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Chromosome pairing

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https://www.readbyqxmd.com/read/28634144/development-of-a-multiplex-pcr-assay-for-the-detection-and-differentiation-of-burkholderia-pseudomallei-burkholderia-mallei-burkholderia-thailandensis-and-burkholderia-cepacia-complex
#1
Irina Zakharova, Natalya Teteryatnikova, Andrey Toporkov, Dmitry Viktorov
Two species of Burkholderia pseudomallei complex (Bpc), B. pseudomallei and B. mallei, can cause severe life-threatening infections. Rapidly discerning individual species within the group and separating them from other opportunistic pathogens of the Burkholderia cepacia complex (Bcc) is essential to establish a correct diagnosis and for epidemiological surveillance. In this study, a multiplex PCR assay based on the detection of an individual set of chromosomal beta-lactamase genes for single-step identification and differentiation of B...
June 17, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28631558/the-overexpression-and-prognostic-role-of-dcaf13-in-hepatocellular-carcinoma
#2
Jianzhong Cao, Pengjiao Hou, Jiemin Chen, Penghui Wang, Wenqin Wang, Wei Liu, Changzheng Liu, Xiaodong He
DDB1 and CUL4 associated factor 13 (DCAF13) is a protein coding gene located on chromosome 8q22.3, which is a hotspot amplified in various cancers. DCAF13 has been reported to be frequently amplified in breast cancer patients. However, the genetic alteration and potential role of DCAF13 in other cancers, including hepatocellular carcinoma, have not been investigated yet. In this study, we found that DCAF13 was amplified in 14.7% of the cases and its expression was upregulated (p < 0.001) in hepatocellular carcinoma samples in The Cancer Genome Atlas dataset...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28630130/how-a-genetically-stable-extremophile-evolves-modes-of-genome-diversification-in-the-archaeon-sulfolobus-acidocaldarius
#3
Dominic Mao, Dennis W Grogan
In order to analyze in molecular terms how Sulfolobus genomes diverge, damage-induced mutations and natural polymorphisms (PMs) were identified in laboratory constructs and wild-type isolates, respectively, of Sulfolobus acidocaldarius Among wild-type isolates drawn from one local population, pairwise nucleotide divergence averaged 4 x 10(-6), which is about 0.15% of the corresponding divergence reported for Sulfolobus islandicus The most variable features of wild-type S. acidocaldarius genomes were homopolymer (mononucleotide) tracts and longer tandem repeats, consistent with the spontaneous mutations that occur under laboratory conditions...
June 19, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28628087/chromatin-enriched-lncrnas-can-act-as-cell-type-specific-activators-of-proximal-gene-transcription
#4
Michael S Werner, Matthew A Sullivan, Rohan N Shah, Rangarajan D Nadadur, Adrian T Grzybowski, Vasiliy Galat, Ivan P Moskowitz, Alexander J Ruthenburg
We recently described a new class of long noncoding RNAs (lncRNAs) that are distinguished by especially tight chromatin association and whose presence is strongly correlated to expression of nearby genes. Here, we examine the cis-enhancer mechanism of this class of chromatin-enriched RNA (cheRNA) across multiple human cell lines. cheRNAs are largely cell type specific and provide the most reliable chromatin signature to predict cis-gene transcription in every human cell type examined. Targeted depletion of three cheRNAs decreases expression of their neighboring genes, indicating potential co-activator function, and single-molecule fluorescence in situ hybridization (smFISH) of one cheRNA-distal target gene pair suggests a spatial overlap consistent with a role in chromosome looping...
June 19, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28627638/meiotic-defects-and-decreased-expression-of-genes-located-around-the-chromosomal-breakpoint-in-the-testis-of-a-patient-with-a-novel-46-x-t-y-1-p11-3-p31-translocation
#5
Guangyuan Li, Furhan Iqbal, Liu Wang, Zhipeng Xu, Xiaoyan Che, Wen Yu, Liang Shi, Tonghang Guo, Guixiang Zhou, Xiaohua Jiang, Huan Zhang, Yuanwei Zhang, Dexin Yu
Balanced translocations are known to be associated with infertility, spontaneous abortions and birth defects in mammals. Spermatocyte spreading and immunostaining were applied to detect meiotic prophase I progression, homologous chromosome pairing, synapsis and recombination in an azoospermic reciprocal translocation 46,X,t(Y;1)(p11.3;p31) carrier. Histological examination of testicular sections revealed a severely reduced number of germ cells with no spermatids or sperm in the carrier. A significant reduction in XY recombination was observed in the patient...
June 14, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28623426/comparative-physical-mapping-of-18s-rdna-in-the-karyotypes-of-six-leafcutter-ant-species-of-the-genera-atta-and-acromyrmex-formicidae-myrmicinae
#6
Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Hilton Jeferson Alves Cardoso de Aguiar, Silvia das Graças Pompolo
Leafcutter ants of the Atta and Acromyrmex genera are important plagues in different cultures. Cytogenetic data on chromosome number, morphology, and chromosomal banding pattern are only available for 17 species of leafcutter ants. Molecular cytogenetic data for the detection of ribosomal genes by the FISH technique are scarce, and only 15 Neotropical ant species have been studied. This study aimed to physically map the 18S ribosomal RNA genes (rDNA) of six leafcutter ants belonging to the genera Atta and Acromyrmex using FISH...
June 16, 2017: Genetica
https://www.readbyqxmd.com/read/28623274/reduction-in-chromosome-mobility-accompanies-nuclear-organization-during-early-embryogenesis-in-caenorhabditis-elegans
#7
Ritsuko Arai, Takeshi Sugawara, Yuko Sato, Yohei Minakuchi, Atsushi Toyoda, Kentaro Nabeshima, Hiroshi Kimura, Akatsuki Kimura
In differentiated cells, chromosomes are packed inside the cell nucleus in an organised fashion. In contrast, little is known about how chromosomes are packed in undifferentiated cells and how nuclear organization changes during development. To assess changes in nuclear organization during the earliest stages of development, we quantified the mobility of a pair of homologous chromosomal loci in the interphase nuclei of Caenorhabditis elegans embryos. The distribution of distances between homologous loci was consistent with a random distribution up to the 8-cell stage but not at later stages...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28621416/all-in-one-integrating-cell-polarity-meiosis-mitosis-and-mechanical-forces-in-early-oocyte-differentiation-in-vertebrates
#8
Yaniv M Elkouby
While the differentiation of oocytes is key for embryonic development, and its investigation is crucial for advancing our understanding of human reproduction and fertility, many fundamental questions in oogenesis have been long standing. However, recent technical advances have led to several breakthroughs mainly in mice and zebrafish. Here I review these recent findings, including regulation and organization of the germline cyst, the mechanistics of chromosomal pairing, establishment of cell polarity, and formation of a universal mRNA-protein (mRNP) granule called the Balbiani body...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/28619849/the-house-fly-y-chromosome-is-young-and-minimally-differentiated-from-its-ancient-x-chromosome-partner
#9
Richard P Meisel, Christopher A Gonzales, Hoang Luu
Canonical ancient sex chromosome pairs consist of a gene rich X (or Z) chromosome and a male- (or female-) limited Y (or W) chromosome that is gene poor. In contrast to highly differentiated sex chromosomes, nascent sex chromosome pairs are homomorphic or very similar in sequence content. Nascent sex chromosomes can arise if an existing sex chromosome fuses to an autosome or an autosome acquires a new sex-determining locus/allele. Sex chromosomes often differ between closely related species and can even be polymorphic within species, suggesting that nascent sex chromosomes arise frequently over the course of evolution...
June 15, 2017: Genome Research
https://www.readbyqxmd.com/read/28614790/genomic-landscape-and-evolution-of-metastatic-chromophobe-renal-cell-carcinoma
#10
Jozefina Casuscelli, Nils Weinhold, Gunes Gundem, Lu Wang, Emily C Zabor, Esther Drill, Patricia I Wang, Gouri J Nanjangud, Almedina Redzematovic, Amrita M Nargund, Brandon J Manley, Maria E Arcila, Nicholas M Donin, John C Cheville, R Houston Thompson, Allan J Pantuck, Paul Russo, Emily H Cheng, William Lee, Satish K Tickoo, Irina Ostrovnaya, Chad J Creighton, Elli Papaemmanuil, Venkatraman E Seshan, A Ari Hakimi, James J Hsieh
Chromophobe renal cell carcinoma (chRCC) typically shows ~7 chromosome losses (1, 2, 6, 10, 13, 17, and 21) and ~31 exonic somatic mutations, yet carries ~5%-10% metastatic incidence. Since extensive chromosomal losses can generate proteotoxic stress and compromise cellular proliferation, it is intriguing how chRCC, a tumor with extensive chromosome losses and a low number of somatic mutations, can develop lethal metastases. Genomic features distinguishing metastatic from nonmetastatic chRCC are unknown. An integrated approach, including whole-genome sequencing (WGS), targeted ultradeep cancer gene sequencing, and chromosome analyses (FACETS, OncoScan, and FISH), was performed on 79 chRCC patients including 38 metastatic (M-chRCC) cases...
June 15, 2017: JCI Insight
https://www.readbyqxmd.com/read/28610615/quantitative-trait-loci-at-the-11q23-3-chromosomal-region-related-to-dyslipidemia-in-the-population-of-andhra-pradesh-india
#11
Rayabarapu Pranavchand, Battini Mohan Reddy
BACKGROUND: Given the characteristic atherogenic dyslipidemia of south Indian population and crucial role of APOA1, APOC3, APOA4 and APOA5 genes clustered in 11q23.3 chromosomal region in regulating lipoprotein metabolism and cholesterol homeostasis, a large number of recently identified variants are to be explored for their role in regulating the serum lipid parameters among south Indians. METHODS: Using fluidigm SNP genotyping platform, a prioritized set of 96 SNPs of the 11q23...
June 13, 2017: Lipids in Health and Disease
https://www.readbyqxmd.com/read/28609254/chromosomal-diversity-of-three-species-of-hypostomus-lac%C3%A3-p%C3%A3-de-1803-siluriformes-loricariidae-from-the-paran%C3%A3-river-basin-brazil-a-species-complex-in-hypostomus-ancistroides-reinforced-by-a-zz-zw-sex-chromosome-system
#12
Marcia Cristina de Souza Lara Kamei, Lucas Baumgärtner, Suzana Paiva, Cláudio Henrique Zawadzki, Isabel Cristina Martins-Santos, Ana Luiza de Brito Portela-Castro
Hypostomus shows wide morphological patterns, corroborated by great chromosomal diversity that has suggested the existence of new species, especially from small tributaries. Cytogenetic analysis has contributed to estimate a cryptic diversity providing important data for taxonomic and evolutionary studies. Cytogenetic techniques were carried out on species from a small tributary of Ivaí River, Keller River (upper Paraná River basin): Hypostomus aff. ancistroides, Hypostomus topavae, and Hypostomus aff. hermanni that presented 2n = 68, 80, and 72 chromosomes, respectively...
June 13, 2017: Zebrafish
https://www.readbyqxmd.com/read/28607452/transmission-of-induced-chromosomal-aberrations-through-successive-mitotic-divisions-in-human-lymphocytes-after-in-vitro-and-%C3%AF-in%C3%AF-vivo-radiation
#13
Akram Kaddour, Bruno Colicchio, Diane Buron, Elie El Maalouf, Eric Laplagne, Claire Borie, Michelle Ricoul, Aude Lenain, William M Hempel, Luc Morat, Mustafa Al Jawhari, Corina Cuceu, Leonhard Heidingsfelder, Eric Jeandidier, Georges Deschênes, Alain Dieterlen, Michèle El May, Theodore Girinsky, Annelise Bennaceur-Griscelli, Patrice Carde, Laure Sabatier, Radhia M'kacher
The mechanisms behind the transmission of chromosomal aberrations (CA) remain unclear, despite a large body of work and major technological advances in chromosome identification. We reevaluated the transmission of CA to second- and third-division cells by telomere and centromere (TC) staining followed by M-FISH. We scored CA in lymphocytes of healthy donors after in vitro irradiation and those of cancer patients treated by radiation therapy more than 12 years before. Our data demonstrate, for the first time, that dicentric chromosomes (DCs) decreased by approximately 50% per division...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28607439/qtl-mapping-reveals-genetic-determinants-of-fungal-disease-resistance-in-the-wild-lentil-species-lens-ervoides
#14
Vijai Bhadauria, Larissa Ramsay, Kirstin E Bett, Sabine Banniza
Lens ervoides, a wild relative of lentil is an important source of allelic diversity for enhancing the genetic resistance of the cultivated species against economically important fungal diseases, such as anthracnose and Stemphylium blight caused by Colletotrichum lentis and Stemphylium botryosum, respectively. To unravel the genetic control underlying resistance to these fungal diseases, a recombinant inbred line (RIL) population (n = 94, F9) originating from a cross between two L. ervoides accessions, L01-827A and IG 72815, was genotyped on the Illumina HiSeq 2500 platform...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28606698/comparative-analyses-of-whole-genome-sequences-of-leishmania-infantum-isolates-from-humans-and-dogs-in-northeastern-brazil
#15
D G Teixeira, G R G Monteiro, D R A Martins, M Z Fernandes, V Macedo-Silva, M Ansaldi, P R P Nascimento, M A Kurtz, J A Streit, M F F M Ximenes, R D Pearson, A Miles, J M Blackwell, M E Wilson, A Kitchen, J E Donelson, J P M S Lima, S M B Jeronimo
The genomic sequences of 20 Leishmania infantum isolates collected in northeastern Brazil were compared with each other and with the available genomic sequences of 29 L. infantum/donovani isolates from Nepal and Turkey. The Brazilian isolates were obtained in the early 1990s or since 2009 from patients with visceral or non-ulcerating cutaneous leishmaniasis, asymptomatic humans, or dogs with visceral leishmaniasis. Two isolates were from the blood and bone marrow of the same visceral leishmaniasis patient. All 20 genomic sequences display 99...
June 10, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28604770/pervasive-antagonistic-interactions-among-hybrid-incompatibility-loci
#16
Rafael F Guerrero, Christopher D Muir, Sarah Josway, Leonie C Moyle
Species barriers, expressed as hybrid inviability and sterility, are often due to epistatic interactions between divergent loci from two lineages. Theoretical models indicate that the strength, direction, and complexity of these genetic interactions can strongly affect the expression of interspecific reproductive isolation and the rates at which new species evolve. Nonetheless, empirical analyses have not quantified the frequency with which loci are involved in interactions affecting hybrid fitness, and whether these loci predominantly interact synergistically or antagonistically, or preferentially involve loci that have strong individual effects on hybrid fitness...
June 12, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28603073/rapid-prenatal-diagnosis-of-aneuploidy-for-chromosomes-21-18-13-x-and-y-using-segmental-duplication-quantitative-fluorescent-pcr-sd-qf-pcr
#17
Lei Sun, Zuqian Fan, Ju Long, Xunjin Weng, Weijun Tang, Wanrong Pang
BACKGROUND: In our previous studies, the rapid diagnosis of aneuploidy has been achieved using the segmental duplication molecular markers-based SD-QF-PCR technique. However, it is also insufficient due to the drawbacks including less detection loci and incompetence in single-tube detection. METHODS: In this paper, we developed 13 new segmental duplications as molecular markers, as well as designed 13 pairs of primers and 1 fluorescence-labeled universal primer, which could detect chromosome aneuploidies in one PCR tube...
June 9, 2017: Gene
https://www.readbyqxmd.com/read/28602622/homoeologous-chromosome-pairing-across-the-eukaryote-phylogeny
#18
REVIEW
Amanda L Grusz, Erin M Sigel, Colby Witherup
During the past quarter century, molecular phylogenetic inferences have significantly resolved evolutionary relationships spanning the eukaryotic tree of life. With improved phylogenies in hand, the focus of systematics will continue to expand from estimating species relationships toward examining the evolution of specific, fundamental traits across the eukaryotic tree. Undoubtedly, this will expose knowledge gaps in the evolution of key traits, particularly with respect to non-model lineages. Here, we examine one such trait across eukaryotes-the regulation of homologous chromosome pairing during meiosis-as an illustrative example...
June 8, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28600900/screening-of-duplicated-loci-reveals-hidden-divergence-patterns-in-a-complex-salmonid-genome
#19
Morten T Limborg, Wesley A Larson, Lisa W Seeb, James E Seeb
A whole genome duplication (WGD) doubles the entire genomic content of a species and is thought to have catalyzed adaptive radiation in some polyploid-origin lineages. However, little is known about general consequences of a WGD since gene duplicates (i.e. paralogs) are commonly filtered in genomic studies; such filtering may remove substantial portions of the genome in data sets from polyploid-origin species. We demonstrate a new method that enables genome-wide scans for signatures of selection at both non-duplicated and duplicated loci by taking locus-specific copy number into account...
June 10, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28600436/accurate-quantification-of-chromosomal-lesions-via-short-tandem-repeat-analysis-using-minimal-amounts-of-dna
#20
Johann-Christoph Jann, Daniel Nowak, Florian Nolte, Stephanie Fey, Verena Nowak, Julia Obländer, Jovita Pressler, Iris Palme, Christina Xanthopoulos, Alice Fabarius, Uwe Platzbecker, Aristoteles Giagounidis, Katharina Götze, Anne Letsch, Detlef Haase, Richard Schlenk, Gesine Bug, Michael Lübbert, Arnold Ganser, Ulrich Germing, Claudia Haferlach, Wolf-Karsten Hofmann, Maximilian Mossner
BACKGROUND: Cytogenetic aberrations such as deletion of chromosome 5q (del(5q)) represent key elements in routine clinical diagnostics of haematological malignancies. Currently established methods such as metaphase cytogenetics, FISH or array-based approaches have limitations due to their dependency on viable cells, high costs or semi-quantitative nature. Importantly, they cannot be used on low abundance DNA. We therefore aimed to establish a robust and quantitative technique that overcomes these shortcomings...
June 9, 2017: Journal of Medical Genetics
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