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Plant function* struct* model*

Faye L Jackson, Robert J Fryer, David M Hannah, Colin P Millar, Iain A Malcolm
The thermal suitability of riverine habitats for cold water adapted species may be reduced under climate change. Riparian tree planting is a practical climate change mitigation measure, but it is often unclear where to focus effort for maximum benefit. Recent developments in data collection, monitoring and statistical methods have facilitated the development of increasingly sophisticated river temperature models capable of predicting spatial variability at large scales appropriate to management. In parallel, improvements in temporal river temperature models have increased the accuracy of temperature predictions at individual sites...
September 14, 2017: Science of the Total Environment
Pramod K Kandoth, Shiming Liu, Elizabeth Prenger, Andrew Ludwig, Naoufal Lakhssassi, Robert Heinz, Zhou Zhou, Amanda Howland, Joshua Gunther, Samantha Eidson, Andi Dhroso, Peter Lafayette, Donna Tucker, Sarah Elizabeth Johnson, James Anderson, Alaa Alaswad, Silvia Cianzio, Wayne Allen Parrott, Dmitry Korkin, Khalid Meksem, Melissa G Mitchum
Rhg4 is a major genetic locus that contributes to soybean cyst nematode (SCN) resistance in the Peking-type resistance of soybean, which also requires the rhg1 gene. By map-based cloning and functional genomic approaches, we previously showed that the Rhg4 gene encodes a predicted cytosolic serine hydroxymethyltransferase (GmSHMT08); however, the novel gain of function of GmSHMT08 in SCN resistance remains to be characterized. Using a forward genetic screen, we identified an allelic series of GmSHMT08 mutants that shed new light on the mechanistic aspects of GmSHMT08-mediated resistance...
September 14, 2017: Plant Physiology
Karl Deisseroth, Peter Hegemann
Channelrhodopsins are light-gated ion channels that, via regulation of flagellar function, enable single-celled motile algae to seek ambient light conditions suitable for photosynthesis and survival. These plant behavioral responses were initially investigated more than 150 years ago. Recently, major principles of function for light-gated ion channels have been elucidated by creating channelrhodopsins with kinetics that are accelerated or slowed over orders of magnitude, by discovering and designing channelrhodopsins with altered spectral properties, by solving the high-resolution channelrhodopsin crystal structure, and by structural model-guided redesign of channelrhodopsins for altered ion selectivity...
September 15, 2017: Science
Taiwo Olayemi Elufioye, Tomayo Ireti Berida, Solomon Habtemariam
Neuroprotection is the preservation of the structure and function of neurons from insults arising from cellular injuries induced by a variety of agents or neurodegenerative diseases (NDs). The various NDs including Alzheimer's, Parkinson's, and Huntington's diseases as well as amyotropic lateral sclerosis affect millions of people around the world with the main risk factor being advancing age. Each of these diseases affects specific neurons and/or regions in the brain and involves characteristic pathological and molecular features...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
Fabiano Jares Contesini, Marcelo Vizoná Liberato, Marcelo Ventura Rubio, Felipe Calzado, Mariane Paludetti Zubieta, Diego Mauricio Riaño Pachón, Fabio Marcio Squina, Fabricio Bracht, Munir S Skaf, André Ricardo Damásio
Carbohydrate-Active Enzymes are key enzymes for biomass-to-bioproducts conversion. α-L-Arabinofuranosidases that belong to the Glycoside Hydrolase family 62 (GH62) have important applications in biofuel production from plant biomass by hydrolyzing arabinoxylans, found in both the primary and secondary cell walls of plants. In this work, we identified a GH62 α-L-arabinofuranosidase (AnAbf62Awt) that was highly secreted when Aspergillus nidulans was cultivated on sugarcane bagasse. The gene AN7908 was cloned and transformed in A...
September 7, 2017: Biochimica et Biophysica Acta
Lloyd L Nackley, Adam G West, Andrew L Skowno, William J Bond
In the Anthropocene, alien species are no longer the only category of biological organism establishing and rapidly spreading beyond historical boundaries. We review evidence showing that invasions by native species are a global phenomenon and present case studies from Southern Africa, and elsewhere, that reveal how climate-mediated expansions of native plants into adjacent communities can emulate the functional and structural changes associated with invasions by alien plant species. We conclude that integrating native invasions into ecological practice and theory will improve mechanistic models and better inform policy and adaptive ecological management in the 21st century...
September 7, 2017: Trends in Ecology & Evolution
Xingtan Zhang, Xuequn Chen, Pingping Liang, Haibao Tang
Structural variation (SV) is a type of genetic variation identified through the comparison of genome structures which often have direct and significant associations with phenotypic variations. Building on the next generation sequencing (NGS) technologies, research on plant structural variations are gaining momentum and have revolutionized our view on the functional impact of the 'hidden' diversity that were largely understudied before. Herein, we first describe the current state of plant genomic SV research based on NGS and in particular focus on the biological insights gained from the large-scale identification of various types of plant SVs...
September 8, 2017: Current Issues in Molecular Biology
Juan G Navea, Emily Richmond, Talia Stortini, Jillian Greenspan
In this study, horizontal attenuated total reflection (HATR) Fourier-transform infrared (FT-IR) spectroscopy was combined with quartz crystal microbalance (QCM) gravimetry to investigate the adsorption isotherms of water on fly ash, a byproduct of coal combustion in power plants. Because of composition variability with the source region, water uptake was studied at room temperature as a function of relative humidity (RH) on fly ash from several regions: United States, India, The Netherlands, and Germany. The FT-IR spectra show water features growth as a function of RH, with water absorbing on the particle surface in both an ordered (ice-like) and a disordered (liquid-like) structure...
September 19, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Ying-Ping Gai, Ya-Nan Zhao, Huai-Ning Zhao, Chuan-Zhong Yuan, Shuo-Shuo Yuan, Shuo Li, Bing-Sen Zhu, Xian-Ling Ji
Biotic stresses are major constraints limiting the leaf quality and productivity of mulberry. MLX56 is a unique chitin-binding protein isolated from Shin-Ichinose (Morus alba) latex that displays toxicity against lepidopteran caterpillars. In this study, the full-length cDNA encoding MLX56 was isolated from Husang 32 (M. multicaulis) and designated HMLX56. Amino acid sequence analysis and protein modeling of three MLX56 proteins showed that they were highly conserved among Morus species. Tissue expression pattern analysis showed that the HMLX56 gene was strongly expressed in mulberry bark and leaves but only slightly expressed in fruits...
2017: Frontiers in Plant Science
Hongyun Liu, Jiajia Qin, Hui Fan, Jinjin Cheng, Lin Li, Zheng Liu
As a member of the GRAS gene family, SCARECROW-LIKE (SCL) genes encode transcriptional regulators that are involved in plant information transmission and signal transduction. In this study, 44 SCL genes including two SCARECROW genes in millet were identified to be distributed on eight chromosomes, except chromosome 6. All the millet genes contain motifs 6-8, indicating that these motifs are conserved during the evolution. SCL genes of millet were divided into eight groups based on the phylogenetic relationship and classification of Arabidopsis SCL genes...
July 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
Fabian Ries, Yvonne Carius, Marina Rohr, Karin Gries, Sandro Keller, C Roy D Lancaster, Felix Willmund
A considerably small fraction of approximately 60-100 proteins of all chloroplast proteins are encoded by the plastid genome. Many of these proteins are major subunits of complexes with central functions within plastids. In comparison with other subcellular compartments and bacteria, many steps of chloroplast protein biogenesis are not well understood. We report here on the first study of chloroplast-localised trigger factor. In bacteria, this molecular chaperone is known to associate with translating ribosomes to facilitate the folding of newly synthesized proteins...
September 6, 2017: Scientific Reports
Kensuke Kawade, Hirokazu Tanimoto, Gorou Horiguchi, Hirokazu Tsukaya
The spatial gradient of signaling molecules is pivotal for establishing developmental patterns of multicellular organisms. It has long been proposed that these gradients could arise from the pure diffusion process of signaling molecules between cells, but whether this simplest mechanism establishes the formation of the tissue-scale gradient remains unclear. Plasmodesmata are unique channel structures in plants that connect neighboring cells for molecular transport. In this study, we measured cellular- and tissue-scale kinetics of molecular transport through plasmodesmata in Arabidopsis thaliana developing leaf primordia by fluorescence recovery assays...
September 5, 2017: Biophysical Journal
Steffen Ehrmann, Jaan Liira, Stefanie Gärtner, Karin Hansen, Jörg Brunet, Sara A O Cousins, Marc Deconchat, Guillaume Decocq, Pieter De Frenne, Pallieter De Smedt, Martin Diekmann, Emilie Gallet-Moron, Annette Kolb, Jonathan Lenoir, Jessica Lindgren, Tobias Naaf, Taavi Paal, Alicia Valdés, Kris Verheyen, Monika Wulf, Michael Scherer-Lorenzen
BACKGROUND: The castor bean tick (Ixodes ricinus) transmits infectious diseases such as Lyme borreliosis, which constitutes an important ecosystem disservice. Despite many local studies, a comprehensive understanding of the key drivers of tick abundance at the continental scale is still lacking. We analyze a large set of environmental factors as potential drivers of I. ricinus abundance. Our multi-scale study was carried out in deciduous forest fragments dispersed within two contrasting rural landscapes of eight regions, along a macroclimatic gradient stretching from southern France to central Sweden and Estonia...
September 6, 2017: BMC Ecology
Khadiza Khatun, Ujjal Kumar Nath, Arif Hasan Khan Robin, Jong-In Park, Do-Jin Lee, Min-Bae Kim, Chang Kil Kim, Ki-Byung Lim, Ill Sup Nou, Mi-Young Chung
BACKGROUND: Zinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription factor family with a conserved DNA binding homeodomain and a zinc finger motif. Members of the ZHD protein family play important roles in plant growth, development, and stress responses. Genome-wide characterization of ZHD genes has been carried out in several model plants, including Arabidopsis thaliana and Oryza sativa, but not yet in tomato (Solanum lycopersicum). RESULTS: In this study, we performed the first comprehensive genome-wide characterization and expression profiling of the ZHD gene family in tomato (Solanum lycopersicum)...
September 6, 2017: BMC Genomics
Sandra M Kerbler, Nicolas L Taylor
The ability to isolate intact and functional mitochondria has greatly deepened our understanding of mitochondrial structure and function. With the advancement of molecular biology techniques and progression into omics-based research over recent decades, mitochondrial research has shifted from crop species such as wheat, pea, and potato to genetically sequenced models such as Arabidopsis thaliana and rice. Although there are many attributes that make model species particularly appealing for plant research, they are often less than ideal for conducting biochemical investigations and as such, considerable modification to mitochondrial isolation methods has been made...
2017: Methods in Molecular Biology
Simone Sello, Roberto Moscatiello, Nicoletta La Rocca, Barbara Baldan, Lorella Navazio
Photosynthetic cell suspension cultures are a useful experimental system to analyze a variety of physiological processes, bypassing the structural complexity of the plant organism in toto. Nevertheless, cell cultures containing functional chloroplasts are quite difficult to obtain, and this process is usually laborious and time-consuming. In this work a novel and rapid method to set up photosynthetic cell suspension cultures from the model plant Arabidopsis thaliana was developed. The direct germination of Arabidopsis seeds on a sucrose-containing agarized culture medium supplemented with 0...
2017: Frontiers in Plant Science
Ye Li, Tongkai Chen, Xiaoqing Miao, Xiang Yi, Xueqing Wang, Haitao Zhao, Simon Ming-Yuen Lee, Ying Zheng
The blood brain barrier (BBB) is the network of capillaries that controls the passage of substances from the blood into the brain and other parts of the central nervous system (CNS). As this barrier is the major obstacle for drug delivery into CNS, a credible BBB model is very necessary to assess the BBB permeability of novel neuroactive compounds including thousands of bioactive compounds which have been extracted from medicinal plants and have the potential for the treatment of CNS diseases. Increasing reports indicated that zebrafish has emerged as a timely, reproducible model for BBB permeability assessment...
August 31, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
Muhammad S Yahya, Muhamad Syafiq, Adham Ashton-Butt, Amal Ghazali, Siti Asmah, Badrul Azhar
Monoculture farming is pervasive in industrial oil palm agriculture, including those RSPO plantations certified as sustainably managed. This farming practice does not promote the maintenance of farmland biodiversity. However, little scientific attention has been given to polyculture farming in oil palm production landscapes. Polyculture farming is likely to increase the floristic diversity and stand structural complexity that underpins biodiversity. Mist nets were used to sample birds at 120 smallholdings in Peninsular Malaysia...
August 2017: Ecology and Evolution
Olga Otrusinová, Gabriel Demo, Petr Padrta, Zuzana Jaseňáková, Blanka Pekárová, Zuzana Gelová, Agnieszka Szmitkowska, Pavel Kadeřávek, Séverine Jansen, Milan Zachrdla, Tomáš Klumpler, Jaromír Marek, Jozef Hritz, Lubomír Janda, Hideo Iwaï, Michaela Wimmerová, Jan Hejátko, Lukáš Žídek
Multistep phosphorelay (MSP) cascades mediate responses to a wide spectrum of stimuli, including plant hormonal signaling, but several aspects of MSP await elucidation. Here, we provide first insight into the key step of MSP-mediated phosphotransfer in a eukaryotic system, the phosphorylation of the receiver domain of the histidine kinase CYTOKININ INDEPENDENT 1 (CKI1RD) from Arabidopsis thaliana We observed that the crystal structures of free, Mg(2+)-bound, and beryllofluoridated CKI1RD (a stable analog of the labile phosphorylated form) were identical and similar to the active state of receiver domains of bacterial response regulators...
August 31, 2017: Journal of Biological Chemistry
Felicity Alcock, Merel Pm Damen, Jesper Levring, Ben C Berks
The twin-arginine translocase (Tat) transports folded proteins across the bacterial cytoplasmic membrane and the plant thylakoid membrane. The Tat translocation site is formed by substrate-triggered oligomerization of the protein TatA. Walther and co-workers have proposed a structural model for the TatA oligomer in which TatA monomers self-assemble using electrostatic 'charge zippers' (Cell (2013) 132: 15945). This model was supported by in vitro analysis of the oligomeric state of TatA variants containing charge-inverting substitutions...
August 31, 2017: ELife
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