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https://www.readbyqxmd.com/read/28931093/synthesis-of-udp-apiose-in-bacteria-the-marine-phototroph-geminicoccus-roseus-and-the-plant-pathogen-xanthomonas-pisi
#1
James Amor Smith, Maor Bar-Peled
The branched-chain sugar apiose was widely assumed to be synthesized only by plant species. In plants, apiose-containing polysaccharides are found in vascularized plant cell walls as the pectic polymers rhamnogalacturonan II and apiogalacturonan. Apiosylated secondary metabolites are also common in many plant species including ancestral avascular bryophytes and green algae. Apiosyl-residues have not been documented in bacteria. In a screen for new bacterial glycan structures, we detected small amounts of apiose in methanolic extracts of the aerobic phototroph Geminicoccus roseus and the pathogenic soil-dwelling bacteria Xanthomonas pisi...
2017: PloS One
https://www.readbyqxmd.com/read/28931073/bacterial-and-diazotrophic-diversities-of-endophytes-in-dendrobium-catenatum-determined-through-barcoded-pyrosequencing
#2
Ou Li, Rong Xiao, Lihua Sun, Chenglin Guan, Dedong Kong, Xiufang Hu
As an epiphyte orchid, Dendrobium catenatum relies on microorganisms for requisite nutrients. Metagenome pyrosequencing based on 16S rRNA and nifH genes was used to characterize the bacterial and diazotrophic communities associated with D. catenatum collected from 5 districts in China. Based on Meta-16S rRNA sequencing, 22 bacterial phyla and 699 genera were identified, distributed as 125 genera from 8 phyla and 319 genera from 10 phyla shared by all the planting bases and all the tissues, respectively. The predominant Proteobacteria varied from 71...
2017: PloS One
https://www.readbyqxmd.com/read/28931057/challenges-and-advances-for-transcriptome-assembly-in-non-model-species
#3
Arnaud Ungaro, Nicolas Pech, Jean-François Martin, R J Scott McCairns, Jean-Philippe Mévy, Rémi Chappaz, André Gilles
Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence)...
2017: PloS One
https://www.readbyqxmd.com/read/28931056/heterogeneity-in-the-expression-and-subcellular-localization-of-polyol-monosaccharide-transporter-genes-in-lotus-japonicus
#4
Lu Tian, Leru Liu, Yehu Yin, Mingchao Huang, Yanbo Chen, Xinlan Xu, Pingzhi Wu, Meiru Li, Guojiang Wu, Huawu Jiang, Yaping Chen
Polyols can serve as a means for the translocation of carbon skeletons and energy between source and sink organs as well as being osmoprotective solutes and antioxidants which may be involved in the resistance of some plants to biotic and abiotic stresses. Polyol/Monosaccharide transporter (PLT) proteins previously identified in plants are involved in the loading of polyols into the phloem and are reported to be located in the plasma membrane. The functions of PLT proteins in leguminous plants are not yet clear...
2017: PloS One
https://www.readbyqxmd.com/read/28931004/the-logic-of-the-floral-transition-reverse-engineering-the-switch-controlling-the-identity-of-lateral-organs
#5
Jean-Louis Dinh, Etienne Farcot, Charlie Hodgman
Much laboratory work has been carried out to determine the gene regulatory network (GRN) that results in plant cells becoming flowers instead of leaves. However, this also involves the spatial distribution of different cell types, and poses the question of whether alternative networks could produce the same set of observed results. This issue has been addressed here through a survey of the published intercellular distribution of expressed regulatory genes and techniques both developed and applied to Boolean network models...
September 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28930140/identification-of-phlogacantholide-c-as-a-novel-adam10-enhancer-from-traditional-chinese-medicinal-plants
#6
Myriam Meineck, Florian Schuck, Sara Abdelfatah, Thomas Efferth, Kristina Endres
Background: Alzheimer's disease is one of the most prevalent dementias in the elderly population with increasing numbers of patients. One pivotal hallmark of this disorder is the deposition of protein aggregates stemming from neurotoxic amyloid-beta peptides. Synthesis of those peptides has been efficiently prevented in AD model mice by activation of an enzyme called alpha-secretase. Therefore, drugs with the capability to increase the expression of this enzyme, named ADAM10, have been suggested as a valuable therapeutic medication...
December 5, 2016: Medicines (Basel, Switzerland)
https://www.readbyqxmd.com/read/28929670/-herbgenomics
#7
Shi-Lin Chen, Jing-Yuan Song
Traditional Chinese medicine (TCM) has contributad greatly to improving human health. However, the biological characteristics and molecular mechanisms of TCM in the treatment of human diseases remain largely unknown. Genomics plays an important role in modern medicine and biology. Here, we introduce genomics and other related omics to the study of herbs to propose a new discipline, Herbgenomics, that aims to uncover the genetic information and regulatory networks of herbs and to clarify their molecular mechanisms in the prevention and treatment of human diseases...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28929648/-cloning-and-expression-analysis-of-tocopherol-cyclase-gene-in-carthamus-tinctorius
#8
Li-Li Guan, Qi Cui, Yu-Tong Han, Yun-Yun Wu, Ren-Ge Hu, Tian-Yao Gu, Hai-Yan Li, Xiao-Kun Li
The tocopherol cyclase was one of the key enzymes in plant vitamin E biosynthesis pathway. According to the study of Carthamus tinctorius transcriptome data,the Tocopherol cyclase gene was obtained using RT-PCR techniques and named CtTC . Bioinformatics analysis showed theopen reading frame (ORF)of CtTC was 1 524 bp. The putative protein contained 507 amino acids with a predicted molecular mass of 62.9 kDa and theoretically isoelectric point was 5.01.Signal peptide analysis showed that it was a non secretory protein, and there was no signal peptide...
October 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28929638/interactions-of-wrky15-and-wrky33-transcription-factors-and-their-roles-in-the-resistance-of-oilseed-rape-to-sclerotinia-infection
#9
Fei Liu, Xiaoxia Li, Meirong Wang, Jing Wen, Bin Yi, Jinxiong Shen, Chaozhi Ma, Tingdong Fu, Jinxing Tu
WRKY transcription factors are known to participate in the defense responses of higher plants. However, little is known about the roles of such proteins, especially regarding their functions in the resistance of oilseed rape (Brassica napus) to Sclerotinia sclerotiorum, a necrotrophic fungal pathogen that causes stem rot. In the present study, we identified BnWRKY33 as a S. sclerotiorum-responsive gene that positively regulates resistance to this pathogen by enhancing the expression of genes involved in camalexin synthesis and genes regulated by salicylic acid (SA) and jasmonic acid (JA)...
September 20, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28929469/chondrocyte-expansion-is-associated-with-loss-of-primary-cilia-and-disrupted-hedgehog-signalling
#10
C L Thompson, J C Plant, A K Wann, C L Bishop, P Novak, H M Mitchison, P L Beales, J P Chapple, M M Knight
Tissue engineering-based therapies targeting cartilage diseases, such as osteoarthritis, require in vitro expansion of articular chondrocytes. A major obstacle for these therapies is the dedifferentiation and loss of phenotype accompanying chondrocyte expansion. Recent studies suggest that manipulation of hedgehog signalling may be used to promote chondrocyte re-differentiation. Hedgehog signalling requires the primary cilium, a microtubule-based signalling compartment, the integrity of which is linked to the cytoskeleton...
September 20, 2017: European Cells & Materials
https://www.readbyqxmd.com/read/28929329/somatic-health-effects-of-chernobyl-30-years-on
#11
REVIEW
Maureen Hatch, Elisabeth Cardis
2016 marked the 30th anniversary of the Chernobyl Nuclear Power Plant accident. We and others wrote reviews for the 25th anniversary. Since then, additional papers have appeared and it seems timely to highlight lessons learned. To present, not a systematic review, but a commentary drawing attention to notable findings. We include not only recent reports and updates on previous results, but key findings from prior Chernobyl studies. The dose-dependent increase in Papillary Thyroid Cancer (PTC) following childhood I-131 exposure in Ukraine and Belarus has now been shown to persist for decades...
September 19, 2017: European Journal of Epidemiology
https://www.readbyqxmd.com/read/28929273/complete-genome-sequence-of-a-novel-lytic-bacteriophage-isolated-from-ralstonia-solanacearum
#12
Jingfang Su, Hongwei Sun, Junjie Liu, Zhaokui Guo, Guoquan Fan, Gang Gu, Guanghua Wang
A lytic podophage RSPI1 was isolated from tobacco field soil collected in Fujian Province, South China using host bacterium Ralstonia solanacearum Tb15-14. Whole genome sequencing of this phage was performed using the high-throughput Ion Torrent PGM Sequencer. The complete genome of RSPI1 was 43,211 bp in length with a mean DNA G + C content of 61.5%. A total of 48 open reading frames were identified with lengths ranging from 132 bp to 5,061 bp, of which, 11, 12 and 25 were identified as functional, structural and unknown genes, respectively...
September 19, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28929212/an-insight-into-phage-diversity-at-environmental-habitats-using-comparative-metagenomics-approach
#13
Krupa Parmar, Nishant Dafale, Rajesh Pal, Hitesh Tikariha, Hemant Purohit
Bacteriophages play significant role in driving microbial diversity; however, little is known about the diversity of phages in different ecosystems. A dynamic predator-prey mechanism called "kill the winner" suggests the elimination of most active bacterial populations through phages. Thus, interaction between phage and host has an effect on the composition of microbial communities in ecosystems. In this study, secondary phage metagenome data from aquatic habitats: wastewater treatment plant (WWTP), fresh, marine, and hot water spring habitat were analyzed using MG-RAST and STAMP tools to explore the diversity of the viruses...
September 19, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28929021/allele-specific-expression-and-methylation-in-the-bumblebee-bombus-terrestris
#14
Zoë Lonsdale, Kate Lee, Maria Kiriakidu, Harindra Amarasinghe, Despina Nathanael, Catherine J O'Connor, Eamonn B Mallon
The social hymenoptera are emerging as models for epigenetics. DNA methylation, the addition of a methyl group, is a common epigenetic marker. In mammals and flowering plants methylation affects allele specific expression. There is contradictory evidence for the role of methylation on allele specific expression in social insects. The aim of this paper is to investigate allele specific expression and monoallelic methylation in the bumblebee, Bombus terrestris. We found nineteen genes that were both monoallelically methylated and monoallelically expressed in a single bee...
2017: PeerJ
https://www.readbyqxmd.com/read/28928963/recent-advances-in-understanding-the-roles-of-whole-genome-duplications-in-evolution
#15
REVIEW
Carol MacKintosh, David E K Ferrier
Ancient whole-genome duplications (WGDs)- paleopolyploidy events-are key to solving Darwin's 'abominable mystery' of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally...
2017: F1000Research
https://www.readbyqxmd.com/read/28928764/exploring-and-harnessing-haplotype-diversity-to-improve-yield-stability-in-crops
#16
REVIEW
Lunwen Qian, Lee T Hickey, Andreas Stahl, Christian R Werner, Ben Hayes, Rod J Snowdon, Kai P Voss-Fels
In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28928761/hormonal-regulation-in-shade-avoidance
#17
REVIEW
Chuanwei Yang, Lin Li
At high vegetation density, shade-intolerant plants sense a reduction in the red (660 nm) to far-red (730 nm) light ratio (R/FR) in addition to a general reduction in light intensity. These light signals trigger a spectrum of morphological changes manifested by growth of stem-like tissue (hypocotyl, petiole, etc.) instead of harvestable organs (leaves, fruits, seeds, etc.)-namely, shade avoidance syndrome (SAS). Common phenotypical changes related to SAS are changes in leaf hyponasty, an increase in hypocotyl and internode elongation and extended petioles...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28928754/responses-of-plant-proteins-to-heavy-metal-stress-a-review
#18
REVIEW
Md Kamrul Hasan, Yuan Cheng, Mukesh K Kanwar, Xian-Yao Chu, Golam J Ahammed, Zhen-Yu Qi
Plants respond to environmental pollutants such as heavy metal(s) by triggering the expression of genes that encode proteins involved in stress response. Toxic metal ions profoundly affect the cellular protein homeostasis by interfering with the folding process and aggregation of nascent or non-native proteins leading to decreased cell viability. However, plants possess a range of ubiquitous cellular surveillance systems that enable them to efficiently detoxify heavy metals toward enhanced tolerance to metal stress...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28928753/peg-induces-high-expression-of-the-cell-cycle-checkpoint-gene-wee1-in-embryogenic-callus-of-medicago-truncatula-potential-link-between-cell-cycle-checkpoint-regulation-and-osmotic-stress
#19
Adel M Elmaghrabi, Hilary J Rogers, Dennis Francis, Sergio J Ochatt
Polyethylene glycol (PEG) can be used to mimic osmotic stress in plant tissue cultures to study mechanisms of tolerance. The aim of this experiment was to investigate the effects of PEG (M.W. 6000) on embryogenic callus of Medicago truncatula. Leaf explants were cultured on MS medium with 2 mg L(-1) NAA and 0.5 mg L(-1) BAP for 5 months. Then, calli were transferred to the same medium further supplemented with 10% (w/v) 6000 PEG for 6 months in order to study physiological and putative molecular markers of water stress...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28928752/climate-clever-clovers-new-paradigm-to-reduce-the-environmental-footprint-of-ruminants-by-breeding-low-methanogenic-forages-utilizing-haplotype-variation
#20
Parwinder Kaur, Rudi Appels, Philipp E Bayer, Gabriel Keeble-Gagnere, Jiankang Wang, Hideki Hirakawa, Kenta Shirasawa, Philip Vercoe, Katia Stefanova, Zoey Durmic, Phillip Nichols, Clinton Revell, Sachiko N Isobe, David Edwards, William Erskine
Mitigating methane production by ruminants is a significant challenge to global livestock production. This research offers a new paradigm to reduce methane emissions from ruminants by breeding climate-clever clovers. We demonstrate wide genetic diversity for the trait methanogenic potential in Australia's key pasture legume, subterranean clover (Trifolium subterraneum L.). In a bi-parental population the broadsense heritability in methanogenic potential was moderate (H(2) = 0.4) and allelic variation in a region of Chr 8 accounted for 7...
2017: Frontiers in Plant Science
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