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https://www.readbyqxmd.com/read/28087829/tracheophytes-contain-conserved-orthologs-of-a-basic-helix-loop-helix-transcription-factor-to-modulate-root-hair-specific-genes
#1
Youra Hwang, Hee-Seung Choi, Hyun-Min Cho, Hyung-Taeg Cho
ROOT HAIR SPECIFIC (RHS) genes, which contain the root hair-specific cis-element (RHE) in their regulatory regions, function in root hair morphogenesis. Here, we demostrate that an Arabidopsis thaliana basic helix-loop-helix transcription factor, ROOT HAIR DEFECTVE SIX-LIKE 4 (RSL4), directly binds to the RHE in vitro and in vivo, up-regulates RHS genes, and stimulates root hair formation in Arabidopsis. Orthologs of RSL4 from a eudicot (poplar, Populus trichocarpa), a monocot (rice, Oryza sativa), and a lycophyte (Selaginella moellendorffii) each restored root hair growth in the Arabidopsis rsl4 mutant...
January 13, 2017: Plant Cell
https://www.readbyqxmd.com/read/28087693/de-novo-genome-and-transcriptome-assembly-of-the-canadian-beaver-castor-canadensis
#2
Si Lok, Tara A Paton, Zhuozhi Wang, Gaganjot Kaur, Susan Walker, Ryan K C Yuen, Wilson W L Sung, Joseph Whitney, Janet A Buchanan, Brett Trost, Naina Singh, Beverly Apresto, Nan Chen, Matthew Coole, Travis J Dawson, Karen Y Ho, Zhizhou Hu, Sanjeev Pullenayegum, Kozue Samler, Arum Shipstone, Fiona Tsoi, Ting Wang, Sergio L Pereira, Pirooz Rostami, Carol Ann Ryan, Amy Hin Yan Tong, Karen Ng, Yogi Sundaravadanam, Jared T Simpson, Burton K Lim, Mark D Engstrom, Christopher J Dutton, Kevin C R Kerr, Maria Franke, William Rapley, Richard F Wintle, Stephen W Scherer
The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long-reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by shortreads (80 ×) and checked for accuracy by congruency against an independent short-read assembly...
January 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28087663/evolution-and-structural-diversification-of-nictaba-like-lectin-genes-in-food-crops-with-a-focus-on-soybean-glycine-max
#3
Sofie Van Holle, Pierre Rougé, Els J M Van Damme
BACKGROUND AND AIMS: The Nictaba family groups all proteins that show homology to Nictaba, the tobacco lectin. So far, Nictaba and an Arabidopsis thaliana homologue have been shown to be implicated in the plant stress response. The availability of more than 50 sequenced plant genomes provided the opportunity for a genome-wide identification of Nictaba-like genes in 15 species, representing members of the Fabaceae, Poaceae, Solanaceae, Musaceae, Arecaceae, Malvaceae and Rubiaceae. Additionally, phylogenetic relationships between the different species were explored...
January 12, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28086804/comparative-analysis-of-the-root-transcriptomes-of-cultivated-sweetpotato-ipomoea-batatas-l-lam-and-its-wild-ancestor-ipomoea-trifida-kunth-g-don
#4
Sathish K Ponniah, Jyothi Thimmapuram, Ketaki Bhide, Venu Kal Kalavacharla, Muthusamy Manoharan
BACKGROUND: The complex process of formation of storage roots (SRs) from adventitious roots affects sweetpotato yield. Identifying the genes that are uniquely expressed in the SR forming cultivated species, Ipomoea batatas (Ib), and its immediate ancestral species, Ipomoea trifida (It), which does not form SRs, may provide insights into the molecular mechanisms underlying SR formation in sweetpotato. RESULTS: Illumina paired-end sequencing generated ~208 and ~200 million reads for Ib and It, respectively...
January 13, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28079890/structural-insight-into-an-evolutionarily-ancient-programmed-cell-death-regulator-the-crystal-structure-of-marine-sponge-bhp2-bound-to-lb-bak-2
#5
Sofia Caria, Mark G Hinds, Marc Kvansakul
Sponges of the porifera family harbor some of the evolutionary most ancient orthologs of the B-cell lymphoma-2 (Bcl-2) family, a protein family critical to regulation of apoptosis. The genome of the sponge Geodia cydonium contains the putative pro-survival Bcl-2 homolog BHP2, which protects sponge tissue as well as mammalian Hek-293 and NIH-3T3 cells against diverse apoptotic stimuli. The Lake Baikal demosponge Lubomirskia baicalensis has been shown to encode both putative pro-survival Bcl-2 (LB-Bcl-2) and pro-apoptotic Bcl-2 members (LB-Bak-2), which have been implied in axis formation (branches) in L...
January 12, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28079523/symbiont-induced-odorant-binding-proteins-mediate-insect-host-hematopoiesis
#6
Joshua B Benoit, Aurélien Vigneron, Nichole A Broderick, Yineng Wu, Jennifer S Sun, John R Carlson, Serap Aksoy, Brian L Weiss
Symbiotic bacteria assist in maintaining homeostasis of the animal immune system. However, the molecular mechanisms that underlie symbiont-mediated host immunity are largely unknown. Tsetse flies (Glossina spp.) house maternally transmitted symbionts that regulate the development and function of their host's immune system. Herein we demonstrate that the obligate mutualist, Wigglesworthia, up-regulates expression of odorant binding protein six in the gut of intrauterine tsetse larvae. This process is necessary and sufficient to induce systemic expression of the hematopoietic RUNX transcription factor lozenge and the subsequent production of crystal cells, which actuate the melanotic immune response in adult tsetse...
January 12, 2017: ELife
https://www.readbyqxmd.com/read/28079255/moonlighting-at-replication-forks-a-new-life-for-homologous-recombination-proteins-brca1-brca2-and-rad51
#7
REVIEW
Arun Mouli Kolinjivadi, Vincenzo Sannino, Anna de Antoni, Hervé Técher, Giorgio Baldi, Vincenzo Costanzo
Coordination between DNA replication and DNA repair ensures maintenance of genome integrity, which is lost in cancer cells. Emerging evidence has linked Homologous Recombination (HR) proteins RAD51, BRCA1 and BRCA2 to the stability of nascent DNA. This function appears to be distinct from Double Strand Break (DSB) repair and is in part due to the prevention of MRE11-mediated degradation of nascent DNA at stalled forks. The role of RAD51 in fork protection resembles the activity described for its prokaryotic ortholog RecA, which prevents nuclease-mediated degradation of DNA and promotes replication fork restart in cells challenged by DNA damaging agents...
January 12, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28079132/critical-role-for-cafen1-and-cafen12-of-candida-albicans-in-cell-wall-integrity-and-biofilm-formation
#8
Md Alfatah, Vinay K Bari, Anubhav S Nahar, Swati Bijlani, K Ganesan
Sphingolipids are involved in several cellular functions, including maintenance of cell wall integrity. To gain insight into the role of individual genes of sphingolipid biosynthetic pathway, we have screened Saccharomyces cerevisiae strains deleted in these genes for sensitivity to cell wall perturbing agents calcofluor white and congo red. Only deletants of FEN1 and SUR4 genes were found to be sensitive to both these agents. Candida albicans strains deleted in their orthologs, CaFEN1 and CaFEN12, respectively, also showed comparable phenotypes, and a strain deleted for both these genes was extremely sensitive to cell wall perturbing agents...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078425/odorant-receptors-and-antennal-lobe-morphology-offer-a-new-approach-to-understanding-olfaction-in-the-asian-longhorned-beetle
#9
Robert F Mitchell, Loyal P Hall, Peter F Reagel, Duane D McKenna, Thomas C Baker, John G Hildebrand
The Asian longhorned beetle Anoplophora glabripennis (Motchulsky) is an exotic forest pest that has repeatedly invaded North America and Europe from Asia, and has the potential to kill millions of trees and cause billions of dollars in damage. Traps baited with an attractive mixture of volatile organic compounds from hosts have been of limited success in monitoring invasion sites. We propose that lures might be improved through studying the olfactory system of adult beetles, especially the gene family of odorant receptors (ORs) and the structure of the antennal lobes of the brain...
January 11, 2017: Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology
https://www.readbyqxmd.com/read/28077643/efficient-vpu-mediated-tetherin-antagonism-by-an-hiv-1-group-o-strain
#10
Katharina Mack, Kathrin Starz, Daniel Sauter, Simon Langer, Frederic Bibollet-Ruche, Gerald H Learn, Christina M Stürzel, Marie Leoz, Jean-Christophe Plantier, Matthias Geyer, Beatrice H Hahn, Frank Kirchhoff
: Simian immunodeficiency viruses (SIVs) use their Nef proteins to counteract the restriction factor tetherin. However, a deletion in human tetherin prevents antagonism by the Nef proteins of SIVcpz and SIVgor, which represent the ape precursors of human immunodeficiency virus type 1 (HIV-1). To promote virus release from infected cells, pandemic HIV-1 group M strains evolved Vpu as tetherin antagonist, while the Nef protein of less widespread HIV-1 group O strains acquired the ability to target a region adjacent to this deletion...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28077388/the-na-taurocholate-cotransporting-polypeptide-ntcp-slc10a1-ortholog-in-the-marine-skate-leucoraja-erinacea-is-not-a-physiological-bile-salt-transporter
#11
Dongke Yu, Han Zhang, Daniel A Lionarons, James L Boyer, Shi-Ying Cai
The Na(+)-dependent taurocholate co-transporting polypeptide (NTCP/SLC10A1) is a hepatocyte specific solute carrier, which plays an important role in maintaining bile salt homeostasis in mammals. The absence of an hepatic Na(+)-dependent bile salt transport system in marine skate and rainbow trout raises a question regarding the function of the Slc10a1 gene in these species. Here we have characterized the Slc10a1 gene in the marine skate, Leucoraja erinacea. The transcript of skate Slc10a1 (skSlc10a1) encodes 319 amino acids and shares 46% identity to human NTCP (hNTCP) with similar topology to mammalian NTCP...
January 11, 2017: American Journal of Physiology. Regulatory, Integrative and Comparative Physiology
https://www.readbyqxmd.com/read/28077092/phylogenetic-analysis-of-ionotropic-l-glutamate-receptor-genes-in-the-bilateria-with-special-notes-on-aplysia-californica
#12
Justin B Greer, Sawsan Khuri, Lynne A Fieber
BACKGROUND: The neurotransmitter L-Glutamate (L-Glu) acting at ionotropic L-Glu receptors (iGluR) conveys fast excitatory signal transmission in the nervous systems of all animals. iGluR-dependent neurotransmission is a key component of the synaptic plasticity that underlies learning and memory. During learning, two subtypes of iGluR, α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPAR) and N-methyl-D-aspartate receptors (NMDAR), are dynamically regulated postsynaptically in vertebrates...
January 11, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28077066/the-essential-requirement-of-an-animal-heme-peroxidase-protein-during-the-wing-maturation-process-in-drosophila
#13
Dondra Bailey, Mohammed Abul Basar, Sanjay Nag, Nivedita Bondhu, Shaloei Teng, Atanu Duttaroy
BACKGROUND: Thus far, a handful of genes have been shown to be related to the wing maturation process in insects. A novel heme peroxidase enzyme known as curly suppressor (Cysu)(formerly CG5873), have been characterized in this report because it is involved in wing morphogenesis. Using bioinformatics tools we found that Cysu is remarkably conserved in the genus Drosophila (>95%) as well as in invertebrates (>70%), although its vertebrate orthologs show poor homology. Time-lapse imaging and histochemical analyses have confirmed that the defective wing phenotype of Cysu is not a result of any underlying cellular alterations; instead, its wings fail to expand in mature adults...
January 11, 2017: BMC Developmental Biology
https://www.readbyqxmd.com/read/28076795/hangover-links-nuclear-rna-signaling-to-camp-regulation-via-the-phosphodiesterase-4d-ortholog-dunce
#14
Manuela Ruppert, Mirjam Franz, Anastasios Saratsis, Laura Velo Escarcena, Oliver Hendrich, Li Ming Gooi, Isabell Schwenkert, Ansgar Klebes, Henrike Scholz
The hangover gene defines a cellular stress pathway that is required for rapid ethanol tolerance in Drosophila melanogaster. To understand how cellular stress changes neuronal function, we analyzed Hangover function on a cellular and neuronal level. We provide evidence that Hangover acts as a nuclear RNA binding protein and we identified the phosphodiesterase 4d ortholog dunce as a target RNA. We generated a transcript-specific dunce mutant that is impaired not only in ethanol tolerance but also in the cellular stress response...
January 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28074535/gene-ages-nomenclatures-and-functional-diversification-of-the-methuselah-methuselah-like-gpcr-family-in-drosophila-and-tribolium
#15
REVIEW
Markus Friedrich, Jeffery W Jones
Affecting lifespan regulation and oxidative stress resistance, the G-protein coupled receptor (GPCR) gene methuselah (mth) plays important roles in the life history of Drosophila melanogaster. Substantial progress has been made in elucidating the molecular pathways by which mth affects these traits, yet conflicting ideas exist as to how old these genetic interactions are as well as how old the mth gene itself is. Root to these issues is the complex gene family history of the Mth/Mthl GPCR family, which experienced independent expansions in a variety of animal clades, leading to at least six subfamilies in insects...
January 11, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28073340/a-comparative-genomic-analysis-of-putative-pathogenicity-genes-in-the-host-specific-sibling-species-colletotrichum-graminicola-and-colletotrichum-sublineola
#16
E A S Buiate, K V Xavier, N Moore, M F Torres, M L Farman, C L Schardl, L J Vaillancourt
BACKGROUND: Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28072865/reading-the-evolution-of-compartmentalization-in-the-ribosome-assembly-toolbox-the-yrg-protein-family
#17
Pablo Mier, Antonio J Pérez-Pulido, Emmanuel G Reynaud, Miguel A Andrade-Navarro
Reconstructing the transition from a single compartment bacterium to a highly compartmentalized eukaryotic cell is one of the most studied problems of evolutionary cell biology. However, timing and details of the establishment of compartmentalization are unclear and difficult to assess. Here, we propose the use of molecular markers specific to cellular compartments to set up a framework to advance the understanding of this complex intracellular process. Specifically, we use a protein family related to ribosome biogenesis, YRG (YlqF related GTPases), whose evolution is linked to the establishment of cellular compartments, leveraging the current genomic data...
2017: PloS One
https://www.readbyqxmd.com/read/28070736/genome-wide-analysis-of-mirnas-and-tasi-rnas-in-zea-mays-in-response-to-phosphate-deficiency
#18
Saurabh Gupta, Manju Kumari, Himansu Kumar, Pritish Kumar Varadwaj
Globally important cereal crop maize provides important nutritions and starch in dietary foods. Low phosphate (LPi) availability in the soil frequently limits the maize quality and yield across the world. Small non-coding RNAs (Snc-RNAs) play crucial roles in growth and adaptation of plants to the environment. Snc-RNAs like microRNAs (miRs) and trans-acting small interfering RNAs (Tasi-Rs) play important functions in posttranscriptional regulation of gene expression, which controls plant development, reproduction, and biotic/abiotic stress responses...
January 9, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28070461/transcriptome-analysis-of-the-oriental-melon-cucumis-melo-l-var-makuwa-during-fruit-development
#19
Ah-Young Shin, Yong-Min Kim, Namjin Koo, Su Min Lee, Seokhyeon Nahm, Suk-Yoon Kwon
BACKGROUND: The oriental melon (Cucumis melo L. var. makuwa) is one of the most important cultivated cucurbits grown widely in Korea, Japan, and northern China. It is cultivated because its fruit has a sweet aromatic flavor and is rich in soluble sugars, organic acids, minerals, and vitamins. In order to elucidate the genetic and molecular basis of the developmental changes that determine size, color, and sugar contents of the fruit, we performed de novo transcriptome sequencing to analyze the genes expressed during fruit development...
2017: PeerJ
https://www.readbyqxmd.com/read/28068920/comparative-transcriptomics-provide-insight-into-the-morphogenesis-and-evolution-of-fistular-leaves-in-allium
#20
Siyuan Zhu, Shouwei Tang, Zhijian Tan, Yongting Yu, Qiuzhong Dai, Touming Liu
BACKGROUND: Fistular leaves frequently appear in Allium species, and previous developmental studies have proposed that the process of fistular leaf formation involves programmed cell death. However, molecular evidence for the role of programmed cell death in the formation of fistular leaf cavities has yet to be reported. RESULTS: In this study, we characterized the leaf transcriptomes of nine Allium species, including six fistular- and three solid-leaved species...
January 10, 2017: BMC Genomics
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