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https://www.readbyqxmd.com/read/28092811/towards-the-structure-of-the-tir-domain-signalosome
#1
REVIEW
Surekha Nimma, Thomas Ve, Simon J Williams, Bostjan Kobe
TIR (Toll/interleukin-1 receptor/resistance protein) domains feature in animal, plant and bacterial proteins involved in innate immunity pathways and associated processes. They function through protein:protein interactions, in particular self-association and homotypic association with other TIR domains. Structures of TIR domains from all phyla have been determined, but common association modes have only emerged for plant and bacterial TIR domains, and not for mammalian TIR domains. Numerous attempts involving hybrid approaches, which have combined structural, computational, mutagenesis and biophysical data, have failed to converge onto common models of how these domains associate and function...
January 13, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28091525/a-fibrolytic-potential-in-the-human-ileum-mucosal-microbiota-revealed-by-functional-metagenomic
#2
Orlane Patrascu, Fabienne Béguet-Crespel, Ludovica Marinelli, Emmanuelle Le Chatelier, Anne-Laure Abraham, Marion Leclerc, Christophe Klopp, Nicolas Terrapon, Bernard Henrissat, Hervé M Blottière, Joël Doré, Christel Béra-Maillet
The digestion of dietary fibers is a major function of the human intestinal microbiota. So far this function has been attributed to the microorganisms inhabiting the colon, and many studies have focused on this distal part of the gastrointestinal tract using easily accessible fecal material. However, microbial fermentations, supported by the presence of short-chain fatty acids, are suspected to occur in the upper small intestine, particularly in the ileum. Using a fosmid library from the human ileal mucosa, we screened 20,000 clones for their activities against carboxymethylcellulose and xylans chosen as models of the major plant cell wall (PCW) polysaccharides from dietary fibres...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28088302/the-cyp79a1-catalyzed-conversion-of-tyrosine-to-e-p-hydroxyphenylacetaldoxime-unravelled-using-an-improved-method-for-homology-modeling
#3
Dario Vazquez-Albacete, Marco Montefiori, Stefan Kol, Mohammed Saddik Motawia, Birger Lindberg Møller, Lars Olsen, Morten H H Nørholm
The vast diversity and membrane-bound nature of plant P450s makes it challenging to study the structural characteristics of this class of enzymes especially with respect to accurate intermolecular enzyme-substrate interactions. To address this problem we here apply a modified hybrid structure strategy for homology modeling of plant P450s. This allows for structural elucidation based on conserved motifs in the protein sequence and secondary structure predictions. We modeled the well-studied Sorghum bicolor cytochrome P450 CYP79A1 catalyzing the first step in the biosynthesis of the cyanogenic glucoside dhurrin...
January 11, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28087663/evolution-and-structural-diversification-of-nictaba-like-lectin-genes-in-food-crops-with-a-focus-on-soybean-glycine-max
#4
Sofie Van Holle, Pierre Rougé, Els J M Van Damme
BACKGROUND AND AIMS: The Nictaba family groups all proteins that show homology to Nictaba, the tobacco lectin. So far, Nictaba and an Arabidopsis thaliana homologue have been shown to be implicated in the plant stress response. The availability of more than 50 sequenced plant genomes provided the opportunity for a genome-wide identification of Nictaba-like genes in 15 species, representing members of the Fabaceae, Poaceae, Solanaceae, Musaceae, Arecaceae, Malvaceae and Rubiaceae. Additionally, phylogenetic relationships between the different species were explored...
January 12, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#5
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28081359/benzoic-acid-enhances-embryo-implantation-through-lif-dependent-expression-of-integrin-%C3%AE-v%C3%AE-3-and-%C3%AE-v%C3%AE-5
#6
Hee-Jung Choi, Tae-Wook Chung, Mi-Ju Park, Hyung Sik Kim, Sooseong You, Myeong Soo Lee, Bo Sun Joo, Kyu Sup Lee, Keuk-Jun Kim, Gabbine Wee, Choong-Yong Kim, Cheorl-Ho Kim, Ki-Tae Ha
The embryo implantation is crucial step for successful pregnancy. Diverse factors including adhesion molecules, growth factors, and cytokines are important to the embryo implantation through improving endometrial receptivity. Benzoic acid (BA), a component of various plants, has been shown to have anti-fungal and anti-oxidant effects. However, the effect of BA on the embryo implantation remains unknown. Here, we showed the contribution of BA for the enhancement of endometrial receptivity through the leukemia inhibitory factor (LIF)-dependent increase of integrin αV, β3, and β5 expression...
January 12, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28081202/characterization-and-functional-analysis-of-five-mads-box-b-class-genes-related-to-floral-organ-identification-in-tagetes-erecta
#7
Ye Ai, Chunling Zhang, Yalin Sun, Weining Wang, Yanhong He, Manzhu Bao
According to the floral organ development ABC model, B class genes specify petal and stamen identification. In order to study the function of B class genes in flower development of Tagetes erecta, five MADS-box B class genes were identified and their expression and putative functions were studied. Sequence comparisons and phylogenetic analyses indicated that there were one PI-like gene-TePI, two euAP3-like genes-TeAP3-1 and TeAP3-2, and two TM6-like genes-TeTM6-1 and TeTM6-2 in T. erecta. Strong expression levels of these genes were detected in stamens of the disk florets, but little or no expression was detected in bracts, receptacles or vegetative organs...
2017: PloS One
https://www.readbyqxmd.com/read/28080984/modelling-coffee-leaf-rust-risk-in-colombia-with-climate-reanalysis-data
#8
Daniel P Bebber, Ángela Delgado Castillo, Sarah J Gurr
Many fungal plant diseases are strongly controlled by weather, and global climate change is thus likely to have affected fungal pathogen distributions and impacts. Modelling the response of plant diseases to climate change is hampered by the difficulty of estimating pathogen-relevant microclimatic variables from standard meteorological data. The availability of increasingly sophisticated high-resolution climate reanalyses may help overcome this challenge. We illustrate the use of climate reanalyses by testing the hypothesis that climate change increased the likelihood of the 2008-2011 outbreak of Coffee Leaf Rust (CLR, Hemileia vastatrix) in Colombia...
December 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28078746/a-gly65val-substitution-in-an-actin-ghact_li1-disrupts-cell-polarity-and-f-actin-organization-resulting-in-dwarf-lintless-cotton-plants
#9
Gregory N Thyssen, David D Fang, Rickie B Turley, Christopher B Florane, Ping Li, Christopher P Mattison, Marina Naoumkina
Actin polymerizes to form part of the cytoskeleton and organize polar growth in all eukaryotic cells. Species with numerous actin genes are especially useful for the dissection of actin molecular function due to redundancy and neofunctionalization. Here, we investigated the role of a cotton (Gossypium hirsutum) actin gene in the organization of actin filaments in lobed cotyledon pavement cells and the highly-elongated single-celled trichomes that comprise cotton lint fibers. Using mapping-by-sequencing, virus-induced gene silencing, and molecular modeling, we identified the causative mutation of the dominant dwarf Ligon-lintless Li1 short fiber mutant as a single Gly65Val amino acid substitution in a polymerization domain of an actin gene, GhACT_LI1 (Gh_D04G0865)...
January 12, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28074936/hygroscopic-motions-of-fossil-conifer-cones
#10
Simon Poppinga, Nikolaus Nestle, Andrea Šandor, Bruno Reible, Tom Masselter, Bernd Bruchmann, Thomas Speck
Conifer cones represent natural, woody compliant structures which move their scales as passive responses to changes in environmental humidity. Here we report on water-driven opening and closing motions in coalified conifer cones from the Eemian Interglacial (approx. 126,000-113,000 years BP) and from the Middle Miocene (approx. 16.5 to 11.5 million years BP). These cones represent by far the oldest documented evidence of plant parts showing full functionality of such passive hydraulically actuated motion. The functional resilience of these structures is far beyond the biological purpose of seed dispersal and protection and is because of a low level of mineralization of the fossils...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28074042/different-clades-and-traits-yield-similar-grassland-functional-responses
#11
Elisabeth J Forrestel, Michael J Donoghue, Erika J Edwards, Walter Jetz, Justin C O du Toit, Melinda D Smith
Plant functional traits are viewed as key to predicting important ecosystem and community properties across resource gradients within and among biogeographic regions. Vegetation dynamics and ecosystem processes, such as aboveground net primary productivity (ANPP), are increasingly being modeled as a function of the quantitative traits of species, which are used as proxies for photosynthetic rates and nutrient and water-use efficiency. These approaches rely on an assumption that a certain trait value consistently confers a specific function or response under given environmental conditions...
January 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28073340/a-comparative-genomic-analysis-of-putative-pathogenicity-genes-in-the-host-specific-sibling-species-colletotrichum-graminicola-and-colletotrichum-sublineola
#12
E A S Buiate, K V Xavier, N Moore, M F Torres, M L Farman, C L Schardl, L J Vaillancourt
BACKGROUND: Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28072861/identification-of-the-molecular-clockwork-of-the-oyster-crassostrea-gigas
#13
Mickael Perrigault, Damien Tran
Molecular clock system constitutes the origin of biological rhythms that allow organisms to anticipate cyclic environmental changes and adapt their behavior and physiology. Components of the molecular clock are largely conserved across a broad range of species but appreciable diversity in clock structure and function is also present especially in invertebrates. The present work aimed at identify and characterize molecular clockwork components in relationship with the monitoring of valve activity behavior in the oyster Crassostrea gigas...
2017: PloS One
https://www.readbyqxmd.com/read/28070306/ecological-genomics-of-local-adaptation-in-cornus-florida-l-by-genotyping-by-sequencing
#14
Andrew L Pais, Ross W Whetten, Qiu-Yun Jenny Xiang
Discovering local adaptation, its genetic underpinnings, and environmental drivers is important for conserving forest species. Ecological genomic approaches coupled with next-generation sequencing are useful means to detect local adaptation and uncover its underlying genetic basis in nonmodel species. We report results from a study on flowering dogwood trees (Cornus florida L.) using genotyping by sequencing (GBS). This species is ecologically important to eastern US forests but is severely threatened by fungal diseases...
January 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28068903/comparative-transcriptome-analysis-reveals-candidate-genes-for-the-biosynthesis-of-natural-insecticide-in-tanacetum-cinerariifolium
#15
Sana Khan, Swati Upadhyay, Feroz Khan, Sudeep Tandon, Rakesh Kumar Shukla, Sumit Ghosh, Vikrant Gupta, Suchitra Banerjee, Laiq Ur Rahman
BACKGROUND: Pyrethrins are monoterpenoids and consist of either a chrysanthemic acid or pyrethric acid with a rethrolone moiety. Natural pyrethrins are safe and eco-friendly while possessing strong insecticidal properties. Despite such advantages of commercial value coming with the eco-friendly tag, most enzymes/genes involved in the pyrethrin biosynthesis pathway remain unidentified and uncharacterized. Since the flowers of Tanacetum cinerariifolium are rich in major pyrethrins, next generation transcriptome sequencing was undertaken to compare the flowers and the leaves of the plant de novo to identify differentially expressed transcripts and ascertain which among them might be involved in and responsible for the differential accumulation of pyrethrins in T...
January 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28068637/assembling-of-multifunctional-latex-based-hybrid-nanocarriers-from-calotropis-gigantea-for-sustained-doxorubicin-dox-releases
#16
Periyakaruppan Pradeepkumar, Dharman Govindaraj, Murugaraj Jeyaraj, Murugan A Munusamy, Mariappan Rajan
Natural rubber Latex (Lax) is a colloidal dispersion of polymer particles in liquid and shows good biodegradable, biocompatibility, and non-toxicity. Natural polymers are the most important materials used in food packaging, micro/nano-drug delivery, tissue engineering, agriculture, and coating. In the present study, natural compounds extracted from plant Lax were designed to function as drug carriers using various surfactants via emulation and solvent evaporation method. Calotropis gigantea belongs to the family Apocynaceae and has received considerable attention in modern medicine, ayurvedeic, siddha, and traditional medicine...
January 6, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28068355/a-methodology-for-cancer-therapeutics-by-systems-pharmacology-based-analysis-a-case-study-on-breast-cancer-related-traditional-chinese-medicines
#17
Yan Li, Jinghui Wang, Feng Lin, Yinfeng Yang, Su-Shing Chen
Breast cancer is the most common carcinoma in women. Comprehensive therapy on breast cancer including surgical operation, chemotherapy, radiotherapy, endocrinotherapy, etc. could help, but still has serious side effect and resistance against anticancer drugs. Complementary and alternative medicine (CAM) may avoid these problems, in which traditional Chinese medicine (TCM) has been highlighted. In this section, to analyze the mechanism through which TCM act on breast cancer, we have built a virtual model consisting of the construction of database, oral bioavailability prediction, drug-likeness evaluation, target prediction, network construction...
2017: PloS One
https://www.readbyqxmd.com/read/28067630/novel-swine-model-of-ricin-induced-acute-respiratory-distress-syndrome
#18
Shahaf Katalan, Reut Falach, Amir Rosner, Michael Goldvaser, Tal Brosh-Nissimov, Ayana Dvir, Avi Mizrachi, Orr Goren, Barak Cohen, Yoav Gal, Anita Sapoznikov, Sharon Ehrlich, Tamar Sabo, Chanoch Kronman
Pulmonary exposure to the plant toxin ricin, leads to respiratory insufficiency and death. To date, in-depth study of the functional disorders ensuing pulmonary intoxication, a prerequisite for establishing a clinically-relevant therapeutic protocol, is hampered by the lack of an appropriate animal model. To this end, we set up the pig, as a large animal model for the comprehensive study of the multifarious clinical manifestations of pulmonary ricinosis.Here we report for the first time, the monitoring of barometric whole body plethysmography for pulmonary function tests in non-anesthetized ricin-intoxicated pigs...
January 6, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28065919/force-of-habit-shrubs-trees-and-contingent-evolution-of-wood-anatomical-diversity-using-croton-euphorbiaceae-as-a-model-system
#19
Rafael Arévalo, Benjamin W van Ee, Ricarda Riina, Paul E Berry, Alex C Wiedenhoeft
BACKGROUND AND AIMS: Wood is a major innovation of land plants, and is usually a central component of the body plan for two major plant habits: shrubs and trees. Wood anatomical syndromes vary between shrubs and trees, but no prior work has explicitly evaluated the contingent evolution of wood anatomical diversity in the context of these plant habits. METHODS: Phylogenetic comparative methods were used to test for contingent evolution of habit, habitat and wood anatomy in the mega-diverse genus Croton (Euphorbiaceae), across the largest and most complete molecular phylogeny of the genus to date...
January 8, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28064392/chemical-composition-structural-properties-and-source-apportionment-of-organic-macromolecules-in-atmospheric-pm10-in-a-coastal-city-of-southeast-china
#20
Yanting Chen, Wenjiao Du, Jinsheng Chen, Youwei Hong, Jinping Zhao, Lingling Xu, Hang Xiao
Particulate matter (PM10) associated with the fractions of organic macromolecules, including humic acid (HA), kerogen + black carbon (KB), and black carbon (BC), was determined during summer and winter at urban and suburban sites in a coastal city of southeast China. The organic macromolecules were characterized by elemental analysis (EA), scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FTIR), and their sources were identified by using stable carbon/nitrogen isotope (δ(13)C/δ(15)N) and the Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) Model...
January 7, 2017: Environmental Science and Pollution Research International
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