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https://www.readbyqxmd.com/read/28926213/whole-genome-amplification-and-sequencing-of-a-daphnia-resting-egg
#1
Justin B Lack, Lawrence J Weider, Punidan D Jeyasingh
Resting eggs banks are unique windows that allow us to directly observe shifts in population genetics, and phenotypes over time as natural populations evolve. Although a variety of planktonic organisms also produce resting stages, the keystone freshwater consumer, Daphnia, is a well-known model for paleogenetics and resurrection ecology. Nevertheless, paleogenomic investigations are limited largely because resting eggs do not contain enough DNA for genomic sequencing. In fact, genomic studies even on extant populations include a laborious preparatory phase of batch culturing dozens of individuals to generate sufficient genomic DNA...
September 19, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28925547/biogeographic-conservation-of-the-cytosine-epigenome-in-the-globally-important-marine-nitrogen-fixing-cyanobacterium-trichodesmium
#2
Nathan G Walworth, David A Hutchins, Egor Dolzhenko, Michael D Lee, Feixue Fu, Andrew D Smith, Eric A Webb
Cytosine methylation has been shown to regulate essential cellular processes and impact biological adaptation. Despite its evolutionary importance, only a handful of bacterial, genome-wide cytosine studies have been conducted, with none for marine bacteria. Here, we examine the genome-wide, C(5) -Methyl-cytosine (m5C) methylome and its correlation to global transcription in the marine nitrogen-fixing cyanobacterium Trichodesmium. We characterize genome-wide methylation and highlight conserved motifs across 3 Trichodesmium isolates and 2 Trichodesmium metagenomes, thereby identifying highly conserved, novel genomic signatures of potential gene regulation in Trichodesmium...
September 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28925542/genome-characteristics-and-environmental-distribution-of-the-first-phage-that-infects-the-ld28-clade-a-freshwater-methylotrophic-bacterial-group
#3
Kira Moon, Ilnam Kang, Suhyun Kim, Sang-Jong Kim, Jang-Cheon Cho
Bacteriophages infecting major groups of freshwater heterotrophic bacteria have been rarely isolated, hampering analyses of freshwater viromes. Here we report the isolation and genomic characterization of P19250A, the first phage that infects the LD28 clade, an abundant freshwater methylotrophic bacterial group. P19250A was isolated from Lake Soyang, an oligotrophic reservoir, using an LD28 strain as a host. Morphological and genomic analyses revealed that P19250A is a lytic siphovirus with a ∼38.6-kb genome...
September 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28925527/one-gene-two-proteins-coordinated-production-of-a-copper-chaperone-by-differential-transcript-formation-and-translational-frameshifting-in-escherichia-coli
#4
Steffen Lorenz Drees, Birgit Klinkert, Stefan Helling, Dominik Fabian Beyer, Katrin Marcus, Franz Narberhaus, Mathias Lübben
Programmed ribosomal frameshifting (PRF) is a translational anomaly causing the ribosome to shift into an alternative reading frame. PRFs are common in viral genomes, using a single nucleotide sequence to code for two proteins in overlapping frames. In bacteria and eukaryota, PRFs are less frequent. We report on a PRF in the copper detoxification system of Escherichia coli where a metallochaperone is generated out of the first 69 amino acids and a C-terminal out-of-frame glycine of the gene copA. copA besides codes for the P1B -ATPase CopA, a membrane-integral protein and principal interaction target of the chaperone...
September 19, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28925399/dock4-promotes-loss-of-proliferation-in-glioblastoma-progenitor-cells-through-nuclear-beta-catenin-accumulation-and-subsequent-mir-302-367-cluster-expression
#5
D N Debruyne, L Turchi, F Burel-Vandenbos, M Fareh, F Almairac, V Virolle, D Figarella-Branger, N Baeza-Kallee, P Lagadec, V Kubiniek, P Paquis, D Fontaine, M-P Junier, H Chneiweiss, T Virolle
Glioblastomas (GBM) are lethal primitive brain tumours characterized by a strong intra-tumour heterogeneity. We observed in GBM tissues the coexistence of functionally divergent micro-territories either enriched in more differentiated and non-mitotic cells or in mitotic undifferentiated OLIG2 positive cells while sharing similar genomic abnormalities. Understanding the formation of such functionally divergent micro-territories in glioblastomas (GBM) is essential to comprehend GBM biogenesis, plasticity and to develop therapies...
September 18, 2017: Oncogene
https://www.readbyqxmd.com/read/28924058/localization-of-cdc7-protein-kinase-during-dna-replication-in-saccharomyces-cerevisiae
#6
Daniel Rossbach, D Suzi Bryan, Jay R Hesselberth, Robert Sclafani
DDK, a conserved serine-threonine protein kinase composed of a regulatory subunit, Dbf4, and a catalytic subunit, Cdc7, is essential for DNA replication initiation during S phase of the cell cycle through MCM2-7 helicase phosphorylation. The biological significance of DDK is well characterized, but the full mechanism of how DDK associates with substrates remains unclear. Cdc7 is bound to chromatin in the Saccharomyces cerevisiae genome throughout the cell cycle, but there is little empirical evidence as to specific Cdc7 binding locations...
September 18, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28924032/staphylococcus-aureus-strain-newman-d2c-contains-mutations-in-major-regulatory-pathways-that-cripple-its-pathogenesis
#7
William E Sause, Richard Copin, Aidan O'malley, Rita Chan, Brian J Morrow, Peter T Buckley, Jeffrey Fernandez, A Simon Lynch, Bo Shopsin, Victor J Torres
Staphylococcus aureus is a major human pathogen that imposes a great burden on the healthcare system. In the development of anti-staphylococcal modalities intended to reduce the burden of staphylococcal disease, it is imperative to select appropriate models of S. aureus strains when assessing the efficacy of novel agents. Here, using whole genome sequencing, we reveal that the commonly used strain Newman D2C from the American Type Culture Collection (ATCC) contains mutations that render the strain essentially avirulent...
September 18, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28923960/igh-isotype-specific-b-cell-receptor-expression-influences-b-cell-fate
#8
Pei Tong, Alessandra Granato, Teng Zuo, Neha Chaudhary, Adam Zuiani, Seung Seok Han, Rakesh Donthula, Akritee Shrestha, Debattama Sen, Jennifer M Magee, Michael P Gallagher, Cees E van der Poel, Michael C Carroll, Duane R Wesemann
Ig heavy chain (IgH) isotypes (e.g., IgM, IgG, and IgE) are generated as secreted/soluble antibodies (sIg) or as membrane-bound (mIg) B cell receptors (BCRs) through alternative RNA splicing. IgH isotype dictates soluble antibody function, but how mIg isotype influences B cell behavior is not well defined. We examined IgH isotype-specific BCR function by analyzing naturally switched B cells from wild-type mice, as well as by engineering polyclonal Ighγ1/γ1 and Ighε/ε mice, which initially produce IgG1 or IgE from their respective native genomic configurations...
September 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28922742/glytoucan-an-accessible-glycan-structure-repository
#9
Michael Tiemeyer, Kazuhiro Aoki, James Paulson, Richard D Cummings, William S York, Niclas G Karlsson, Frederique Lisacek, Nicolle H Packer, Matthew P Campbell, Nobuyuki P Aoki, Akihiro Fujita, Masaaki Matsubara, Daisuke Shinmachi, Shinichiro Tsuchiya, Issaku Yamada, Michael Pierce, René Ranzinger, Hisashi Narimatsu, Kiyoko F Aoki-Kinoshita
Rapid and continued growth in the generation of glycomic data has revealed the need for enhanced development of basic infrastructure for presenting and interpreting these datasets in a manner that engages the broader biomedical research community. Early in their growth, the genomic and proteomic fields implemented mechanisms for assigning unique gene and protein identifiers that were essential for organizing data presentation and for enhancing bioinformatic approaches to extracting knowledge. Similar unique identifiers are currently absent from glycomic data...
October 1, 2017: Glycobiology
https://www.readbyqxmd.com/read/28922188/new-insights-into-the-role-of-glycosylation-in-lipoprotein-metabolism
#10
Marjolein A W van den Boogert, Daniel J Rader, Adriaan G Holleboom
PURPOSE OF REVIEW: Human genetics has provided new insights into the role of protein glycosylation in regulating lipoprotein metabolism. Here we review these new developments and discuss the biological insights they provide. RECENT FINDINGS: Case descriptions of patients with congenital defects in N-glycosylation (CDG-I) frequently describe a distinct hypocholesterolemia in these rare multisystem clinical syndromes. Two novel CDGs with disturbed Golgi homeostasis and trafficking defects result in mixed glycosylation disorders, hepatic steatosis and hypercholesterolemia...
September 15, 2017: Current Opinion in Lipidology
https://www.readbyqxmd.com/read/28920489/primer-in-genetics-and-genomics-article-5-further-defining-the-concepts-of-genotype-and-phenotype-and-exploring-genotype-phenotype-associations
#11
Fay Wright, Kristen Fessele
As nurses begin to incorporate genetic and genomic sciences into clinical practice, education, and research, it is essential that they have a working knowledge of the terms foundational to the science. The first article in this primer series provided brief definitions of the basic terms (e.g., genetics and genomics) and introduced the concept of phenotype during the discussion of Mendelian inheritance. These terms, however, are inconsistently used in publications and conversations, and the linkage between genotype and phenotype requires clarification...
October 2017: Biological Research for Nursing
https://www.readbyqxmd.com/read/28920001/zoledronic-acid-inhibits-nfat-and-il-2-signaling-pathways-in-regulatory-t-cells-and-diminishes-their-suppressive-function-in-patients-with-metastatic-cancer
#12
Dhifaf Sarhan, Caroline Leijonhufvud, Shannon Murray, Kristina Witt, Christina Seitz, Majken Wallerius, Hanjing Xie, Anders Ullén, Ulrika Harmenberg, Elisabet Lidbrink, Charlotte Rolny, John Andersson, Andreas Lundqvist
Regulatory T cells (Treg) suppress anti-tumor immune responses and their infiltration in the tumor microenvironment is associated with inferior prognosis in cancer patients. Thus, in order to enhance anti-tumor immune responses, selective depletion of Treg is highly desired. We found that treatment with zoledronic acid (ZA) resulted in a selective decrease in the frequency of Treg that was associated with a significant increase in proliferation of T cells and natural killer (NK) cells in peripheral blood of patients with metastatic cancer...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28919745/dose-and-time-effect-of-cdte-quantum-dots-on-antioxidant-capacities-of-the-liver-and-kidneys-in-mice
#13
Jilong Wang, Hubo Sun, Peijun Meng, Mengmeng Wang, Mi Tian, Yamin Xiong, Xueying Zhang, Peili Huang
Although quantum dot (QD)-induced toxicity occurs due to free radicals, generation of oxidative stress mediated by reactive oxygen species (ROS) formation is considered an important mechanism. However, free radical mechanisms are essentially difficult to elucidate at the molecular level because most biologically relevant free radicals are highly reactive and short-lived, making them difficult to directly detect, especially in vivo. Antioxidants play an important role in preventing or, in most cases, limiting the damage caused by ROS...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/28919019/epithelial-to-mesenchymal-transition-epigenetic-reprogramming-driving-cellular-plasticity
#14
REVIEW
Nicolas Skrypek, Steven Goossens, Eva De Smedt, Niels Vandamme, Geert Berx
Epithelial-to-mesenchymal transition (EMT) is a process in which epithelial cells lose their junctions and polarity to gain a motile mesenchymal phenotype. EMT is essential during embryogenesis and adult physiological processes like wound healing, but is aberrantly activated in pathological conditions like fibrosis and cancer. A series of transcription factors (EMT-inducing transcription factor; EMT-TF) regulate the induction of EMT by repressing the transcription of epithelial genes while activating mesenchymal genes through mechanisms still debated...
September 14, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28918903/saga-is-a-general-cofactor-for-rna-polymerase-ii-transcription
#15
Tiago Baptista, Sebastian Grünberg, Nadège Minoungou, Maria J E Koster, H T Marc Timmers, Steve Hahn, Didier Devys, László Tora
Prior studies suggested that SAGA and TFIID are alternative factors that promote RNA polymerase II transcription, with about 10% of genes in S. cerevisiae dependent on SAGA. We reassessed the role of SAGA by mapping its genome-wide location and role in global transcription in budding yeast. We find that SAGA maps to the UAS elements of most genes, overlapping with Mediator binding and irrespective of previous designations of SAGA- or TFIID-dominated genes. Disruption of SAGA through mutation or rapid subunit depletion reduces transcription from nearly all genes, measured by newly synthesized RNA...
September 11, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28918527/alterations-in-epididymal-proteomics-and-antioxidant-activity-of-mice-exposed-to-fluoride
#16
Zilong Sun, Sujuan Li, Yuxiang Yu, Hongyu Chen, Mohammad Mehdi Ommati, Ram Kumar Manthari, Ruiyan Niu, Jundong Wang
It is well known that high fluoride results in low fertility. Epididymis is the important place for spermatozoa maturation, which is essential for successful fertilization. In the previous studies, fluoride was reported to damage the epididymal structure of mouse and rabbit. However, the mechanism underlying sodium fluoride (NaF)-induced epididymal toxicity has not yet been well elucidated. The aim of this study is to explore the global protein alterations in epididymis of mice exposed to NaF using the iTRAQ technique...
September 16, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/28916929/trace-elements-and-healthcare-a-bioinformatics-perspective
#17
Yan Zhang
Biological trace elements are essential for human health. Imbalance in trace element metabolism and homeostasis may play an important role in a variety of diseases and disorders. While the majority of previous researches focused on experimental verification of genes involved in trace element metabolism and those encoding trace element-dependent proteins, bioinformatics study on trace elements is relatively rare and still at the starting stage. This chapter offers an overview of recent progress in bioinformatics analyses of trace element utilization, metabolism, and function, especially comparative genomics of several important metals...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28915715/epigenetic-regulation-during-the-differentiation-of-stem-cells-to-germ-cells
#18
REVIEW
Yuan-Chao Sun, Yong-Yong Wang, Wei Ge, Shun-Feng Cheng, Paul W Dyce, Wei Shen
Gametogenesis is an essential process to ensure the transfer of genetic information from one generation to the next. It also provides a mechanism by which genetic evolution can take place. Although the genome of primordial germ cells (PGCs) is exactly the same with somatic cells within an organism, there are significant differences between their developments. For example, PGCs eventually undergo meiosis to become functional haploid gametes, and prior to that they undergo epigenetic imprinting which greatly alter their genetic regulation...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915707/augmented-expression-of-polo-like-kinase-1-indicates-poor-clinical-outcome-for-breast-patients-a-systematic-review-and-meta-analysis
#19
REVIEW
Yunfeng Zhang, Zhibin Wu, Dapeng Liu, Meng Wang, Guodong Xiao, Peili Wang, Xin Sun, Hong Ren, Shou-Ching Tang, Ning Du
Polo-like kinases 1 (PLK1), a key regulator of mitosis, plays an essential role in maintaining genomic stability. Up-regulation of PLK1 was found in tumorigenesis and tumor progression of diverse cancers. However, the clinicopathological and prognostic implications of PLK1 in breast cancer (BC) have yet to be unveiled. Therefore, using PubMed, Web of Science, Embase, and Chinese databases, we conducted a meta-analysis to define the potential clinical value of PLK1 in BC. Eleven eligible articles with 2481 patients enrolled were included in the present meta-analysis, of which eight studies reported on the relationship between PLK1 expression and clinicopathological features, and nine studies provided survival data in BC patients...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915706/the-role-of-autophagy-in-hepatocellular-carcinoma-friend-or-foe
#20
REVIEW
Lian Liu, Jia-Zhi Liao, Xing-Xing He, Pei-Yuan Li
Autophagy is an evolutionarily conserved lysosome-dependent catabolic process which degrades cell's components in order to recycle substrates to exert optimally and adapt to tough circumstances. It is a critical cellular homeostatic mechanism with stress resistance, immunity, antiaging, and pro-tumor or anti-tumor effects. Among these, the role of autophagy in cancer is the most eye-catching that is not immutable but dynamic and highly complex. Basal autophagy acts as a tumor suppressor by maintaining genomic stability in normal cells...
August 22, 2017: Oncotarget
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