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https://www.readbyqxmd.com/read/28214450/in-silico-structural-and-functional-analysis-of-mesorhizobium-acc-deaminase
#1
Krishnendu Pramanik, Tithi Soren, Soumik Mitra, Tushar Kanti Maiti
Nodulation is one of the very important processes of legume plants as it is the initiating event of fixing nitrogen. Although ethylene has essential role in normal plant metabolism but it has also negative impact on plants particularly in nodule formation in legume plants. It is also produced due to a variety of biotic or abiotic stresses. 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase is a rhizobial enzyme which cleaves ACC (immediate precursor of ethylene) into α-ketobutyrate and ammonia. As a result, the level of ethylene from the plant cells is decreased and the negative impact of ethylene on nodule formation is reduced...
February 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28213686/the-iswi-remodeler-in-plants-protein-complexes-biochemical-functions-and-developmental-roles
#2
REVIEW
Dongjie Li, Jie Liu, Wu Liu, Guang Li, Zhongnan Yang, Peng Qin, Lin Xu
Imitation Switch (ISWI) is a member of the ATP-dependent chromatin remodeling factor family, whose members move or restructure nucleosomes using energy derived from ATP hydrolysis. ISWI proteins are conserved in eukaryotes and usually form complexes with DDT (DNA-binding homeobox and different transcription factors)-domain proteins. Here, we review recent research on ISWI in the model plant Arabidopsis thaliana (AtISWI). AtISWI forms complexes with AtDDT-domain proteins, many of which have domain structures that differ from those of DDT-domain proteins in yeast and animals...
February 17, 2017: Chromosoma
https://www.readbyqxmd.com/read/28211331/sulfamethoxazole-and-cod-increase-abundance-of-sulfonamide-resistance-genes-and-change-bacterial-community-structures-within-sequencing-batch-reactors
#3
Xueping Guo, Weihai Pang, Chunling Dou, Daqiang Yin
The abundant microbial community in biological treatment processes in wastewater treatment plants (WWTPs) may potentially enhance the horizontal gene transfer of antibiotic resistance genes with the presence of antibiotics. A lab-scale sequencing batch reactor was designed to investigate response of sulfonamide resistance genes (sulI, sulII) and bacterial communities to various concentrations of sulfamethoxazole (SMX) and chemical oxygen demand (COD) of wastewater. The SMX concentrations (0.001 mg/L, 0.1 mg/L and 10 mg/L) decreased with treatment time and higher SMX level was more difficult to remove...
February 1, 2017: Chemosphere
https://www.readbyqxmd.com/read/28207822/identification-classification-and-transcription-profiles-of-the-b-type-response-regulator-family-in-pear
#4
Junbei Ni, Songling Bai, Ling Gao, Minjie Qian, Linbing Zhong, Yuanwen Teng
Type-B response regulators (B-RRs) are transcription factors that function in the final step of two-component signaling systems. In model plants, B-RRs have been shown to play important roles in cytokinin signal transduction. However, the functions of B-RRs in pear have not been well studied. In this report, we conducted a genome-wide analysis and identified 11 putative genes encoding B-PpRR proteins based on the published genome sequence of Pyrus bretschneideri. A phylogenetic tree of the B-PpRR family was constructed, and the motif distribution, chromosome localization, and gene structure of B-PpRR family genes were determined...
2017: PloS One
https://www.readbyqxmd.com/read/28198676/global-transcriptome-analysis-reveals-extensive-gene-remodeling-alternative-splicing-and-differential-transcription-profiles-in-non-seed-vascular-plant-selaginella-moellendorffii
#5
Yan Zhu, Longxian Chen, Chengjun Zhang, Pei Hao, Xinyun Jing, Xuan Li
BACKGROUND: Selaginella moellendorffii, a lycophyte, is a model plant to study the early evolution and development of vascular plants. As the first and only sequenced lycophyte to date, the genome of S. moellendorffii revealed many conserved genes and pathways, as well as specialized genes different from flowering plants. Despite the progress made, little is known about long noncoding RNAs (lncRNA) and the alternative splicing (AS) of coding genes in S. moellendorffii. Its coding gene models have not been fully validated with transcriptome data...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28197167/vviaprt3-and-vvifsex-two-genes-involved-in-sex-specification-able-to-distinguish-different-flower-types-in-vitis
#6
João L Coito, Miguel J N Ramos, Jorge Cunha, Helena G Silva, Sara Amâncio, Maria M R Costa, Margarida Rocheta
Vitis vinifera vinifera is a hermaphrodite subspecies, while its ancestor, Vitis vinifera sylvestris, is dioecious. We have identified two genes that together allow the discrimination between male, female and hermaphrodite Vitis plants. The sex locus region on chromosome 2 was screened resulting in the discovery of a new gene, VviFSEX. The same screening revealed another gene, VviAPRT3, located in the sex region, that be used as a sex marker. Both genes are good candidates to be involved in flower sex differentiation in grapevine...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28190466/the-total-triterpenoid-saponins-of-xanthoceras-sorbifolia-improve-learning-and-memory-impairments-through-against-oxidative-stress-and-synaptic-damage
#7
Xue-Fei Ji, Tian-Yan Chi, Peng Liu, Lu-Yi Li, Ji-Kai Xu, Qian Xu, Li-Bo Zou, Da-Li Meng
BACKGROUND: X. sorbifolia is a widely cultivated ecologicalcrop in the north of China which is used to produce biodiesel fuel. It also possesses special medicinal value and has attracted keen interests of researchers to explore its bioactivity. PURPOSE: To extract the total triterpenoid saponins from the husk of X. sorbifolia (TSX) and investigate its effects on Alzheimer's disease (AD). STUDY DESIGN: TSX was prepared via modern extraction techniques...
February 15, 2017: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
https://www.readbyqxmd.com/read/28181244/plant-functional-traits-and-canopy-structure-control-the-relationship-between-photosynthetic-co2-uptake-and-far-red-sun-induced-fluorescence-in-a-mediterranean-grassland-under-different-nutrient-availability
#8
Mirco Migliavacca, Oscar Perez-Priego, Micol Rossini, Tarek S El-Madany, Gerardo Moreno, Christiaan van der Tol, Uwe Rascher, Anna Berninger, Verena Bessenbacher, Andreas Burkart, Arnaud Carrara, Francesco Fava, Jin-Hong Guan, Tiana W Hammer, Kathrin Henkel, Enrique Juarez-Alcalde, Tommaso Julitta, Olaf Kolle, M Pilar Martín, Talie Musavi, Javier Pacheco-Labrador, Andrea Pérez-Burgueño, Thomas Wutzler, Sönke Zaehle, Markus Reichstein
Sun-induced fluorescence (SIF) in the far-red region provides a new noninvasive measurement approach that has the potential to quantify dynamic changes in light-use efficiency and gross primary production (GPP). However, the mechanistic link between GPP and SIF is not completely understood. We analyzed the structural and functional factors controlling the emission of SIF at 760 nm (F760 ) in a Mediterranean grassland manipulated with nutrient addition of nitrogen (N), phosphorous (P) or nitrogen-phosphorous (NP)...
February 9, 2017: New Phytologist
https://www.readbyqxmd.com/read/28177687/curcumin-protects-neuronal-cells-against-status-epilepticus-induced-hippocampal-damage-through-induction-of-autophagy-and-inhibition-of-necroptosis
#9
Jin Wang, Yuan Liu, Xiao-Hui Li, Xiang-Chang Zeng, Jian Li, Jun Zhou, Bo Xiao, Kai Hu
Status epilepticus, the most severe form of epilepsy, is characterized by progressive functional and structural damage in the hippocampus, ultimately leading to the development and clinical appearance of spontaneous, recurrent seizures. Though the pathogenesis underlying epileptogenesis processes remains unclear, a substantial body of evidence has shown that status epilepticus acts as an important initial factor in triggering epileptogenesis. Notably, besides classical cell death mechanisms such as apoptosis and necrosis, two novel regulators of cell fate known as necroptosis and autophagy, are demonstrated to be involved in neuronal damage in various neurodegenerative and neuropsychiatric disorders...
December 9, 2016: Canadian Journal of Physiology and Pharmacology
https://www.readbyqxmd.com/read/28177216/bacterioferritin-structure-dynamics-and-protein-protein-interactions-at-play-in-iron-storage-and-mobilization
#10
Mario Rivera
Despite its essentiality to life, iron presents significant challenges to cells: the exceedingly low solubility of Fe(3+) limits its bioavailability, and the reactivity of Fe(2+) toward H2O2 is a source of the toxic hydroxyl radical (HO(•)). Consequently, cellular levels of free iron are highly regulated to ensure sufficiency while preventing iron-induced toxicity. Relatively little is known about the fate of iron in the bacterial cytosol or how cells balance the need for relatively high cytosolic iron concentrations with the potential toxicity of the nutrient...
February 8, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28174680/structural-evidence-for-arabidopsis-glutathione-transferase-atgstf2-functioning-as-a-transporter-of-small-organic-ligands
#11
Laziana Ahmad, Elizabeth L Rylott, Neil C Bruce, Robert Edwards, Gideon Grogan
Glutathione transferases (GSTs) are involved in many processes in plant biochemistry, with their best characterised role being the detoxification of xenobiotics through their conjugation with glutathione. GSTs have also been implicated in noncatalytic roles, including the binding and transport of small heterocyclic ligands such as indole hormones, phytoalexins and flavonoids. Although evidence for ligand binding and transport has been obtained using gene deletions and ligand binding studies on purified GSTs, there has been no structural evidence for the binding of relevant ligands in noncatalytic sites...
February 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28166763/how-anthropogenic-changes-may-affect-soil-borne-parasite-diversity-plant-parasitic-nematode-communities-associated-with-olive-trees-in-morocco-as-a-case-study
#12
Nadine Ali, Johannes Tavoillot, Guillaume Besnard, Bouchaib Khadari, Ewa Dmowska, Grażyna Winiszewska, Odile Fossati-Gaschignard, Mohammed Ater, Mohamed Aït Hamza, Abdelhamid El Mousadik, Aïcha El Oualkadi, Abdelmajid Moukhli, Laila Essalouh, Ahmed El Bakkali, Elodie Chapuis, Thierry Mateille
BACKGROUND: Plant-parasitic nematodes (PPN) are major crop pests. On olive (Olea europaea), they significantly contribute to economic losses in the top-ten olive producing countries in the world especially in nurseries and under cropping intensification. The diversity and the structure of PPN communities respond to environmental and anthropogenic forces. The olive tree is a good host plant model to understand the impact of such forces on PPN diversity since it grows according to different modalities (wild, feral and cultivated olives)...
February 6, 2017: BMC Ecology
https://www.readbyqxmd.com/read/28161893/identification-and-characterization-of-a-stable-intermediate-in-photosystem-i-assembly-in-tobacco
#13
Gal Wittenberg, Sari Järvi, Marta Hojka, Szilvia Z Tóth, Etienne H Meyer, Eva-Mari Aro, Mark Aurel Schöttler, Ralph Bock
PSI is the most efficient bioenergetic nanomachine in nature and one of the largest membrane protein complexes known. It is composed of 18 protein subunits that bind more than 200 co-factors and prosthetic groups. While the structure and function of PSI have been studied in great detail, very little is known about the PSI assembly process. In this work, we have characterized a PSI assembly intermediate in tobacco plants, which we named PSI*. We found PSI* to contain only a specific subset of the core subunits of PSI...
February 5, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28158264/recognition-of-prokaryotic-and-eukaryotic-promoters-using-convolutional-deep-learning-neural-networks
#14
Ramzan Kh Umarov, Victor V Solovyev
Accurate computational identification of promoters remains a challenge as these key DNA regulatory regions have variable structures composed of functional motifs that provide gene-specific initiation of transcription. In this paper we utilize Convolutional Neural Networks (CNN) to analyze sequence characteristics of prokaryotic and eukaryotic promoters and build their predictive models. We trained a similar CNN architecture on promoters of five distant organisms: human, mouse, plant (Arabidopsis), and two bacteria (Escherichia coli and Bacillus subtilis)...
2017: PloS One
https://www.readbyqxmd.com/read/28149162/artificial-root-foraging-optimizer-algorithm-with-hybrid-strategies
#15
Yang Liu, Junfei Liu, Lianbo Ma, Liwei Tian
In this work, a new plant-inspired optimization algorithm namely the hybrid artificial root foraging optimizion (HARFO) is proposed, which mimics the iterative root foraging behaviors for complex optimization. In HARFO model, two innovative strategies were developed: one is the root-to-root communication strategy, which enables the individual exchange information with each other in different efficient topologies that can essentially improve the exploration ability; the other is co-evolution strategy, which can structure the hierarchical spatial population driven by evolutionary pressure of multiple sub-populations that ensure the diversity of root population to be well maintained...
February 2017: Saudi Journal of Biological Sciences
https://www.readbyqxmd.com/read/28145590/molecular-modeling-and-dynamic-simulation-of-arabidopsis-thaliana-carotenoid-cleavage-dioxygenase-gene-a-comparison-with-bixa-orellana-and-crocus-sativus
#16
Priya R, Sneha P, Renata Rivera Madrid, George Priya Doss C, Pooja Singh, Siva Ramamoorthy
Carotenoid cleavage dioxygenase (CCD) gene, ubiquitously found in numerous types of plants, are eminent in synthesizing the various volatile compounds (β-ionone, C13 -norisoprenoid, geranylacetone) known as apocarotenoids. These apocarotenoids have various biological functions such as volatile signals, allelopathic interaction and plant defense. In Arabidopsis genome sequence, four potential CCD genes have been identified namely CCD1, CCD4, CCD7, and CCD8. These four genes give rise to diverse biological functions with almost similar sequence identity...
February 1, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28135760/landscape-scale-gpp-and-carbon-density-inform-patterns-and-impacts-of-an-invasive-tree-across-wet-forests-of-hawaii
#17
Jomar M Barbosa, Gregory P Asner, R Flint Hughes, M Tracy Johnson
Plant invasion typically occurs within a landscape-scale framework of abiotic and biotic conditions, often resulting in emergent feedbacks among environment, ecosystem functions, and the dominance of invasive species. Understanding the mechanisms underlying successful invasions is an important component of conservation and management efforts, but this has been poorly investigated in a spatially explicit manner. Knowing where and why invasion patterns change throughout the landscape enables managers to use context-specific controls on the spread of invasive species...
October 3, 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28135022/structural-overshoot-of-tree-growth-with-climate-variability-and-the-global-spectrum-of-drought-induced-forest-dieback
#18
Alistair S Jump, Paloma Ruiz-Benito, Sarah Greenwood, Craig D Allen, Thomas Kitzberger, Rod Fensham, Jordi Martínez-Vilalta, Francisco Lloret
Ongoing climate change poses significant threats to plant function and distribution. Increased temperatures and altered precipitation regimes amplify drought frequency and intensity, elevating plant stress and mortality. Large-scale forest mortality events will have far-reaching impacts on carbon and hydrological cycling, biodiversity, and ecosystem services. However, biogeographical theory and global vegetation models poorly represent recent forest die-off patterns. Furthermore, since trees are sessile and long-lived, their responses to climate extremes are substantially dependent on historical factors...
January 30, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28131339/review-epistasis-and-dominance-in-the-emergence-of-catalytic-function-as-exemplified-by-the-evolution-of-plant-terpene-synthases
#19
REVIEW
Jitender Cheema, Juan A Faraldos, Paul E O'Maille
Epistasis, the interaction between mutations and the genetic background, is a pervasive force in evolution that is difficult to predict yet derives from a simple principle - biological systems are interconnected. Therefore, one effect may be intimately linked to another, hence interdependent. Untangling epistatic interactions between and within genes is a vibrant area of research. Deriving a mechanistic understanding of epistasis is a major challenge. Particularly, elucidating how epistasis can attenuate the effects of otherwise dominant mutations that control phenotypes...
February 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28130300/proteins-with-chad-domains-conserved-histidine-%C3%AE-helical-domain-are-attached-to-polyphosphate-polyp-granules-in-vivo-and-constitute-a-novel-family-of-polyp-associated-proteins-phosins
#20
Tony Tumlirsch, Dieter Jendrossek
: Based on bioinformatic evidence, we suspected that proteins with a CYTH domain (CyaB thiamine tri-phosphatase) and/or a CHAD motif (conserved-histidine-α-helical-domain) could represent polyP granule-associated proteins. No evidence for a polyP-targeting function was found for proteins with CYTH domains. By contrast, the two CHAD motif-containing proteins of Ralstonia eutropha H16 (A0104 and B1017) co-localized with polyP granules when they were expressed as fusions with the enhanced-yellow-fluorescent-protein (eYFP)...
January 27, 2017: Applied and Environmental Microbiology
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