Structural and functional insights into Mimivirus ORFans

<p>Abstract</p> <p>Background</p> <p>Mimivirus isolated from A. <it>polyphaga </it>is the largest virus discovered so far. It is unique among all the viruses in having genes related to translation, DNA repair and replication which bear close homology to eukaryotic genes. Nevertheless, only a small fraction of the proteins (33%) encoded in this genome has been assigned a function. Furthermore, a large fraction of the unassigned protein sequences bear no sequence similarity to proteins from other genomes. These sequences are referred to as ORFans. Because of their lack of sequence similarity to other proteins, they can not be assigned putative functions using standard sequence comparison methods. As part of our genome-wide computational efforts aimed at characterizing Mimivirus ORFans, we have applied fold-recognition methods to predict the structure of these ORFans and further functions were derived based on conservation of functionally important residues in sequence-template alignments.</p> <p>Results</p> <p>Using fold recognition, we have identified highly confident computational 3D structural assignments for 21 Mimivirus ORFans. In addition, highly confident functional predictions for 6 of these ORFans were derived by analyzing the conservation of functional motifs between the predicted structures and proteins of known function. This analysis allowed us to classify these 6 previously unannotated ORFans into their specific protein families: carboxylesterase/thioesterase, metal-dependent deacetylase, P-loop kinases, 3-methyladenine DNA glycosylase, BTB domain and eukaryotic translation initiation factor eIF4E.</p> <p>Conclusion</p> <p>Using stringent fold recognition criteria we have assigned three-dimensional structures for 21 of the ORFans encoded in the Mimivirus genome. Further, based on the 3D models and an analysis of the conservation of functionally important residues and motifs, we were able to derive functional attributes for 6 of the ORFans. Our computational identification of important functional sites in these ORFans can be the basis for a subsequent experimental verification of our predictions. Further computational and experimental studies are required to elucidate the 3D structures and functions of the remaining Mimivirus ORFans.</p

MiR-221 influences effector functions and actin cytoskeleton in mast cells.

Mast cells have essential effector and immunoregulatory functions in IgE-associated allergic disorders and certain innate and adaptive immune responses, but the role of miRNAs in regulating mast cell functions is almost completely unexplored. To examine the role of the activation-induced miRNA miR-221 in mouse mast cells, we developed robust lentiviral systems for miRNA overexpression and depletion. While miR-221 favored mast cell adhesion and migration towards SCF or antigen in trans-well migration assays, as well as cytokine production and degranulation in response to IgE-antigen complexes, neither miR-221 overexpression, nor its ablation, interfered with mast cell differentiation. Transcriptional profiling of miR-221-overexpressing mast cells revealed modulation of many transcripts, including several associated with the cytoskeleton; indeed, miR-221 overexpression was associated with reproducible increases in cortical actin in mast cells, and with altered cellular shape and cell cycle in murine fibroblasts. Our bioinformatics analysis showed that this effect was likely mediated by the composite effect of miR-221 on many primary and secondary targets in resting cells. Indeed, miR-221-induced cellular alterations could not be recapitulated by knockdown of one of the major targets of miR-221. We propose a model in which miR-221 has two different roles in mast cells: in resting cells, basal levels of miR-221 contribute to the regulation of the cell cycle and cytoskeleton, a general mechanism probably common to other miR-221-expressing cell types, such as fibroblasts. Vice versa, upon induction in response to mast cell stimulation, miR-221 effects are mast cell-specific and activation-dependent, contributing to the regulation of degranulation, cytokine production and cell adherence. Our studies provide new insights into the roles of miR-221 in mast cell biology, and identify novel mechanisms that may contribute to mast cell-related pathological conditions, such as asthma, allergy and mastocytosis

miRBase: tools for microRNA genomics.

miRBase is the central online repository for microRNA (miRNA) nomenclature, sequence data, annotation and target prediction. The current release (10.0) contains 5071 miRNA loci from 58 species, expressing 5922 distinct mature miRNA sequences: a growth of over 2000 sequences in the past 2 years. miRBase provides a range of data to facilitate studies of miRNA genomics: all miRNAs are mapped to their genomic coordinates. Clusters of miRNA sequences in the genome are highlighted, and can be defined and retrieved with any inter-miRNA distance. The overlap of miRNA sequences with annotated transcripts, both protein- and non-coding, are described. Finally, graphical views of the locations of a wide range of genomic features in model organisms allow for the first time the prediction of the likely boundaries of many miRNA primary transcripts. miRBase is available at http://microrna.sanger.ac.uk/

Profiling of Plant Derived Natural Constituents by Using Magnetic Resonance Techniques

Plants are reservoirs of naturally occurring chemical constituents with a wide range of structural diversity. These biological compounds can be derived from different parts of plants such as leaves, barks, seeds, seed coats, flowers, and roots. A broad array of secondary metabolic compounds is present in the plants such as antibiotics, alkaloids, antimicrobials, food-grade pigments, and phenolics which have been reported to possess numerous health-related benefits, including antioxidant, anti-inflammatory, anticancer, and antiobesity activities. Therefore, the identification and detection of these compounds are of utmost importance in order to utilise their benefits into various fields. Wherein, magnetic resonance techniques, such as NMR (nuclear magnetic resonance), MRI (magnetic resonance imaging), and EPR (electron paramagnetic resonance), being far more reproducible, nondestructive, than other analytical techniques such as liquid chromatography, mass spectroscopy, and high-performance liquid chromatography cover a much wider dynamic range of metabolites with easy sample preparation techniques with high speed and fidelity. Hence, these magnetic resonance techniques have been proven to be extremely useful in plant metabolite profiling and disease metabolomics, along with structural elucidation of bioactive compounds from plant sources. Therefore, the present review focuses on the effectiveness of magnetic resonance for the detection of plant-derived metabolites that may lead to new areas of research in various fields such as drug discovery and development, metabolomics, combinatorial chemistry, and assessing overall food safety and quality

MiR-221 influences effector functions and actin cytoskeleton in mast cells

Mast cells have essential effector and immunoregulatory functions in IgE-associated allergic disorders and certain innate and adaptive immune responses, but the role of miRNAs in regulating mast cell functions is almost completely unexplored. To examine the role of the activation-induced miRNA miR-221 in mouse mast cells, we developed robust lentiviral systems for miRNA overexpression and depletion. While miR-221 favored mast cell adhesion and migration towards SCF or antigen in trans-well migration assays, as well as cytokine production and degranulation in response to IgE-antigen complexes, neither miR-221 overexpression, nor its ablation, interfered with mast cell differentiation. Transcriptional profiling of miR-221-overexpressing mast cells revealed modulation of many transcripts, including several associated with the cytoskeleton; indeed, miR-221 overexpression was associated with reproducible increases in cortical actin in mast cells, and with altered cellular shape and cell cycle in murine fibroblasts. Our bioinformatics analysis showed that this effect was likely mediated by the composite effect of miR-221 on many primary and secondary targets in resting cells. Indeed, miR- 221-induced cellular alterations could not be recapitulated by knockdown of one of the major targets of miR-221. We propose a model in which miR-221 has two different roles in mast cells: in resting cells, basal levels of miR-221 contribute to the regulation of the cell cycle and cytoskeleton, a general mechanism probably common to other miR-221- expressing cell types, such as fibroblasts. Vice versa, upon induction in response to mast cell stimulation, miR-221 effects are mast cell-specific and activation-dependent, contributing to the regulation of degranulation, cytokine production and cell adherence. Our studies provide new insights into the roles of miR-221 in mast cell biology, and identify novel mechanisms that may contribute to mast cell-related pathological conditions, such as asthma, allergy and mastocytosis

Color Opponency Modulates Feature Integration Through Bayesian Priors

Stimulus color, even irrelevant to the task, has been shown to modulate high-level cognitive functions, producing different behavioral outcomes. However, the effect of color on lower-level perceptual processes remains unclear. To address this gap, we investigated whether color affects feature integration, an early-stage visual process, using the flash-jump illusion. Our results demonstrated that color modulates the integration of color and motion features, as red and blue flashes resulted in more veridical estimates of flash location, compared to green and yellow. We provide a novel interpretation of our current results in respect to a Bayesian perceptual framework, where the color of the flash is inherently assigned different Bayesian weights, resulting in different levels of perceptual shifts. Furthermore, in reviewing pertinent literature and empirical evidence, we have proposed a novel theory outlining three putative mechanisms, predictions and underlying neural circuitry using Bayesian frameworks to explain such color-dependent modulations in visual processing

Sequence-structure alignment ORFan L529 and yeast translation initiation factor (PDB code: 1ap8)

<p><b>Copyright information:</b></p><p>Taken from "Structural and functional insights into Mimivirus ORFans"</p><p>http://www.biomedcentral.com/1471-2164/8/115</p><p>BMC Genomics 2007;8():115-115.</p><p>Published online 9 May 2007</p><p>PMCID:PMC1876218.</p><p></p> The eight conserved tryptophans of 1ap8 are numbered as 1–8. The conserved terminal tryptophans (Trp-1 & Trp-8) are shown in yellow boxes. The consensus motif (S/T)VxxxFW is highlighted in green color. Ribbon diagram of predicted model of ORFan L529. The model was built from FFAS03 [55] and refined using Nest [53]. The model shows curved antiparallel β-sheet with two long helices present on one side. The conserved tryptophan residues (Trp25 and Trp124) required for cap recognition are shown in ball-and-sticks