Artykuły w czasopismach na temat „Wide hybridisation”
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Knipler, Monica L., Mark Dowton i Katarina Maryann Mikac. "Genome-Wide SNPs Detect Hybridisation of Marsupial Gliders (Petaurus breviceps breviceps × Petaurus norfolcensis) in the Wild". Genes 12, nr 9 (27.08.2021): 1327. http://dx.doi.org/10.3390/genes12091327.
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Petaurus breviceps and Petaurus norfolcensis have produced hybrids in captivity, however there are no reported cases of Petaurus hybridisation in the wild. This study uses morphological data, mitochondrial DNA, and nuclear genome-wide SNP markers to confirm P. breviceps breviceps × P. norfolcensis hybridisation within their natural range on the central coast of New South Wales, Australia. Morphological data identified a potential hybrid that was confirmed with next-generation sequencing technology and 10,111 genome-wide SNPs. Both STRUCTURE and NewHybrid analyses identified the hybrid as a P. norfolcensis backcross, which suggests an initial F1 hybrid was fertile. The mitochondrial DNA matched that of a P. b. breviceps, indicating that a P. b. breviceps female initially mated with a P. norfolcensis male to produce a fertile female offspring. Our study is an important example of how genome-wide SNPs can be used to identify hybrids where the distribution of congeners overlaps. Hybridisation between congeners is likely to become more frequent as climate changes and habitats fragment, resulting in increased interactions and competition for resources and mates.
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Tiesmeyer, Annika, Luana Ramos, José Manuel Lucas, Katharina Steyer, Paulo C. Alves, Christos Astaras, Mareike Brix i in. "Range-wide patterns of human-mediated hybridisation in European wildcats". Conservation Genetics 21, nr 2 (25.01.2020): 247–60. http://dx.doi.org/10.1007/s10592-019-01247-4.
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Burke, Katherine, i Angus Clarke. "The challenge of consent in clinical genome-wide testing". Archives of Disease in Childhood 101, nr 11 (28.04.2016): 1048–52. http://dx.doi.org/10.1136/archdischild-2013-304109.
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Genome-wide testing methods include array comparative genomic hybridisation (aCGH), multiple gene panels, whole exome sequencing (WE) and whole genome sequencing (WGS). Here we introduce some of the key ethical and social considerations relating to informed consent for the testing of children, particularly the management of incidental findings and variants of unknown significance.
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Ebersbach, Jana, Natalia Tkach, Martin Röser i Adrien Favre. "The Role of Hybridisation in the Making of the Species-Rich Arctic-Alpine Genus Saxifraga (Saxifragaceae)". Diversity 12, nr 11 (23.11.2020): 440. http://dx.doi.org/10.3390/d12110440.
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Evolutionary processes fuelling rapid species diversification are not yet fully understood, although their major contribution to overall patterns of plant biodiversity is well established. Hybridisation is among the least understood of these processes, despite its multifaceted role in speciation processes being widely accepted. Species of the large arctic-alpine genus Saxifraga are notorious for their ability to hybridise; however, the overall role of hybridisation and polyploidisation for the diversification of this genus remains unknown. Here, we provide a comprehensive genus-wide review of hybridisation accounts and ploidy levels. We find that the sections of Saxifraga vary greatly in their propensity to hybridise. The majority of natural hybridisation accounts are from recent localised events (n = 71). Hybridisation hotspots were located in the Pyrenees and the European Alps, thus contrasting with the overall distribution of species richness in the genus. Hybrids or hybrid populations are often short-lived in Saxifraga due to a multitude of reproductive barriers, most commonly low F1 hybrid fertility. However, these barriers are not always fully effective, allowing for backcrossing and the formation of hybrid swarms. In addition, we find that the incidence of polyploidy varies widely across different sections of Saxifraga, with species-rich sections Porphyrion and Saxifraga showing divergent polyploidy proportions. Overall, we show that hybridisation and polyploidisation played differential roles in the diversification of this large genus. Nevertheless, a significant proportion of species are yet to be scrutinised, particularly among the Asian Saxifraga species, illustrating the need for systematic further study to fully unravel the role of hybridisation during the evolution of Saxifraga.
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Canestrelli, Daniele, Roberta Bisconti, Andrea Chiocchio, Luigi Maiorano, Mauro Zampiglia i Giuseppe Nascetti. "Climate change promotes hybridisation between deeply divergent species". PeerJ 5 (23.03.2017): e3072. http://dx.doi.org/10.7717/peerj.3072.
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Rare hybridisations between deeply divergent animal species have been reported for decades in a wide range of taxa, but have often remained unexplained, mainly considered chance events and reported as anecdotal. Here, we combine field observations with long-term data concerning natural hybridisations, climate, land-use, and field-validated species distribution models for two deeply divergent and naturally sympatric toad species in Europe (Bufo bufoandBufotes viridisspecies groups). We show that climate warming and seasonal extreme temperatures are conspiring to set the scene for these maladaptive hybridisations, by differentially affecting life-history traits of both species. Our results identify and provide evidence of an ultimate cause for such events, and reveal that the potential influence of climate change on interspecific hybridisations goes far beyond closely related species. Furthermore, climate projections suggest that the chances for these events will steadily increase in the near future.
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Weiss, M. M. "Genome wide array comparative genomic hybridisation analysis of premalignant lesions of the stomach". Molecular Pathology 56, nr 5 (1.10.2003): 293–98. http://dx.doi.org/10.1136/mp.56.5.293.
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Partridge, Wu i Bucknall. "Investigation on the Impact of Degree of Hybridisation for a Fuel Cell Supercapacitor Hybrid Bus with a Fuel Cell Variation Strategy". Vehicles 2, nr 1 (19.12.2019): 1–17. http://dx.doi.org/10.3390/vehicles2010001.
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This paper presents the development of a control strategy for a fuel cell and supercapacitor hybrid power system for application in a city driving bus. This aims to utilise a stable fuel cell power output during normal operation whilst allowing variations to the power output based on the supercapacitor state-of-charge. This provides flexibility to the operation of the system, protection against over-charge and under-charge of the supercapacitor and gives flexibility to the sizing of the system components. The proposed control strategy has been evaluated using validated Simulink models against real-world operating data collected from a double-decker bus operating in London. It was demonstrated that the control strategy was capable of meeting the operating power demands of the bus and that a wide range of degrees of hybridisation are viable for achieving this. Comparison between the degree of hybridisation proposed in this study and those in operational fuel cell (FC) hybrid buses was carried out. It was found that the FC size requirement and FC variation can be significantly reduced through the use of the degree of hybridisation identified in this study.
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Kumari, Madhu, Raj Kumar Mittal, Rakesh Kumar Chahota, Kalpna Thakur, Swaran Lata i Dorin Gupta. "Assessing genetic potential of elite interspecific and intraspecific advanced lentil lines for agronomic traits and their reaction to rust (Uromyces viciae-fabae)". Crop and Pasture Science 69, nr 10 (2018): 999. http://dx.doi.org/10.1071/cp17145.
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The narrow genetic base of lentil (Lens culinaris) has challenged the efforts of breeders to increase its productivity under changing environmental conditions. Inclusion of wild species and diverse cultivated genotypes offers an opportunity to generate new variation through wide hybridisation to broaden the genetic base of cultivated lentil. We evaluated 96 elite, interspecific (L. culinaris × L. orientalis) and intraspecific advanced lentil genotypes along with four checks to determine the extent of genetic variation, resistance to lentil rust (Uromyces viciae-fabae), and the nature and magnitude of their genetic divergence. Sufficient genetic variability was revealed for all of the traits. High heritability and genetic advance were recorded for number of seeds per pod, number of pods per plant, seed yield per plant and biomass per plant. A positive correlation was recorded between grain yield and ten important plant traits. Statistical (D2) and molecular analyses grouped all genotypes into two main clusters and revealed sufficient genetic diversity among advanced lines. Our study showed promising results for creating new variation through wide hybridisation and identified lines L-354 and L-437-1 (rust-resistant) and HPLL-32 (moderately rust-resistant) superior for seed yield and related traits.
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Healey, Adam, David J. Lee, Agnelo Furtado i Robert J. Henry. "Evidence of inter-sectional chloroplast capture in Corymbia among sections Torellianae and Maculatae". Australian Journal of Botany 66, nr 5 (2018): 369. http://dx.doi.org/10.1071/bt18028.
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Chloroplast capture through hybridisation and introgression is well described within Eucalyptus. Despite the propensity of the Corymbia genus (eucalypts) to form hybrids from wide crosses, description of chloroplast capture in Corymbia has, until recently, been limited. In this study our aim was to investigate evidence of intersectional chloroplast capture between sections Torellianae and Maculatae. Using whole-genome next-generation sequencing data, the complete chloroplast genomes were assembled from four Corymbia taxa: Corymbia citriodora subspecies citriodora (Hook.) K.D.Hill & L.A.S.Johnson, Corymbia citriodora subspecies variegata (F.Muell.) A.R.Bean & M.W.McDonald, Corymbia henryi (S.T.Blake) K.D.Hill & L.A.S.Johnson, and Corymbia torelliana (F.Muell.) K.D.Hill & L.A.S.Johnson, represented by eight genotypes. Phylogenetic analysis and comparison among Corymbia chloroplast genomes and nuclear external transcribed spacer (ETS) sequences revealed chloroplast capture among Corymbia species across distinct sections Torellianae and Maculatae within subgenus Blakella. Reticulate evolution, along with Eucalyptus, likely extends into Corymbia as evidenced by incongruent plastid and nuclear phylogenetic trees, suggestive of its importance of hybridisation and introgression during the evolution of eucalypts.
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Ghani, Muhammad Awais, Qian Sun, Junxing Li, Liwen Cao, Linli Rao, Xiaoxia Zou i Liping Chen. "Phenotypic and genetic variation occurred during wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra". Scientia Horticulturae 176 (wrzesień 2014): 22–31. http://dx.doi.org/10.1016/j.scienta.2014.06.029.
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Ab Rahim, Emi S., Thuy T. T. Nguyen, Brett Ingram, Cynthia Riginos, Kim J. Weston i Craig D. H. Sherman. "Species composition and hybridisation of mussel species (Bivalvia: Mytilidae) in Australia". Marine and Freshwater Research 67, nr 12 (2016): 1955. http://dx.doi.org/10.1071/mf15307.
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Mussels belonging to the Mytilus edulis species complex have been the focus of numerous studies exploring the systematics and origin of this commercially and ecologically important genus. Species have wide geographical ranges and hybridise where their distributions overlap, making identification difficult. Several molecular markers have been used to distinguish between the species within the M. edulis species complex; however, no single marker system has been found to be completely diagnostic, and a combination of markers are used. Here, we used a combination of three nuclear genes and a mitochondrial gene region to assess the species composition of Mytilus mussels collected across its geographical range in Australia. Our results show that the majority (98.5%) of individuals sampled from Australian populations are Mytilus galloprovincialis, with 56.2% of them displaying a southern hemisphere haplotype, 10.3% displaying a putatively northern hemisphere haplotype, and 32% having M. galloprovincialis genotypes consistent with either northern or southern hemisphere M. galloprovincialis lineages. The taxonomic origin of the remaining 1.5% of samples (n=3) could not be conclusively determined. Our results suggest that there have been significant introductions of non-native M. galloprovincialis lineages into both southern and northern hemisphere populations.
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Cursino, Marina S., Lana Harriott, Benjamin L. Allen, Matthew Gentle i Luke K. P. Leung. "Do female dingo–dog hybrids breed like dingoes or dogs?" Australian Journal of Zoology 65, nr 2 (2017): 112. http://dx.doi.org/10.1071/zo17005.
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Hybridisation between animals that breed once (e.g. dingoes) and twice (e.g. domestic dogs) annually may produce offspring that breed either way. This question was investigated by determining the breeding seasonality of female dingo–dog hybrids in south-east Queensland, Australia, through evaluating macroscopic and histological features of 71 female reproductive tracts. All animals were sourced from urban areas where levels of hybridisation are generally high. Most animals trapped in summer were pups less than 6 months of age. A peak of uterus diameter and weight coincided with a peak of corpus luteum in winter. The follicular phase was characterised by growing follicles, ~1–3 mm wide, in late summer and autumn. Only two of the animals (1.4%) showed out-of-season reproductive cycles: one was found with corpus luteum in summer and another in autumn. Our data clearly show that hybrids have a single annual breeding season in winter, exhibiting the same breeding seasonality as dingoes. Our findings are similar to those found in the New Guinea singing dog. Future studies should be conducted to understand and exploit the mechanism and drivers of the breeding seasonality of dingo–dog hybrids to develop more effective management of their populations.
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Willi, Yvonne, i Josh Van Buskirk. "Genomic compatibility occurs over a wide range of parental genetic similarity in an outcrossing plant". Proceedings of the Royal Society B: Biological Sciences 272, nr 1570 (15.06.2005): 1333–38. http://dx.doi.org/10.1098/rspb.2005.3077.
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The theory of inbreeding and outbreeding suggests that there is a hump-shaped relationship between the genetic similarity of sexually reproducing parents and the performance of their offspring. Inbreeding depression occurs when genetic similarity is high, whereas hybrid breakdown is expected when genetic similarity is low. Between these extremes, the effect of genetic similarity on fitness is unclear. We studied the shape of this relationship by crossing 65 target genotypes of the clonal, self-incompatible Ranunculus reptans with partner genotypes spanning a broad scale of genetic similarity, ranging from crosses within populations to between-population crosses and hybridisation with a closely related species. Offspring were raised in outdoor tubs. Results revealed a quadratic relationship between parental genetic distance and offspring performance, with the clonal component of fitness more strongly hump-shaped than the sexual component. Optimal genetic similarity encompassed a broad range of within-population and between-population crosses. This pattern of genomic compatibility has important implications for the evolution of mating systems and mate choice.
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Song, Fengping, Zuqing Meng, Tao Luo, Jiajia Xin, Mengzhu Xian, Na Rao, Quan Chen, Yuhao Wang, Mohammad Nauman Khan i Liyong Hu. "Cytological identification of new-type Brassica napus materials and their physiological response to drought". Crop and Pasture Science 70, nr 10 (2019): 876. http://dx.doi.org/10.1071/cp19015.
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The naturally drought-prone climate of the Tibetan Plateau has produced highly drought-resistant Brassica juncea. The objective of the present study was to examine improvement in drought resistance in B. napus by distant hybridisation between B. juncea and B. napus. Distant hybridisation was performed to generate F1 hybrids, which were open-pollinated by a set of breeding lines of B. napus. Continuous self-crossing was then performed to produce the F2–F6 generations, and 74 lines of new-type Brassica napus with stable fertility and morphological phenotypes were selected. The drought resistance of the 74 lines was evaluated during the germination stage by simulating drought stress at 15% PEG-6000, and a wide range of genetic variation in drought resistance was scored. Cytological identification of four lines chosen from strongly, intermediate and weakly drought-resistant clusters demonstrated that their chromosomes had gradually stabilised to B. napus (2n = 38) after advanced self-crossing. A drought-resistant line (line 290) and a drought-susceptible line (line 299) were selected to determine the physiological response to drought stress at the seedling stage. The results showed that proline, soluble protein and malondialdehyde contents of the drought-resistant line were always lower than those of the drought-susceptible line and other common rapeseed variety under drought stress and rewatering conditions. This indicates that the drought-resistant line may have a better reactive oxygen species scavenging system with a less extreme reaction to drought stress. Additionally, the results revealed that the genetic diversity of B. napus under drought resistance was broadened by distant hybridisation, which could encourage breeders to utilise the germplasm resources of B. juncea in the Tibetan Plateau to achieve the goal of drought resistance.
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Ghani, Muhammad Awais, Junxing Li, Linli Rao, Muhammad Ammar Raza, Liwen Cao, Ningning Yu, Xiaoxia Zou i Liping Chen. "The high-throughput sequencing of small RNAs profiling in wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra". Genomics Data 3 (marzec 2015): 1–3. http://dx.doi.org/10.1016/j.gdata.2014.10.021.
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Gogoi, Biswadeep. "Capsicum chinense Jacq. (Bhut Jolokia) – rich source of capsaicin with wide application and economic potential". Annals of Plant Sciences 6, nr 8 (6.08.2017): 1664. http://dx.doi.org/10.21746/aps.2017.8.3.
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Bhut jolokia, which is a cultivar of Capsicum chinense Jacq. is known to the world for its high capsaicinoids content. While wild C. chinense forms may be found in eastern lowland of South America, bhut jolokia is grown in the northeastern states of India. Evidences show that bhut jolokia has interspecific origin with introgression of genes of C. frutecens into C. chinense a natural hybridisation. The fruit of the plant and its leaves has been used as ethnobotanical medicine in different parts of the world. Phytochemical analysis has shown that the fruit is rich in capsaicinoids, which is the reason for its high pungency. Capsaicin and dihydrocapsaicin are the two major capsaicinoids adding pungency to chilli. Higher the capsaicin higher is the pungency. Recent studies has shown wide medicinal applications of capsaicin such as pain relief, anti-obesity treatment, as an antioxidant, antimicrobial agent and even as anticancer molecule. The government of Nagaland has patent rights and geographical indications for naga chilli, which will certainly help in the economic prospect of the region from its cultivation. Thus, this review is an attempt to highlight the latest research and developments in bhut jolokia, which has a huge economic potential to prosper the northeastern region of India.
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Sandywell, Barry, i David Beer. "Stylistic Morphing: Notes on the Digitisation of Contemporary Music Culture". Convergence: The International Journal of Research into New Media Technologies 11, nr 4 (listopad 2005): 106–21. http://dx.doi.org/10.1177//1354856505061057.
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This article is a series of notes concerned with tracking the social and cultural implications of the digitisation of music. In this piece we explore a number of emerging questions and phenomena with the explicit intention of opening new sets of questions and creating opportunities for further reflections and more detailed empirical case studies. This article, therefore, is not intended as a final word or a definitive statement on the phenomenon of cultural morphing, but rather it represents an attempt to experiment, to develop, and to explore the field of hybridisation and popular cultural change. It is hoped that these exploratory notes will illuminate some of the cultural transformations resulting from the proliferation and appropriation of a wide range of digital music technologies.
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Lohani, Neeta, Saeid Babaei, Mohan B. Singh i Prem L. Bhalla. "Genome-Wide In Silico Identification and Comparative Analysis of Dof Gene Family in Brassica napus". Plants 10, nr 4 (7.04.2021): 709. http://dx.doi.org/10.3390/plants10040709.
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DNA binding with one finger (DOF) proteins are plant-specific transcription factors that play roles in diverse plant functions. However, little is known about the DOF protein repertoire of the allopolyploid crop, Brassica napus. This in silico study identified 117 Brassica napus Dof genes (BnaDofs) and classified them into nine groups (A, B1, B2, C1, C2.1, C2.2, C3, D1, and D2), based on phylogenetic analysis. Most members belonging to a particular group displayed conserved gene structural organisation and protein motif distribution. Evolutionary analysis exemplified that the divergence of the Brassica genus from Arabidopsis, the whole-genome triplication event, and the hybridisation of Brassica oleracea and Brassica rapa to form B. napus, followed by gene loss and rearrangements, led to the expansion and divergence of the Dof transcription factor (TF) gene family in B. napus. So far, this is the largest number of Dof genes reported in a single eudicot species. Functional annotation of BnaDof proteins, cis-element analysis of their promoters, and transcriptomic analysis suggested potential roles in organ development, the transition from the vegetative to the reproductive stage, light responsiveness, phytohormone responsiveness, as well as potential regulatory roles in abiotic stress. Overall, our results provide a comprehensive understanding of the molecular structure, evolution, and possible functional roles of Dof genes in plant development and abiotic stress response.
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Wagner, Natascha D., Mark A. Clements, Lalita Simpson i Katharina Nargar. "Conservation in the face of hybridisation: genome-wide study to evaluate taxonomic delimitation and conservation status of a threatened orchid species". Conservation Genetics 22, nr 1 (29.01.2021): 151–68. http://dx.doi.org/10.1007/s10592-020-01325-y.
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Mckellar, MA, i KH Quesenberry. "Chromosome-Pairing and Pollen Viability in Desmodium ovalifolium Wall × Desmodium heterocarpon (L) DC. Hybrids". Australian Journal of Botany 40, nr 2 (1992): 243. http://dx.doi.org/10.1071/bt9920243.
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Lack of genetic compatibility can result in low viable seed production in wide crosses. One year of an ongoing hybridisation program, during which 1333 Desmodium ovalifolium × Desmodium heterocarpon crosses were made, resulted in only two F1 plants. An examination of four stages of microsporogenesis (metaphase I, first division segregation, late tetrad microspore production, and pollen shed) was conducted for two lines of D. ovalifolium, three lines of D. heterocarpon and five D. ovalifolium × D. heterocarpon F1 hybrids made over a 2- year period. Both parental lines and hybrids had low levels of metaphase I univalents, anaphase I laggards, abnormal tetrad microspore production, and had high percentages of pollen stainability. Lack of chromosome homology does not appear to be the reason for low hybrid production in controlled crosses between D. ovalifolium and D. heterocarpon.
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Lamb, Jacob J., i Odne S. Burheim. "Lithium-Ion Capacitors: A Review of Design and Active Materials". Energies 14, nr 4 (12.02.2021): 979. http://dx.doi.org/10.3390/en14040979.
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Lithium-ion capacitors (LICs) have gained significant attention in recent years for their increased energy density without altering their power density. LICs achieve higher capacitance than traditional supercapacitors due to their hybrid battery electrode and subsequent higher voltage. This is due to the asymmetric action of LICs, which serves as an enhancer of traditional supercapacitors. This culminates in the potential for pollution-free, long-lasting, and efficient energy-storing that is required to realise a renewable energy future. This review article offers an analysis of recent progress in the production of LIC electrode active materials, requirements and performance. In-situ hybridisation and ex-situ recombination of composite materials comprising a wide variety of active constituents is also addressed. The possible challenges and opportunities for future research based on LICs in energy applications are also discussed.
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Colmer, T. D., R. Munns i T. J. Flowers. "Improving salt tolerance of wheat and barley: future prospects". Australian Journal of Experimental Agriculture 45, nr 11 (2005): 1425. http://dx.doi.org/10.1071/ea04162.
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Cropping on saline land is restricted by the low tolerance of crops to salinity and waterlogging. Prospects for improving salt tolerance in wheat and barley include the use of: (i) intra-specific variation, (ii) variation for salt tolerance in the progenitors of these cereals, (iii) wide-hybridisation with halophytic ‘wild’ relatives (an option for wheat, but not barley), and (iv) transgenic techniques. In this review, key traits contributing to salt tolerance, and sources of variation for these within the Triticeae, are identified and recommendations for use of these traits in screening for salt tolerance are summarised. The potential of the approaches to deliver substantial improvements in salt tolerance is discussed, and the importance of adverse interactions between waterlogging and salinity are emphasised. The potential to develop new crops from the diverse halophytic flora is also considered.
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Chow, L. Y., Merce Garcia-Barcelo, Y. K. Wing i Mary M. Y. Waye. "Schizophrenia and Hypocalcaemia: Variable Phenotype of Deletion at Chromosome 22q11". Australian & New Zealand Journal of Psychiatry 33, nr 5 (październik 1999): 760–62. http://dx.doi.org/10.1080/j.1440-1614.1999.00617.x.
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Objective: The aim of this paper is to report the diagnosis of velo-cardio-facial syndrome (VCFS) in a patient presenting with schizophrenia and hypocalcaemia. Screening of deletion 22q11 in patients with schizophrenia is discussed. Clinical picture: We report a schizophrenic patient presenting with hypocalcaemia as the only feature of VCFS. Deletion 22q11 was confirmed by fluorescent in situ hybridisation (FISH). Treatment: The patient was treated with haloperidol 3 mg/day with resolution of psychotic symptoms. Outcome: The patient harboured some residual psychotic symptoms probably related to her irregular compliance. Conclusions: The wide range of phenotypic variability of VCFS makes screening of 22q11 deletion in schizophrenia difficult. It is proposed that screening of 22q11 deletion in schizophrenia should be selectively targeted only at patients with specific features of VCFS highly predictive of the presence of 22q11 deletion.
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Ashton, DH, i EM Sandiford. "Natural Hybridisation Between Eucalyptus regnans F. Muell. And E. macrorhyncha F. Muell. in the Cathedral Range, Victoria". Australian Journal of Botany 36, nr 1 (1988): 1. http://dx.doi.org/10.1071/bt9880001.
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Intermediates between E. regnans and E. macrorhyncha occur in E. macrorhyncha forests on the Cathedral Range sandstones up to 5 km from the nearest stands of E. regnans. Such intermediates are regarded as F1 hybrids, primarily because of their low variability. Except for one site adjacent to E. regnans, no introgression to E. macrorhyncha is found, suggesting that hybridization is a rare event. The presence of hybrids is likely to be a result of a 'third order reaction' requiring heavy synchronous flowering, attraction of suitable pollinators and the occurrence of bushfires within the retention time of capsules in the canopies. Intermediate trees exhibit water relation characteristics and essential oil contents similar to those of E. macrorhyncha but morphological features closer to those of E. regnans. Progeny of intermediates display wide variability, both morphologically and physiologically, between the putative parent species. Such rare, widely dispersed hybrid events may eventually lead to increased local variation of E. macrorhyncha and as such may have implications for evolution of eucalypt taxa in diverse habitats.
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Howard‐McCombe, Jo, Daniel Ward, Andrew C. Kitchener, Daniel Lawson, Helen V. Senn i Mark Beaumont. "On the use of genome‐wide data to model and date the time of anthropogenic hybridisation: An example from the Scottish wildcat". Molecular Ecology 30, nr 15 (lipiec 2021): 3688–702. http://dx.doi.org/10.1111/mec.16000.
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Quennell, J. H., J. L. Stanton i P. R. Hurst. "227. FSH receptor expression in small human ovarian follicles". Reproduction, Fertility and Development 17, nr 9 (2005): 88. http://dx.doi.org/10.1071/srb05abs227.
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Follicle-stimulating hormone (FSH) is pivotal in ovarian follicle development; the granulosa cells are the targets of FSH action in the ovary via FSH receptors. Granulosa cell growth and division mark initial follicle recruitment. The acquisition of FSH receptors on granulosa cells is regarded as a key event in hormone responsiveness and consequently follicle development. Due to the low abundance of FSH receptors and low expression of its mRNA it has been difficult to definitively characterise FSH receptor expression patterns. Here, localisation of FSH receptor in different follicle populations has been assessed with in situ hybridisation and real-time PCR of laser microdissected samples. We have used non-radioactive in situ hybridisation to investigate FSH receptor mRNA on a wide range of follicle stages. Biopsies from healthy fertile women (28–33 years) were frozen, embedded and cryosectioned at 10 µm. DIG-labelled RNA probes were designed to detect all splice variants. Hybridised probes were detected with NBT/BCIP in a colorimetric reaction. Secondly, follicles of different morphometric stages were isolated with a laser microscope. RNA extraction, reverse transcription and real-time PCR were used to confirm RNA presence and quantify relative expression. All follicle stages (from primordial to large antral) showed the presence of FSH receptor mRNA in their granulosa cells; sense controls were negative. Observations from real-time PCR indicate FSH receptor mRNA is present in all follicle stages observed and relative expression levels increase over early follicle development. These results challenge the existing doctrine that FSH receptor is absent in the smallest follicles. This suggests initial follicle recruitment may involve gonadotrophins. The use of sensitive molecular techniques will be crucial in elucidating this further.
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Raghavan, Manoj, Debra Lillington, Spyros Skoulakis, Silvana Debernardi, Tracy Chaplin, Nicola J. Foot, T. Andrew Lister i Bryan D. Young. "Genome Wide SNP Analysis Reveals Frequent Uniparental Disomy (UPD) Due to Somatic Recombination in Acute Myeloid Leukemias." Blood 104, nr 11 (16.11.2004): 139. http://dx.doi.org/10.1182/blood.v104.11.139.139.
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Abstract Many cases of AML have either a normal karyotype or non-recurrent chromosomal abnormalities and hence their pathogenesis remains obscure. The introduction of array-based analysis of single nucleotide polymorphisms (SNPs) allows the rapid determination of genome-wide allelic information at a high density for a DNA sample. High-resolution SNP genotype analysis was performed on 64 presentation AML samples with full karyotype information as follows: normal karyotype [40], t(8;21) [5], t(15;17) [4], inv16 [3], 11q23 [2],−7 [3],+8 [2] and other structural abnormalities [7]. Using the 10K SNP array (Affymetrix, Inc., Santa Clara) 9, a mean call rate of 93.3% yielded more than 10,000 SNP genotype calls per sample. Large unexpected regions of homozygosity were observed in 12 AMLs (18.75%). These regions ranged in size from 16 million base pairs to 113 million base pairs and would have been visible in the karyotypes if due to deletion. Remission bone marrow samples from 5 of those patients were subjected to SNP genotype analysis. The SNP call data demonstrated clearly that the homozygosity seen in the leukemic DNA was not present in the respective remission bone marrow DNA. Fluorescence in situ hybridisation (FISH) demonstrated 2 signals for probes within regions of homozygosity. Furthermore, hybridisation signal values on the SNP arrays demonstrated that regions of homozygosity did not differ from the rest of the chromosome. It was therefore concluded that such homozygous regions corresponded to uniparental disomy (UPD) due to somatic recombination events occurring during development of the leukemias. There appears to be a non-random distribution of UPD with 5 events on chromosome 11, 2 on chromosome 6, 2 on chromosome 9 and 1 on chromosomes 13, 19 and 21. As expected for somatic recombination, homozygosity continued to the telomere in most cases. Any parental bias in UPD could be evidence of a role for imprinted genes. This issue was investigated using the H19 gene, which is located at 11p15 and is normally methylated only on the paternal allele. Two leukemias exhibited UPD including 11p15 and the methylation status of the H19 gene was therefore determined by bisulfite sequencing. One leukemia with UPD11p exhibited a homozygous methylated paternal pattern, while the other example of UPD11p showed a homozygous non-methylated maternal pattern. These data show that the UPD seen on 11p is not restricted to a single parental origin. In a previous analysis, the leukemia with UPD19q was shown to be homozygous for a CEBPA mutation and FISH demonstrated 2 copies of the CEBPA gene. This gene is located at 19q13.1, within the area of UPD and we conclude that the mutation occurred prior to the UPD. We can therefore speculate that an important consequence of UPD could be to unmask pre-existing mutations. A total of 8 different chromosomal regions have been shown to be affected by UPD in this study and this may suggest that there are at least this number of mutational targets. The discovery of widespread, somatically acquired, UPD in leukemias has potentially important clinical implications. 20% of the normal karyotype AMLs was found to have UPD, and this could offer a valuable new approach to the classification of this important subgroup of AML. The prognostic consequences of such cryptic abnormalities for the patient are uncertain, and larger studies will be required to assess the clinical significance of this phenomenon.
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Faulkner, Roy. "Genetics and breeding of Sitka spruce". Proceedings of the Royal Society of Edinburgh. Section B. Biological Sciences 93, nr 1-2 (1987): 41–50. http://dx.doi.org/10.1017/s0269727000006266.
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SynopsisSitka spruce is a monoecious, wind-pollinated, cross-fertilising species showing wide genetic variation which suggests heterozygosity for many alleles and natural selection against self-fertilisation. Phenotypic selection for the important trait of vigour is ineffective, so testing progenies of selected individuals and clonal testing is an essential and time-consuming part of any improvement programme. Old trees can be vegetatively propagated by grafting and very young trees by rooted cuttings.The British tree improvement programme is based, in the short term, on the use of seed collected from superior plantation trees of desirable origins; in the mid term on seed derived from clonal orchards based on mixtures of clones previously tested for superiority in family tests; and in the longer term on highly superior seed or clones derived from a system of recurrent mating with family selection. Three populations are being developed. There is a small interspecific hybridisation programme.
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Leach, John. "The Functional Psychoses – Are Oncogenes Involved in Their Pathogenesis? Some Speculations". British Journal of Psychiatry 158, nr 4 (kwiecień 1991): 563–68. http://dx.doi.org/10.1192/bjp.158.4.563.
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Oncogenes are genes whose expression has been associated with malignant transformation of cells in tissue culture and with neoplastic change in vivo (Bishop, 1987). Much of the current understanding of their nature and action has stemmed from work, over the past 20 years, on tumour viruses (Temin, 1971; Rapp, 1983). One group of tumour viruses, the retroviruses, are unique in possessing an enzyme, reverse transcriptase, which transcribes to the cell DNA a copy of the viral RNA genome (Marks, 1987). After the discovery of viral oncogenes, such DNA copies were used as probes in hybridisation studies (Stehelin et al, 1976; Frankel & Fischinger, 1976). These probes, capable of annealing to complementary DNA sequences, revealed the existence of the latter in normal, unaffected cells (Willecke & Schäfer, 1984). These sequences, called cellular or proto-oncogenes, exist in a wide range of eukaryotic organisms, from yeast to man.
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Neat, Michael J., Mufaddal T. Moonim, Robert G. Dunn, Helen Geoghegan i Nicola J. Foot. "Fluorescence in situ hybridisation analysis of bone marrow trephine biopsy specimens; an additional tool in the diagnostic armoury". Journal of Clinical Pathology 66, nr 1 (4.10.2012): 54–57. http://dx.doi.org/10.1136/jclinpath-2012-201131.
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Fluorescence in situ hybridisation (FISH) analysis is now widely employed in the diagnosis and risk stratification of a wide range of malignant diseases. While this technique is used successfully with formalin-fixed paraffin-embedded (FFPE) sections from numerous tissue types, FISH analysis of FFPE tissue sections from trephine biopsy specimens has been less widely reported, possibly due to technical limitations relating to the decalcification protocols employed. During the last 4 years FISH analysis has been carried out successfully in 42 out of 55 (76%) consecutive trephine biopsy specimens received as part of the standard diagnostic service at our institution. Samples decalcified using EDTA-based protocols were analysed successfully in 31/31 cases (100%), whereas only 11/24 samples (46%) decalcified using formic acid-based protocols were successful. In our experience, FISH analysis of trephine biopsy specimens is a highly reproducible technique and a very useful adjunctive tool in the diagnostic armoury; however, its use in a standard diagnostic setting relies on the use of EDTA-based decalcification protocols.
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Tuhina-Khatun, Mst, Mohamed M. Hanafi, Mohd Rafii Yusop, M. Y. Wong, Faezah M. Salleh i Jannatul Ferdous. "Genetic Variation, Heritability, and Diversity Analysis of Upland Rice (Oryza sativaL.) Genotypes Based on Quantitative Traits". BioMed Research International 2015 (2015): 1–7. http://dx.doi.org/10.1155/2015/290861.
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Upland rice is important for sustainable crop production to meet future food demands. The expansion in area of irrigated rice faces limitations due to water scarcity resulting from climate change. Therefore, this research aimed to identify potential genotypes and suitable traits of upland rice germplasm for breeding programmes. Forty-three genotypes were evaluated in a randomised complete block design with three replications. All genotypes exhibited a wide and significant variation for 22 traits. The highest phenotypic and genotypic coefficient of variation was recorded for the number of filled grains/panicle and yields/plant (g). The highest heritability was found for photosynthetic rate, transpiration rate, stomatal conductance, intercellular CO2, and number of filled grains/panicle and yields/plant (g). Cluster analysis based on 22 traits grouped the 43 rice genotypes into five clusters. Cluster II was the largest and consisted of 20 genotypes mostly originating from the Philippines. The first four principle components of 22 traits accounted for about 72% of the total variation and indicated a wide variation among the genotypes. The selected best trait of the number of filled grains/panicle and yields/plant (g), which showed high heritability and high genetic advance, could be used as a selection criterion for hybridisation programmes in the future.
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Kamei, Noriko, i Charles G. Glabe. "Subtractive analysis of S. franciscanus and S. purpuratus ovary mRNA: what kinds of genes determine species-specificity?" Zygote 8, S1 (grudzień 1999): S64. http://dx.doi.org/10.1017/s0967199400130333.
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Our goal is to identify and understand points of regulation in sperm–egg recognition as well as in steps of early development. These processes are species-specific and are the key to understanding speciation. In both vertebrates and invertebrates, the interaction of the sperm and egg displays a wide range of species-specificity. The questions we would like to answer are: What kinds of molecules determine the specificity and control the fertilisation process? Are early steps in development regulated in a species-specific manner?As an approach to identifying genes that determine species-specificity, in two different species, S. purpuratus (S. p.) and S. franciscanus (S. f.), we used a new subtractive hybridisation method known as RDA (representational difference analysis) (Lisitsyn et al., 1993; Hubank et al., 1994). Several species-specific clones were isolated from S. f. ovary mRNA by this method using mRNA from another species but the same genus of sea urchin, S. p. Four different clones were obtained and the species-specificity of the sequence was confirmed by hybridisation. One of them has four tandem EGF repeats and is homologous to the S. p. EGF-II gene (Yang et al., 1989) and A. crassispina EGIP (exogastrula inducing protein) gene (Ishihara et al., 1982). The first three EGF repeats (EGF 1–3) have 60% similarity among these species, but the fourth EGF domain (EGF 4) is highly divergent. The EGF-II protein is believed to be involved in the signalling events of early development, because purified EGF causes exogastrulation when it is added to the seawater prior to gastrulation (Ishihara et al., 1982). Recombinant EGF 3 from S. f. induces exogastrulation in both S. f. and S. p.
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Volery, Lara, Tim M. Blackburn, Sandro Bertolino, Thomas Evans, Piero Genovesi, Sabrina Kumschick, Helen E. Roy, Kevin G. Smith i Sven Bacher. "Improving the Environmental Impact Classification for Alien Taxa (EICAT): a summary of revisions to the framework and guidelines". NeoBiota 62 (15.10.2020): 547–67. http://dx.doi.org/10.3897/neobiota.62.52723.
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The Environmental Impact Classification for Alien Taxa (EICAT) classifies the impacts caused by alien species in their introduced range in standardised terms across taxa and recipient environments. Impacts are classified into one of five levels of severity, from Minimal Concern to Massive, via one of 12 impact mechanisms. Here, we explain revisions based on an IUCN-wide consultation process to the previously-published EICAT framework and guidelines, to clarify why these changes were necessary. These changes mainly concern: the distinction between the two highest levels of impact severity (Major and Massive impacts), the scenarios of the five levels of severity for the hybridisation and disease transmission mechanisms, the broadening of existing impact mechanisms to capture overlooked mechanisms, the Current (Maximum) Impact, and the way uncertainty of individual impact assessments is evaluated. Our aim in explaining this revision process is to ensure consistency of EICAT assessments, by improving the understanding of the framework.
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White, Christine A., i Lois A. Salamonsen. "A guide to issues in microarray analysis: application to endometrial biology". Reproduction 130, nr 1 (lipiec 2005): 1–13. http://dx.doi.org/10.1530/rep.1.00685.
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Within the last decade, the development of DNA microarray technology has enabled the simultaneous measurement of thousands of gene transcripts in a biological sample. Conducting a microarray study is a multi-step process; starting with a well-defined biological question, moving through experimental design, target RNA preparation, microarray hybridisation, image acquisition and data analysis – finishing with a biological interpretation requiring further study. Advances continue to be made in microarray quality and methods of statistical analysis, improving the reliability and therefore appeal of microarray analysis for a wide range of biological questions. The purpose of this review is to provide both an introduction to microarray methodology, as well as a practical guide to the use of microarrays for gene expression analysis, using endometrial biology as an example of the applications of this technology. While recommendations are based on previous experience in our laboratory, this review also summarises the methods currently considered to be best practice in the field.
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Hilu, Khidir W. "Phylogenetics and chromosomal evolution in the Poaceae (grasses)". Australian Journal of Botany 52, nr 1 (2004): 13. http://dx.doi.org/10.1071/bt03103.
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The wide range in basic chromosome number (x = 2–18) and prevalence of polyploidy and hybridisation have resulted in contrasting views on chromosomal evolution in Poaceae. This study uses information on grass chromosome number and a consensus phylogeny to determine patterns of chromosomal evolution in the family. A chromosomal parsimony hypothesis is proposed that underscores (1) the evolution of the Joinvilleaceae/Ecdeiocoleaceae/Poaceae lineage from Restionaceae ancestors with x = 9, (2) aneuploid origin of x�=�11 in Ecdeiocoleaceae and Poaceae (Streptochaeta, Anomochlooideae), (3) reduction to x = 9, followed by chromosome doubling within Anomochlooideae to generate the x = 18 in Anomochloa, and (4) aneuploid increase from the ancestral x = 11 to x = 12 in Pharoideae and Puelioideae, and further diversification in remaining taxa (Fig. 3b). Higher basic chromosome numbers are maintained in basal taxa of all grass subfamilies, whereas smaller numbers are found in terminal species. This finding refutes the 'secondary polyploidy hypothesis', but partially supports the 'reduction hypothesis' previously proposed for chromosomal evolution in the Poaceae.
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Weinmaster, G., V. J. Roberts i G. Lemke. "Notch2: a second mammalian Notch gene". Development 116, nr 4 (1.12.1992): 931–41. http://dx.doi.org/10.1242/dev.116.4.931.
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Notch is a cell surface receptor that mediates a wide variety of cellular interactions that specify cell fate during Drosophila development. Recently, homologs of Drosophila Notch have been isolated from Xenopus, human and rat, and the expression patterns of these vertebrate proteins suggest that they may be functionally analogous to their Drosophila counterpart. We have now identified a second rat gene that exhibits substantial nucleic and amino acid sequence identity to Drosophila Notch. This gene, designated Notch2, encodes a protein that contains all the structural motifs characteristic of a Notch protein. Thus, mammals differ from Drosophila in having more than one Notch gene. Northern and in situ hybridisation analyses in the developing and adult rat identify distinct spatial and temporal patterns of expression for Notch1 and Notch2, indicating that these genes are not redundant. These results suggest that the great diversity of cell-fate decisions regulated by Notch in Drosophila may be further expanded in vertebrates by the activation of distinct Notch proteins.
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Pasricha, Sharda, i Pragya Gahlot. "Synthetic Strategies and Biological Potential of Coumarin-Chalcone Hybrids: A New Dimension to Drug Design". Current Organic Chemistry 24, nr 4 (9.05.2020): 402–38. http://dx.doi.org/10.2174/1385272824666200219091830.
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Privileged scaffolds are ubiquitous as effective templates in drug discovery regime. Natural and synthetically derived hybrid molecules are one such attractive scaffold for therapeutic agent development due to their dual or multiple modes of action, minimum or no side effects, favourable pharmacokinetics and other advantages. Coumarins and chalcone are two important classes of natural products affording diverse pharmacological activities which make them ideal templates for building coumarin-chalcone hybrids as effective biological scaffold for drug discovery research. Provoked by the promising medicinal application of hybrid molecules as well as those of coumarins and chalcones, the medicinal chemists have used molecular hybridisation strategy to report dozens of coumarin- chalcone hybrids with a wide spectrum of biological properties including anticancer, antimicrobial, antimalarial, antioxidant, anti-tubercular and so on. The present review provides a systematic summary on synthetic strategies, biological or chemical potential, SAR studies, some mechanisms of action and some plausible molecular targets of synthetic coumarin-chalcone hybrids published from 2001 till date. The review is expected to assist medicinal chemists in the effective and successful development of coumarin- chalcone hybrid based drug discovery regime.
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Drew, R. A., S. V. Siar, C. M. O'Brien i A. G. C. Sajise. "Progress in backcrossing between Carica papaya × Vasconcellea quercifolia intergeneric hybrids and C. papaya". Australian Journal of Experimental Agriculture 46, nr 3 (2006): 419. http://dx.doi.org/10.1071/ea04248.
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Papaya is a major tropical fruit crop worldwide, however, all genotypes are susceptible to Papaya ringspot virus type P (PRSV-P). Protocols have been developed to produce large numbers of intergeneric hybrids between Carica papaya L. and Vasconcellea quercifolia, which is PRSV-P resistant. Although pollen fertility of these hybrids was low, backcross populations were produced in both Australia and the Philippines when papaya flowers were pollinated with pollen from 11 hybrid plants that had been identified as having some pollen fertility and were PRSV-P resistant. Plantlets were produced after embryo rescue and culture in vitro. Second backcross generations (BC2) were easier to produce than first backcross (BC1) generations as pollen fertility was >80% in male BC1 plants. Variation in time to PRSV-P symptom expression and severity of virus symptoms in the backcross generations was observed in both countries. Commercially acceptable fruit were produced in the BC2 generation. The results demonstrate that efforts in wide hybridisation to transfer PRSV-P resistance to C. papaya, are better directed towards crosses between C. papaya and V. quercifolia than with other Vasconcellea species.
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Mijnsbrugge, Kristine Vander, K. Cox i J. Van Slycken. "Conservation Approaches For Autochthonous Woody Plants in Flanders". Silvae Genetica 54, nr 1-6 (1.12.2005): 197–206. http://dx.doi.org/10.1515/sg-2005-0029.
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Abstract Autochthonous genetic resources of woody plants have become seriously endangered in Flanders because of the particularly low and fragmented forest cover, centuries of intensive forest use in this highly populated area and the wide-spread usage of non-autochthonous planting stock in reforestation and landscape plantings. Intraspecific hybridisation between remnant autochthonous populations and foreign genotypes, which can show inadequate adaptation, may influence the autochthonous genetic constitution and fitness in the long term. As several European countries face similar problems, the objective of this paper is to outline the conservation measures that are taken in Flanders. The central aim is to maintain and create the necessary conditions for natural and flexible evolution of the genetic diversity of autochthonous trees and shrubs. An inventory survey to locate remaining autochthonous populations was started in 1997 and will be completed in 2006. Relict populations are preserved in clonal banks. Central issues are the production of autochthonous planting stock through in situ seed collection, the approval of seed sources and stands and the creation of seed orchards. Conservation actions are discussed.
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Hopkins, Stephen, Jeremy Turk, Adeniyi Daramola i Marinos Kyriakopoulos. "Autism spectrum mixed neurodevelopmental disorder associated with 6q27 deletion and multiple copies within 20q11.23: a case study". Advances in Mental Health and Intellectual Disabilities 8, nr 3 (29.04.2014): 210–15. http://dx.doi.org/10.1108/amhid-07-2013-0050.
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Purpose – Copy Number Variations (CNVs) are not infrequently observed in aberrant neurodevelopment. CNVs can alter gene expression and have been linked to a wide range of neuropsychiatric disorders. The purpose of this case study is to report the association of CNVs with a mixed neurodevelopmental disorder. Design/methodology/approach – Array-Comparative Genomic Hybridisation analysis was carried out in a case of an eight-year-old boy presenting with a mixed neurodevelopmental disorder including autism spectrum disorder, intellectual disability, tic disorder, anxiety and severe aggression. The child's parents also underwent the same investigation. Findings – A 6q27 deletion and multiple copies within 20q11.23 were identified. The boy's father shared the 6q27 deletion and his mother also had multiple copies within 20q11.23. Originality/value – This is the first report linking the combination of 6p27 and 20q11 CNVs with a mixed neurodevelopmental presentation. Identifying CNVs that may underlie aberrant neurodevelopment is likely to assist in unravelling the aetiology of neurodevelopmental and psychiatric disorders and lead to more effective strategies for their characterisation and management.
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Zanni, Fabrizio. "In-between. Frammenti pubblici interposti: una risorsa per il disegno urbano". TERRITORIO, nr 48 (maj 2009): 62–69. http://dx.doi.org/10.3280/tr2009-048011.
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- We are all too familiar with the failure to appreciate urban public spaces and the splintering of the latter that has resulted as the cities have spread outwards. There are many conceptual implications of this type of interstitial space. The notion of ‘in-between' has been treated from to a wide range of perspectives. From an initial meaning of terrain vague, i.e. an abandoned but not necessarily barren area, one moves on to an interesting cultural approach which interprets these peripheral zones as a new wilderness, a ‘dirty' second or third level reality that goes hand in hand with the concept of urban ‘pore' or ‘porosity', understood not only in the physical- settlement sense, but also in sociological terms (Lévesque, 2001-2003). A further related concept is that of liminal space (Paredes, 2005), an ‘interstitial passage' between ‘fixed identities' (Heidegger, 1950). Finally, the ‘space of flows' character of this particular spatial category has been noted by various commentators and has been linked, both in architecture and urban planning, with hybridity and/or hybridisation.
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Duncan, W. C., P. J. Illingworth i H. M. Fraser. "Expression of tissue inhibitor of metalloproteinases-1 in the primate ovary during induced luteal regression". Journal of Endocrinology 151, nr 2 (listopad 1996): 203–13. http://dx.doi.org/10.1677/joe.0.1510203.
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Abstract Although tissue inhibitor of metalloproteinases-1 (TIMP-1) is one of the major secretory products of the corpus luteum, the functional significance of this is not clear. In addition to its role as a specific inhibitor of the matrix metalloproteinase enzymes involved in tissue remodelling, it has recently been suggested that TIMP-1 is also a potent stimulator of steroidogenesis in vitro. However, in the ruminant, TIMP-1 expression increases during luteal regression. This study sought to determine (i) the effect of induced luteal regression on ovarian TIMP-1 expression in the primate and (ii) the expression of TIMP-1 in other steroidogenic and non-steroidogenic tissues. Marmoset ovaries were studied on day 10 of the normal luteal phase and 12 and 24 h after induced luteolysis, with either gonadotrophin-releasing hormone (GnRH) antagonist or prostaglandin F2α analogue. Ovaries from different stages of the normal ovarian cycle were also studied. Expression of TIMP-1 was investigated by isotopic in situ hybridisation. TIMP-1 expression was also examined in a wide range of other marmoset tissues by Northern blotting and in situ hybridisation. TIMP-1 was found to be highly expressed in the marmoset corpus luteum. Luteolysis induced with either prostaglandin F2α or GnRH antagonist was associated with a significant fall in TIMP-1 expression in luteal tissue. TIMP-1 mRNA was also localised to ovarian follicles throughout the ovarian cycle. Expression occurred in the thecal layer of smaller follicles (<1·5 mm) and the granulosal layer of larger pre-ovulatory follicles. In atretic follicles, TIMP-1 was highly expressed at the interface between the thecal and granulosal cells. TIMP-1 was found to be predominantly expressed in steroidogenic tissues, particularly the ovary, adrenal and placenta. These data support a role for changes in TIMP-1 expression in tissue remodelling in the ovary and are consistent with an additional function of TIMP-1 as a facilitator of steroidogenesis. Journal of Endocrinology (1996) 151, 203–213
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Holland, AM, JK Findlay i JA Clements. "Kallikrein gene expression in the gonadotrophin-stimulated rat ovary". Journal of Endocrinology 170, nr 1 (1.07.2001): 243–50. http://dx.doi.org/10.1677/joe.0.1700243.
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The kallikreins (KLKs) are a highly conserved multi-gene family of serine proteases that are expressed in a wide variety of tissues and act on a diverse range of substrates. KLK-like enzyme activity has variously been reported to increase or decrease during the period leading up to ovulation in the equine chorionic gonadotrophin (eCG)primed, human chorionic gonadotrophin (hCG)-stimulated immature rat ovary. These earlier studies, which used biochemical assays to detect enzyme activity, lacked the specificity and sensitivity necessary to characterise conclusively the activity of the individual KLK gene family members. In this study, we have used a gene-specific RT-PCR/Southern hybridisation strategy to delineate the expression patterns of six of the individual KLK genes expressed in the rat ovary (rKLK1-3 and rKLK7-9). We have identified three broad patterns of expression in the eCG/hCG-stimulated ovary in which there is either a post-eCG increase/pre-ovulatory decrease in rKLK expression (rKLK1, rKLK3), a peri-ovulatory decrease in expression (rKLK2, rKLK8) or a relatively unchanged pattern of expression (rKLK7, rKLK9). In addition to clarifying the earlier biochemical studies, these findings support a differential role for the individual KLKs in the ovulatory process.
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Larcombe, Matthew J., René E. Vaillancourt, Rebecca C. Jones i Brad M. Potts. "Assessing a Bayesian Approach for Detecting Exotic Hybrids between Plantation and Native Eucalypts". International Journal of Forestry Research 2014 (2014): 1–13. http://dx.doi.org/10.1155/2014/650202.
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Eucalyptus globulusis grown extensively in plantations outside its native range in Australia. Concerns have been raised that the species may pose a genetic risk to native eucalypt species through hybridisation and introgression. Methods for identifying hybrids are needed to enable assessment and management of this genetic risk. This paper assesses the efficiency of a Bayesian approach for identifying hybrids between the plantation speciesE. globulusandE. nitensand four at-risk native eucalypts. Range-wide DNA samples ofE. camaldulensis,E. cypellocarpa,E. globulus,E. nitens,E. ovataandE. viminalis, and pedigreed and putative hybrids (n= 606), were genotyped with 10 microsatellite loci. Using a two-way simulation analysis (two species in the model at a time), the accuracy of identification was 98% for first and 93% for second generation hybrids. However, the accuracy of identifying simulated backcross hybrids was lower (74%). A six-way analysis (all species in the model together) showed that as the number of species increases the accuracy of hybrid identification decreases. Despite some difficulties identifying backcrosses, the two-way Bayesian modelling approach was highly effective at identifyingF1s, which, in the context ofE. globulusplantations, are the primary management concern.
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Ryland, Georgina L., Kate Jones, Melody Chin, John Markham, Elle Aydogan, Yamuna Kankanige, Marisa Caruso i in. "Novel genomic findings in multiple myeloma identified through routine diagnostic sequencing". Journal of Clinical Pathology 71, nr 10 (14.05.2018): 895–99. http://dx.doi.org/10.1136/jclinpath-2018-205195.
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AimsMultiple myeloma is a genomically complex haematological malignancy with many genomic alterations recognised as important in diagnosis, prognosis and therapeutic decision making. Here, we provide a summary of genomic findings identified through routine diagnostic next-generation sequencing at our centre.MethodsA cohort of 86 patients with multiple myeloma underwent diagnostic sequencing using a custom hybridisation-based panel targeting 104 genes. Sequence variants, genome-wide copy number changes and structural rearrangements were detected using an inhouse-developed bioinformatics pipeline.ResultsAt least one mutation was found in 69 (80%) patients. Frequently mutated genes included TP53 (36%), KRAS (22.1%), NRAS (15.1%), FAM46C/DIS3 (8.1%) and TET2/FGFR3 (5.8%), including multiple mutations not previously described in myeloma. Importantly we observed TP53 mutations in the absence of a 17 p deletion in 8% of the cohort, highlighting the need for sequencing-based assessment in addition to cytogenetics to identify these high-risk patients. Multiple novel copy number changes and immunoglobulin heavy chain translocations are also discussed.ConclusionsOur results demonstrate that many clinically relevant genomic findings remain in multiple myeloma which have not yet been identified through large-scale sequencing efforts, and provide important mechanistic insights into plasma cell pathobiology.
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Schäfer, Richard A., i Björn Voß. "RNAnue: efficient data analysis for RNA–RNA interactomics". Nucleic Acids Research 49, nr 10 (21.05.2021): 5493–501. http://dx.doi.org/10.1093/nar/gkab340.
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Abstract RNA–RNA inter- and intramolecular interactions are fundamental for numerous biological processes. While there are reasonable approaches to map RNA secondary structures genome-wide, understanding how different RNAs interact to carry out their regulatory functions requires mapping of intermolecular base pairs. Recently, different strategies to detect RNA–RNA duplexes in living cells, so called direct duplex detection (DDD) methods, have been developed. Common to all is the Psoralen-mediated in vivo RNA crosslinking followed by RNA Proximity Ligation to join the two interacting RNA strands. Sequencing of the RNA via classical RNA-seq and subsequent specialised bioinformatic analyses the result in the prediction of inter- and intramolecular RNA–RNA interactions. Existing approaches adapt standard RNA-seq analysis pipelines, but often neglect inherent features of RNA–RNA interactions that are useful for filtering and statistical assessment. Here we present RNAnue, a general pipeline for the inference of RNA–RNA interactions from DDD experiments that takes into account hybridisation potential and statistical significance to improve prediction accuracy. We applied RNAnue to data from different DDD studies and compared our results to those of the original methods. This showed that RNAnue performs better in terms of quantity and quality of predictions.
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Armstrong, Susan J., F. Christopher H. Franklin i Gareth H. Jones. "Nucleolus-associated telomere clustering and pairing precede meiotic chromosome synapsis in Arabidopsis thaliana". Journal of Cell Science 114, nr 23 (1.12.2001): 4207–17. http://dx.doi.org/10.1242/jcs.114.23.4207.
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The intranuclear arrangements of centromeres and telomeres during meiotic interphase and early prophase I of meiosis in Arabidopsis thaliana were analysed by fluorescent in situ hybridisation to spread pollen mother cells and embryo-sac mother cells. Meiocyte identification, staging and progression were established by spreading and sectioning techniques, including various staining procedures and bromodeoxyuridine labeling of replicating DNA. Centromere regions of Arabidopsis are unpaired, widely dispersed and peripherally located in nuclei during meiotic interphase, and they remain unpaired and unassociated throughout leptotene. Eventually they associate pairwise during zygotene, as part of the nucleus-wide synapsis of homologous chromosomes. Telomeres, by contrast, show a persistent association with the nucleolus throughout meiotic interphase. Variation in telomere signal number indicates that telomeres undergo pairing during this interval, preceding the onset of general chromosome synapsis. During leptotene the paired telomeres lose their association with the nucleolus and become widely dispersed. As the chromosomes synapse during zygotene, the telomeres reveal a loose clustering within one hemisphere, which may represent a degenerate or relic bouquet configuration. We propose that in Arabidopsis the classical leptotene/zygotene bouquet is absent and is replaced functionally by nucleolus-associated telomere clustering.
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Hall, Andrew G., Lisa C. Bloodworth, Linda A. Hogarth, Nick P. Bown i Julie A. Irving. "Loss of Heterozygosity in Childhood Acute Lymphoblastic Leukaemia Detected by Genome-Wide Microarray Single Nucleotide Polymorphism Analysis." Blood 104, nr 11 (16.11.2004): 1088. http://dx.doi.org/10.1182/blood.v104.11.1088.1088.
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Abstract Loss of heterozygosity (LOH) is detectable in many forms of malignancy, including leukaemia, using techniques such as microsatellite analysis and comparative genomic hybridisation. However, these techniques are laborious and require the use of relatively large amounts of DNA if the whole genome is to be examined. Here we describe the use of oligonucleotide microarrays to characterise single nucleotide polymorphisms (SNPs) in lymphoblasts isolated from children with acute lymphoblastic leukaemia for the pan-genomic mapping of LOH with a resolution of 100–200kb. Results were compared with DNA obtained during remission and on relapse. Abnormalities were seen in 8 of 10 cases. The two cases with no abnormalities and one case which showed identical changes affecting whole chromosomes at relapse and presentation remain in remission 1–9 years following retreatment. The 7 cases which showed LOH not affecting entire chromosomes died following relapse, suggesting that partial LOH may be associated with a poor prognosis. In 4 cases LOH was only detectable at relapse suggesting that progressive LOH may be a cause of disease progression and/or drug resistance. This was supported by detailed analysis of one case in which LOH involving the glucocorticoid receptor (GR) was associated with mutation of the remaining allele. In cell line models the loss of a functional GR is associated with profound resistance to steroids. The most frequent abnormality detected in this series involved chromosome 9p. In each of the four cases where this was observed LOH included the INK4 locus. In three of the four cases INK4 loss was only observed at relapse (see figure), suggesting that this abnormality may be commonly associated with treatment failure, supporting previous reports that 9p abnormailities are associated with a poor prognosis. One case was reported as showing monosomy 20 as the sole cytogenetic aberration but LOH analysis identified 9p LOH and loss of 20q, with retention of heterozygocity for 20p. These findings strongly implicate unbalanced translocation der(9)t(9;20),-20 as described by Clark et al (Leukaemia, 2000, 14:241). Our observations demonstrate that SNP array analysis is a powerful new tool for the analysis of allelic imbalance and unbalanced translocations in leukaemic blasts.
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de Leeuw, N., R. Pfundt, D. A. Koolen, I. Neefs, I. Scheltinga, H. Mieloo, E. A. Sistermans i in. "A newly recognised microdeletion syndrome involving 2p15p16.1: narrowing down the critical region by adding another patient detected by genome wide tiling path array comparative genomic hybridisation analysis". Journal of Medical Genetics 45, nr 2 (24.09.2007): 122–24. http://dx.doi.org/10.1136/jmg.2007.054049.
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Hassan, Azmi, Muhammad Ridwan Andi Purnomo i Putri Dwi Annisa. "Clustering Using Genetic Algorithm-Based Self-Organising Map". Advanced Materials Research 1115 (lipiec 2015): 573–77. http://dx.doi.org/10.4028/www.scientific.net/amr.1115.573.
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This paper presents a comparative study of clustering using Artificial Intelligence (AI) techniques. There are 3 methods to be compared, two methods are pure method, called Self Organising Map (SOM) which is branch of Artificial Neural Network (ANN) and Genetic Algorithm (GA), while one method is hybrid between GA and SOM, called GA-based SOM. SOM is one of the most popular method for cluster analysis. SOM will group objects based on the nearest distance between object and updateable cluster centres. However, there are disadvantages of SOM. Solution quality is depend on initial cluster centres that are generated randomly and cluster centres update algorithm is just based on a delta value without considering the searching direction. Basically, clustering case could be modelled as optimisation case. The objective function is to minimise total distance of all data to their cluster centre. Hence, GA has potentiality to be applied for clustering. Advantage of GA is it has multi searching points in finding the solution and stochastic movement from a phase to the next phase. Therefore, possibility of GA to find global optimum solution will be higher. However, there is still some possibility of GA just find near-optimum solution. The advantage of SOM is the smooth iterative procedure to improve existing cluster centres. Hybridisation of GA and SOM believed could provide better solution. In this study, there are 2 data sets used to test the performance of the three techniques. The study shows that when the solution domain is very wide then SOM and GA-based SOM perform better compared to GA while when the solution domain is not very wide then GA performs better.