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https://www.readbyqxmd.com/read/29222751/reconstruction-and-analysis-of-central-metabolism-in-microbes
#1
Janaka N Edirisinghe, José P Faria, Nomi L Harris, Benjamin H Allen, Christopher S Henry
Genome-scale metabolic models (GEMs) generated from automated reconstruction pipelines often lack accuracy due to the need for extensive gapfilling and the inference of periphery metabolic pathways based on lower-confidence annotations. The central carbon pathways and electron transport chains are among the most well-understood regions of microbial metabolism, and these pathways contribute significantly toward defining cellular behavior and growth conditions. Thus, it is often useful to construct a simplified core metabolic model (CMM) that is comprised of only the high-confidence central pathways...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222292/uncoding-the-genetic-heterogeneity-of-myelodysplastic-syndrome
#2
REVIEW
R Coleman Lindsley
Myelodysplastic syndrome (MDS) is a clinically heterogeneous disease characterized by functional impairment of hematopoiesis and abnormal bone marrow morphology. The type and severity of hematopoietic dysfunction in MDS are highly variable, and the kinetics of disease progression are difficult to predict. Genomic studies have shown that MDS is typically driven by a multistep somatic genetic process affecting a core set of genes. By definition, recurrent MDS driver mutations all drive clonal dominance, although they can have stereotyped positions in the clonal hierarchy or patterns of comutation association and exclusivity...
December 8, 2017: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/29222100/diversity-of-lactococcus-lactis-in-undefined-mixed-dairy-starter-cultures-revealed-by-comparative-genome-analyses-and-targeted-amplicon-sequencing-of-epsd
#3
Cyril A Frantzen, Hans Petter Kleppen, Helge Holo
Undefined mesophilic mixed (DL) starter cultures are used in the production of continental cheeses and contain unknown strain mixtures of Lactococcus lactis and leuconostocs. The choice of starter culture affects the taste, aroma and quality of the final product. To gain insight into the diversity of Lactococcus lactis strains in starter cultures, we whole-genome sequenced 95 isolates from three different starter cultures. Pan-genomic analyses, which included 30 publically available complete genomes, grouped the strains into 21 subsp...
December 8, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29217450/cadm2-regulates-body-weight-and-energy-homeostasis-in-mice
#4
Xin Yan, Zhen Wang, Vanessa Schmidt, Anton Gauert, Thomas E Willnow, Matthias Heinig, Matthew N Poy
OBJECTIVE: Obesity is strongly linked to genes regulating neuronal signaling and function, implicating the central nervous system in the maintenance of body weight and energy metabolism. Genome-wide association studies identified significant associations between body mass index (BMI) and multiple loci near Cell adhesion molecule2 (CADM2), which encodes a mediator of synaptic signaling enriched in the brain. Here we sought to further understand the role of Cadm2 in the pathogenesis of hyperglycemia and weight gain...
November 22, 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/29216180/the-ink4a-arf-locus-operates-as-a-regulator-of-the-circadian-clock-modulating-ras-activity
#5
Rukeia El-Athman, Nikolai N Genov, Jeannine Mazuch, Kaiyang Zhang, Yong Yu, Luise Fuhr, Mónica Abreu, Yin Li, Thomas Wallach, Achim Kramer, Clemens A Schmitt, Angela Relógio
The mammalian circadian clock and the cell cycle are two major biological oscillators whose coupling influences cell fate decisions. In the present study, we use a model-driven experimental approach to investigate the interplay between clock and cell cycle components and the dysregulatory effects of RAS on this coupled system. In particular, we focus on the Ink4a/Arf locus as one of the bridging clock-cell cycle elements. Upon perturbations by the rat sarcoma viral oncogene (RAS), differential effects on the circadian phenotype were observed in wild-type and Ink4a/Arf knock-out mouse embryonic fibroblasts (MEFs), which could be reproduced by our modelling simulations and correlated with opposing cell cycle fate decisions...
December 2017: PLoS Biology
https://www.readbyqxmd.com/read/29215000/the-evolution-of-the-macrophage-specific-enhancer-fms-intronic-regulatory-element-within-the-csf1r-locus-of-vertebrates
#6
David A Hume, Evi Wollscheid-Lengeling, Rocio Rojo, Clare Pridans
The Csf1r locus encodes the receptor for macrophage colony-stimulating factor, which controls the proliferation, differentiation and survival of macrophages. The 300 bp Fms intronic regulatory element (FIRE), within the second intron of Csf1r, is necessary and sufficient to direct macrophage-specific transcription. We have analysed the conservation and divergence of the FIRE DNA sequence in vertebrates. FIRE is present in the same location in the Csf1r locus in reptile, avian and mammalian genomes. Nearest neighbor analysis based upon this element alone largely recapitulates phylogenies inferred from much larger genomic sequence datasets...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29214581/newborn-screening-beyond-the-spot
#7
Tiina K Urv, Melissa A Parisi
The newborn screening paradigm of testing all newborns in the United States for treatable conditions within the first few hours of birth has proven to be a remarkable success story in the realm of public health by reducing neonatal and childhood morbidity and mortality. The Newborn Screening Saves Lives Act of 2007 and its successor, the Reauthorization Act of 2014, legislated the establishment of a Department of Health and Human Services Advisory Committee to make recommendations around newborn screening and a methodology to establish and add new conditions to a Recommended Uniform Screening Panel (RUSP) which currently includes 34 core conditions...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29213333/comparative-genomic-analysis-of-clostridium-difficile-ribotype-027-strains-including-the-newly-sequenced-strain-nckuh-21-isolated-from-a-patient-in-taiwan
#8
Haruo Suzuki, Masaru Tomita, Pei-Jane Tsai, Wen-Chien Ko, Yuan-Pin Hung, I-Hsiu Huang, Jenn-Wei Chen
Background: Clostridium difficile is a Gram-positive anaerobe and the leading cause of antibiotic-associated diarrhea worldwide. The emergence of ribotype 027 (RT027) strains is associated with increased incidence of infection and mortality. To further understand the relationship between C. difficile NCKUH-21, a RT027 strain isolated from a patient in Taiwan, and other RT027 strains, we performed whole-genome shotgun sequencing on NCKUH-21 and comparative genomic analyses. Results: The genome size, G+C content, and gene number for the NCKUH-21 strain were determined to be similar to those for other C...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/29212533/subtracting-the-sequence-bias-from-partially-digested-mnase-seq-data-reveals-a-general-contribution-of-tfiis-to-nucleosome-positioning
#9
Gabriel Gutiérrez, Gonzalo Millán-Zambrano, Daniel A Medina, Antonio Jordán-Pla, José E Pérez-Ortín, Xenia Peñate, Sebastián Chávez
BACKGROUND: TFIIS stimulates RNA cleavage by RNA polymerase II and promotes the resolution of backtracking events. TFIIS acts in the chromatin context, but its contribution to the chromatin landscape has not yet been investigated. Co-transcriptional chromatin alterations include subtle changes in nucleosome positioning, like those expected to be elicited by TFIIS, which are elusive to detect. The most popular method to map nucleosomes involves intensive chromatin digestion by micrococcal nuclease (MNase)...
December 7, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29212286/regulation-of-dna-replication-coupled-histone-gene-expression
#10
REVIEW
Qianyun Mei, Junhua Huang, Wanping Chen, Jie Tang, Chen Xu, Qi Yu, Ying Cheng, Lixin Ma, Xilan Yu, Shanshan Li
The expression of core histone genes is cell cycle regulated. Large amounts of histones are required to restore duplicated chromatin during S phase when DNA replication occurs. Over-expression and excess accumulation of histones outside S phase are toxic to cells and therefore cells need to restrict histone expression to S phase. Misregulation of histone gene expression leads to defects in cell cycle progression, genome stability, DNA damage response and transcriptional regulation. Here, we discussed the factors involved in histone gene regulation as well as the underlying mechanism...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29211859/transformation-asymmetry-and-the-evolution-of-the-bacterial-accessory-genome
#11
Katinka J Apagyi, Christophe Fraser, Nicholas J Croucher
Bacterial transformation can insert or delete genomic islands (GIs), depending on the donor and recipient genotypes, if an homologous recombination spans the GI's integration site and includes sufficiently long flanking homologous arms. Combining mathematical models of recombination with experiments using pneumococci found GI insertion rates declined geometrically with the GI's size. The decrease in acquisition frequency with length (1.08x10-3 bp-1) was higher than a previous estimate of the analogous rate at which core genome recombinations terminated...
December 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29208896/mechanistic-insight-into-trip13-catalyzed-mad2-structural-transition-and-spindle-checkpoint-silencing
#12
Melissa L Brulotte, Byung-Cheon Jeong, Faxiang Li, Bing Li, Eric B Yu, Qiong Wu, Chad A Brautigam, Hongtao Yu, Xuelian Luo
The spindle checkpoint maintains genomic stability and prevents aneuploidy. Unattached kinetochores convert the latent open conformer of the checkpoint protein Mad2 (O-Mad2) to the active closed conformer (C-Mad2), bound to Cdc20. C-Mad2-Cdc20 is incorporated into the mitotic checkpoint complex (MCC), which inhibits the anaphase-promoting complex/cyclosome (APC/C). The C-Mad2-binding protein p31comet and the ATPase TRIP13 promote MCC disassembly and checkpoint silencing. Here, using nuclear magnetic resonance (NMR) spectroscopy, we show that TRIP13 and p31comet catalyze the conversion of C-Mad2 to O-Mad2, without disrupting its stably folded core...
December 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/29208606/emerging-role-of-crispr-cas9-technology-for-micrornas-editing-in-cancer-research
#13
REVIEW
Guillermo Aquino-Jarquin
MicroRNAs (miRNA) are small, noncoding RNA molecules with a master role in the regulation of important tasks in different critical processes of cancer pathogenesis. Because there are different miRNAs implicated in all the stages of cancer, for example, functioning as oncogenes, this makes these small molecules suitable targets for cancer diagnosis and therapy. RNA-mediated interference has been one major approach for sequence-specific regulation of gene expression in eukaryotic organisms. Recently, the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system, first identified in bacteria and archaea as an adaptive immune response to invading genetic material, has been explored as a sequence-specific molecular tool for editing genomic sequences for basic research in life sciences and for therapeutic purposes...
December 5, 2017: Cancer Research
https://www.readbyqxmd.com/read/29208121/whole-genome-sequencing-of-bloodstream-staphylococcus-aureus-isolates-does-not-distinguish-bacteraemia-from-endocarditis
#14
Berit Lilje, Rasmus Vedby Rasmussen, Anders Dahl, Marc Stegger, Robert Leo Skov, Vance G Fowler, Kim Lee Ng, Kristoffer Kiil, Anders Rhod Larsen, Andreas Petersen, Helle Krogh Johansen, Henrik Carl Schønheyder, Magnus Arpi, Flemming S Rosenvinge, Eva Korup, Ulla Høst, Christian Hassager, Sabine Ute Alice Gill, Thomas Fritz Hansen, Thor Bech Johannesen, Jesper Smit, Peter Søgaard, Paal Skytt Andersen, Niels Eske-Bruun
Most Staphylococcus aureus isolates can cause invasive disease given the right circumstances, but it is unknown if some isolates are more likely to cause severe infections than others. S. aureus bloodstream isolates from 120 patients with definite infective endocarditis and 121 with S. aureus bacteraemia without infective endocarditis underwent whole-genome sequencing. Genome-wide association analysis was performed using a variety of bioinformatics approaches including SNP analysis, accessory genome analysis and k-mer based analysis...
November 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29207277/laser-captured-microglia-in-the-alzheimer-s-and-parkinson-s-brain-reveal-unique-regional-expression-profiles-and-suggest-a-potential-role-for-hepatitis-b-in-the-alzheimer-s-brain
#15
Diego Mastroeni, Jennifer Nolz, Shobana Sekar, Elaine Delvaux, Geidy Serrano, Lori Cuyugan, Winnie S Liang, Thomas G Beach, Joseph Rogers, Paul D Coleman
Expression array data from dozens of laboratories, including our own, show significant changes in expression of many genes in Alzheimer's disease (AD) patients compared with normal controls. These data typically rely on brain homogenates, and information about transcripts specific to microglia and other central nervous system (CNS) cell types, which far outnumber microglia-specific transcripts, is lost. We therefore used single-cell laser capture methods to assess the full range of microglia-specific expression changes that occur in different brain regions (substantia nigra and hippocampus CA1) and disease states (AD, Parkinson's disease, and normal controls)...
November 1, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/29205864/a-bifunctional-cellulase-xylanase-of-a-new-chryseobacterium-strain-isolated-from-the-dung-of-a-straw-fed-cattle
#16
Hao Tan, Renyun Miao, Tianhai Liu, Lufang Yang, Yumin Yang, Chunxiu Chen, Jianrong Lei, Yuhui Li, Jiabei He, Qun Sun, Weihong Peng, Bingcheng Gan, Zhongqian Huang
A new cellulolytic strain of Chryseobacterium genus was screened from the dung of a cattle fed with cereal straw. A putative cellulase gene (cbGH5) belonging to glycoside hydrolase family 5 subfamily 46 (GH5_46) was identified and cloned by degenerate PCR plus genome walking. The CbGH5 protein was overexpressed in Pichia pastoris, purified and characterized. It is the first bifunctional cellulase-xylanase reported in GH5_46 as well as in Chryseobacterium genus. The enzyme showed an endoglucanase activity on carboxymethylcellulose of 3237 μmol min-1  mg-1 at pH 9, 90 °C and a xylanase activity on birchwood xylan of 1793 μmol min-1  mg-1 at pH 8, 90 °C...
December 4, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/29204787/the-complete-genome-sequence-of-a-third-distinct-baculovirus-isolated-from-the-true-armyworm-mythimna-unipuncta-contains-two-copies-of-the-lef-7-gene
#17
Robert L Harrison, Joseph D Mowery, Daniel L Rowley, Gary R Bauchan, David A Theilmann, George F Rohrmann, Martin A Erlandson
A baculovirus isolate from a USDA Forest Service collection was characterized by electron microscopy and analysis of its genome sequence. The isolate, formerly referred to as Pseudoletia (Mythimna) sp. nucleopolyhedrovirus #7 (MyspNPV#7), was determined by barcoding PCR to derive from the host species Mythimna unipuncta (true armyworm) and was renamed Mythimna unipuncta nucleopolyhedrovirus #7 (MyunNPV#7). The occlusion bodies (OBs) and virions exhibited a size and morphology typical for OBs produced by the species of genus Alphabaculovirus, with occlusion-derived virions consisting of 2-5 nucleocapsids within a single envelope...
December 4, 2017: Virus Genes
https://www.readbyqxmd.com/read/29203924/nemertean-and-phoronid-genomes-reveal-lophotrochozoan-evolution-and-the-origin-of-bilaterian-heads
#18
Yi-Jyun Luo, Miyuki Kanda, Ryo Koyanagi, Kanako Hisata, Tadashi Akiyama, Hirotaka Sakamoto, Tatsuya Sakamoto, Noriyuki Satoh
Nemerteans (ribbon worms) and phoronids (horseshoe worms) are closely related lophotrochozoans-a group of animals including leeches, snails and other invertebrates. Lophotrochozoans represent a superphylum that is crucial to our understanding of bilaterian evolution. However, given the inconsistency of molecular and morphological data for these groups, their origins have been unclear. Here, we present draft genomes of the nemertean Notospermus geniculatus and the phoronid Phoronis australis, together with transcriptomes along the adult bodies...
December 4, 2017: Nature Ecology & Evolution
https://www.readbyqxmd.com/read/29203696/treasure-your-exceptions-an-interview-with-2017-george-beadle-award-recipient-susan-a-gerbi
#19
Susan A Gerbi
THE Genetics Society of America's (GSA) George W. Beadle Award honors individuals who have made outstanding contributions to the community of genetics researchers and who exemplify the qualities of its namesake. The 2017 recipient is Susan A. Gerbi, who has been a prominent leader and advocate for the scientific community. In the course of her research on DNA replication, Gerbi helped develop the method of Replication Initiation Point (RIP) mapping to map replication origins at the nucleotide level, improving resolution by two orders of magnitude...
December 2017: Genetics
https://www.readbyqxmd.com/read/29203652/divergence-of-regulatory-networks-governed-by-the-orthologous-transcription-factors-flc-and-pep1-in-brassicaceae-species
#20
Julieta L Mateos, Vicky Tilmes, Pedro Madrigal, Edouard Severing, René Richter, Colin W M Rijkenberg, Paweł Krajewski, George Coupland
Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively...
December 4, 2017: Proceedings of the National Academy of Sciences of the United States of America
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