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J J Zhao, Y L Zhang, S J Zhang, J Zhou, F K Yu, Y L Zu, H F Zhao, Z Li, Y P Song
Objective: To investigate the molecular-cytogenetic characterization and impact on tyrosine kinase inhibitors (TKIs) therapy in chronic phase of chronic myeloid leukemia (CML-CP) patients with variant Ph chromosome (vPh). Methods: The clinical data of 32 patients with vPh chromosomes were collected and compared with 703 patients with typical Ph chromosome in newly diagnosed CML-CP who were on first-line imatinib (IM) and with BCR-ABL transcript of P210. Results: There was no significant difference in demographic and hematological characteristics between vPh and classic Ph patients...
March 14, 2018: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
J Feng, X Y Gong, Y J Jia, K Q Liu, Y Li, X B Dong, Q Y Fang, K Ru, Q H Li, H J Wang, X L Zhao, Y N Jia, Y Song, Z Tian, M Wang, K J Tang, J X Wang, Y C Mi
Objective: To investigate the spectrum of gene mutations in adult patients with B-acute lymphoblastic leukemia (B-ALL), and to analyze the influences of different gene mutations on prognosis. Methods: DNA samples from 113 adult B-ALL patients who administered from June 2009 to September 2015 were collected. Target-specific next generation sequencing (NGS) approach was used to analyze the mutations of 112 genes (focused on the specific mutational hotspots) and all putative mutations were compared against multiple databases to calculate the frequency spectrum...
February 14, 2018: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
A J Christensen, Venkatraman Srinivasan, John C Hart, Amy Marshall-Colon
Sustainable crop production is a contributing factor to current and future food security. Innovative technologies are needed to design strategies that will achieve higher crop yields on less land and with fewer resources. Computational modeling coupled with advanced scientific visualization enables researchers to explore and interact with complex agriculture, nutrition, and climate data to predict how crops will respond to untested environments. These virtual observations and predictions can direct the development of crop ideotypes designed to meet future yield and nutritional demands...
March 17, 2018: Nutrition Reviews
Véronique Hugouvieux, Catarina S Silva, Agnès Jourdain, Arnaud Stigliani, Quentin Charras, Vanessa Conn, Simon J Conn, Cristel C Carles, François Parcy, Chloe Zubieta
The MADS transcription factors (TF) constitute an ancient family of TF found in all eukaryotes that bind DNA as obligate dimers. Plants have dramatically expanded the functional diversity of the MADS family during evolution by adding protein-protein interaction domains to the core DNA-binding domain, allowing the formation of heterotetrameric complexes. Tetramerization of plant MADS TFs is believed to play a central role in the evolution of higher plants by acting as one of the main determinants of flower formation and floral organ specification...
March 19, 2018: Nucleic Acids Research
Héctor Cervera, Silvia Ambrós, Guillermo P Bernet, Guillermo Rodrigo, Santiago F Elena
Determining the fitness of viral genotypes has become a standard practice in virology as it is essential to evaluate their evolutionary potential. Darwinian fitness, defined as the advantage of a given genotype with respect to a reference, is a complex property that captures, in a single figure, differences in performance at every stage of viral infection. To what extent does viral fitness result from specific molecular interactions with host factors and regulatory networks during infection? Can we identify host genes in functional classes whose expression depends on viral fitness? Here, we compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyvirus (TEV) that differ in fitness...
March 19, 2018: Molecular Biology and Evolution
Joel A Boyd, Ben J Woodcroft, Gene W Tyson
Large-scale metagenomic datasets enable the recovery of hundreds of population genomes from environmental samples. However, these genomes do not typically represent the full diversity of complex microbial communities. Gene-centric approaches can be used to gain a comprehensive view of diversity by examining each read independently, but traditional pairwise comparison approaches typically over-classify taxonomy and scale poorly with increasing metagenome and database sizes. Here we introduce GraftM, a tool that uses gene specific packages to rapidly identify gene families in metagenomic data using hidden Markov models (HMMs) or DIAMOND databases, and classifies these sequences using placement into pre-constructed gene trees...
March 19, 2018: Nucleic Acids Research
Adam Wright, Pamela M Neri, Skye Aaron, Thu-Trang T Hickman, Francine L Maloney, Daniel A Solomon, Dustin McEvoy, Angela Ai, Kevin Kron, Gianna Zuccotti
Background: Microbiology laboratory results are complex and cumbersome to review. We sought to develop a new review tool to improve the ease and accuracy of microbiology results review. Methods: We observed and informally interviewed clinicians to determine areas in which existing microbiology review tools were lacking. We developed a new tool that reorganizes microbiology results by time and organism. We conducted a scenario-based usability evaluation to compare the new tool to existing legacy tools, using a balanced block design...
March 17, 2018: Journal of the American Medical Informatics Association: JAMIA
Arthur Aronson
The spore coat of Bacilli is a relatively complex structure comprised of about 70 species of proteins in 2 or 3 layers. While some are involved in assembly or protection, the regulation of many are not well defined so lacZ transcriptional fusions were constructed to six Bacillus anthracis spore coat genes in order to gain insight into their possible functions. The genes were selected on the basis of the location of the encoded proteins within the coat and distribution among spore forming species. Conditions tested were temperature and media either as solid or liquid...
March 17, 2018: FEMS Microbiology Letters
Parminder Raina, Anne Gilsing, Heinz Freisling, Edwin van den Heuvel, Nazmul Sohel, Mazda Jenab, Pietro Ferrari, Anne Tjønneland, Vassiliki Benetou, Susan Picavet, Sture Eriksson, Ben Schöttker, Hermann Brenner, Kai-Uwe Saum, Laura Perna, Tom Wilsgaard, Antonia Trichopoulou, Paolo Boffetta, Lauren E Griffith
Background: The number of older people living with cancer and cardio-metabolic conditions is increasing but little is known about how specific combinations of these conditions impact mortality. Methods: A total of 22,692 participants aged 65 years and older from four international cohorts were followed-up for mortality for an average of 10 years (8,596 deaths). Data were harmonized across cohorts and mutually exclusive groups of disease combinations were created for cancer, MI, stroke, and diabetes at baseline...
March 19, 2018: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
Ulrike Bechtold, John N Ferguson, Philip M Mullineaux
The emergence of Arabidopsis as a model species and the availability of genetic and genomic resources have resulted in the identification and detailed characterisation of abiotic stress signalling pathways. However, this has led only to limited success in engineering abiotic stress tolerance in crops. This is because there needs to be a deeper understanding in how to combine resistances to a range of stresses with growth and productivity. The natural variation and genomic resources of Arabidopsis thaliana (Arabidopsis) is a great asset to understand the mechanisms of multiple stress tolerances...
March 17, 2018: Journal of Experimental Botany
Haijun Xiao, Yanghong Xu, Chenzi Ni, Qiannan Zhang, Feiya Zhong, Jishuai Huang, Wei Liu, Leilei Peng, Yingguo Zhu, Jun Hu
In flowering plants, various RNA editing events occur in the mitochondria and chloroplasts as part of post-transcriptional processes. Although several PPRs and MORFs have been identified as RNA editing factors, the underlying mechanism of PPRs and the cooperation among these proteins are still obscure. Here, we identified a rice dual-localized PPR protein, OsPGL1. The loss of function of OsPGL1 resulted in defects in both chloroplast RNA editing of ndhD-878 and mitochondrial RNA editing of ccmFc-543, both of which could be restored via complementary validation...
March 17, 2018: Journal of Experimental Botany
Heitor S P de Souza, Claudio Fiocchi
Despite unquestionable progress in the management of inflammatory bowel disease (IBD) and the much improved clinical results achievable today in Crohn's disease (CD) and ulcerative colitis (UC) patients, the overall therapeutic outcome remains far from optimal. The main reason of this partial success is that all current medications only block individual components of a highly complex disease process that results from the integration of multiple and incompletely identified pathogenic components. Thus, if further progress is to be achieved in IBD therapeutics and we want to move from the current success rate to nearly 100%, bold new ideas must be entertained and new approaches put into practice...
March 19, 2018: Inflammatory Bowel Diseases
Bruno Leite Rodrigues, Luís Fernando Carvalho-Costa, Israel de Souza Pinto, José Manuel Macário Rebêlo
Sand fly (Diptera: Psychodidae) taxonomy is complex and time-consuming, which hampers epidemiological efforts directed toward controlling leishmaniasis in endemic regions such as northeastern Brazil. Here, we used a fragment of the mitochondrial cytochrome c oxidase I (COI) gene to identify sand fly species in Maranhão State (northeastern Brazil) and to assess cryptic diversity occurring at different spatial scales. For this, we obtained 148 COI sequences of 15 sand fly species (10 genera) from Maranhão (fine spatial scale), and joined them to COI sequences from other Brazilian localities (distant about 2,000 km from Maranhão, broad spatial scale) available in GenBank...
March 17, 2018: Journal of Medical Entomology
Penny J Tricker, Abdeljalil ElHabti, Jessica Schmidt, Delphine Fleury
Drought and heat stress cause losses in wheat productivity in major growing regions worldwide, and both the occurrence and the severity of these events is likely to increase with global climate change. Water deficits and high temperatures frequently occur simultaneously at sensitive growth stages, reducing wheat yields by reducing grain number or weight. Although genetic variation and underlying quantitative trait loci for either individual stress are known, the combination of the two stresses has rarely been studied...
March 17, 2018: Journal of Experimental Botany
Evan M Zhao, Yanfei Zhang, Justin Mehl, Helen Park, Makoto A Lalwani, Jared E Toettcher, José L Avalos
The optimization of engineered metabolic pathways requires careful control over the levels and timing of metabolic enzyme expression. Optogenetic tools are ideal for achieving such precise control, as light can be applied and removed instantly without complex media changes. Here we show that light-controlled transcription can be used to enhance the biosynthesis of valuable products in engineered Saccharomyces cerevisiae. We introduce new optogenetic circuits to shift cells from a light-induced growth phase to a darkness-induced production phase, which allows us to control fermentation with only light...
March 21, 2018: Nature
Neha Maurya, Mehraj Ud Din Parray, Jitendra Kumar Maurya, Amit Kumar, Rajan Patel
The binding nature of amphiphilic drugs viz. promethazine hydrochloride (PMT) and adiphenine hydrochloride (ADP), with human hemoglobin (Hb) was unraveled by fluorescence, absorbance, time resolved fluorescence, fluorescence resonance energy transfer (FRET) and circular dichroism (CD) spectral techniques in combination with molecular docking and molecular dynamic simulation methods. The steady state fluorescence spectra indicated that both PMT and ADP quenches the fluorescence of Hb through static quenching mechanism which was further confirmed by time resolved fluorescence spectra...
March 11, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Karl Kuntzelman, L Jack Rhodes, Lillian N Harrington, Vladimir Miskovic
There is a broad family of statistical methods for capturing time series regularity, with increasingly widespread adoption by the neuroscientific community. A common feature of these methods is that they permit investigators to quantify the entropy of brain signals - an index of unpredictability/complexity. Despite the proliferation of algorithms for computing entropy from neural time series data there is scant evidence concerning their relative stability and efficiency. Here we evaluated several different algorithmic implementations (sample, fuzzy, dispersion and permutation) of multiscale entropy in terms of their stability across sessions, internal consistency and computational speed, accuracy and precision using a combination of electroencephalogram (EEG) and synthetic 1/ƒ noise signals...
March 18, 2018: Brain and Cognition
Youn Jung Choi, James W Bowman, Jae U Jung
Hosts respond to viral infection by expressing interferon-stimulated genes, of which IFITs are potent inhibitors of viral RNA translation. Johnson et al. (2018) solved the structure of the IFIT1-IFIT3 complex bound cap 0 RNA and explored their concerted antiviral activity.
March 20, 2018: Immunity
Dale I Godfrey, Jérôme Le Nours, Daniel M Andrews, Adam P Uldrich, Jamie Rossjohn
Most studies on the immunotherapeutic potential of T cells have focused on CD8 and CD4 T cells that recognize peptide antigens (Ag) presented by polymorphic major histocompatibility complex (MHC) class I and MHC class II molecules, respectively. However, unconventional T cells, which interact with MHC class Ib and MHC-I like molecules, are also implicated in tumor immunity, although their role therein is unclear. These include unconventional T cells targeting MHC class Ib molecules such as HLA-E and its murine ortholog Qa-1b, natural killer T (NKT) cells, mucosal associated invariant T (MAIT) cells, and γδ T cells...
March 20, 2018: Immunity
Lukas M von Ziegler, Nathalie Selevsek, Ry Y Tweedie-Cullen, Eloïse Kremer, Isabelle M Mansuy
The hippocampal formation is a brain structure essential for higher-order cognitive functions. It has a complex anatomical organization and cellular composition, and hippocampal subregions have different properties and functional roles. In this study, we used SWATH-MS to determine whether the proteomes of hippocampus areas CA1 and CA3 can explain the commonalities or specificities of these subregions in basal conditions and after recognition memory. We show that the proteomes of areas CA1 and CA3 are largely different in basal conditions and that differential changes and dynamics in protein expression are induced in these areas after recognition of an object or object location...
March 20, 2018: Cell Reports
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