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Plant function* struct* model*

Anne-Laure Chateigner-Boutin, José J Ordaz-Ortiz, Camille Alvarado, Brigitte Bouchet, Sylvie Durand, Yves Verhertbruggen, Yves Barrière, Luc Saulnier
Cell walls are comprised of networks of entangled polymers that differ considerably between species, tissues and developmental stages. The cell walls of grasses, a family that encompasses major crops, contain specific polysaccharide structures such as xylans substituted with feruloylated arabinose residues. Ferulic acid is involved in the grass cell wall assembly by mediating linkages between xylan chains and between xylans and lignins. Ferulic acid contributes to the physical properties of cell walls, it is a hindrance to cell wall degradability (thus biomass conversion and silage digestibility) and may contribute to pest resistance...
2016: Frontiers in Plant Science
Maoulida Toueni, Cécile Ben, Aurélie Le Ru, Laurent Gentzbittel, Martina Rickauer
Resistance mechanisms to Verticillium wilt are well-studied in tomato, cotton, and Arabidopsis, but much less in legume plants. Because legume plants establish nitrogen-fixing symbioses in their roots, resistance to root-attacking pathogens merits particular attention. The interaction between the soil-borne pathogen Verticillium alfalfae and the model legume Medicago truncatula was investigated using a resistant (A17) and a susceptible (F83005.5) line. As shown by histological analyses, colonization by the pathogen was initiated similarly in both lines...
2016: Frontiers in Plant Science
Luis F Aristizábal, Gabriel Moura Mascarin, Ron Cherry, Bernardo Chaves-Cordoba, Steven P Arthurs
The development of simple and reliable pest sampling programs is needed for growers to adopt economic or aesthetic injury levels. We developed a sampling plan for monitoring chilli thrips Scirtothrips dorsalis Hood populations on KnockOut shrub roses under simulated nursery conditions. The distribution of S. dorsalis among different plant structures revealed that most adults and larvae are found on foliar terminals, when compared with buds and flowers. Based on thrips distribution, the third leaf of actively growing terminals was used to determine a sequential sampling model...
October 15, 2016: Journal of Economic Entomology
Georgia Sioupouli, George Lambrinidis, Emmanuel Mikros, Sotiris Amillis, George Diallinas
NCS1 proteins are H(+) or Na(+) symporters responsible for the uptake of purines, pyrimidines or related metabolites in bacteria, fungi and some plants. Fungal NCS1 are classified into two evolutionary and structurally distinct subfamilies, known as Fur- and Fcy-like transporters. These subfamilies have expanded and functionally diversified by gene duplications. The Fur subfamily of the model fungus Aspergillus nidulans includes both major and cryptic transporters specific for uracil, 5-fluorouracil, allantoin or/and uric acid...
October 14, 2016: Molecular Microbiology
Jean-Christophe Domec, Duncan D Smith, Kate McCulloh
Here we summarize studies on the effects of elevated [CO2 ] (CO2(e) ) on the structure and function of plant hydraulic architecture, and explore the implications of those changes using a model. Changes in conduit diameter and hydraulic conductance due to CO2(e) vary among species. Ring-porous species tend toward an increase in conduit size and consequently conductivity. The effect in diffuse-porous species is much more limited. In conifers the results are mixed, some species showing minor changes in xylem structure, while other studies found increases in tracheid density and diameter...
October 14, 2016: Plant, Cell & Environment
Huiwu Tang, Xingmei Zheng, Chuliang Li, Xianrong Xie, Yuanling Chen, Letian Chen, Xiucai Zhao, Huiqi Zheng, Jiajian Zhou, Shan Ye, Jingxin Guo, Yao-Guang Liu
New gene origination is a major source of genomic innovations that confer phenotypic changes and biological diversity. Generation of new mitochondrial genes in plants may cause cytoplasmic male sterility (CMS), which can promote outcrossing and increase fitness. However, how mitochondrial genes originate and evolve in structure and function remains unclear. The rice Wild Abortive type of CMS is conferred by the mitochondrial gene WA352c (previously named WA352) and has been widely exploited in hybrid rice breeding...
October 11, 2016: Cell Research
Elena Barghini, Flavia Mascagni, Lucia Natali, Tommaso Giordani, Andrea Cavallini
Short Interspersed Nuclear Elements (SINEs) are nonautonomous retrotransposons in the genome of most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, SINE identification has been carried out only in a limited number of plant species. This lack of information is apparent especially in non-model plants whose genome has not been sequenced yet. The aim of this work was to produce a specific bioinformatics pipeline for analysing second generation sequence reads of a non-model species and identifying SINEs...
October 6, 2016: Molecular Genetics and Genomics: MGG
A V Raevsky, M Sharifi, D A Samofalova, P A Karpov, Y B Blume
Histone lysine acetylation is a reversible post-translational modification that does not involve changes in DNA sequences. Enzymes play an important role in developmental processes and their deregulation has been linked to the progression of diverse disorders. The HAT enzyme family fulfills an important role in various developmental processes mediated by the state of chromatin, and have been attributed to its deregulation. To understand acetylation mechanisms and their role in cell signaling, transcriptional regulation, and apoptosis, it is crucial to identify and analyze acetylation sites...
November 2016: Journal of Molecular Modeling
Qian-Feng Li, Min Xiong, Peng Xu, Li-Chun Huang, Chang-Quan Zhang, Qiao-Quan Liu
Brassinosteroids (BRs), essential plant-specific steroidal hormones, function in a wide spectrum of plant growth and development events, including seed germination. Rice is not only a monocotyledonous model plant but also one of the most important staple food crops of human beings. Rice seed germination is a decisive event for the next-generation of plant growth and successful seed germination is critical for rice yield. However, little is known about the molecular mechanisms on how BR modulates seed germination in rice...
October 5, 2016: Scientific Reports
Florian D Schneider, Ulrich Brose, Björn C Rall, Christian Guill
Species diversity is changing globally and locally, but the complexity of ecological communities hampers a general understanding of the consequences of animal species loss on ecosystem functioning. High animal diversity increases complementarity of herbivores but also increases feeding rates within the consumer guild. Depending on the balance of these counteracting mechanisms, species-rich animal communities may put plants under top-down control or may release them from grazing pressure. Using a dynamic food-web model with body-mass constraints, we simulate ecosystem functions of 20,000 communities of varying animal diversity...
October 5, 2016: Nature Communications
Robert J Huber, Danton H O'Day
BACKGROUND: The extracellular matrix (ECM) is a dynamic complex of glycoproteins, proteoglycans, carbohydrates, and collagen that serves as an interface between mammalian cells and their extracellular environment. Essential for normal cellular homeostasis, physiology, and events that occur during development, it is also a key functionary in a number of human diseases including cancer. The social amoeba Dictyostelium discoideum secretes an ECM during multicellular development that regulates multicellularity, cell motility, cell differentiation, and morphogenesis, and provides structural support and protective layers to the resulting differentiated cell types...
September 28, 2016: Biochimica et Biophysica Acta
Lihui Wang, Xiujuan Bei, Jiansheng Gao, Yaxuan Li, Yueming Yan, Yingkao Hu
BACKGROUND: Multidrug and toxic compound extrusion (MATE) transporter proteins are present in all organisms. Although the functions of some MATE gene family members have been studied in plants, few studies have investigated the gene expansion patterns, functional divergence, or the effects of positive selection. RESULTS: Forty-five MATE genes from rice and 56 from Arabidopsis were identified and grouped into four subfamilies. MATE family genes have similar exon-intron structures in rice and Arabidopsis; MATE gene structures are conserved in each subfamily but differ among subfamilies...
September 26, 2016: BMC Plant Biology
Aurélie Désamoré, Jairo Patiño, Patrick Mardulyn, Stuart F Mcdaniel, Florian Zanatta, Benjamin Laenen, Alain Vanderpoorten
Paleontological evidence and current patterns of angiosperm species richness suggest that European biota experienced more severe bottlenecks than North American ones during the last glacial maximum. How well this pattern fits other plant species is less clear. Bryophytes offer a unique opportunity to contrast the impact of the last glacial maximum in North America and Europe because about 60% of the European bryoflora is shared with North America. Here, we use population genetic analyses based on approximate Bayesian computation on eight amphi-Atlantic species to test the hypothesis that North American populations were less impacted by the last glacial maximum, exhibiting higher levels of genetic diversity than European ones and ultimately serving as a refugium for the postglacial recolonization of Europe...
September 23, 2016: Molecular Ecology
Aiyatullah Shah, Nawab John Dar, Qazi Parvaiz Hassan, Muzamil Ahmad
Neurodegeneration is progressive loss of functional and structural integrity of the central nervous system. Neurodegenerative disorders are yet without any reliable therapy because the neurons of the central nervous system have limited ability to regenerate. Current therapeutic approaches rely mainly on abrogation of symptoms and leave the dying neurons to their fate. Protective and/or rescuing treatments need to be explored fully to suppress neuronal death that will automatically alleviate the symptoms. Adequate precedent exists in literature regarding the neuroprotective activity of endophytes...
September 19, 2016: CNS & Neurological Disorders Drug Targets
Pranay Srivastava, Rajesh Singh Yadav
Neurodegenerative disorders represent clusters of serious diseases that results in progressive deterioration of normal structure and physiology of central nervous system. Pathophysiology of Alzheimer's, Parkinson's or other neurodegenerative disorders involves multifaceted permutation of genetic and environmental factors. Combinations of lifestyle modification linked with environmental factor jointly or alone represent the largest share of cases of these disorders. Etiology of such neuronal degeneration involves manifestation of toxic reaction in the form of functional anomalies leading to dysfunction of the ubiquitin-proteasome system, activated inflammatory cascade, compromised neuronal survival pathway, mitochondrial dysfunction and finally neuronal apoptosis/necrosis and cell death...
2016: Advances in Neurobiology
Vidya Pawar, Axel Poulet, Gwénaëlle Détourné, Christophe Tatout, Emmanuel Vanrobays, David E Evans, Katja Graumann
This paper describes the characterisation of a new family of higher plant nuclear envelope-associated proteins (NEAPs) that interact with other proteins of the nuclear envelope. In the model plant Arabidopsis thaliana, the family consists of three genes expressed ubiquitously (AtNEAP1-3) and a pseudogene (AtNEAP4). NEAPs consist of extensive coiled-coil domains, followed by a nuclear localisation signal and a C-terminal predicted transmembrane domain. Domain deletion mutants confirm the presence of a functional nuclear localisation signal and transmembrane domain...
October 2016: Journal of Experimental Botany
Tomasz Nodzyński, Steffen Vanneste, Marta Zwiewka, Markéta Pernisová, Jan Hejátko, Jiří Friml
Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and thus directional cell-to-cell transport. Regardless of the developmental importance of PINs the structure of these transporters is poorly characterised. Here, we present experimental data concerning protein topology of plasma membrane-localised PINs. Utilizing techniques based on pH-dependant quenching of fluorescent reporters combined with immunolocalization techniques we mapped PIN membrane topology cross-validating our results using available topology modelling software...
September 10, 2016: Molecular Plant
Ji Eun Kim, Jun Go, Eun Kyoung Koh, Sung Hwa Song, Ji Eun Sung, Hyun Ah Lee, Young Hee Lee, Jin Tae Hong, Dae Youn Hwang
Several natural products containing tannins are used as traditional medicines for treatment of constipation; however, their pharmacological mechanism is not well understood. The laxative effects of gallotannin-enriched extract isolated from Galla Rhois (GEGR) were investigated using a constipation model induced by loperamide (Lop) injection. After analysis for antioxidant activity of GEGR, alterations in the excretion parameters, histological structure, mucin secretion, and related protein levels were measured in the transverse colon of Sprague Dawley (SD) rats with Lop-induced constipation following treatment with 250, 500 and 1,000 mg/ml of GEGR...
2016: PloS One
Jung Ro Lee, Xiaoyuan Xie, Kailu Yang, Junjie Zhang, Sang Yeol Lee, Dorothy E Shippen
Telomeres are the essential nucleoprotein structures that provide a physical cap for the ends of linear chromosomes. The highly conserved CST (CTC1/STN1/TEN1) protein complex facilitates telomeric DNA replication and promotes telomere stability. Here we report three unexpected properties of Arabidopsis thaliana TEN1 that indicate it possesses functions distinct from other previously characterized telomere proteins. First, we show that telomeres in ten1 mutants are highly sensitive to thermal stress. Heat shock causes abrupt and dramatic loss of telomeric DNA in ten1 plants, likely via deletional recombination...
September 8, 2016: Plant Cell
Mesfin T Gebremikael, Hanne Steel, David Buchan, Wim Bert, Stefaan De Neve
The role of soil fauna in crucial ecosystem services such as nutrient cycling remains poorly quantified, mainly because of the overly reductionistic approach adopted in most experimental studies. Given that increasing nitrogen inputs in various ecosystems influence the structure and functioning of soil microbes and the activity of fauna, we aimed to quantify the role of the entire soil nematode community in nutrient mineralization in an experimental set-up emulating nutrient-rich field conditions and accounting for crucial interactions amongst the soil microbial communities and plants...
2016: Scientific Reports
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