Effect of Inlet Jet injection angle on a calandria based reactor-An investigation with numerical analysis of heat and mass transfer for an optimum reactor design

Heat and mass transfer studies in a calandria based reactor is quite complex both due to geometry and due to the complex mixing flow. It is challenging to devise optimum operating conditions with efficient but safe working range for such a complex configuration. Numerical study known to be very effective is taken up for investigation. In the present study a 3D RANS code with turbulence model has been used to compute the flow fields and to get the heat transfer characteristics to understand certain design parameters of engineering importance. The angle of injection and of the coolant liquid has a large effect on the heat transfer within the reactor.

Adiabatic Eigenfunction Based Approach to Coherent Transfer: Application to the Fenna-Matthews-Olson (FMO) Complex and the Role of Correlations in the Efficiency of Energy Transfer

We have recently suggested a method (Pallavi Bhattacharyya and K. L. Sebastian, Physical Review E 2013, 87, 062712) for the analysis of coherence in finite-level systems that are coupled to the surroundings and used it to study the process of energy transfer in the Fenna-Matthews-Olson (FMO) complex. The method makes use of adiabatic eigenstates of the Hamiltonian, with a subsequent transformation of the Hamiltonian into a form where the terms responsible for decoherence and population relaxation could be separated out at the lowest order. Thus one can account for decoherence nonperturbatively, and a Markovian type of master equation could be used for evaluating the population relaxation. In this paper, we apply this method to a two-level system as well as to a seven-level system. Comparisons with exact numerical results show that the method works quite well and is in good agreement with numerical calculations. The technique can be applied with ease to systems with larger numbers of levels as well. We also investigate how the presence of correlations among the bath degrees of freedom of the different bacteriochlorophyll a molecules of the FMO Complex affect the rate of energy transfer. Surprisingly, in the cases that we studied, our calculations suggest that the presence of anticorrelations, in contrast to correlations, make the excitation transfer more facile.

Inactivation of the Bacterial RNA Polymerase Due to Acquisition of Secondary Structure by the omega Subunit

The widely conserved omega subunit encoded by rpoZ is the smallest subunit of Escherichia coli RNA polymerase (RNAP) but is dispensable for bacterial growth. Function of omega is known to be substituted by GroEL in omega-null strain, which thus does not exhibit a discernable phenotype. In this work, we report isolation of omega variants whose expression in vivo leads to a dominant lethal phenotype. Studies show that in contrast to omega, which is largely unstructured, omega mutants display substantial acquisition of secondary structure. By detailed study with one of the mutants, omega(6) bearing N60D substitution, the mechanism of lethality has been deciphered. Biochemical analysis reveals that omega(6) binds to beta ` subunit in vitro with greater affinity than that of omega. The reconstituted RNAP holoenzyme in the presence of omega(6) in vitro is defective in transcription initiation. Formation of a faulty RNAP in the presence of mutant omega results in death of the cell. Furthermore, lethality of omega(6) is relieved in cells expressing the rpoC2112 allele encoding beta ` (2112), a variant beta ` bearing Y457S substitution, immediately adjacent to the beta ` catalytic center. Our results suggest that the enhanced omega(6)-beta ` interaction may perturb the plasticity of the RNAP active center, implicating a role for omega and its flexible state.

Transcriptional Repression of Tumor Suppressor CDC73, Encoding an RNA Polymerase II Interactor, by Wilms Tumor 1 Protein (WT1) Promotes Cell Proliferation IMPLICATION FOR CANCER THERAPEUTICS

The Wilms tumor 1 gene (WT1) can either repress or induce the expression of genes. Inconsistent with its tumor suppressor role, elevated WT1 levels have been observed in leukemia and solid tumors. WT1 has also been suggested to act as an oncogene by inducing the expression of MYC and BCL-2. However, these are only the correlational studies, and no functional study has been performed to date. Consistent with its tumor suppressor role, CDC73 binds to RNA polymerase II as part of a PAF1 transcriptional regulatory complex and causes transcriptional repression of oncogenes MYC and CCND1. It also represses beta-catenin-mediated transcription. Based on the reduced level of CDC73 in oral squamous cell carcinoma (OSCC) samples in the absence of loss-of-heterozygosity, promoter methylation, and mutations, we speculated that an inhibitory transcription factor is regulating its expression. The bioinformatics analysis predicted WT1 as an inhibitory transcription factor to regulate the CDC73 level. Our results showed that overexpression of WT1 decreased CDC73 levels and promoted proliferation of OSCC cells. ChIP and EMSA results demonstrated binding of WT1 to the CDC73 promoter. The 5-azacytidine treatment of OSCC cells led to an up-regulation of WT1 with a concomitant down-regulation of CDC73, further suggesting regulation of CDC73 by WT1. Exogenous CDC73 attenuated the protumorigenic activity of WT1 by apoptosis induction. An inverse correlation between expression levels of CDC73 and WT1 was observed in OSCC samples. These observations indicated that WT1 functions as an oncogene by repressing the expression of CDC73 in OSCC. We suggest that targeting WT1 could be a therapeutic strategy for cancer, including OSCC.

Transfer free suspended graphene devices on silicon using electrodeposited copper

Transfer free processes using Cu films greatly simplify the fabrication of reliable suspended graphene devices. In this paper, the authors report on the use of electrodeposited Cu films on Si for transfer free fabrication of suspended graphene devices. The quality of graphene layers on optimized electrodeposited Cu and Cu foil are found to be the same. By selectively etching the underlying Cu, the authors have realized by a transfer free process metal contacted, suspended graphene beams up to 50 mu m in length directly on Si. The suspended graphene beams do not show any increase in defect levels over the as grown state indicating the efficiency of the transfer free process. Measured room temperature electronic mobilities of up to 5200 cm(2)/V.s show that this simpler and CMOS compatible route has the potential to replace the foil based route for such suspended nano and micro electromechanical device arrays. (C) 2014 American Vacuum Society.

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