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https://www.readbyqxmd.com/read/28724081/genome-wide-screening-for-lectin-motifs-in-arabidopsis-thaliana
#1
Lore Eggermont, Bruno Verstraeten, Els J M Van Damme
For more than three decades, served as a model for plant biology research. At present only a few protein families have been studied in detail in . This study focused on all sequences with lectin motifs in the genome of . Based on amino acid sequence similarity (BLASTp searches), 217 putative lectin genes were retrieved belonging to 9 out of 12 different lectin families. The domain organization and genomic distribution for each lectin family were analyzed. Domain architecture analysis revealed that most of these lectin gene sequences are linked to other domains, often belonging to protein families with catalytic activity...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28723971/termination-factor-rho-from-the-control-of-pervasive-transcription-to-cell-fate-determination-in-bacillus-subtilis
#2
Vladimir Bidnenko, Pierre Nicolas, Aleksandra Grylak-Mielnicka, Olivier Delumeau, Sandrine Auger, Anne Aucouturier, Cyprien Guerin, Repoila Francis, Jacek Bardowski, Stéphane Aymerich, Elena Bidnenko
In eukaryotes, RNA species originating from pervasive transcription are regulators of various cellular processes, from the expression of individual genes to the control of cellular development and oncogenesis. In prokaryotes, the function of pervasive transcription and its output on cell physiology is still unknown. Most bacteria possess termination factor Rho, which represses pervasive, mostly antisense, transcription. Here, we investigate the biological significance of Rho-controlled transcription in the Gram-positive model bacterium Bacillus subtilis...
July 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28723592/effects-of-near-infrared-radiation-on-dna-dls-and-atr-ftir-study
#3
Katarzyna Szymborska-Małek, Małgorzata Komorowska, Marlena Gąsior-Głogowska
We presume that the primary effect of Near Infrared (NIR) radiation on aqueous solutions of biological molecules concerns modification of hydrogen bonded structures mainly the global and the hydration shell water molecules. Since water has a significant influence on the DNA structure, we expect that the thermal stability of DNA could be modified by NIR radiation. The herring sperm DNA was exposed to NIR radiation (700-1100nm) for 5, 10, and 20min periods. The temperature dependent infrared measurements were done for the thin films formed on the diamond ATR crystal from evaporated DNA solutions exposed and unexposed to NIR radiation...
July 12, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28722507/polyglutamine-tracts-regulate-autophagy
#4
Avraham Ashkenazi, Carla F Bento, Thomas Ricketts, Mariella Vicinanza, Farah Siddiqi, Mariana Pavel, Ferdinando Squitieri, Maarten C Hardenberg, Sara Imarisio, Fiona M Menzies, David C Rubinsztein
Expansions of polyglutamine (polyQ) tracts in different proteins cause 9 neurodegenerative conditions, such as Huntington disease and various ataxias. However, many normal mammalian proteins contain shorter polyQ tracts. As these are frequently conserved in multiple species, it is likely that some of these polyQ tracts have important but unknown biological functions. Here we review our recent study showing that the polyQ domain of the deubiquitinase ATXN3/ataxin-3 enables its interaction with BECN1/beclin 1, a key macroautophagy/autophagy initiator...
July 19, 2017: Autophagy
https://www.readbyqxmd.com/read/28721317/ameloblastic-fibrodentinoma-a-case-with-varied-patterns-of-dysplastic-dentin
#5
Radhika M Bavle, Sudhakara Muniswammappa, Reshma Venugopal, Amulya S R
Ameloblastic fibrodentinoma is a benign odontogenic tumor belonging to the category of "odontogenic epithelium with odontogenic ectomesenchyme" along with recognition of induction in the form of dentin in atypical or dysplastic forms. The biological behaviour of ameloblastic fibrodentinoma is not very different from ameloblastic fibroma; hence, it is treated similarly by conservative procedures. It is important to understand the histopathogenesis of these rare tumors. Though rare, they are an independent entity awaiting recognition...
June 14, 2017: Curēus
https://www.readbyqxmd.com/read/28720789/evolutionarily-conserved-bil4-suppresses-the-degradation-of-brassinosteroid-receptor-bri1-and-regulates-cell-elongation
#6
Ayumi Yamagami, Chieko Saito, Miki Nakazawa, Shozo Fujioka, Tomohiro Uemura, Minami Matsui, Masaaki Sakuta, Kazuo Shinozaki, Hiroyuki Osada, Akihiko Nakano, Tadao Asami, Takeshi Nakano
Brassinosteroids (BRs), plant steroid hormones, play important roles in plant cell elongation and differentiation. To investigate the mechanisms of BR signaling, we previously used the BR biosynthesis inhibitor Brz as a chemical biology tool and identified the Brz-insensitive-long hypocotyl4 mutant (bil4). Although the BIL4 gene encodes a seven-transmembrane-domain protein that is evolutionarily conserved in plants and animals, the molecular function of BIL4 in BR signaling has not been elucidated. Here, we demonstrate that BIL4 is expressed in early elongating cells and regulates cell elongation in Arabidopsis...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720734/lack-of-acrb-efflux-function-confers-loss-of-virulence-on-salmonella-enterica-serovar-typhimurium
#7
Xuan Wang-Kan, Jessica M A Blair, Barbara Chirullo, Jonathan Betts, Roberto M La Ragione, Alasdair Ivens, Vito Ricci, Timothy J Opperman, Laura J V Piddock
AcrAB-TolC is the paradigm resistance-nodulation-division (RND) multidrug resistance efflux system in Gram-negative bacteria, with AcrB being the pump protein in this complex. We constructed a nonfunctional AcrB mutant by replacing D408, a highly conserved residue essential for proton translocation. Western blotting confirmed that the AcrB D408A mutant had the same native level of expression of AcrB as the parental strain. The mutant had no growth deficiencies in rich or minimal medium. However, compared with wild-type SL1344, the mutant had increased accumulation of Hoechst 33342 dye and decreased efflux of ethidium bromide and was multidrug hypersusceptible...
July 18, 2017: MBio
https://www.readbyqxmd.com/read/28719655/protein-analysis-and-gene-expression-indicate-differential-vulnerability-of-iberian-fish-species-under-a-climate-change-scenario
#8
Tiago F Jesus, João M Moreno, Tiago Repolho, Alekos Athanasiadis, Rui Rosa, Vera M F Almeida-Val, Maria M Coelho
Current knowledge on the biological responses of freshwater fish under projected scenarios of climate change remains limited. Here, we examine differences in the protein configuration of two endemic Iberian freshwater fish species, Squalius carolitertii and the critically endangered S. torgalensis that inhabit in the Atlantic-type northern and in the Mediterranean-type southwestern regions, respectively. We performed protein structure modeling of fourteen genes linked to protein folding, energy metabolism, circadian rhythms and immune responses...
2017: PloS One
https://www.readbyqxmd.com/read/28719649/differential-expression-of-small-rna-pathway-genes-associated-with-the-biomphalaria-glabrata-schistosoma-mansoni-interaction
#9
Fábio Ribeiro Queiroz, Luciana Maria Silva, Wander de Jesus Jeremias, Élio Hideo Babá, Roberta Lima Caldeira, Paulo Marcos Zech Coelho, Matheus de Souza Gomes
The World Health Organization (WHO) estimates that approximately 240 million people in 78 countries require treatment for schistosomiasis, an endemic disease caused by trematodes of the genus Schistosoma. In Brazil, Schistosoma mansoni is the only species representative of the genus whose passage through an invertebrate host, snails of the genus Biomphalaria, is obligatory before infecting a mammalian host, including humans. The availability of the genome and transcriptome of B. glabrata makes studying the regulation of gene expression, particularly the regulation of miRNA and piRNA processing pathway genes, possible...
2017: PloS One
https://www.readbyqxmd.com/read/28719054/evolutionary-cell-biology-of-proteins-from-protists-to-humans-and-plants
#10
REVIEW
Helmut Plattner
During evolution, the cell as a fine-tuned machine had to undergo permanent adjustments to match changes in its environment, while "closed for repair work" was not possible. Evolution from protists (protozoa and unicellular algae) to multicellular organisms may have occurred in basically two lineages, Unikonta and Bikonta, culminating in mammals and angiosperms (flowering plants), respectively. Unicellular models for unikont evolution are myxamoebae (Dictyostelium) and increasingly also choanoflagellates, whereas, for bikonts, ciliates are preferred models...
July 18, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28718764/crispr-mediated-genetic-interaction-profiling-identifies-rna-binding-proteins-controlling-metazoan-fitness
#11
Adam D Norris, Xicotencatl Gracida, John Calarco
<span style="font-size: 12pt; font-family: 'Times';">Genetic interaction screens have aided our understanding of complex genetic traits,</span><span style="font-size: 11.000000pt; font-family: 'Calibri';"> </span><span style="font-size: 12pt; font-family: 'Times';">diseases, and biological pathways. However, approaches for synthetic genetic analysis with</span><span style="font-size: 11.000000pt; font-family: 'Calibri';"> </span><span style="font-size: 12pt; font-family: 'Times';">null-alleles in metazoans have not been feasible...
July 18, 2017: ELife
https://www.readbyqxmd.com/read/28717235/protein-protein-binding-selectivity-and-network-topology-constrain-global-and-local-properties-of-interface-binding-networks
#12
David O Holland, Benjamin H Shapiro, Pei Xue, Margaret E Johnson
Protein-protein interactions networks (PPINs) are known to share a highly conserved structure across all organisms. What is poorly understood, however, is the structure of the child interface interaction networks (IINs), which map the binding sites proteins use for each interaction. In this study we analyze four independently constructed IINs from yeast and humans and find a conserved structure of these networks with a unique topology distinct from the parent PPIN. Using an IIN sampling algorithm and a fitness function trained on the manually curated PPINs, we show that IIN topology can be mostly explained as a balance between limits on interface diversity and a need for physico-chemical binding complementarity...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716949/biochemical-regulatory-features-of-aid-remain-conserved-from-lamprey-to-humans
#13
Emma M Quinlan, Justin J King, Chris T Amemiya, Ellen Hsu, Mani Larijani
Activation induced cytidine deaminase (AID) is a genome-mutating enzyme that initiates class switch recombination and somatic hypermutation of antibodies in jawed vertebrates. We previously described the biochemical properties of human AID and found that it is an unusual enzyme in that it exhibits binding affinities for its substrate DNA and catalytic rates several orders of magnitude higher and lower, respectively, than a typical enzyme. Recently, we solved the functional structure of AID and demonstrated that these properties are due to non-specific DNA binding on its surface, along with a catalytic pocket that predominantly assumes a closed conformation...
July 17, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28716860/novel-mechanisms-of-piezo1-dysfunction-in-hereditary-xerocytosis
#14
Edyta Glogowska, Eve R Schneider, Yelena Maksimova, Vincent P Schulz, Kimberly Lezon-Geyda, John Wu, Kottayam Radhakrishnan, Siobán B Keel, Donald Mahoney, Alison M Freidmann, Rachel A Altura, Elena O Gracheva, Sviatoslav N Bagriantsev, Theodosia A Kalfa, Patrick G Gallagher
Mutations in PIEZO1 are the primary cause of hereditary xerocytosis, a clinically heterogeneous, dominantly inherited disorder of erythrocyte dehydration. We utilized next generation sequencing-based techniques to identify PIEZO1 mutations in individuals from 9 kindreds referred with suspected HX and/or undiagnosed congenital hemolytic anemia. Mutations were primarily found in the highly conserved, COOH-terminal pore region domain. Several mutations were novel and demonstrated ethnic specificity. We characterized these mutations using genomic, bioinformatic, cell biology, and physiology-based functional assays...
July 17, 2017: Blood
https://www.readbyqxmd.com/read/28716386/comparing-the-rankings-obtained-from-two-biodiversity-indices-the-fair-proportion-index-and-the-shapley-value
#15
Kristina Wicke, Mareike Fischer
The Shapley Value and the Fair Proportion Index of phylogenetic trees have been frequently discussed as prioritization tools in conservation biology. Both indices rank species according to their contribution to total phylogenetic diversity, allowing for a simple conservation criterion. While both indices have their specific advantages and drawbacks, it has recently been shown that both values are closely related. However, as different authors use different definitions of the Shapley Value, the specific degree of relatedness depends on the specific version of the Shapley Value - it ranges from a high correlation index to equality of the indices...
July 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28714397/prognostic-value-of-copeptin-in-chronic-kidney-disease-from-general-population-to-end-stage-renal-disease
#16
Edyta Golembiewska, Anna Machowska, Peter Stenvinkel, Bengt Lindholm
Arginine vasopressin (AVP), also known as antidiuretic hormone (ADH), is released in response to osmotic and non-osmotic stimuli and plays a key role in many physiologic and pathologic processes. The main function of AVP is the control of fluid homeostasis by inducing water conservation by the kidney, but it also stimulates arteriolar vasoconstriction and the release of adrenocorticotropic hormone (ACTH). These actions are mediated by different AVP receptors located on various target cells. Produced in hypothalamus from a larger precursor, pre-proAVP, AVP is produced in equimolar amounts to copeptin, a glycopeptide with yet unknown biologic function...
July 14, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28713421/analyses-of-genomic-trna-reveal-presence-of-novel-trnas-in-oryza-sativa
#17
Tapan K Mohanta, Hanhong Bae
Transfer rRNAs are important molecules responsible for the translation event during protein synthesis. tRNAs are widespread found in unicellular to multi-cellular organisms. Analysis of tRNA gene family members in Oryza sativa revealed the presence of 750 tRNA genes distributed unevenly in different chromosomes. The length of O. sativa tRNAs genes were ranged from 66 to 91 nucleotides encoding 52 isoacceptor in total. tRNA(Ser) found in chromosome 8 of O. sativa encoded only 66 nucleotides which is the smallest tRNA of O...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28713413/identification-of-conserved-and-novel-micrornas-in-blueberry
#18
Junyang Yue, Xiaohui Lu, Huan Zhang, Jiao Ge, Xueling Gao, Yongsheng Liu
MicroRNAs (miRNAs) are a class of small endogenous RNAs that play important regulatory roles in cells by negatively affecting gene expression at both transcriptional and post-transcriptional levels. There have been extensive studies aiming to identify miRNAs and to elucidate their functions in various plant species. In the present study, we employed the high-throughput sequencing technology to profile miRNAs in blueberry fruits. A total of 9,992,446 small RNA tags with sizes ranged from 18 to 30 nt were obtained, indicating that blueberry fruits have a large and diverse small RNA population...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28713404/genome-wide-identification-and-analysis-of-genes-conserved-between-japonica-and-indica-rice-cultivars-that-respond-to-low-temperature-stress-at-the-vegetative-growth-stage
#19
Manu Kumar, Yun-Shil Gho, Ki-Hong Jung, Seong-Ryong Kim
Cold stress is very detrimental to crop production. However, only a few genes in rice have been identified with known functions related to cold tolerance. To meet this agronomic challenge more effectively, researchers must take global approaches to select useful candidate genes and find the major regulatory factors. We used five Gene expression omnibus series data series of Affymetrix array data, produced with cold stress-treated samples from the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), and identified 502 cold-inducible genes common to both japonica and indica rice cultivars...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28713244/regulatory-roles-of-long-non-coding-rnas-in-the-central-nervous-system-and-associated-neurodegenerative-diseases
#20
REVIEW
Zhenzhen Quan, Da Zheng, Hong Qing
Accumulating studies have revealed that the human genome encodes tens of thousands of long non-coding RNAs (lncRNAs), which participate in multiple biological networks modulating gene expression via transcriptional, post-transcriptional and epigenetic regulation. Strikingly, a large fraction of tissue-specific lncRNAs are expressed in the Central Nervous System (CNS) with precisely regulated temporal and spatial expression patterns. These brain-specific lncRNAs are also featured with the cell-type specificity, the highest signals of evolutionary conservation, and their preferential location adjacent to brain-expressed protein-coding genes...
2017: Frontiers in Cellular Neuroscience
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