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Molecular Biosciences

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https://www.readbyqxmd.com/read/28911313/-letter-to-the-editor-incorrect-assignment-of-affected-nucleotides-in-footprinting-probing-experiments
#1
Sergey Belikov, Fredrik Lackmann, Lars Wieslander
Address correspondence to Sergey Belikov or Lars Wieslander, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden. E-mail: sergey.belikov@su.se or lars.wieslander@su.se.
September 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28899979/clinical-performance-evaluation-of-the-idylla-nras-braf-mutation-test-on-retrospectively-collected-formalin-fixed-paraffin-embedded-colorectal-cancer-tissue
#2
Louise Johnston, Michael Power, Philip Sloan, Anna Long, Angela Silmon, Ben Chaffey, Andrea Jane Lisgo, Liam Little, Ellen Vercauteren, Torben Steiniche, Tine Meyer, John Simpson
AIMS: Understanding the molecular mechanisms of underlying disease has led to a movement away from the one-drug-fits-all paradigm towards treatment tailored to the genetic profile of the patient. The Biocartis Idylla platform is a novel fully automated, real-time PCR-based in vitro diagnostic system. The Idylla NRAS-BRAF mutation test has been developed for the qualitative detection of mutations in NRAS and BRAF oncogenes, facilitating genetic profiling of patients with cancer. The aim of this study was to carry out a formal clinical performance evaluation...
September 12, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28891636/cuaac-based-click-chemistry-in-self-healing-polymers
#3
Diana Döhler, Philipp Michael, Wolfgang H Binder
Click chemistry has emerged as a significant tool for materials science, organic chemistry, and bioscience. Based on the initial concept of Barry Sharpless in 2001, the copper(I)-catalyzed azide/alkyne cycloaddition (CuAAC) reaction has triggered a plethora of chemical concepts for linking molecules and building blocks under ambient conditions, forming the basis for applications in autonomous cross-linking materials. Self-healing systems on the other hand are often based on mild cross-linking chemistries that are able to react either autonomously or upon an external trigger...
September 11, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28859321/course-based-undergraduate-research-experiences-in-molecular-biosciences-patterns-trends-and-faculty-support
#4
Jack T H Wang
Inquiry-driven learning, research internships and course-based undergraduate research experiences all represent mechanisms through which educators can engage undergraduate students in scientific research. In life sciences education, the benefits of undergraduate research have been thoroughly evaluated, but limitations in infrastructure and training can prevent widespread uptake of these practices. It is not clear how faculty members can integrate complex laboratory techniques and equipment into their unique context, while finding the time and resources to implement undergraduate research according to best practice guidelines...
August 15, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28839929/why-an-extended-evolutionary-synthesis-is-necessary
#5
REVIEW
Gerd B Müller
Since the last major theoretical integration in evolutionary biology-the modern synthesis (MS) of the 1940s-the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and multiple inheritance systems, the '-omics' revolution and the science of systems biology, among other developments, have provided a wealth of new knowledge about the factors responsible for evolutionary change. Some of these results are in agreement with the standard theory and others reveal different properties of the evolutionary process...
October 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/28837659/in-vivo-cloning-of-up-to-16-kb-plasmids-in-e-coli-is-as-simple-as-pcr
#6
Faqing Huang, Joseph Rankin Spangler, Allen Yang Huang
The precise assembly of defined DNA sequences into plasmids is an essential task in bioscience research. While a number of molecular cloning techniques have been developed, many methods require specialized expensive reagents or laborious experimental procedure. Not surprisingly, conventional cloning techniques based on restriction digestion and ligation are still commonly used in routine DNA cloning. Here, we describe a simple, fast, and economical cloning method based on RecA- and RecET-independent in vivo recombination of DNA fragments with overlapping ends using E...
2017: PloS One
https://www.readbyqxmd.com/read/28833759/can-rapid-negative-exclusion-of-blood-cultures-by-a-molecular-method-enzyme-template-generation-and-amplification-technique-cognitor-%C3%A2-minus-aid-antimicrobial-stewardship
#7
Matthew Dryden, Agnes Sitjar, Zoe Gunning, Sophie Lewis, Richard Healey, Praneeth Satchithananthan, Natalie Parker, Taryn Keyser, Kordo Saeed, Helen V Bennett
OBJECTIVES: Antimicrobial review is an important part of antimicrobial stewardship. A novel enzyme template generation and amplification technique (ETGA), the Cognitor(®) Minus (Momentum Bioscience, Long Hanborough, UK) test, has a 99.5% negative predictive value for bacteraemia and fungaemia. This observational study asked two questions: (1) Does a negative ETGA, indicating no bacteraemia or fungaemia, aid antimicrobial review within 48 h of admission; (2) In this real-life clinical setting, does a negative ETGA mean no bacteraemia or fungaemia? METHODS: Consecutive blood cultures in patients with clinical infection were tested by ETGA...
August 18, 2017: International Journal of Pharmacy Practice
https://www.readbyqxmd.com/read/28758332/a-biosafety-level-2-virology-lab-for-biotechnology-undergraduates
#8
Sigal Matza-Porges, Dafna Nathan
Medical, industrial, and basic research relies heavily on the use of viruses and vectors. Therefore, it is important that bioscience undergraduates learn the practicalities of handling viruses. Teaching practical virology in a student laboratory setup presents safety challenges, however. The aim of this article is to describe the design and implementation of a virology laboratory, with emphasis on student safety, for biotechnology undergraduates. Cell culture techniques, animal virus infection, quantification, and identification are taught at a biosafety level 2 for a diverse group of undergraduates ranging from 20 to 50 students per group...
July 30, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28755976/g-quadruplexes-prediction-characterization-and-biological-application
#9
REVIEW
Chun Kit Kwok, Catherine J Merrick
Guanine (G)-rich sequences in nucleic acids can assemble into G-quadruplex structures that involve G-quartets linked by loop nucleotides. The structural and topological diversity of G-quadruplexes have attracted great attention for decades. Recent methodological advances have advanced the identification and characterization of G-quadruplexes in vivo as well as in vitro, and at a much higher resolution and throughput, which has greatly expanded our current understanding of G-quadruplex structure and function...
July 26, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28748222/an-improved-plasmodium-cynomolgi-genome-assembly-reveals-an-unexpected-methyltransferase-gene-expansion
#10
Erica M Pasini, Ulrike Böhme, Gavin G Rutledge, Annemarie Voorberg-Van der Wel, Mandy Sanders, Matt Berriman, Clemens Hm Kocken, Thomas Dan Otto
BACKGROUND: Plasmodium cynomolgi, a non-human primate malaria parasite species, has been an important model parasite since its discovery in 1907. Similarities in the biology of P. cynomolgi to the closely related, but less tractable, human malaria parasite P. vivax make it the model parasite of choice for liver biology and vaccine studies pertinent to P. vivax malaria. Molecular and genome-scale studies of P. cynomolgi have relied on the current reference genome sequence, which remains highly fragmented with 1,649 unassigned scaffolds and little representation of the subtelomeres...
2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28711585/global-outbreak-of-severe-mycobacterium-chimaera-disease-after-cardiac-surgery-a-molecular-epidemiological-study
#11
Jakko van Ingen, Thomas A Kohl, Katharina Kranzer, Barbara Hasse, Peter M Keller, Anna Katarzyna Szafrańska, Doris Hillemann, Meera Chand, Peter Werner Schreiber, Rami Sommerstein, Christoph Berger, Michele Genoni, Christian Rüegg, Nicolas Troillet, Andreas F Widmer, Sören L Becker, Mathias Herrmann, Tim Eckmanns, Sebastian Haller, Christiane Höller, Sylvia B Debast, Maurice J Wolfhagen, Joost Hopman, Jan Kluytmans, Merel Langelaar, Daan W Notermans, Jaap Ten Oever, Peter van den Barselaar, Alexander B A Vonk, Margreet C Vos, Nada Ahmed, Timothy Brown, Derrick Crook, Theresa Lamagni, Nick Phin, E Grace Smith, Maria Zambon, Annerose Serr, Tim Götting, Winfried Ebner, Alexander Thürmer, Christian Utpatel, Cathrin Spröer, Boyke Bunk, Ulrich Nübel, Guido V Bloemberg, Erik C Böttger, Stefan Niemann, Dirk Wagner, Hugo Sax
BACKGROUND: Since 2013, over 100 cases of Mycobacterium chimaera prosthetic valve endocarditis and disseminated disease were notified in Europe and the USA, linked to contaminated heater-cooler units (HCUs) used during cardiac surgery. We did a molecular epidemiological investigation to establish the source of these patients' disease. METHODS: We included 24 M chimaera isolates from 21 cardiac surgery-related patients in Switzerland, Germany, the Netherlands, and the UK, 218 M chimaera isolates from various types of HCUs in hospitals, from LivaNova (formerly Sorin; London, UK) and Maquet (Rastatt, Germany) brand HCU production sites, and unrelated environmental sources and patients, as well as eight Mycobacterium intracellulare isolates...
July 12, 2017: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/28670468/institutional-profile-the-national-swedish-academic-drug-discovery-development-platform-at-scilifelab
#12
EDITORIAL
Per I Arvidsson, Kristian Sandberg, Kjell S Sakariassen
The Science for Life Laboratory Drug Discovery and Development Platform (SciLifeLab DDD) was established in Stockholm and Uppsala, Sweden, in 2014. It is one of ten platforms of the Swedish national SciLifeLab which support projects run by Swedish academic researchers with large-scale technologies for molecular biosciences with a focus on health and environment. SciLifeLab was created by the coordinated effort of four universities in Stockholm and Uppsala: Stockholm University, Karolinska Institutet, KTH Royal Institute of Technology and Uppsala University, and has recently expanded to other Swedish university locations...
June 2017: Future Science OA
https://www.readbyqxmd.com/read/28606056/comparative-genome-and-transcriptome-analysis-reveals-distinctive-surface-characteristics-and-unique-physiological-potentials-of-pseudomonas-aeruginosa-atcc-27853
#13
Huiluo Cao, Yong Lai, Salim Bougouffa, Zeling Xu, Aixin Yan
BACKGROUND: Pseudomonas aeruginosa ATCC 27853 was isolated from a hospital blood specimen in 1971 and has been widely used as a model strain to survey antibiotics susceptibilities, biofilm development, and metabolic activities of Pseudomonas spp.. Although four draft genomes of P. aeruginosa ATCC 27853 have been sequenced, the complete genome of this strain is still lacking, hindering a comprehensive understanding of its physiology and functional genome. RESULTS: Here we sequenced and assembled the complete genome of P...
June 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28604319/establishing-an-academic-biobank-in-a-resource-challenged-environment
#14
Cassandra Claire Soo, Freedom Mukomana, Scott Hazelhurst, Michele Ramsay
Past practices of informal sample collections and spreadsheets for data and sample management fall short of best-practice models for biobanking, and are neither cost effective nor efficient to adequately serve the needs of large research studies. The biobank of the Sydney Brenner Institute for Molecular Bioscience serves as a bioresource for institutional, national and international research collaborations. It provides high-quality human biospecimens from African populations, secure data and sample curation and storage, as well as monitored sample handling and management processes, to promote both non-communicable and infectious-disease research...
May 24, 2017: South African Medical Journal, Suid-Afrikaanse Tydskrif Vir Geneeskunde
https://www.readbyqxmd.com/read/28572312/four-complete-paenibacillus-larvae-genome-sequences
#15
Douglas W Dingman
Four complete genome sequences of genetically distinct Paenibacillus larvae strains have been determined. Pacific BioSciences single-molecule real-time (SMRT) sequencing technology was used as the sole method of sequence determination and assembly. The chromosomes exhibited a G+C content of 44.1 to 44.2% and a molecular size range of 4.29 to 4.67 Mbp.
June 1, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28572170/new-developments-in-crystallography-exploring-its-methods-technology-and-scope%C3%A2-in-the-molecular-biosciences
#16
John R Helliwell
Since the Protein Data Bank was founded in 1971 there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database, founded in 1965, there are more than 800,000 'small molecule' crystal structure depositions, and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs...
June 1, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28558786/lost-in-plasmids-next-generation-sequencing-and-the-complex-genome-of-the-tick-borne-pathogen-borrelia-burgdorferi
#17
G Margos, S Hepner, C Mang, D Marosevic, S E Reynolds, S Krebs, A Sing, M Derdakova, M A Reiter, V Fingerle
BACKGROUND: Borrelia (B.) burgdorferi sensu lato, including the tick-transmitted agents of human Lyme borreliosis, have particularly complex genomes, consisting of a linear main chromosome and numerous linear and circular plasmids. The number and structure of plasmids is variable even in strains within a single genospecies. Genes on these plasmids are known to play essential roles in virulence and pathogenicity as well as host and vector associations. For this reason, it is essential to explore methods for rapid and reliable characterisation of molecular level changes on plasmids...
May 30, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28503305/three-dimensional-conjugation-of-recombinant-n-cadherin-to-a-hydrogel-for-in-vitro-anisotropic-neural-growth
#18
Johana C M Vega L, Min Kyung Lee, Ellen C Qin, Max Rich, Kwan Young Lee, Dong Hyun Kim, Hee Jung Chung, Deborah E Leckband, Hyunjoon Kong
Living cells are extensively being studied to build functional tissues that are useful for both fundamental and applied bioscience studies. Increasing evidence suggests that cell-cell adhesion controlled by intercellular cadherin junction plays important roles in the quality of the resulting engineered tissue. These findings prompted efforts to interrogate biological effects of cadherin at a molecular scale; however, few efforts were made to harness the effects of cadherin on cells cultured in an in vivo-like three dimensional matrix...
November 14, 2016: Journal of Materials Chemistry. B, Materials for Biology and Medicine
https://www.readbyqxmd.com/read/28487882/identification-of-a-novel-rasd1-somatic-mutation-in-a-usp8-mutated-corticotroph-adenoma
#19
Andrew V Uzilov, Khadeen C Cheesman, Marc Y Fink, Leah C Newman, Chetanya Pandya, Yelena Lalazar, Marco Hefti, Mary Fowkes, Gintaras Deikus, Chun Yee Lau, Aye S Moe, Yayoi Kinoshita, Yumi Kasai, Micol Zweig, Arpeta Gupta, Daniela Starcevic, Milind Mahajan, Eric E Schadt, Kalmon D Post, Michael J Donovan, Robert Sebra, Rong Chen, Eliza B Geer
Cushing's disease (CD) is caused by pituitary corticotroph adenomas that secrete excess adrenocorticotropic hormone (ACTH). In these tumors, somatic mutations in the gene USP8 have been identified as recurrent and pathogenic and are the sole known molecular driver for CD. Although other somatic mutations were reported in these studies, their contribution to the pathogenesis of CD remains unexplored. No molecular drivers have been established for a large proportion of CD cases and tumor heterogeneity has not yet been investigated using genomics methods...
May 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28425189/the-global-ethics-corner-foundations-beliefs-and-the-teaching-of-biomedical-and-scientific-ethics-around-the-world
#20
Henry Jakubowski, Jianping Xie, Arup Kumar Mitra, Ravindra Ghooi, Saman Hosseinkhani, Mohsen Alipour, Behnam Hajipour, George Obiero
The profound advances in the biomolecular sciences over the last decades have enabled similar advances in biomedicine. These advances have increasingly challenged our abilities to deploy them in an equitable and ethically acceptable manner. As such, it has become necessary and important to teach biomedical and scientific ethics to our students who will become the researchers, medical professionals, and global citizens of the future. As advances in the biosciences and medicine are made, developed, and used across the globe, our survival on an endangered planet requires global dialog and consensual action...
April 19, 2017: Biochemistry and Molecular Biology Education
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