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https://www.readbyqxmd.com/read/27903806/oschx14-is-involved-in-the-k-homeostasis-in-rice-oryza-sativa-flowers
#1
Yi Chen, Jingkun Ma, Anthony J Miller, Bingbing Luo, Mei Wang, Zhen Zhu, Pieter B F Ouwerkerk
Previously we showed in the osjar1 mutants that the lodicule senescence which controls the closing of rice flowers was delayed. This resulted in florets staying open longer when compared with the wild type. The gene OsJAR1 is silenced in osjar1 mutants and is a key member of the jasmonic acid (JA) signaling pathway. We found that K concentrations in lodicules and flowers of osjar1-2 were significantly elevated compared with the wild type, indicating that K(+) homeostasis may play a role in regulating the closure of rice flowers...
July 2016: Plant & Cell Physiology
https://www.readbyqxmd.com/read/27902874/spodoptera-litura-autophagy-related-protein-1-interacts-with-autophagy-related-protein-5-and-enhances-its-degradation
#2
N Zhang, Y Yang, H Lu, Y Xiang, X Huang, R Hu, Z Chen, W Yuan, R Peng, J Peng, H Ai, K Liu
It is known that the autophagy-related protein 1 (ATG1) plays critical roles in the regulation of autophagy in mammals and yeast, whereas the function of ATG1 in lepidopteran insects is not well elucidated. Here Spodoptera litura ATG1 (SlATG1) and its interactions with other ATG proteins were characterized. Alternative splicing of SlAtg1 produced at least four transcript variants. Over-expression and RNA interference knockdown of SlAtg1 demonstrated that SlATG1 enhanced autophagy. SlATG1A-Green fluorescent protein (GFP) tagged localized in the cytoplasm and formed some punctuate dots, which were colocalized with red fluorescent protein mCherry tagged Spodoptera exigua ATG5 (SeATG5)...
November 30, 2016: Insect Molecular Biology
https://www.readbyqxmd.com/read/27902702/selective-inhibitor-of-nuclear-export-sine-compounds-alter-new-world-alphavirus-capsid-localization-and-reduce-viral-replication-in-mammalian-cells
#3
Lindsay Lundberg, Chelsea Pinkham, Cynthia de la Fuente, Ashwini Brahms, Nazly Shafagati, Kylie M Wagstaff, David A Jans, Sharon Tamir, Kylene Kehn-Hall
The capsid structural protein of the New World alphavirus, Venezuelan equine encephalitis virus (VEEV), interacts with the host nuclear transport proteins importin α/β1 and CRM1. Novel selective inhibitor of nuclear export (SINE) compounds, KPT-185, KPT-335 (verdinexor), and KPT-350, target the host's primary nuclear export protein, CRM1, in a manner similar to the archetypical inhibitor Leptomycin B. One major limitation of Leptomycin B is its irreversible binding to CRM1; which SINE compounds alleviate because they are slowly reversible...
November 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27899627/improvements-to-patric-the-all-bacterial-bioinformatics-database-and-analysis-resource-center
#4
Alice R Wattam, James J Davis, Rida Assaf, Sébastien Boisvert, Thomas Brettin, Christopher Bun, Neal Conrad, Emily M Dietrich, Terry Disz, Joseph L Gabbard, Svetlana Gerdes, Christopher S Henry, Ronald W Kenyon, Dustin Machi, Chunhong Mao, Eric K Nordberg, Gary J Olsen, Daniel E Murphy-Olson, Robert Olson, Ross Overbeek, Bruce Parrello, Gordon D Pusch, Maulik Shukla, Veronika Vonstein, Andrew Warren, Fangfang Xia, Hyunseung Yoo, Rick L Stevens
The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27895115/shared-subunits-of-tetrahymena-telomerase-holoenzyme-and-replication-protein-a-have-different-functions-in-different-cellular-complexes
#5
Heather E Upton, Henry Chan, Juli Feigon, Kathleen Collins
In most eukaryotes, telomere maintenance relies on telomeric repeat synthesis by a reverse transcriptase named telomerase. To synthesize telomeric repeats, the catalytic subunit telomerase reverse transcriptase (TERT) uses the RNA subunit (TER) as a template. In the ciliate Tetrahymena thermophila,the telomerase holoenzyme consists of TER, TERT, and eight additional proteins including the telomeric-repeat single-stranded DNA binding protein Teb1 and its heterotrimer partners Teb2 and Teb3. Teb1 is paralogous to the large subunit of the general single-stranded DNA binding heterotrimer Replication Protein A (RPA)...
November 28, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27894276/small-proteins-in-cyanobacteria-provide-a-paradigm-for-the-functional-analysis-of-the-bacterial-micro-proteome
#6
Desiree Baumgartner, Matthias Kopf, Stephan Klähn, Claudia Steglich, Wolfgang R Hess
BACKGROUND: Despite their versatile functions in multimeric protein complexes, in the modification of enzymatic activities, intercellular communication or regulatory processes, proteins shorter than 80 amino acids (μ-proteins) are a systematically underestimated class of gene products in bacteria. Photosynthetic cyanobacteria provide a paradigm for small protein functions due to extensive work on the photosynthetic apparatus that led to the functional characterization of 19 small proteins of less than 50 amino acids...
November 28, 2016: BMC Microbiology
https://www.readbyqxmd.com/read/27893425/tag-snps-of-long-non-coding-rna-tincr-affect-the-genetic-susceptibility-to-gastric-cancer-in-a-chinese-population
#7
Xiang Ma, Chi Huang, Dakui Luo, Younan Wang, Ran Tang, Xiangkun Huan, Yi Zhu, Zekuan Xu, Ping Liu, Li Yang
Tissue differentiation-inducing non-protein coding RNA (TINCR) is required for normal epidermal differentiation. TINCR is also strongly overexpressed in human gastric cancer (GC) and contributes to carcinogenesis and tumor progression. However, the association between TINCR polymorphisms and the risk of any diseases, such as GC, remains unknown. In the present study, the tag single nucleotide polymorphisms rs8113645, rs2288947, rs8105637, and rs12610531 were analyzed in 602 patients with GC and 602 age- and sex-matched controls...
November 23, 2016: Oncotarget
https://www.readbyqxmd.com/read/27879391/rice-leaf-angle-and-grain-size-are-affected-by-the-osbul1-transcriptional-activator-complex
#8
Seonghoe Jang, Gynheung An, Hsing-Yi Li
Rice atypical HLH protein Oryza sativa BRASSINOSTEROID UPREGULATED 1-LIKE 1 (OsBUL1) is preferentially expressed in the laminar joint where it controls cell elongation and positively affects leaf angles. OsBUL1 knockout mutant (osbul1) and transgenic rice for double stranded RNA interference (dsRNAi) of OsBUL1 produced erected leaves with smaller grains whereas OsBUL1 overexpressors and an activation tagging line of OsBUL1 exhibited increased laminar inclination and grain size. Moreover, OsBUL1 expression was induced by brassinolide (BL) and osbul1 did not respond to BL treatment...
November 22, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27875576/small-rna-library-preparation-method-for-next-generation-sequencing-using-chemical-modifications-to-prevent-adapter-dimer-formation
#9
Sabrina Shore, Jordana M Henderson, Alexandre Lebedev, Michelle P Salcedo, Gerald Zon, Anton P McCaffrey, Natasha Paul, Richard I Hogrefe
For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants...
2016: PloS One
https://www.readbyqxmd.com/read/27864674/interactions-between-giardia-duodenalis-sm-proteins-and-their-association-with-spliceosomal-snrnas
#10
Vanessa Gómez, Moisés Wasserman
Giardia duodenalis is a parasite that colonises the intestines of humans and other vertebrates, causing diarrhoea and poor nutrient absorption. G. duodenalis is sometimes considered an early diverging eukaryote, and its genome exhibits simplified molecular machinery for many cellular processes, which makes it an interesting model to study. The spliceosome, one of the most complex molecular machines in the eukaryotic cell, is responsible for intron excision and exon splicing. Just over a decade ago, it was believed that the G...
November 18, 2016: Parasitology Research
https://www.readbyqxmd.com/read/27854567/metagenomic-evaluation-of-bacteria-from-voles
#11
Katja A Koskela, Laura Kalin-Mänttäri, Heidi Hemmilä, Teemu Smura, Paula M Kinnunen, Jukka Niemimaa, Heikki Henttonen, Simo Nikkari
Voles (Arvicolinae, Rodentia) are known carriers of zoonotic bacteria such as Bartonella spp. and Francisella tularensis. However, apart from F. tularensis, the bacterial microbiome of voles has not previously been determined in Finland and rarely elsewhere. Therefore, we studied liver samples from 61 voles using 16S ribosomal RNA gene PCR analysis, followed by Sanger sequencing. Twenty-three of these samples were also studied with tag-encoded pyrosequencing. The samples originated from 21 field voles (Microtus agrestis), 37 tundra voles (Microtus oeconomus), and 3 bank voles (Myodes glareolus)...
November 17, 2016: Vector Borne and Zoonotic Diseases
https://www.readbyqxmd.com/read/27852860/nes-masking-regulates-hiv-1-rev-trafficking-and-viral-rna-nuclear-export
#12
Ryan T Behrens, Mounavya Aligeti, Ginger M Pocock, Christina A Higgins, Nathan M Sherer
: HIV-1's Rev protein forms a homooligomeric adaptor complex linking viral RNAs to the cellular CRM1/Ran-GTP nuclear export machinery through the activity of Rev's prototypical leucine-rich nuclear export signal (NES). In this study we used a functional fluorescently-tagged Rev fusion protein as a platform to study the effects of modulating Rev NES identity, number, position, or strength on Rev subcellular trafficking, viral RNA nuclear export, and infectious virion production. We found Rev activity to be remarkably tolerant of diverse NES sequences including supraphysiological NES (SNES) peptides that otherwise arrest CRM1 transport complexes at nuclear pores...
November 16, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27825944/the-u6-biogenesis-like-1-plays-an-important-role-in-maize-kernel-and-seedling-development-by-affecting-the-3-end-processing-of-u6-snrna
#13
Jiankun Li, Junjie Fu, Yan Chen, Kaijian Fan, Cheng He, Zhiqiang Zhang, Li Li, Yunjun Liu, Jun Zheng, Dongtao Ren, Guoying Wang
The regulation of gene expression at the post-transcriptional level is of crucial importance in the development of an organism. Here, we present a maize gene, U6 biogenesis like 1 (UBL1), which plays an important role in kernel and seedling development by influencing pre-mRNA splicing. The ubl1 mutant, revealing the phenotype of small kernel and weak seedling, was isolated from a Mutator-tagged population. Transgenic complementation and three independent mutant alleles confirmed that UBL1 is responsible for the phenotype of ubl1...
November 4, 2016: Molecular Plant
https://www.readbyqxmd.com/read/27825887/electrochemical-immunosensor-for-n6-methyladenosine-detection-in-human-cell-lines-based-on-biotin-streptavidin-system-and-silver-sio2-signal-amplification
#14
Huanshun Yin, Haiyan Wang, Wenjing Jiang, Yunlei Zhou, Shiyun Ai
N6-methyladenosine (m6A), a kind of RNA methylation form and important epigenetic event, plays crucial roles in many biological progresses. Thus it is essential to quantitatively detect m6A in complicated biological samples. Herein, a simple and sensitive electrochemical method was developed for m6A detection using N6-methyladenosine-5'-triphosphate (m6ATP) as detection target molecule. In this detection strategy, anti-m6A antibody was selected as m6A recognition and capture reagent, silver nanoparticles and amine-PEG3-biotin functionalized SiO2 nanospheres (Ag@SiO2) was prepared and used as signal amplification label, and phos-tag-biotin played a vital role of "bridge" to link m6ATP and Ag@SiO2 through the two forms of specific interaction between phosphate group of m6ATP and phos-tag, biotin and streptavidin, respectively...
October 27, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27822450/a-simple-and-effective-method-for-ultrastructural-analysis-of-mitosis-in-drosophila-s2-cells
#15
Anton Strunov, Lidiya V Boldyreva, Gera A Pavlova, Alexey V Pindyurin, Maurizio Gatti, Elena Kiseleva
The Drosophila S2 tissue culture cells are a widely used system for studies on mitosis. S2 cells are particularly sensitive to gene silencing by RNA interference (RNAi), allowing targeted inactivation of mitotic genes. S2 cells are also well suited for high-resolution light microscopy analysis of mitosis in fixed cells, and can be easily immunostained to detect mitotic components. In addition, S2 cells are amenable to transformation with plasmid encoding fluorescently tagged mitotic proteins, allowing in vivo analysis of their behavior throughout cell division...
2016: MethodsX
https://www.readbyqxmd.com/read/27821849/detailed-analysis-of-protein-topology-of-extracellular-vesicles-evidence-of-unconventional-membrane-protein-orientation
#16
Aleksander Cvjetkovic, Su Chul Jang, Barbora Konečná, Johanna L Höög, Carina Sihlbom, Cecilia Lässer, Jan Lötvall
Extracellular vesicles (EVs) are important mediators of intercellular communication that change the recipient cell by shuttling lipids, RNA, or protein cargo between cells. Here, we investigate the topology of the protein cargo found in EVs, as this topology can fundamentally influence the biological effects of EVs. A multiple proteomics approach, combining proteinase treatment and biotin tagging, shows that many proteins of cytosolic origin are localized on the surface of EVs. A detailed analysis of the EV proteome at the peptide level revealed that a number of EV membrane proteins are present in a topologically reversed orientation compared to what is annotated...
November 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27811180/a-new-marker-sequence-for-systematics-of-medically-important-fungi-based-on-amino-acid-sequence-of-the-largest-subunit-of-rna-polymerase-i
#17
Chiaki Yamanishi, Mohamed Mahdi Alshahni, Ayako Sano, Ikuo Nakamura, Koichi Makimura
Molecular evolution has dominated taxonomic studies for decades, replacing traditional methods for identification and classification. However, there is a need for better markers to resolve the problems that have limited their usefulness. In this report, we introduce the protein tag (Ptag) sequence, a highly polymorphic amino acid sequence within the C-terminal region of the largest subunit of RNA polymerase I, as a new systematic tag sequence for delineating the evolutionary history of medically important fungi...
November 2, 2016: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/27807710/two-isoforms-of-hormone-sensitive-lipase-b-are-generated-by-alternative-exons-usage-and-transcriptional-regulation-by-insulin-in-grass-carp-ctenopharyngodon-idella
#18
Jian Sun, Zhou Yang, PeiZhen Xiao, Yong Liu, Hong Ji, ZhenYu Du, LiQiao Chen
The aim of this study was to investigate the gene structure of two hormone-sensitive lipase b (HSLb) isoforms and their transcriptional regulation by insulin in grass carp (Ctenopharyngodon idella). HSL is an important lipolytic enzyme responsible for the hydrolysis of triacylglycerols (TAGs). Two isoforms (HSLa and HSLb) have been cloned in fish, but information about their gene structure and function is very few. In this study, a novel grass carp HSLb isoform (HSLb2) were firstly isolated and characterized from grass carp, encoding peptides of 848 amino acid residues...
November 2, 2016: Fish Physiology and Biochemistry
https://www.readbyqxmd.com/read/27795410/deep-sequence-identification-and-role-in-virus-replication-of-a-jc-virus-quasispecies-in-patients-with-progressive-multifocal-leukoencephalopathy
#19
Kenta Takahashi, Tsuyoshi Sekizuka, Hitomi Fukumoto, Kazuo Nakamichi, Tadaki Suzuki, Yuko Sato, Hideki Hasegawa, Makoto Kuroda, Harutaka Katano
: JC virus (JCV) is a DNA virus causing progressive multifocal leukoencephalopathy (PML) in immunodeficient patients. In the present study, 22 genetic quasispecies with more than 1.5% variant frequency were detected in JCV genomes from six clinical samples of PML by next-generation sequencing. A mutation from A to C at nt 3495 in JCV Mad1 resulting in a V to G amino acid substitution at aa position 392 of the large T antigen (TAg) was identified in all six cases of PML at 3%-19% variant frequencies...
October 19, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27793802/a-sequence-upstream-of-canonical-pdz-binding-motif-within-cftr-c-terminus-enhances-nherf1-interaction
#20
Neeraj Sharma, Jessica LaRusch, Patrick Sosnay, Laura B Gottschalk, Andrea Lopez, Matthew J Pellicore, Taylor Evans, Emily Davis, Melis Atalar, Chan-Hyun Na, Gedge D Rosson, Deborah Belchis, Michal Milewski, Akhilesh Pandey, Garry R Cutting
The development of CFTR targeted therapy for cystic fibrosis has generated interest in maximizing membrane residence of mutant forms of CFTR by manipulating interactions with scaffold proteins such as NHERF1. In this study, we explored whether C-terminal sequences in CFTR beyond the PDZ-binding motif influence its interaction with NHERF1. NHERF1 displayed minimal self-association in blot overlays (NHERF1, Kd = 1382 ± 61.1 nM) at concentrations well above physiologic levels, estimated at 240 nM from RNA-Seq and 260 nM by LC-MS/MS in sweat gland, a key site of CFTR function in vivo...
October 28, 2016: American Journal of Physiology. Lung Cellular and Molecular Physiology
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