RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state

Flaviviral RNA-dependent RNA polymerases (RdRps) initiate replication of the single-stranded RNA genome in the absence of a primer. The template sequence 5'-CU-3' at the 3'-end of the flaviviral genome is highly conserved. Surprisingly, flaviviral RdRps require high concentrations of the second incoming nucleotide GTP to catalyze de novo template-dependent RNA synthesis. We show that GTP stimulates de novo RNA synthesis by RdRp from Japanese encephalitis virus (jRdRp) also. Crystal structures of jRdRp complexed with GTP and ATP provide a basis for specific recognition of GTP. Comparison of the jRdRp(GTP) structure with other viral RdRp-GTP structures shows that GTP binds jRdRp in a novel conformation. Apo-jRdRp structure suggests that the conserved motif F of jRdRp occupies multiple conformations in absence of GTP. Motif F becomes ordered on GTP binding and occludes the nucleotide triphosphate entry tunnel. Mutational analysis of key residues that interact with GTP evinces that the jRdRp(GTP) structure represents a novel pre-initiation state. Also, binding studies show that GTP binding reduces affinity of RdRp for RNA, but the presence of the catalytic Mn2+ ion abolishes this inhibition. Collectively, these observations suggest that the observed pre-initiation state may serve as a check-point to prevent erroneous template-independent RNA synthesis by jRdRp during initiation.

Mechanistic studies on the diazo transfer reaction

The mechanism of the diazo transfer reaction which converts amines to azides has been studied with labeled amino acids and labeled imidazole-l-sulfonyl azides. Retention of amine nitrogen in the amine, and transfer of the two terminal nitrogen atoms of the imidazole-l-sulfonyl azide to the product, were unambiguously established. (C) 2014 Elsevier Ltd. All rights reserved.

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.

Effect of angle of incidence on mixed convective wake dynamics and heat transfer past a square cylinder in cross flow at Re=100

In this paper, a numerical investigation is performed to study the mixed convective flow and heat transfer characteristics past a square cylinder in cross flow at incidence. Utilizing air (Pr = 0.71) as an operating fluid, computations are carried out at a representative Reynolds number (Re) of 100. Angles of incidences are varied as, 0 degrees <= alpha <= 45 degrees. Effect of superimposed positive and negative cross-flow buoyancy is brought about by varying the Richardson number (RI) in the range -1.0 <= Ri <= 1.0. The detail features of flow topology and heat transport are analyzed critically for different angles of incidences. The thermo fluidic forces acting on the cylinder during mixed convection are captured in terms of the drag (C-D), lift (C-L), and moment (C-M) coefficients. The results show that the lateral width of the cylinder wake reduces with increasing alpha and the isotherms spread out far wide. In the range 0 degrees < alpha < 45 degrees, C-D reduces with increasing Ri. The functional dependence of C-M with Ri reveals a linear relationship. Thermal boundary layer thickness reduces with increasing angle of incidences. The global rate of heat transfer from the cylinder increases with increasing alpha. (C) 2014 Elsevier Ltd. All rights reserved.

Exploring Transfer Learning Approaches for Head Pose Classification from Multi-view Surveillance Images

Head pose classification from surveillance images acquired with distant, large field-of-view cameras is difficult as faces are captured at low-resolution and have a blurred appearance. Domain adaptation approaches are useful for transferring knowledge from the training (source) to the test (target) data when they have different attributes, minimizing target data labeling efforts in the process. This paper examines the use of transfer learning for efficient multi-view head pose classification with minimal target training data under three challenging situations: (i) where the range of head poses in the source and target images is different, (ii) where source images capture a stationary person while target images capture a moving person whose facial appearance varies under motion due to changing perspective, scale and (iii) a combination of (i) and (ii). On the whole, the presented methods represent novel transfer learning solutions employed in the context of multi-view head pose classification. We demonstrate that the proposed solutions considerably outperform the state-of-the-art through extensive experimental validation. Finally, the DPOSE dataset compiled for benchmarking head pose classification performance with moving persons, and to aid behavioral understanding applications is presented in this work.

Metal-metal charge transfer and interfacial charge transfer mechanism for the visible light photocatalytic activity of cerium and nitrogen co-doped TiO2

Nanosized cerium and nitrogen co-doped TiO2 (Ce-TiO2-xNx) was synthesized by sol gel method and characterized by powder X-ray diffraction (PXRD), X-ray photoelectron spectroscopy (XPS), FESEM, Fourier transform infrared, N-2 adsorption and desorption methods, photoluminescence and ultraviolet-visible (UV-vis) DRS techniques. PXRD analysis shows the dopant decreases the crystallite sizes and slows the crystallization of the titania matrix. XPS confirm the existence of cerium ion in +3 or +4 state, and nitrogen in -3 state in Ce-TiO2-xNx. The modified surface of TiO2 provides highly active sites for the dyes at the periphery of the Ce-O-Ti interface and also inhibits Ce particles from sintering. UV-visible DRS studies show that the metal-metal charge transfer (MMCT) of Ti/Ce assembly (Ti4+/Ce3+ -> Ti3+/Ce4+) is responsible for the visible light photocatalytic activity. Photoluminescence was used to determine the effect of cerium ion on the electron-hole pair separation between the two interfaces Ce-TiO2-xNx and Ce2O3. This separation increases with the increase of cerium and nitrogen ion concentrations of doped samples. The degradation kinetics of methylene blue and methyl violet dyes in the presence of sol gel TiO2, Ce-TiO2-xNx and commercial Degussa P25 was determined. The higher visible light activity of Ce-TiO2-xNx was due to the participation of MMCT and interfacial charge transfer mechanism.

3 `-Amino-5 `-carboxymethy1-3 `,5 `-dideoxy nucleosides for the synthesis of fully amide-linked RNA mimics

A convenient protocol is developed for the synthesis of 3 `-N-(fluorenylmethoxycarbonyl)-amino]-5 `-carboxymethyl derivatives of all four natural ribonucleosides from cheap chiral pool compound glucose. Synthesis of fully amide-linked RNA analogues of small oligonucleotides containing, for the first time, all four nucleoside amino acids using standard solid phase Fmoc-chemistry is described. (C) 2014 Elsevier Ltd. All rights reserved.

Mycobacterium tuberculosis Rho Is an NTPase with Distinct Kinetic Properties and a Novel RNA-Binding Subdomain

Two mechanisms - factor independent and dependent termination - ensure the completion of RNA synthesis in eubacteria. Factor-dependent mechanism relies on the Rho protein to terminate transcription by interacting with RNA polymerase. Although well studied in Escherichia coli, the properties of the Rho homologs from most bacteria are not known. The rho gene is unusually large in genus Mycobacterium and other members of actinobacteria, having,150 additional residues towards the amino terminal end. We describe the distinct properties of Rho from Mycobacterium tuberculosis. It is an NTPase with a preference for purine nucleoside triphosphates with kinetic properties different from E. coli homolog and an ability to use various RNA substrates. The N-terminal subdomain of MtbRho can bind to RNA by itself, and appears to contribute to the interaction of the termination factor with RNAs. Furthermore, the interaction with RNA induces changes in conformation and oligomerization of MtbRho.

Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA

In this study, we combine available high resolution structural information on eukaryotic ribosomes with low resolution cryo-EM data on the Hepatitis C Viral RNA (IRES) human ribosome complex. Aided further by the prediction of RNA-protein interactions and restrained docking studies, we gain insights on their interaction at the residue level. We identified the components involved at the major and minor contact regions, and propose that there are energetically favorable local interactions between 40S ribosomal proteins and IRES domains. Domain II of the IRES interacts with ribosomal proteins S5 and S25 while the pseudoknot and the downstream domain IV region bind to ribosomal proteins S26, S28 and S5. We also provide support using UV cross-linking studies to validate our proposition of interaction between the S5 and IRES domains II and IV. We found that domain IIIe makes contact with the ribosomal protein S3a (S1e). Our model also suggests that the ribosomal protein S27 interacts with domain IIIc while S7 has a weak contact with a single base RNA bulge between junction IIIabc and IIId. The interacting residues are highly conserved among mammalian homologs while IRES RNA bases involved in contact do not show strict conservation. IRES RNA binding sites for S25 and S3a show the best conservation among related viral IRESs. The new contacts identified between ribosomal proteins and RNA are consistent with previous independent studies on RNA-binding properties of ribosomal proteins reported in literature, though information at the residue level is not available in previous studies.

Local Structural and Environmental Factors Define the Efficiency of an RNA Pseudoknot Involved in Programmed Ribosomal Frameshift Process

In programmed -1 ribosomal frameshift, an RNA pseudoknot stalls the ribosome at specific sequence and restarts translation in a new reading frame. A precise understanding of structural characteristics of these pseudoknots and their PRF inducing ability has not been clear to date. To investigate this phenomenon, we have studied various structural aspects of a -1 PRF inducing RNA pseudoknot from BWYV using extensive molecular dynamics simulations. A set of functional and poorly functional forms, for which previous mutational data were available, were chosen for analysis. These structures differ from each other by either single base substitutions or base-pair replacements from the native structure. We have rationalized how certain mutations in RNA pseudoknot affect its function; e.g., a specific base substitution in loop 2 stabilizes the junction geometry by forming multiple noncanonical hydrogen bonds, leading to a highly rigid structure that could effectively resist ribosome-induced unfolding, thereby increasing efficiency. While, a CG to AU pair substitution in stem 1 leads to loss of noncanonical hydrogen bonds between stems and loop, resulting in a less stable structure and reduced PRF inducing ability, inversion of a pair in stem 2 alters specific base-pair geometry that might be required in ribosomal recognition of nucleobase groups, negatively affecting pseudoknot functioning. These observations illustrate that the ability of an RNA pseudoknot to induce -1 PRF with an optimal rate depends on several independent factors that contribute to either the local conformational variability or geometry

Discerning heat transfer in building materials

The function of a building is to ensure safety and thermal comfort for healthy living conditions. Buildings primarily comprise an envelope, which acts as an interface separating the external environment from the indoors environment. The building envelope is primarily responsible for regulating indoor thermal comfort in response to external climatic conditions. It usually comprises a configuration of building materials to thus far provide requisite structural performance. However, studies into building-envelope configurations to provide a particular thermal performance are limited. As the building envelope is exposed to the external environment there will be heat and moisture transfer to the indoor environment through it. The overall phenomenon of heat and moisture transfer depends on the microstructure and configuration within the building material. Further, thermal property of a material is generally dependent on its microstructure, which comprises a network of pores and particles arranged in a definite structure. Thermal behaviour of a building material thus depends on the thermal conductivities of the solid particles, pore micro-structure and its constituent fluid (air and/or moisture). The thermal response of a building envelope is determined by the thermal characteristics of the individual building materials and its configuration. Understanding the heat transfer influenced by the complex networks of pores and particles is a relatively new study in the area of building climatic-response. The current study reviews the heat-transfer mechanisms that determine the thermal performance of a building material attributed to its micro-structure. A theoretical basis for the same is being evolved and its relevance in regulating heat-transfer through building envelopes, walls in particular, is reviewed in this paper. (C) 2014 N.C. Balaji. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

Interaction of Sesbania mosaic virus (SeMV) RNA-dependent RNA polymerase (RdRp) with the p10 domain of polyprotein 2a and its implications in SeMV replication

Identification of viral encoded proteins that interact with RNA-dependent RNA polymerase (RdRp) is an important step towards unraveling the mechanism of replication. Sesbania mosaic virus (SeMV) RdRp was shown to interact strongly with p10 domain of polyprotein 2a and moderately with the protease domain. Mutational analysis suggested that the C-terminal disordered domain of RdRp is involved in the interaction with p10. Coexpression of full length RdRp and p10 resulted in formation of RdRp-p10 complex which showed significantly higher polymerase activity than RdRp alone. Interestingly, C Delta 43 RdRp also showed a similar increase in activity. Thus, p10 acts as a positive regulator of RdRp by interacting with the C-terminal disordered domain of RdRp. (C) 2014 The Authors. Published by Elsevier B.V.

Stacking Interactions in RNA and DNA: Roll-Slide Energy Hyperspace for Ten Unique Dinucleotide Steps

Understanding dinucleotide sequence directed structures of nuleic acids and their variability from experimental observation remained ineffective due to unavailability of statistically meaningful data. We have attempted to understand this from energy scan along twist, roll, and slide degrees of freedom which are mostly dependent on dinucleotide sequence using ab initio density functional theory. We have carried out stacking energy analysis in these dinucleotide parameter phase space for all ten unique dinucleotide steps in DNA and RNA using DFT-D by B97X-D/6-31G(2d,2p), which appears to satisfactorily explain conformational preferences for AU/AU step in our recent study. We show that values of roll, slide, and twist of most of the dinucleotide sequences in crystal structures fall in the low energy region. The minimum energy regions with large twist values are associated with the roll and slide values of B-DNA, whereas, smaller twist values correspond to higher stability to RNA and A-DNA like conformations. Incorporation of solvent effect by CPCM method could explain the preference shown by some sequences to occur in B-DNA or A-DNA conformations. Conformational preference of BII sub-state in B-DNA is preferentially displayed mainly by pyrimidine-purine steps and partly by purine-purine steps. The purine-pyrimidine steps show largest effect of 5-methyl group of thymine in stacking energy and the introduction of solvent reduces this effect significantly. These predicted structures and variabilities can explain the effect of sequence on DNA and RNA functionality. (c) 2014 Wiley Periodicals, Inc. Biopolymers 103: 134-147, 2015.

Synthesis of mixed glycosyl disulfides/selenenylsulfides using benzyltriethylammonium tetrathiomolybdate as a sulfur transfer reagent

An easy and mild method has been developed for the synthesis of mixed glycosyl disulfides/selenenylsulfides from glycosyl halides and diaryl/dialkyl dichalcogenides in the presence of benzyltriethylammonium tetrathiomolybdate (BnEt3N)(2)MoS4]. The salient feature of this method is the sulfur transfer from BnEt3N](2)MoS4 to form glycosyl disulfides which with excess tetrathiomolybdate further undergo exchange reaction with other dichalcogenides in a one-pot operation. (C) 2014 Elsevier Ltd. All rights reserved.

Investigations on pressure and thickness profiles in carbon fiber-reinforced polymers during vacuum assisted resin transfer molding

Systematic experiments have been carried out by monitoring the in-situ pressure and thickness profiles for three different configurations, viz., flat plate, flat plate with a central circular hole, and an L-section using vacuum assisted resin transfer molding (VARTM) process. The effect of anisotropy on resin flow has been quantified by considering uni-directional carbon fiber preforms with 0 degrees and 90 degrees orientation to the flow direction for each configuration. A quasi-isotropic 45 degrees/0 degrees/-45 degrees/90 degrees](S) layup has also been included for flat plate case. Additionally, the study has been extended to understand the effect of using high permeability medium for each configuration. Fluid pressure profiles and thickness variation profiles have been obtained using an array of pressure sensors and linear variable differential transformers for each configuration. Experimental data reveal that anisotropy (due to changing fiber orientations), configuration, and gravity significantly change fluid pressure and displacement fields obtained during VARTM.