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https://www.readbyqxmd.com/read/29165230/para-like-protein-influences-the-distribution-of-multi-copy-chromosomes-in-cyanobacterium-synechococcus-elongatus-pcc-7942
#1
Satoru Watanabe, Aska Noda, Ryudo Ohbayashi, Kana Uchioke, Ami Kurihara, Shizuka Nakatake, Sayumi Morioka, Yu Kanesaki, Taku Chibazakura, Hirofumi Yoshikawa
While many bacteria, such as Escherichia coli and Bacillus subtilis, harbour a single-copy chromosome, freshwater cyanobacteria have multiple copies of each chromosome per cell. Although it has been reported that multi-copy chromosomes are evenly distributed along the major axis of the cell in cyanobacterium Synechococcus elongatus PCC 7942, the distribution mechanism of these chromosomes remains unclear. In S. elongatus, the carboxysome, a metabolic microcompartment for carbon fixation that is distributed in a similar manner to the multi-copy chromosomes, is regulated by ParA-like protein (hereafter ParA)...
November 21, 2017: Microbiology
https://www.readbyqxmd.com/read/29163436/promoting-simultaneous-onset-of-viral-gene-expression-among-cells-infected-with-herpes-simplex-virus-1
#2
Maya Ralph, Marina Bednarchik, Enosh Tomer, Dor Rafael, Sefi Zargarian, Motti Gerlic, Oren Kobiler
Synchronous viral infection facilitates the study of viral gene expression, viral host interactions, and viral replication processes. However, the protocols for achieving synchronous infections were hardly ever tested in proper temporal resolution at the single-cell level. We set up a fluorescence-based, time lapse microscopy assay to study sources of variability in the timing of gene expression during herpes simplex virus-1 (HSV-1) infection. We found that with the common protocol, the onset of gene expression within different cells can vary by more than 3 h...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163388/genomic-comparison-of-two-family-level-groups-of-the-uncultivated-nag1-archaeal-lineage-from-chemically-and-geographically-disparate-hot-springs
#3
Eric D Becraft, Jeremy A Dodsworth, Senthil K Murugapiran, Scott C Thomas, J Ingemar Ohlsson, Ramunas Stepanauskas, Brian P Hedlund, Wesley D Swingley
Recent progress based on single-cell genomics and metagenomic investigations of archaea in a variety of extreme environments has led to significant advances in our understanding of the diversity, evolution, and metabolic potential of archaea, yet the vast majority of archaeal diversity remains undersampled. In this work, we coordinated single-cell genomics with metagenomics in order to construct a near-complete genome from a deeply branching uncultivated archaeal lineage sampled from Great Boiling Spring (GBS) in the U...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163026/generation-of-urine-cell-derived-non-integrative-human-ipscs-and-inscs-a-step-by-step-optimized-protocol
#4
Lin Cheng, Qiannan Lei, Chen Yin, Hui-Yun Wang, Kangxin Jin, Mengqing Xiang
Objective: Establishing a practical procedure to generate induced pluripotent stem cells (iPSCs) and induced neural stem cells (iNSCs) from human urine cells (UCs). In this report, we optimized a non-integrative protocol to generate patient-specific iPSC and iNSC lines with high reprogramming efficiency. Methods: UCs were electroporated with the pEP4-EO2S-ET2K and pEP4-M2L plasmids containing the OCT4, SOX2, KLF4, SV40LT, c-MYC, and LIN28 genes, and then cultured with N2B27 medium plus four small molecule compounds (A83-01, PD0325901, Thiazovivin, and CHIR99021)...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29162929/genomic-assessment-in-lactobacillus-plantarum-links-the-butyrogenic-pathway-with-glutamine-metabolism
#5
Cristian Botta, Alberto Acquadro, Anna Greppi, Lorenzo Barchi, Marta Bertolino, Luca Cocolin, Kalliopi Rantsiou
The butyrogenic capability of Lactobacillus (L.) plantarum is highly dependent on the substrate type and so far not assigned to any specific metabolic pathway. Accordingly, we compared three genomes of L. plantarum that showed a strain-specific capability to produce butyric acid in human cells growth media. Based on the genomic analysis, butyric acid production was attributed to the complementary activities of a medium-chain thioesterase and the fatty acid synthase of type two (FASII). However, the genomic islands of discrepancy observed between butyrogenic L...
November 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29162700/double-strand-dna-breaks-are-mainly-repaired-by-the-homologous-recombination-pathway-in-early-developing-swine-embryos
#6
Rodrigo C Bohrer, Naomi Dicks, Karina Gutierrez, Raj Duggavathi, Vilceu Bordignon
DNA double-strand breaks (DSBs) are less frequent than single-strand breaks but have more harmful consequences on cell survival and physiology. Homologous recombination (HR) and nonhomologous end-joining (NHEJ) are the two main pathways that are responsible for DSB repair in eukaryotic cells, but their importance for the preservation of genome stability in totipotent blastomeres of early developing embryos has not been determined. In this study, we observed that the chemical inhibition of HR or both pathways, but not NHEJ alone, increased the number of DSBs, reduced embryo development to the blastocyst stage, and resulted in embryos with higher proportions of apoptotic cells...
November 21, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29162636/quantitative-proteomic-profiling-reveals-novel-plasmodium-falciparum-surface-antigens-and-possible-vaccine-candidates
#7
Sandra K Nilsson Bark, Rushdy Ahmad, Kathleen Dantzler, Amanda K Lukens, Mariana De Niz, Matthew J Szucs, Xiaojing Jin, Joanne Cotton, Dietmar Hoffmann, Eva Bric-Furlong, Ray Oomen, Mark Parrington, Dan Milner, Daniel E Neafsey, Steven A Carr, Dyann F Wirth, Matthias Marti
Despite recent efforts towards control and elimination, malaria remains a major public health problem worldwide. Plasmodium falciparum resistance against artemisinin, used in front line combination drugs, is on the rise, and the only approved vaccine shows limited efficacy. Combinations of novel and tailored drug and vaccine interventions are required to maintain the momentum of the current malaria elimination program. Current evidence suggests that strain-transcendent protection against malaria infection can be achieved using whole organism vaccination or with a polyvalent vaccine covering multiple antigens or epitopes...
November 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29162237/inter-individual-gene-variants-associated-with-trabecular-bone-plasticity-a-step-forward-in-the-personal-genomics-of-degenerative-bone-disease
#8
Enrique Caso, Cristina C Sabiers, Daniel López-Guillén, Jaime Caso, Manuel Toledano, Raquel Osorio, Estrella Osorio, Carmen Lozano, Enrique Guerado
Continuing tissue destruction in osteoarthrosis is maintained by molecular pathways related to an unbalanced chondrocyte metabolism, the loss of reactive oxygen species (ROS) homeostasis, increase catabolism in a degraded matrix and the limited response to growth factors due to cell aging. Rare deleterious gene variants driving relevant molecular pathways may play a key role in the pathogenesis and genetic control of common diseases and may also influence the common gene variants observed in GWAS. We use molecular profiling technologies based on massive sequencing of genes to interrogate clinical samples for a variety of molecules involved in the pathogenesis pathways of OA and also to derive new insights for drug targeting discovery at an early stage of the disease...
November 2017: Injury
https://www.readbyqxmd.com/read/29161623/functions-of-myosin-motors-tailored-for-parasitism
#9
REVIEW
Christina Mueller, Arnault Graindorge, Dominique Soldati-Favre
Myosin motors are one of the largest protein families in eukaryotes that exhibit divergent cellular functions. Their roles in protozoans, a diverse group of anciently diverged, single celled organisms with many prominent members known to be parasitic and to cause diseases in human and livestock, are largely unknown. In the recent years many different approaches, among them whole genome sequencing, phylogenetic analyses and functional studies have increased our understanding on the distribution, protein architecture and function of unconventional myosin motors in protozoan parasites...
November 18, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29158893/evaluation-of-a-stenotrophomonas-maltophilia-bacteremia-cluster-in-hematopoietic-stem-cell-transplantation-recipients-using-whole-genome-sequencing
#10
Stefanie Kampmeier, Mike H Pillukat, Aleksandra Pettke, Annelene Kossow, Evgeny A Idelevich, Alexander Mellmann
Background: Stenotrophomonas maltophilia ubiquitously occurs in the hospital environment. This opportunistic pathogen can cause severe infections in immunocompromised hosts such as hematopoietic stem cell transplantation (HSCT) recipients. Between February and July 2016, a cluster of four patients on the HSCT unit suffered from S. maltophilia bloodstream infections (BSI). Methods: For epidemiological investigation we retrospectively identified the colonization status of patients admitted to the ward during this time period and performed environmental monitoring of shower heads, shower outlets, washbasins and toilets in patient rooms...
2017: Antimicrobial Resistance and Infection Control
https://www.readbyqxmd.com/read/29158564/long-read-genome-sequence-assembly-provides-insight-into-ongoing-retroviral-invasion-of-the-koala-germline
#11
Matthew Hobbs, Andrew King, Ryan Salinas, Zhiliang Chen, Kyriakos Tsangaras, Alex D Greenwood, Rebecca N Johnson, Katherine Belov, Marc R Wilkins, Peter Timms
The koala retrovirus (KoRV) is implicated in several diseases affecting the koala (Phascolarctos cinereus). KoRV provirus can be present in the genome of koalas as an endogenous retrovirus (present in all cells via germline integration) or as exogenous retrovirus responsible for somatic integrations of proviral KoRV (present in a limited number of cells). This ongoing invasion of the koala germline by KoRV provides a powerful opportunity to assess the viral strategies used by KoRV in an individual. Analysis of a high-quality genome sequence of a single koala revealed 133 KoRV integration sites...
November 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29158545/a-potent-cas9-derived-gene-activator-for-plant-and-mammalian-cells
#12
Zhenxiang Li, Dandan Zhang, Xiangyu Xiong, Bingyu Yan, Wei Xie, Jen Sheen, Jian-Feng Li
Overexpression of complementary DNA represents the most commonly used gain-of-function approach for interrogating gene functions and for manipulating biological traits. However, this approach is challenging and inefficient for multigene expression due to increased labour for cloning, limited vector capacity, requirement of multiple promoters and terminators, and variable transgene expression levels. Synthetic transcriptional activators provide a promising alternative strategy for gene activation by tethering an autonomous transcription activation domain (TAD) to an intended gene promoter at the endogenous genomic locus through a programmable DNA-binding module...
November 20, 2017: Nature Plants
https://www.readbyqxmd.com/read/29158515/a-programmed-cell-division-delay-preserves-genome-integrity-during-natural-genetic-transformation-in-streptococcus-pneumoniae
#13
Matthieu J Bergé, Chryslène Mercy, Isabelle Mortier-Barrière, Michael S VanNieuwenhze, Yves V Brun, Christophe Grangeasse, Patrice Polard, Nathalie Campo
Competence for genetic transformation is a differentiation program during which exogenous DNA is imported into the cell and integrated into the chromosome. In Streptococcus pneumoniae, competence develops transiently and synchronously in all cells during exponential phase, and is accompanied by a pause in growth. Here, we reveal that this pause is linked to the cell cycle. At least two parallel pathways impair peptidoglycan synthesis in competent cells. Single-cell analyses demonstrate that ComM, a membrane protein induced during competence, inhibits both initiation of cell division and final constriction of the cytokinetic ring...
November 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/29157061/the-dna-pol-%C3%AF%C2%B5-stimulatory-activity-of-mrc1-is-modulated-by-phosphorylation
#14
Zhong-Xin Zhang, Jingjing Zhang, Qinhong Cao, Judith L Campbell, Huiqiang Lou
DNA replication checkpoint (Mec1-Mrc1-Rad53 in budding yeast) is an evolutionarily conserved surveillance system to ensure proper DNA replication and genome stability in all eukaryotes. Compared to its well-known function as a mediator of replication checkpoint, the exact role of Mrc1 as a component of normal replication forks remains relatively unclear. In this study, we provide in vitro biochemical evidence to support that yeast Mrc1 is able to enhance the activity of DNA polymerase ϵ (Pol ϵ), the major leading strand replicase...
November 20, 2017: Cell Cycle
https://www.readbyqxmd.com/read/29156626/surface-plasmon-resonance-sensing-of-biorecognition-interactions-within-the-tumor-suppressor-p53-network
#15
REVIEW
Ilaria Moscetti, Salvatore Cannistraro, Anna Rita Bizzarri
Surface Plasmon Resonance (SPR) is a powerful technique to study the kinetics of biomolecules undergoing biorecognition processes, particularly suited for protein-protein interactions of biomedical interest. The potentiality of SPR was exploited to sense the interactions occurring within the network of the tumor suppressor p53, which is crucial for maintaining genome integrity and whose function is inactivated, mainly by down regulation or by mutation, in the majority of human tumors. This study includes p53 down-regulators, p53 mutants and also the p53 family members, p63 and p73, which could vicariate p53 protective function...
November 20, 2017: Sensors
https://www.readbyqxmd.com/read/29155789/efficient-generation-and-editing-of-feeder-free-ipscs-from-human-pancreatic-cells-using-the-crispr-cas9-system
#16
Anjali Nandal, Barbara Mallon, Bhanu P Telugu
Embryonic and induced pluripotent stem cells can self-renew and differentiate into multiple cell types of the body. The pluripotent cells are thus coveted for research in regenerative medicine and are currently in clinical trials for eye diseases, diabetes, heart diseases, and other disorders. The potential to differentiate into specialized cell types coupled with the recent advances in genome editing technologies including the CRISPR/Cas system have provided additional opportunities for tailoring the genome of iPSC for varied applications including disease modeling, gene therapy, and biasing pathways of differentiation, to name a few...
November 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155127/mdr1-gene-c3435t-polymorphism-in-chronic-hepatitis-c-patients
#17
Mehdi Parsanahad, Manoochehr Makvandi, Ali Teimoori, Shahram Jalilian, Gholamabas Kayedani, Sara Mahmoodi
BACKGROUND: MDR1 is a highly polymorphic gene that encodes P-glycoprotein (P-gp). This protein anchor to the cell membrane and transports toxins, xenobiotic, chemicals, and drugs from the intracellular to extracellular and thus protect cells. Polymorphism of the MDR1 gene seems to be effective in gene expression and response to treatment. Since one of the main mechanisms of drug resistance is the removal of the drug from the cell by ATP-dependent efflux proteins, thus MDR1, single nucleotide polymorphism (SNP) C3435T can be used as a predictor for treatment outcomes...
November 15, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29153976/image-based-ex-vivo-drug-screening-for-patients-with-aggressive-haematological-malignancies-interim-results-from-a-single-arm-open-label-pilot-study
#18
Berend Snijder, Gregory I Vladimer, Nikolaus Krall, Katsuhiro Miura, Ann-Sofie Schmolke, Christoph Kornauth, Oscar Lopez de la Fuente, Hye-Soo Choi, Emiel van der Kouwe, Sinan Gültekin, Lukas Kazianka, Johannes W Bigenzahn, Gregor Hoermann, Nicole Prutsch, Olaf Merkel, Anna Ringler, Monika Sabler, Georg Jeryczynski, Marius E Mayerhoefer, Ingrid Simonitsch-Klupp, Katharina Ocko, Franz Felberbauer, Leonhard Müllauer, Gerald W Prager, Belgin Korkmaz, Lukas Kenner, Wolfgang R Sperr, Robert Kralovics, Heinz Gisslinger, Peter Valent, Stefan Kubicek, Ulrich Jäger, Philipp B Staber, Giulio Superti-Furga
BACKGROUND: Patients with refractory or relapsed haematological malignancies have few treatment options and short survival times. Identification of effective therapies with genomic-based precision medicine is hampered by intratumour heterogeneity and incomplete understanding of the contribution of various mutations within specific cancer phenotypes. Ex-vivo drug-response profiling in patient biopsies might aid effective treatment identification; however, proof of its clinical utility is limited...
November 15, 2017: Lancet Haematology
https://www.readbyqxmd.com/read/29153527/short-communication-genomic-prediction-using-imputed-whole-genome-sequence-variants-in-brown-swiss-cattle
#19
Mirjam Frischknecht, Theodorus H E Meuwissen, Beat Bapst, Franz R Seefried, Christine Flury, Dorian Garrick, Heidi Signer-Hasler, Christian Stricker, Anna Bieber, Ruedi Fries, Ingolf Russ, Johann Sölkner, Alessandro Bagnato, Birgit Gredler-Grandl
The accuracy of genomic prediction determines response to selection. It has been hypothesized that accuracy of genomic breeding values can be increased by a higher density of variants. We used imputed whole-genome sequence data and various single nucleotide polymorphism (SNP) selection criteria to estimate genomic breeding values in Brown Swiss cattle. The extreme scenarios were 50K SNP chip data and whole-genome sequence data with intermediate scenarios using linkage disequilibrium-pruned whole-genome sequence variants, only variants predicted to be missense, or the top 50K variants from genome-wide association studies...
November 15, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29153167/a-100-year-review-reproductive-technologies-in-dairy-science
#20
S G Moore, J F Hasler
Reproductive technology revolutionized dairy production during the past century. Artificial insemination was first successfully applied to cattle in the early 1900s. The next major developments involved semen extenders, invention of the electroejaculator, progeny testing, addition of antibiotics to semen during the 1930s and 1940s, and the major discovery of sperm cryopreservation with glycerol in 1949. The 1950s and 1960s were particularly productive with the development of protocols for the superovulation of cattle with both pregnant mare serum gonadotrophin/equine chorionic gonadotrophin and FSH, the first successful bovine embryo transfer, the discovery of sperm capacitation, the birth of rabbits after in vitro fertilization, and the development of insulated liquid nitrogen tanks...
December 2017: Journal of Dairy Science
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