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https://www.readbyqxmd.com/read/29679929/a-phylogenetic-framework-facilitates-y-str-variant-discovery-and-classification-via-massively-parallel-sequencing
#1
Tunde I Huszar, Mark A Jobling, Jon H Wetton
Short tandem repeats on the male-specific region of the Y chromosome (Y-STRs) are permanently linked as haplotypes, and therefore Y-STR sequence diversity can be considered within the robust framework of a phylogeny of haplogroups defined by single nucleotide polymorphisms (SNPs). Here we use massively parallel sequencing (MPS) to analyse the 23 Y-STRs in Promega's prototype PowerSeq™ Auto/Mito/Y System kit (containing the markers of the PowerPlex® Y23 [PPY23] System) in a set of 100 diverse Y chromosomes whose phylogenetic relationships are known from previous megabase-scale resequencing...
April 12, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29679774/comparable-results-of-autologous-and-allogeneic-haematopoietic-stem-cell-transplantation-for-adults-with-philadelphia-positive-acute-lymphoblastic-leukaemia-in-first-complete-molecular-remission-an-analysis-by-the-acute-leukemia-working-party-of-the-ebmt
#2
Sebastian Giebel, Myriam Labopin, Michael Potter, Xavier Poiré, Henrik Sengeloev, Gerard Socié, Anne Huynh, Boris V Afanasyev, Urs Schanz, Olle Ringden, Peter Kalhs, Dietrich W Beelen, Antonio M Campos, Tamás Masszi, Jonathan Canaani, Mohamad Mohty, Arnon Nagler
BACKGROUND: Allogeneic haematopoietic stem cell transplantation (alloHSCT) is considered a standard treatment for patients with Philadelphia chromosome-positive acute lymphoblastic leukaemia (Ph+ ALL) achieving complete remission after induction containing tyrosine kinase inhibitors (TKIs). METHODS: We retrospectively compared results of myeloablative alloHSCT from either matched sibling donor (MSD) or unrelated donor (URD) with autologous (auto) HSCT for adults with Ph+ ALL in molecular remission, treated between 2007 and 2014...
April 18, 2018: European Journal of Cancer
https://www.readbyqxmd.com/read/29679654/the-vanillin-derivative-6-bromine-5-hydroxy-4-methoxybenzaldehyde-induces-aberrant-mitotic-progression-and-enhances-radio-sensitivity-accompanying-suppression-the-expression-of-plk1-in-esophageal-squamous-cell-carcinoma
#3
Meng-Meng Gu, Ming Li, Dexuan Gao, Lang-Huan Liu, Yue Lang, Si-Ming Yang, Hongling Ou, Bo Huang, Ping-Kun Zhou, Zeng-Fu Shang
Esophageal squamous cell carcinoma (ESCC) is the most common form of esophageal cancer in China. Since chemotherapy is the standard clinical intervention for advanced ESCC, the development of highly effective and minimal/non-toxic drugs is essential to improve the clinical outcome and prognosis of the patients. A novel derivative of vanillin, 6-bromine-5-hydroxy-4-methoxybenzaldehyde (BVAN08), has been recently reported to activate different cell death pathways in cancer cells. In this study, we demonstrate that BVAN08 exhibits a potent anti-proliferation effect on ESCC cells (TE-1 and ECA-109) by inhibiting the expression of PLK1, an important mitotic kinase...
April 18, 2018: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29679205/changes-in-the-position-and-volume-of-inactive-x-chromosomes-during-the-g0-g1-transition
#4
Guoliang Lyu, Tan Tan, Yiting Guan, Lei Sun, Qianjin Liang, Wei Tao
In female mammals, each cell silences one X chromosome by converting it into transcriptionally inert heterochromatin. The inactivation is concomitant with epigenetic changes including methylation of specific histone residues and incorporation of macroH2A. Such epigenetic changes may exert influence on the positioning of the inactive X chromosome (Xi) within the nucleus beyond the level of chromatin structure. However, the dynamic positioning of the inactive X chromosome during cell cycle remains unclear. Here, we show that H3K27me3 is a cell-cycle-independent marker for the inactivated X chromosomes in WI38 cells...
April 21, 2018: Chromosome Research
https://www.readbyqxmd.com/read/29679127/-basic-principles-of-diagnosis-and-treatment-of-gliomas
#5
REVIEW
H-G Wirsching, T Weiss, P Roth, M Weller
BACKGROUND: Traditionally, gliomas were classified based on histopathological features alone. The revised World Health Organization (WHO) classification of tumors of the central nervous system from 2016 integrated molecular features into the histopathological diagnosis. OBJECTIVE: To summarize key aspects of the WHO classification from 2016 and implications for the clinical management of glioma patients. An overview of novel treatment approaches is also provided...
April 20, 2018: Der Nervenarzt
https://www.readbyqxmd.com/read/29679004/the-linc01138-drives-malignancies-via-activating-arginine-methyltransferase-5-in-hepatocellular-carcinoma
#6
Zhe Li, Jiwei Zhang, Xinyang Liu, Shengli Li, Qifeng Wang, Di Chen, Zhixiang Hu, Tao Yu, Jie Ding, Jinjun Li, Ming Yao, Jia Fan, Shenglin Huang, Qiang Gao, Yingjun Zhao, Xianghuo He
Recurrent chromosomal aberrations have led to the discovery of oncogenes or tumour suppressors involved in carcinogenesis. Here we characterized an oncogenic long intergenic non-coding RNA in the frequent DNA-gain regions in hepatocellular carcinoma (HCC), LINC01138 (long intergenic non-coding RNA located on 1q21.2). The LINC01138 locus is frequently amplified in HCC; the LINC01138 transcript is stabilized by insulin like growth factor-2 mRNA-binding proteins 1/3 (IGF2BP1/IGF2BP3) and is associated with the malignant features and poor outcomes of HCC patients...
April 20, 2018: Nature Communications
https://www.readbyqxmd.com/read/29678955/studying-x-chromosome-inactivation-in-the-single-cell-genomic-era
#7
REVIEW
Andrew Keniry, Marnie E Blewitt
Single-cell genomics is set to revolutionise our understanding of how epigenetic silencing works; by studying specific epigenetic marks or chromatin conformations in single cells, it is possible to ask whether they cause transcriptional silencing or are instead a consequence of the silent state. Here, we review what single-cell genomics has revealed about X chromosome inactivation, perhaps the best characterised mammalian epigenetic process, highlighting the novel findings and important differences between mouse and human X inactivation uncovered through these studies...
April 20, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29678281/an-orphan-g-protein-coupled-receptor-causes-human-gigantism-and-or-acromegaly-molecular-biology-and-clinical-correlations
#8
REVIEW
Giampaolo Trivellin, Laura C Hernández-Ramírez, Jeremy Swan, Constantine A Stratakis
X-linked acrogigantism (X-LAG) is a recently described form of familial or sporadic pituitary gigantism characterized by very early onset GH and IGF-1 excess, accelerated growth velocity, gigantism and/or acromegaloid features. Germline or somatic microduplications of the Xq26.3 chromosomal region, invariably involving the GPR101 gene, constitute the genetic defect leading to X-LAG. GPR101 encodes a class A G protein-coupled receptor that activates the 3',5'-cyclic adenosine monophosphate signaling pathway...
April 2018: Best Practice & Research. Clinical Endocrinology & Metabolism
https://www.readbyqxmd.com/read/29678154/genomic-regions-responsible-for-seminal-and-crown-root-lengths-identified-by-2d-3d-root-system-image-analysis
#9
Yusaku Uga, Ithipong Assaranurak, Yuka Kitomi, Brandon G Larson, Eric J Craft, Jon E Shaff, Susan R McCouch, Leon V Kochian
BACKGROUND: Genetic improvement of root system architecture is a promising approach for improved uptake of water and mineral nutrients distributed unevenly in the soil. To identify genomic regions associated with the length of different root types in rice, we quantified root system architecture in a set of 26 chromosome segment substitution lines derived from a cross between lowland indica rice, IR64, and upland tropical japonica rice, Kinandang Patong, (IK-CSSLs), using 2D & 3D root phenotyping platforms...
April 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29678151/analysis-of-human-es-cell-differentiation-establishes-that-the-dominant-isoforms-of-the-lncrnas-rmst-and-firre-are-circular
#10
Osagie G Izuogu, Abd A Alhasan, Carla Mellough, Joseph Collin, Richard Gallon, Jonathon Hyslop, Francesco K Mastrorosa, Ingrid Ehrmann, Majlinda Lako, David J Elliott, Mauro Santibanez-Koref, Michael S Jackson
BACKGROUND: Circular RNAs (circRNAs) are predominantly derived from protein coding genes, and some can act as microRNA sponges or transcriptional regulators. Changes in circRNA levels have been identified during human development which may be functionally important, but lineage-specific analyses are currently lacking. To address this, we performed RNAseq analysis of human embryonic stem (ES) cells differentiated for 90 days towards 3D laminated retina. RESULTS: A transcriptome-wide increase in circRNA expression, size, and exon count was observed, with circRNA levels reaching a plateau by day 45...
April 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29677489/transvection-goes-live-visualizing-enhancer-promoter-communication-between-chromosomes
#11
Albert Tsai, Robert H Singer, Justin Crocker
Lim et al. (2018) use live imaging in Drosophila embryos to show that enhancers can drive transcription from promoters on another chromosome when they are in close proximity. In addition, they show that multiple promoters can access the same enhancer without competition, potentially sharing a pool of factors in a transcriptional "hub."
April 19, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29677183/divergent-genome-evolution-caused-by-regional-variation-in-dna-gain-and-loss-between-human-and-mouse
#12
Reuben M Buckley, R Daniel Kortschak, David L Adelson
The forces driving the accumulation and removal of non-coding DNA and ultimately the evolution of genome size in complex organisms are intimately linked to genome structure and organisation. Our analysis provides a novel method for capturing the regional variation of lineage-specific DNA gain and loss events in their respective genomic contexts. To further understand this connection we used comparative genomics to identify genome-wide individual DNA gain and loss events in the human and mouse genomes. Focusing on the distribution of DNA gains and losses, relationships to important structural features and potential impact on biological processes, we found that in autosomes, DNA gains and losses both followed separate lineage-specific accumulation patterns...
April 20, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29676727/characterization-of-sccmec-type-iv-methicillin-resistant-staphylococcus-aureus-clones-increased-in-japanese-hospitals
#13
Hidemasa Nakaminami, Shunsuke Takadama, Ayumu Ito, Mariko Hasegawa, Chika Jono, Miyuki Noguchi, Manami Shoshi, Takeaki Wajima, Takeshi Fujii, Hiroshi Maruyama, Haruo Sakamoto, Yutaka Ito, Satsuki Okamoto, Yukiyoshi Masaki, Kayoko Tsuchiya, Susumu Nishinarita, Norihisa Noguchi
Recently, the prevalence of staphylococcal cassette chromosome mec (SCCmec) type IV isolates, which are the major community-acquired methicillin-resistant Staphylococcus aureus (MRSA), have increased in Japanese hospitals. The aim of this study was to elucidate the detailed molecular epidemiological features of the SCCmec type IV clones in Japanese hospitals. When 2589 MRSA isolated from four hospitals in Tokyo, Japan between 2010 and 2014 were analysed, the proportion of SCCmec type IV overtook that of type II, which was the major type of hospital-acquired MRSA in 2014...
April 20, 2018: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/29676638/identification-of-novel-targets-for-lung-cancer-therapy-using-an-induced-pluripotent-stem-cell-model
#14
Vivek Shukla, Mahadev Rao, Hongen Zhang, Jeanette Beers, Darawalee Wangsa, Danny Wangsa, Floryne O Buishand, Yonghong Wang, Zhiya Yu, Holly Stevenson, Emily Reardon, Kaitlin C McLoughlin, Andrew Kaufman, Eden Payabyab, Julie A Hong, Mary Zhang, Sean R Davis, Daniel C Edelman, Guokai Chen, Markku Miettinen, Nicholas Restifo, Thomas Ried, Paul S Meltzer, David S Schrump
RATIONALE: Despite extensive studies, the genetic and epigenetic mechanisms that mediate initiation and progression of lung cancers have not been fully elucidated. Previously, we have demonstrated that via complementary mechanisms, including DNA methylation, polycomb repressive complexes, and noncoding RNAs, cigarette smoke induces stem-like phenotypes that coincide with progression to malignancy in normal respiratory epithelia as well as enhanced growth and metastatic potential of lung cancer cells...
April 2018: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29676042/meta-analysis-of-chromosome-scale-crossover-rate-variation-in-eukaryotes-and-its-significance-to-evolutionary-genomics
#15
Quiterie Haenel, Telma G Laurentino, Marius Roesti, Daniel Berner
Understanding the distribution of crossovers along chromosomes is crucial to evolutionary genomics because the crossover rate determines how strongly a genome region is influenced by natural selection on linked sites. Nevertheless, generalities in the chromosome-scale distribution of crossovers have not been investigated formally. We fill this gap by synthesizing joint information on genetic and physical maps across 62 animal, plant, and fungal species. Our quantitative analysis reveals a strong and taxonomically wide-spread reduction of the crossover rate in the center of chromosomes relative to their peripheries...
April 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29675996/streptococcus-endopeptidases-promote-hpv-infection-in-vitro
#16
Sylvia I Pavlova, Reid V Wilkening, Michael J Federle, Yu Lu, Joel Schwartz, Lin Tao
Both cervical and throat cancers are associated with human papillomavirus (HPV). HPV infection requires cleavage of the minor capsid protein L2 by furin. While furin is present in the vaginal epithelium, it is absent in oral epithelial basal cells where HPV infection occurs. The objective of this study was to investigate whether common oral bacteria express furin-like peptidases. By screening strains representing 12 oral Streptococcus and Enterococcus species, we identified that eight Streptococcus strains displayed high levels of furin-like peptidase activity, with S...
April 19, 2018: MicrobiologyOpen
https://www.readbyqxmd.com/read/29675645/fine-mapping-and-identification-of-a-novel-locus-qgl12-2-control-grain-length-in-wild-rice-oryza-rufipogon-griff
#17
Lan Qi, Yingbin Ding, Xiaoming Zheng, Rui Xu, Lizhen Zhang, Yanyan Wang, Xiaoning Wang, Lifang Zhang, Yunlian Cheng, Weihua Qiao, Qingwen Yang
A wild rice QTL qGL12.2 for grain length was fine mapped to an 82-kb interval in chromosome 12 containing six candidate genes and none was reported previously. Grain length is an important trait for yield and commercial value in rice. Wild rice seeds have a very slender shape and have many desirable genes that have been lost in cultivated rice during domestication. In this study, we identified a quantitative trait locus, qGL12.2, which controls grain length in wild rice. First, a wild rice chromosome segment substitution line, CSSL41, was selected that has longer glume and grains than does the Oryza sativa indica cultivar, 9311...
April 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29675468/decline-of-genetic-diversity-in-ancient-domestic-stallions-in-europe
#18
Saskia Wutke, Edson Sandoval-Castellanos, Norbert Benecke, Hans-Jürgen Döhle, Susanne Friederich, Javier Gonzalez, Michael Hofreiter, Lembi Lõugas, Ola Magnell, Anna-Sapfo Malaspinas, Arturo Morales-Muñiz, Ludovic Orlando, Monika Reissmann, Alexandra Trinks, Arne Ludwig
Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages...
April 2018: Science Advances
https://www.readbyqxmd.com/read/29675466/parallel-evolution-of-batesian-mimicry-supergene-in-two-papilio-butterflies-p-polytes-and-p-memnon
#19
Takuro Iijima, Rei Kajitani, Shinya Komata, Chung-Ping Lin, Teiji Sota, Takehiko Itoh, Haruhiko Fujiwara
Batesian mimicry protects animals from predators when mimics resemble distasteful models. The female-limited Batesian mimicry in Papilio butterflies is controlled by a supergene locus switching mimetic and nonmimetic forms. In Papilio polytes , recent studies revealed that a highly diversified region (HDR) containing doublesex ( dsx -HDR) constitutes the supergene with dimorphic alleles and is likely maintained by a chromosomal inversion. In the closely related Papilio memnon , which exhibits a similar mimicry polymorphism, we performed whole-genome sequence analyses in 11 butterflies, which revealed a nearly identical dsx -HDR containing three genes ( dsx , Nach-like , and UXT ) with dimorphic sequences strictly associated with the mimetic/nonmimetic phenotypes...
April 2018: Science Advances
https://www.readbyqxmd.com/read/29675319/technique-of-laser-chromosome-welding-for-chromosome-repair-and-artificial-chromosome-creation
#20
Yao-Xiong Huang, Lin Li, Liu Yang, Yi Zhang
Here we report a technique of laser chromosome welding that uses a violet pulse laser micro-beam for welding. The technique can integrate any size of a desired chromosome fragment into recipient chromosomes by combining with other techniques of laser chromosome manipulation such as chromosome cutting, moving, and stretching. We demonstrated that our method could perform chromosomal modifications with high precision, speed and ease of use in the absence of restriction enzymes, DNA ligases and DNA polymerases...
April 1, 2018: Biomedical Optics Express
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