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https://www.readbyqxmd.com/read/28107688/sequencing-and-de-novo-assembly-of-visceral-mass-transcriptome-of-the-critically-endangered-land-snail-satsuma-myomphala-annotation-and-ssr-discovery
#1
Se Won Kang, Bharat Bhusan Patnaik, Hee-Ju Hwang, So Young Park, Jong Min Chung, Dae Kwon Song, Hongray Howrelia Patnaik, Jae Bong Lee, Changmu Kim, Soonok Kim, Young-Su Park, Hong Seog Park, Seung-Hwan Park, Yeon Soo Han, Jun Sang Lee, Yong Seok Lee
Satsuma myomphala is critically endangered through loss of natural habitats, predation by natural enemies, and indiscriminate collection. It is a protected species in Korea but lacks genomic resources for an understanding of varied functional processes attributable to evolutionary success under natural habitats. For assessing the genetic information of S. myomphala, we performed for the first time, de novo transcriptome sequencing and functional annotation of expressed sequences using Illumina Next-Generation Sequencing (NGS) platform and bioinformatics analysis...
October 29, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28106839/the-importance-of-the-nucleus-during-flavivirus-replication
#2
REVIEW
Adam J Lopez-Denman, Jason M Mackenzie
Flaviviruses are a large group of arboviruses of significant medical concern worldwide. With outbreaks a common occurrence, the need for efficient viral control is required more than ever. It is well understood that flaviviruses modulate the composition and structure of membranes in the cytoplasm that are crucial for efficient replication and evading immune detection. As the flavivirus genome consists of positive sense RNA, replication can occur wholly within the cytoplasm. What is becoming more evident is that some viral proteins also have the ability to translocate to the nucleus, with potential roles in replication and immune system perturbation...
January 19, 2017: Viruses
https://www.readbyqxmd.com/read/28106836/the-astrovirus-capsid-a-review
#3
REVIEW
Carlos F Arias, Rebecca M DuBois
Astroviruses are enterically transmitted viruses that cause infections in mammalian and avian species. Astroviruses are nonenveloped, icosahedral viruses comprised of a capsid protein shell and a positive-sense, single-stranded RNA genome. The capsid protein undergoes dramatic proteolytic processing both inside and outside of the host cell, resulting in a coordinated maturation process that affects cellular localization, virus structure, and infectivity. After maturation, the capsid protein controls the initial phases of virus infection, including virus attachment, endocytosis, and genome release into the host cell...
January 19, 2017: Viruses
https://www.readbyqxmd.com/read/28106804/ultrafast-electronic-deactivation-dynamics-of-xanthosine-monophosphate
#4
Katharina Röttger, Rebecca Stellmacher, Mayra C Stuhldreier, Friedrich Temps
Ultrafast energy dissipation is a crucial factor for the photostability of DNA and RNA, but even some of the key electronic deactivation pathways in monomeric nucleic acid building stones are still controversial. Here, we report on the excited-state dynamics of the rare nucleotide xanthosine monophosphate as a function of deprotonation state (XMP vs. XMP - ) and excitation wavelength ( λ pump = 278-243 nm) by femtosecond time-resolved fluorescence and absorption spectroscopy. We show that the predominating relaxation channel leads to a return of the photo-excited molecules to the electronic ground state in τ∼1 ps...
January 18, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28106786/sulfolobus-acidocaldarius-udg-can-remove-du-from-the-rna-backbone-insight-into-the-specific-recognition-of-uracil-linked-with-deoxyribose
#5
Gang-Shun Yi, Wei-Wei Wang, Wei-Guo Cao, Feng-Ping Wang, Xi-Peng Liu
Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG). Two recombinant S. acidocaldarius UDGs (SacUDG) were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU) base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond...
January 18, 2017: Genes
https://www.readbyqxmd.com/read/28106722/using-network-extracted-ontologies-to-identify-novel-genes-with-roles-in-appressorium-development-in-the-rice-blast-fungus-magnaporthe-oryzae
#6
Ryan M Ames
Magnaporthe oryzae is the causal agent of rice blast disease, the most important infection of rice worldwide. Half the world's population depends on rice for its primary caloric intake and, as such, rice blast poses a serious threat to food security. The stages of M. oryzae infection are well defined, with the formation of an appressorium, a cell type that allows penetration of the plant cuticle, particularly well studied. However, many of the key pathways and genes involved in this disease stage are yet to be identified...
January 17, 2017: Microorganisms
https://www.readbyqxmd.com/read/28106375/acinetodin-and-klebsidin-rna-polymerase-targeting-lasso-peptides-produced-by-human-isolates-of-acinetobacter-gyllenbergii-and-klebsiella-pneumoniae
#7
Mikhail Metelev, Anatolii Arseniev, Leah B Bushin, Konstantin Kuznedelov, Tatiana O Artamonova, Ruslan Kondratenko, Mikhail Khodorkovskii, Mohammad R Seyedsayamdost, Konstantin Severinov
We report the bioinformatic prediction and structural validation of two lasso peptides, acinetodin and klebsidin, encoded by the genomes of several human-associated strains of Acinetobacter and Klebsiella. Computation of the three-dimensional structures of these peptides using NMR NOESY constraints verifies that they contain a lasso motif. Despite the lack of sequence similarity to each other or to microcin J25, a prototypical lasso peptide and transcription inhibitor from Escherichia coli, acinetodin and klebsidin also inhibit transcript elongation by the E...
January 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28105941/the-loss-of-photosynthetic-pathways-in-the-plastid-and-nuclear-genomes-of-the-non-photosynthetic-mycoheterotrophic-eudicot-monotropa-hypopitys
#8
Nikolai V Ravin, Eugeny V Gruzdev, Alexey V Beletsky, Alexander M Mazur, Egor B Prokhortchouk, Mikhail A Filyushin, Elena Z Kochieva, Vitaly V Kadnikov, Andrey V Mardanov, Konstantin G Skryabin
BACKGROUND: Chloroplasts of most plants are responsible for photosynthesis and contain a conserved set of about 110 genes that encode components of housekeeping gene expression machinery and photosynthesis-related functions. Heterotrophic plants obtaining nutrients from other organisms and their plastid genomes represent model systems in which to study the effects of relaxed selective pressure on photosynthetic function. The most evident is a reduction in the size and gene content of the plastome, which correlates with the loss of genes encoding photosynthetic machinery which become unnecessary...
November 16, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28105940/integrated-single-cell-data-analysis-reveals-cell-specific-networks-and-novel-coactivation-markers
#9
Shila Ghazanfar, Adam J Bisogni, John T Ormerod, David M Lin, Jean Y H Yang
BACKGROUND: Large scale single cell transcriptome profiling has exploded in recent years and has enabled unprecedented insight into the behavior of individual cells. Identifying genes with high levels of expression using data from single cell RNA sequencing can be useful to characterize very active genes and cells in which this occurs. In particular single cell RNA-Seq allows for cell-specific characterization of high gene expression, as well as gene coexpression. RESULTS: We offer a versatile modeling framework to identify transcriptional states as well as structures of coactivation for different neuronal cell types across multiple datasets...
December 5, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28105919/snoreport-2-0-new-features-and-a-refined-support-vector-machine-to-improve-snorna-identification
#10
João Victor de Araujo Oliveira, Fabrizio Costa, Rolf Backofen, Peter Florian Stadler, Maria Emília Machado Telles Walter, Jana Hertel
BACKGROUND: snoReport uses RNA secondary structure prediction combined with machine learning as the basis to identify the two main classes of small nucleolar RNAs, the box H/ACA snoRNAs and the box C/D snoRNAs. Here, we present snoReport 2.0, which substantially improves and extends in the original method by: extracting new features for both box C/D and H/ACA box snoRNAs; developing a more sophisticated technique in the SVM training phase with recent data from vertebrate organisms and a careful choice of the SVM parameters C and γ; and using updated versions of tools and databases used for the construction of the original version of snoReport...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105914/homology-modeling-and-molecular-dynamics-provide-structural-insights-into-tospovirus-nucleoprotein
#11
Rayane Nunes Lima, Muhammad Faheem, João Alexandre Ribeiro Gonçalves Barbosa, Marcelo Depólo Polêto, Hugo Verli, Fernando Lucas Melo, Renato Oliveira Resende
BACKGROUND: Tospovirus is a plant-infecting genus within the family Bunyaviridae, which also includes four animal-infecting genera: Hantavirus, Nairovirus, Phlebovirus and Orthobunyavirus. Compared to these members, the structures of Tospovirus proteins still are poorly understood. Despite multiple studies have attempted to identify candidate N protein regions involved in RNA binding and protein multimerization for tospovirus using yeast two-hybrid systems (Y2HS) and site-directed mutagenesis, the tospovirus ribonucleocapsids (RNPs) remains largely uncharacterized at the molecular level and the lack of structural information prevents detailed insight into these interactions...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105853/identification-of-potential-molecular-associations-between-chikungunya-virus-non-structural-protein-2-and-human-host-proteins
#12
J Rana, S Gulati, S Rajasekharan, A Gupta, V Chaudhary, S Gupta
Chikungunya virus (CHIKV) non-structural protein 2 (nsP2) is considered to be the master regulator of viral RNA replication and host responses generated during viral infection. This protein has two main functional domains: an N-terminal domain which exhibits NTPase, RNA triphosphatase and helicase activities and a C-terminal protease domain. Understanding how CHIKV nsP2 interacts with its host proteins is essential for elucidating all the required processes for viral replication and pathogenesis along with the identification of potential targets for antiviral therapy...
January 19, 2017: Acta Virologica
https://www.readbyqxmd.com/read/28105473/recent-applications-of-the-combination-of-mesoporous-silica-nanoparticles-with-nucleic-acids-development-of-bioresponsive-devices-carriers-and-sensors
#13
REVIEW
Rafael R Castillo, Alejandro Baeza, María Vallet-Regí
The discovery and control of the biological roles mediated by nucleic acids have turned them into a powerful tool for the development of advanced biotechnological materials. Such is the importance of these gene-keeping biomacromolecules that even nanomaterials have succumbed to the claimed benefits of DNA and RNA. Currently, there could be found in the literature a practically intractable number of examples reporting the use of combination of nanoparticles with nucleic acids, so boundaries are demanded. Following this premise, this review will only cover the most recent and powerful strategies developed to exploit the possibilities of nucleic acids as biotechnological materials when in combination with mesoporous silica nanoparticles...
January 20, 2017: Biomaterials Science
https://www.readbyqxmd.com/read/28104569/interaction-of-octahedral-ruthenium-ii-polypyridyl-complex-ru-bpy-2-pip-2-with-poly-u-%C3%A2-poly-a-poly-u-triplex-increasing-third-strand-stabilization-of-the-triplex-without-affecting-the-stability-of-the-duplex
#14
Zhiyuan Zhu, Mengna Peng, Jingwen Zhang, Lifeng Tan
Triple-helical RNA are of interest because of possible biological roles as well as the potential therapeutic uses of these structures, while the stability of triplexes is usually weaker than that of the Watson-Crick base pairing duplex strand due to the electrostatic repulsion between three polyanionic strands. Therefore, how to increase the stability of the specific sequences of triplexes are of importance. In this paper the binding of a Ru(II) complex, [Ru(bpy)2(PIP)](2+) (bpy=2.2'-bipyridine, PIP=2-phenyl-1H-imidazo[4,5-f]- [1,10]-phenanthroline), with poly(U)·poly(A)*poly(U) triplex has been investigated by spectrophotometry, spectrofluorometry, viscosimetry and circular dichroism...
January 4, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28104453/alphavirus-polymerase-and-rna-replication
#15
REVIEW
Maija K Pietilä, Kirsi Hellström, Tero Ahola
Alphaviruses are typically arthropod-borne, and many are important pathogens such as chikungunya virus. Alphaviruses encode four nonstructural proteins (nsP1-4), initially produced as a polyprotein P1234. nsP4 is the core RNA-dependent RNA polymerase but all four nsPs are required for RNA synthesis. The early replication complex (RC) formed by the polyprotein P123 and nsP4 synthesizes minus RNA strands, and the late RC composed of fully processed nsP1-nsP4 is responsible for the production of genomic and subgenomic plus strands...
January 16, 2017: Virus Research
https://www.readbyqxmd.com/read/28104452/cystoviral-rna-directed-rna-polymerases-regulation-of-rna-synthesis-on-multiple-time-and-length-scales
#16
REVIEW
Sébastien Alphonse, Ranajeet Ghose
P2, an RNA-directed RNA polymerase (RdRP), is encoded on the largest of the three segments of the double-stranded RNA genome of cystoviruses. P2 performs the dual tasks of replication and transcription de novo on single-stranded RNA templates, and plays a critical role in the viral life-cycle. Work over the last few decades has yielded a wealth of biochemical and structural information on the functional regulation of P2, on its role in the spatiotemporal regulation of RNA synthesis and its variability across the Cystoviridae family...
January 16, 2017: Virus Research
https://www.readbyqxmd.com/read/28104450/polymerases-of-paramyxoviruses-and-pneumoviruses
#17
REVIEW
Rachel Fearns, Richard K Plemper
The paramyxo- and pneumoviruses are members of the order Mononegavirales, a group of viruses with non-segmented, negative strand RNA genomes. The polymerases of these viruses are multi-functional complexes, capable of transcribing subgenomic capped and polyadenylated mRNAs and replicating the genome. Although there is no native structure available for any complete paramyxo- or pneumovirus polymerase, functional and structural studies of a fragment of a pneumovirus polymerase protein and mutation analyses and resistance profiling of small-molecule inhibitors have generated a wealth of mechanistic information...
January 16, 2017: Virus Research
https://www.readbyqxmd.com/read/28104311/comprehensive-profiling-of-the-androgen-receptor-in-liquid-biopsies-from-castration-resistant-prostate-cancer-reveals-novel-intra-ar-structural-variation-and-splice-variant-expression-patterns
#18
Bram De Laere, Pieter-Jan van Dam, Tom Whitington, Markus Mayrhofer, Emanuela Henao Diaz, Gert Van den Eynden, Jean Vandebroek, Jurgen Del-Favero, Steven Van Laere, Luc Dirix, Henrik Grönberg, Johan Lindberg
BACKGROUND: Expression of the androgen receptor splice variant 7 (AR-V7) is associated with poor response to second-line endocrine therapy in castration-resistant prostate cancer (CRPC). However, a large fraction of nonresponding patients are AR-V7-negative. OBJECTIVE: To investigate if a comprehensive liquid biopsy-based AR profile may improve patient stratification in the context of second-line endocrine therapy. DESIGN, SETTING, AND PARTICIPANTS: Peripheral blood was collected from patients with CRPC (n=30) before initiation of a new line of systemic therapy...
January 16, 2017: European Urology
https://www.readbyqxmd.com/read/28103684/activation-pathway-of-a-nucleoside-analog-inhibiting-respiratory-syncytial-virus-polymerase
#19
Paul C Jordan, Sarah K Stevens, Yuen Tam, Ryan P Pemberton, Shuvam Chaudhuri, Antitsa D Stoycheva, Natalia Dyatkina, Guangyi Wang, Julian A Symons, Jerome Deval, Leo Beigelman
Human respiratory syncytial virus (RSV) is a negative-sense RNA virus and a significant cause of respiratory infection in infants and the elderly. No effective vaccines or antiviral therapies are available for the treatment of RSV. ALS-8176 is a first-in-class nucleoside prodrug inhibitor of RSV replication currently under clinical evaluation. ALS-8112, the parent molecule of ALS-8176, undergoes intracellular phosphorylation, yielding the active 5'-triphosphate metabolite. The host kinases responsible for this conversion are not known...
January 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28103252/comparative-and-evolutionary-analysis-of-grass-pollen-allergens-using-brachypodium-distachyon-as-a-model-system
#20
Akanksha Sharma, Niharika Sharma, Prem Bhalla, Mohan Singh
Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses...
2017: PloS One
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