Annab's gsseminar [8 articles]

Abstract

MicroRNAs are small regulatory RNA molecules that exert post-transcriptional control overexpression of specific target mRNAs. AU-rich elements (AREs) are highly conserved 3'UTR sequences that alter the stability and translation of mRNAs of clinical importance as a rapid and transient response to external and internal changes. We recently demonstrated that a reporter mRNA containing the tumor necrosis factor alpha (TNFalpha) ARE activates translation in response to quiescence via microRNA target sites in the ARE. Further studies revealed that microRNAs in general have ...

Abstract

A new generation of DNA sequencers that can rapidly and inexpensively sequence billions of bases is transforming genomic science. These new machines are quickly becoming the technology of choice for whole-genome sequencing and for a variety of sequencing-based assays, including gene expression, DNA-protein interaction, human resequencing and RNA splicing studies. ...

Abstract

Genomes are more than linear sequences. In vivo they exist as elaborate physical structures, and their functional properties are strongly determined by their cellular organization. I discuss here the functional relevance of spatial and temporal genome organization at three hierarchical levels: the organization of nuclear processes, the higher-order organization of the chromatin fiber, and the spatial arrangement of genomes within the cell nucleus. Recent insights into the cell biology of genomes have overturned long-held dogmas and have led to new models ...

Abstract

10.1101/gr.088922.108 Recent studies have revealed that insertions and deletions (indels) are more different in their formation than previously assumed. What remains enigmatic is how the local DNA sequence context contributes to these differences. To investigate the relative impact of various molecular mechanisms to indel formation, we analyzed sequence contexts of indels in the non protein- or RNA-coding, nonrepetitive (NCNR) portion of the human genome. We considered small (≤30-bp) indels occurring in the human lineage since its divergence from chimpanzee and used ...

Abstract

In order to gain a better understanding of gene expression during early malaria infection, we conducted microarray analysis of early blood responses in mice infected with erythrocytic-stage Plasmodium chabaudi. Immediately following infection, we observed coordinated and sequential waves of immune responses, with interferon-associated gene transcripts dominating by 16 h postinfection, followed by strong increases in natural killer (NK) cell-associated and major histocompatibility complex class I-related transcripts by 32 h postinfection. We showed by flow cytometry that the observed elevation in NK ...

Abstract

Our notions of family, population and race may need revising in the age of personal genomics, argues Aravinda Chakravarti. ...

Abstract

Vibrio cholerae, the causative agent of the human disease cholera, uses cell-to-cell communication to control pathogenicity and biofilm formation1, 2. This process, known as quorum sensing, relies on the secretion and detection of signalling molecules called autoinducers. At low cell density V. cholerae activates the expression of virulence factors and forms biofilms. At high cell density the accumulation of two quorum-sensing autoinducers represses these traits. These two autoinducers, cholerae autoinducer-1 (CAI-1) and autoinducer-2 (AI-2), function synergistically to control gene regulation, although ...

Abstract

The origin of cooperation is a central challenge to our understanding of evolution1, 2, 3. The fact that microbial interactions can be manipulated in ways that animal interactions cannot has led to a growing interest in microbial models of cooperation4, 5, 6, 7, 8, 9, 10 and competition11, 12. For the budding yeast Saccharomyces cerevisiae to grow on sucrose, the disaccharide must first be hydrolysed by the enzyme invertase13, 14. This hydrolysis reaction is performed outside the cytoplasm in the periplasmic ...