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https://www.readbyqxmd.com/read/29454117/the-differentially-expressed-genes-of-human-sporadic-cerebral-cavernous-malformations
#1
Xiangjiang Lin, Guolu Meng, Xing Liu, Tengfei Yu, Chuanfeng Bai, Xiaobin Fei, Shengze Deng, Jizong Zhao, Shulin Ren, Junting Zhang, Zhen Wu, Shuo Wang, Jianguo Zhang, Liwei Zhang
OBJECTIVES: To understand the development of Sporadic cerebral cavernous malformations (SCCM) comprehensively, we analyzed gene expression profiles in SCCMs by the gene microarray. METHODS: The total number of the specimens collected in our study was 14, 7 of which were SCCMs, and the others were controls that were obtained from normal brain vessels. The total RNA was extracted and hybridized with Oligonucleotide array containing 21522 genes. The analysis of Gene Ontology (GO) items and molecular pathways was performed based on the GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases...
February 14, 2018: World Neurosurgery
https://www.readbyqxmd.com/read/29453633/comparative-analysis-of-the-mitochondrial-genome-of-the-fungus-colletotrichum-lindemuthianum-the-causal-agent-of-anthracnose-in-common-beans
#2
Casley Borges de Queiroz, Mateus Ferreira Santana, Pedro M Pereira Vidigal, Marisa Vieira de Queiroz
Fungi of the genus Colletotrichum are economically important and are used as models in plant-pathogen interaction studies. In this study, the complete mitochondrial genomes of two Colletotrichum lindemuthianum isolates were sequenced and compared with the mitochondrial genomes of seven species of Colletotrichum. The mitochondrial genome of C. lindemuthianum is a typical circular molecule 37,446 bp (isolate 89 A 2 2-3) and 37,440 bp (isolate 83.501) in length. The difference of six nucleotides between the two genomes is the result of a deletion in the ribosomal protein S3 (rps3) gene in the 83...
February 16, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29452455/complex-hur-function-in-pancreatic-cancer-cells
#3
REVIEW
Jonathan R Brody, Dan A Dixon
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers with dismal patient outcomes. The underlying core genetic drivers of disease have been identified in human tumor specimens and described in genetically engineered mouse models. These genetic drivers of PDAC include KRAS signaling, TP53 mutations, and genetic loss of the SMAD4 tumor suppressor protein. Beyond the known mutational landscape of PDAC genomes, alternative disrupted targets that extend beyond conventional genetic mutations have been elusive and understudied in the context of PDAC cell therapeutic resistance and survival...
February 16, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29449436/mixed-species-rnaseq-analysis-of-human-lymphoma-cells-adhering-to-mouse-stromal-cells-identifies-a-core-gene-set-that-is-also-differentially-expressed-in-the-lymph-node-microenvironment-of-mantle-cell-lymphoma-and-chronic-lymphocytic-leukemia-patients
#4
Gustav Arvidsson, Johan Henriksson, Birgitta Sander, Anthony P Wright
A subset of hematological cancer patients is refractory to treatment or suffers relapse, due in part to minimal residual disease, whereby some cancer cells survive treatment. Cell-adhesion mediated drug resistance is an important mechanism, whereby cancer cells receive survival signals via interaction with e.g. stromal cells. No genome-wide studies of in vitro systems have yet been performed to compare gene expression in different cell subsets within a co-culture and cells grown separately. Using RNA sequencing and species-specific read mapping, we compared transcript levels in human Jeko-1 mantle cell lymphoma cells stably adhered to mouse MS-5 stromal cells or in suspension within a co-culture or cultured separately as well as in stromal cells in co-culture or in separate culture...
February 15, 2018: Haematologica
https://www.readbyqxmd.com/read/29447373/coupling-the-core-of-the-anticancer-drug-etoposide-to-an-oligonucleotide-induces-topoisomerase-ii-mediated-cleavage-at-specific-dna-sequences
#5
Lorena Infante Lara, Sabine Fenner, Steven Ratcliffe, Albert Isidro-Llobet, Michael Hann, Ben Bax, Neil Osheroff
Etoposide and other topoisomerase II-targeted drugs are important anticancer therapeutics. Unfortunately, the safe usage of these agents is limited by their indiscriminate induction of topoisomerase II-mediated DNA cleavage throughout the genome and by a lack of specificity toward cancer cells. Therefore, as a first step toward constraining the distribution of etoposide-induced DNA cleavage sites and developing sequence-specific topoisomerase II-targeted anticancer agents, we covalently coupled the core of etoposide to oligonucleotides centered on a topoisomerase II cleavage site in the PML gene...
February 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29445826/genome-based-comparison-of-clostridioides-difficile-average-amino-acid-identity-analysis-of-core-genomes
#6
Adriana Cabal, Se-Ran Jun, Piroon Jenjaroenpun, Visanu Wanchai, Intawat Nookaew, Thidathip Wongsurawat, Mary J Burgess, Atul Kothari, Trudy M Wassenaar, David W Ussery
Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores...
February 14, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/29444947/hepatitis-c-virus-core-1-arfp-modulates-cyclin-d1-prb-pathway-and-promotes-carcinogenesis
#7
Savvina Moustafa, Ioannis Karakasiliotis, Penelope Mavromara
Viruses often encompass overlapping reading frames and unconventional translation mechanisms in order to maximize the output from a minimum genome and to orchestrate timely their gene expression. HCV possesses such an unconventional open reading frame (ORF) within the core-coding region, encoding an additional protein designated initially as ARFP or F or core+1. Two predominant isoforms of core+1/ARFP have been reported, core+1/L initiating from codon 26 and core+1/S initiating from codons 85/87 of the polyprotein coding region, respectively...
February 14, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29444944/the-38k-mediated-specific-dephosphorylation-of-the-viral-core-protein-p6-9-plays-an-important-role-in-the-nucleocapsid-assembly-of-autographa-californica-multiple-nucleopolyhedrovirus
#8
Qingying Lai, Wenbi Wu, Ao Li, Wei Wang, Meijin Yuan, Kai Yang
Encapsidation of the viral genomes, leading to the assembly of the nucleocapsids to form infectious progeny virions, is a key step in many virus life cycles. Baculovirus nucleocapsid assembly is a complex process that involves many proteins. Our previous studies showed that the deletion of the core gene, 38K ( ac98 ) interrupted the nucleocapsid assembly by producing capsid sheaths devoid of viral genomes under unknown mechanism. All homologs of 38K contain conserved motifs of the haloacid dehalogenase superfamily, which are involved in phosphoryl transfer...
February 14, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29442331/role-of-zic-family-proteins-in-transcriptional-regulation-and-chromatin-remodeling
#9
Minoru Hatayama, Jun Aruga
Proper functions of Zic proteins are essential for animals in health and disease. Here, we summarize our current understanding of the molecular properties and functions of the Zic family across animal species and paralog subtypes. Zics are basic proteins with some posttranslational modifications and can move to the cell nucleus via importin- and CRM1-based nucleocytoplasmic shuttling mechanisms. Degradation is mediated by the ubiquitin proteasome system. Many Zic proteins are capable of binding to two types of target DNA sequences (CTGCTG-core-type and GC-stretch-type)...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29439438/rna-dependent-rna-polymerases-insights-from-structure-function-and-evolution
#10
REVIEW
Sangita Venkataraman, Burra V L S Prasad, Ramasamy Selvarajan
RNA dependent RNA polymerase (RdRp) is one of the most versatile enzymes of RNA viruses that is indispensable for replicating the genome as well as for carrying out transcription. The core structural features of RdRps are conserved, despite the divergence in their sequences. The structure of RdRp resembles that of a cupped right hand and consists of fingers, palm and thumb subdomains. The catalysis involves the participation of conserved aspartates and divalent metal ions. Complexes of RdRps with substrates, inhibitors and metal ions provide a comprehensive view of their functional mechanism and offer valuable insights regarding the development of antivirals...
February 10, 2018: Viruses
https://www.readbyqxmd.com/read/29439026/rev-erb%C3%AE-dynamically-modulates-chromatin-looping-to-control-circadian-gene-transcription
#11
Yong Hoon Kim, Sajid A Marhon, Yuxiang Zhang, David J Steger, Kyoung-Jae Won, Mitchell A Lazar
Mammalian physiology exhibits 24-hour cyclicity due to circadian rhythms of gene expression controlled by transcription factors (TF) that comprise molecular clocks. Core clock TFs bind to the genome at enhancer sequences to regulate circadian gene expression, but not all binding sites are equally functional. Here we demonstrate that circadian gene expression in mouse liver is controlled by rhythmic chromatin interactions between enhancers and promoters. Rev-erbα, a core repressive TF of the clock, opposes functional loop formation between Rev-erbα-regulated enhancers and circadian target gene promoters by recruitment of the NCoR-HDAC3 corepressor complex, histone deacetylation, and eviction of the elongation factor BRD4 and the looping factor MED1...
February 8, 2018: Science
https://www.readbyqxmd.com/read/29434842/comprehensive-characterization-of-cancer-genes-in-hepatocellular-carcinoma-genomes
#12
Zhihao Zhang, Liping Xu, Changyu Sun
The present study was performed to detect moderate or low-frequency mutated cancer driver genes in hepatocellular carcinoma (HCC), using OncodriveFM and Dendrix. Following this, integrated analyses were conducted on these novel cancer driver genes. A total of 112,980 somatic mutations were retrieved from TCGA and classified into 11 categories based on their function. Driver genes and pathways were predicted by OncodriveFM and Dendrix, followed by differential expression, DNA-methylation, copy number variations and survival analyses...
February 2018: Oncology Letters
https://www.readbyqxmd.com/read/29434737/identification-of-core-pathways-based-on-attractor-and-crosstalk-in-ischemic-stroke
#13
Xiufang Diao, Aijuan Liu
Ischemic stroke is a leading cause of mortality and disability around the world. It is an important task to identify dysregulated pathways which infer molecular and functional insights existing in high-throughput experimental data. Gene expression profile of E-GEOD-16561 was collected. Pathways were obtained from the database of Kyoto Encyclopedia of Genes and Genomes and Retrieval of Interacting Genes was used to download protein-protein interaction sets. Attractor and crosstalk approaches were applied to screen dysregulated pathways...
February 2018: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29434220/the-plant-specific-histone-residue-phe41-is-important-for-genome-wide-h3-1-distribution
#14
Li Lu, Xiangsong Chen, Shuiming Qian, Xuehua Zhong
The dynamic incorporation of histone variants influences chromatin structure and many biological processes. In Arabidopsis, the canonical variant H3.1 differs from H3.3 in four residues, one of which (H3.1Phe41) is unique and conserved in plants. However, its evolutionary significance remains unclear. Here, we show that Phe41 first appeared in H3.1 in ferns and became stable during land plant evolution. Unlike H3.1, which is specifically enriched in silent regions, H3.1F41Y variants gain ectopic accumulation at actively transcribed regions...
February 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29433445/comparative-genomic-analysis-reveals-the-evolution-and-environmental-adaptation-strategies-of-vibrios
#15
Heyu Lin, Min Yu, Xiaolei Wang, Xiao-Hua Zhang
BACKGROUND: Vibrios are among the most diverse and ecologically important marine bacteria, which have evolved many characteristics and lifestyles to occupy various niches. The relationship between genome features and environmental adaptation strategies is an essential part for understanding the ecological functions of vibrios in the marine system. The advent of complete genome sequencing technology has provided an important method of examining the genetic characteristics of vibrios on the genomic level...
February 13, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29432421/the-rate-and-potential-relevance-of-new-mutations-in-a-colonizing-plant-lineage
#16
Moises Exposito-Alonso, Claude Becker, Verena J Schuenemann, Ella Reiter, Claudia Setzer, Radka Slovak, Benjamin Brachi, Jörg Hagmann, Dominik G Grimm, Jiahui Chen, Wolfgang Busch, Joy Bergelson, Rob W Ness, Johannes Krause, Hernán A Burbano, Detlef Weigel
By following the evolution of populations that are initially genetically homogeneous, much can be learned about core biological principles. For example, it allows for detailed studies of the rate of emergence of de novo mutations and their change in frequency due to drift and selection. Unfortunately, in multicellular organisms with generation times of months or years, it is difficult to set up and carry out such experiments over many generations. An alternative is provided by "natural evolution experiments" that started from colonizations or invasions of new habitats by selfing lineages...
February 12, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29430445/mechanical-stretch-modulates-cell-migration-in-the-lungs
#17
REVIEW
Cecilia López-Martínez, Covadonga Huidobro, Guillermo M Albaiceta, Inés López-Alonso
Cell migration is a core process to preserve homeostasis. Release of chemotactic signals induces changes in cell cytoskeleton to facilitate migration. This includes the rearrangement of cytoskeleton, genomic reprogramming and the modification of the surrounding extracellular matrix (ECM) to allow the motion of cells through. In the special case of repair after acute lung injury, cells must migrate while exposed to an increased mechanical stretch caused either by an increased work of breathing or positive-pressure ventilation...
January 2018: Annals of Translational Medicine
https://www.readbyqxmd.com/read/29428968/differentiation-analysis-for-estimating-individual-ancestry-from-the-tibetan-plateau-by-an-archaic-altitude-adaptation-epas1-haplotype-among-east-asian-populations
#18
Li Jiang, Jianxiong Peng, Meisha Huang, Jing Liu, Ling Wang, Quan Ma, Hui Zhao, Xin Yang, Anquan Ji, Caixia Li
Tibetans have adapted to the extreme environment of high altitude for hundreds of generations. A highly differentiated 5-SNP (Single Nucleotide Polymorphism) haplotype motif (AGGAA) on a hypoxic pathway gene, EPAS1, is observed in Tibetans and lowlanders. To evaluate the potential usage of the 5-SNP haplotype in ancestry inference for Tibetan or Tibetan-related populations, we analyzed this haplotype in 1053 individuals of 12 Chinese populations residing on the Tibetan Plateau, peripheral regions of Tibet, and plain regions...
February 10, 2018: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29427605/a-mathematical-framework-for-yield-versus-rate-optimization-in-constraint-based-modeling-and-applications-in-metabolic-engineering
#19
Steffen Klamt, Stefan Müller, Georg Regensburger, Jürgen Zanghellini
BACKGROUND: The optimization of metabolic rates (as linear objective functions) represents the methodical core of flux-balance analysis techniques which have become a standard tool for the study of genome-scale metabolic models. Besides (growth and synthesis) rates, metabolic yields are key parameters for the characterization of biochemical transformation processes, especially in the context of biotechnological applications. However, yields are ratios of rates, and hence the optimization of yields (as nonlinear objective functions) under arbitrary linear constraints is not possible with current flux-balance analysis techniques...
February 7, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29427526/nup98-bptf-gene-fusion-identified-in-primary-refractory-acute-megakaryoblastic-leukemia-of-infancy
#20
Mathieu Roussy, Mélanie Bilodeau, Loubna Jouan, Pauline Tibout, Louise Laramée, Emmanuelle Lemyre, Sophie Cardin, Camille Sauvageau, Françoise Couture, Aurélien Choblet, Natalie Patey, Patrick Gendron, Michel Duval, Pierre Teira, Josée Hébert, Brian T Wilhelm, John K Choi, Tanja A Gruber, Henrique Bittencourt, Sonia Cellot
The advent of large scale genomic sequencing technologies significantly improved the molecular classification of acute megakaryoblastic leukaemia (AMKL). AMKL represents a subset (∼10%) of high fatality pediatric acute myeloid leukemia (AML). Recurrent and mutually exclusive chimeric gene fusions associated with pediatric AMKL are found in 60-70% of cases and include RBM15-MKL1, CBFA2T3-GLIS2, NUP98-KDM5A and MLL rearrangements. In addition, another 4% of AMKL harbor NUP98 rearrangements (NUP98r), with yet undetermined fusion partners...
February 10, 2018: Genes, Chromosomes & Cancer
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