Interploid St. Augustinegrass [<Emphasis Type="Italic">Stenotaphrum secundatum</Emphasis> (Walt.) Kuntze] hybrids recovered by embryo rescue

St. Augustinegrass is one of the most important warm season turfgrasses in the southern United States because of its shade tolerance. Most cultivars are diploids (2n = 2x = 18) and are susceptible to various diseases and insects. Polyploid cultivars in the species have some resistance to pests, but most lack cold tolerance. In this study, eight polyploid genotypes were crossed with six diploid cultivars to transfer pest resistance to the diploids. Because interploid crosses often result in aborted seed, it was necessary to use in vitro techniques. Using embryo rescue, 268 plants were recovered from 2,463 emasculated and pollinated florets (10.88% crossability). Because of the heterogeneous nature of the species, these purported hybrids could not be verified by phenotype. DNA markers were used for hybrid identification. A subset of 25 plants from crosses between the aneuploid cultivar Floratam (2n = 4x = 32) and five diploid cultivars were analyzed using 144 expressed sequence tags–simple sequence repeats (EST-SSRs) developed from buffelgrass cDNA sequence data. Chi-square tests for paternal-specific markers revealed that all analyzed progeny were true F₁ hybrids and none originated from self-fertilization or unintended outcrossing. In addition to identifying DNA polymorphism, the EST-SSRs revealed that genetic variation exists among all analyzed cultivars and is not partitioned between ploidy levels. The findings demonstrate that these embryo rescue techniques will enable the entire spectrum of St. Augustinegrass genetic variation to be better used through the recovery of interploid hybrids.     

flowCore: a Bioconductor package for high throughput flow cytometry

Background  

Recent advances in automation technologies have enabled the use of flow cytometry for high throughput screening, generating large complex data sets often in clinical trials or drug discovery settings. However, data management and data analysis methods have not advanced sufficiently far from the initial small-scale studies to support modeling in the presence of multiple covariates.     

Enhanced dark field microscopy for rapid artifact-free detection of nanoparticle binding to Candida albicans cells and hyphae

We surveyed a panel of 13 metal nanoparticle (NP) catalysts for their antifungal activities against Candida albicans ATCC 90028. Initial characterization using scanning electron microscopy (SEM) suggested that our ability to detect NP binding to Candida surfaces with this method was impeded by preparation artifacts. As an alternative method for visualizing NP binding, we used an enhanced dark field illumination system (CytoViva®) attached to a standard light microscope. When viewed using this system, all NP produced intense optical signals due to resonant light scattering. To assay binding, NP were allowed to interact with C. albicans hyphae and cells in spent RPMI broth for 15 min with gentle inversion, followed by viewing with the CytoViva® system. The antifungal efficacy of NP preparations was determined separately using a 24-h broth microdilution test. For single-metal NP, observations of binding at 15 min made via CytoViva® corresponded to antifungal efficacy at 24 h, with the most antifungal NP yielding complete coverage of hyphal surfaces. Our work suggests the utility of visual screening using the CytoViva® system for rapid, simple and artifact-free viewing of NP-cell interactions in support of antimicrobial screening efforts. This approach provides a quick and accessible alternative to SEM for imaging of NP-cell interactions.     

Clinical Utility of Waist Circumference in Predicting All‐cause Mortality in a Preventive Cardiology Clinic Population: A PreCIS Database Study

Although obesity is a risk factor for mortality, it is unclear whether waist circumference (WC) is a better predictor of mortality than BMI in a clinical setting of patients at high risk for coronary artery disease (CAD). Thus, we compared the association between WC and BMI with all‐cause mortality in relation to traditional CAD risk factors in a high‐risk cohort. Study population included 5,453 consecutive new patients seen between 1996 and 2005 for management of CAD risk factors in a preventive cardiology clinic. Mortality was determined from the Social Security Death Index. There were 359 deaths over a median follow‐up of 5.2 years. Mortality was greater in high (>102 cm in men and >88 cm in women) vs. normal WC in both genders (P < 0.01). The unadjusted Cox proportional hazard ratio (HR) for continuous WC (per cm) was 1.02 (P < 0.001) in both genders and remained significant after adjustment for CAD risk factors (HR = 1.01 in men, HR = 1.03 in women, both P < 0.05). BMI did not associate statistically with mortality. WC associated with diabetes mellitus (DM) and CAD prevalence (P < 0.001). BMI associated only with DM (P < 0.001) and this association disappeared when WC was added to the model. We conclude that WC is an independent predictor of all‐cause mortality in a preventive cardiology population. These data affirm the clinical importance of WC measurements for mortality, DM, and CAD risk prediction and suggest that obesity‐specific interventions targeting WC in addition to traditional risk factor management may favorably impact these outcomes.     

Species versus genotypic diversity of a nitrogen-fixing plant functional group in a metacommunity

Exploring species and genetic diversity interactions provides new opportunities for furthering our understanding of the ecology and evolution of population and community dynamics, and for predicting responses of ecosystems to environmental change. Theory predicts that species diversity within communities and genetic diversity within populations will covary positively, because either species and genetic diversity interact synergistically or they respond in parallel fashion to common habitat conditions. We tested the hypothesis of positive covariation between species and genotypic diversity in a metacommunity of the species-rich southwest Australian flora. We hypothesised that the connection between genotypic diversity and species diversity is strong within functional groups, but weak or non-existent if the species considered extend beyond the functional group. We show that allelic richness of Daviesia triflora, an ant-dispersed pea, covaries positively with the species richness of six co-occurring nitrogen-fixing legume species. No pattern can be detected between allelic richness of D. triflora and species richness of ant-dispersed species when four non-legumes are added. We also show that genetic diversity of D. triflora is not governed by the same environmental factors that determine the presence of a group of large-shrub/small-tree species in the same metacommunity. This study shows that species and genetic diversity covariation are more likely to be confined to within, rather than between, plant functional groups.     

Temperature controls on aquatic bacterial production and community dynamics in arctic lakes and streams

The impact of temperature on bacterial activity and community composition was investigated in arctic lakes and streams in northern Alaska. Aquatic bacterial communities incubated at different temperatures had different rates of production, as measured by ¹⁴C‐leucine uptake, indicating that populations within the communities had different temperature optima. Samples from Toolik Lake inlet and outlet were collected at water temperatures of 14.2°C and 15.9°C, respectively, and subsamples incubated at temperatures ranging from 6°C to 20°C. After 5 days, productivity rates varied from 0.5 to ～13.7 µg C l^?1 day^?1 and two distinct activity optima appeared at 12°C and 20°C. At these optima, activity was 2‐ to 11‐fold higher than at other incubation temperatures. The presence of two temperature optima indicates psychrophilic and psychrotolerant bacteria dominate under different conditions. Community fingerprinting via denaturant gradient gel electrophoresis (DGGE) of 16S rRNA genes showed strong shifts in the composition of communities driven more by temperature than by differences in dissolved organic matter source; e.g. four and seven unique operational taxonomic units (OTUs) were found only at 2°C and 25°C, respectively, and not found at other incubation temperatures after 5 days. The impact of temperature on bacteria is complex, influencing both bacterial productivity and community composition. Path analysis of measurements of 24 streams and lakes sampled across a catchment 12 times in 4 years indicates variable timing and strength of correlation between temperature and bacterial production, possibly due to bacterial community differences between sites. As indicated by both field and laboratory experiments, shifts in dominant community members can occur on ecologically relevant time scales (days), and have important implications for understanding the relationship of bacterial diversity and function.     

The Drosophila calcipressin sarah is required for several aspects of egg activation

Activation of mature oocytes initiates development by releasing the prior arrest of female meiosis, degrading certain maternal mRNAs while initiating the translation of others, and modifying egg coverings. In vertebrates and marine invertebrates, the fertilizing sperm triggers activation events through a rise in free calcium within the egg. In insects, egg activation occurs independently of sperm and is instead triggered by passage of the egg through the female reproductive tract ; it is unknown whether calcium signaling is involved. We report here that mutations in sarah, which encodes an inhibitor of the calcium-dependent phosphatase calcineurin, disrupt several aspects of egg activation in Drosophila. Eggs laid by sarah mutant females arrest in anaphase of meiosis I and fail to fully polyadenylate and translate bicoid mRNA. Furthermore, sarah mutant eggs show elevated cyclin B levels, indicating a failure to inactivate M-phase promoting factor (MPF). Taken together, these results demonstrate that calcium signaling is involved in Drosophila egg activation and suggest a molecular mechanism for the sarah phenotype. We also find the conversion of the sperm nucleus into a functional male pronucleus is compromised in sarah mutant eggs, indicating that the Drosophila egg's competence to support male pronuclear maturation is acquired during activation.     

Mouse-adapted scrapie infection of SN56 cells: greater efficiency with microsome-associated versus purified PrP-res

The process by which transmissible spongiform encephalopathy agents, or prions, infect cells is unknown. We employed a new differentiable cell line (SN56) susceptible to infection with three mouse-adapted scrapie strains to gain insight into the cellular infection process. The effect of disease-associated PrP (PrP-res) association with microsomal membranes on infection efficiency was examined by comparing sustained PrP-res production in cells treated with either scrapie brain microsomes or purified, detergent-extracted PrP-res. When normalized for quantity of input PrP-res, scrapie brain microsomes induced dramatically enhanced persistent PrP-res formation compared to purified PrP-res. Infected SN56 cells released low levels of PrP-res into the culture supernatant, which also efficiently initiated infection in recipient cells. Interestingly, microsomes labeled with a fluorescent marker were internalized by SN56 cells in small vesicles, which were subsequently found in neuritic processes. When bound to culture wells to reduce internalization during the infection process, scrapie microsomes induced less long-term PrP-res production than suspended microsomes. Long-term differentiation of infected SN56 cells was accompanied by a decrease in PrP-res formation. Our observations provide evidence that infection of cells is aided by the association of PrP-res with membranes and/or other microsomal constituents.     

Whole-exome sequencing links a variant in DHDDS to retinitis pigmentosa

Increasingly, mutations in genes causing Mendelian disease will be supported by individual and small families only; however, exome sequencing studies have thus far focused on syndromic phenotypes characterized by low locus heterogeneity. In contrast, retinitis pigmentosa (RP) is caused by >50 known genes, which still explain only half of the clinical cases. In a single, one-generation, nonsyndromic RP family, we have identified a gene, dehydrodolichol diphosphate synthase (DHDDS), demonstrating the power of combining whole-exome sequencing with rapid in vivo studies. DHDDS is a highly conserved essential enzyme for dolichol synthesis, permitting global N-linked glycosylation. Zebrafish studies showed virtually identical photoreceptor defects as observed with N-linked glycosylation-interfering mutations in the light-sensing protein rhodopsin. The identified Lys42Glu variant likely arose from an ancestral founder, because eight of the nine identified alleles in 27,174 control chromosomes were of confirmed Ashkenazi Jewish ethnicity. These findings demonstrate the power of exome sequencing linked to functional studies when faced with challenging study designs and, importantly, link RP to the pathways of N-linked glycosylation, which promise new avenues for therapeutic interventions.