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https://www.readbyqxmd.com/read/29150511/sulfolobus-acidocaldarius-uptakes-pentoses-via-a-cut2-type-abc-transporter-and-metabolizes-them-through-the-aldolase-independent-weimberg-pathway
#1
Michaela Wagner, Lu Shen, Andreas Albersmeier, Nienke van der Kolk, Sujin Kim, Jaeho Cha, Christopher Bräsen, Jörn Kalinowski, Bettina Siebers, Sonja-Verena Albers
Sulfolobus spp. possess a great metabolic versatility and grow heterotrophically on various carbon sources such as different sugars and peptides. Known sugar transporters in Archaea predominantly belong to ABC transport systems. Although several ABC transporters for sugar uptake have been characterized in the crenarchaeon Sulfolobus solfataricus, only one homologue of these transporters, the maltose/maltooligomer transporter, could be identified in the closely related Sulfolobus acidocaldarius Comparison of the transcriptome of S...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29149845/early-nutritional-programming-affects-liver-transcriptome-in-diploid-and-triploid-atlantic-salmon-salmo-salar
#2
L M Vera, C Metochis, J F Taylor, M Clarkson, K H Skjærven, H Migaud, D R Tocher
BACKGROUND: To ensure sustainability of aquaculture, plant-based ingredients are being used in feeds to replace marine-derived products. However, plants contain secondary metabolites which can affect food intake and nutrient utilisation of fish. The application of nutritional stimuli during early development can induce long-term changes in animal physiology. Recently, we successfully used this approach to improve the utilisation of plant-based diets in diploid and triploid Atlantic salmon...
November 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29149417/spl13-regulates-shoot-branching-and-flowering-time-in-medicago-sativa
#3
Ruimin Gao, Margaret Y Gruber, Lisa Amyot, Abdelali Hannoufa
Our results show SPL13 plays a crucial role in regulating vegetative and reproductive development in Medicago sativa L. (alfalfa), and that MYB112 is targeted and downregulated by SPL13 in alfalfa. We previously showed that transgenic Medicago sativa (alfalfa) plants overexpressing microRNA156 (miR156) show a bushy phenotype, reduced internodal length, delayed flowering time, and enhanced biomass yield. In alfalfa, transcripts of seven SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, including SPL13, are targeted for cleavage by miR156...
November 17, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29149092/analysis-of-the-roles-of-the-arabidopsis-nmat2-and-pmh2-proteins-provided-with-new-insights-into-the-regulation-of-group-ii-intron-splicing-in-land-plant-mitochondria
#4
Michal Zmudjak, Sofia Shevtsov, Laure D Sultan, Ido Keren, Oren Ostersetzer-Biran
Plant mitochondria are remarkable with respect to the presence of numerous group II introns which reside in many essential genes. The removal of the organellar introns from the coding genes they interrupt is essential for respiratory functions, and is facilitated by different enzymes that belong to a diverse set of protein families. These include maturases and RNA helicases related proteins that function in group II intron splicing in different organisms. Previous studies indicate a role for the nMAT2 maturase and the RNA helicase PMH2 in the maturation of different pre-RNAs in Arabidopsis mitochondria...
November 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29146266/endophytism-or-saprophytism-decoding-the-lifestyle-transition-of-the-generalist-fungus-phomopsis-liquidambari
#5
Jun Zhou, Xin Li, Peng-Wei Huang, Chuan-Chao Dai
Filamentous ascomycete Phomopsis sp. are common inhabitants of natural ecosystems and, as saprophytes, are largely responsible for the destructive decay of litterfall, promoting the carbon and nitrogen cycles. Phomopsis liquidambari B3 can establish mutualistic symbiosis with a broad spectrum of crop plants. Colonizing dynamics observations and a growth promotion assay of rice and Arabidopsis thaliana revealed that the B3 colonization strategy is host-adapted and resulted in different growth promotions influenced by N availability...
January 2018: Microbiological Research
https://www.readbyqxmd.com/read/29145496/insights-into-soybean-transcriptome-reconfiguration-under-hypoxic-stress-functional-regulatory-structural-and-compositional-characterization
#6
Thiago J Nakayama, Fabiana A Rodrigues, Norman Neumaier, Juliana Marcolino-Gomes, Hugo B C Molinari, Thaís R Santiago, Eduardo F Formighieri, Marcos F Basso, José R B Farias, Beatriz M Emygdio, Ana C B de Oliveira, Ângela D Campos, Aluízio Borém, Frank G Harmon, Liliane M Mertz-Henning, Alexandre L Nepomuceno
Soybean (Glycine max) is one of the major crops worldwide and flooding stress affects the production and expansion of cultivated areas. Oxygen is essential for mitochondrial aerobic respiration to supply the energy demand of plant cells. Because oxygen diffusion in water is 10,000 times lower than in air, partial (hypoxic) or total (anoxic) oxygen deficiency is important component of flooding. Even when oxygen is externally available, oxygen deficiency frequently occurs in bulky, dense or metabolically active tissues such as phloem, meristems, seeds, and fruits...
2017: PloS One
https://www.readbyqxmd.com/read/29144434/the-role-of-non-coding-rnas-in-cytoplasmic-male-sterility-in-flowering-plants
#7
REVIEW
Helena Štorchová
The interactions between mitochondria and nucleus substantially influence plant development, stress response and morphological features. The prominent example of a mitochondrial-nuclear interaction is cytoplasmic male sterility (CMS), when plants produce aborted anthers or inviable pollen. The genes responsible for CMS are located in mitochondrial genome, but their expression is controlled by nuclear genes, called fertility restorers. Recent explosion of high-throughput sequencing methods enabled to study transcriptomic alterations in the level of non-coding RNAs under CMS biogenesis...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29144204/specific-hypersensitive-response-associated-recognition-of-new-apoplastic-effectors-from-cladosporium-fulvum-in-wild-tomato
#8
Carl H Mesarich, Bilal Ӧkmen, Hanna Rovenich, Scott A Griffiths, Changchun Wang, Mansoor Karimi Jashni, Aleksandar Mihajlovski, Jérôme Collemare, Lukas Hunziker, Cecilia H Deng, Ate van der Burgt, Henriek G Beenen, Matthew D Templeton, Rosie E Bradshaw, Pierre J G M de Wit
Tomato leaf mold disease is caused by the biotrophic fungus Cladosporium fulvum. During infection, C. fulvum produces extracellular small secreted protein (SSP) effectors that function to promote colonization of the leaf apoplast. Resistance to the disease is governed by Cf immune receptor genes that encode receptor-like proteins (RLPs). These RLPs recognize specific SSP effectors to initiate a hypersensitive response (HR) that renders the pathogen avirulent. C. fulvum strains capable of overcoming one or more of all cloned Cf genes have now emerged...
November 16, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29143556/datalbase-a-database-for-genomic-and-transcriptomic-data-related-to-tal-effectors
#9
Alvaro L Pérez-Quintero, Léo Lamy, Carlos A Zarate, Sébastien Cunnac, Erin L Doyle, Adam J Bogdanove, Boris Szurek, Alexis Derepeer
Transcription activator-like effectors (TALEs) are proteins found in the genus Xanthomonas of phytopathogenic bacteria. These proteins enter the nucleus of cells in the host plant and can induce the expression of susceptibility S genes, triggering disease. TALEs bind the promoter region of S genes following a specific code, which allows the prediction of binding sites based on TALEs' amino acid sequence. New candidate susceptibility genes can then be discovered by finding the intersection between genes induced in the presence of TALEs and genes containing predicted effector binding elements (EBEs)...
November 16, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29141585/transcriptome-analysis-in-petals-and-leaves-of-chrysanthemums-with-different-chlorophyll-levels
#10
Akemi Ohmiya, Katsutomo Sasaki, Kenji Nashima, Chihiro Oda-Yamamizo, Masumi Hirashima, Katsuhiko Sumitomo
BACKGROUND: Chlorophylls (Chls) are magnesium-containing tetrapyrrole macromolecules responsible for the green color in plants. The Chl metabolic pathway has been intensively studied and nearly all the enzymes involved in the pathway have been identified and characterized. Synthesis and activity of these enzymes are tightly regulated in tissue- and developmental stage-specific manners. Leaves contain substantial amounts of Chls because Chls are indispensable for photosynthesis. In contrast, petals generally contain only trace amounts of Chls, which if present would mask the bright petal color...
November 15, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29138433/transcriptomic-analysis-of-the-regulation-of-stalk-development-in-flowering-chinese-cabbage-brassica-campestris-by-rna-sequencing
#11
Xinmin Huang, Yuling Lei, Hongling Guan, Yanwei Hao, Houcheng Liu, Guangwen Sun, Riyuan Chen, Shiwei Song
Flowering Chinese cabbage is a stalk vegetable whose quality and yield are directly related to stalk development. However, no comprehensive investigations on stalk development have been performed. To address this issue, the present study used RNA sequencing to investigate transcriptional regulation at three key stages (seedling, bolting, and flowering) of stalk development in flowering Chinese cabbage. Anatomical analysis revealed that cell division was the main mode of stalk thickening and elongation at all key stages...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29137184/cell-type-specific-metabolic-flux-analysis-a-challenge-for-metabolic-phenotyping-and-a-potential-solution-in-plants
#12
Merja T Rossi, Monika Kalde, Chaiyakorn Srisakvarakul, Nicholas J Kruger, R George Ratcliffe
Stable isotope labelling experiments are used routinely in metabolic flux analysis (MFA) to determine the metabolic phenotype of cells and tissues. A complication arises in multicellular systems because single cell measurements of transcriptomes, proteomes and metabolomes in multicellular organisms suggest that the metabolic phenotype will differ between cell types. In silico analysis of simulated metabolite isotopomer datasets shows that cellular heterogeneity confounds conventional MFA because labelling data averaged over multiple cell types does not necessarily yield averaged flux values...
November 13, 2017: Metabolites
https://www.readbyqxmd.com/read/29136191/genome-sequence-of-the-small-brown-planthopper-laodelphax-striatellus
#13
Junjie Zhu, Feng Jiang, Xianhui Wang, Pengcheng Yang, Yanyuan Bao, Wan Zhao, Wei Wang, Hong Lu, Qianshuo Wang, Na Cui, Jing Li, Xiaofang Chen, Lan Luo, Jinting Yu, Le Kang, Feng Cui
Background: Laodelphax striatellus Fallén (Hemiptera: Delphacidae) is one of the most destructive rice pests. L. striatellus is different from two other rice planthoppers with a released genome sequence, Sogatella furcifera and Nilaparvata lugens, in many biological characteristics, such as host range, dispersal capacity, and vectoring plant viruses. Deciphering the genome of L. striatellus will help to understand the genetic basis of the biological differences among the three rice planthoppers...
November 10, 2017: GigaScience
https://www.readbyqxmd.com/read/29135360/transcriptome-profiling-of-melaleuca-quinquenervia-challenged-by-myrtle-rust-reveals-differences-in-defense-responses-among-resistant-individuals
#14
Ji-Fan Hsieh, Aaron Chuah, Hardip R Patel, Karanjeet Sandhu, William J Foley, Carsten Külheim
Plants have developed complex defense mechanisms to protect themselves against pathogens. A wide-host range fungus, Austropuccinia psidii (G. Winter) Beenken comb. nov., which has caused severe damage to ecosystems and plantations worldwide, is a major threat to Australian ecosystems dominated by Myrtaceae. In particular, the east coast wetland foundation tree species Melaleuca quinquenervia appears to be variably susceptible to this pathogen. Understanding the molecular basis of host resistance would enable better management of this rust disease...
November 14, 2017: Phytopathology
https://www.readbyqxmd.com/read/29134709/light-sensing-by-opsins-and-fungal-ecology-nop-1-modulates-entry-into-sexual-reproduction-in-response-to-environmental-cues
#15
Zheng Wang, Junrui Wang, Ning Li, Jigang Li, Frances Trail, Jay C Dunlap, Jeffrey P Townsend
Understanding the genetic basis of the switch from asexual to sexual lifestyles in response to sometimes rapid environmental changes is one of the major challenges in fungal ecology. Light appears to play a critical role in the switch-but fungal genomes harbor diverse light sensors. Fungal opsins are homologous to bacterial green-light sensory rhodopsins, and their organismal functions in fungi have not been well understood. Three of these opsin-like proteins were widely distributed across fungal genomes, but homologs of the Fusarium opsin-like protein CarO were present only in plant-associated fungi...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134529/transcriptional-changes-measured-in-rice-roots-after-exposure-to-arsenite-contaminated-sediments
#16
Alexandra Brinke, Georg Reifferscheid, Roland Klein, Ute Feiler, Sebastian Buchinger
Transcriptional analyses are discussed to provide a deeper understanding of the molecular mechanisms underlying toxic effects. Thus, they can complement classic ecotoxicological test methods and potentially allow the identification of biomarkers associated to the exposure of chemical stressors and or adverse biological effects. This feasibility study intended to identify a set of potential gene expression biomarkers for arsenite-exposure in rice roots that could complement the informative value of an existing sediment-contact test with rice...
November 13, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29134148/transcriptome-dynamics-along-axolotl-regenerative-development-are-consistent-with-an-extensive-reduction-in-gene-expression-heterogeneity-in-dedifferentiated-cells
#17
Carlos Díaz-Castillo
Although in recent years the study of gene expression variation in the absence of genetic or environmental cues or gene expression heterogeneity has intensified considerably, many basic and applied biological fields still remain unaware of how useful the study of gene expression heterogeneity patterns might be for the characterization of biological systems and/or processes. Largely based on the modulator effect chromatin compaction has for gene expression heterogeneity and the extensive changes in chromatin compaction known to occur for specialized cells that are naturally or artificially induced to revert to less specialized states or dedifferentiate, I recently hypothesized that processes that concur with cell dedifferentiation would show an extensive reduction in gene expression heterogeneity...
2017: PeerJ
https://www.readbyqxmd.com/read/29133375/spatial-control-of-gene-expression-by-mir319-regulated-tcp-transcription-factors-in-leaf-development
#18
Edgardo G Bresso, Uciel Chorostecki, Ramiro E Rodriguez, Javier Fernando Palatnik, Carla Schommer
The characteristic leaf shapes we see in all plants are in good part outcome of the combined action of several transcription factor networks that translate into cell division activity during the early development of the organ. We show here that wild-type leaves have distinct transcriptomic profiles in center and marginal regions. Certain transcripts are enriched in margins, including those of CINCINNATA-like TCPs, and members of the NGATHA (NGA) and STYLISH (STY) gene families. We study in detail the contribution of miR319 regulated TCP (Teosinte branched, Cycloidea, PCF1/2) transcription factors to the development of the center and marginal regions of Arabidopsis leaves...
November 13, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29133370/a-mucin-like-protein-of-planthopper-is-required-for-feeding-and-induces-immunity-response-in-plants
#19
Xinxin Shangguan, Jing Zhang, Bingfang Liu, Yan Zhao, Huiying Wang, Zhizheng Wang, Jianping Guo, Weiwei Rao, Shengli Jing, Wei Guan, Yinhua Ma, Yan Wu, Liang Hu, Rongzhi Chen, Bo Du, Lili Zhu, Dazhao Yu, Guangcun He
The brown planthopper, Nilaparvata lugens (Stål), is a pest that threatens rice production worldwide. While feeding on rice plants, planthoppers secrete saliva, which plays crucial roles in nutrient ingestion and modulating plant defense responses, although the specific functions of salivary proteins remain largely unknown. We identified a N. lugens-secreted mucin-like protein (NlMLP) by transcriptome and proteome analyses and characterized its function, both in brown planthopper and in plants. NlMLP is highly expressed in salivary glands and is secreted into rice during feeding...
November 13, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29132375/comparative-transcriptome-analysis-of-soybean-response-to-bean-pyralid-larvae
#20
Weiying Zeng, Zudong Sun, Zhaoyan Cai, Huaizhu Chen, Zhenguang Lai, Shouzhen Yang, Xiangmin Tang
BACKGROUND: Soybean is one of most important oilseed crop worldwide, however, its production is often limited by many insect pests. Bean pyralid is one of the major soybean leaf-feeding insects in China. To explore the defense mechanisms of soybean resistance to bean pyralid, the comparative transcriptome sequencing was completed between the leaves infested with bean pyralid larvae and no worm of soybean (Gantai-2-2 and Wan82-178) on the Illumina HiSeq™ 2000 platform. RESULTS: In total, we identified 1744 differentially expressed genes (DEGs) in the leaves of Gantai-2-2 (1064) and Wan82-178 (680) fed by bean pyralid for 48 h, compared to 0 h...
November 13, 2017: BMC Genomics
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