Virtual Socializing: Its Motives and Spread

Virtual communities constitute an important attribute through which social dialogues are mediated. The emergence of online communities is the outcome of the prevalence of web based technologies. In the world of inter and intra connectedness individuals have the prerogative to get connected to the community of their choice. The present study examines the magnitude and motivations of online social networking through field survey method.virtual socializing, online communities, social networking, virtual platforms, virtual communities

Genome-wide expression profile of RNA polymerase II subunit mutant of yeast using microarray technology

Rpb4, the non-essential core subunit of RNA polymerase II has been assigned a function of regulating stress response in S. cerevisiae based mainly on phenotypes associated with its deletion. The actual mechanism has been elusive, although various hypotheses have been put forth. We have shown previously that it plays a significant role in activation of a subset of genes, rather than causing generalized defect in transcription. We used the microarray technology to look at the effect of this RNA polymerase subunit on the expression pattern of the entire S. cerevisiae genome. Many surprises emerged when we compared the genome-wide expression patterns of wild type and a mutant lacking the RPB4 gene (rpb4Δ) subjected to heat shock. The initial analysis of genes downregulated in the mutant showed that the co-regulation of genes is not position-dependent, although the locus carrying the deletion had unexpectedly a large cluster of down-regulated genes. We also found that among the known down-regulated genes, a majority is involved in hexose uptake and utilization. We speculate that this could potentially contribute to the slow growth rate of the mutant. Compared to the other components of the transcription machinery, the Rpb4 subunit affects a unique set of genes

DyNAVacS: an integrative tool for optimized DNA vaccine design

DNA vaccines have slowly emerged as keystones in preventive immunology due to their versatility in inducing both cell-mediated as well as humoral immune responses. The design of an efficient DNA vaccine, involves choice of a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses and providing additional sequence signals for efficient translation. DyNAVacS is a web-based tool created for rapid and easy design of DNA vaccines. It follows a step-wise design flow, which guides the user through the various sequential steps in the design of the vaccine. Further, it allows restriction enzyme mapping, design of primers spanning user specified sequences and provides information regarding the vectors currently used for generation of DNA vaccines. The web version uses Apache HTTP server. The interface was written in HTML and utilizes the Common Gateway Interface scripts written in PERL for functionality. DyNAVacS is an integrated tool consisting of user-friendly programs, which require minimal information from the user. The software is available free of cost, as a web based application at URL:

Metal complexation of crosslinked polyacrylamide-supported dithiocarbamates: effect of the molecular character and extent of crosslinking on complexation

Dithiocarbamate functions were incorporated into different polyacrylamide matrices crosslinked with a flexible and hydrophilic crosslinking agent, tetraethyleneglycol diacrylate (TEGDA), and their complexation behaviours were investigated. Crosslinked polyacrylamides with varying extents of the tetrafunctional TEGDA crosslinks were prepared by free radical solution polymerization at 60°C using potassium persulphate as initiator in ethanol. The dithiocarbamate functionality was incorporated into these polyacrylamides by a two-step polymer-analogous reaction involving (i)trans-amidation with ethylenediamine and (ii) dithiocarbamylation of the aminopolyacrylamide with carbon disulphide and alkali. The complexations of dithiocarbamate with Cu(II), Ni(II), Zn(II), Co(II) and Hg(II) ions were followed under different conditions. The metal ion intake varied with the extent of the crosslinking agent and the observed trend in complexation is Hg(II) >Cu(II)>Zn(II)>Co(II)> Ni (II). The time-course of complexation, the possibility of recycling, swelling characteristics, and spectral and thermal analyses were carried out. The thermal stability increases upon complexation with metal ions

Host-virus interaction: a new role for microRNAs

MicroRNAs (miRNAs) are a new class of 18–23 nucleotide long non-coding RNAs that play critical roles in a wide spectrum of biological processes. Recent reports also throw light into the role of microRNAs as critical effectors in the intricate host-pathogen interaction networks. Evidence suggests that both virus and hosts encode microRNAs. The exclusive dependence of viruses on the host cellular machinery for their propagation and survival also make them highly susceptible to the vagaries of the cellular environment like small RNA mediated interference. It also gives the virus an opportunity to fight and/or modulate the host to suite its needs. Thus the range of interactions possible through miRNA-mRNA cross-talk at the host-pathogen interface is large. These interactions can be further fine-tuned in the host by changes in gene expression, mutations and polymorphisms. In the pathogen, the high rate of mutations adds to the complexity of the interaction network. Though evidence regarding microRNA mediated cross-talk in viral infections is just emerging, it offers an immense opportunity not only to understand the intricacies of host-pathogen interactions, and possible explanations to viral tropism, latency and oncogenesis, but also to develop novel biomarkers and therapeutics

A Role for Voltage-Dependent Anion Channel Vdac1 in Polyglutamine-Mediated Neuronal Cell Death

Expansion of trinucleotide repeats in coding and non-coding regions of genes is associated with sixteen neurodegenerative disorders. However, the molecular effects that lead to neurodegeneration have remained elusive. We have explored the role of transcriptional dysregulation by TATA-box binding protein (TBP) containing an expanded polyglutamine stretch in a mouse neuronal cell culture based model. We find that mouse neuronal cells expressing a variant of human TBP harboring an abnormally expanded polyQ tract not only form intranuclear aggregates, but also show transcription dysregulation of the voltage dependent anion channel, Vdac1, increased cytochrome c release from the mitochondria and upregulation of genes involved in localized neuronal translation. On the other hand, unfolded protein response seemed to be unaffected. Consistent with an increased transcriptional effect, we observe an elevated promoter occupancy by TBP in vivo in TATA containing and TATA-less promoters of differentially expressed genes. Our study suggests a link between transcriptional dysfunction and cell death in trinucleotide repeat mediated neuronal dysfunction through voltage dependent anion channel, Vdac1, which has been recently recognized as a critical determinant of cell death

Metal ion complexation of hydrophilic polymeric amino ligands derived from tetraethyleneglycol diacrylate (TTEGDA)-crosslinked polyacrylamides

Complexation behaviour of amino ligands supported on polyacrylamides with 2–20 mol% of tetraethyleneglycol diacrylate crosslinks was investigated towards Co(II), Ni(II), Cu(II), Zn(II) and Hg(II) ions. The metal ion intake was dependent on the extent of crosslinking and followed the order: Hg(II) > Cu(II) > Zn(II) > Ni(II) > Co(II). The aminopolyacrylamides and their metal complexes were characterised by IR and EPR techniques. The absorptions of the ligands were shifted by complexation with metal ions and the EPR spectrum suggested distorted tetragonal geometry for the Cu(II) complex. The thermogravimetric analysis of the metal complexes revealed a pattern of variation of thermal stability on incorporation of metal ions. The kinetics and adsorption parameters of complexation, swelling characteristics, recyclability and specificity of metal-desorbed systems are also described

A kinetic model of TBP auto-regulation exhibits bistability

<p>Abstract</p> <p>Background</p> <p>TATA Binding Protein (TBP) is required for transcription initiation by all three eukaryotic RNA polymerases. It participates in transcriptional initiation at the majority of eukaryotic gene promoters, either by direct association to the TATA box upstream of the transcription start site or by indirectly localizing to the promoter through other proteins. TBP exists in solution in a dimeric form but binds to DNA as a monomer. Here, we present the first mathematical model for auto-catalytic TBP expression and use it to study the role of dimerization in maintaining the steady state TBP level.</p> <p>Results</p> <p>We show that the autogenous regulation of TBP results in a system that is capable of exhibiting three steady states: an unstable low TBP state, one stable state corresponding to a physiological TBP concentration, and another stable steady state corresponding to unviable cells where no TBP is expressed. Our model predicts that a basal level of TBP is required to establish the transcription of the TBP gene, and hence for cell viability. It also predicts that, for the condition corresponding to a typical mammalian cell, the high-TBP state and cell viability is sensitive to variation in DNA binding strength. We use the model to explore the effect of the dimer in buffering the response to changes in TBP levels, and show that for some physiological conditions the dimer is not important in buffering against perturbations.</p> <p>Conclusions</p> <p>Results on the necessity of a minimum basal TBP level support the in vivo observations that TBP is maternally inherited, providing the small amount of TBP required to establish its ubiquitous expression. The model shows that the system is sensitive to variations in parameters indicating that it is vulnerable to mutations in TBP. A reduction in TBP-DNA binding constant can lead the system to a regime where the unviable state is the only steady state. Contrary to the current hypotheses, we show that under some physiological conditions the dimer is not very important in restoring the system to steady state. This model demonstrates the use of mathematical modelling to investigate system behaviour and generate hypotheses governing the dynamics of such nonlinear biological systems.</p> <p>Reviewers</p> <p>This article was reviewed by Tomasz Lipniacki, James Faeder and Anna Marciniak-Czochra.</p

Virtual Socializing: Its Motives and Spread

Virtual communities constitute an important attribute through which social dialogues are mediated. The emergence of online communities is the outcome of the prevalence of web based technologies. In the world of inter and intra connectedness individuals have the prerogative to get connected to the community of their choice. The present study examines the magnitude and motivations of online social networking through field survey method

Whole genome expression profiles of yeast RNA polymerase II core subunit, Rpb4, in stress and nonstress conditions

Organisms respond to environmental stress by adopting changes in gene expression at the transcriptional level. Rpb4, a nonessential subunit of the core RNA polymerase II has been proposed to play a role in non-stress-specific transcription and in the regulation of stress response in yeast. We find that in addition to the temperature sensitivity of the null mutant of Rpb4, diploid null mutants are also compromised in sporulation and show morphological changes associated with nitrogen starvation. Using whole genome expression analysis, we report here the effects of Rpb4 on expression of genes during normal growth and following heat shock and nutritional starvation. Our analysis shows that Rpb4 affects expression of a small yet significant fraction of the genome in both stress and normal conditions. We found that genes involved in galactose metabolism were dependent on the presence of Rpb4 irrespective of the environmental condition. Rpb4 was also found to affect the expression of several other genes specifically in conditions of nutritional starvation. The general defect in the absence of Rpb4 is in the expression of metabolic genes, especially those involved in carbon metabolism and energy generation. We report that various stresses are affected byRPB4 and that on overexpression the stress-specific activators can partially rescue the corresponding defects