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https://www.readbyqxmd.com/read/29332992/experiment-design-for-early-molecular-events-in-hiv-infection
#1
Aditya Jagarapu, LaMont Cannon, Ryan Zurakowski
The recent introduction of integrase inhibitors to the HIV antiviral repertoire permits us to create in vitro experiments that reliably terminate HIV infection at the point of chromosomal integration. This allows us to isolate the dynamics of a single round of infection, without needing to account for the influence of multiple overlapping rounds of infection. By measuring the various nucleic acid concentrations in a population of infected target cells at multiple time points, we can infer the rates of these molecular events with great accuracy, which allows us to compare the rates between target cells with different functional phenotypes...
May 2017: Proceedings of the ... American Control Conference
https://www.readbyqxmd.com/read/29332159/transposable-elements-genome-innovation-chromosome-diversity-and-centromere-conflict
#2
REVIEW
Savannah J Klein, Rachel J O'Neill
Although it was nearly 70 years ago when transposable elements (TEs) were first discovered "jumping" from one genomic location to another, TEs are now recognized as contributors to genomic innovations as well as genome instability across a wide variety of species. In this review, we illustrate the ways in which active TEs, specifically retroelements, can create novel chromosome rearrangements and impact gene expression, leading to disease in some cases and species-specific diversity in others. We explore the ways in which eukaryotic genomes have evolved defense mechanisms to temper TE activity and the ways in which TEs continue to influence genome structure despite being rendered transpositionally inactive...
January 13, 2018: Chromosome Research
https://www.readbyqxmd.com/read/29331932/cnv-biology-in-neurodevelopmental-disorders
#3
REVIEW
Toru Takumi, Kota Tamada
Copy number variants (CNVs), characterized in recent years by cutting-edge technology, add complexity to our knowledge of the human genome. CNVs contribute not only to human diversity but also to different kinds of diseases including neurodevelopmental delay, autism spectrum disorder and neuropsychiatric diseases. Interestingly, many pathogenic CNVs are shared among these diseases. Studies suggest that pathophysiology of disease may not be simply attributed to a single driver gene within a CNV but also that multifactorial effects may be important...
January 10, 2018: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/29330432/developing-genome-wide-snps-and-constructing-an-ultrahigh-density-linkage-map-in-oil-palm
#4
Bin Bai, Le Wang, Ying Jun Zhang, May Lee, Rahmadsyah Rahmadsyah, Yuzer Alfiko, Bao Qing Ye, Sigit Purwantomo, Antonius Suwanto, Nam-Hai Chua, Gen Hua Yue
Oil palm (Elaeis guineensis Jacq.) is the leading oil-producing crops and the most important edible oil resource worldwide. DNA markers and genetic linkage maps are essential resources for marker-assisted selection to accelerate genetic improvement. We conducted RAD-seq on an Illumina NextSeq500 to discover genome-wide SNPs, and used the SNPs to construct a linkage map for an oil palm (Tenera) population derived from a cross between a Deli Dura and an AVROS Pisifera. The RAD-seq produced 1,076 million single-end reads across the breeding population containing 155 trees...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330416/virtual-genome-walking-across-the-32%C3%A2-gb-ambystoma-mexicanum-genome-assembling-gene-models-and-intronic-sequence
#5
Teri Evans, Andrew D Johnson, Matthew Loose
Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330284/novel-intergenically-spliced-chimera-nfatc3-pla2g15-is-associated-with-aggressive-t-all-biology-and-outcome
#6
Jonathan Bond, Christine Tran Quang, Guillaume Hypolite, Mohamed Belhocine, Aurélie Bergon, Gaëlle Cordonnier, Jacques Ghysdael, Elizabeth Macintyre, Nicolas Boissel, Salvatore Spicuglia, Vahid Asnafi
Leukemias are frequently characterized by the expression of oncogenic fusion chimeras that normally arise due to chromosomal rearrangements. Intergenically-spliced chimeric RNAs (ISCs) are transcribed in the absence of structural genomic changes, and aberrant ISC expression is now recognized as a potential driver of cancer. To better understand these potential oncogenic drivers, high-throughput RNA-sequencing (RNA-seq) was performed on T-acute lymphoblastic leukemia (T-ALL) patient specimens (n=24) and candidate T-ALL-related ISCs were identified (n=55; a median of 4 per patient)...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29329249/scaffolding-for-repair-understanding-molecular-functions-of-the-smc5-6-complex
#7
REVIEW
Mariana Diaz, Ales Pecinka
Chromosome organization, dynamics and stability are required for successful passage through cellular generations and transmission of genetic information to offspring. The key components involved are Structural maintenance of chromosomes (SMC) complexes. Cohesin complex ensures proper chromatid alignment, condensin complex chromosome condensation and the SMC5/6 complex is specialized in the maintenance of genome stability. Here we summarize recent knowledge on the composition and molecular functions of SMC5/6 complex...
January 12, 2018: Genes
https://www.readbyqxmd.com/read/29325627/epigenetic-mechanisms-underlying-nervous-system-diseases
#8
Irfan A Qureshi, Mark F Mehler
Epigenetic mechanisms act as control systems for modulating genomic structure and activity in response to evolving profiles of cell-extrinsic, cell-cell, and cell-intrinsic signals. These dynamic processes are responsible for mediating cell- and tissue-specific gene expression and function and gene-gene and gene-environmental interactions. The major epigenetic mechanisms include DNA methylation and hydroxymethylation; histone protein posttranslational modifications, nucleosome remodeling/repositioning, and higher-order chromatin reorganization; noncoding RNA regulation; and RNA editing...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29325559/pangenome-analyses-of-the-wheat-pathogen-zymoseptoria-tritici-reveal-the-structural-basis-of-a-highly-plastic-eukaryotic-genome
#9
Clémence Plissonneau, Fanny E Hartmann, Daniel Croll
BACKGROUND: Structural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence...
January 11, 2018: BMC Biology
https://www.readbyqxmd.com/read/29325123/packaging-of-dinoroseobacter-shibae-dna-into-gene-transfer-agent-particles-is-not-random
#10
Jürgen Tomasch, Hui Wang, April T K Hall, Diana Patzelt, Matthias Preusse, Jörn Petersen, Henner Brinkmann, Boyke Bunk, Sabin Bhuju, Michael Jarek, Robert Geffers, Andrew S Lang, Irene Wagner-Döbler
Gene transfer agents (GTAs) are phage-like particles which contain a fragment of genomic DNA of the bacterial or archaeal producer and deliver this to a recipient cell. GTA gene clusters are present in the genomes of almost all marine Rhodobacteraceae (Roseobacters) and might be important contributors to horizontal gene transfer (HGT) in the world's oceans. For all organisms studied so far, no obvious evidence of sequence specificity or other non-random process responsible for packaging genomic DNA into GTAs has been found...
January 9, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29324881/genome-wide-analysis-and-expression-profiles-of-glyoxalase-gene-families-in-chinese-cabbage-brassica-rapa-l
#11
Guixin Yan, Xin Xiao, Nian Wang, Fugui Zhang, Guizhen Gao, Kun Xu, Biyun Chen, Jiangwei Qiao, Xiaoming Wu
The glyoxalase pathway is composed of glyoxalase I (GLYI) and glyoxalase II (GLYII) and is responsible for the detoxification of a cytotoxic metabolite methylglyoxal (MG) into the nontoxic S-D-lactoylglutathione. The two glyoxalase enzymes play a crucial role in stress tolerance in various plant species. Recently, the GLY gene families have well been analyzed in Arabidopsis, rice and soybean, however, little is known about them in Chinese cabbage (Brassica rapa). Here, 16 BrGLYI and 15 BrGLYII genes were identified in the B...
2018: PloS One
https://www.readbyqxmd.com/read/29324636/simple-sequence-repeat-ssr-genetic-linkage-map-of-d-genome-diploid-cotton-derived-from-an-interspecific-cross-between-gossypium-davidsonii-and-gossypium-klotzschianum
#12
Joy Nyangasi Kirungu, Yanfeng Deng, Xiaoyan Cai, Richard Odongo Magwanga, Zhongli Zhou, Xingxing Wang, Yuhong Wang, Zhenmei Zhang, Kunbo Wang, Fang Liu
The challenge in tetraploid cotton cultivars is the narrow genetic base and therefore, the bottleneck is how to obtain interspecific hybrids and introduce the germplasm directly from wild cotton to elite cultivars. Construction of genetic maps has provided insight into understanding the genome structure, interrelationships between organisms in relation to evolution, and discovery of genes that carry important agronomic traits in plants. In this study, we generated an interspecific hybrid between two wild diploid cottons, Gossypium davidsonii and Gossypium klotzschianum, and genotyped 188 F2:3 populations in order to develop a genetic map...
January 11, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29323637/autocatalytic-microtubule-nucleation-determines-the-size-and-mass-of-xenopus-laevis-egg-extract-spindles
#13
Franziska Decker, David Oriola, Benjamin Dalton, Jan Brugues
Regulation of size and growth is a fundamental problem in biology. A prominent example is the formation of the mitotic spindle, where protein concentration gradients around chromosomes are thought to regulate spindle growth by controlling microtubule nucleation. Previous evidence suggests that microtubules nucleate throughout the spindle structure. However, the mechanisms underlying microtubule nucleation and its spatial regulation are still unclear. Here, we developed an assay based on laser ablation to directly probe microtubule nucleation events in Xenopuslaevis egg extracts...
January 11, 2018: ELife
https://www.readbyqxmd.com/read/29322592/predicting-the-intrauterine-fetal-death-of-fetuses-with-cystic-hygroma-in-early-pregnancy
#14
Mai Shimura, Hiroshi Ishikawa, Hiromi Nagase, Akihiko Mochizuki, Futoshi Sekiguchi, Naho Koshimizu, Toshiyuki Itai, Mizuha Odagami
We investigated whether it was possible to predict the prognosis of fetuses with cystic hygroma (CH) in early pregnancy based on the degree of neck thickening. We retrospectively analyzed 57 singleton pregnancies with fetuses with CH who were examined before the 22nd week of pregnancy. The fetuses were categorized according to the outcome, structural abnormalities at birth, and chromosomal abnormalities. Here, we proposed a new sonographic predictor with which we assessed neck thickening by dividing the width of the neck thickening by the biparietal diameter (BPD), which is expressed as the CH/BPD ratio (CBR)...
January 11, 2018: Congenital Anomalies
https://www.readbyqxmd.com/read/29322240/ki-67-more-than-a-proliferation-marker
#15
REVIEW
Xiaoming Sun, Paul D Kaufman
Ki-67 protein has been widely used as a proliferation marker for human tumor cells for decades. In recent studies, multiple molecular functions of this large protein have become better understood. Ki-67 has roles in both interphase and mitotic cells, and its cellular distribution dramatically changes during cell cycle progression. These localizations correlate with distinct functions. For example, during interphase, Ki-67 is required for normal cellular distribution of heterochromatin antigens and for the nucleolar association of heterochromatin...
January 10, 2018: Chromosoma
https://www.readbyqxmd.com/read/29322237/genome-wide-association-study-of-cold-tolerance-of-chinese-indica-rice-varieties-at-the-bud-burst-stage
#16
Mengchen Zhang, Jing Ye, Qun Xu, Yue Feng, Xiaoping Yuan, Hanyong Yu, Yiping Wang, Xinghua Wei, Yaolong Yang
A region containing three genes on chromosome 1 of indica rice was associated with cold tolerance at the bud burst stage; these results may be useful for breeding cold-tolerant lines. Low temperature at the bud burst stage is one of the major abiotic stresses limiting rice growth, especially in regions where rice seeds are sown directly. In this study, we investigated cold tolerance of rice at the bud burst stage and conducted a genome-wide association study (GWAS) based on the 5K rice array of 249 indica rice varieties widely distributed in China...
January 10, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29321672/phenotypic-interpretation-of-complex-chromosomal-rearrangements-informed-by-nucleotide-level-resolution-and-structural-organization-of-chromatin
#17
Cinthya J Zepeda-Mendoza, Alexandra Bardon, Tammy Kammin, David J Harris, Helen Cox, Claire Redin, Zehra Ordulu, Michael E Talkowski, Cynthia C Morton
Molecular characterization of balanced chromosomal abnormalities constitutes a powerful tool in understanding the pathogenic mechanisms of complex genetic disorders. Here we report a male with severe global developmental delay in the presence of a complex karyotype and normal microarray and exome studies. The subject, referred to as DGAP294, has two de novo apparently balanced translocations involving chromosomes 1 and 14, and chromosomes 4 and 10, disrupting several different transcripts of adhesion G protein-coupled receptor L2 (ADGRL2) and protocadherin 15 (PCDH15)...
January 10, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29321632/genome-wide-association-study-in-asia-adapted-tropical-maize-reveals-novel-and-explored-genomic-regions-for-sorghum-downy-mildew-resistance
#18
Zerka Rashid, Pradeep Kumar Singh, Hindu Vemuri, Pervez Haider Zaidi, Boddupalli Maruthi Prasanna, Sudha Krishnan Nair
Globally, downy mildews are among the important foliar diseases of maize that cause significant yield losses. We conducted a genome-wide association study for sorghum downy mildew (SDM; Peronosclerospora sorghi) resistance in a panel of 368 inbred lines adapted to the Asian tropics. High density SNPs from Genotyping-by-sequencing were used in GWAS after controlling for population structure and kinship in the panel using a single locus mixed model. The study identified a set of 26 SNPs that were significantly associated with SDM resistance, with Bonferroni corrected P values ≤ 0...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321342/association-between-ssr-markers-and-fibre-traits-in-sea-island-cotton-gossypium-barbadense-germplasm-resources
#19
Qi Ma, Jing Zhao, Hai Lin, Xinzhu Ning, Ping Liu, Fujun Deng, Aijun Si, Jilian Li
Identification of molecular markers associated with fibre traits can accelerate cotton marker-assisted selection (MAS) programmes. In this study, Gossypium barbadense germplasm accessions with diverse origins (n = 123) were used to perform association analysis of fibre traits with 120 polymorphic simple sequence repeat (SSR) markers. In total, 120 polymorphic primer pairs amplified 258 loci with a mean of 2.15 loci per primer. Population structure analysis identified three main clusters for the accessions, which indicated agreement of genetic and predefined populations...
December 1, 2017: Journal of Genetics
https://www.readbyqxmd.com/read/29321280/analysis-of-mitotic-checkpoint-function-in-xenopus-egg-extracts
#20
Yinghui Mao
Accurate sister chromatid segregation is pivotal in the faithful transmission of genetic information during each cell division. To ensure accurate segregation, eukaryotic organisms have evolved a "mitotic (or spindle assembly) checkpoint" to prevent premature advance to anaphase before successful attachment of every chromosome to the microtubules of the mitotic spindle. An unattached kinetochore generates a diffusible signal that inhibits ubiquitination of substrates such as cyclin B and securins. This protocol presents an in vitro assay for studying the mitotic checkpoint using Xenopus laevis egg extracts...
January 10, 2018: Cold Spring Harbor Protocols
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