorithms prevent levels with undesired traits to be evaluated during the simulation phase of the SB procedures. An Angry Birds clone is used for conducting the experiments and results report improvement using the combined approach against every SB algorithm by itself.
30
Delandre, Océane, Ombeline Lamer, Jean-Marie Loreau, Nasserdine Papa Mze, Isabelle Fonta, Joel Mosnier, Nicolas Gomez, Emilie Javelle e Bruno Pradines. "Long-Read Sequencing and De Novo Genome Assembly Pipeline of Two Plasmodium falciparum Clones (Pf3D7, PfW2) Using Only the PromethION Sequencer from Oxford Nanopore Technologies without Whole-Genome Amplification". Biology 13, n. 2 (31 gennaio 2024): 89. http://dx.doi.org/10.3390/biology13020089.
Abstract (sommario):
Antimalarial drug resistance has become a real public health problem despite WHO measures. New sequencing technologies make it possible to investigate genomic variations associated with resistant phenotypes at the genome-wide scale. Based on the use of hemisynthetic nanopores, the PromethION technology from Oxford Nanopore Technologies can produce long-read sequences, in contrast to previous short-read technologies used as the gold standard to sequence Plasmodium. Two clones of P. falciparum (Pf3D7 and PfW2) were sequenced in long-read using the PromethION sequencer from Oxford Nanopore Technologies without genomic amplification. This made it possible to create a processing analysis pipeline for human Plasmodium with ONT Fastq only. De novo assembly revealed N50 lengths of 18,488 kb and 17,502 kb for the Pf3D7 and PfW2, respectively. The genome size was estimated at 23,235,407 base pairs for the Pf3D7 clone and 21,712,038 base pairs for the PfW2 clone. The average genome coverage depth was estimated at 787X and 653X for the Pf3D7 and PfW2 clones, respectively. This study proposes an assembly processing pipeline for the human Plasmodium genome using software adapted to large ONT data and the high AT percentage of Plasmodium. This search provides all the parameters which were optimized for use with the software selected in the pipeline.
31
Castañeda-Sánchez, Jorge I., Everardo Curiel-Quesada, Miguel Pedrosa-Seres, Mario E. Cancino-Diaz, Sandra Rodríguez-Martínez e Juan C. Cancino-Diaz. "Peptidic sequence “HSEAETGPP” is recognized by the sera of pars planitis patients". Clinical & Investigative Medicine 32, n. 3 (1 giugno 2009): 206. http://dx.doi.org/10.25011/cim.v32i3.6109.
Abstract (sommario):
Purpose: HLA class II, p-36 protein, heat shock protein and retinal antigens have been associated with pars planitis (PP), but their participation in the development of the disease are unknown. A search for new molecules related to PP is necessary. This work focused on the identification of peptides recognized by PP patient sera using the phage display method. Methods: Sera of PP patients were used to isolate peptides fused to M13-phage pIII protein. The response of PP and healthy sera to peptides was determined by ELISA. PCR amplification and sequencing of peptide-encoding fragments from clones with high recognition by PP sera were used to characterize displayed peptides. Results: One hundred clones were randomly selected from a phage display library after three panning rounds using serum proteins from a PP patient. The immunologic response level of 100 clones selected were determined with a major number of patients, it was found that one clone was recognized stronger in PP patients sera than in healthy sera (PP vs. healthy; P < 0.05). The peptide-encoding region of this clone was sequenced and translated. The peptide sequence corresponded to HSEAETGPP. An identical amino acid sequence to HSEAETGPP is found in the human proline-rich transmembrane protein 2 which has not been related with eye diseases. Conclusion: These results suggest that the peptide HSEAETGPP is associated with PP.
32
Rokka, V. M., M. S. Clark, D. L. Knudson, E. Pehu e NLV Lapitan. "Cytological and molecular characterization of repetitive DNA sequences of Solanum brevidens and Solanum tuberosum". Genome 41, n. 4 (1 agosto 1998): 487–94. http://dx.doi.org/10.1139/g98-047.
Abstract (sommario):
The chromosomal distribution, copy numbers, and nucleotide sequences were determined for four repetitive DNA clones, pSB1 and pSB7 of Solanum brevidens and pST3 and pST10 of Solanum tuberosum. Using fluorescence in situ hybridization (FISH), pSB1 and pSB7 were localized near the telomeres and in some centromeric and interstitial sites of S. brevidens chromosomes, but not in S. tuberosum chromosomes, after high stringency washes. The clone pST3 showed signals in the telomeric areas of a few chromosomes in S. tuberosum, but signals were not detected in S. brevidens. All three repeated sequences (pSB1, pSB7, and pST3) were detected in chromosomal areas that are typically known to contain tandemly repeated sequences. The S. tuberosum clone pST10 did not show signals in either species even at low stringency conditions. The estimated copy numbers of the four clones were 1500, 6750, 300, and 400 for pSB1, pSB7, pST3, and pST10, respectively, in the corresponding haploid genomes (S. brevidens and S. tuberosum). The inserts of the four clones pSB1, pSB7, pST3, and pST10 were 322, 167, 845, and 121 bp, respectively. After sequencing, no significant sequence homologies were found among the four clones. A homology search in sequence data bases showed that pSB7 has variable homology (78-100%) with another repetitive sequence of S. brevidens Sb4/2 depending on its subrepeat. It also showed some homology with one repeat of tomato (pLEG15) and one repeat of Solanum circaeifolium (pSC15).Key words: chromosome, copy number, fluorescence in situ hybridization, FISH, nucleotide sequence, potato.
33
Fritzler, M. J., J. C. Hamel, R. L. Ochs e E. K. Chan. "Molecular characterization of two human autoantigens: unique cDNAs encoding 95- and 160-kD proteins of a putative family in the Golgi complex." Journal of Experimental Medicine 178, n. 1 (1 luglio 1993): 49–62. http://dx.doi.org/10.1084/jem.178.1.49.
Abstract (sommario):
Serum autoantibodies from a patient with autoantibodies directed against the Golgi complex were used to screen clones from a HepG2 lambda Zap cDNA library. Three related clones, designated SY2, SY10, and SY11, encoding two distinct polypeptides were purified for further analysis. Antibodies affinity purified by adsorption to the lambda Zap-cloned recombinant proteins and antibodies from NZW rabbits immunized with purified recombinant proteins reproduced Golgi staining and bound two different proteins, 95 and 160 kD, from whole cell extracts. The SY11 protein was provisionally named golgin-95 and the SY2/SY10 protein was named golgin-160. The deduced amino acid sequence of the cDNA clone of SY2 and SY11 represented 58.7- and 70-kD proteins of 568 and 620 amino acids. The in vitro translation products of SY2 and SY11 cDNAs migrated in SDS-PAGE at 65 and 95 kD, respectively. The in vitro translated proteins were immunoprecipitated by human anti-Golgi serum or immune rabbit serum, but not by normal human serum or preimmune rabbit serum. Features of the cDNA suggested that SY11 was a full-length clone encoding golgin-95 but SY2 and SY10 together encoded a partial sequence of golgin-160. Analysis of the SY11 recombinant protein identified a leucine zipper spanning positions 419-455, a glutamic acid-rich tract spanning positions 322-333, and a proline-rich tract spanning positions 67-73. A search of the SwissProt data bank indicated sequence similarity of SY11 to human restin, the heavy chain of kinesin, and the heavy chain of myosin. SY2 shared sequence similarity with the heavy chain of myosin, the USO1 transport protein from yeast, and the 150-kD cytoplasmic dynein-associated polypeptide. Sequence analysis demonstrated that golgin-95 and golgin-160 share 43% sequence similarity and, therefore, may be functionally related proteins.
34
Pagani, I. S., P. Dang, V. A. Saunders, R. Grose, N. Shanmuganathan, L. Carne, Z. Rwodzi et al. "S885 IN SEARCH OF THE RESIDUAL LEUKAEMIC CLONE IN CHRONIC MYELOID LEUKAEMIA PATIENTS IN TREATMENT-FREE REMISSION". HemaSphere 3, S1 (giugno 2019): 398. http://dx.doi.org/10.1097/01.hs9.0000561820.12198.70.
35
Trusty, Andrew, Santiago Santiago Ontañón e Ashwin Ram. "Stochastic Plan Optimization in Real-Time Strategy Games". Proceedings of the AAAI Conference on Artificial Intelligence and Interactive Digital Entertainment 4, n. 1 (27 settembre 2021): 126–31. http://dx.doi.org/10.1609/aiide.v4i1.18684.
Abstract (sommario):
We present a domain independent off-line adaptation technique called Stochastic Plan Optimization for finding and improving plans in real-time strategy games. Our method is based on ideas from genetic algorithms but we utilize a different representation for our plans and an alternate initialization procedure for our search process. The key to our technique is the use of expert plans to initialize our search in the most relevant parts of plan space. Our experiments validate this approach using our existing case based reasoning system Darmok in the real-time strategy game Wargus, a clone of Warcraft II.
36
Sobrinho-Simões, Manuel, Vicki Wilczek, Joannah Score, Nicholas C. P. Cross, Jane F. Apperley e Junia V. Melo. "In search of the original leukemic clone in chronic myeloid leukemia patients in complete molecular remission after stem cell transplantation or imatinib". Blood 116, n. 8 (26 agosto 2010): 1329–35. http://dx.doi.org/10.1182/blood-2009-11-255109.
Abstract (sommario):
Abstract It is not clear if absence of BCR-ABL transcripts—complete molecular response (CMR)—is synonymous with, or required for, cure of chronic myeloid leukemia (CML). Some patients achieve CMR with imatinib (IM), but most relapse shortly after treatment discontinuation. Furthermore, most patients in long-term remission (LTR) post–stem cell transplantation (SCT) are considered functionally cured, although some remain occasionally positive for low-level BCR-ABL mRNA. Interpretation of the latter is complicated because it has been observed in healthy subjects. We designed a patient-specific, highly sensitive, DNA quantitative polymerase chain reaction to test follow-up samples for the original leukemic clone, identified by its unique genomic BCR-ABL fusion (gBCR-ABL). In 5 IM-treated patients in CMR, gBCR-ABL was detected in transcript-negative samples; 4 patients became gBCR-ABL-negative with continuing IM therapy. In contrast, of 9 patients in LTR (13-27 years) post-SCT, gBCR-ABL was detected in only 1, despite occasional transcript-positive samples in 8 of them. In conclusion, in IM-treated patients, absence of transcripts should not be interpreted as absence of the leukemic clone, although continuing IM after achievement of CMR may lead to further reduction of residual disease. Post-SCT, we found little evidence that the transcripts occasionally detected originate from the leukemic clone.
37
Serce, S., e J. F. Hancock. "195 Sexual and Vegetative Performance of Native and Cultivated Day-neutral Strawberries under Moderate and High Temperatures". HortScience 35, n. 3 (giugno 2000): 424D—424. http://dx.doi.org/10.21273/hortsci.35.3.424d.
Abstract (sommario):
A common complaint with day-neutral strawberries is that they perform poorly in mid-summer heat. Since most modern day-neutral cultivars are derived from the same Fragaria virginiana ssp. glauca clone from Utah, we felt it prudent to search for alternate sources of day-neutrality that were more heat-tolerant. We compared the sexual and vegetative performance of nine F. virginiana clones from a wide range of environments including the Utah site, and four F. × ananassa day-neutral types (`Aromas', `Fort Laramie', `Ogallala', and `Tribute') under constant temperatures of 18, 22, 26, and 30 °C and 12-h days. `Aromas' and `Tribute' carry the Utah source of day-neutrality, while `Fort Laramie' and `Ogallala' are old cultivars that have a different, complex background. After a 4-week period of acclimation, we counted the number of crowns, inflorescences, flowers, stolons, and daughter plants that emerged over a 10-week period, and measured the dry weights of component parts. ANOVA tables revealed that temperature regime (T), genotypes (G), and T*G were significant for flower number (FLN) and total dry matter accumulation, while species and T*G were significant for daughter plant number (DPN). Mean FLNs across the four temperatures were 6.8, 3.7, 3.3, and 1.2, while mean DPNs were 0.7, 0.9, 0.7, and 1.8. F. virginiana clones averaged 3.8 FLNs and 1.8 DPNs, while the F. × ananassa clones averaged 4.1 FLNs and 0.2 DPNs. There was generally more variability among the F. virginiana clones than the F. × ananassa clones, but the F. × ananassa cultivars, `Fort Laramie' and `Ogallala', performed best at 30 °C. The Wasatch clone did not flower in any treatment, suggesting it is not day-neutral.
38
Heath, Victoria, Elaine Cloutman-Green, Samuel Watkin, Magdalena Karlikowska, Derren Ready, James Hatcher, Nicola Pearce-Smith, Colin Brown e Alicia Demirjian. "Staphylococcus capitis: Review of Its Role in Infections and Outbreaks". Antibiotics 12, n. 4 (29 marzo 2023): 669. http://dx.doi.org/10.3390/antibiotics12040669.
Abstract (sommario):
In June 2021, a national incident team was formed due to an increased detection of Staphylococcus capitis in samples from hospitalised infants. Staphylococcus capitis has been known to cause outbreaks in neonatal units across the globe, but the extent of the UK spread was unclear. A literature review was undertaken to support case identification, clinical management and environmental infection control. A literature search was undertaken on multiple databases from inception to 24 May 2021, using keywords such as “Staphylococcus capitis”, “NRCS-A”, “S. capitis”, “neonate”, “newborn” and “neonatal intensive care unit” (NICU). After screening, 223 articles of relevance were included. Results show incidences of S. capitis outbreaks have frequently been associated with the outbreak clone (NRCS-A) and environmental sources. The NRCS-A harbours a multidrug resistance profile that includes resistance to beta-lactam antibiotics and aminoglycosides, with several papers noting resistance or heteroresistance to vancomycin. The NRCS-A clone also harbours a novel SCCmec-SCCcad/ars/cop composite island and increased vancomycin resistance. The S. capitis NRCS-A clone has been detected for decades, but the reasons for the potentially increased frequency are unclear, as are the most effective interventions to manage outbreaks associated with this clone. This supports the need for improvements in environmental control and decontamination strategies to prevent transmission.
39
G, Anbarasi, e Vishnupriya B. "Molecular identification and phylogenetic analysis of suaeda maritima from parangipettai coastal areas, southeast coast of india". Kongunadu Research Journal 7, n. 1 (15 aprile 2020): 28–34. http://dx.doi.org/10.26524/krj.2020.5.
Abstract (sommario):
Conventional taxonomy is limited with delineating species and controversies arise with DNA barcoding based identifications. Hence, an alternative supporting approach is very much needed to identify species and differentiate them within the species based on the genetic material. 18S rRNA genes have been particularly helpful in analyzing phylogeny at the species level. In addition, bioinformatics which represents a new, growing area of science uses computational approaches to answer biological questions. Salt tolerant costal salt marsh plant of Suaeda maritima was selected for 18s rRNA sequencing to solve the ambiguity in itsspecies level identification. Similarity search of study species shared 99% similarity with 5 species of Atriplex canescens clone s128, Atriplex torreyi var. griffithsii clone p508, Spinacia oleracea, Oenothera laciniata clone,Beta vulgaris. Phylogenetic tree infer that S.maritima is closely related to Spinacia oleracea and Oenothera laciniata. Atriplex canescens (fourwing saltbush), Atriplex torreyi and Phaulothamnus spinescens, Celosia argentea found to be closely related and are in one group. Hence, this study result clearly shows thus study species evaluated from angiosperm and provides key step in understanding the evolution of salt tolerance in angiosperm.
40
Pawlik, Piotr, Kristiana K. Grigoriadis, Abigail Bunkum, Simone Zaccaria, Nicholas McGranahan e Charles Swanton. "Abstract 1200: A novel algorithm for deconvolving cancer allele-specific clone copy number and copy number evolution". Cancer Research 84, n. 6_Supplement (22 marzo 2024): 1200. http://dx.doi.org/10.1158/1538-7445.am2024-1200.
Abstract (sommario):
Abstract Both single nucleotide variants (SNVs) and somatic copy number alterations (SCNAs) accumulate in cancer cells during tumor development, fuelling clonal evolution. However, accurate inference of their coevolution from bulk DNA sequencing is challenging. We present ALPACA (ALlele-specific Phylogenetic Analysis of clone Copy number Alterations), a novel algorithm to allow the practical inference of SNV and SCNA coevolution. ALPACA is framed as an optimisation problem, that takes as input bulk tumor sample copy number mixtures and the tumor phylogenetic tree constructed from SNVs, and deconvolves the optimal, allele-specific integer copy number profiles for every distinct clone present in the tumor. To circumvent the challenge of joint SNV/SCNA inference, we postulate that in high mutation burden tumors all relevant SCNA clones are identifiable by their unique SNVs, hence ALPACA leverages phylogenetic trees constructed from bulk tumor sequencing data using SNVs. Secondly, to restrict the clone-specific copy number search space, ALPACA leverages constraints imposed by multisample sequencing, specifically in cases where clones are present across multiple samples or clones from different samples are phylogenetically related. Finally, ALPACA relies on parsimony and biologically informed constraints to further guide the deconvolution process. We demonstrate that ALPACA infers the copy number evolution of complex simulated tumors with higher accuracy than current state-of-the-art methods. We apply ALPACA to the large, multisample non-small cell lung cancer (NSCLC) cohort from the recent longitudinal, prospective TRACERx421 study, and show that ALPACA uncovers loss of heterozygosity and amplification events in minor subclones that were previously missed using standard approaches. ALPACA's assignment of SCNA driver events to branches of the phylogenetic tree reveals the evolutionary ordering of SNVs and SCNAs during NSCLC tumor evolution, such as late focal amplifications affecting the TERT gene locus occurring in subclones which expand and dominate a tumor sample. ALPACA enables an in-depth analysis of the coevolution of mutations and SCNAs in the tumor’s evolutionary history, revealing distinct patterns of copy number evolution. Notably, ALPACA identifies common patterns of copy number changes across the genome characterizing metastatic seeding clones, revealing that they harbor an increased number of SCNAs compared to clones that do not metastasize. Additionally, ALPACA uncovers subclonal enrichment for CCND1 amplification in primary tumor subclones that seed metastasis, and an overall increase of SCNA events occurring in both tumors with polyclonal seeding and extrathoracic metastases. Clone-level results obtained with ALPACA can offer new clinical insights and enable new types of analysis, e.g. copy number signature analysis including temporal order of SCNA acquisition. Citation Format: Piotr Pawlik, Kristiana K. Grigoriadis, Abigail Bunkum, Simone Zaccaria, Nicholas McGranahan, Charles Swanton. A novel algorithm for deconvolving cancer allele-specific clone copy number and copy number evolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1200.
41
Bowell, Edward, Robert L. Millis, Edward W. Dunham, Bruce W. Koehn e Byron W. Smith. "Searching for NEOs using Lowell observatorys Discovery Channel Telescope (DCT)". Proceedings of the International Astronomical Union 2, S236 (agosto 2006): 363–70. http://dx.doi.org/10.1017/s1743921307003432.
Abstract (sommario):
AbstractWe discuss the potential contribution of the Discovery Channel Telescope (or a clone) to a detection program aimed at discovering 90% of potentially hazardous objects (PHOs) larger than 140 m in diameter. Three options are described, each involving different levels of investment. We believe that LSST, Pan-STARRS, and DCT, working in a coordinated fashion, offer a cost-effective, low-risk way to accomplish the objectives of the extended NEO search program.
42
Zha, Zhihua, Chaoqun Li, Jing Xiao, Yao Zhang, Hu Qin, Yang Liu, Jie Zhou e Jie Wu. "An Improved Adaptive Clone Genetic Algorithm for Task Allocation Optimization in ITWSNs". Journal of Sensors 2021 (5 aprile 2021): 1–12. http://dx.doi.org/10.1155/2021/5582646.
Abstract (sommario):
Research on intelligent transportation wireless sensor networks (ITWSNs) plays a very important role in an intelligent transportation system. ITWSNs deploy high-yield and low-energy-consumption traffic remote sensing sensor nodes with complex traffic parameter coordination on both sides of the road and use the self-organizing capabilities of each node to automatically establish the entire network. In the large-scale self-organization process, the importance of tasks undertaken by each node is different. It is not difficult to prove that the task allocation of traffic remote sensing sensors is an NP-hard problem, and an efficient task allocation strategy is necessary for the ITWSNs. This paper proposes an improved adaptive clone genetic algorithm (IACGA) to solve the problem of task allocation in ITWSNs. The algorithm uses a clonal expansion operator to speed up the convergence rate and uses an adaptive operator to improve the global search capability. To verify the performance of the IACGA for task allocation optimization in ITWSNs, the algorithm is compared with the elite genetic algorithm (EGA), the simulated annealing (SA), and the shuffled frog leaping algorithm (SFLA). The simulation results show that the execution performance of the IACGA is higher than EGA, SA, and SFLA. Moreover, the convergence speed of the IACGA is faster. In addition, the revenue of ITWSNs using IACGA is higher than those of EGA, SA, and SFLA. Therefore, the proposed algorithm can effectively improve the revenue of the entire ITWSN system.
43
ZHU, HUILI, LIXIN XU, RUOFENG YAN, XIAOKAI SONG, FANG TANG, SONG WANG e XIANGRUI LI. "Identification and characterization of a cDNA clone-encoding antigen of Eimeria acervulina". Parasitology 139, n. 13 (21 agosto 2012): 1711–19. http://dx.doi.org/10.1017/s0031182012001163.
Abstract (sommario):
SUMMARYEimeria spp. are the causative agents of coccidiosis, a major disease affecting the poultry industry. So far, only a few antigen genes of E. acervulina have been reported. In this study, a clone, named as cSZ-JN2, was identified from a cDNA expression library prepared from E. acervulina sporozoite stage with the ability to stimulate the chicken immune response. The sequence analysis showed that the open reading fragment (ORF) of cSZ-JN2 was 153 bp in size and encoded a predicted protein of 50 amino acids of Mr 5·3 kDa. BLASTN search revealed that cSZ-JN2 had no significant homology with the known genes of E. acervulina or any other organism (GenBank). The recombinant cSZ-JN2 antigen expressed in E. coli was recognized strongly by serum from chickens experimentally infected with E. acervulina. Immunofluorescence analysis using antibody against recombinant cSZ-JN2 indicated that this protein was expressed in sporozoite and merozoite developmental stages. Animal challenge experiments demonstrated that the recombinant protein of cSZ-JN2 and DNA vaccine carrying cSZ-JN2 could significantly increase the average body weight gains, decrease the mean lesion scores and the oocyst outputs of the immunized chickens and presented anti-coccidial indices of more than 165. All the above results suggested that the cSZ-JN2 was a novel E. acervulina antigen and could be an effective candidate for the development of a new vaccine against E. acervulina infection.
44
Doosti, Abbas, Ghasemi Dehkordi e Hosein Khodabakhsh. "cDNA cloning and sequencing of ostrich Growth hormone". Archives of Biological Sciences 64, n. 2 (2012): 445–49. http://dx.doi.org/10.2298/abs1202445d.
Abstract (sommario):
In recent years, industrial breeding of ostrich (Struthio camelus) has been widely developed in Iran. Growth hormone (GH) is a peptide hormone that stimulates growth and cell reproduction in different animals. The aim of this study was to clone and sequence the ostrich growth hormone gene in E. coli, done for the first time in Iran. The cDNA that encodes ostrich growth hormone was isolated from total mRNA of the pituitary gland and amplified by RT-PCR using GH specific PCR primers. Then GH cDNA was cloned by T/A cloning technique and the construct was transformed into E. coli. Finally, GH cDNA sequence was submitted to the GenBank (Accession number: JN559394). The results of present study showed that GH cDNA was successfully cloned in E. coli. Sequencing confirmed that GH cDNA was cloned and that the length of ostrich GH cDNA was 672 bp; BLAST search showed that the sequence of growth hormone cDNA of the ostrich from Iran has 100% homology with other records existing in GenBank.
45
Yin-Hua, Chen, Ouyang Bo, Li Han-Xia e Ye Zhi-Biao. "Cloning of ACO gene and inhibition of ethylene evolution in tomatoes with RNAi". Chinese Journal of Agricultural Biotechnology 4, n. 3 (dicembre 2007): 193–97. http://dx.doi.org/10.1017/s1479236207001775.
Abstract (sommario):
AbstractA 1018 bp fragment of the ACO gene cDNA sequence was cloned from tomato (Lycopersicon esculentum) leaves incubated with a pathogen mixture using reverse transcriptase-polymerase chain reaction (RT-PCR) with two PCR primers designed according to the sequence of a tomato cDNA clone (E11). A BLAST search showed the sequence presenting a very high match with the ACO genes in other plants, with 83–99% homology. Using this sequence, an RNA interference (RNAi) transformation vector (pD311) was constructed and transformed into tomato. Twenty-seven regenerated plants with kanamycin resistance were obtained, showing that the transgene was integrated into the tomato genome; this was confirmed by PCR and Southern blotting. Ethylene production by the RNAi transgenic tomato plants was measured by gas chromatography, and showed that ethylene evolution was specifically inhibited in leaves and fruits of the transgenic plants.
46
Beer, Philip A., François Delhommeau, Jean-Pierre LeCouédic, Mark A. Dawson, Edwin Chen, David Bareford, Rajko Kušec et al. "Two routes to leukemic transformation after a JAK2 mutation–positive myeloproliferative neoplasm". Blood 115, n. 14 (8 aprile 2010): 2891–900. http://dx.doi.org/10.1182/blood-2009-08-236596.
Abstract (sommario):
Abstract Acute myeloid leukemia (AML) may follow a JAK2-positive myeloproliferative neoplasm (MPN), although the mechanisms of disease evolution, often involving loss of mutant JAK2, remain obscure. We studied 16 patients with JAK2-mutant (7 of 16) or JAK2 wild-type (9 of 16) AML after a JAK2-mutant MPN. Primary myelofibrosis or myelofibrotic transformation preceded all 7 JAK2-mutant but only 1 of 9 JAK2 wild-type AMLs (P = .001), implying that JAK2-mutant AML is preceded by mutation(s) that give rise to a “myelofibrosis” phenotype. Loss of the JAK2 mutation by mitotic recombination, gene conversion, or deletion was excluded in all wild-type AMLs. A search for additional mutations identified alterations of RUNX1, WT1, TP53, CBL, NRAS, and TET2, without significant differences between JAK2-mutant and wild-type leukemias. In 4 patients, mutations in TP53, CBL, or TET2 were present in JAK2 wild-type leukemic blasts but absent from the JAK2-mutant MPN. By contrast in a chronic-phase patient, clones harboring mutations in JAK2 or MPL represented the progeny of a shared TET2-mutant ancestral clone. These results indicate that different pathogenetic mechanisms underlie transformation to JAK2 wild-type and JAK2-mutant AML, show that TET2 mutations may be present in a clone distinct from that harboring a JAK2 mutation, and emphasize the clonal heterogeneity of the MPNs.
47
Saunders, Charlie N., Subhayan Chattopadhyay, Stefanie Huhn, Niels Weinhold, Per Hoffmann, Markus M. Nöthen, Karl-Heinz Jöckel et al. "Search for AL amyloidosis risk factors using Mendelian randomization". Blood Advances 5, n. 13 (6 luglio 2021): 2725–31. http://dx.doi.org/10.1182/bloodadvances.2021004423.
Abstract (sommario):
In amyloid light chain (AL) amyloidosis, amyloid fibrils derived from immunoglobulin light chain are deposited in many organs, interfering with their function. The etiology of AL amyloidosis is poorly understood. Summary data from genome-wide association studies (GWASs) of multiple phenotypes can be exploited by Mendelian randomization (MR) methodology to search for factors influencing AL amyloidosis risk. We performed a 2-sample MR analyzing 72 phenotypes, proxied by 3461 genetic variants, and summary genetic data from a GWAS of 1129 AL amyloidosis cases and 7589 controls. Associations with a Bonferroni-defined significance level were observed for genetically predicted increased monocyte counts (P = 3.8 × 10−4) and the tumor necrosis factor receptor superfamily member 17 (TNFRSF17) gene (P = 3.4 × 10−5). Two other associations with the TNFRSF (members 6 and 19L) reached a nominal significance level. The association between genetically predicted decreased fibrinogen levels may be related to roles of fibrinogen other than blood clotting. be related to its nonhemostatic role. It is plausible that a causal relationship with monocyte concentration could be explained by selection of a light chain–producing clone during progression of monoclonal gammopathy of unknown significance toward AL amyloidosis. Because TNFRSF proteins have key functions in lymphocyte biology, it is entirely plausible that they offer a potential link to AL amyloidosis pathophysiology. Our study provides insight into AL amyloidosis etiology, suggesting high circulating levels of monocytes and TNFRSF proteins as risk factors.
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Lionberger, Jack M., Ninder K. Panesar, Bharat Panuganti, Ahmad Rajeh e Carl E. Freter. "Detecting Accumulated Somatic Mutations in Healthy Aged Female Myeloid Cells". Blood 128, n. 22 (2 dicembre 2016): 5045. http://dx.doi.org/10.1182/blood.v128.22.5045.5045.
Abstract (sommario):
Abstract Background: Acute Myeloid Leukemia and Myelodysplasia are diseases associated with age and with genetic mutations driving evolution of clonal dominance. The earliest steps leading to genetic variation occur in a milieu of normal hematopoiesis by as a matter of course because genomic divergence is a fundamental element of biology. Organism speciation implicates genetic variation is the first step of evolution, followed by resource restriction pressure (a bottleneck). Such conditions create an environment where competitive advantages arise for genetically unique sub-species. Our work is based on the hypothesis that these rules also apply to the rise of pathologic clonal dominance. Consequentially, a low level of mutations in normal hematopoietic stem cells should be detectable and increase with age. Mutations can serve as lineage markers to allow the definition of the kinetics of competing myeloid sub-clones. Also, individual clones with higher rates of mutation might serve as a pre-condition for pathological clonal dominance and disease initiation. Methods: Healthy 78 year old female myeloid progenitors were single cell sorted and cultured for 6 weeks in expansion media. Clones were harvested and typed apropos X-Chromosome Inactivation state (XCI state) as either "Xa" or "Xb" using a methylation specific polymerase chain reaction strategy after DNA was bisulfite modified. Remaining unmodified DNA was whole genome amplified and placed on an Affymetrix 6.0 Single Nucleotide Polymorphism (SNP) array (2.5 million SNP calls/array). Partek Genome Suite software interpreted raw SNP intensity signals as copy number variants (CNV) or loss of heterozygosity (LOH) calls using a stringent search strategy of a > 30 SNP markers, and an average variance of 0.5 (p<0.001). Mutations were compared between XCI states and within XCI states (i.e: individual Xa or Xb clones). Results: SNP comparison between XCI defined phylogenetic lineages showed significant somatic LOH and CNV variance, as did comparison of clones within specific XCI states (e.g: between Xa clones). Mutations represent accumulated genetic drift over the 78.75 years since subject conception and are summarized in Table 1. Regarding call parameters, LOH analysis was unpaired, using Partek internal references. For CNV calls, subtractive comparison was made between related data sets. For example, raw Xa data from clones A1 and A2 were averaged, CNV calls were generated and compared to Xb averaged clone data (B1 and B2) to reveal specific XCI state variance (i.e.: A-Ave vs B-Ave). Individual clones were compared within the XCI state (i.e.: clone A1 compared directly to A2 to reveal unique A1 calls). An example of our data interpretation: 8 LOH and 558 CNV are specific to and shared among XCI state Xa clones (i.e.: A-both). Clone A1 had 35 specific, unique LOH and 1402 CNV calls, while clone A2 had 15 unique, specific LOH and 650 CNV calls. Xb clone data (B1, B2, B-both) are displayed in Table 1. Conclusions: Recent studies reveal frequent mutations in the blood of healthy individuals; however within a person there a no model to identify normal myeloid sub-clones. Therefore we have no accurate data on stem cell kinetics or clonal evolution in healthy marrow. Herein we describe the feasibility of using SNP calls variation in un-diseased aged human myeloid cells to define stem cell specific progeny. To our knowledge, this is the first use of both inclusive (somatic mutations) and exclusive (XCI state) markers to develop a phylogenetic lineage map of normal aged marrow. Importantly, all clones had progenitors with an identical genetic background (the fertilized egg) at a single time point (conception). Therefore, this innovative approach allows for the somatic variation rate to be monitored in primary cells occupying the same organism environment as a function of age and stress events (i.e.: chemo, radiation, etc). Disclosures No relevant conflicts of interest to declare.
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Wilson, G. L., C. H. Fox, A. S. Fauci e J. H. Kehrl. "cDNA cloning of the B cell membrane protein CD22: a mediator of B-B cell interactions." Journal of Experimental Medicine 173, n. 1 (1 gennaio 1991): 137–46. http://dx.doi.org/10.1084/jem.173.1.137.
Abstract (sommario):
We have cloned a full-length cDNA for the B cell membrane protein CD22, which is referred to as B lymphocyte cell adhesion molecule (BL-CAM). Using subtractive hybridization techniques, several B lymphocyte-specific cDNAs were isolated. Northern blot analysis with one of the clones, clone 66, revealed expression in normal activated B cells and a variety of B cell lines, but not in normal activated T cells, T cell lines, Hela cells, or several tissues, including brain and placenta. One major transcript of approximately 3.3 kb was found in B cells although several smaller transcripts were also present in low amounts (approximately 2.6, 2.3, and 1.6 kb). Sequence analysis of a full-length cDNA clone revealed an open reading frame of 2,541 bases coding for a predicted protein of 847 amino acids with a molecular mass of 95 kD. The BL-CAM cDNA is nearly identical to a recently isolated cDNA clone for CD22, with the exception of an additional 531 bases in the coding region of BL-CAM. BL-CAM has a predicted transmembrane spanning region and a 140-amino acid intracytoplasmic domain. Search of the National Biological Research Foundation protein database revealed that this protein is a member of the immunoglobulin super family and that it had significant homology with three homotypic cell adhesion proteins: carcinoembryonic antigen (29% identity over 460 amino acids), myelin-associated glycoprotein (27% identity over 425 amino acids), and neural cell adhesion molecule (21.5% over 274 amino acids). Northern blot analysis revealed low-level BL-CAM mRNA expression in unactivated tonsillar B cells, which was rapidly increased after B cell activation with Staphylococcus aureus Cowan strain 1 and phorbol myristate acetate, but not by various cytokines, including interleukin 4 (IL-4), IL-6, and gamma interferon. In situ hybridization with an antisense BL-CAM RNA probe revealed expression in B cell-rich areas in tonsil and lymph node, although the most striking hybridization was in the germinal centers. COS cells transfected with a BL-CAM expression vector were immunofluorescently stained positively with two different CD22 antibodies, each of which recognizes a different epitope. Additionally, both normal tonsil B cells and a B cell line were found to adhere to COS transfected with BL-CAM in the sense but not the antisense direction.(ABSTRACT TRUNCATED AT 400 WORDS)
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Kunta, Madhurababu, H. Sonia del Rio e Eliezer Louzada. "(86) Isolation and Molecular Characterization of Putative Ascorbate Peroxidase from Citrus". HortScience 41, n. 4 (luglio 2006): 1021D—1021. http://dx.doi.org/10.21273/hortsci.41.4.1021d.
Abstract (sommario):
Reactive oxygen species (ROS) are continuously produced during the normal aerobic metabolism and also under environmental stress conditions. They are the major damaging factors to the photosynthetic machinery under stress conditions and need to be scavenged for the normal growth of the plant. Ascorbate peroxidase (APX) is the key enzyme in detoxifying H2O2, one of ROS from chloroplast and cytosol. A cDNA encoding a putative APXcit was isolated from mature `Dancy' tangerine (Citrus reticulata Blanco) juice vesicles using differential display reverse transcription-polymerase chain reaction (RT-PCR). Subsequently, full-length APXcit cDNA clone and genomic clone were obtained and sequenced. The full-length APXcit sequence is composed by 1082-bp nucleotides, including an open reading frame (ORF) of 753 bp, encoding a protein of 250 amino acids (27 kDa). The 5' un-translated region (UTR) of the APXcit gene consisted of 91 nucleotides and the 3' UTR consisted of 238 nucleotides. Homology search for APXcit at GenBank database showed high similarity to APX from several plant species.