239 research outputs found
A totally Self-Checking Dynamic Asynchronous Datapath
This paper investigates the inherent totally self-checking (TSC) property of one type of dynamic asynchronous datapath based on Differential Cascode Voltage Logic (DCVSL). As a result, a totally self-checking dynamic asynchronous datapath architecture is proposed. It is simpler than other similar approaches and represents a new approach to fault tolerant design.published_or_final_versio
A robust computational algorithm for inverse photomask synthesis in optical projection lithography
Inverse lithography technology formulates the photomask synthesis as an inverse mathematical problem. To solve this, we propose a variational functional and develop a robust computational algorithm, where the proposed functional takes into account the process variations and incorporates several regularization terms that can control the mask complexity. We establish the existence of the minimizer of the functional, and in order to optimize it effectively, we adopt an alternating minimization procedure with Chambolle's fast duality projection algorithm. Experimental results show that our proposed algorithm is effective in synthesizing high quality photomasks as compared with existing methods.published_or_final_versio
Design for self-checking and self-timed datapath
This work examines the inherent self-checking property of a latch-free dynamic asynchronous datapath (LFDAD) using differential cascode voltage switch logic (DCVSL). Consequently, a highly efficient self-checking (SC) dynamic asynchronous datapath architecture is presented. In this architecture, no hardware needs to be added to the datapath to achieve self-checking. The presented implementation is efficient in terms of speed and area and represents a new approach to fault-tolerant design.published_or_final_versio
The adipocyte: a model for integration of endocrine and metabolic signaling in energy metabolism regulation
The ability to ensure continuous availability of energy despite highly variable
supplies in the environment is a major determinant of the survival of all
species. In higher organisms, including mammals, the capacity to efficiently
store excess energy as triglycerides in adipocytes, from which stored energy
could be rapidly released for use at other sites, was developed. To orchestrate
the processes of energy storage and release, highly integrated systems operating
on several physiological levels have evolved. The adipocyte is no longer
considered a passive bystander, because fat cells actively secrete many members
of the cytokine family, such as leptin, tumor necrosis factor-alpha, and
interleukin-6, among other cytokine signals, which influence peripheral fuel
storage, mobilization, and combustion, as well as energy homeostasis. The
existence of a network of adipose tissue signaling pathways, arranged in a
hierarchical fashion, constitutes a metabolic repertoire that enables the
organism to adapt to a wide range of different metabolic challenges, such as
starvation, stress, infection, and short periods of gross energy excess
The N-Terminus of GalE Induces tmRNA Activity in Escherichia coli
BACKGROUND: The tmRNA quality control system recognizes stalled translation complexes and facilitates ribosome recycling in a process termed 'ribosome rescue'. During ribosome rescue, nascent chains are tagged with the tmRNA-encoded SsrA peptide, which targets tagged proteins for degradation. In Escherichia coli, tmRNA rescues ribosomes arrested on truncated messages, as well as ribosomes that are paused during elongation and termination. METHODOLOGY/PRINCIPAL FINDINGS: Here, we describe a new translational pausing determinant that leads to SsrA peptide tagging of the E. coli GalE protein (UDP-galactose 4-epimerase). GalE chains are tagged at more than 150 sites, primarily within distinct clusters throughout the C-terminal domain. These tagging sites do not correspond to rare codon clusters and synonymous recoding of the galE gene had little effect on tagging. Moreover, tagging was largely unaffected by perturbations that either stabilize or destabilize the galE transcript. Examination of GalE-thioredoxin (TrxA) fusion proteins showed that the GalE C-terminal domain is no longer tagged when fused to an N-terminal TrxA domain. Conversely, the N-terminus of GalE induced tagging within the fused C-terminal TrxA domain. CONCLUSIONS/SIGNIFICANCE: These findings suggest that translation of the GalE N-terminus induces subsequent tagging of the C-terminal domain. We propose that co-translational maturation of the GalE N-terminal domain influences ribosome pausing and subsequent tmRNA activity
Regulation of Septin Dynamics by the Saccharomyces cerevisiae Lysine Acetyltransferase NuA4
In the budding yeast Saccharomyces cerevisiae, the lysine acetyltransferase NuA4 has been linked to a host of cellular processes through the acetylation of histone and non-histone targets. To discover proteins regulated by NuA4-dependent acetylation, we performed genome-wide synthetic dosage lethal screens to identify genes whose overexpression is toxic to non-essential NuA4 deletion mutants. The resulting genetic network identified a novel link between NuA4 and septin proteins, a group of highly conserved GTP-binding proteins that function in cytokinesis. We show that acetyltransferase-deficient NuA4 mutants have defects in septin collar formation resulting in the development of elongated buds through the Swe1-dependent morphogenesis checkpoint. We have discovered multiple sites of acetylation on four of the five yeast mitotic septins, Cdc3, Cdc10, Cdc12 and Shs1, and determined that NuA4 can acetylate three of the four in vitro. In vivo we find that acetylation levels of both Shs1 and Cdc10 are reduced in a catalytically inactive esa1 mutant. Finally, we determine that cells expressing a Shs1 protein with decreased acetylation in vivo have defects in septin localization that are similar to those observed in NuA4 mutants. These findings provide the first evidence that yeast septin proteins are acetylated and that NuA4 impacts septin dynamics
Mouse models of rhinovirus-induced disease and exacerbation of allergic airway inflammation
Rhinoviruses cause serious morbidity and mortality as the major etiological agents of asthma exacerbations and the common cold. A major obstacle to understanding disease pathogenesis and to the development of effective therapies has been the lack of a small-animal model for rhinovirus infection. Of the 100 known rhinovirus serotypes, 90% (the major group) use human intercellular adhesion molecule-1 (ICAM-1) as their cellular receptor and do not bind mouse ICAM-1; the remaining 10% (the minor group) use a member of the low-density lipoprotein receptor family and can bind the mouse counterpart. Here we describe three novel mouse models of rhinovirus infection: minor-group rhinovirus infection of BALB/c mice, major-group rhinovirus infection of transgenic BALB/c mice expressing a mouse-human ICAM-1 chimera and rhinovirus-induced exacerbation of allergic airway inflammation. These models have features similar to those observed in rhinovirus infection in humans, including augmentation of allergic airway inflammation, and will be useful in the development of future therapies for colds and asthma exacerbations
Identification of a Novel Marine Fish Virus, Singapore Grouper Iridovirus-Encoded MicroRNAs Expressed in Grouper Cells by Solexa Sequencing
BACKGROUND: MicroRNAs (miRNAs) are ubiquitous non-coding RNAs that regulate gene expression at the post-transcriptional level. An increasing number of studies has revealed that viruses can also encode miRNAs, which are proposed to be involved in viral replication and persistence, cell-mediated antiviral immune response, angiogenesis, and cell cycle regulation. Singapore grouper iridovirus (SGIV) is a pathogenic iridovirus that has severely affected grouper aquaculture in China and Southeast Asia. Comprehensive knowledge about the related miRNAs during SGIV infection is helpful for understanding the infection and the pathogenic mechanisms. METHODOLOGY/PRINCIPAL FINDINGS: To determine whether SGIV encoded miRNAs during infection, a small RNA library derived from SGIV-infected grouper (GP) cells was constructed and sequenced by Illumina/Solexa deep-sequencing technology. We recovered 6,802,977 usable reads, of which 34,400 represented small RNA sequences encoded by SGIV. Sixteen novel SGIV-encoded miRNAs were identified by a computational pipeline, including a miRNA that shared a similar sequence to herpesvirus miRNA HSV2-miR-H4-5p, which suggests miRNAs are conserved in far related viruses. Generally, these 16 miRNAs are dispersed throughout the SGIV genome, whereas three are located within the ORF057L region. Some SGIV-encoded miRNAs showed marked sequence and length heterogeneity at their 3' and/or 5' end that could modulate their functions. Expression levels and potential biological activities of these viral miRNAs were examined by stem-loop quantitative RT-PCR and luciferase reporter assay, respectively, and 11 of these viral miRNAs were present and functional in SGIV-infected GP cells. CONCLUSIONS: Our study provided a genome-wide view of miRNA production for iridoviruses and identified 16 novel viral miRNAs. To the best of our knowledge, this is the first experimental demonstration of miRNAs encoded by aquatic animal viruses. The results provide a useful resource for further in-depth studies on SGIV infection and iridovirus pathogenesis
Identification, Replication, and Functional Fine-Mapping of Expression Quantitative Trait Loci in Primary Human Liver Tissue
The discovery of expression quantitative trait loci (“eQTLs”) can
help to unravel genetic contributions to complex traits. We identified genetic
determinants of human liver gene expression variation using two independent
collections of primary tissue profiled with Agilent
(n = 206) and Illumina (n = 60)
expression arrays and Illumina SNP genotyping (550K), and we also incorporated
data from a published study (n = 266). We found that
∼30% of SNP-expression correlations in one study failed to replicate
in either of the others, even at thresholds yielding high reproducibility in
simulations, and we quantified numerous factors affecting reproducibility. Our
data suggest that drug exposure, clinical descriptors, and unknown factors
associated with tissue ascertainment and analysis have substantial effects on
gene expression and that controlling for hidden confounding variables
significantly increases replication rate. Furthermore, we found that
reproducible eQTL SNPs were heavily enriched near gene starts and ends, and
subsequently resequenced the promoters and 3′UTRs for 14 genes and tested
the identified haplotypes using luciferase assays. For three genes, significant
haplotype-specific in vitro functional differences correlated
directly with expression levels, suggesting that many bona fide
eQTLs result from functional variants that can be mechanistically isolated in a
high-throughput fashion. Finally, given our study design, we were able to
discover and validate hundreds of liver eQTLs. Many of these relate directly to
complex traits for which liver-specific analyses are likely to be relevant, and
we identified dozens of potential connections with disease-associated loci.
These included previously characterized eQTL contributors to diabetes, drug
response, and lipid levels, and they suggest novel candidates such as a role for
NOD2 expression in leprosy risk and
C2orf43 in prostate cancer. In general, the work presented
here will be valuable for future efforts to precisely identify and functionally
characterize genetic contributions to a variety of complex traits
The first global deep-sea stable isotope assessment reveals the unique trophic ecology of Vampire Squid Vampyroteuthis infernalis (Cephalopoda)
Vampyroteuthis infernalis Chun, 1903, is a widely distributed deepwater cephalopod with unique morphology and phylogenetic position. We assessed its habitat and trophic ecology on a global scale via stable isotope analyses of a unique collection of beaks from 104 specimens from the Atlantic, Pacific and Indian Oceans. Cephalopods typically are active predators occupying a high trophic level (TL) and exhibit an ontogenetic increase in δ15N and TL. Our results, presenting the first global comparison for a deep-sea invertebrate, demonstrate that V. infernalis has an ontogenetic decrease in δ15N and TL, coupled with niche broadening. Juveniles are mobile zooplanktivores, while larger Vampyroteuthis are slow-swimming opportunistic consumers and ingest particulate organic matter. Vampyroteuthis infernalis occupies the same TL (3.0–4.3) over its global range and has a unique niche in deep-sea ecosystems. These traits have enabled the success and abundance of this relict species inhabiting the largest ecological realm on the planet.Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
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