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https://www.readbyqxmd.com/read/29332829/synchronous-detection-of-ebolavirus-conserved-rna-sequences-and-ebolavirus-encoded-mirna-like-fragment-based-on-a-zwitterionic-copper-ii-metal-organic-framework
#1
Gui-Hua Qiu, Zi-Hua Weng, Pei-Pei Hu, Wen-Jun Duan, Bao-Ping Xie, Bin Sun, Xiao-Yan Tang, Jin-Xiang Chen
From a three-dimensional (3D) metal-organic framework (MOF) of {[Cu(Cmdcp)(phen)(H2O)]2·9H2O}n (1, H3CmdcpBr = N-carboxymethyl-(3,5-dicarboxyl)pyridinium bromide, phen = phenanthroline), a sensitive and selective fluorescence sensor has been developed for the simultaneous detection of ebolavirus conserved RNA sequences and ebolavirus-encoded microRNA-like (miRNA-like) fragment. The results from molecular dynamics simulation confirmed that MOF 1 absorbs carboxyfluorescein (FAM)-tagged and 5(6)-carboxyrhodamine, triethylammonium salt (ROX)-tagged probe ss-DNA (probe DNA, P-DNA) by π…π stacking and hydrogen bonding, as well as additional electrostatic interactions to form a sensing platform of P-DNAs@1 with quenched FAM and ROX fluorescence...
April 1, 2018: Talanta
https://www.readbyqxmd.com/read/29330702/ptac10-an-s1-domain-containing-component-of-the-transcriptionally-active-chromosome-complex-is-essential-for-plastid-gene-expression-in-arabidopsis-thaliana-and-is-phosphorylated-by-chloroplast-targeted-casein-kinase-ii
#2
Qing-Bo Yu, Tuan-Tuan Zhao, Lin-Shan Ye, Ling Cheng, Ying-Qian Wu, Chao Huang, Zhong-Nan Yang
In higher plant chloroplasts, the plastid-encoded RNA polymerase (PEP) consists of four catalytic subunits and numerous nuclear-encoded accessory proteins, including pTAC10, an S1-domain-containing protein. In this study, pTAC10 knockout lines were characterized. Two ptac10 mutants had an albino phenotype and severely impaired chloroplast development. The pTAC10 genomic sequence fused to a four-tandem MYC tag driven by its own promoter functionally complemented the ptac10-1 mutant phenotype. pTAC10 was present in both the chloroplast stroma and thylakoids...
January 12, 2018: Photosynthesis Research
https://www.readbyqxmd.com/read/29324359/progress-toward-an-enhanced-vaccine-eight-marked-attenuated-viruses-to-porcine-reproductive-and-respiratory-disease-virus
#3
Allyn Spear, Feng-Xue Wang, Matthew A Kappes, Phani B Das, Kay S Faaberg
Recombinant viruses of strain Ingelvac® PRRS porcine reproductive and respiratory syndrome virus (PRRSV) modified live virus vaccine were produced with two individual small in-frame deletions in nonstructural protein 2 (nsp2; Δ23 and Δ87) and also the same deletions supplanted with foreign tags (Δ23-V5, Δ23-FLAG, Δ23-S, Δ87-V5, Δ87-FLAG, Δ87-S). The viruses, but one (Δ87-FLAG), were stable for 10 passages and showed minimal effects on in vitro growth. Northern hybridization showed that the Δ23-tagged probe detected intracellular viral genome RNA as well as shorter RNAs that may represent heteroclite species, while the Δ87-tagged probe detected predominantly only genome length RNAs...
January 8, 2018: Virology
https://www.readbyqxmd.com/read/29323290/clonal-analysis-of-lineage-fate-in-native-haematopoiesis
#4
Alejo E Rodriguez-Fraticelli, Samuel L Wolock, Caleb S Weinreb, Riccardo Panero, Sachin H Patel, Maja Jankovic, Jianlong Sun, Raffaele A Calogero, Allon M Klein, Fernando D Camargo
Haematopoiesis, the process of mature blood and immune cell production, is functionally organized as a hierarchy, with self-renewing haematopoietic stem cells and multipotent progenitor cells sitting at the very top. Multiple models have been proposed as to what the earliest lineage choices are in these primitive haematopoietic compartments, the cellular intermediates, and the resulting lineage trees that emerge from them. Given that the bulk of studies addressing lineage outcomes have been performed in the context of haematopoietic transplantation, current models of lineage branching are more likely to represent roadmaps of lineage potential than native fate...
January 11, 2018: Nature
https://www.readbyqxmd.com/read/29322297/nuclear-distribution-of-the-trypanosoma-cruzi-rna-pol-i-subunit-rpa31-during-growth-and-metacyclogenesis-and-characterization-of-its-nuclear-localization-signal
#5
Israel Canela-Pérez, Imelda López-Villaseñor, Ana María Cevallos, Roberto Hernández
Trypanosoma cruzi is the aetiologic agent of Chagas disease. Our research group studies ribosomal RNA (rRNA) gene transcription and nucleolus dynamics in this species of trypanosomes. RPA31 is an essential subunit of RNA polymerase I (Pol I) whose presence is apparently restricted to trypanosomes. Using fluorescent-tagged versions of this protein (TcRPA31-EGFP), we describe its nuclear distribution during growth and metacyclogenesis. Our findings indicate that TcRPA31-EGFP alters its nuclear presence from concentrated nucleolar localization in exponentially growing epimastigotes to a dispersed granular distribution in the nucleoplasm of stationary epimastigotes and metacyclic trypomastigotes...
January 10, 2018: Parasitology Research
https://www.readbyqxmd.com/read/29315273/aeginetia-indica-decoction-inhibits-hepatitis-c-virus-life-cycle
#6
Cheng-Wei Lin, Chieh-Wen Lo, Chia-Ni Tsai, Ting-Chun Pan, Pin-Yin Chen, Ming-Jiun Yu
Chronic hepatitis C virus (HCV) infection is still a global epidemic despite the introduction of several highly effective direct-acting antivirals that are tagged with sky-high prices. The present study aimed to identify an herbal decoction that ameliorates HCV infection. Among six herbal decoctions tested, the Aeginetia indica decoction had the most profound effect on the HCV reporter activity in infected Huh7.5.1 liver cells in a dose- and time-dependent manner. The Aeginetia indica decoction exerted multiple inhibitory effects on the HCV life cycle...
January 9, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29311362/novel-transcriptional-activity-and-extensive-allelic-imbalance-in-the-human-mhc-region
#7
Elizabeth Gensterblum-Miller, Weisheng Wu, Amr H Sawalha
The MHC region encodes HLA genes and is the most complex region in the human genome. The extensively polymorphic nature of the HLA hinders accurate localization and functional assessment of disease risk loci within this region. Using targeted capture sequencing and constructing individualized genomes for transcriptome alignment, we identified 908 novel transcripts within the human MHC region. These include 593 novel isoforms of known genes, 137 antisense strand RNAs, 119 novel long intergenic noncoding RNAs, and 5 transcripts of 3 novel putative protein-coding human endogenous retrovirus genes...
January 8, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29301188/a-boy-with-46-x-mar-presenting-gynecomastia-and-short-stature
#8
Ki Eun Kim, Ye Jin Kim, Mo Kyoung Jung, Hyun-Wook Chae, Ah Reum Kwon, Woo Jung Lee, Duk-Hee Kim, Ho-Seong Kim
A 15-year-old boy was referred due to gynecomastia and short stature. He was overweight and showed the knuckle-dimple sign on the left hand, a short fourth toe on the left foot, and male external genitalia with a small phallus. His levels of estradiol and follicle-stimulating hormone were increased, and his testosterone concentration was normal. Other hormonal tests were within the normal range. Radiographs showed short fourth and fifth metacarpals and fourth metatarsal bones. The karyotype was reported as 46,X,+mar, and the marker chromosome was shown to originate from the Y chromosome, which was identified by fluorescence in situ hybridization...
December 2017: Annals of Pediatric Endocrinology & Metabolism
https://www.readbyqxmd.com/read/29295864/harnessing-an-rna-mediated-chaperone-for-the-assembly-of-influenza-hemagglutinin-in-an-immunologically-relevant-conformation
#9
Seung Won Yang, Yo Han Jang, Soon Bin Kwon, Yoon Jae Lee, Wonil Chae, Young Ho Byun, Paul Kim, Chan Park, Young Jae Lee, Choon Kang Kim, Young Seok Kim, Seong Il Choi, Baik Lin Seong
A novel protein-folding function of RNA has been recognized, which can outperform previously known molecular chaperone proteins. The RNA as a molecular chaperone (chaperna) activity is intrinsic to some ribozymes and is operational during viral infections. Our purpose was to test whether influenza hemagglutinin (HA) can be assembled in a soluble, trimeric, and immunologically activating conformation by means of an RNA molecular chaperone (chaperna) activity. An RNA-interacting domain (RID) from the host being immunized was selected as a docking tag for RNA binding, which served as a transducer for the chaperna function for de novo folding and trimeric assembly of RID-HA1...
January 2, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29286477/biotinylated-cell-penetrating-peptides-to-study-intracellular-protein-protein-interactions
#10
Myriam Jaraíz-Rodríguez, Ana González-Sánchez, Laura García-Vicente, Jose M Medina, Arantxa Tabernero
Here we present a protocol to study intracellular protein-protein interactions that is based on the widely used biotin-avidin pull-down system. The modification presented includes the combination of this technique with cell-penetrating sequences. We propose to design cell-penetrating baits that can be incubated with living cells instead of cell lysates and therefore the interactions found will reflect those that occur within the intracellular context. Connexin43 (Cx43), a protein that forms gap junction channels and hemichannels is down-regulated in high-grade gliomas...
December 20, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29286136/proteomic-investigation-of-the-effects-of-preimplantation-factor-on-human-embryo-implantation
#11
Min Yang, Yixuan Yang, Sha She, Sanglin Li
Despite the use of adjuvant therapies, the cumulative proportion of live births remains at ~40%. Accumulating data show that low pregnancy rates, even in the presence of high fertility rates, are due to implantation failure. The present study aimed to identify and construct a profile of proteins that react with preimplantation factor (PIF) and to provide an understanding into the molecular mechanisms by which PIF promotes trophoblast invasion. Cytoplasmic proteins were immunoprecipitated with biotin‑labeled synthetic PIF or intralipid and scrambled PIF (PIFscr)...
December 22, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29261807/characterization-of-host-proteins-interacting-with-the-lymphocytic-choriomeningitis-virus-l-protein
#12
Kseniya Khamina, Alexander Lercher, Michael Caldera, Christopher Schliehe, Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, Anannya Bhattacharya, Peter Májek, Alexey Stukalov, Roberto Sacco, Leo C James, Daniel D Pinschewer, Keiryn L Bennett, Jörg Menche, Andreas Bergthaler
RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics...
December 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29250754/high-level-production-of-dna-specific-endonuclease-asendi-with-synonymous-codon-and-its-potential-utilization-for-removing-dna-contamination
#13
Yuan Wang, Peng Jia, Rahat Sharif, Zhengchen Li, Yuhong Li, Peng Chen
Endonuclease I is a widely distributed periplasmic or extracellular enzyme. A method for the high-level production of recombinant AsEndI (endonuclease I from Aliivibrio salmonicida) in Escherichia coli with secretion expression is investigated. The coding sequence of AsEndI gene was assembled according to the E. coli codon usage bias, and AsEndI was expressed in the periplasm of E. coli TOP10 with a C-terminal 6× His-tagged fusion. The recombinant AsEndI (His-AsEndI) was purified by Ni-NTA resin with a yield of 1...
December 18, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/29248385/a-cytosolic-sensor-pmddx41-mediates-antiviral-immune-response-in-black-tiger-shrimp-penaeus-monodon
#14
Suthinee Soponpong, Piti Amparyup, Anchalee Tassanakajon
DEAD (Asp-Glu-Ala-Asp)-box polypeptide 41 (DDX41), a receptor belonging to the DExD family, has recently been identified as an intracellular DNA sensor in vertebrates. Here, we report on the identification and functional characterization of PmDDX41, the first cytosolic DNA sensor in shrimp. By searching a Penaeus monodon expressed sequence tag (EST) database (http://pmonodon.biotec.or.th), three cDNA fragments exhibiting similarity to DDX41 in various species were identified and assembled, resulting in a complete open reading frame of PmDDX41 that contains 1868-bp and encodes a putative protein of 620 amino acids...
December 14, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/29246928/identification-of-mir-29b-targets-using-3-cyanovinylcarbazole-containing-mimics
#15
Anupma Choudhary, Darya Vanichkina, Christine Ender, Joanna Crawford, Gregory Baillie, Andrew Calcino, Kelin Ru, Ryan Taft
MicroRNAs (miRNAs) are highly conserved ~22nt small noncoding RNAs that bind partially complementary sequences in target transcripts. MicroRNAs regulate both translation and transcript stability, and play important roles in development, cellular homeostasis and disease. There are limited approaches available to agnostically identify microRNA targets transcriptome-wide, and methods employing miRNA mimics, which in principle identify direct miRNA:transcript pairs, have low sensitivity and specificity. Here we describe a novel method to identify microRNA targets using miR-29b mimics containing 3-cyanovinylcarbazole (CNVK), a photolabile nucleoside analogue...
December 15, 2017: RNA
https://www.readbyqxmd.com/read/29245388/the-complete-mitochondrial-genome-of-the-jumping-grasshopper-i-sinopodisma-i-i-pieli-i-orthoptera-acrididae-and-the-phylogenetic-analysis-of-melanoplinae
#16
Huaxuan Liu, Liyun Yan, Guofang Jiang
In this study, we reported the complete mitochondrial genome (mitogenome) of Sinopodisma pieli by polymerase chain reaction method for the first time, the type species of the genus Sinopodisma. Its mitogenome was a circular DNA molecule of 15,625 bp in length, with 76.0% A+T, and contained 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes and one A+T control region. The overall base composition of the S. pieli mitogenome was 42.8% for A, 33.2% for T, 13.5% for C, and 10.5% for G, respectively...
December 12, 2017: Zootaxa
https://www.readbyqxmd.com/read/29239600/exonuclease-iii-assisted-upconversion-resonance-energy-transfer-in-a-wash-free-suspension-dna-assay
#17
Yinghui Chen, Hien Duong, Shihui Wen, Chao Mi, Yingzhu Zhou, Olga Shimoni, Stella M Valenzuela, Dayong Jin
Sensitivity is the key in optical detection of low-abundant analytes, such as circulating RNA or DNA. The enzyme Exonuclease III (Exo III) is a useful tool in this regard; its ability to recycle target DNA molecules results in markedly improved detection sensitivity. Lower limits of detection may be further achieved if the detection background of auto-fluorescence can be removed. Here we report an ultrasensitive and specific method to quantify trace amounts of DNA analytes in a wash-free suspension assay. In the presence of target DNA, the Exo III recycles the target DNA by selectively digesting the dye-tagged sequence-matched probe DNA strand only, so that the amount of free dye removed from the probe DNA is proportional to the number of target DNAs...
December 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29235545/one-plasmid-double-expression-his-tag-system-for-rapid-production-and-easy-purification-of-ms2-phage-like-particles
#18
Pavel Mikel, Petra Vasickova, Petr Kralik
MS2 phage-like particles (MS2 PLP) are artificially constructed pseudo-viral particles derived from bacteriophage MS2. They are able to carry a specific single stranded RNA (ssRNA) sequence of choice inside their capsid, thus protecting it against the effects of ubiquitous nucleases. Such particles are able to mimic ssRNA viruses and, thus, may serve as the process control for molecular detection and quantification of such agents in several kinds of matrices, vaccines and vaccine candidates, drug delivery systems, and systems for the display of immunologically active peptides or nanomachines...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29230863/characterization-of-a-nilaparvata-lugens-st%C3%A3-l-brummer-gene-and-analysis-of-its-role-in-lipid-metabolism
#19
Jinming Zhou, Jing Yan, Keke You, Xia Chen, Zhineng Yuan, Qiang Zhou, Kai Lu
The brummer (bmm) genes encode the lipid storage droplet-associated triacylglycerols (TAG) lipases, which belong to the Brummer/Nutrin subfamily. These enzymes hydrolyze the ester bonds in TAG in lipid metabolism and act in insect energy homeostasis. Exposure to some agricultural chemicals leads to increased fecundity, which necessarily involves lipid metabolism, in some planthopper species. However, the biological roles of bmm in planthopper lipid storage and mobilization have not been investigated. Here, the open reading frame (ORF) of bmm (Nlbmm) was cloned and sequenced from the brown planthopper (BPH; Nilaparvata lugens)...
December 12, 2017: Archives of Insect Biochemistry and Physiology
https://www.readbyqxmd.com/read/29224073/cleantag-adapters-improve-small-rna-next-generation-sequencing-library-preparation-by-reducing-adapter-dimers
#20
Sabrina Shore, Jordana M Henderson, Anton P McCaffrey
Next-generation small RNA sequencing is a valuable tool which is increasing our knowledge regarding small noncoding RNAs and their function in regulating genetic information. Library preparation protocols for small RNA have thus far been restricted due to higher RNA input requirements (>10 ng), long workflows, and tedious manual gel purifications. Small RNA library preparation methods focus largely on the prevention or depletion of a side product known as adapter dimer that tends to dominate the reaction...
2018: Methods in Molecular Biology
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