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Plant phenotyping

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https://www.readbyqxmd.com/read/29141230/sub-minute-phosphoregulation-of-cell-cycle-systems-during-plasmodium-gamete-formation
#1
Brandon M Invergo, Mathieu Brochet, Lu Yu, Jyoti Choudhary, Pedro Beltrao, Oliver Billker
The transmission of malaria parasites to mosquitoes relies on the rapid induction of sexual reproduction upon their ingestion into a blood meal. Haploid female and male gametocytes become activated and emerge from their host cells, and the males enter the cell cycle to produce eight microgametes. The synchronized nature of gametogenesis allowed us to investigate phosphorylation signaling during its first minute in Plasmodium berghei via a high-resolution time course of the phosphoproteome. This revealed an unexpectedly broad response, with proteins related to distinct cell cycle events undergoing simultaneous phosphoregulation...
November 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/29140512/a-novel-tetratricopeptide-repeat-protein-white-to-green1-is-required-for-early-chloroplast-development-and-affects-rna-editing-in-chloroplasts
#2
Fei Ma, Yingchun Hu, Yan Ju, Qianru Jiang, Zhijun Cheng, Quan Zhang, Sodmergen
The chloroplast is essential for plant photosynthesis and production, but the regulatory mechanism of chloroplast development is still elusive. Here, a novel gene, WHITE TO GREEN1 (WTG1), was identified to have a function in chloroplast development and plastid gene expression by screening Arabidopsis leaf coloration mutants. WTG1 encodes a chloroplast-localized tetratricopeptide repeat protein that is expressed widely in Arabidopsis cells. Disruption of WTG1 suppresses plant growth, retards leaf greening and chloroplast development, and represses photosynthetic gene expression, but complemented expression of WTG1 restored a normal phenotype...
November 11, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29138939/responses-of-he-ne-laser-on-agronomic-traits-and-the-crosstalk-between-uvr8-signaling-and-phytochrome-b-signaling-pathway-in-arabidopsis-thaliana-subjected-to-supplementary-ultraviolet-b-uv-b-stress
#3
Limei Gao, Yongfeng Li, Zhihua Shen, Rong Han
UV-B acclimation effects and UV-B damage repair induced by a 632.8-nm He-Ne laser were investigated in Arabidopsis thaliana plants in response to supplementary UV-B stress. There was an increasing trend in growth parameters in the combination-treated plants with He-Ne laser and UV-B light compared to those stressed with enhanced UV-B light alone during different developmental stages of plants. The photosynthetic efficiency (Pn) and survival rates of seedlings were significantly higher in the combination treatments than UV-B stress alone...
November 14, 2017: Protoplasma
https://www.readbyqxmd.com/read/29138904/rice-diversity-panel-provides-accurate-genomic-predictions-for-complex-traits-in-the-progenies-of-biparental-crosses-involving-members-of-the-panel
#4
M Ben Hassen, T V Cao, J Bartholomé, G Orasen, C Colombi, J Rakotomalala, L Razafinimpiasa, C Bertone, C Biselli, A Volante, F Desiderio, L Jacquin, G Valè, N Ahmadi
Rice breeding programs based on pedigree schemes can use a genomic model trained with data from their working collection to predict performances of progenies produced through rapid generation advancement. So far, most potential applications of genomic prediction in plant improvement have been explored using cross validation approaches. This is the first empirical study to evaluate the accuracy of genomic prediction of the performances of progenies in a typical rice breeding program. Using a cross validation approach, we first analyzed the effects of marker selection and statistical methods on the accuracy of prediction of three different heritability traits in a reference population (RP) of 284 inbred accessions...
November 14, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29138309/loss-of-popz-at-activity-in-agrobacterium-tumefaciens-by-deletion-or-depletion-leads-to-multiple-growth-poles-minicells-and-growth-defects
#5
Romain Grangeon, John Zupan, Yeonji Jeon, Patricia C Zambryski
Agrobacterium tumefaciens grows by addition of peptidoglycan (PG) at one pole of the bacterium. During the cell cycle, the cell needs to maintain two different developmental programs, one at the growth pole and another at the inert old pole. Proteins involved in this process are not yet well characterized. To further characterize the role of pole-organizing protein A. tumefaciens PopZ (PopZ At ), we created deletions of the five PopZ At domains and assayed their localization. In addition, we created a popZAt deletion strain (ΔpopZAt ) that exhibited growth and cell division defects with ectopic growth poles and minicells, but the strain is unstable...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29137281/hic-5-regulates-epithelial-to-mesenchymal-transition-in-ovarian-cancer-cells-in-a-tgf%C3%AE-1-independent-manner
#6
Razan Sheta, Zhi-Qiang Wang, Magdalena Bachvarova, Marie Plante, Jean Gregoire, Marie-Claude Renaud, Alexandra Sebastianelli, Stephane Gobeil, Chantale Morin, Elizabeth Macdonald, Barbara Vanderhyden, Dimcho Bachvarov
The molecular basis of epithelial ovarian cancer (EOC) dissemination is still poorly understood. We have previously identified the hydrogen peroxide-inducible clone-5 (Hic-5) gene as hypomethylated in high-grade (HG) serous EOC tumors, compared to normal ovarian tissues. Hic-5 is a focal adhesion scaffold protein and has been primarily studied for its role as a key mediator of TGF-β-induced epithelial-to-mesenchymal transition (EMT) in epithelial cells of both normal and malignant origin; however, its role in EOC has been never investigated...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137184/cell-type-specific-metabolic-flux-analysis-a-challenge-for-metabolic-phenotyping-and-a-potential-solution-in-plants
#7
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/29134741/contemporary-evolution-of-a-lepidopteran-species-heliothis-virescens-in-response-to-modern-agricultural-practices
#8
Megan L Fritz, Alexandra M DeYonke, Alexie Papanicolaou, Stephen Micinski, John Westbrook, Fred Gould
Adaptation to human-induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where anthropogenic selection pressure is strong. Heliothis virescens primarily feeds on cotton in its larval stages and US populations have been declining since the widespread planting of transgenic cotton, which endogenously expresses proteins derived from Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so adaptation in this altered environment could involve: 1) shifts in host plant selection mechanisms to avoid cotton, 2) changes in detoxification mechanisms required for cotton-feeding versus feeding on other hosts, or 3) loss of resistance to previously used management practices including insecticides...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134739/phenotypic-plasticity-in-response-to-environmental-heterogeneity-contributes-to-fluctuating-asymmetry-in-plants-first-empirical-evidence
#9
Branka Tucić, Sanja Budečević, Sanja Manitašević Jovanović, Ana Vuleta, Christian Peter Klingenberg
Fluctuating asymmetry (FA) is widely used to quantify developmental instability (DI) in ecological and evolutionary studies. It has long been recognized that FA may not exclusively originate from DI for sessile organisms such as plants, because phenotypic plasticity in response to heterogeneities in the environment might also produce FA. This study provides the first empirical evidence for this hypothesis. We reasoned that solar irradiance, which is greater on the southern side than on the northern side of plants growing in the temperate zone of the northern hemisphere, would cause systematic morphological differences and asymmetry associated with the orientation of plant parts...
November 13, 2017: Journal of Evolutionary Biology
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
#10
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
#11
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
#12
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/29133511/which-individuals-to-choose-to-update-the-reference-population-minimizing-the-loss-of-genetic-diversity-in-animal-genomic-selection-programs
#13
S E Eynard, P Croiseau, D Laloë, S Fritz, M P L Calus, G Restoux
Genomic selection is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, genomic selection allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study we propose a modification of the reference population composition to mitigate diversity loss...
November 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29133376/distinct-functions-of-starch-synthase-4-domains-in-starch-granule-formation
#14
Kuan-Jen Lu, Barbara Pfister, Camilla Jenny, Simona Eicke, Samuel C Zeeman
The formation of normal starch granules in Arabidopsis leaf chloroplasts requires STARCH SYNTHASE 4 (SS4). In plants lacking SS4, chloroplasts typically produce only one round granule rather than multiple lenticular granules. The mechanisms by which SS4 determines granule number and morphology are not understood. The N-terminal region of SS4 is unique among SS isoforms and contains several long coiled-coil motifs, typically implicated in protein-protein interactions. The C-terminal region contains the catalytic glucosyltransferase domains, which are widely conserved in plant SS and bacterial glycogen synthase (GS) isoforms...
November 13, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29133369/transcription-factor-wrky75-interacts-with-della-proteins-to-affect-flowering
#15
Ligang Chen, Liping Zhang, Diqiu Yu
Flowering time is tightly controlled by both endogenous and exogenous signals. Although several lines of evidence have suggested the involvement of WRKY transcription factors in floral initiation, the underlying mechanisms and signaling pathways involved remain elusive. Here, we newly identified Arabidopsis thaliana WRKY DNA binding protein75 (WRKY75) as a positive regulator of flowering initiation. Mutation of WRKY75 resulted in a delay in flowering, whereas overexpression of WRKY75 significantly accelerated flowering in Arabidopsis...
November 13, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29132313/comparative-transcriptome-analysis-of-a-lowly-virulent-strain-of-erwinia-amylovora-in-shoots-of-two-apple-cultivars-susceptible-and-resistant-to-fire-blight
#16
Joanna Puławska, Monika Kałużna, Wojciech Warabieda, Artur Mikiciński
BACKGROUND: Erwinia amylovora is generally considered to be a homogeneous species in terms of phenotypic and genetic features. However, strains show variation in their virulence, particularly on hosts with different susceptibility to fire blight. We applied the RNA-seq technique to elucidate transcriptome-level changes of the lowly virulent E. amylovora 650 strain during infection of shoots of susceptible (Idared) and resistant (Free Redstar) apple cultivars. RESULTS: The highest number of differentially expressed E...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29128357/osprx2-contributes-to-stomatal-closure-and-improves-potassium-deficiency-tolerance-in-rice
#17
Xiaohui Mao, Yanmei Zheng, Kaizhuan Xiao, Yidong Wei, Yongsheng Zhu, Qiuhua Cai, Liping Chen, Huaan Xie, Jianfu Zhang
Peroxiredoxins (Prxs) which are thiol-based peroxidases have been implicated in the toxic reduction and intracellular concentration regulation of hydrogen peroxide. In Arabidopsis thaliana At2-CysPrxB (At5g06290) has been demonstrated to be essential in maintaining the water-water cycle for proper H2O2 scavenging. Although the mechanisms of 2-Cys Prxs have been extensively studied in Arabidopsis thaliana, the function of 2-Cys Prxs in rice is unclear. In this study, a rice homologue gene of At2-CysPrxB, OsPRX2 was investigated aiming to characterize the effect of 2-Cys Prxs on the K(+)-deficiency tolerance in rice...
November 8, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29127883/metabolic-engineering-of-yeast-for-lignocellulosic-biofuel-production
#18
REVIEW
Yong-Su Jin, Jamie Hd Cate
Production of biofuels from lignocellulosic biomass remains an unsolved challenge in industrial biotechnology. Efforts to use yeast for conversion face the question of which host organism to use, counterbalancing the ease of genetic manipulation with the promise of robust industrial phenotypes. Saccharomyces cerevisiae remains the premier host for metabolic engineering of biofuel pathways, due to its many genetic, systems and synthetic biology tools. Numerous engineering strategies for expanding substrate ranges and diversifying products of S...
November 8, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/29127501/characterization-of-a-novel-yeast-species-metschnikowia-persimmonesis-kctc-12991bp-kiom-g15050-type-strain-isolated-from-a-medicinal-plant-korean-persimmon-calyx-diospyros-kaki-thumb
#19
Young Min Kang, Ji Eun Choi, Richard Komakech, Jeong Hwan Park, Dae Wook Kim, Kye Man Cho, Seung Mi Kang, Sang Haeng Choi, Kun Chul Song, Chung Min Ryu, Keun Chul Lee, Jung-Sook Lee
The yeast strain Metschnikowia persimmonesis Kang and Choi et al., sp. nov. [type strain KIOM_G15050 = Korean Collection for Type Cultures (KCTC) 12991BP] was isolated from the stalk of native persimmon cultivars (Diospyros kaki Thumb) obtained from different regions of South Korea and was characterized phenotypically, genetically, and physiologically. The isolate grew between 4 and 40 °C (optimum temperature: 24-28 °C), pH 3-8 (pH optimum = 6.0), and in 0-4% NaCl solution (with optimal growth in absence of NaCl)...
November 10, 2017: AMB Express
https://www.readbyqxmd.com/read/29127260/an-improved-brome-mosaic-virus-silencing-vector-greater-insert-stability-and-more-extensive-vigs
#20
Xin Shun Ding, Stephen W Mannas, Bethany A Bishop, Xiaolan Rao, Mitchell Lecoultre, Soonil Kwon, Richard S Nelson
Virus-induced gene silencing (VIGS) is used extensively for gene function studies in plants. VIGS is inexpensive and rapid compared with silencing conducted through stable transformation, but many virus silencing vectors, especially in grasses, induce only transient silencing phenotypes. A major reason for transient phenotypes is instability of the foreign gene fragment (insert) in the vector during VIGS. Here we report the development of a Brome mosaic virus (BMV)-based vector that better maintains inserts through modification of the original BMV vector RNA sequence...
November 10, 2017: Plant Physiology
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