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https://www.readbyqxmd.com/read/28437583/natural-selection-on-mhc-ii%C3%AE-in-parapatric-lake-and-stream-stickleback-balancing-divergent-both-or-neither
#1
William E Stutz, Daniel I Bolnick
Major histocompatibility (MHC) genes encode proteins that play a central role in vertebrates' adaptive immunity to parasites. MHC loci are among the most polymorphic in vertebrates' genomes, inspiring many studies to identify evolutionary processes driving MHC polymorphism within populations, and divergence between populations. Leading hypotheses include balancing selection favoring rare alleles within populations, and spatially divergent selection. These hypotheses do not always produce diagnosably distinct predictions, causing many studies of MHC to yield inconsistent or ambiguous results...
April 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28437572/nearly-a-decade-long-repeatable-seasonal-diversity-patterns-of-bacterioplankton-communities-in-the-eutrophic-lake-donghu-wuhan-china
#2
Qingyun Yan, James C Stegen, Yuhe Yu, Ye Deng, Xinghao Li, Shu Wu, LilI Dai, Xiang Zhang, Jinjin Li, Chun Wang, Jiajia Ni, Xuemei Li, Hongjuan Hu, Fanshu Xiao, Weisong Feng, Daliang Ning, Zhili H E, Joy D Van Nostrand, Liyou Wu, Jizhong Zhou
Uncovering which environmental factors govern community diversity patterns and how ecological processes drive community turnover are key questions related to understand the community assembly. However, the ecological mechanisms regulating long-term variations of bacterioplankton communities in lake ecosystems remains poorly understood. Here we present nearly a decade-long study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing with MiSeq platform...
April 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28436944/active-and-poised-promoter-states-drive-folding-of-the-extended-hoxb-locus-in-mouse-embryonic-stem-cells
#3
Mariano Barbieri, Sheila Q Xie, Elena Torlai Triglia, Andrea M Chiariello, Simona Bianco, Inês de Santiago, Miguel R Branco, David Rueda, Mario Nicodemi, Ana Pombo
Gene expression states influence the 3D conformation of the genome through poorly understood mechanisms. Here, we investigate the conformation of the murine HoxB locus, a gene-dense genomic region containing closely spaced genes with distinct activation states in mouse embryonic stem (ES) cells. To predict possible folding scenarios, we performed computer simulations of polymer models informed with different chromatin occupancy features that define promoter activation states or binding sites for the transcription factor CTCF...
April 24, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28436004/engineering-of-an-h2-o2-auto-scavenging-in-vivo-cascade-for-pinoresinol-production
#4
Yongkun Lv, Xiaozhong Cheng, Guocheng Du, Jingwen Zhou, Jian Chen
Pinoresinol is a natural lignan with a high market value that has potential pharmacological and food supplement applications. Pinoresinol is currently isolated from plants, which suffers from low efficiency and yield. To produce pinoresinol from inexpensive and industrially available eugenol, an in vivo enzymatic cascade composed of vanillyl alcohol oxidase and peroxidase was designed, which scavenges H2 O2 automatically and eliminates protein purification and cofactor addition. Two peroxidases were screened and identified from Escherichia coli BL21 (DE3), and tested in the enzymatic cascade...
April 24, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28435878/evolutionary-dynamics-of-crispr-gene-drives
#5
Charleston Noble, Jason Olejarz, Kevin M Esvelt, George M Church, Martin A Nowak
The alteration of wild populations has been discussed as a solution to a number of humanity's most pressing ecological and public health concerns. Enabled by the recent revolution in genome editing, clustered regularly interspaced short palindromic repeats (CRISPR) gene drives-selfish genetic elements that can spread through populations even if they confer no advantage to their host organism-are rapidly emerging as the most promising approach. However, before real-world applications are considered, it is imperative to develop a clear understanding of the outcomes of drive release in nature...
April 2017: Science Advances
https://www.readbyqxmd.com/read/28435837/staphylococcus-aureus-type-i-signal-peptidase-essential-or-not-essential-that-s-the-question
#6
COMMENT
Wouter L Hazenbos, Elizabeth Skippington, Man-Wah Tan
Secretion of proteins into the extracellular environment is crucial for the normal physiology and virulence of pathogenic bacteria. Type I signal peptidase (SPase I) mediates the final step of bacterial secretion, by cleaving proteins at their signal peptide once they are translocated by the Sec or twin-arginine (Tat) translocon. SPase I has long been thought to be essential for viability in multiple bacterial pathogens. Challenging this view, we and others have recently created Staphylococcus aureus bacteria lacking the SPase I SpsB that are viable and able to grow in vitro when over-expressing a native gene cassette encoding for a putative ABC transporter...
March 17, 2017: Microbial Cell
https://www.readbyqxmd.com/read/28435138/proteomic-analysis-of-a-mosquito-host-cell-response-to-persistent-wolbachia-infection
#7
Gerald Baldridge, LeeAnn Higgins, Bruce Witthuhn, Todd Markowski, Abigail Baldridge, Anibal Armien, Ann Fallon
Wolbachia pipientis, an obligate intracellular bacterium associated with arthropods and filarial worms, is a target for filarial disease treatment and provides a gene drive agent for insect vector population suppression/replacement. We compared proteomes of Aedes albopictus mosquito C/wStr1 cells persistently infected with Wolbachia strain wStr, relative to uninfected C7-10 control cells. Among approximately 2,500 proteins, iTRAQ data identified 815 differentially abundant proteins. As functional classes, energy and central intermediary metabolism proteins were elevated in infected cells, while suppressed proteins with roles in host DNA replication, transcription and translation suggested that Wolbachia suppresses pathways that support host cell growth and proliferation...
April 20, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28434151/cbf2a-cbf4b-genomic-region-copy-numbers-alongside-the-circadian-clock-play-key-regulatory-mechanisms-driving-expression-of-fr-h2-cbfs
#8
Taniya Dhillon, Kengo Morohashi, Eric J Stockinger
The C-Repeat Binding Factors (CBFs) are DNA-binding transcriptional activators that were identified using Arabidopsis thaliana. In barley, Hordeum vulgare, a cluster of CBF genes reside at FROST RESISTANCE-H2, one of two loci having major effects on winter-hardiness. FR-H2 was revealed in a population derived from the winter barley 'Nure' and the spring barley 'Trèmois'. 'Nure' harbors two to three copies of CBF2A and CBF4B as a consequence of tandem iteration of the genomic region encompassing these genes whereas 'Trèmois' harbors single copies, and these copy number differences are associated with their transcript level differences...
April 22, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28433771/a-versatile-tumor-gene-deletion-system-reveals-a-crucial-role-for-fgfr1-in-breast-cancer-metastasis
#9
Wei Wang, Yanling Meng, Bingning Dong, Jie Dong, Michael M Ittmann, Chad J Creighton, Lu Yang, Hong Zhang, Tao Shen, Jianghua Wang, David R Rowley, Yi Li, Fengju Chen, David D Moore, Feng Yang
RCAS avian viruses have been used to deliver oncogene expression and induce tumors in transgenic mice expressing the virus receptor TVA. Here we report the generation and characterization of a novel RCAS-Cre-IRES-PyMT (RCI-PyMT) virus designed to specifically knockout genes of interest in tumors generated in appropriate mutant mouse hosts. FGF receptor 1 (FGFR1) is a gene that is amplified in human breast cancer, but there have been no definitive studies on its function in mammary tumorigenesis, progression, and metastasis in vivo in spontaneous tumors in mice...
April 20, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28433419/disconnect-between-alcohol-induced-alterations-in-chromatin-structure-and-gene-transcription-in-a-mouse-embryonic-stem-cell-model-of-exposure
#10
Kylee J Veazey, Haiqing Wang, Yudhishtar S Bedi, William M Skiles, Richard Cheng-An Chang, Michael C Golding
Alterations to chromatin structure induced by environmental insults have become an attractive explanation for the persistence of exposure effects into subsequent life stages. However, a growing body of work examining the epigenetic impact that alcohol and other drugs of abuse exert consistently notes a disconnection between induced changes in chromatin structure and patterns of gene transcription. Thus, an important question is whether perturbations in the 'histone code' induced by prenatal exposures to alcohol implicitly subvert gene expression, or whether the hierarchy of cellular signaling networks driving development is such that they retain control over the transcriptional program...
January 11, 2017: Alcohol
https://www.readbyqxmd.com/read/28432287/advantages-of-unfair-quantum-ground-state-sampling
#11
Brian Hu Zhang, Gene Wagenbreth, Victor Martin-Mayor, Itay Hen
The debate around the potential superiority of quantum annealers over their classical counterparts has been ongoing since the inception of the field. Recent technological breakthroughs, which have led to the manufacture of experimental prototypes of quantum annealing optimizers with sizes approaching the practical regime, have reignited this discussion. However, the demonstration of quantum annealing speedups remains to this day an elusive albeit coveted goal. We examine the power of quantum annealers to provide a different type of quantum enhancement of practical relevance, namely, their ability to serve as useful samplers from the ground-state manifolds of combinatorial optimization problems...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432098/inhibitory-effect-of-coumarin-on-syntrophic-fatty-acid-oxidizing-and-methanogenic-cultures-and-biogas-reactor-microbiomes
#12
Denny Popp, Caroline M Plugge, Sabine Kleinsteuber, Hauke Harms, Heike Sträuber
Coumarins are widely found in plants as natural constituents having antimicrobial activity. When considering plants rich in coumarins for biogas production, adverse effects on microorganisms driving the anaerobic digestion process are expected. Furthermore, coumarin derivatives like warfarin, which are used as anti-coagulating medicine, are found in wastewater affecting its treatment. Coumarin as the structure common to all coumarins inhibits the anaerobic digestion process. However, details of this inhibition are still elusive...
April 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28431105/extinction-vs-rapid-radiation-the-juxtaposed-evolutionary-histories-of-coelotine-spiders-support-the-eocene-oligocene-orogenesis-of-the-tibetan-plateau
#13
Zhe Zhao, Shuqiang Li
Evolutionary biology has long been concerned with how changing environments affect and drive the spatiotemporal development of organisms. Coelotine spiders (Agelenidae: Coelotinae) are common species in the temperate and subtropical areas of the Northern Hemisphere. Their long evolutionary history and the extremely imbalanced distribution of species richness suggest that Eurasian environments, especially since the Cenozoic, are the drivers of their diversification. We use phylogenetics, molecular dating, ancestral area reconstructions, diversity, and ecological niche analyses to investigate the spatiotemporal evolution of 286 coelotine species from throughout the region...
April 20, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28430989/gene-fractionation-and-function-in-the-ancient-subgenomes-of-maize
#14
Simon Renny-Byfield, Eli Rodgers-Melnick, Jeffrey Ross-Ibarra
The maize genome experienced an ancient whole genome duplication approximately 10 million years ago and the duplicate subgenomes have since experienced reciprocal gene loss (fractionation) such that many genes have returned to single-copy status. This process has not affected the subgenomes equally; reduced gene expression in one of the subgenomes mitigates the consequences of mutations and gene deletions and is thought to drive higher rates of fractionation. Here we take advantage of published genome-wide SNP and phenotype association data to show that, in accordance with predictions of this model, paralogs with greater expression contribute more to phenotypic variation compared to their lowly expressed counterparts...
April 19, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28430105/switching-of-metabolic-programs-in-response-to-light-availability-is-an-essential-function-of-the-cyanobacterial-circadian-output-pathway
#15
Anna M Puszynska, Erin K O'Shea
The transcription factor RpaA is the master regulator of circadian transcription in cyanobacteria, driving genome-wide oscillations in mRNA abundance. Deletion of rpaA has no effect on viability in constant light conditions, but renders cells inviable in cycling conditions when light and dark periods alternate. We investigated the mechanisms underlying this viability defect, and demonstrate that the rpaA(-) strain cannot maintain appropriate energy status at night, does not accumulate carbon reserves during the day, and is defective in transcription of genes crucial for utilization of carbohydrate stores at night...
April 21, 2017: ELife
https://www.readbyqxmd.com/read/28429085/the-role-of-rna-alternative-splicing-in-regulating-cancer-metabolism
#16
REVIEW
Itamar Kozlovski, Zahava Siegfried, Adi Amar-Schwartz, Rotem Karni
Tumor cells alter their metabolism by a wide array of mechanisms to promote growth and proliferation. Dysregulated expression and/or somatic mutations of key components of the glycolytic pathway/TCA cycle as well as other metabolic pathways allow tumor cells to improve their ability to survive harsh conditions such as hypoxia and the presence of reactive oxygen species, as well as the ability to obtain nutrients to increase lipids, protein, and nucleic acids biogenesis. Approximately 95% of the human protein encoding genes undergo alternative splicing (AS), a regulated process of gene expression that greatly diversifies the proteome by creating multiple proteins from a single gene...
April 20, 2017: Human Genetics
https://www.readbyqxmd.com/read/28428858/genetic-diversity-and-spatial-structure-of-the-rufous-throated-antbird-gymnopithys-rufigula-an-amazonian-obligate-army-ant-follower
#17
Juliana Menger, Klaus Henle, William E Magnusson, Antonella Soro, Martin Husemann, Martin Schlegel
Amazonian understory antbirds are thought to be relatively sedentary and to have limited dispersal ability; they avoid crossing forest gaps, and even narrow roads through a forest may limit their territories. However, most evidence for sedentariness in antbirds comes from field observations and plot-based recapture of adult individuals, which do not provide evidence for lack of genetic dispersal, as this often occurs through juveniles. In this study, we used microsatellite markers and mitochondrial control-region sequences to investigate contemporary and infer historical patterns of genetic diversity and structure of the Rufous-throated Antbird (Gymnopithys rufigula) within and between two large reserves in central Amazonia...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28428362/hepatic-lipid-accumulation-cause-and-consequence-of-dysregulated-glucoregulatory-hormones
#18
Caroline E Geisler, Benjamin Jennings Renquist
Fatty liver can be diet, endocrine, genetic, viral, or drug induced. Independent of cause, hepatic lipid accumulation promotes systemic metabolic dysfunction. By acting as peroxisome proliferator activated receptor (PPAR) ligands, hepatic non-esterified fatty acids upregulate expression of gluconeogenic, beta-oxidative, lipogenic, and ketogenic genes, promoting hyperglycemia, hyperlipidemia, and ketosis. The typical hormonal environment in fatty liver disease consists of hyperinsulinemia, hyperglucagonemia, hypercortisolemia, growth hormone deficiency, and elevated sympathetic tone...
April 20, 2017: Journal of Endocrinology
https://www.readbyqxmd.com/read/28428277/immune-gene-expression-is-associated-with-genomic-aberrations-in-breast-cancer
#19
Anton Safonov, Tingting Jiang, Giampaolo Bianchini, Balázs Győrffy, Thomas Karn, Christos Hatzis, Lajos Pusztai
The presence of tumor-infiltrating lymphocytes (TIL) is a favorable prognostic factor in breast cancer, but what drives immune infiltration remains unknown. Here we examine if clonal heterogeneity, total mutation load, neoantigen load, copy number variations (CNV), gene- or pathway-level somatic mutations, or germline polymorphisms (SNP) are associated with immune metagene expression in breast cancer subtypes. Thirteen published immune metagenes correlated separately with genomic metrics in the 3 major breast cancer subtypes...
April 20, 2017: Cancer Research
https://www.readbyqxmd.com/read/28428276/micellar-delivery-of-mir-34a-modulator-rubone-and-paclitaxel-in-resistant-prostate-cancer
#20
Di Wen, Yang Peng, Feng Lin, Rakesh K Singh, Ram I Mahato
Treatment of prostate cancer with paclitaxel (PTX) often fails due to development of chemoresistance caused by downregulation of the tumor suppressor gene miR-34a. In this study, we demonstrate that co-delivery of PTX and 2'-hydroxy-2,4,4',5,6'-pentamethoxychalcone (termed rubone) drives upregulation of miR-34a and chemosensitizes PTX-resistant prostate cancer cells, killing both cancer stem-like cells (CSCs) and bulk tumor cells. Rubone upregulated miR-34a and reversed its downstream target genes in DU145-TXR and PC3-TXR cells...
April 20, 2017: Cancer Research
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