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https://www.readbyqxmd.com/read/29350065/molecular-typing-of-lactobacillus-brevis-isolates-from-korean-food-using-repetitive-element-polymerase-chain-reaction
#1
Jasmine Kaur, Anshul Sharma, Sulhee Lee, Young-Seo Park
Lactobacillus brevis is a part of a large family of lactic acid bacteria that are present in cheese, sauerkraut, sourdough, silage, cow manure, feces, and the intestinal tract of humans and rats. It finds its use in food fermentation, and so is considered a "generally regarded as safe" organism. L. brevis strains are extensively used as probiotics and hence, there is a need for identifying and characterizing these strains. For identification and discrimination of the bacterial species at the subspecific level, repetitive element-polymerase chain reaction method is a reliable genomic fingerprinting tool...
January 1, 2018: Food Science and Technology International, Ciencia y Tecnología de Los Alimentos Internacional
https://www.readbyqxmd.com/read/29346625/complete-genomic-and-transcriptional-landscape-analysis-using-third-generation-sequencing-a-case-study-of-saccharomyces-cerevisiae-cen-pk113-7d
#2
Piroon Jenjaroenpun, Thidathip Wongsurawat, Rui Pereira, Preecha Patumcharoenpol, David W Ussery, Jens Nielsen, Intawat Nookaew
Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism and a cell factory, was selected for this study to demonstrate the superior capability of very long sequence reads for de novo genome assembly. We generated long reads using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)) and used short reads obtained using Illumina sequencing for error correction...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29344755/mathematical-modelling-of-bone-adaptation-of-the-metacarpal-subchondral-bone-in-racehorses
#3
Peta L Hitchens, Peter Pivonka, Fatemeh Malekipour, R Chris Whitton
In Thoroughbred racehorses, fractures of the distal limb are commonly catastrophic. Most of these fractures occur due to the accumulation of fatigue damage from repetitive loading, as evidenced by microdamage at the predilection sites for fracture. Adaptation of the bone in response to training loads is important for fatigue resistance. In order to better understand the mechanism of subchondral bone adaptation to its loading environment, we utilised a square root function defining the relationship between bone volume fraction [Formula: see text] and specific surface [Formula: see text] of the subchondral bone of the lateral condyles of the third metacarpal bone (MCIII) of the racehorse, and using this equation, developed a mathematical model of subchondral bone that adapts to loading conditions observed in vivo...
January 17, 2018: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/29343575/high-resolution-sequencing-of-viral-populations-during-early-siv-infection-reveals-evolutionary-strategies-for-rapid-escape-from-emerging-env-specific-antibody-responses
#4
Sergio Ita, Alison K Hill, Evan C Lam, Fay J Dufort, Xiao Yang, Ruchi Newman, Sivan Leviyang, Ismael B Fofana, Welkin E Johnson
Primate lentiviruses, including the human and simian immunodeficiency viruses (HIV and SIV), produce infections marked by persistent, ongoing viral replication. This occurs despite the presence of virus-specific adaptive immune responses, including antibodies targeting the viral envelope glycoprotein (Env), and evolution of antibody-escape variants is a well-documented feature of lentiviral infection. Here, we examined the evolutionary dynamics of the SIV env gene during early infection (≤ 29 weeks post-infection) in a cohort of four SIVmac251-infected rhesus macaques...
January 17, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29331298/spatiotemporal-characterization-of-microdamage-accumulation-in-rat-ulnae-in-response-to-uniaxial-compressive-fatigue-loading
#5
Xuhui Zhang, Xiyu Liu, Zedong Yan, Jing Cai, Fei Kang, Shuai Shan, Pan Wang, Mingming Zhai, X Edward Guo, Erping Luo, Da Jing
Repetitive fatigue loading can induce microdamage accumulation in bone matrix, which results in impaired mechanical properties and increased fracture susceptibility. However, the spatial distribution and time-variant process of microdamage accumulation in fatigue-loaded skeleton, especially for linear microcracks which are known to initiate bone remodeling, remain not fully understood. In this study, the time-varying process of the morphology and distribution of microcracks in rat ulnae subjected to uniaxial compressive fatigue loading was investigated...
January 10, 2018: Bone
https://www.readbyqxmd.com/read/29317055/scapholunate-interosseous-ligament-dysfunction-as-a-source-of-elbow-pain-syndromes-possible-mechanisms-and-implications-for-hand-surgeons-and-therapists
#6
Cigdem Ayhan, Seval Tanrıkulu, Gursel Leblebicioglu
Elbow pain syndromes are common upper extremity musculoskeletal disorders, and they are usually associated with repetitive occupational exposure. Ligaments are often one of the sources of musculoskeletal disorders because of their mechanical and neurological properties. The wrist ligaments are some of the ligaments most vulnerable to occupational exposure. Since most occupational tasks require wrist extension for handling tools and loading, the scapholunate interosseous ligament (SLIL) bears greater strain during loading, which results in creep deformation and hysteresis...
January 2018: Medical Hypotheses
https://www.readbyqxmd.com/read/29309948/molecular-characterization-and-epidemiology-of-extended-spectrum-beta-lactamase-producing-klebsiella-pneumoniae-isolates-from-immunocompromised-patients-in-tunisia
#7
Farah Ben Tanfous, Wafa Achour, Anis Raddaoui, Assia Ben Hassen
OBJECTIVES: This study investigated the prevalence of extended-spectrum β-lactamase producing K. pneumoniae (ESBL-KP) strains in the National Bone Marrow Transplant Center of Tunis between 2002 and 2011, their associated antibiotics resistance patterns and their molecular features. METHODS: Antimicrobial susceptibility was determined by the disk diffusion method according to CA-SFM guidelines. All the strains were screened for beta-lactamase genes, plasmidic AmpC genes and integrons...
January 5, 2018: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29307335/miru-vntr-analysis-of-mycobacterium-tuberculosis-from-tehran-sistan-baluchestan-kermanshah-and-hormozgan-during-2014-and-2015
#8
Mahroo Baghbanian, Hengameh Zandi, Samin Zamani, Sedigheh Javadpour, Gholam Reza Hamzehloo, Mohammad Mahdi Feizabadi
Standard 15-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing of Mycobacterium tuberculosis (MTB) is a valuable instrumentation for TB control. Our knowledge about the genetic diversity of MTB and population structure of MTB circulating in Iran is limited. During 2014-2015, 98 MTB isolates were collected from the TB centers of four provinces of Iran. Isolates were genetically characterized using 15-locus based MIRU-VNTR typing. Ninety-five distinct mycobacterial interspersed repetitive unit MIRU-VNTR patterns were found among 98 isolates...
December 30, 2017: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/29301493/pacbio-sequencing-of-copper-tolerant-xanthomonas-citri-reveals-presence-of-a-chimeric-plasmid-structure-and-provides-insights-into-reassortment-and-shuffling-of-transcription-activator-like-effectors-among-x-citri-strains
#9
Alberto M Gochez, Jose C Huguet-Tapia, Gerald V Minsavage, Deepak Shantaraj, Neha Jalan, Annett Strauß, Thomas Lahaye, Nian Wang, Blanca I Canteros, Jeffrey B Jones, Neha Potnis
BACKGROUND: Xanthomonas citri, a causal agent of citrus canker, has been a well-studied model system due to recent availability of whole genome sequences of multiple strains from different geographical regions. Major limitations in our understanding of the evolution of pathogenicity factors in X. citri strains sequenced by short-read sequencing methods have been tracking plasmid reshuffling among strains due to inability to accurately assign reads to plasmids, and analyzing repeat regions among strains...
January 4, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29276725/markerless-gene-editing-in-the-hyperthermophilic-archaeon-thermococcus-kodakarensis
#10
Alexandra M Gehring, Travis J Sanders, Thomas J Santangelo
The advent of single cell genomics and the continued use of metagenomic profiling in diverse environments has exponentially increased the known diversity of life. The recovered and assembled genomes predict physiology, consortium interactions and gene function, but experimental validation of metabolisms and molecular pathways requires more directed approaches. Gene function-and the correlation between phenotype and genotype is most obviously studied with genetics, and it is therefore critical to develop techniques permitting rapid and facile strain construction...
November 20, 2017: Bio-protocol
https://www.readbyqxmd.com/read/29274468/molecular-characterization-of-carbapenem-resistant-enterobacter-cloacae-complex-in-colombia-blakpc-and-the-changing-landscape
#11
Elsa De La Cadena, Adriana Correa, Juan Sebastián Muñoz, Laura J Rojas, Cristhian Hernández-Gómez, Christian Pallares, Federico Perez, Robert A Bonomo, Maria V Villegas
OBJECTIVES: To examine the population structure of representative carbapenem resistant Enterobacter cloacae complex (CR-Ecl) isolates from 8 different Colombian regions and to characterize their asociated β-lactamases. METHODS: Twenty-eight CR-Ecl isolates collected in Colombia between 2009 and 2013 through the Colombian Nosocomial Network were included. Antimicrobial susceptibility testing was performed by broth microdilution. Molecular detection of carbapenemases and extended-spectrum β-lactamases (ESBL), and the presence of Tn4401 was evaluated by PCR and sequencing...
December 20, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29273626/minion-based-long-read-sequencing-and-assembly-extends-the-caenorhabditis-elegans-reference-genome
#12
John R Tyson, Nigel J O'Neil, Miten Jain, Hugh E Olsen, Philip Hieter, Terrance P Snutch
Advances in long read single molecule sequencing have opened new possibilities for 'benchtop' whole genome sequencing. The Oxford Nanopore Technologies MinION is a portable device that uses nanopore technology that can directly sequence DNA molecules. MinION single molecule long sequence reads are well suited for de novo assembly of complex genomes as they facilitate the construction of highly contiguous physical genome maps obviating the need for labor-intensive physical genome mapping. Long sequence reads can also be used to delineate complex chromosomal rearrangements, such as those that occur in tumour cells, that can confound analysis using short reads...
December 22, 2017: Genome Research
https://www.readbyqxmd.com/read/29250959/formation-of-ruddlesden-popper-faults-and-their-effect-on-magnetic-properties-in-pr0-5sr0-5coo3-thin-films
#13
Hongmei Jing, Sheng Cheng, Shao-Bo Mi, Lu Lu, Ming Liu, Shao-Dong Cheng, Chunlin Jia
The Pr0.5Sr0.5CoO3 thin films have been epitaxially grown on single-crystalline (La0.289 Sr0.712)(Al0.633Ta 0.356)O3 (001) substrates by a pulsed laser deposition technique. By changing the laser repetition rate Ruddleson-Popper faults are induced in the films. The segregation of Pr at the Ruddleson-Popper faults is characterized by atomic-resolution chemical mapping. It is found that the formation of the Ruddleson-Popper faults not only contributes to epitaxial strain relaxation, but also significantly decreases the ferromagnetic long-range-order of the films, resulting in low spontaneous magnetizations compared with the defect-free films...
December 18, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29249565/comparative-study-of-rflp-is6110-and-miru-vntr-from-mycobacterium-tuberculosis-isolated-in-the-state-of-minas-gerais-brazil
#14
Cláudio José Augusto, Wânia da Silva Carvalho, Isabela Neves de Almeida, Lida Jouca de Assis Figueiredo, Nayanne Gama Teixeira Dantas, Philip Noel Suffys, Silvana Spíndola de Miranda
DNA genotyping of Mycobacterium tuberculosis has been widely applied in the understanding of disease transmission in many countries. The purpose of this study was to genotype the strains of M. tuberculosis isolated in patients with new tuberculosis (TB) cases in Minas Gerais, as well as to compare the similarity, discriminatory power, and agreement of the clusters between the IS6110 Restriction Fragment Length Polymorfism (RFLP) and 12 loci Variable Number Tandem Repeat - Mycobacterial Interspersed Repetitive Units (MIRU-VNTR) techniques...
December 11, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29246454/reliability-construct-validity-and-interpretability-of-the-brazilian-version-of-the-rapid-upper-limb-assessment-rula-and-strain-index-si
#15
Daniela Pereira Valentim, Tatiana de Oliveira Sato, Maria Luiza Caíres Comper, Anderson Martins da Silva, Cristiana Villas Boas, Rosimeire Simprini Padula
BACKGROUND: There are very few observational methods for analysis of biomechanical exposure available in Brazilian-Portuguese. OBJECTIVE: This study aimed to cross-culturally adapt and test the measurement properties of the Rapid Upper Limb Assessment (RULA) and Strain Index (SI). METHODS: The cross-cultural adaptation and measurement properties test were established according to Beaton et al. and COSMIN guidelines, respectively. Several tasks that required static posture and/or repetitive motion of upper limbs were evaluated (n>100)...
November 26, 2017: Brazilian Journal of Physical Therapy
https://www.readbyqxmd.com/read/29242289/mild-telomere-dysfunction-as-a-force-for-altering-the-adaptive-potential-of-subtelomeric-genes
#16
Jennifer M O Mason, Michael J McEachern
Subtelomeric regions have several unusual characteristics including complex repetitive structures, increased rates of evolution, and enrichment for genes involved in niche adaptation. The adaptive telomere failure hypothesis suggests that certain environmental stresses can induce a low level of telomere failure, potentially leading to elevated subtelomeric recombination that could result in adaptive mutational changes within subtelomeric genes. Here, we tested a key prediction of the adaptive telomere failure hypothesis; that telomere dysfunction mild enough to have little or no overall effect on cell fitness could still lead to substantial increases in the mutation rates of subtelomeric genes...
December 14, 2017: Genetics
https://www.readbyqxmd.com/read/29237455/molecular-and-histological-effects-of-mr-guided-pulsed-focused-ultrasound-to-the-rat-heart
#17
Kee W Jang, Tsang-Wei Tu, Matthew E Nagle, Bobbi K Lewis, Scott R Burks, Joseph A Frank
BACKGROUND: Image-guided high intensity focused ultrasound has been used as an extracorporeal cardiac pacing tool and to enhance homing of stem cells to targeted tissues. However, molecular changes in the myocardium after sonication have not been widely investigated. Magnetic-resonance (MR)-guided pulsed focused ultrasound (pFUS) was targeted to the rat myocardium over a range of pressures and the microenvironmental and histological effects were evaluated over time. METHODS: Eight-to-ten-week-old Sprague-Dawley rats received T2-weighted MR images to target pFUS to the left ventricular and septum without cardiac or respiratory gating...
December 13, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29221460/goldenpics-a-golden-gate-derived-modular-cloning-system-for-applied-synthetic-biology-in-the-yeast-pichia-pastoris
#18
Roland Prielhofer, Juan J Barrero, Stefanie Steuer, Thomas Gassler, Richard Zahrl, Kristin Baumann, Michael Sauer, Diethard Mattanovich, Brigitte Gasser, Hans Marx
BACKGROUND: State-of-the-art strain engineering techniques for the host Pichia pastoris (syn. Komagataella spp.) include overexpression of homologous and heterologous genes, and deletion of host genes. For metabolic and cell engineering purposes the simultaneous overexpression of more than one gene would often be required. Very recently, Golden Gate based libraries were adapted to optimize single expression cassettes for recombinant proteins in P. pastoris. However, an efficient toolbox allowing the overexpression of multiple genes at once was not available for P...
December 8, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29218781/in-vitro-invasion-capacity-of-salmonella-typhimurium-dt9-isolates-sourced-from-humans-and-layer-hen-environments
#19
A R McWhorter, G Phan, H Hocking, K K Chousalkar
In Australia, Salmonella Typhimurium definitive type 9 is frequently isolated during foodborne outbreaks of salmonellosis. Multiple-locus variable number tandem repeat analysis (MLVA) trace back investigations frequently identify isolate distribution patterns that may be epidemiologically linked to disease outbreaks. In this study, the in vitro virulence potential of S. Typhimurium DT9 isolates possessing different MLVA patterns (03 15 07 11 550, 03 24 11 10 523, 03 15 08 11 550 and 03 14 08 11 550) isolated from either humans or layer hens was assessed using a human colon carcinoma cell line...
December 8, 2017: Zoonoses and Public Health
https://www.readbyqxmd.com/read/29216285/myocardial-adaption-to-hi-r-t-in-previously-untrained-men-with-a-randomized-longitudinal-cardiac-mr-imaging-study-physical-adaptions-in-untrained-on-strength-and-heart-trial-push-trial
#20
RANDOMIZED CONTROLLED TRIAL
Michael Scharf, Derya Oezdemir, Axel Schmid, Wolfgang Kemmler, Simon von Stengel, Matthias S May, Michael Uder, Michael M Lell
OBJECTIVE: Although musculoskeletal effects in resistance training are well described, little is known about structural and functional cardiac adaption in formerly untrained subjects. We prospectively evaluated whether short term high intensity (resistance) training (HI(R)T) induces detectable morphologic cardiac changes in previously untrained men in a randomized controlled magnetic resonance imaging (MRI) study. MATERIALS AND METHODS: 80 untrained middle-aged men were randomly assigned to a HI(R)T-group (n = 40; 43...
2017: PloS One
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