Inferring a single variable from an assemblage with multiple controls: getting into deep water with cladoceran lake-depth transfer functions

Transfer functions have proved very useful for quantitative reconstruction of past environments. Inferring values of a single parameter based on changes in a community with multiple controls may result in unreliable inferences. To assess this unreliability cladoceran surface sediment assemblages from 53 lakes in Greenland, which have substantial variations in lake depth and fish abundance, both of which shape cladoceran communities, were analysed in this study. Redundancy analysis (RDA) revealed that maximum lake depth and either fish abundance or fish presence/absence exerted substantial and significant control on the cladoceran assemblage. Partial RDA showed that maximum lake depth and fish abundance uniquely explained 7.9 and 5.1%, respectively, with 5.3% variance being shared. A transfer function to infer lake depth from cladoceran sub-fossils was constructed and performed moderately well [coefficient of determination (r ²) = 0.65; root mean square error of prediction (RMSEP) = 0.32 log maximum depth] on the full dataset. When outliers, defined by a bootstrapped prediction error greater than 25% of the total depth gradient, were excluded, the model performed well (r ² = 0.74, RMSEP = 0.25 log maximum depth). The improved transfer function was then applied to sedimentary assemblage from a sediment core from Lake Bores?, in North-eastern Greenland, covering 9,000 years. A large increase in lake depth was inferred around 6250 bp. Whilst the climate was wetter at that time, the inferred changes in depth likely reflect the alteration of the food web, which resulted from the arrival of fish in the lake. This highlights the risks of using single-variable inference models for hindcasting change in lake physical and/or food web structure when there are other important co-variables.     

Association between discrimination and obesity in African-American men

The objective of this study was to examine the association between discrimination and obesity among a U.S. nationally representative sample of African-American men. Data from the 2001–2003 National Survey of American Life (NSAL) were used to collect measures of everyday and major discrimination, and body mass index (BMI) taken from self-reports. Poisson regression with robust standard errors was applied to estimate the prevalence ratios of everyday and major discrimination as it relates to obesity (BMI ≥ 30 kg/m²), controlling for potential confounders. In the model that included both everyday and major discrimination, men who experienced any major discrimination had a higher likelihood of obesity (prevalence ratio [PR] = 1.33, 95% confidence interval [CI], 1.06, 1.66) than those who did not experience any major discrimination, controlling for age, marital status, income, education, major stressors, two or more chronic conditions, and physical activity. Exposure to any major discrimination was found to be associated with obesity in African-American men. Future studies among this population are needed to examine whether the observed changes in self-reports of major discrimination are associated with obesity, measured by BMI, over time. The health of African-American men must be a priority in reducing excess disparities in disease, disability, and death.     

Non-targeted metabolomics of saliva to explore potential biomarkers for gastric ulceration in pigs fed hemp

Gastric ulceration is a common disease in pig production worldwide and is associated with economic losses as well as animal health and welfare issues. The aim of this study was to explore potential salivary biomarkers for gastric ulceration in pigs. In addition, the aim was to study the effect of hemp on the incidence of gastric ulcers. Approximately 440 growing-finishing pigs in the period from 30 to 110 kg BW were allocated to four different diets: meal feed (Meal); pelleted feed (Pellets); pelleted feed added 4% hempseed cake (Hemp Cake); pelleted feed added 4% hempseed hulls (Hemp Hulls). The day before slaughter, saliva samples from each pig were collected. After slaughter, the stomachs were emptied to assess the consistency of the stomach content and examined for gastric ulceration using an index scale (0–10). Noticeable changes of the gastric mucosa (total index score ≥ 6) were observed in 291 pigs. The odds of having index scores 0–5 relative to index scores 6–8 and 9–10, respectively, were higher (P < 0.001) for pigs fed Meal compared to pigs fed Pellets. The odds of suffering from severe gastric ulcers tended (P = 0.08) to be lower in pigs fed Hemp Hulls compared to pigs fed Pellets. A non-targeted liquid chromatography mass spectrometry based metabolomics analysis was performed on saliva samples to determine any separation between pigs with healthy stomachs and those with gastric ulcers and to examine a possible correlation between gastric ulcer index and potential biomarkers. Partial least-squares discriminant analysis showed a separation between pigs with ulcers and those with healthy stomachs/hyperkeratosis (HK). Metabolites contributing to the separation between groups were identified. Levels of oxylipins deriving from linoleic acid were lower (P < 0.001) in pigs with ulcers compared to healthy/HK pigs. This may indicate a shift in the metabolic pathways towards more pro-inflammatory arachidonic acid-derived eicosanoids, which might reflect an increased inflammatory response. Thus, reduced levels of oxylipins derived from linoleic acid seemed to be associated with active gastric ulcers, and thereby they might function as biomarkers for gastric ulceration in pigs. In addition, supplementation of hempseed hulls had a beneficial effect on severe gastric ulcers, as hempseed hulls changed the consistency of the gastric content by conferring more solidness. However, it was not possible to observe any reliable separation between pigs fed pellets supplemented with hemp products and pigs fed non-supplemented pellets according to the identified salivary metabolites.     

The formation of filamentous structures from iodinated neurotubules

The porcine neurotubule and its basic subunit were found to be modified in vitro by iodination of amino acids (principally tyrosine) using lactoperoxidase. Iodide ion, H₂O₂, or lactoperoxidase singly or in any pairwise combination had virtually no effect on neurotubules. However, when all three reagents were present, permitting covalent iodination, it was found that at 0.1 iodotyrosines per tubulin dimer the microtubules unravel to form structures which morphologically resemble strands of protofilaments twisted or wound around each other. These abnormal tubules are stable at room temperature and 4°C. Both monomers of tubulin are labeled to approximately the same extent. Iodinated tubulin (0.1 iodotyrosines/dimer) is unable to assemble in vitro under normal assembly conditions. Heavily iodinated microtubules (8 iodines per tubulin dimer) are similar in morphology to the slightly iodinated structures.     

High throughput detection of antibody self-interaction by bio-layer interferometry

Self-interaction of an antibody may lead to aggregation, low solubility or high viscosity. Rapid identification of highly developable leads remains challenging, even though progress has been made with the introduction of techniques such as self-interaction chromatography (SIC) and cross-interaction chromatography (CIC). Here, we report a high throughput method to detect antibody clone self-interaction (CSI) using bio-layer interferometry (BLI) technology. Antibodies with strong self-interaction responses in the CSI-BLI assay also show delayed retention times in SIC and CIC. This method allows hundreds of candidates to be screened in a matter of hours with minimal material consumption.     

Enzyme-linked enzyme-binding assay for Pin1 WW domain ligands

Peptidyl prolyl cis-trans isomerase (PPIase) interacting with NIMA-1 (Pin1) catalyzes the cis-trans isomerization of pSer/pThr-Pro amide bonds. Pin1 is a two-domain protein that represents a promising target for the treatment of cancer. Both domains of Pin1 bind the pSer/pThr-Pro motif; PPIase enzymatic activity occurs in the catalytic domain, and the WW domain acts as a recognition module for the pSer/pThr-Pro motif. An assay we call an enzyme-linked enzyme-binding assay (ELEBA) was developed to measure the K_d of ligands that bind selectively to the WW domain. A ligand specific for the WW domain of Pin1 was covalently immobilized in a 96-well plate. Commercially available Pin1 conjugated to horseradish peroxidase was used for chemiluminescent detection of ligands that block the association of the WW domain with immobilized ligand. The peptide ligands were derived from the cell cycle regulatory phosphatase, Cdc25c, residues 45-50. The K_d values for Fmoc-VPRpTPVGGGK-NH₂ and Ac-VPRpTPV-NH₂ were determined to be 36 ± 4 and 110 ± 30 μM, respectively. The ELEBA offers a selective approach for detecting ligands that bind to the Pin1 WW domain, even in the presence of the catalytic domain. This method may be applied to any dual specificity, multidomain protein.