Global biogeographical data bases on marine fishes: caveat emptor

A review of georeferenced collection‐site records for Caribbean shore‐fishes served by major online distributors of aggregated biodiversity data found large‐scale errors in over a third of the species and genera, in nearly two‐thirds of the families. To avoid compromising the value of their services to the global science community online providers must actively address the question of data quality.     

Stopping Rules for Clinical Trials Implicitly Incorporating Safety Information

Clinical trials research is mainly conducted for the purpose of evaluating the relative efficacy of two or more treatments. However, a positive response due to treatment is not sufficient to put forward a new product because one must also demonstrate safety. In such cases, clinical trials which show a positive effect would need to accrue enough patients to also demonstrate that the new treatment is safe. It is our purpose to show how the efficacy and safety problems can be combined to yield a more practical clinical trial design. In this paper we propose an asymmetric stopping rule which allows the experimenter to terminate a clinical trial early for a sufficiently negative result and to continue to a specified number of patients otherwise. As it turns out, a few interim tests will have negligible effects on the overall significance level.     

Identification of kin structure among Guam rail founders: a comparison of pedigrees and DNA profiles

Kin structure among founders can have a significant effect on subsequent population structure. Here we use the correlation between DNA profile similarity and relatedness calculated from pedigrees to test hypotheses regarding kin structure among founders to the captive Guam rail (Rallus owstoni) population. Five different pedigrees were generated under the following hypotheses: (i) founders are unrelated; (ii) founders are unrelated except for same-nest chicks; (iii) founders from the same major site are siblings; (iv) founders from the same local site are siblings; and (v) founders are related as defined by a UPGMA cluster analysis of DNA similarity data. Relatedness values from pedigrees 1, 2 and 5 had the highest correlation with DNA similarity but the correlation between relatedness and similarity were not significantly different among pedigrees. Pedigree 5 resulted in the highest correlation overall when using only relatedness values that changed as a result of different founder hypotheses. Thus, founders were assigned relatedness based on pedigree 5 because it had the highest correlations with DNA similarity, was the most conservative approach, and incorporated all field data. The analyses indicated that estimating relatedness using DNA profiles remains problematic, therefore we compared mean kinship, a measure of genetic importance, with mean DNA profile similarity to determine if genetic importance among individuals could be determined via use of DNA profiles alone. The significant correlation suggests this method may provide more information about population structure than was previously thought. Thus, DNA profiles can provide a reasonable explanation for founder relatedness and mean DNA profile similarity may be helpful in determining relative genetic importance of individuals when detailed pedigrees are absent.     

Bacterial diversity, organic pollutants and their metabolites in two aeration lagoons of common effluent treatment plant (CETP) during the degradation and detoxification of tannery wastewater

In this study, PCR-RFLP and GC-MS approaches were used to characterize the bacterial diversity, organic pollutants and metabolites during the tannery wastewater treatment process at common effluent treatment plant (CETP). Results revealed that the bacterial communities growing in aeration lagoon-I were dominated with Escherichia sp., Stenotrophomonas sp., Bacillus sp. and Cronobacter sp. while that of aeration lagoon-II prevailed with Stenotrophomonas sp., and Burkholderiales bacterium, respectively. The HPLC and GC-MS analysis revealed that most of the organic pollutants detected in untreated tannery wastewater samples were diminished from bacterial treated tannery wastewater samples. Only two pollutants i.e. L-(+)-lactic acid and acetic acid could not be degraded by bacteria whereas benzene and 2-hydroxy-3-methyl-butanoic acid was produced as new metabolites during the bacterial treatment of tannery wastewater in aeration lagoon II of CETP. Further, it was observed that after bacterial treatment, the toxicity of tannery effluent was reduced significantly allowing 90% seed germination.     

Water quality effectiveness of ditch fencing and culvert crossing in the Lake Okeechobee basin, southern Florida, USA

Ditch fencing and culvert cattle crossing Best Management Practice (BMP) was evaluated in this study with regard to phosphorus (P) and nitrogen (N) load reductions and economic feasibility in the Lake Okeechobee (LO) basin. The BMP was implemented at a 170 m section of a drainage ditch within a ranch in the LO basin and flow and concentration (N and P) data at the upstream and downstream of the ditch were collected for one pre-BMP (June-October, 2005) and three post-BMP (June-October, 2006-2008) periods. During the pre-BMP period, downstream total P (TP) load was 20% (67.0 kg) higher than the upstream, indicating the cattle crossing to be a source of P. Downstream loads of TP in 2006 and 2008 (post-BMP periods) became 26% (14.7 kg) and 11% (85.9 kg) lower than the upstream loads, respectively indicating that the BMP reduced the P loads. The site was a sink for N for all periods except the 2007. Unusual dry conditions during 2007 resulted in the addition of P and N at the BMP site, probably due to the release of P and N from soil and plants. Average of three post-BMP period load showed a 10% reduction of TP loads at the downstream (251.8 kg) compared to the upstream (281.0 kg) location. To consider potential P contributions from the soil and plant, two scenarios, conservative and liberal, were considered to estimate P load reductions due to the BMP. For the conservative scenario, P contribution from soil and plant was considered, while for liberal it was not. Reductions in P loads for conservative and liberal scenarios were 0.35 and 0.44 kg/day, respectively. Phosphorus removal cost for the conservative scenario was $12.61/kg of P, which is considerably less than the cost of other P reduction strategies in the basin. Overall, results show that the BMP can reduce P concentration and loads from ranches without causing adverse impact on cattle production.     

Modelling beef cows’ individual response to short nutrient restriction in different lactation stages

Short-term nutrient restrictions can occur naturally in extensive beef cattle production systems due to low feed quality or availability. The aims of the study were to (1) model the curves of milk yield, plasma non-esterified fatty acids (NEFAs) and β-hydroxybutyrate (BHB) contents of beef cows in response to short nutritional challenges throughout lactation; (2) identify clusters of cows with different response profiles; (3) quantify differences in cows’ response between the clusters and lactation stages. Data of BW, body condition score (BCS), milk yield, NEFA, and BHB plasma concentration from 31 adult beef cows (626 ± 48 kg at calving) were used to study the effect of 4-day feed restriction repeated over months 2, 3 and 4 of lactation. On each month, all cows received a single diet calculated to meet the requirements of the average cow: 100 % requirements for 4 days (d-4 to d-1, basal period), 55 % requirements on the next 4 days (d0 to d3, restriction period) and 100 % requirements for 4 days (d4 to d7, refeeding period). Natural cubic splines were used to model the response of milk yield, NEFA and BHB to restriction and refeeding in the 3 months. The new response variables [baseline value, peak value, days to peak and to regain baseline, and areas under the curve (AUC) during restriction and refeeding] were used to cluster cows according to their metabolic response (MR) into two groups: Low MR and High MR. The month of lactation affected all the traits, and basal values decreased as lactation advanced. Cows from both clusters had similar BW and BCS values, but those in the High MR cluster had higher basal milk yield, NEFA and BHB contents, and responded more intensely to restriction, with more marked peaks and AUCs. Reaction times were similar, and baseline values recovered during refeeding in both clusters. Our results suggest that the response was driven by cows’ milk potential rather than size or body reserves, and despite high-responding cattle’s higher milk yield, they were able to activate metabolic pathways to respond to and recover from the challenge.     

Variance component tests of multivariate mediation effects under composite null hypotheses

Mediation effects of multiple mediators are determined by two associations: one between an exposure and mediators (‐) and the other between the mediators and an outcome conditional on the exposure (‐). The test for mediation effects is conducted under a composite null hypothesis, that is, either one of the ‐ and ‐ associations is zero or both are zeros. Without accounting for the composite null, the type 1 error rate within a study containing a large number of multimediator tests may be much less than the expected. We propose a novel test to address the issue. For each mediation test , , we examine the ‐ and ‐ associations using two separate variance component tests. Assuming a zero‐mean working distribution with a common variance for the element‐wise ‐ (and ‐) associations, score tests for the variance components are constructed. We transform the test statistics into two normally distributed statistics under the null. Using a recently developed result, we conduct hypothesis tests accounting for the composite null hypothesis by adjusting for the variances of the normally distributed statistics for the ‐ and ‐ associations. Advantages of the proposed test over other methods are illustrated in simulation studies and a data application where we analyze lung cancer data from The Cancer Genome Atlas to investigate the smoking effect on gene expression through DNA methylation in 15 114 genes.     

Comparative proteomic analysis of biofilm and planktonic cells of Lactobacillus plantarum DB200

This study investigated the relative abundance of extracellular and cell wall associated proteins (exoproteome), cytoplasmic proteins (proteome), and related phenotypic traits of Lactobacillus plantarum grown under planktonic and biofilm conditions. Lactobacillus plantarum DB200 was preliminarily selected due to its ability to form biofilms and to adhere to Caco2 cells. As shown by fluorescence microscope analysis, biofilm cells became longer and autoaggregated at higher levels than planktonic cells. The molar ratio between glucose consumed and lactate synthesised was markedly decreased under biofilm compared to planktonic conditions. DIGE analysis showed a differential exoproteome (115 protein spots) and proteome (44) between planktonic and biofilm L. plantarum DB200 cells. Proteins up‐ or downregulated by at least twofold (p < 0.05) were found to belong mainly to the following functional categories: cell wall and catabolic process, cell cycle and adhesion, transport, glycolysis and carbohydrate metabolism, exopolysaccharide metabolism, amino acid and protein metabolisms, fatty acid and lipid biosynthesis, purine and nucleotide metabolism, stress response, oxidation/reduction process, and energy metabolism. Many of the above proteins showed moonlighting behavior. In accordance with the high expression levels of stress proteins (e.g., DnaK, GroEL, ClpP, GroES, and catalase), biofilm cells demonstrated enhanced survival under conditions of environmental stress.