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https://www.readbyqxmd.com/read/28528444/assembly-and-egress-of-an-alphaherpesvirus-clockwork
#1
Gregory A Smith
All viruses produce infectious particles that possess some degree of stability in the extracellular environment yet disassemble upon cell contact and entry. For the alphaherpesviruses, which include many neuroinvasive viruses of mammals, these metastable virions consist of an icosahedral capsid surrounded by a protein matrix (referred to as the tegument) and a lipid envelope studded with glycoproteins. Whereas the capsid of these viruses is a rigid structure encasing the DNA genome, the tegument and envelope are dynamic assemblies that orchestrate a sequential series of events that ends with the delivery of the genome into the nucleus...
2017: Advances in Anatomy, Embryology, and Cell Biology
https://www.readbyqxmd.com/read/28528358/dna-topoisomerase-targeting-chemotherapeutics-what-s-new
#2
REVIEW
Selma M Cuya, Mary-Ann Bjornsti, Robert C A M van Waardenburg
To resolve the topological problems that threaten the function and structural integrity of nuclear and mitochondrial genomes and RNA molecules, human cells encode six different DNA topoisomerases including type IB enzymes (TOP1 and TOP1mt), type IIA enzymes (TOP2α and TOP2β) and type IA enzymes (TOP3α and TOP3β). DNA entanglements and the supercoiling of DNA molecules are regulated by topoisomerases through the introduction of transient enzyme-linked DNA breaks. The covalent topoisomerase-DNA complexes are the cellular targets of a diverse group of cancer chemotherapeutics, which reversibly stabilize these reaction intermediates...
May 20, 2017: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/28527137/genome-based-identification-of-heterotic-patterns-in-rice
#3
Ulrike Beukert, Zuo Li, Guozheng Liu, Yusheng Zhao, Nadhigade Ramachandra, Vilson Mirdita, Fabiano Pita, Klaus Pillen, Jochen Christoph Reif
BACKGROUND: Hybrid rice breeding facilitates to increase grain yield and yield stability. Long-term success of hybrid breeding depends on the recognition of high-yielding complementary heterotic patterns, which is lacking in crops like rice. RESULT: The main goal of this study was to evaluate the potential and limits to use genomics for establishing heterotic patterns in rice. For this purpose, data of a commercial hybrid rice breeding program targeted to India was analyzed, including 1,960 phenotyped hybrids from three market segments and 262 genotyped parental lines...
December 2017: Rice
https://www.readbyqxmd.com/read/28524267/synaptic-activity-suppresses-expression-of-neurogenic-differentiation-factor-2-in-an-nmda-receptor-dependent-manner
#4
Fading Chen, Benjamin J Hall
Neurogenic differentiation factor 2 (NeuroD2) is a highly expressed transcription factor in the developing central nervous system. In newborn neurons, NeuroD2-mediated gene expression promotes differentiation, maturation, and survival. In addition to these early, cell-intrinsic developmental processes, NeuroD2 in post-mitotic neurons also regulates synapse growth and ion channel expression to control excitability. While NeuroD2 transactivation can be induced in an activity-dependent manner, little is known about how expression of NeuroD2 itself is regulated...
May 19, 2017: Synapse
https://www.readbyqxmd.com/read/28523359/arginine-cga-codons-as-a-source-of-nonsense-mutations-a-possible-role-in-multivariant-gene-expression-control-of-mrna-quality-and-aging
#5
Georgy A Romanov, Victor S Sukhoverov
Methylation of cytosine residues in DNA of higher eukaryotes, including humans, creates "hot spots" of C→T transitions in the genome. The predominantly methylated sequence in mammalian DNAs is CG (CpG). Among CG-containing codons, CGA codons for arginine are unique due to their ability to create stop codons TGA (UGA in mRNA) upon epigenetic-mediated mutation. As such nonsense mutations can have a strong adverse effect on the cell and organism, we have performed a study, on the example of human genes, aimed to characterise the anticipated effects of epigenetic-mediated nonsense mutations CGA→TGA in somatic cells...
May 18, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28521416/a-proposed-method-for-the-relative-quantification-of-levels-of-circulating-micrornas-in-the-plasma-of-gastric-cancer-patients
#6
Mayra-Cecilia Suárez-Arriaga, Javier Torres, Margarita Camorlinga-Ponce, Alejandro Gómez-Delgado, Patricia Piña-Sánchez, Hilda-Alicia Valdez-Salazar, Rosa-María Ribas-Aparicio, Ezequiel M Fuentes-Pananá, Martha-Eugenia Ruiz-Tachiquín
Gastric cancer (GC) is the fifth most common type of malignancy and the third leading cause of cancer-associated mortality worldwide. It is necessary to identify novel methods aimed at improving the early diagnosis and treatment of GC. MicroRNA expression profiles in the plasma of patients with GC have demonstrated a potential use in the opportune diagnosis of this neoplasm. However, there are currently no standardized targets for use in the normalization of microRNA Cq values for different neoplasms. The present study tested two normalization approaches while analyzing plasma derived from patients with GC and non-atrophic gastritis...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28520982/genome-wide-mrna-processing-in-methanogenic-archaea-reveals-post-transcriptional-regulation-of-ribosomal-protein-synthesis
#7
Lei Qi, Lei Yue, Deqin Feng, Fengxia Qi, Jie Li, Xiuzhu Dong
Unlike stable RNAs that require processing for maturation, prokaryotic cellular mRNAs generally follow an 'all-or-none' pattern. Herein, we used a 5΄ monophosphate transcript sequencing (5΄P-seq) that specifically captured the 5΄-end of processed transcripts and mapped the genome-wide RNA processing sites (PSSs) in a methanogenic archaeon. Following statistical analysis and stringent filtration, we identified 1429 PSSs, among which 23.5% and 5.4% were located in 5΄ untranslated region (uPSS) and intergenic region (iPSS), respectively...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520869/comparative-pathogenomic-characterization-of-a-non-invasive-serotype-m71-strain-streptococcus-pyogenes-ns53-reveals-incongruent-phenotypic-implications-from-distinct-genotypic-markers
#8
Yun-Juan Bao, Yang Li, Zhong Liang, Garima Agrahari, Shaun W Lee, Victoria A Ploplis, Francis J Castellino
The strains serotyped as M71 from group A Streptococcus are common causes of pharyngeal and skin diseases worldwide. Here we characterize the genome of a unique non-invasive M71 human isolate, NS53. The genome does not contain structural rearrangements or large-scale gene gains/losses, but encodes a full set of non-truncated known virulence factors, thus providing an ideal reference for comparative studies. However, the NS53 genome showed incongruent phenotypic implications from distinct genotypic markers. NS53 is characterized as an emm pattern D and FCT (fibronectin-collagen-T-antigen) type-3 strain, typical of skin tropic strains, but is phylogenetically close to emm pattern E strains with preference for both skin and pharyngeal infections...
May 17, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28516230/diverse-roles-of-dpb2-the-non-catalytic-subunit-of-dna-polymerase-%C3%AE%C2%B5
#9
REVIEW
Michał Dmowski, Iwona J Fijałkowska
Timely progression of living cells through the cell cycle is precisely regulated. This involves a series of phosphorylation events which are regulated by various cyclins, activated in coordination with the cell cycle progression. Phosphorylated proteins govern cell growth, division as well as duplication of the genetic material and transcriptional activation of genes involved in these processes. A subset of these tightly regulated genes, which depend on the MBF transcription factor and are mainly involved in DNA replication and cell division, is transiently activated at the transition from G1 to S phase...
May 17, 2017: Current Genetics
https://www.readbyqxmd.com/read/28515050/the-mapping-of-predicted-triplex-dna-rna-in-the-drosophila-genome-reveals-a-prominent-location-in-development-and-morphogenesis-related-genes
#10
Claude Pasquier, Sandra Agnel, Alain Robichon
Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand. A nucleic acid triplex occurs according to Hoogsteen rules that predict the stability and affinity of the third strand bound to the Watson-Crick duplex. The "triplex-forming oligonucleotide" (TFO) can be a short sequence of RNA that binds to the major groove of the targeted duplex only when this duplex presents a sequence of purine or pyrimidine bases in one of the DNA strands. Many nuclear proteins are known to bind triplex DNA or DNA:RNA, but their biological functions are unexplored...
May 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28514650/the-ino80-complex-removes-h2a-z-to-promote-presynaptic-filament-formation-during-homologous-recombination
#11
Claudio A Lademann, Jörg Renkawitz, Boris Pfander, Stefan Jentsch
The INO80 complex (INO80-C) is an evolutionarily conserved nucleosome remodeler that acts in transcription, replication, and genome stability. It is required for resistance against genotoxic agents and is involved in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). However, the causes of the HR defect in INO80-C mutant cells are controversial. Here, we unite previous findings using a system to study HR with high spatial resolution in budding yeast. We find that INO80-C has at least two distinct functions during HR-DNA end resection and presynaptic filament formation...
May 16, 2017: Cell Reports
https://www.readbyqxmd.com/read/28510637/telomeres-nutrition-and-longevity-can-we-really-navigate-our-aging
#12
Nikolina Škrobot Vidacek, Lucia Nanic, Sanda Ravlic, Mary Sopta, Marko Geric, Goran Gajski, Vera Garaj-Vrhovac, Ivica Rubelj
Telomeres are dynamic chromosome-end structures that serve as guardians of genome stability. They are known to be one of the major determinants of aging and longevity in higher mammals. Studies have demonstrated a direct correlation between telomere length and life expectancy, stress, DNA damage, and onset of aging-related diseases. This review discusses the most important factors that influence our telomeres. Various genetic and environmental factors such as diet, physical activity, obesity, and stress are known to influence health and longevity as well as telomere dynamics...
May 16, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28508487/accuracy-of-genomic-breeding-values-revisited-assessment-of-two-established-approaches-and-a-novel-one-to-determine-the-accuracy-in-two-step-genomic-prediction
#13
G Ni, S Kipp, H Simianer, M Erbe
Selection decisions in genomic selection schemes are made based on genomic breeding values (GBV) of candidates. Thus, the accuracy of GBV is a relevant parameter, as it reflects the stability of prediction and the possibility that the GBV might change when more information becomes available. Accuracy of genomic prediction defined as the correlation between GBV and true breeding values (TBV), however, is difficult to assess, considering TBV of the candidates are not available in reality. In previous studies, several methods were proposed to assess the accuracy of GBV including methods using population parameters or parameters inferred from mixed-model equations...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508482/solving-efficiently-large-single-step-genomic-best-linear-unbiased-prediction-models
#14
I Strandén, K Matilainen, G P Aamand, E A Mäntysaari
Single-step genomic BLUP (ssGBLUP) requires a dense matrix of the size equal to the number of genotyped animals in the coefficient matrix of mixed model equations (MME). When the number of genotyped animals is high, solving time of MME will be dominated by this matrix. The matrix is the difference of two inverse relationship matrices: genomic (G) and pedigree (A22 ). Different approaches were used to ease computations, reduce computing time and improve numerical stability. Inverse of A22 can be computed as A22-1=A22-A21A11-1A12 where A(ij) , i, j = 1,2, are sparse sub-matrices of A(-1) , and numbers 1 and 2 refer to non-genotyped and genotyped animals, respectively...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508214/efficient-reverse-genetic-systems-for-rapid-genetic-manipulation-of-emergent-and-preemergent-infectious-coronaviruses
#15
Adam S Cockrell, Anne Beall, Boyd Yount, Ralph Baric
Emergent and preemergent coronaviruses (CoVs) pose a global threat that requires immediate intervention. Rapid intervention necessitates the capacity to generate, grow, and genetically manipulate infectious CoVs in order to rapidly evaluate pathogenic mechanisms, host and tissue permissibility, and candidate antiviral therapeutic efficacy. CoVs encode the largest viral RNA genomes at about 28-32,000 nucleotides in length, and thereby complicate efficient engineering of the genome. Deconstructing the genome into manageable fragments affords the plasticity necessary to rapidly introduce targeted genetic changes in parallel and assort mutated fragments while maximizing genome stability over time...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28508213/reverse-genetics-of-zika-virus
#16
Chao Shan, Xuping Xie, Pei-Yong Shi
We have established a reverse genetic system for Zika virus (ZIKV). Five shuttle plasmids were constructed and assembled into the full-length cDNA clone of ZIKV genome. To ensure the stability of the cDNA clone, we used a low copy vector (pACYC177) and a set of unique restriction enzyme sites on the ZIKV genome to assemble the full-length cDNA clone. A T7 promoter was engineered in front of the viral 5' UTR for in vitro transcription. A hepatitis delta virus ribozyme (HDVr) sequence was engineered following the viral 3' UTR for generation of the authentic 3' end of the RNA transcript...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28507282/p53-suppresses-ribonucleotide-reductase-via-inhibiting-mtorc1
#17
Zhengfu He, Xing Hu, Weijin Liu, Adrienne Dorrance, Ramiro Garzon, Peter J Houghton, Changxian Shen
Balanced deoxyribonucleotides pools are essential for cell survival and genome stability. Ribonucleotide reductase is the rate-limiting enzyme for the production of deoxyribonucleotides. We report here that p53 suppresses ribonucleotide reductase subunit 1 (RRM1) and 2 (RRM2) via inhibiting mammalian target of rapamycin complex 1 (mTORC1). In vitro, cancer cell lines and mouse embryonic fibroblast cells were treated with different concentrations of pharmacological inhibitors for different times. In vivo, rhabdomyosarcoma Rh30 cell tumor-bearing mice were treated with rapamycin or AZD8055...
April 26, 2017: Oncotarget
https://www.readbyqxmd.com/read/28507061/rnf8-mediates-histone-h3-ubiquitylation-and-promotes-glycolysis-and-tumorigenesis
#18
Yan Xia, Weiwei Yang, Ming Fa, Xinjian Li, Yugang Wang, Yuhui Jiang, Yanhua Zheng, Jong-Ho Lee, Jing Li, Zhimin Lu
Disassembly of nucleosomes in which genomic DNA is packaged with histone regulates gene expression. However, the mechanisms underlying nucleosome disassembly for gene expression remain elusive. We show here that epidermal growth factor receptor activation results in the binding of the RNF8 forkhead-associated domain to pyruvate kinase M2-phosphorylated histone H3-T11, leading to K48-linked polyubiquitylation of histone H3 at K4 and subsequent proteasome-dependent protein degradation. In addition, H3 polyubiquitylation induces histone dissociation from chromatin, nucleosome disassembly, and binding of RNA polymerase II to MYC and CCND1 promoter regions for transcription...
May 15, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28506294/hssb1-associates-with-and-promotes-stability-of-the-blm-helicase
#19
Laura V Croft, Nicholas W Ashton, Nicolas Paquet, Emma Bolderson, Kenneth J O'Byrne, Derek J Richard
BACKGROUND: Maintenance of genome stability is critical in human cells. Mutations in or loss of genome stability pathways can lead to a number of pathologies including cancer. hSSB1 is a critical DNA repair protein functioning in the repair and signalling of stalled DNA replication forks, double strand DNA breaks and oxidised DNA lesions. The BLM helicase is central to the repair of both collapsed DNA replication forks and double strand DNA breaks by homologous recombination. RESULTS: In this study, we demonstrate that hSSB1 and BLM helicase form a complex in cells and the interaction is altered in response to ionising radiation (IR)...
May 15, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28505184/steadycom-predicting-microbial-abundances-while-ensuring-community-stability
#20
Siu Hung Joshua Chan, Margaret N Simons, Costas D Maranas
Genome-scale metabolic modeling has become widespread for analyzing microbial metabolism. Extending this established paradigm to more complex microbial communities is emerging as a promising way to unravel the interactions and biochemical repertoire of these omnipresent systems. While several modeling techniques have been developed for microbial communities, little emphasis has been placed on the need to impose a time-averaged constant growth rate across all members for a community to ensure co-existence and stability...
May 15, 2017: PLoS Computational Biology
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