Relative dominance of epitope-specific cytotoxic T-lymphocyte responses in human immunodeficiency virus type 1-infected persons with shared HLA alleles.

Cytotoxic T lymphocytes (CTL) target multiple epitopes in human immunodeficiency virus (HIV)-infected persons, and are thought to influence the viral set point. The extent to which HLA class I allele expression predicts the epitopes targeted has not been determined, nor have the relative contributions of responses restricted by different class I alleles within a given individual. In this study, we performed a detailed analysis of the CTL response to optimally defined CTL epitopes restricted by HLA class I A and B alleles in individuals who coexpressed HLA A2, A3, and B7. The eight HIV-1-infected subjects studied included two subjects with acute HIV infection, five subjects with chronic HIV infection, and one long-term nonprogressor. Responses were heterogeneous with respect to breadth and magnitude of CTL responses in individuals of the same HLA type. Of the 27 tested epitopes that are presented by A2, A3, and B7, 25 were targeted by at least one person. However, there was wide variation in the number of epitopes targeted, ranging from 2 to 17. The A2-restricted CTL response, which has been most extensively studied in infected persons, was found to be narrowly directed in most individuals, and in no cases was it the dominant contributor to the total HIV-1-specific CTL response. These results indicate that HLA type alone does not predict CTL responses and that numerous potential epitopes may not be targeted by CTL in a given individual. These data also provide a rationale for boosting both the breadth and the magnitude of HIV-1-specific CTL responses by immunotherapy in persons with chronic HIV-1 infection.     

The lysophosphatidic acid receptor LPA1 links pulmonary fibrosis to lung injury by mediating fibroblast recruitment and vascular leak

Aberrant wound-healing responses to injury have been implicated in the development of pulmonary fibrosis, but the mediators directing these pathologic responses have yet to be fully identified. We show that lysophosphatidic acid levels increase in bronchoalveolar lavage fluid following lung injury in the bleomycin model of pulmonary fibrosis, and that mice lacking one of its receptors, LPA1, are markedly protected from fibrosis and mortality in this model. The absence of LPA1 led to reduced fibroblast recruitment and vascular leak, two responses that may be excessive when injury leads to fibrosis rather than to repair, whereas leukocyte recruitment was preserved during the first week after injury. In persons with idiopathic pulmonary fibrosis, lysophosphatidic acid levels in bronchoalveolar lavage fluid were also increased, and inhibition of LPA1 markedly reduced fibroblast responses to the chemotactic activity of this fluid. LPA1 therefore represents a new therapeutic target for diseases in which aberrant responses to injury contribute to fibrosis, such as idiopathic pulmonary fibrosis.     

Ground wētā in vines of the Awatere Valley,Marlborough: biology,density and distribution

The endemic New Zealand ground wētā (Hemiandrus sp. ‘promontorius’) has a Naturally Uncommon conservation status. This is because of the paucity of information on its density and distribution. Here, the biology, density and distribution of a population of this wētā found in and around vineyards in the Awatere Valley, Marlborough was studied. Wētā density was assessed in vineyards, paddocks and shrublands in this valley. Soil moisture, penetration resistance, pH and organic matter were recorded at locations with and without wētā. Wētā density in vineyards was significantly higher than in either paddocks or shrub habitats. In vineyards, the density of this insect was significantly higher under-vines than in the inter-rows. Higher numbers of this wētā were found in moist soils that required lower force to burrow. Females laid an average of 55 eggs between March and April, which hatched in September. These findings highlight the intersection between agriculture and conservation.     

The relation between cartilage biomarkers (C2C,C1,2C,CS846, and CPII) and the long-term outcome of rheumatoid arthritis patients within the CAMERA trial

Introduction  

The aim of this study was to investigate whether serum biomarker levels of C2C, C1,2C, CS846, and CPII can predict the long-term course of disease activity and radiographic progression early in the disease course of rheumatoid arthritis (RA).     

High Dietary Magnesium Intake Is Associated with Low Insulin Resistance in the Newfoundland Population

Background

Magnesium plays a role in glucose and insulin homeostasis and evidence suggests that magnesium intake is associated with insulin resistance (IR). However, data is inconsistent and most studies have not adequately controlled for critical confounding factors.

Objective

The study investigated the association between magnesium intake and IR in normal-weight (NW), overweight (OW) and obese (OB) along with pre- and post- menopausal women.

Design

A total of 2295 subjects (590 men and 1705 women) were recruited from the CODING study. Dietary magnesium intake was computed from the Willett Food Frequency Questionnaire (FFQ). Adiposity (NW, OW and OB) was classified by body fat percentage (%BF) measured by Dual-energy X-ray absorptiometry according to the Bray criteria. Multiple regression analyses were used to test adiposity-specific associations of dietary magnesium intake on insulin resistance adjusting for caloric intake, physical activity, medication use and menopausal status.

Results

Subjects with the highest intakes of dietary magnesium had the lowest levels of circulating insulin, HOMA-IR, and HOMA-ß and subjects with the lowest intake of dietary magnesium had the highest levels of these measures, suggesting a dose effect. Multiple regression analysis revealed a strong inverse association between dietary magnesium with IR. In addition, adiposity and menopausal status were found to be critical factors revealing that the association between dietary magnesium and IR was stronger in OW and OB along with Pre-menopausal women.

Conclusion

The results of this study indicate that higher dietary magnesium intake is strongly associated with the attenuation of insulin resistance and is more beneficial for overweight and obese individuals in the general population and pre-menopausal women. Moreover, the inverse correlation between insulin resistance and dietary magnesium intake is stronger when adjusting for %BF than BMI.     

Image Corruption Detection in Diffusion Tensor Imaging for Post-Processing and Real-Time Monitoring

Due to the high sensitivity of diffusion tensor imaging (DTI) to physiological motion, clinical DTI scans often suffer a significant amount of artifacts. Tensor-fitting-based, post-processing outlier rejection is often used to reduce the influence of motion artifacts. Although it is an effective approach, when there are multiple corrupted data, this method may no longer correctly identify and reject the corrupted data. In this paper, we introduce a new criterion called “corrected Inter-Slice Intensity Discontinuity” (cISID) to detect motion-induced artifacts. We compared the performance of algorithms using cISID and other existing methods with regard to artifact detection. The experimental results show that the integration of cISID into fitting-based methods significantly improves the retrospective detection performance at post-processing analysis. The performance of the cISID criterion, if used alone, was inferior to the fitting-based methods, but cISID could effectively identify severely corrupted images with a rapid calculation time. In the second part of this paper, an outlier rejection scheme was implemented on a scanner for real-time monitoring of image quality and reacquisition of the corrupted data. The real-time monitoring, based on cISID and followed by post-processing, fitting-based outlier rejection, could provide a robust environment for routine DTI studies.     

An approach to functionally relevant clustering of the protein universe: Active site profile‐based clustering of protein structures and sequences

Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification—amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two‐Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure‐Function Linkage Database, SFLD) self‐identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self‐identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well‐curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP‐identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F‐measure and performance analysis on the enolase search results and comparison to GEMMA and SCI‐PHY demonstrate that TuLIP avoids the over‐division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results.     

Dietary Supplementation with S-Adenosyl Methionine was Associated with Protracted Reduction of Seizures in a Line of Transgenic Mice

Transgenic mice, although useful for analyses of gene function, can present unanticipated phenotypic manifestations, including behavioral problems, that may not be directly associated with the gene of interest but rather due to the complex interplay inherent in genomes. These unexpected events can present unique insight into gene function, leading to an advantage in some situations, yet in others can confound interpretation and compromise usefulness of the transgenic line. Here we document that short-term supplementation with S-adenosyl methionine (SAM)—a nutriceutical known to regulate neurotransmitter levels, improve working memory, and reduce aggression—reduced handling- and startling-induced seizures that otherwise precluded behavioral analyses in a transgenic line. This effect lasted for at least 1 mo after withdrawal of SAM and allowed mice to be used in standard maze analyses. These findings suggest that short-term administration of a neurotropic nutriceutical may provide a functional rescue for behavioral studies in an otherwise intractable transgenic mouse line as well as improve the welfare of similar lines.Abbreviations: SAH, S-adenosyl homocysteine; SAM, S-adenosyl methionineSite-directed mutagenesis, gene deletion, and the insertion of exogenous genes present powerful tools for genetic analyses. Incorporation of such genetic alterations into the murine germline, and the resultant generation of transgenic strains of mice, has provided novel insight into the roles of genes, and their interaction with other genes, at all stages of life. However, transgenic mice can present unanticipated behavioral problems that may not be associated directly with the gene of interest but rather are due to the complex interplay inherent in genomes.²⁰ This unexpected outcome can present unique insight into gene function, leading to an advantage in some situations, yet in others can confound interpretation and compromise usefulness of the transgenic line. Genetic variability of inbred strains can confound interpretation of behavior,¹⁸ especially if behavioral analyses are part of the regimen to be studied.²⁶The presence of 1 or more ApoE4 alleles is associated with an increased risk of Alzheimer disease.¹³ Transgenic mice in which the single murine ApoE allele has been ablated and replaced with human apolipoprotein E isoforms have been useful models for studying the impact of ApoE on age-related cognitive decline and Alzheimer disease. In addition to impaired cognition, mice lacking murine ApoE and expressing human ApoE4 (ApoE4 mice) display increased aggression as compared with normal mice, mice lacking murine ApoE, or mice lacking murine ApoE and expressing other human ApoE alleles.^5,6 These behavioral manifestations of ApoE4 mice are useful in that Alzheimer disease is often accompanied by behavioral trauma, including pyschosis and agitation,⁷ and ApoE4 has been associated with an increase psychotic symptoms in humans.²⁷Recent shipments of ApoE4 mice displayed violent spontaneous and handling-induced convulsions (hereafter referred to as seizures for the sake of simplicity), which included jumping and eventual prostration due to overt exhaustion. These seizures occurred regardless of how quietly or slowly the handler or caregiver moved. These seizures, which persisted for more than 1 mo, had not previously been observed in ApoE4 mice or other mice in our facility and precluded the intended use of the ApoE4 mice in standard maze trials.⁵In our ongoing studies, we had observed that dietary supplementation with the nutriceutical S-adenosyl methionine (SAM) reduced aggressive behavior in ApoE4 mice.⁵ SAM also restores neurotransmitter balance, increases working memory, and modulates neuronal activity.^6,8,17,19 We therefore hypothesized that SAM supplementation would reduce or alleviate handling-induced seizures. Here we document that short-term administration of SAM reduced of seizures for extended periods, to the extent that these mice could be used in behavioral studies. We discuss the possibility that such an approach may be useful for habituation of other mouse lines displaying similar behavior difficulties.