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https://www.readbyqxmd.com/read/29165610/gramene-2018-unifying-comparative-genomics-and-pathway-resources-for-plant-research
#1
Marcela K Tello-Ruiz, Sushma Naithani, Joshua C Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J Geniza, Yinping Jiao, Young Koung Lee, Bo Wang, Joseph Mulvaney, Kapeel Chougule, Justin Elser, Noor Al-Bader, Sunita Kumari, James Thomason, Vivek Kumar, Daniel M Bolser, Guy Naamati, Electra Tapanari, Nuno Fonseca, Laura Huerta, Haider Iqbal, Maria Keays, Alfonso Munoz-Pomer Fuentes, Amy Tang, Antonio Fabregat, Peter D'Eustachio, Joel Weiser, Lincoln D Stein, Robert Petryszak, Irene Papatheodorou, Paul J Kersey, Patti Lockhart, Crispin Taylor, Pankaj Jaiswal, Doreen Ware
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29164368/3d-reconstruction-of-endoplasmic-reticulum-in-a-hydrocarbon-secreting-green-alga-botryococcus-braunii-race-b
#2
Reiko Suzuki, Ichiro Nishii, Shigeru Okada, Tetsuko Noguchi
Based on 3D sections through cells of Botryococcus braunii, the structure of three domains of endoplasmic reticulum, and their spatial and functional relationships to other organelles are clarified. Oil production by photosynthetic microalgae has attracted attention since these oils can be converted into renewable, carbon-neutral fuels. The green alga B. braunii accumulates large amounts of hydrocarbons, 30-50% of cell dry weight, in extracellular spaces rather than its cytoplasm. To advance the knowledge of hydrocarbon biosynthesis and transport pathways in this alga, we utilized transmission EM combined with rapid freezing and image reconstruction...
November 22, 2017: Planta
https://www.readbyqxmd.com/read/29156572/assembly-of-the-cutin-polyester-from-cells-to-extracellular-cell-walls
#3
REVIEW
Bénédicte Bakan, Didier Marion
Cuticular matrices covering aerial plant organs or delimiting compartments in these organs are composed of an insoluble hydrophobic polymer of high molecular mass, i.e., cutin, that encompass some cell wall polysaccharides and is filled by waxes. Cutin is a polyester of hydroxy and-or epoxy fatty acids including a low amount of glycerol. Screening of Arabidopsis and more recently of tomato (Solanum lycopersicum) mutants allowed the delineation of the metabolic pathway involved in the formation of cutin monomers, as well as their translocation in the apoplast...
November 18, 2017: Plants (Basel, Switzerland)
https://www.readbyqxmd.com/read/29154940/ebulin-rp-a-novel-member-of-the-ebulin-gene-family-with-low-cytotoxicity-as-a-result-of-deficient-sugar-binding-domains
#4
Rosario Iglesias, J Miguel Ferreras, Antimo Di Maro, Lucía Citores
BACKGROUND: Sambucus ebulus is a rich source of ribosome-inactivating proteins (RIPs) and RIP-related lectins generated from multiple genes. These proteins differ in their structure, enzymatic activity and sugar binding specificity. METHODS: We have purified and characterized ebulin-RP from S. ebulus leaves and determined the amino acid sequence by cDNA cloning. Cytotoxicity was studied in a variety of cancer cells and a comparative study of the ability of ebulin-RP to bind sugars using "in vitro" and "in silico" approaches was performed...
November 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29149288/overexpression-of-seipin1-increases-oil-in-hydroxy-fatty-acid-accumulating-seeds
#5
Daniel Lunn, James G Wallis, John Browse
While plant oils are an important source of food, plants also produce oils containing specialized fatty acids with chemical and physical properties valued in industry. Ricinoleic acid, a hydroxy-fatty acid (HFA) produced in the seed of castor (Ricinus communis), is of particular value with a wide range of applications. Since castor cultivation is currently successful only in tropic climates, and because castor seed contain the toxin ricin, there are ongoing efforts to develop a temperate crop capable of HFA biosynthesis...
November 15, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29140084/characterization-of-a-ugt84-family-glycosyltransferase-provides-new-insights-into-substrate-binding-and-reactivity-of-galloylglucose-ester-forming-ugts
#6
Alexander E Wilson, Xiaoxue Feng, Nadia N Ono, Doron Holland, Rachel Amir, Li Tian
Galloylated plant specialized metabolites play important roles in plant-environment interactions as well as the promotion of human and animal health. The galloylation reactions are mediated by the formation of galloylglucose esters from gallic acid and UDP-glucose, catalyzed by the plant UGT84 family glycosyltransferases. To explore and exploit the structural determinants of UGT84 activities, we performed homology modeling and substrate docking of PgUGT84A23, a galloylglucose ester-forming family 84 UGT, as well as sequence comparisons of PgUGT84A23 with other functionally characterized plant UGTs...
November 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/29138829/resveratrol-ameliorates-inflammatory-damage-and-protects-against-osteoarthritis-in-a-rat-model-of-osteoarthritis
#7
Yulong Wei, Jie Jia, Xin Jin, Wei Tong, Hongtao Tian
Resveratrol is a non‑flavonoid polyphenol compound with a stilbene structure. As a type of phytoalexin produced under stress in plants, it improves the plant's resistance against pathogens and environment deterioration, and performs important functions beneficial to human health, such as anti‑cancer, anti‑oxidation, regulating blood lipid levels and prolonging life span. The effects of resveratrol were examined in a rat model of osteoarthritis (OA) and observed to ameliorate inflammatory damage and protect against OA...
November 13, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29134738/fungal-community-reveals-less-dispersal-limitation-and-potentially-more-connected-network-than-that-of-bacteria-in-bamboo-forest-soils
#8
Xian Xiao, Yuting Liang, Sai Zhou, Shunyao Zhuang, Bo Sun
A central aim of current microbial ecology research is to investigate the mechanisms shaping the assembly of soil microbial communities. Despite the importance of bacterial and fungal mediation of carbon cycling in forest ecosystems, knowledge concerning their distribution patterns and underlying mechanisms remains insufficient. Here, soils were sampled from six bamboo forests across the main planting area of Moso bamboo in southern China. The bacterial and fungal diversities were assessed by sequencing 16S rRNA and ITS gene amplicons, respectively, with an Illumina MiSeq...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134140/genome-wide-identification-and-characterization-of-gras-transcription-factors-in-tomato-solanum-lycopersicum
#9
Yiling Niu, Tingting Zhao, Xiangyang Xu, Jingfu Li
Solanum lycopersicum, belonging to Solanaceae, is one of the commonly used model plants. The GRAS genes are transcriptional regulators, which play a significant role in plant growth and development, and the functions of several GRAS genes have been recognized, such as, axillary shoot meristem formation, radial root patterning, phytohormones (gibberellins) signal transduction, light signaling, and abiotic/biotic stress; however, only a few of these were identified and functionally characterized. In this study, a gene family was analyzed comprehensively with respect to phylogeny, gene structure, chromosomal localization, and expression pattern; the 54 GRAS members were screened from tomato by bioinformatics for the first time...
2017: PeerJ
https://www.readbyqxmd.com/read/29133911/species-pool-distributions-along-functional-trade-offs-shape-plant-productivity-diversity-relationships
#10
Loïc Chalmandrier, Camille Albouy, Loïc Pellissier
Grasslands deliver the resources for food production and are among the most biologically diverse ecosystems. These characteristics are often in conflict as increasing yield through fertilization can lead to biodiversity loss. Thus, the challenge in grassland management is to sustain both yield and diversity. Biodiversity-ecosystem functioning experiments typically reveal a positive relationship between manipulated species diversity and productivity. In contrast, observations of the effect of increasing productivity via fertilization suggest a negative association with biodiversity...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29132315/comprehensive-genomic-analysis-of-the-cngc-gene-family-in-brassica-oleracea-novel-insights-into-synteny-structures-and-transcript-profiles
#11
Kaleem U Kakar, Zarqa Nawaz, Khadija Kakar, Essa Ali, Abdulwareth A Almoneafy, Raqeeb Ullah, Xue-Liang Ren, Qing-Yao Shu
BACKGROUND: The cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this gene family has not been performed in Brassica oleracea, an important vegetable crop and genomic model organism. RESULTS: In present study, we identified 26 CNGC genes in B. oleracea genome, which are non-randomly localized on eight chromosomes, and classified into four major (I-IV) and two sub-groups (i...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29131478/gene-isolation-using-degenerate-primers-targeting-protein-motif-a-laboratory-exercise
#12
Brandon Pei Hui Yeo, Lian Chee Foong, Sheh May Tam, Vivian Lee, Siaw San Hwang
Structures and functions of protein motifs are widely included in many biology-based course syllabi. However, little emphasis is placed to link this knowledge to applications in biotechnology to enhance the learning experience. Here, the conserved motifs of nucleotide binding site-leucine rich repeats (NBS-LRR) proteins, successfully used for the isolation and characterization of many plant resistance gene analogues (RGAs), is featured in the development of a series of laboratory experiments using important molecular biology techniques...
November 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29126135/habitat-modification-by-the-leaf-cutter-ant-atta-cephalotes-and-patterns-of-leaf-litter-arthropod-communities
#13
Rachel L Wells, Serena K Murphy, Matthew D Moran
Ecosystem engineers are profoundly important in many biological communities. A Neotropical taxonomic group considered to have engineering effects is the Formicidae (ants). Leaf-cutter ants (LCAs), in particular, which form extensive colonies of millions of individuals, can be important ecosystem engineers in these environments. While the effects of LCAs on plant community structure and soil chemistry are well-studied, their effects on consumers are poorly understood. Therefore, we examined the indirect effects of the LCA Atta cephalotes L...
November 4, 2017: Environmental Entomology
https://www.readbyqxmd.com/read/29120516/carbon-cycle-confidence-and-uncertainty-exploring-variation-among-soil-biogeochemical-models
#14
William R Wieder, Melannie D Hartman, Benjamin Sulman, Ying-Ping Wang, Charles D Koven, Gordon B Bonan
Emerging insights into factors responsible for soil organic matter stabilization and decomposition are being applied in a variety of contexts, but new tools are needed to facilitate the understanding, evaluation and improvement of soil biogeochemical theory and models at regional to global scales. To isolate the effects of model structural uncertainty on the global distribution of soil carbon stocks and turnover times we developed a soil biogeochemical testbed that forces three different soil models with consistent climate and plant productivity inputs...
November 9, 2017: Global Change Biology
https://www.readbyqxmd.com/read/29119916/cytoprotective-polyphenols-against-chronological-skin-aging-and-cutaneous-photodamage
#15
Sergio Davinelli, Juan Carlos Bertoglio, Ascanio Polimeni, Giovanni Scapagnini
BACKGROUND: Skin aging is a complex biological process influenced by a combination of intrinsic and extrinsic factors, leading to cumulative alterations of skin structure, function and appearance. Polyphenols, which are secondary plant metabolites, represent one of the largest classes of compounds used in dermatology and nutricosmetics to combat skin aging. The main objective is to provide an overview of the existing literature linking skin aging and the ability of polyphenols as regulatory elements able to maintain skin homeostasis...
November 8, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/29115619/administration-of-chlorogenic-acid-alleviates-spinal-cord-injury-via-tlr4-nf%C3%A2-%C3%AE%C2%BAb-and-p38-signaling-pathway-anti%C3%A2-inflammatory-activity
#16
Dayong Chen, Dan Pan, Shaolong Tang, Zhihong Tan, Yanan Zhang, Yunfeng Fu, Guohua Lü, Qinghua Huang
Chlorogenic acid, as a secondary metabolite of plants, exhibits a variety of effects including free radical scavenging, antiseptic, anti‑inflammatory and anti‑viral, in addition to its ability to reduce blood glucose, protect the liver and act as an anti‑hyperlipidemic agent and cholagogue. The present study demonstrated that administration of chlorogenic acid alleviated spinal cord injury (SCI) via anti‑inflammatory activity mediated by nuclear factor (NF)‑κB and p38 signaling pathways. Wistar rats were used to structure a SCI model rat to explore the effects of administration of chlorogenic acid on SCI...
November 6, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29109147/structural-and-dynamical-characterization-of-the-ph-dependence-of-the-pectin-methylesterase-pectin-methylesterase-inhibitor-complex
#17
Fabien Senechal, Olivier Habrylo, Ludivine Hocq, Jean-Marc Domon, Paulo Marcelo, Valérie Lefebvre, Jerome Pelloux, Davide Mercadante
Pectin methylesterases (PMEs) catalyze the demethylesterification of pectin, one of the main polysaccharides in the plant cell wall, and are of critical importance in plant development. PME activity generates highly negatively charged pectin and mutates the physiochemical properties of the plant cell wall in such that remodeling of the plant cell can occur. PMEs are therefore tightly regulated by proteinaceous inhibitors (PMEIs) some of which become active upon changes in cellular pH. <br /><br />Nevertheless, a detailed picture of how this pH-dependent inhibition of PME occurs at the molecular level is missing...
November 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29106606/increased-affinity-for-rna-targets-evolved-early-in-animal-and-plant-dicer-lineages-through-different-structural-mechanisms
#18
Haiyan Jia, Oralia Kolaczkowski, James Rolland, Bryan Kolaczkowski
Understanding the structural basis for evolutionary changes in protein function is central to molecular evolutionary biology and can help determine the extent to which functional convergence occurs through similar or different structural mechanisms. Here, we combine ancestral sequence reconstruction with functional characterization and structural modeling to directly examine the evolution of sequence-structure-function across the early differentiation of animal and plant Dicer/DCL proteins, which perform the first molecular step in RNA interference by identifying target RNAs and processing them into short interfering products...
July 5, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29096605/genome-wide-identification-and-expression-analysis-of-calmodulin-like-cml-genes-in-chinese-cabbage-brassica-rapa-l-ssp-pekinensis
#19
Shanshan Nie, Minjuan Zhang, Lugang Zhang
BACKGROUND: Calmodulin-like (CML) proteins are a primary family of plant-specific Ca(2+) sensors that specifically bind to Ca(2+) and deliver a Ca(2+) signal. CML proteins have been identified and characterized in many plant species, such as the model plant Arabidopsis and rice. Based on considerable evidence, the roles of CML proteins are crucial in plant growth and development and in the response to various external stimuli. Nevertheless, the characterization and expression profiling of CML genes in Chinese cabbage (Brassica rapa L...
November 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29077763/spatial-temporal-dynamics-of-neotropical-velvet-ant-hymenoptera-mutillidae-communities-along-a-forest-savanna-gradient
#20
Júlio Miguel Alvarenga, Cecília Rodrigues Vieira, Leandro Braga Godinho, Pedro Henrique Campelo, James Purser Pitts, Guarino Rinaldi Colli
Understanding how and why biological communities are organized over space and time is a major challenge and can aid biodiversity conservation in times of global changes. Herein, spatial-temporal variation in the structure of velvet ant communities was examined along a forest-savanna gradient in the Brazilian Cerrado to assess the roles of environmental filters and interspecific interactions upon community assembly. Velvet ants were sampled using 25 arrays of Y-shaped pitfall traps with drift fences for one year along an environmental gradient from cerrado sensu stricto (open canopy, warmer, drier) to cerradão (closed canopy, cooler, moister)...
2017: PloS One
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