42 research outputs found
Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products
We developed a low-cost, high-throughput microbiome profiling method that
uses combinatorial sequence tags attached to PCR primers that amplify the rRNA
V6 region. Amplified PCR products are sequenced using an Illumina paired-end
protocol to generate millions of overlapping reads. Combinatorial sequence
tagging can be used to examine hundreds of samples with far fewer primers than
is required when sequence tags are incorporated at only a single end. The
number of reads generated permitted saturating or near-saturating analysis of
samples of the vaginal microbiome. The large number of reads al- lowed an
in-depth analysis of errors, and we found that PCR-induced errors composed the
vast majority of non-organism derived species variants, an ob- servation that
has significant implications for sequence clustering of similar high-throughput
data. We show that the short reads are sufficient to assign organisms to the
genus or species level in most cases. We suggest that this method will be
useful for the deep sequencing of any short nucleotide region that is
taxonomically informative; these include the V3, V5 regions of the bac- terial
16S rRNA genes and the eukaryotic V9 region that is gaining popularity for
sampling protist diversity.Comment: 28 pages, 13 figure
Wall roughness induces asymptotic ultimate turbulence
Turbulence is omnipresent in Nature and technology, governing the transport
of heat, mass, and momentum on multiple scales. For real-world applications of
wall-bounded turbulence, the underlying surfaces are virtually always rough;
yet characterizing and understanding the effects of wall roughness for
turbulence remains a challenge, especially for rotating and thermally driven
turbulence. By combining extensive experiments and numerical simulations, here,
taking as example the paradigmatic Taylor-Couette system (the closed flow
between two independently rotating coaxial cylinders), we show how wall
roughness greatly enhances the overall transport properties and the
corresponding scaling exponents. If only one of the walls is rough, we reveal
that the bulk velocity is slaved to the rough side, due to the much stronger
coupling to that wall by the detaching flow structures. If both walls are
rough, the viscosity dependence is thoroughly eliminated in the boundary layers
and we thus achieve asymptotic ultimate turbulence, i.e. the upper limit of
transport, whose existence had been predicted by Robert Kraichnan in 1962
(Phys. Fluids {\bf 5}, 1374 (1962)) and in which the scalings laws can be
extrapolated to arbitrarily large Reynolds numbers
Chronic Antagonism of the Mineralocorticoid Receptor Ameliorates Hypertension and End Organ Damage in a Rodent Model of Salt-Sensitive Hypertension
We investigated the effects of chronic mineralocorticoid receptor blockade with eplerenone on the development and progression of hypertension and end organ damage in Dahl salt-sensitive rats. Eplerenone significantly attenuated the progressive rise in systolic blood pressure (SBP) (204 ± 3 vs. 179±3 mmHg, p < 0.05), reduced proteinuria (605.5 ± 29.6 vs. 479.7 ± 26.1 mg/24h, p < 0.05), improved injury scores of glomeruli, tubules, renal interstitium, and vasculature in Dahl salt-sensitive rats fed a high-salt diet. These results demonstrate that mineralocorticoid receptor antagonism provides target organ protection and attenuates the development of elevated blood pressure (BP) in a model of salt-sensitive hypertension
The HIV Tat protein affects processing of ribosomal RNA precursor
<p>Abstract</p> <p>Background</p> <p>Inside the cell, the HIV Tat protein is mainly found in the nucleus and nucleolus. The nucleolus, the site of ribosome biogenesis, is a highly organized, non-membrane-bound sub-compartment where proteins with a high affinity for nucleolar components are found. While it is well known that Tat accumulates in the nucleolus via a specific nucleolar targeting sequence, its function in this compartment it still unknown.</p> <p>Results</p> <p>To clarify the significance of the Tat nucleolar localization, we induced the expression of the protein during oogenesis in <it>Drosophila melanogaster </it>strain transgenic for HIV-<it>tat </it>gene. Here we show that Tat localizes in the nucleoli of <it>Drosophila </it>oocyte nurse cells, where it specifically co-localizes with fibrillarin. Tat expression is accompanied by a significant decrease of cytoplasmic ribosomes, which is apparently related to an impairment of ribosomal rRNA precursor processing. Such an event is accounted for by the interaction of Tat with fibrillarin and U3 snoRNA, which are both required for pre-rRNA maturation.</p> <p>Conclusion</p> <p>Our data contribute to understanding the function of Tat in the nucleolus, where ribosomal RNA synthesis and cell cycle control take place. The impairment of nucleolar pre-rRNA maturation through the interaction of Tat with fibrillarin-U3snoRNA complex suggests a process by which the virus modulates host response, thus contributing to apoptosis and protein shut-off in HIV-uninfected cells.</p
Cortical Surround Interactions and Perceptual Salience via Natural Scene Statistics
Spatial context in images induces perceptual phenomena associated with salience and modulates the responses of neurons in primary visual cortex (V1). However, the computational and ecological principles underlying contextual effects are incompletely understood. We introduce a model of natural images that includes grouping and segmentation of neighboring features based on their joint statistics, and we interpret the firing rates of V1 neurons as performing optimal recognition in this model. We show that this leads to a substantial generalization of divisive normalization, a computation that is ubiquitous in many neural areas and systems. A main novelty in our model is that the influence of the context on a target stimulus is determined by their degree of statistical dependence. We optimized the parameters of the model on natural image patches, and then simulated neural and perceptual responses on stimuli used in classical experiments. The model reproduces some rich and complex response patterns observed in V1, such as the contrast dependence, orientation tuning and spatial asymmetry of surround suppression, while also allowing for surround facilitation under conditions of weak stimulation. It also mimics the perceptual salience produced by simple displays, and leads to readily testable predictions. Our results provide a principled account of orientation-based contextual modulation in early vision and its sensitivity to the homogeneity and spatial arrangement of inputs, and lends statistical support to the theory that V1 computes visual salience
When Right Feels Left: Referral of Touch and Ownership between the Hands
Feeling touch on a body part is paradigmatically considered to require stimulation of tactile afferents from the body part in question, at least in healthy non-synaesthetic individuals. In contrast to this view, we report a perceptual illusion where people experience “phantom touches” on a right rubber hand when they see it brushed simultaneously with brushes applied to their left hand. Such illusory duplication and transfer of touch from the left to the right hand was only elicited when a homologous (i.e., left and right) pair of hands was brushed in synchrony for an extended period of time. This stimulation caused the majority of our participants to perceive the right rubber hand as their own and to sense two distinct touches – one located on the right rubber hand and the other on their left (stimulated) hand. This effect was supported by quantitative subjective reports in the form of questionnaires, behavioral data from a task in which participants pointed to the felt location of their right hand, and physiological evidence obtained by skin conductance responses when threatening the model hand. Our findings suggest that visual information augments subthreshold somatosensory responses in the ipsilateral hemisphere, thus producing a tactile experience from the non-stimulated body part. This finding is important because it reveals a new bilateral multisensory mechanism for tactile perception and limb ownership
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage
Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of γ-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25–1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition