Analysis of errors in the structure determination of MsbA

An analysis is presented of the methodological errors that led to the incorrect structure of MsbA

Identification of candidate genes and molecular markers for heat-induced brown discoloration of seed coats in cowpea [Vigna unguiculata (L.) Walp].

BackgroundHeat-induced browning (Hbs) of seed coats is caused by high temperatures which discolors the seed coats of many legumes, affecting the visual appearance and quality of seeds. The genetic determinants underlying Hbs in cowpea are unknown.ResultsWe identified three QTL associated with the heat-induced browning of seed coats trait, Hbs-1, Hbs-2 and Hbs-3, using cowpea RIL populations IT93K-503-1 (Hbs positive) x CB46 (hbs negative) and IT84S-2246 (Hbs positive) x TVu14676 (hbs negative). Hbs-1 was identified in both populations, accounting for 28.3% -77.3% of the phenotypic variation. SNP markers 1_0032 and 1_1128 co-segregated with the trait. Within the syntenic regions of Hbs-1 in soybean, Medicago and common bean, several ethylene forming enzymes, ethylene responsive element binding factors and an ACC oxidase 2 were observed. Hbs-1 was identified in a BAC clone in contig 217 of the cowpea physical map, where ethylene forming enzymes were present. Hbs-2 was identified in the IT93K-503-1 x CB46 population and accounted for of 9.5 to 12.3% of the phenotypic variance. Hbs-3 was identified in the IT84S-2246 x TVu14676 population and accounted for 6.2 to 6.8% of the phenotypic variance. SNP marker 1_0640 co-segregated with the heat-induced browning phenotype. Hbs-3 was positioned on BAC clones in contig512 of the cowpea physical map, where several ACC synthase 1 genes were present.ConclusionThe identification of loci determining heat-induced browning of seed coats and co-segregating molecular markers will enable transfer of hbs alleles into cowpea varieties, contributing to higher quality seeds

Immune-Mediated Inflammation May Contribute to the Pathogenesis of Cardiovascular Disease in Mucopolysaccharidosis Type I.

BackgroundCardiovascular disease, a progressive manifestation of α-L-iduronidase deficiency or mucopolysaccharidosis type I, continues in patients both untreated and treated with hematopoietic stem cell transplantation or intravenous enzyme replacement. Few studies have examined the effects of α-L-iduronidase deficiency and subsequent glycosaminoglycan storage upon arterial gene expression to understand the pathogenesis of cardiovascular disease.MethodsGene expression in carotid artery, ascending, and descending aortas from four non-tolerized, non-enzyme treated 19 month-old mucopolysaccharidosis type I dogs was compared with expression in corresponding vascular segments from three normal, age-matched dogs. Data were analyzed using R and whole genome network correlation analysis, a bias-free method of categorizing expression level and significance into discrete modules. Genes were further categorized based on module-trait relationships. Expression of clusterin, a protein implicated in other etiologies of cardiovascular disease, was assessed in canine and murine mucopolysaccharidosis type I aortas via Western blot and in situ immunohistochemistry.ResultsGene families with more than two-fold, significant increased expression involved lysosomal function, proteasome function, and immune regulation. Significantly downregulated genes were related to cellular adhesion, cytoskeletal elements, and calcium regulation. Clusterin gene overexpression (9-fold) and protein overexpression (1.3 to 1.62-fold) was confirmed and located specifically in arterial plaques of mucopolysaccharidosis-affected dogs and mice.ConclusionsOverexpression of lysosomal and proteasomal-related genes are expected responses to cellular stress induced by lysosomal storage in mucopolysaccharidosis type I. Upregulation of immunity-related genes implicates the potential involvement of glycosaminoglycan-induced inflammation in the pathogenesis of mucopolysaccharidosis-related arterial disease, for which clusterin represents a potential biomarker

A decadally-resolved paleohurricane record archived in the late Holocene sediments of a Florida sinkhole

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Marine Geology 287 (2011): 14-30, doi:10.1016/j.margeo.2011.07.001.A 4500-year record of hurricane-induced storm surges is developed from sediment cores collected from a coastal sinkhole near Apalachee Bay, Florida. Recent deposition of sand layers in the upper sediments of the pond was found to be contemporaneous with significant, historic storm surges at the site modeled using SLOSH and the Best Track, post-1851 A.D. dataset. Using the historic portion of the record for calibration, paleohurricane deposits were identified by sand content and dated using radiocarbon-based age models. Marine-indicative foraminifera, some originating at least 5 km offshore, were present in several modern and ancient storm deposits. The presence and long-term preservation of offshore foraminifera suggest that this site and others like it may yield promising microfossil-based paleohurricane reconstructions in the future. Due to the sub-decadal (~ 7 year) resolution of the record and the site’s high susceptibility to hurricane-generated storm surges, the average, local frequency of recorded events, approximately 3.9 storms per century, is greater than that of previously published paleohurricane records from the region. The high incidence of recorded events permitted a time series of local hurricane frequency during the last five millennia to be constructed. Variability in the frequency of the largest storm layers was found to be greater than what would likely occur by chance alone, with intervals of both anomalously high and low storm frequency identified. However, the rate at which smaller layers were deposited was relatively constant over the last five millennia. This may suggest that significant variability in hurricane frequency has occurred only in the highest magnitude events. The frequency of high magnitude events peaked near 6 storms per century between 2800 and 2300 years ago. High magnitude events were relatively rare with about 0-3 storms per century occurring between 1900 to 1600 years ago and between 400 to 150 years ago. A marked decline in the number of large storm deposits, which began around 600 years ago, has persisted through present with below average frequency over the last 150 years when compared to the preceding five millennia.Funding for this research was supported by the National Science Foundation and the Coastal Ocean Institute. the model. The Florida State University Marine Laboratory provided lodging during fieldwork. This research was completed during an American Meteorological Society Graduate Fellowship, National Science Foundation Graduate Fellowship and Coastal Ocean Institute Fellowship. This work was further supported by National Science Foundation award #OCE-0903020

Genetic mapping and legume synteny of aphid resistance in African cowpea (Vigna unguiculata L. Walp.) grown in California.

The cowpea aphid Aphis craccivora Koch (CPA) is a destructive insect pest of cowpea, a staple legume crop in Sub-Saharan Africa and other semiarid warm tropics and subtropics. In California, CPA causes damage on all local cultivars from early vegetative to pod development growth stages. Sources of CPA resistance are available in African cowpea germplasm. However, their utilization in breeding is limited by the lack of information on inheritance, genomic location and marker linkage associations of the resistance determinants. In the research reported here, a recombinant inbred line (RIL) population derived from a cross between a susceptible California blackeye cultivar (CB27) and a resistant African breeding line (IT97K-556-6) was genotyped with 1,536 SNP markers. The RILs and parents were phenotyped for CPA resistance using field-based screenings during two main crop seasons in a 'hotspot' location for this pest within the primary growing region of the Central Valley of California. One minor and one major quantitative trait locus (QTL) were consistently mapped on linkage groups 1 and 7, respectively, both with favorable alleles contributed from IT97K-556-6. The major QTL appeared dominant based on a validation test in a related F2 population. SNP markers flanking each QTL were positioned in physical contigs carrying genes involved in plant defense based on synteny with related legumes. These markers could be used to introgress resistance alleles from IT97K-556-6 into susceptible local blackeye varieties by backcrossing

Sentinel surveillance of HIV-1 transmitted drug resistance, acute infection and recent infection.

BackgroundHIV-1 acute infection, recent infection and transmitted drug resistance screening was integrated into voluntary HIV counseling and testing (VCT) services to enhance the existing surveillance program in San Francisco. This study describes newly-diagnosed HIV cases and characterizes correlates associated with infection.Methodology/principal findingsA consecutive sample of persons presenting for HIV VCT at the municipal sexually transmitted infections (STI) clinic from 2004 to 2006 (N = 9,868) were evaluated by standard enzyme-linked immunoassays (EIA). HIV antibody-positive specimens were characterized as recent infections using a less-sensitive EIA. HIV-RNA pooled testing was performed on HIV antibody-negative specimens to identify acute infections. HIV antibody-positive and acute infection specimens were evaluated for drug resistance by sequence analysis. Multivariable logistic regression was performed to evaluate associations. The 380 newly-diagnosed HIV cases included 29 acute infections, 128 recent infections, and 47 drug-resistant cases, with no significant increases or decreases in prevalence over the three years studied. HIV-1 transmitted drug resistance prevalence was 11.0% in 2004, 13.4% in 2005 and 14.9% in 2006 (p = 0.36). Resistance to non-nucleoside reverse transcriptase inhibitors (NNRTI) was the most common pattern detected, present in 28 cases of resistance (59.6%). Among MSM, recent infection was associated with amphetamine use (AOR = 2.67; p<0.001), unprotected anal intercourse (AOR = 2.27; p<0.001), sex with a known HIV-infected partner (AOR = 1.64; p = 0.02), and history of gonorrhea (AOR = 1.62; p = 0.03).ConclusionsNew HIV diagnoses, recent infections, acute infections and transmitted drug resistance prevalence remained stable between 2004 and 2006. Resistance to NNRTI comprised more than half of the drug-resistant cases, a worrisome finding given its role as the backbone of first-line antiretroviral therapy in San Francisco as well as worldwide. The integration of HIV-1 drug resistance, recent infection, and acute infection testing should be considered for existing HIV/STI surveillance and prevention activities, particularly in an era of enhanced efforts for early diagnosis and treatment

Tropical cyclone wind speed constraints from resultant storm surge deposition : a 2500 year reconstruction of hurricane activity from St. Marks, FL

Author Posting. © American Geophysical Union, 2013. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry, Geophysics, Geosystems 14 (2013): 2993–3008, doi:10.1002/ggge.20217.Recent work suggests that the patterns of intense (≥category 3 on the Saffir-Simpson scale) hurricane strikes over the last few millennia might differ from that of overall hurricane activity during this period. Prior studies typically rely on assigning a threshold storm intensity required to produce a sedimentological overwash signal at a particular coastal site based on historical analogs. Here, we improve on this approach by presenting a new inverse-model technique that constrains the most likely wind speeds required to transport the maximum grain size within resultant storm deposits. As a case study, the technique is applied to event layers observed in sediments collected from a coastal sinkhole in northwestern Florida. We find that (1) simulated wind speeds for modern deposits are consistent with the intensities for historical hurricanes affecting the site, (2) all deposits throughout the ∼2500 year record are capable of being produced by hurricanes, and (3) a period of increased intense hurricane frequency is observed between ∼1700 and ∼600 years B.P. and decreased intense storm frequency is observed from ∼2500 to ∼1700 and ∼600 years B.P. to the present. This is consistent with prior reconstructions from nearby sites. Changes in the frequency of intense hurricane strikes may be related to the degree of penetration of the Loop Current in the Gulf of Mexico.This work was supported by the National Science Foundation.2014-02-2

Assessing sedimentary records of paleohurricane activity using modeled hurricane climatology

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 9 (2008): Q09V10, doi:10.1029/2008GC002043.Patterns of overwash deposition observed within back-barrier sediment archives can indicate past changes in tropical cyclone activity; however, it is necessary to evaluate the significance of observed trends in the context of the full range of variability under modern climate conditions. Here we present a method for assessing the statistical significance of patterns observed within a sedimentary hurricane-overwash reconstruction. To alleviate restrictions associated with the limited number of historical hurricanes affecting a specific site, we apply a recently published technique for generating a large number of synthetic storms using a coupled ocean-atmosphere hurricane model set to simulate modern climatology. Thousands of overwash records are generated for a site using a random draw of these synthetic hurricanes, a prescribed threshold for overwash, and a specified temporal resolution based on sedimentation rates observed at a particular site. As a test case we apply this Monte Carlo technique to a hurricane-induced overwash reconstruction developed from Laguna Playa Grande (LPG), a coastal lagoon located on the island of Vieques, Puerto Rico in the northeastern Caribbean. Apparent overwash rates in the LPG overwash record are observed to be four times lower between 2500 and 1000 years B.P. when compared to apparent overwash rates during the last 300 years. However, probability distributions based on Monte Carlo simulations indicate that as much as 65% of this drop can be explained by a reduction in the temporal resolution for older sediments due to a decrease in sedimentation rates. Periods of no apparent overwash activity at LPG between 2500 and 3600 years B.P. and 500–1000 years B.P. are exceptionally long and are unlikely to occur (above 99% confidence) under the current climate conditions. In addition, breaks in activity are difficult to produce even when the hurricane model is forced to a constant El Niño state. Results from this study continue to support the interpretation that the western North Atlantic has exhibited significant changes in hurricane climatology over the last 5500 years.Funding for this research was provided by the Earth Systems History Program of the National Science Foundation, Risk Prediction Initiative, National Geographic Society, Coastal Ocean Institute at WHOI, and the Andrew W. Mellon Foundation Endowed Fund for Innovative Research