The properties of Msh2-Msh6 ATP binding mutants suggest a signal amplification mechanism in DNA mismatch repair.

DNA mismatch repair (MMR) corrects mispaired DNA bases and small insertion/deletion loops generated by DNA replication errors. After binding a mispair, the eukaryotic mispair recognition complex Msh2-Msh6 binds ATP in both of its nucleotide-binding sites, which induces a conformational change resulting in the formation of an Msh2-Msh6 sliding clamp that releases from the mispair and slides freely along the DNA. However, the roles that Msh2-Msh6 sliding clamps play in MMR remain poorly understood. Here, using Saccharomyces cerevisiae, we created Msh2 and Msh6 Walker A nucleotide-binding site mutants that have defects in ATP binding in one or both nucleotide-binding sites of the Msh2-Msh6 heterodimer. We found that these mutations cause a complete MMR defect in vivo The mutant Msh2-Msh6 complexes exhibited normal mispair recognition and were proficient at recruiting the MMR endonuclease Mlh1-Pms1 to mispaired DNA. At physiological (2.5 mm) ATP concentration, the mutant complexes displayed modest partial defects in supporting MMR in reconstituted Mlh1-Pms1-independent and Mlh1-Pms1-dependent MMR reactions in vitro and in activation of the Mlh1-Pms1 endonuclease and showed a more severe defect at low (0.1 mm) ATP concentration. In contrast, five of the mutants were completely defective and one was mostly defective for sliding clamp formation at high and low ATP concentrations. These findings suggest that mispair-dependent sliding clamp formation triggers binding of additional Msh2-Msh6 complexes and that further recruitment of additional downstream MMR proteins is required for signal amplification of mispair binding during MMR

Affymetrix probes containing runs of contiguous guanines are not gene-specific

High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in the designated probe set will provide a consistent message signifying the gene's presence. However, we demonstrate by data mining thousands of CEL files from NCBI's GEO database that 4G-probes (defined as probes containing sequences of four or more consecutive guanine (G) bases) do not react in the intended way. Rather, possibly due to the formation of G-quadruplexes, most 4G-probes are correlated, irrespective of the expression of the thousands of genes for which they were separately intended. It follows that 4G-probes should be ignored when calculating gene expression levels. Furthermore, future microarray designs should make no use of 4G-probes

Cow, farm, and herd management factors in the dry period associated with raised somatic cell counts in early lactation

This study investigated cow characteristics, farm facilities, and herd management strategies during the dry period to examine their joint influence on somatic cell counts (SCC) in early lactation. Data from 52 commercial dairy farms throughout England and Wales were collected over a 2-yr period. For the purpose of analysis, cows were separated into those housed for the dry period (6,419 cow-dry periods) and those at pasture (7,425 cow-dry periods). Bayesian multilevel models were specified with 2 response variables: ln SCC (continuous) and SCC >199,000 cells/mL (binary), both within 30 d of calving. Cow factors associated with an increased SCC after calving were parity, an SCC >199,000 cells/mL in the 60 d before drying off, increasing milk yield 0 to 30 d before drying off, and reduced DIM after calving at the time of SCC estimation. Herd management factors associated with an increased SCC after calving included procedures at drying off, aspects of bedding management, stocking density, and method of pasture grazing. Posterior predictions were used for model assessment, and these indicated that model fit was generally good. The research demonstrated that specific dry-period management strategies have an important influence on SCC in early lactation

Seasonal variability in ichthyoplankton abundance and assemblage composition in the northern Gulf of Mexico off Alabama

Multiyear ichthyoplankton surveys used to monitor larval fish seasonality, abundance, and assemblage structure can provide early indicators of regional ecosystem changes. Numerous ichthyoplankton surveys have been conducted in the northern Gulf of Mexico, but few have had high levels of temporal resolution and sample replication. In this study, ichthyoplankton samples were collected monthly (October 2004–October 2006) at a single station off the coast of Alabama as part of a long-term biological survey. Four seasonal periods were identified from observed and historic water temperatures, including a relatively long (June–October) “summer” period (water temperature >26°C). Fish egg abundance, total larval abundance, and larval taxonomic diversity were significantly related to water temperature (but not salinity), with peaks in the spring, spring–summer, and summer periods, respectively. Larvae collected during the survey represented 58 different families, of which engraulids, sciaenids, carangids, and clupeids were the most prominent. The most abundant taxa collected were unidentified engraulids (50%), sand seatrout (Cynoscion arenarius, 7.5%), Atlantic bumper (Chloroscombrus chrysurus, 5.4%), Atlantic croaker (Micropogonias undulatus, 4.4%), Gulf menhaden (Brevoortia patronus, 3.8%), and unidentified gobiids (3.6%). Larval concentrations for dominant taxa were highly variable between years, but the timing of seasonal occurrence for these taxa was relatively consistent. Documented increases in sea surface temperature on the Alabama shelf may have various implications for larval fish dynamics, as indicated by the presence of tropical larval forms (e.g., fistularids, labrids, scarids, and acanthurids) in our ichthyoplankton collections and in recent juvenile surveys of Alabama and northern Gulf of Mexico seagrass habitats

Process-based modelling of decadal trends in growth, survival, and smolting of wild salmon (Salmo salar) parr in a Scottish upland stream

This paper reports a new model of the freshwater stages of an anadromous fish, at the core of which is a stochastic description of the size-at-age dynamics of a growing cohort. Emigration is assumed to require the individual to exceed a threshold size at a critical time of year, thus making the distributions of survival to, and age at, smolting emergent properties of the model. The model is applied to a long-term data set on juvenile Atlantic salmon (Salmo salar) in the Girnock Burn, Scotland, to understand the role played by decadal temperature trends in generating changes in smolt production and age distribution. We conclude that changes in age at smolting are compatible with causation by shifts in the temperature regime. However, the large attenuation between a dramatic fall in spawner numbers and a relatively minor diminution in total smolt production does not result from the physiological effects of temperature but is rather a result of strongly density-dependent mortality between the deposition of ova and the appearance of catchable fry the following summer

A One-Hole Cu\u3csub\u3e4\u3c/sub\u3eS Cluster with N\u3csub\u3e2\u3c/sub\u3eO Reductase Activity: A Structural and Functional Model for Cu\u3csub\u3eZ\u3c/sub\u3e

During bacterial denitrification, two-electron reduction of N2O occurs at a [Cu4(μ4-S)] catalytic site (CuZ*) embedded within the nitrous oxide reductase (N2OR) enzyme. In this Communication, an amidinate-supported [Cu4(μ4-S)] model cluster in its one-hole (S = 1/2) redox state is thoroughly characterized. Along with its two-hole redox partner and fully reduced clusters reported previously, the new species completes the two-electron redox series of [Cu4(μ4-S)] model complexes with catalytically relevant oxidation states for the first time. More importantly, N2O is reduced by the one-hole cluster to produce N2 and the two-hole cluster, thereby completing a closed cycle for N2O reduction. Not only is the title complex thus the best structural model for CuZ* to date, but it also serves as a functional CuZ* mimic

Role of BacA in Lipopolysaccharide Synthesis, Peptide Transport, and Nodulation by \u3cem\u3eRhizobium\u3c/em\u3e sp. Strain NGR234

BacA of Sinorhizobium meliloti plays an essential role in the establishment of nitrogen-fixing symbioses with Medicago plants, where it is involved in peptide import and in the addition of very-long-chain fatty acids (VLCFA) to lipid A of lipopolysaccharide (LPS). We investigated the role of BacA in Rhizobium species strain NGR234 by mutating the bacA gene. In the NGR234 bacA mutant, peptide import was impaired, but no effect on VLCFA addition was observed. More importantly, the symbiotic ability of the mutant was comparable to that of the wild type for a variety of legume species. Concurrently, an acpXL mutant of NGR234 was created and assayed. In rhizobia, AcpXL is a dedicated acyl carrier protein necessary for the addition of VLCFA to lipid A. LPS extracted from the NGR234 mutant lacked VLCFA, and this mutant was severely impaired in the ability to form functional nodules with the majority of legumes tested. Our work demonstrates the importance of VLCFA in the NGR234-legume symbiosis and also shows that the necessity of BacA for bacteroid differentiation is restricted to specific legume-Rhizobium interactions

Impact of imperfect test sensitivity on determining risk factors : the case of bovine tuberculosis

Background Imperfect diagnostic testing reduces the power to detect significant predictors in classical cross-sectional studies. Assuming that the misclassification in diagnosis is random this can be dealt with by increasing the sample size of a study. However, the effects of imperfect tests in longitudinal data analyses are not as straightforward to anticipate, especially if the outcome of the test influences behaviour. The aim of this paper is to investigate the impact of imperfect test sensitivity on the determination of predictor variables in a longitudinal study. Methodology/Principal Findings To deal with imperfect test sensitivity affecting the response variable, we transformed the observed response variable into a set of possible temporal patterns of true disease status, whose prior probability was a function of the test sensitivity. We fitted a Bayesian discrete time survival model using an MCMC algorithm that treats the true response patterns as unknown parameters in the model. We applied our approach to epidemiological data of bovine tuberculosis outbreaks in England and investigated the effect of reduced test sensitivity in the determination of risk factors for the disease. We found that reduced test sensitivity led to changes to the collection of risk factors associated with the probability of an outbreak that were chosen in the ‘best’ model and to an increase in the uncertainty surrounding the parameter estimates for a model with a fixed set of risk factors that were associated with the response variable. Conclusions/Significance We propose a novel algorithm to fit discrete survival models for longitudinal data where values of the response variable are uncertain. When analysing longitudinal data, uncertainty surrounding the response variable will affect the significance of the predictors and should therefore be accounted for either at the design stage by increasing the sample size or at the post analysis stage by conducting appropriate sensitivity analyses

Imaging of the Stellar Population of IC10 with Laser Guide Star Adaptive Optics and the Hubble Space Telescope

We present adaptive optics (AO) images of the central starburst region of the dwarf irregular galaxy IC10. The Keck 2 telescope laser guide star was used to achieve near diffraction-limited performance at H and K' (Strehls of 18% and 32%, respectively). The images are centered on the putative Wolf-Rayet (W-R) object [MAC92]24. We combine our AO images with F814W data from HST. By comparing the K' vs. [F814W]-K' color-magnitude diagram (CMD) with theoretical isochrones, we find that the stellar population is best represented by at least two bursts of star formation, one ~ 10 Myr ago and one much older (150-500 Myr). Young, blue stars are concentrated in the vicinity of [MAC92]24. This population represents an OB association with a half-light radius of about 3 pc. We resolve the W-R object [MAC92]24 into at least six blue stars. Four of these components have near-IR colors and luminosities that make them robust WN star candidates. By matching the location of C-stars in the CMD with those in the SMC we derive a distance modulus for IC10 of about 24.5 mag. and a foreground reddening of E(B-V) = 0.95. We find a more precise distance by locating the tip of the giant branch in the F814W, H, and K' luminosity functions. We find a weighted mean distance modulus of 24.48 +/- 0.08. The systematic error in this measurement, due to a possible difference in the properties of the RGB populations in IC10 and the SMC, is +/- 0.16 mag.Comment: 13 pages, 13 figures, ApJ in pres