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https://www.readbyqxmd.com/read/28550453/exchange-of-genetic-sequences-between-viruses-and-hosts
#1
Robin A Weiss
Although genetic transfer between viruses and vertebrate hosts occurs less frequently than gene flow between bacteriophages and prokaryotes, it is extensive and has affected the evolution of both parties. With retroviruses, the integration of proviral DNA into chromosomal DNA can result in the activation of adjacent host gene expression and in the transduction of host transcripts into retroviral genomes as oncogenes. Yet in contrast to lysogenic phage, there is little evidence that viral oncogenes persist in a chain of natural transmission or that retroviral transduction is a significant driver of the horizontal spread of host genes...
May 28, 2017: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/28550064/transient-silencing-of-dna-repair-genes-improves-targeted-gene-integration-in-the-filamentous-fungus-trichoderma-reesei
#2
Pak Yang Chum, Georg Schmidt, Markku Saloheimo, Christopher P Landowski
Trichoderma reesei is a filamentous fungus that is used world-wide to produce industrial enzymes. Industrial strains have traditionally been created though systematic strain improvement by mutagenesis and screening approaches. It is also desirable to specifically manipulate genes of the organism to further improve and modify the strain. Targeted integration in filamentous fungi is typically hampered by very low frequencies of homologous recombination. To address this limitation we have developed a simple transient method for silencing genes in T...
May 26, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28549825/metabolic-integration-of-bacterial-endosymbionts-through-antimicrobial-peptides
#3
REVIEW
Peter Mergaert, Yoshitomo Kikuchi, Shuji Shigenobu, Eva C M Nowack
Antimicrobial peptides (AMPs) are massively produced by eukaryotic hosts during symbiotic interactions with bacteria. Among other roles, these symbiotic AMPs have the capacity to permeabilize symbiont membranes and facilitate metabolite flow across the host-symbiont interface. We propose that an ancestral role of these peptides is to facilitate metabolic exchange between the symbiotic partners through membrane permeabilization. This function may be particularly critical for integration of endosymbiont and host metabolism in interactions involving bacteria with strongly reduced genomes lacking most small metabolite transporters...
May 23, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28549257/human-somatic-cells-deficient-for-rad52-are-impaired-for-viral-integration-and-compromised-for-most-aspects-of-homology-directed-repair
#4
Yinan Kan, Nizar N Batada, Eric A Hendrickson
Homology-directed repair (HDR) maintains genomic integrity by eliminating lesions such as DNA double-strand breaks (DSBs), interstrand crosslinks (ICLs) and stalled replication forks and thus a deficiency in HDR is associated with genomic instability and cancer predisposition. The mechanism of HDR is best understood and most rigorously characterized in yeast. The inactivation of the fungal radiation sensitive 52 (RAD52) gene, which has both recombination mediator and single-strand annealing (SSA) activities in vitro, leads to severe HDR defects in vivo...
May 10, 2017: DNA Repair
https://www.readbyqxmd.com/read/28549184/coiled-coil-interactions-mediate-serine-integrase-directionality
#5
Kushol Gupta, Robert Sharp, Jimmy B Yuan, Huiguang Li, Gregory D Van Duyne
Serine integrases are bacteriophage enzymes that carry out site-specific integration and excision of their viral genomes. The integration reaction is highly directional; recombination between the phage attachment site attP and the host attachment site attB to form the hybrid sites attL and attR is essentially irreversible. In a recent model, extended coiled-coil (CC) domains in the integrase subunits are proposed to interact in a way that favors the attPxattB reaction but inhibits the attLxattR reaction. Here, we show for the Listeria innocua integrase (LI Int) system that the CC domain promotes self-interaction in isolated Int and when Int is bound to attachment sites...
May 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28549128/atad3-gene-cluster-deletions-cause-cerebellar-dysfunction-associated-with-altered-mitochondrial-dna-and-cholesterol-metabolism
#6
Radha Desai, Ann E Frazier, Romina Durigon, Harshil Patel, Aleck W Jones, Ilaria Dalla Rosa, Nicole J Lake, Alison G Compton, Hayley S Mountford, Elena J Tucker, Alice L R Mitchell, Deborah Jackson, Abdul Sesay, Miriam Di Re, Lambert P van den Heuvel, Derek Burke, David Francis, Sebastian Lunke, George McGillivray, Simone Mandelstam, Fanny Mochel, Boris Keren, Claude Jardel, Anne M Turner, P Ian Andrews, Jan Smeitink, Johannes N Spelbrink, Simon J Heales, Masakazu Kohda, Akira Ohtake, Kei Murayama, Yasushi Okazaki, Anne Lombès, Ian J Holt, David R Thorburn, Antonella Spinazzola
Although mitochondrial disorders are clinically heterogeneous, they frequently involve the central nervous system and are among the most common neurogenetic disorders. Identifying the causal genes has benefited enormously from advances in high-throughput sequencing technologies; however, once the defect is known, researchers face the challenge of deciphering the underlying disease mechanism. Here we characterize large biallelic deletions in the region encoding the ATAD3C, ATAD3B and ATAD3A genes. Although high homology complicates genomic analysis of the ATAD3 defects, they can be identified by targeted analysis of standard single nucleotide polymorphism array and whole exome sequencing data...
June 1, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28548087/the-distinct-metabolic-phenotype-of-lung-squamous-cell-carcinoma-defines-selective-vulnerability-to-glycolytic-inhibition
#7
Justin Goodwin, Michael L Neugent, Shin Yup Lee, Joshua H Choe, Hyunsung Choi, Dana M R Jenkins, Robin J Ruthenborg, Maddox W Robinson, Ji Yun Jeong, Masaki Wake, Hajime Abe, Norihiko Takeda, Hiroko Endo, Masahiro Inoue, Zhenyu Xuan, Hyuntae Yoo, Min Chen, Jung-Mo Ahn, John D Minna, Kristi L Helke, Pankaj K Singh, David B Shackelford, Jung-Whan Kim
Adenocarcinoma (ADC) and squamous cell carcinoma (SqCC) are the two predominant subtypes of non-small cell lung cancer (NSCLC) and are distinct in their histological, molecular and clinical presentation. However, metabolic signatures specific to individual NSCLC subtypes remain unknown. Here, we perform an integrative analysis of human NSCLC tumour samples, patient-derived xenografts, murine model of NSCLC, NSCLC cell lines and The Cancer Genome Atlas (TCGA) and reveal a markedly elevated expression of the GLUT1 glucose transporter in lung SqCC, which augments glucose uptake and glycolytic flux...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28547323/a-shortened-two-enzyme-pathway-for-2-3-butanediol-production-in-escherichia-coli
#8
Shamlan M S Reshamwala, Shalini S Deb, Arvind M Lali
The platform chemical 2,3-butanediol (2,3-BDO) is produced by a number of microorganisms via a three-enzyme pathway starting from pyruvate. Here, we report production of 2,3-BDO via a shortened, two-enzyme pathway in Escherichia coli. A synthetic operon consisting of the acetolactate synthase (ALS) and acetoin reductase (AR) genes from Enterobacter under control of the T7 promoter was cloned in an episomal plasmid. E. coli transformed with this plasmid produced 2,3-BDO and the pathway intermediate acetoin, demonstrating that the shortened pathway was functional...
May 25, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28546923/homocysteine-mediates-transcriptional-changes-of-the-inflammatory-pathway-signature-genes-in-human-retinal-pigment-epithelial-cells
#9
Mahavir Singh, Suresh C Tyagi
AIM: To test whether homocysteine (Hcy) can influence the transcriptional profile, we hypothesized that Hcy can lead to the induction of proinflammatory molecules in the retinal cells of aging people. METHODS: An unbiased in vitro inflammatory pathway focused study was designed employing retinal pigment epithelial (RPE) cell line, ARPE-19. Cells were cultured in the presence or absence of Hcy to capture target genes' expression profile. Three different concentrations of Hcy were added in the culture medium of confluent monolayers...
2017: International Journal of Ophthalmology
https://www.readbyqxmd.com/read/28545995/systematic-studies-on-ciliates-alveolata-ciliophora-in-china-progress-and-achievements-based-on-molecular-information
#10
REVIEW
Feng Gao, Jie Huang, Yan Zhao, Lifang Li, Weiwei Liu, Miao Miao, Qianqian Zhang, Jiamei Li, Zhenzhen Yi, Hamed A El-Serehy, Alan Warren, Weibo Song
Due to complex morphological and convergent morphogenetic characters, the systematics of ciliates has long been ambiguous. Since 1990, the Laboratory of Protozoology, Ocean University of China, in collaboration with other research groups worldwide, has carried out a series of integrative investigations on ciliate systematics. To date, genomic DNA has been extracted from about 1700 ciliate strains, and phylogenetic analyses have been performed for two-thirds of orders. Main findings are: (1) Classifications of about 50 hypotrichous species have been resolved, although the monophylies of three hypotrichous orders remain unconfirmed; (2) Euplotia and two orders and all seven families within them are monophyletic assemblages; (3) Lynnella represents an order-level taxon, and is separated from two sister monophyletic subclasses Oligotrichia and Choreotrichia; (4) the peritrich families Zoothamniidae and Vorticellidae are separated from each other, and Zoothamnium exhibits a high genetic diversity; (5) the scuticociliate order Philasterida is monophyletic and separated from loxocephalids, and the thigmotrichids is a suborder within Pleuronematida; (6) 14 classes were recovered including one new class Protocruziea, and Mesodiniea is basal to subphyla Intramacronucleata and Postciliodesmatophora; (7) mitochondrial cytochrome c oxidase subunit I heteroplasmy was reported in ciliates for the first time, and candidate barcoding genes for Frontonia species identification were identified...
May 6, 2017: European Journal of Protistology
https://www.readbyqxmd.com/read/28545165/highly-recurrent-h3f3a-mutations-with-additional-epigenetic-regulator-alterations-in-giant-cell-tumor-of-bone
#11
Koichi Ogura, Fumie Hosoda, Hiromi Nakamura, Natsuko Hama, Yasushi Totoki, Akihiko Yoshida, Shoko Ohashi, Hirofumi Rokutan, Erina Takai, Shinichi Yachida, Akira Kawai, Sakae Tanaka, Tatsuhiro Shibata
Recurrent H3F3A and IDH2 mutations have been reported in giant cell tumor of bone (GCTB). However, the reported incidences have varied, and other molecular genetic alterations have not been identified due to the small number of cases analyzed with comprehensive methods. Moreover, the relative sensitivities of Sanger sequencing and next-generation sequencing (NGS) for the detection of H3F3A mutations in DNA extracted from archival formalin-fixed paraffin-embedded (FFPE) for clinical diagnosis have not been assessed...
May 25, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28545026/identification-of-novel-long-non-coding-rna-biomarkers-for-prognosis-prediction-of-papillary-thyroid-cancer
#12
Qiuying Li, Haihong Li, Lu Zhang, Chunming Zhang, Wentao Yan, Chao Wang
Papillary thyroid carcinoma (PTC) is the most frequent type of malignant thyroid tumor. Several lncRNA signatures have been established for prognosis prediction in some cancers. However, the prognostic value of lncRNAs has not been investigated in PTC yet. In this study, we performed genome-wide analysis of lncRNA expression profiles in a large cohort of PTC patients from The Cancer Genome Atlas and identified 111 differentially expressed lncRNAs between tumor and non-tumor samples and between recurrent and recurrence-free samples...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28544881/mammalian-systems-biotechnology-reveals-global-cellular-adaptations-in-a-recombinant-cho-cell-line
#13
Faraaz Noor Khan Yusufi, Meiyappan Lakshmanan, Ying Swan Ho, Bernard Liat Wen Loo, Pramila Ariyaratne, Yuansheng Yang, Say Kong Ng, Tessa Rui Min Tan, Hock Chuan Yeo, Hsueh Lee Lim, Sze Wai Ng, Ai Ping Hiu, Chung Ping Chow, Corrine Wan, Shuwen Chen, Gavin Teo, Gao Song, Ju Xin Chin, Xiaoan Ruan, Ken Wing Kin Sung, Wei-Shou Hu, Miranda Gek Sim Yap, Muriel Bardor, Niranjan Nagarajan, Dong-Yup Lee
Effective development of host cells for therapeutic protein production is hampered by the poor characterization of cellular transfection. Here, we employed a multi-omics-based systems biotechnology approach to elucidate the genotypic and phenotypic differences between a wild-type and recombinant antibody-producing Chinese hamster ovary (CHO) cell line. At the genomic level, we observed extensive rearrangements in specific targeted loci linked to transgene integration sites. Transcriptional re-wiring of DNA damage repair and cellular metabolism in the antibody producer, via changes in gene copy numbers, was also detected...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28544514/dynamic-enhancer-function-in-the-chromatin-context
#14
REVIEW
Ido Goldstein, Gordon L Hager
Enhancers serve as critical regulatory elements in higher eukaryotic cells. The characterization of enhancer function has evolved primarily from genome-wide methodologies, including chromatin immunoprecipitation (ChIP-seq), DNase-I hypersensitivity (DNase-seq), digital genomic footprinting (DGF), and the chromosome conformation capture techniques (3C, 4C, and Hi-C). These population-based assays average signals across millions of cells and lead to enhancer models characterized by static and sequential binding...
May 22, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28542811/integrative-analyses-reveal-biological-pathways-and-key-genes-in-psoriasis
#15
J Dou, L Zhang, X Xie, L Ye, C Yang, L Wen, C Shen, C Zhu, S Zhao, Z Zhu, B Liang, Z Wang, H Li, X Fan, S Liu, X Yin, X Zheng, L Sun, S Yang, Y Cui, F Zhou, X Zhang
BACKGROUND: Psoriasis is a complex disease that is influenced by both genetic and environmental factors with abnormal gene expression in lesional skin. However, no studies are available on genome-scale gene expression of psoriatic lesions in the Chinese population. In addition, systematic studies on the biological pathways, pathogenicity and interaction networks of psoriasis-related genes with abnormal expression profiles require further investigation. OBJECTIVES: To further explore the associated pathways in psoriasis by functional analysis and to identify the key genes by gene pathogenicity analysis...
May 25, 2017: British Journal of Dermatology
https://www.readbyqxmd.com/read/28542565/promiscuous-signaling-by-a-regulatory-system-unique-to-the-pandemic-pmen1-pneumococcal-lineage
#16
Anagha Kadam, Rory A Eutsey, Jason Rosch, Xinyu Miao, Mark Longwell, Wenjie Xu, Carol A Woolford, Todd Hillman, Anfal Shakir Motib, Hasan Yesilkaya, Aaron P Mitchell, N Luisa Hiller
Streptococcus pneumoniae (pneumococcus) is a leading cause of death and disease in children and elderly. Genetic variability among isolates from this species is high. These differences, often the product of gene loss or gene acquisition via horizontal gene transfer, can endow strains with new molecular pathways, diverse phenotypes, and ecological advantages. PMEN1 is a widespread and multidrug-resistant pneumococcal lineage. Using comparative genomics we have determined that a regulator-peptide signal transduction system, TprA2/PhrA2, was acquired by a PMEN1 ancestor and is encoded by the vast majority of strains in this lineage...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28542390/analysis-of-early-mesothelial-cell-responses-to-staphylococcus-epidermidis-isolated-from-patients-with-peritoneal-dialysis-associated-peritonitis
#17
Amanda L McGuire, Kieran T Mulroney, Christine F Carson, Ramesh Ram, Grant Morahan, Aron Chakera
The major complication of peritoneal dialysis (PD) is the development of peritonitis, an infection within the abdominal cavity, primarily caused by bacteria. PD peritonitis is associated with significant morbidity, mortality and health care costs. Staphylococcus epidermidis is the most frequently isolated cause of PD-associated peritonitis. Mesothelial cells are integral to the host response to peritonitis, and subsequent clinical outcomes, yet the effects of infection on mesothelial cells are not well characterised...
2017: PloS One
https://www.readbyqxmd.com/read/28542371/whole-genome-sequencing-of-spermatocytic-tumors-provides-insights-into-the-mutational-processes-operating-in-the-male-germline
#18
Eleni Giannoulatou, Geoffrey J Maher, Zhihao Ding, Ad J M Gillis, Lambert C J Dorssers, Alexander Hoischen, Ewa Rajpert-De Meyts, Gilean McVean, Andrew O M Wilkie, Leendert H J Looijenga, Anne Goriely
Adult male germline stem cells (spermatogonia) proliferate by mitosis and, after puberty, generate spermatocytes that undertake meiosis to produce haploid spermatozoa. Germ cells are under evolutionary constraint to curtail mutations and maintain genome integrity. Despite constant turnover, spermatogonia very rarely form tumors, so-called spermatocytic tumors (SpT). In line with the previous identification of FGFR3 and HRAS selfish mutations in a subset of cases, candidate gene screening of 29 SpTs identified an oncogenic NRAS mutation in two cases...
2017: PloS One
https://www.readbyqxmd.com/read/28542306/gene-signature-associated-with-benign-neurofibroma-transformation-to-malignant-peripheral-nerve-sheath-tumors
#19
Marta Martínez, Carlos O S Sorzano, Alberto Pascual-Montano, Jose M Carazo
Benign neurofibromas, the main phenotypic manifestations of the rare neurological disorder neurofibromatosis type 1, degenerate to malignant tumors associated to poor prognosis in about 10% of patients. Despite efforts in the field of (epi)genomics, the lack of prognostic biomarkers with which to predict disease evolution frustrates the adoption of appropriate early therapeutic measures. To identify potential biomarkers of malignant neurofibroma transformation, we integrated four human experimental studies and one for mouse, using a gene score-based meta-analysis method, from which we obtained a score-ranked signature of 579 genes...
2017: PloS One
https://www.readbyqxmd.com/read/28542178/uncovering-direct-and-indirect-molecular-determinants-of-chromatin-loops-using-a-computational-integrative-approach
#20
Raphaël Mourad, Lang Li, Olivier Cuvier
Chromosomal organization in 3D plays a central role in regulating cell-type specific transcriptional and DNA replication timing programs. Yet it remains unclear to what extent the resulting long-range contacts depend on specific molecular drivers. Here we propose a model that comprehensively assesses the influence on contacts of DNA-binding proteins, cis-regulatory elements and DNA consensus motifs. Using real data, we validate a large number of predictions for long-range contacts involving known architectural proteins and DNA motifs...
May 23, 2017: PLoS Computational Biology
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