The Cleavable Carboxyl-Terminus of the Small Coat Protein of Cowpea Mosaic Virus Is Involved in RNA Encapsidation

AbstractThe site of cleavage of the small coat protein of cowpea mosaic virus has been precisely mapped and the proteolysis has been shown to result in the loss of 24 amino acids from the carboxyl-terminus of the protein. A series of premature termination and deletion mutants was constructed to investigate the role or roles of these carboxyl-terminal amino acids in the viral replication cycle. Mutants containing premature termination codons at or downstream of the cleavage site were viable but reverted to wild-type after a single passage through cowpea plants, indicating that the carboxyl-terminal amino acids are important. Mutants with the equivalent deletions were genetically stable and shown to be debilitated with respect to virus accumulation. The specific infectivity of preparations of a deletion mutant (DM4) lacking all 24 amino acids was 6-fold less than that of a wild-type preparation. This was shown to be a result of DM4 preparations containing a much increased percentage (73%) of empty (RNA-free) particles, a finding that implicates the cleavable carboxyl-terminal residues in the packaging of the virion RNAs

Major Subject: Computer ScienceTECHNIQUES FOR MODELING AND ANALYZING RNA AND PROTEIN FOLDING ENERGY LANDSCAPES

Major Subject: Computer Scienceiii Techniques for Modeling and Analyzing RNA and Protein Folding Energ

Pre- and Perinatal Ischemia-Hypoxia, the Ischemia-Hypoxia Response Pathway, and ADHD Risk

This review focuses on how measured pre- and perinatal environmental and (epi)genetic risk factors are interrelated and potentially influence one, of many, common developmental pathway towards ADHD. Consistent with the Developmental Origins of Health and Disease hypothesis, lower birth weight is associated with increased ADHD risk. Prenatal ischemia-hypoxia (insufficient blood and oxygen supply in utero) is a primary pathway to lower birth weight and produces neurodevelopmental risk for ADHD. To promote tissue survival in the context of ischemia-hypoxia, ischemia-hypoxia response (IHR) pathway gene expression is altered in the developing brain and peripheral tissues. Although altered IHR gene expression is adaptive in the context of ischemia-hypoxia, lasting IHR epigenetic modifications may lead to increased ADHD risk. Taken together, IHR genetic vulnerability to ischemia-hypoxia and IHR epigenetic alterations following prenatal ischemia-hypoxia may result in neurodevelopmental vulnerability for ADHD. Limitations of the extant literature and future directions for genetically-informed research are discussed

Passive \u3cem\u3er\u3c/em\u3eGE or Developmental Gene-Environment Cascade? An Investigation of the Role of Xenobiotic Metabolism Genes in the Association Between Smoke Exposure During Pregnancy and Child Birth Weight

There is considerable evidence that smoke exposure during pregnancy (SDP) environmentally influences birth weight after controlling for genetic influences and maternal characteristics. However, maternal smoking during pregnancy—the behavior that leads to smoke exposure during pregnancy—is also genetically-influenced, indicating the potential role of passive gene-environment correlation. An alternative to passive gene-SDP correlation is a cascading effect whereby maternal and child genetic influences are causally linked to prenatal exposures, which then have an ‘environmental’ effect on the development of the child’s biology and behavior. We describe and demonstrate a conceptual framework for disentangling passive rGE from this cascading GE effect using a systems-based polygenic scoring approach comprised of genes shown to be important in the xenobiotic (substances foreign to the body) metabolism pathway. Data were drawn from 5044 families from the Avon Longitudinal Study of Parents and Children with information on maternal SDP, birth weight, and genetic polymorphisms in the xenobiotic pathway. Within a k-fold cross-validation approach (k = 5), we created weighted maternal and child polygenic scores using 18 polymorphisms from 10 genes that have been implicated in the xenobiotic metabolism pathway. Mothers and children shared variation in xenobiotic metabolism genes. Amongst mothers who smoked during pregnancy, neither maternal nor child xenobiotic metabolism polygenic scores were associated with a higher likelihood of smoke exposure during pregnancy, or the severity of smoke exposure during pregnancy (and therefore, neither proposed mechanism was supported), or with child birth weight. SDP was consistently associated with lower child birth weight controlling for the polygenic scores, maternal educational attainment, social class, psychiatric problems, and age. Limitations of the study design and the potential of the framework using other designs are discussed

Improving signal intensities for genes with low-expression on oligonucleotide microarrays

BACKGROUND: DNA microarrays using long oligonucleotide probes are widely used to evaluate gene expression in biological samples. These oligonucleotides are pre-synthesized and sequence-optimized to represent specific genes with minimal cross-hybridization to homologous genes. Probe length and concentration are critical factors for signal sensitivity, particularly when genes with various expression levels are being tested. We evaluated the effects of oligonucleotide probe length and concentration on signal intensity measurements of the expression levels of genes in a target sample. RESULTS: Selected genes of various expression levels in a single cell line were hybridized to oligonucleotide arrays of four lengths and four concentrations of probes to determine how these critical parameters affected the intensity of the signal representing their expression. We found that oligonucleotides of longer length significantly increased the signals of genes with low-expression in the target. High-expressing gene signals were also boosted but to a lesser degree. Increasing the probe concentration, however, did not linearly increase the signal intensity for either low- or high-expressing genes. CONCLUSIONS: We conclude that the longer the oligonuclotide probe the better the signal intensities of low expressing genes on oligonucleotide arrays

Layout optimization in ultra deep submicron VLSI design

As fabrication technology keeps advancing, many deep submicron (DSM) effects have become increasingly evident and can no longer be ignored in Very Large Scale Integration (VLSI) design. In this dissertation, we study several deep submicron problems (eg. coupling capacitance, antenna effect and delay variation) and propose optimization techniques to mitigate these DSM effects in the place-and-route stage of VLSI physical design. The place-and-route stage of physical design can be further divided into several steps: (1) Placement, (2) Global routing, (3) Layer assignment, (4) Track assignment, and (5) Detailed routing. Among them, layer/track assignment assigns major trunks of wire segments to specific layers/tracks in order to guide the underlying detailed router. In this dissertation, we have proposed techniques to handle coupling capacitance at the layer/track assignment stage, antenna effect at the layer assignment, and delay variation at the ECO (Engineering Change Order) placement stage, respectively. More specifically, at layer assignment, we have proposed an improved probabilistic model to quickly estimate the amount of coupling capacitance for timing optimization. Antenna effects are also handled at layer assignment through a linear-time tree partitioning algorithm. At the track assignment stage, timing is further optimized using a graph based technique. In addition, we have proposed a novel gate splitting methodology to reduce delay variation in the ECO placement considering spatial correlations. Experimental results on benchmark circuits showed the effectiveness of our approaches

The STAPL pList

We present the design and implementation of the Standard Template Adap- tive Parallel Library (stapl) pList, a parallel container that has the properties of a sequential list, but allows for scalable concurrent access when used in a paral- lel program. The stapl is a parallel programming library that extends C with support for parallelism. stapl provides a collection of distributed data structures (pContainers) and parallel algorithms (pAlgorithms) and a generic methodology for extending them to provide customized functionality. stapl pContainers are thread-safe, concurrent objects, providing appropriate interfaces (pViews) that can be used by generic pAlgorithms. The pList provides Standard Template Library (stl) equivalent methods, such as insert, erase, and splice, additional methods such as split, and efficient asyn- chronous (non-blocking) variants of some methods for improved parallel performance. List related algorithms such as list ranking, Euler Tour (ET), and its applications to compute tree based functions can be computed efficiently and expressed naturally using the pList. Lists are not usually considered useful in parallel algorithms because they do not allow random access to its elements. Instead, they access elements through a serializing traversal of the list. Our design of the pList, which consists of a collec- tion of distributed lists (base containers), provides almost random access to its base containers. The degree of parallelism supported can be tuned by setting the number of base containers. Thus, a key feature of the pList is that it offers the advantages of a classical list while enabling scalable parallelism. We evaluate the performance of the stapl pList on an IBM Power 5 cluster and on a CRAY XT4 massively parallel processing system. Although lists are generally not considered good data structures for parallel processing, we show that pList methods and pAlgorithms, and list related algorithms such as list ranking and ET technique operating on pLists provide good scalability on more than 16, 000 processors. We also show that the pList compares favorably with other dynamic data structures such as the pVector that explicitly support random access

The Living Planet Index: using species population time series to track trends in biodiversity.

The Living Planet Index was developed to measure the changing state of the world's biodiversity over time. It uses time-series data to calculate average rates of change in a large number of populations of terrestrial, freshwater and marine vertebrate species. The dataset contains about 3000 population time series for over 1100 species. Two methods of calculating the index are outlined: the chain method and a method based on linear modelling of log-transformed data. The dataset is analysed to compare the relative representation of biogeographic realms, ecoregional biomes, threat status and taxonomic groups among species contributing to the index. The two methods show very similar results: terrestrial species declined on average by 25% from 1970 to 2000. Birds and mammals are over-represented in comparison with other vertebrate classes, and temperate species are over-represented compared with tropical species, but there is little difference in representation between threatened and non-threatened species. Some of the problems arising from over-representation are reduced by the way in which the index is calculated. It may be possible to reduce this further by post-stratification and weighting, but new information would first need to be collected for data-poor classes, realms and biomes

Tissue‐resident macrophages actively suppress IL‐1beta release via a reactive prostanoid/IL‐10 pathway

The alarm cytokine interleukin‐1β (IL‐1β) is a potent activator of the inflammatory cascade following pathogen recognition. IL‐1β production typically requires two signals: first, priming by recognition of pathogen‐associated molecular patterns leads to the production of immature pro‐IL‐1β; subsequently, inflammasome activation by a secondary signal allows cleavage and maturation of IL‐1β from its pro‐form. However, despite the important role of IL‐1β in controlling local and systemic inflammation, its overall regulation is still not fully understood. Here we demonstrate that peritoneal tissue‐resident macrophages use an active inhibitory pathway, to suppress IL‐1β processing, which can otherwise occur in the absence of a second signal. Programming by the transcription factor Gata6 controls the expression of prostacyclin synthase, which is required for prostacyclin production after lipopolysaccharide stimulation and optimal induction of IL‐10. In the absence of secondary signal, IL‐10 potently inhibits IL‐1β processing, providing a previously unrecognized control of IL‐1β in tissue‐resident macrophages

How Does Blood-Retinal Barrier Breakdown Relate to Death and Disability in Pediatric Cerebral Malaria?

Background In cerebral malaria, the retina can be used to understand disease pathogenesis. The mechanisms linking sequestration, brain swelling and death remain poorly understood. We hypothesized that retinal vascular leakage would be associated with brain swelling. Methods We used retinal angiography to study blood-retinal barrier integrity. We analyzed retinal leakage, histopathology, brain MRI, and associations with death and neurological disability in prospective cohorts of Malawian children with cerebral malaria. Results Three types of retinal leakage were seen: Large focal leak (LFL), punctate leak (PL) and vessel leak. LFL and PL were associated with death (OR 13.20, 95%CI 5.21-33.78 and 8.58, 2.56-29.08 respectively), and brain swelling (p<0.05). Vessel leak and macular non-perfusion were associated with neurological disability (3.71, 1.26-11.02 and 9.06, 1.79-45.90). LFL was observed as an evolving retinal hemorrhage. A core of fibrinogen and monocytes was found in 39 (93%) white-centered hemorrhages. Conclusions Blood-retina barrier breakdown occurs in three patterns in cerebral malaria. Associations between LFL, brain swelling, and death suggest that the rapid accumulation of cerebral hemorrhages, with accompanying fluid egress, may cause fatal brain swelling. Vessel leak from barrier dysfunction, and non-perfusion were not associated with severe brain swelling, but with neurological deficits, suggesting hypoxic injury in survivors