179 research outputs found
Kinematic dynamo in spherical Couette flow
We investigate numerically kinematic dynamos driven by flow of electrically
conducting fluid in the shell between two concentric differentially rotating
spheres, a configuration normally referred to as spherical Couette flow. We
compare between axisymmetric (2D) and fully three dimensional flows, between
low and high global rotation rates, between prograde and retrograde
differential rotations, between weak and strong nonlinear inertial forces,
between insulating and conducting boundaries, and between two aspect ratios.
The main results are as follows. Azimuthally drifting Rossby waves arising from
the destabilisation of the Stewartson shear layer are crucial to dynamo action.
Differential rotation and helical Rossby waves combine to contribute to the
spherical Couette dynamo. At a slow global rotation rate, the direction of
differential rotation plays an important role in the dynamo because of
different patterns of Rossby waves in prograde and retrograde flows. At a rapid
global rotation rate, stronger flow supercriticality (namely the difference
between the differential rotation rate of the flow and its critical value for
the onset of nonaxisymmetric instability) facilitates the onset of dynamo
action. A conducting magnetic boundary condition and a larger aspect ratio both
favour dynamo action
Chandrasekhar-Kendall functions in astrophysical dynamos
Some of the contributions of Chandrasekhar to the field of
magnetohydrodynamics are highlighted. Particular emphasis is placed on the
Chandrasekhar-Kendall functions that allow a decomposition of a vector field
into right- and left-handed contributions. Magnetic energy spectra of both
contributions are shown for a new set of helically forced simulations at
resolutions higher than what has been available so far. For a forcing function
with positive helicity, these simulations show a forward cascade of the
right-handed contributions to the magnetic field and nonlocal inverse transfer
for the left-handed contributions. The speed of inverse transfer is shown to
decrease with increasing value of the magnetic Reynolds number.Comment: 10 pages, 5 figures, proceedings of the Chandrasekhar Centenary
Conference, to be published in PRAMANA - Journal of Physic
Force spectroscopy in studying infection
Biophysical force spectroscopy tools - for example optical tweezers, magnetic
tweezers, atomic force microscopy, - have been used to study elastic,
mechanical, conformational and dynamic properties of single biological
specimens from single proteins to whole cells to reveal information not
accessible by ensemble average methods such as X-ray crystallography, mass
spectroscopy, gel electrophoresis and so on. Here we review the application of
these tools on a range of infection-related questions from antibody-inhibited
protein processivity to virus-cell adhesion. In each case we focus on how the
instrumental design tailored to the biological system in question translates
into the functionality suitable for that particular study. The unique insights
that force spectroscopy has gained to complement knowledge learned through
population averaging techniques in interrogating biomolecular details prove to
be instrumental in therapeutic innovations such as those in structure-based
drug design
Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis
<p>Abstract</p> <p>Background</p> <p><it>Candida parapsilosis </it>is one of the most common causes of <it>Candida </it>infection worldwide. However, the genome sequence annotation was made without experimental validation and little is known about the transcriptional landscape. The transcriptional response of <it>C. parapsilosis </it>to hypoxic (low oxygen) conditions, such as those encountered in the host, is also relatively unexplored.</p> <p>Results</p> <p>We used next generation sequencing (RNA-seq) to determine the transcriptional profile of <it>C. parapsilosis </it>growing in several conditions including different media, temperatures and oxygen concentrations. We identified 395 novel protein-coding sequences that had not previously been annotated. We removed > 300 unsupported gene models, and corrected approximately 900. We mapped the 5' and 3' UTR for thousands of genes. We also identified 422 introns, including two introns in the 3' UTR of one gene. This is the first report of 3' UTR introns in the Saccharomycotina. Comparing the introns in coding sequences with other species shows that small numbers have been gained and lost throughout evolution. Our analysis also identified a number of novel transcriptional active regions (nTARs). We used both RNA-seq and microarray analysis to determine the transcriptional profile of cells grown in normoxic and hypoxic conditions in rich media, and we showed that there was a high correlation between the approaches. We also generated a knockout of the <it>UPC2 </it>transcriptional regulator, and we found that similar to <it>C. albicans</it>, Upc2 is required for conferring resistance to azole drugs, and for regulation of expression of the ergosterol pathway in hypoxia.</p> <p>Conclusion</p> <p>We provide the first detailed annotation of the <it>C. parapsilosis </it>genome, based on gene predictions and transcriptional analysis. We identified a number of novel ORFs and other transcribed regions, and detected transcripts from approximately 90% of the annotated protein coding genes. We found that the transcription factor Upc2 role has a conserved role as a major regulator of the hypoxic response in <it>C. parapsilosis </it>and <it>C. albicans</it>.</p
Nephele: genotyping via complete composition vectors and MapReduce
<p>Abstract</p> <p>Background</p> <p>Current sequencing technology makes it practical to sequence many samples of a given organism, raising new challenges for the processing and interpretation of large genomics data sets with associated metadata. Traditional computational phylogenetic methods are ideal for studying the evolution of gene/protein families and using those to infer the evolution of an organism, but are less than ideal for the study of the whole organism mainly due to the presence of insertions/deletions/rearrangements. These methods provide the researcher with the ability to group a set of samples into distinct genotypic groups based on sequence similarity, which can then be associated with metadata, such as host information, pathogenicity, and time or location of occurrence. Genotyping is critical to understanding, at a genomic level, the origin and spread of infectious diseases. Increasingly, genotyping is coming into use for disease surveillance activities, as well as for microbial forensics. The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, these traditional single-processor methods are suboptimal for rapidly growing sequence datasets being generated by next-generation DNA sequencing machines, because they increase in computational complexity quickly with the number of sequences.</p> <p>Results</p> <p>Nephele is a suite of tools that uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers by passing the need for multiple sequence alignment, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods run on traditional hardware. Nephele can use the open-source Hadoop implementation of MapReduce to parallelize execution using multiple compute nodes. We were able to generate a neighbour-joined tree of over 10,000 16S samples in less than 2 hours.</p> <p>Conclusions</p> <p>We conclude that using Nephele can substantially decrease the processing time required for generating genotype trees of tens to hundreds of organisms at genome scale sequence coverage.</p
South Atlantic paleobathymetry since early Cretaceous
We present early Cretaceous to present paleobathymetric reconstructions and quantitative uncertainty estimates for the South Atlantic, offering a strong basis for studies of paleocirculation, paleoclimate and paleobiogeography. Circulation in an initially salty and anoxic ocean, restricted by the topography of the Falkland Plateau, Rio Grande Ridge and Walvis Rise, favoured deposition of thick evaporites in shallow water of the Brazilian-Angolan margins. This ceased as sea oor spreading propagated northwards, opening an equatorial gateway to shallow and intermediate circulation. This gateway, together with subsiding volcano-tectonic barriers would have played a key role in Late Cretaceous climate changes. Later deepening and widening of the South Atlantic, together with gateway opening at Drake Passage would lead, by mid-Miocene (∼15 Ma) to the establishment of modern-style thermohaline circulation
Mesozoic Alpine facies deposition as a result of past latitudinal plate motion
The fragmentation of Pangaea as a consequence of the opening of the Atlantic Ocean is documented in the Alpine-Mediterranean region by the onset of widespread pelagic sedimentation1. Shallow-water sediments were replaced by mainly pelagic limestones in the Early Jurassic period, radiolarian cherts in the Middle-Late Jurassic period, and again pelagic limestones in the Late Jurassic-Cretaceous period. During initial extension, basin subsidence below the carbonate compensation depth (CCD) is thought to have triggered the transition from Early Jurassic limestones to Middle-Late Jurassic radiolarites. It has been proposed that the transition from radiolarites to limestones in the Late Jurassic period was due to an increase in calcareous nannoplankton abundance when the CCD was depressed below the ocean floor. But in modern oceans, sediments below the CCD are not necessarily radiolaritic. Here we present palaeomagnetic samples from the Jurassic-Cretaceous pelagic succession exposed in the Lombardian basin, Italy. On the basis of an analysis of our palaeolatitudinal data in a broader palaeogeographic context, we propose an alternative explanation for the above facies tripartition. We suggest that the Lombardian basin drifted initially towards, and subsequently away from, a near-equatorial upwelling zone of high biosiliceous productivity. Our tectonic model for the genesis of radiolarites adds an essential horizontal plate motion component to explanations involving only vertical variations of CCD relative to the ocean floor. It may explain the deposition of radiolarites throughout the Mediterranean and Middle Eastern region during the Jurassic period
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