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https://www.readbyqxmd.com/read/28809850/function-related-replacement-of-bacterial-siderophore-pathways
#1
Hilke Bruns, Max Crüsemann, Anne-Catrin Letzel, Mohammad Alanjary, James O McInerney, Paul R Jensen, Stefan Schulz, Bradley S Moore, Nadine Ziemert
Bacterial genomes are rife with orphan biosynthetic gene clusters (BGCs) associated with secondary metabolism of unrealized natural product molecules. Often up to a tenth of the genome is predicted to code for the biosynthesis of diverse metabolites with mostly unknown structures and functions. This phenomenal diversity of BGCs coupled with their high rates of horizontal transfer raise questions about whether they are really active and beneficial, whether they are neutral and confer no advantage, or whether they are carried in genomes because they are parasitic or addictive...
August 15, 2017: ISME Journal
https://www.readbyqxmd.com/read/28796277/talking-the-talk-but-not-walking-the-walk-rt-qpcr-as-a-paradigm-for-the-lack-of-reproducibility-in-molecular-research
#2
REVIEW
Stephen Bustin, Tania Nolan
Poorly executed and inadequately reported molecular measurement methods are amongst the causes underlying the lack of reproducibility of much biomedical research. Although several high impact factor journals have acknowledged their past failure to scrutinise adequately the technical soundness of manuscripts, there is a perplexing reluctance to implement basic corrective measures. The reverse transcription real time quantitative PCR (RT-qPCR) is probably the most straightforward measurement technique available for RNA quantification and is widely used in research, diagnostic, forensic and biotechnology applications...
August 10, 2017: European Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28761006/unpacking-the-species-conundrum-philosophy-practice-and-a-way-forward
#3
Kartik Shanker, S P Vijayakumar, K N Ganeshaiah
The history of ecology and evolutionary biology is rife with attempts to define and delimit species. However, there has been confusion between concepts and criteria, which has led to discussion, debate, and conflict, eventually leading to lack of consistency in delimitation. Here, we provide a broad review of species concepts, a clarification of category versus concept, an account of the general lineage concept (GLC), and finally a way forward for species discovery and delimitation. Historically, species were considered as varieties bound together by reproduction...
July 2017: Journal of Genetics
https://www.readbyqxmd.com/read/28654659/environmental-change-drives-accelerated-adaptation-through-stimulated-copy-number-variation
#4
Ryan M Hull, Cristina Cruz, Carmen V Jack, Jonathan Houseley
Copy number variation (CNV) is rife in eukaryotic genomes and has been implicated in many human disorders, particularly cancer, in which CNV promotes both tumorigenesis and chemotherapy resistance. CNVs are considered random mutations but often arise through replication defects; transcription can interfere with replication fork progression and stability, leading to increased mutation rates at highly transcribed loci. Here we investigate whether inducible promoters can stimulate CNV to yield reproducible, environment-specific genetic changes...
June 2017: PLoS Biology
https://www.readbyqxmd.com/read/28615462/posttranslational-modification-as-a-critical-determinant-of-cytoplasmic-innate-immune-recognition
#5
REVIEW
Paul J Baker, Dominic De Nardo, Fiona Moghaddas, Le Son Tran, Annabell Bachem, Tan Nguyen, Thomas Hayman, Hazel Tye, James E Vince, Sammy Bedoui, Richard L Ferrero, Seth L Masters
Cell surface innate immune receptors can directly detect a variety of extracellular pathogens to which cytoplasmic innate immune sensors are rarely exposed. Instead, within the cytoplasm, the environment is rife with cellular machinery and signaling pathways that are indirectly perturbed by pathogenic microbes to activate intracellular sensors, such as pyrin, NLRP1, NLRP3, or NLRC4. Therefore, subtle changes in key intracellular processes such as phosphorylation, ubiquitination, and other pathways leading to posttranslational protein modification are key determinants of innate immune recognition in the cytoplasm...
July 1, 2017: Physiological Reviews
https://www.readbyqxmd.com/read/28609580/metabolic-defense-against-oxidative-stress-the-road-less-travelled-so-far
#6
REVIEW
Joe Lemire, Azhar Alhasawi, Varun P Appanna, Sujeenthar Tharmalingam, Vasu D Appanna
Bacteria have survived, and many have thrived, since antiquity in the presence of the highly-reactive chalcogen - oxygen (O2 ). They are known to evoke intricate strategies to defend themselves from the reactive by-products of oxygen - reactive oxygen species (ROS). Many of these detoxifying mechanisms have been extensively characterized; superoxide dismutase (SOD), catalases, alkyl hydroperoxide reductase and the glutathione (GSH)-cycling system are responsible for neutralizing specific ROS. Meanwhile, a pool of NADPH - the reductive engine of many ROS-combating enzymes - is maintained by metabolic enzymes including, but not exclusively, glucose-6 phosphate dehydrogenase (G6PDH) and NADP-dependent isocitrate dehydrogenase (ICDH-NADP)...
June 13, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28576578/understanding-solid-phase-hla-antibody-assays-and-the-value-of-mfi
#7
REVIEW
Harold C Sullivan, Howard M Gebel, Robert A Bray
As the practice of medicine becomes more reliant on imaging and laboratory tests, medical decisions will be increasingly based on numbers. Accordingly, following the introduction of solid-phase testing to the HLA testing repertoire, laboratory directors and physicians have employed preset mean fluorescence intensity (MFI) thresholds as the basis for decisions in the management of transplant patients. However, what do MFI values mean? The literature is rife with reports detailing numerous factors that influence antibody assessment including (but not limited to) sensitization history of the patient, level of mismatch between donor and recipient, presence of interfering substances in the serum, whether the antigen on multiplex beads is native or denatured, day-to-day and technologist variability, and the historical performance of an assay in a given institution...
May 30, 2017: Human Immunology
https://www.readbyqxmd.com/read/28501896/what-do-biologists-make-of-the-species-problem
#8
Bruno Pušić, Pavel Gregorić, Damjan Franjević
The concept of species is one of the core concepts in biology and one of the cornerstones of evolutionary biology, yet it is rife with conceptual problems. Philosophers of biology have been discussing the concept of species for decades, and in doing so they sometimes appeal to the views of biologists. However, their statements as to what biologists think are seldom supported by empirical data. In order to investigate what biologists actually think about the key issues related to the problem of species, we have conducted a survey on the sample of 193 biologists from the population of biologists from over 150 biology departments at universities in the US and the EU...
May 13, 2017: Acta Biotheoretica
https://www.readbyqxmd.com/read/28438256/clinical-profile-and-outcome-of-patients-with-biopsy-proven-acute-interstitial-nephritis-in-cape-town-a-10-year-review%C3%A2
#9
Emmanuel E Effa, Udeme E Ekrikpo, Megan Borkum, Brian L Rayner, Peter Heering, Ikechi G Okpechi
BACKGROUND: Acute interstitial nephritis (AIN) is a common cause of acute kidney injury that has not been adequately characterized in Sub-Saharan Africa (SSA) despite an increasing use of potentially inciting agents for the treatment of human immunodeficiency virus (HIV) and tuberculosis in the region. METHODS: A retrospective audit of records of patients with biopsy-proven AIN diagnosed at Groote Schuur Hospital, Cape Town from the 1st of January, 2006, to the 31st of December, 2015...
April 25, 2017: Clinical Nephrology
https://www.readbyqxmd.com/read/28421932/learning-disability-nurse-numbers-heading-in-the-wrong-direction
#10
(no author information available yet)
The UK's record on supporting people with learning disabilities is patchy to say the least. For decades people were housed in inappropriate institutions where abuse was rife, and attempts to improve their lives by delivering better services in the community have come up short because they have not been afforded sufficient priority.
April 19, 2017: Nursing Standard
https://www.readbyqxmd.com/read/28419609/band-aids-for-buchnera-and-b-vitamins-for-all
#11
Jacob A Russell, Kerry M Oliver, Allison K Hansen
Evolution lacks foresight, and hence, key adaptations may produce major challenges over the long run. The natural world is rife with examples of long-term 'side effects' associated with quick-fix tinkering, including blind spots in vertebrate eyes. An important question is how nature compensates for imperfections once evolution has set a course. The symbioses associated with sap-feeding insects present a fascinating opportunity to address this issue. On one hand, the substantial diversity and biomass of sap-feeding insects are largely due to ancient acquisitions of nutrient-provisioning bacterial symbionts...
April 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28400787/silicification-in-grasses-variation-between-different-cell-types
#12
REVIEW
Santosh Kumar, Milan Soukup, Rivka Elbaum
Plants take up silicon as mono-silicic acid, which is released to soil by the weathering of silicate minerals. Silicic acid can be taken up by plant roots passively or actively, and later it is deposited in its polymerized form as amorphous hydrated silica. Major silica depositions in grasses occur in root endodermis, leaf epidermal cells, and outer epidermal cells of inflorescence bracts. Debates are rife about the mechanism of silica deposition, and two contrasting scenarios are often proposed to explain it...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28366126/prescriptions-filled-following-an-opioid-related-hospitalization
#13
Ellen Herbst, Tauheed Zaman, Tessa Rife
No abstract text is available yet for this article.
April 1, 2017: Psychiatric Services: a Journal of the American Psychiatric Association
https://www.readbyqxmd.com/read/28355975/the-potential-of-collective-intelligence-in-emergency-medicine-pooling-medical-students-independent-decisions-improves-diagnostic-performance
#14
Juliane E Kämmer, Wolf E Hautz, Stefan M Herzog, Olga Kunina-Habenicht, Ralf H J M Kurvers
BACKGROUND: Evidence suggests that pooling multiple independent diagnoses can improve diagnostic accuracy in well-defined tasks. We investigated whether this is also the case for diagnostics in emergency medicine, an ill-defined task environment where diagnostic errors are rife. METHODS: A computer simulation study was conducted based on empirical data from 2 published experimental studies. In the computer experiments, 285 medical students independently diagnosed 6 simulated patients arriving at the emergency room with dyspnea...
August 2017: Medical Decision Making: An International Journal of the Society for Medical Decision Making
https://www.readbyqxmd.com/read/28337689/managing-chronic-pain-in-primary-care-it-really-does-take-a-village
#15
Karen Seal, William Becker, Jennifer Tighe, Yongmei Li, Tessa Rife
Some healthcare systems are relieving primary care providers (PCPs) of "the burden" of managing chronic pain and opioid prescribing, instead offloading chronic pain management to pain specialists. Last year the Centers for Disease Control and Prevention recommended a biopsychosocial approach to pain management that discourages opioid use and promotes exercise therapy, cognitive behavioral therapy and non-opioid medications as first-line patient-centered, multi-modal treatments best delivered by an interdisciplinary team...
August 2017: Journal of General Internal Medicine
https://www.readbyqxmd.com/read/28336175/the-academic-industrial-complex-navigating-the-translational-and-cultural-divide
#16
REVIEW
Stephen Freedman, Kevin Mullane
In general, the fruits of academic discoveries can only be realized through joint efforts with industry. However, the poor reproducibility of much academic research has damaged credibility and jeopardized translational efforts that could benefit patients. Meanwhile, journals are rife with articles bemoaning the limited productivity and increasing costs of the biopharmaceutical industry and its resultant predilection for mergers and reorganizations while decreasing internal research efforts. The ensuing disarray and uncertainty has created tremendous opportunities for academia and industry to form even closer ties, and to embrace new operational and financial models to their joint benefit...
March 20, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/28242753/sequencing-errors-rife-in-genome-databases
#17
(no author information available yet)
Low-frequency genetic variants in cancer genome datasets are often simply artifacts of DNA damage introduced by routine sample preparation, not tumor-driving mutations. A new algorithm found that around three quarters of all the samples in The Cancer Genome Atlas contain large numbers of these sequencing errors.
April 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28235883/ethical-questions-identified-in-a-study-of-local-and-expatriate-responders-perspectives-of-vulnerability-in-the-2010-haiti-earthquake
#18
Evelyne Durocher, Ryoa Chung, Christiane Rochon, Jean-Hugues Henrys, Catherine Olivier, Matthew Hunt
BACKGROUND: Situations of disaster that prompt international humanitarian responses are rife with ethical tensions. The 2010 Haiti earthquake caused great destruction and prompted a massive humanitarian response. The widespread needs experienced by the population and the scale of the response inevitably rendered priority-setting difficult, and gave rise to ethical challenges. PURPOSE: This paper presents four ethical questions identified in the analysis of a study on vulnerability and equity in the humanitarian response to the 2010 Haiti earthquake...
February 24, 2017: Journal of Medical Ethics
https://www.readbyqxmd.com/read/28211601/biogeography-of-nodulated-legumes-and-their-nitrogen-fixing-symbionts
#19
REVIEW
Janet I Sprent, Julie Ardley, Euan K James
Contents I. II. III. IV. V. VI. VII. VIII. References SUMMARY: In the last decade, analyses of both molecular and morphological characters, including nodulation, have led to major changes in our understanding of legume taxonomy. In parallel there has been an explosion in the number of genera and species of rhizobia known to nodulate legumes. No attempt has been made to link these two sets of data or to consider them in a biogeographical context. This review aims to do this by relating the data to the evolution of the two partners: it highlights both longitudinal and latitudinal trends and considers these in relation to the location of major land masses over geological time...
February 17, 2017: New Phytologist
https://www.readbyqxmd.com/read/28125645/gbs-based-deconvolution-of-the-surviving-north-american-collection-of-cold-hardy-kiwifruit-actinidia-spp-germplasm
#20
Arthur T O Melo, Robert S Guthrie, Iago Hale
Plant germplasm collections can be invaluable resources to plant breeders, provided they are well-characterized. After 140 years of acquisition and curation efforts by a wide and largely non-coordinated array of private and institutional actors, the current US collection of cold-hardy kiwifruit (Actinidia spp.) is rife with misclassifications, misnomers, and mix-ups. To facilitate the systematic improvement and resource-efficient curation of these species of long-recognized horticultural potential, we used genotyping-by-sequencing (GBS) data to deconvolute this historic collection...
2017: PloS One
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