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Molecular Biosciences

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https://www.readbyqxmd.com/read/29741723/a-single-molecule-sequencing-assay-for-the-comprehensive-profiling-of-t4-dna-ligase-fidelity-and-bias-during-dna-end-joining
#1
Vladimir Potapov, Jennifer L Ong, Bradley W Langhorst, Katharina Bilotti, Dan Cahoon, Barry Canton, Thomas F Knight, Thomas C Evans, Gregory Js Lohman
DNA ligases are key enzymes in molecular and synthetic biology that catalyze the joining of breaks in duplex DNA and the end-joining of DNA fragments. Ligation fidelity (discrimination against the ligation of substrates containing mismatched base pairs) and bias (preferential ligation of particular sequences over others) have been well-studied in the context of nick ligation. However, almost no data exist for fidelity and bias in end-joining ligation contexts. In this study, we applied Pacific Biosciences Single-Molecule Real-Time sequencing technology to directly sequence the products of a highly multiplexed ligation reaction...
May 8, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29643861/-targeted-sequencing-by-gene-synteny-a-new-strategy-for-polyploid-species-sequencing-and-physical-structure-of-a-complex-sugarcane-region
#2
Melina C Mancini, Claudio B Cardoso-Silva, Danilo A Sforça, Anete Pereira de Souza
Sugarcane exhibits a complex genome mainly due to its aneuploid nature and high ploidy level, and sequencing of its genome poses a great challenge. Closely related species with well-assembled and annotated genomes can be used to help assemble complex genomes. Here, a stable quantitative trait locus (QTL) related to sugar accumulation in sorghum was successfully transferred to the sugarcane genome. Gene sequences related to this QTL were identified in silico from sugarcane transcriptome data, and molecular markers based on these sequences were developed to select bacterial artificial chromosome (BAC) clones from the sugarcane variety SP80-3280...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29607989/-research-misconduct-in-japan-and-how-it-is-covered-by-the-media
#3
Eisuke Enoki
 Cases of research misconduct (fabrication, falsification, and plagiarism) have been increasing worldwide, including in Japan. In particular, since 2006, many cases of research misconduct have been reported in Japan, and these cases have also been covered by the media. The 2014 case of the withdrawal of articles on STAP cells followed a rare course in which research misconduct became a full-blown social phenomenon. In recent years, even the University of Tokyo has experienced reported cases of research misconduct...
2018: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
https://www.readbyqxmd.com/read/29599423/atypical-presentation-of-gelsolin-amyloidosis-in-a-man-of-african-descent-with-a-novel-mutation-in-the-gelsolin-gene
#4
Karlos Z Oregel, Geoffrey P Shouse, Cyrus Oster, Freddy Martinez, Jun Wang, Michael Rosenzweig, Jeremy K Deisch, Chien-Shing Chen, Gayathri Nagaraj
BACKGROUND Gelsolin amyloidosis is a very rare systemic disease presenting with a pathognomonic triad of corneal lattice dystrophy, cutis laxa, and polyneuropathy. The disease is mostly restricted to a Finnish population with known mutations (G654A, G654T) in exon 4 of the gelsolin gene. The mutations lead to errors in protein processing and folding, and ultimately leads to deposition of an amyloidogenic fragment in the extracellular space, causing the symptoms of disease. CASE REPORT We present a case of gelsolin amyloidosis in a male of African descent with an atypical clinical presentation including fevers, skin rash, polyneuropathy, and anemia...
March 30, 2018: American Journal of Case Reports
https://www.readbyqxmd.com/read/29572005/programmed-cell-death-ligand-1-pd-l1-expression-is-associated-with-ras-tp53-mutations-in-lung-adenocarcinoma
#5
Pierre Serra, Arthur Petat, Jean-Michel Maury, Françoise Thivolet-Bejui, Lara Chalabreysse, Marc Barritault, Nathalie Ebran, Gérard Milano, Nicolas Girard, Marie Brevet
INTRODUCTION: The systematic assessment of anti-programmed cell death ligand 1 (PD-L1) expression by immunohistochemistry (IHC) in lung adenocarcinomas is becoming standard practice. However, the assessment of PD-L1 expression on small tissue specimens needs to be evaluated and the association with other features more thoroughly analyzed. METHODS: This retrospective single center study evaluated the immunohistochemical expression of the SP263 anti-PD-L1 antibody on tissue microarrays (TMA) of 152 surgically resected lung adenocarcinomas, using a 25% positivity threshold...
April 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29448102/a-universal-mini-vector-and-an-annealing-of-pcr-products-app-based-cloning-strategy-for-convenient-molecular-biological-manipulations
#6
Xia Liu, Tuoping Li, Darren J Hart, Song Gao, Hongling Wang, Herui Gao, Shumin Xu, Yifeng Zhang, Yifei Liu, Yingfeng An
Currently, the most widely used strategies for molecular cloning are sticky-end ligation-based cloning, TA cloning, blunt-end ligation-based cloning and ligase-independent cloning. In this study we have developed a novel mini-vector pANY1 which can simultaneously meet the requirements of all these cloning strategies. In addition, the selection of appropriate restriction digestion sites is difficult in some cases because of the presence of internal sites. In this study, an annealing of PCR products (APP)-based sticky-end cloning strategy was introduced to avoid this issue...
March 18, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29321824/high-frequency-of-cd34-cd38-low-immature-leukemia-cells-is-correlated-with-unfavorable-prognosis-in-acute-myeloid-leukemia
#7
Adriana Plesa, Charles Dumontet, Eve Mattei, Ines Tagoug, Sandrine Hayette, Pierre Sujobert, Isabelle Tigaud, Marie Pierre Pages, Youcef Chelghoum, Fiorenza Baracco, Helene Labussierre, Sophie Ducastelle, Etienne Paubelle, Franck Emmanuel Nicolini, Mohamed Elhamri, Lydia Campos, Claudiu Plesa, Stéphane Morisset, Gilles Salles, Yves Bertrand, Mauricette Michallet, Xavier Thomas
AIM: To evaluate the importance of the CD34+CD38- cell population when compared to the CD34+CD38+/low and CD34+CD38+/high leukemic cell sub-populations and to determine its correlations with leukemia characteristics and known prognostic factors, as well as with response to therapy and survival. METHODS: Two hundred bone marrow samples were obtained at diagnosis from 200 consecutive patients with newly diagnosed acute myeloid leukemia (AML) were studied between September 2008 and December 2010 at our Institution (Hematology Department, Lyon, France)...
December 26, 2017: World Journal of Stem Cells
https://www.readbyqxmd.com/read/29275251/emerging-whole-cell-modeling-principles-and-methods
#8
REVIEW
Arthur P Goldberg, Balázs Szigeti, Yin Hoon Chew, John Ap Sekar, Yosef D Roth, Jonathan R Karr
Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment. Whole-cell models have great potential to transform bioscience, bioengineering, and medicine. However, numerous challenges remain to achieve whole-cell models. Nevertheless, researchers are beginning to leverage recent progress in measurement technology, bioinformatics, data sharing, rule-based modeling, and multi-algorithmic simulation to build the first whole-cell models...
December 21, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29222463/the-genome-sequence-of-bipolaris-cookei-reveals-mechanisms-of-pathogenesis-underlying-target-leaf-spot-of-sorghum
#9
Alex Z Zaccaron, Burton H Bluhm
Bipolaris cookei (=Bipolaris sorghicola) causes target leaf spot, one of the most prevalent foliar diseases of sorghum. Little is known about the molecular basis of pathogenesis in B. cookei, in large part due to a paucity of resources for molecular genetics, such as a reference genome. Here, a draft genome sequence of B. cookei was obtained and analyzed. A hybrid assembly strategy utilizing Illumina and Pacific Biosciences sequencing technologies produced a draft nuclear genome of 36.1 Mb, organized into 321 scaffolds with L50 of 31 and N50 of 378 kb, from which 11,189 genes were predicted...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29206036/the-design-and-development-of-a-potent-and-selective-novel-diprolyl-derivative-that-binds-to-the-n-domain-of-angiotensin-i-converting-enzyme
#10
Stephen Fienberg, Gyles E Cozier, K Ravi Acharya, Kelly Chibale, Edward D Sturrock
Angiotensin-I converting enzyme (ACE) is a zinc metalloprotease consisting of two catalytic domains (N- and C-). Most clinical ACE inhibitor(s) (ACEi) have been shown to inhibit both domains nonselectively, resulting in adverse effects such as cough and angioedema. Selectively inhibiting the individual domains is likely to reduce these effects and potentially treat fibrosis in addition to hypertension. ACEi from the GVK Biosciences database were inspected for possible N-domain selective binding patterns. From this set, a diprolyl chemical series was modeled using docking simulations...
January 11, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29166127/bat-biology-genomes-and-the-bat1k-project-to-generate-chromosome-level-genomes-for-all-living-bat-species
#11
Emma C Teeling, Sonja C Vernes, Liliana M Dávalos, David A Ray, M Thomas P Gilbert, Eugene Myers
Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene...
February 15, 2018: Annual Review of Animal Biosciences
https://www.readbyqxmd.com/read/29132146/identification-of-unique-neoantigen-qualities-in-long-term-survivors-of-pancreatic-cancer
#12
Vinod P Balachandran, Marta Łuksza, Julia N Zhao, Vladimir Makarov, John Alec Moral, Romain Remark, Brian Herbst, Gokce Askan, Umesh Bhanot, Yasin Senbabaoglu, Daniel K Wells, Charles Ian Ormsby Cary, Olivera Grbovic-Huezo, Marc Attiyeh, Benjamin Medina, Jennifer Zhang, Jennifer Loo, Joseph Saglimbeni, Mohsen Abu-Akeel, Roberta Zappasodi, Nadeem Riaz, Martin Smoragiewicz, Z Larkin Kelley, Olca Basturk, Mithat Gönen, Arnold J Levine, Peter J Allen, Douglas T Fearon, Miriam Merad, Sacha Gnjatic, Christine A Iacobuzio-Donahue, Jedd D Wolchok, Ronald P DeMatteo, Timothy A Chan, Benjamin D Greenbaum, Taha Merghoub, Steven D Leach
Pancreatic ductal adenocarcinoma is a lethal cancer with fewer than 7% of patients surviving past 5 years. T-cell immunity has been linked to the exceptional outcome of the few long-term survivors, yet the relevant antigens remain unknown. Here we use genetic, immunohistochemical and transcriptional immunoprofiling, computational biophysics, and functional assays to identify T-cell antigens in long-term survivors of pancreatic cancer. Using whole-exome sequencing and in silico neoantigen prediction, we found that tumours with both the highest neoantigen number and the most abundant CD8+ T-cell infiltrates, but neither alone, stratified patients with the longest survival...
November 23, 2017: Nature
https://www.readbyqxmd.com/read/29115536/advances-in-the-t7-phage-display-system-review
#13
Xiangying Deng, Li Wang, Xiaolong You, Pei Dai, Yanhua Zeng
The present review describes the advantages and updated applications of the T7 phage display system in bioscience and medical science. Current phage display systems are based on various bacteriophage vectors, including M13, T7, T4 and f1. Of these, the M13 phage display is the most frequently used, however, the present review highlights the advantages of the T7 system. As a phage display platform, M13 contains single‑stranded DNA, while the T7 phage consists of double‑stranded DNA, which exhibits increased stability and is less prone to mutation during replication...
January 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29108958/novel-physical-chemistry-approaches-in-biophysical-researches-with-advanced-application-of-lasers-detection-and-manipulation
#14
REVIEW
Koichi Iwata, Masahide Terazima, Hiroshi Masuhara
Novel methodologies utilizing pulsed or intense CW irradiation obtained from lasers have a major impact on biological sciences. In this article, recent development in biophysical researches fully utilizing the laser irradiation is described for three topics, time-resolved fluorescence spectroscopy, time-resolved thermodynamics, and manipulation of the biological assemblies by intense laser irradiation. First, experimental techniques for time-resolved fluorescence spectroscopy are concisely explained in Section 2...
February 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29041927/diagnostic-performance-of-the-loop-mediated-isothermal-amplification-lamp-based-illumigene-%C3%A2-malaria-assay-in-a-non-endemic-region
#15
Anne-Sophie De Koninck, Lieselotte Cnops, Mattias Hofmans, Jan Jacobs, Dorien Van den Bossche, Jan Philippé
BACKGROUND: Light microscopy and antigen-based rapid diagnostic tests are the primary diagnostic tools for detecting malaria, although being labour-intensive and frequently challenged by lack of personnel's experience and low levels of parasite density. The latter being especially important in non-endemic settings. Novel molecular techniques aim to overcome this drawback. The objective of this study was to assess the diagnostic performance of the illumigene malaria assay® (Meridian Bioscience) compared to microscopy, RDT and real-time PCR...
October 17, 2017: Malaria Journal
https://www.readbyqxmd.com/read/29018576/key-differences-between-13-kras-mutation-detection-technologies-and-their-relevance-for-clinical-practice
#16
James L Sherwood, Helen Brown, Alessandro Rettino, Amelie Schreieck, Graeme Clark, Bart Claes, Bhuwnesh Agrawal, Ria Chaston, Benjamin S G Kong, Paul Choppa, Anders O H Nygren, Ina L Deras, Alexander Kohlmann
INTRODUCTION: This study assessed KRAS mutation detection and functional characteristics across 13 distinct technologies and assays available in clinical practice, in a blinded manner. METHODS: Five distinct KRAS -mutant cell lines were used to study five clinically relevant KRAS mutations: p.G12C, p.G12D, p.G12V, p.G13D and p.Q61H. 50 cell line admixtures with low (50 and 100) mutant KRAS allele copies at 20%, 10%, 5%, 1% and 0.5% frequency were processed using quantitative PCR (qPCR) (n=3), matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF) (n=2), next-generation sequencing (NGS) (n=6), digital PCR (n=1) and Sanger capillary sequencing (n=1) assays...
2017: ESMO Open
https://www.readbyqxmd.com/read/28981959/chiral-molecular-science-how-were-the-absolute-configurations-of-chiral-molecules-determined-experimental-results-and-theories
#17
Nobuyuki Harada
Molecular chirality is a key concept in chemistry, bioscience, and molecular technology, like the invention of a light-powered chiral molecular motor explained in this review. Thus, the primary research subject is how to determine the absolute configuration (AC) of chiral compounds. This review article focuses on the principle, theory, and practice of the nonempirical methods for determining ACs of chiral compounds, i.e., the Bijvoet method in X-ray crystallography and the circular dichroism (CD) exciton chirality method, together with the historical aspects of AC determination...
December 2017: Chirality
https://www.readbyqxmd.com/read/28911313/-letter-to-the-editor-incorrect-assignment-of-affected-nucleotides-in-footprinting-probing-experiments
#18
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
#19
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...
April 2018: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28891636/cuaac-based-click-chemistry-in-self-healing-polymers
#20
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...
October 17, 2017: Accounts of Chemical Research
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