A study of glycoproteins in human serum and plasma reference standards (HUPO) using multilectin affinity chromatography coupled with RPLC-MS/MS

The glycoproteome is a major subproteome present in human plasma. In this study, we isolated and characterized approximately 150 glycoproteins from the human plasma and serum samples provided by HUPO using a multilectin affinity column. The corresponding tryptic digest was separated by RP-HPLC coupled to an IT mass spectrometer (3-D LCQ). Also in this study, a new system, namely an Ettan MDLC system coupled to a linear ITLTQ, was compared with the previous LCQ platform and gave a greater number of protein identifications, as well as better quality. When we compared the composition of the glycoproteomes for the plasma and serum samples there was a close correlation between the samples, except for the absence of fibrinogen from the identified-protein list in the latter sample, which was presumably as a result of the clotting process. In addition, the analysis of the samples from three ethnic specimens, Caucasian American, Asian American, and African American, were very similar but showed a higher angiotensinogen plasma level and a lower histidine-rich glycoprotein level in Caucasian American samples, and a lower vitronectin level in African American blood samples.     

Altered CXCR2 signaling in beta-arrestin-2-deficient mouse models

CXCR2 is a G-protein-coupled receptor (GPCR) that binds the CXC chemokines, CXCL1-3 and CXCL5-8, and induces intracellular signals associated with chemotaxis. Many adaptor proteins are actively involved in the sequestration, internalization, and trafficking of CXCR2 and transduction of agonist-induced intracellular signaling. We have previously shown that adaptor protein beta-arrestin-2 (betaarr2) plays a crucial role in transducing signals mediated through CXCR2. To further investigate the role of betaarr2 on CXCR2-mediated signaling during acute inflammation, zymosan-induced neutrophils were isolated from peritoneal cavities of betaarr2-deficient (betaarr2(-/-)) and their wild-type (betaarr2(+/+)) littermate mice, and neutrophil CXCR2 signaling activities were determined by measurement of Ca(2+) mobilization, receptor internalization, GTPase activity, and superoxide anion production. The results showed that the deletion of betaarr2 resulted in increased Ca(2+) mobilization, superoxide anion production, and GTPase activity in neutrophils, but decreased receptor internalization relative to wild-type mice. Two animal models, the dorsal air pouch model and the excisional wound healing model, were used to further study the in vivo effects of betaarr2 on CXCR2-mediated neutrophil chemotaxis and on cutaneous wound healing. Surprisingly, the recruitment of neutrophils was increased in response to CXCL1 in the air pouch model and in the excisional wound beds of betaarr2(-/-) mice. Wound re-epithelialization was also significantly faster in betaarr2(-/-) mice than in betaarr2(+/+) mice. Taken together, the data indicate that betaarr2 is a negative regulator for CXCR2 in vivo signaling.     

Exploiting collider bias to apply two-sample summary data Mendelian randomization methods to one-sample individual level data

Over the last decade the availability of SNP-trait associations from genome-wide association studies has led to an array of methods for performing Mendelian randomization studies using only summary statistics. A common feature of these methods, besides their intuitive simplicity, is the ability to combine data from several sources, incorporate multiple variants and account for biases due to weak instruments and pleiotropy. With the advent of large and accessible fully-genotyped cohorts such as UK Biobank, there is now increasing interest in understanding how best to apply these well developed summary data methods to individual level data, and to explore the use of more sophisticated causal methods allowing for non-linearity and effect modification.In this paper we describe a general procedure for optimally applying any two sample summary data method using one sample data. Our procedure first performs a meta-analysis of summary data estimates that are intentionally contaminated by collider bias between the genetic instruments and unmeasured confounders, due to conditioning on the observed exposure. These estimates are then used to correct the standard observational association between an exposure and outcome. Simulations are conducted to demonstrate the method’s performance against naive applications of two sample summary data MR. We apply the approach to the UK Biobank cohort to investigate the causal role of sleep disturbance on HbA1c levels, an important determinant of diabetes.Our approach can be viewed as a generalization of Dudbridge et al. (Nat. Comm. 10: 1561), who developed a technique to adjust for index event bias when uncovering genetic predictors of disease progression based on case-only data. Our work serves to clarify that in any one sample MR analysis, it can be advantageous to estimate causal relationships by artificially inducing and then correcting for collider bias.     

Ontogeny of total body oxygen stores and aerobic dive potential in Steller sea lions (Eumetopias jubatus)

Two key factors influence the diving and hence foraging ability of marine mammals: increased oxygen stores prolong aerobic metabolism and decreased metabolism slows rate of fuel consumption. In young animals, foraging ability may be physiologically limited due to low total body oxygen stores and high mass specific metabolic rates. To examine the development of dive physiology in Steller sea lions, total body oxygen stores were measured in animals from 1 to 29 months of age and used to estimate aerobic dive limit (ADL). Blood oxygen stores were determined by measuring hematocrit, hemoglobin, and plasma volume, while muscle oxygen stores were determined by measuring myoglobin concentration and total muscle mass. Around 2 years of age, juveniles attained mass specific total body oxygen stores that were similar to those of adult females; however, their estimated ADL remained less than that of adults, most likely due to their smaller size and higher mass specific metabolic rates. These findings indicate that juvenile Steller sea lion oxygen stores remain immature for more than a year, and therefore may constrain dive behavior during the transition to nutritional independence.     

The Behavioural Response of Mayfly Nymphs (Stenonema sp.) to Chemical Cues from Crayfish (Orconectes rusticus)

Artificial reef systems play an important role in the increase of natural production of biological marine resources and they have been deployed worldwide. In Portugal, seven artificial systems have been deployed along the southern coast of the Algarve. Research to date has focussed mainly on fish populations, particularly those of economical importance. The present work aims to study the macrobenthic communities of the artificial reef structures, as these will enhance the food resources and shelter, making the reefs more attractive to fish. In particular, we experimentally analysed the sequence of colonisation of macrobenthic communities of the Ancão artificial reef system, which was deployed in the summer of 2002. The study of the colonisation of benthic communities was done using samples of concrete cubic units (15 × 15 cm) that were suspended at the reef modules at a depth of 20 m, at the time of the reef immersion. Four replicate samples were collected by SCUBA diving from two groups of the Ancão reef every three months from the starting date. Sampling was done using essentially non-destructive methods to assess the percentage cover of macrobenthic organisms in both vertical and horizontal surfaces. The percentage cover of the taxonomic groups was compared within the different surfaces of the samples and between the two reef groups. The bottom surface of cubic samples had a significantly higher colonisation related to the dominance of barnacle cover, probably due to lower sedimentation levels. Samples from both reef groups showed a similar pattern of colonisation. Barnacles, bryozoans and serpulids dominated the samples three months immediately after the beginning of the experiment. Other invertebrates groups, such as Porifera, Hydrozoa, Anthozoa, other sessile Polychaeta, Decapoda, Gastropoda and Bivalvia, were more abundant after six months of colonisation.     

Role of Binding and Nucleoside Diphosphate Kinase A in the Regulation of the Cystic Fibrosis Transmembrane Conductance Regulator by AMP-activated Protein Kinase

Cystic fibrosis transmembrane conductance regulator (CFTR) Cl⁻ channel mutations cause cystic fibrosis lung disease. A better understanding of CFTR regulatory mechanisms could suggest new therapeutic strategies. AMP-activated protein kinase (AMPK) binds to and phosphorylates CFTR, attenuating PKA-activated CFTR gating. However, the requirement for AMPK binding to CFTR and the potential role of other proteins in this regulation are unclear. We report that nucleoside diphosphate kinase A (NDPK-A) interacts with both AMPK and CFTR in overlay blots of airway epithelial cell lysates. Binding studies in Xenopus oocytes and transfected HEK-293 cells revealed that a CFTR peptide fragment that binds AMPK (CFTR-1420-57) disrupted the AMPK-CFTR interaction. Introduction of CFTR-1420-57 into human bronchial Calu-3 cells enhanced forskolin-stimulated whole cell conductance in patch clamp measurements. Similarly, injection of CFTR-1420-57 into Xenopus oocytes blocked the inhibition of cAMP-stimulated CFTR conductance by AMPK in two-electrode voltage clamp studies. AMPK also inhibited CFTR conductance with co-expression of WT NDPK-A in two-electrode voltage clamp studies, but co-expression of a catalytically inactive H118F mutant or various Ser-120 NDPK-A mutants prevented this inhibition. In vitro phosphorylation of WT NDPK-A was enhanced by purified active AMPK, but phosphorylation was prevented in H118F and phosphomimic Ser-120 NDPK-A mutants. AMPK does not appear to phosphorylate NDPK-A directly but rather promotes an NDPK-A autophosphorylation event that involves His-118 and Ser-120. Taken together, these results suggest that NDPK-A exists in a functional cellular complex with AMPK and CFTR in airway epithelia, and NDPK-A catalytic function is required for the AMPK-dependent regulation of CFTR.     

Mechanistic and spectroscopic studies of metallo-β-lactamase NDM-1

In an effort to biochemically characterize metallo-β-lactamase NDM-1, we cloned, overexpressed, purified, and characterized several maltose binding protein (MBP)-NDM-1 fusion proteins with different N-termini (full-length, Δ6, Δ21, and Δ36). All MBP-NDM-1 fusion proteins were soluble; however, only one, MBP-NDM-1Δ36, exhibited high activity and bound 2 equiv of Zn(II). Thrombin cleavage of this fusion protein resulted in the truncated NDM-1Δ36 variant, which exhibited a k(cat) of 16 s(-1) and a K(m) of 1.1 μM when using nitrocefin as a substrate, bound 2 equiv of Zn(II), and was monomeric in solution. Extended X-ray absorption fine structure studies of the NDM-1Δ36 variant indicate the average metal binding site for Zn(II) in this variant consists of four N/O donors (two of which are histidines) and 0.5 sulfur donor per zinc, with a Zn-Zn distance of 3.38 ?. This metal binding site is very similar to those of other metallo-β-lactamases that belong to the B1 subclass. Pre-steady-state kinetic studies using nitrocefin and chromacef and the NDM-1Δ36 variant indicate that the enzyme utilizes a kinetic mechanism similar to that used by metallo-β-lactamases L1 and CcrA, in which a reactive nitrogen anion is stabilized and its protonation is rate-limiting. While they are very different in terms of amino acid sequence, these studies demonstrate that NDM-1 is structurally and mechanistically very similar to metallo-β-lactamase CcrA.     

Hand pressure distribution during Oldowan stone tool production

Modern humans possess a highly derived thumb that is robust and long relative to the other digits, with enhanced pollical musculature compared with extant apes. Researchers have hypothesized that this anatomy was initially selected for in early Homo in part to withstand high forces acting on the thumb during hard hammer percussion when producing stone tools. However, data are lacking on loads experienced during stone tool production and the distribution of these loads across the hand.Here we report the first quantitative data on manual normal forces (N) and pressures (kPa) acting on the hand during Oldowan stone tool production, captured at 200 Hz. Data were collected from six experienced subjects replicating Oldowan bifacial choppers. Our data do not support hypotheses asserting that the thumb experiences relatively high loads when making Oldowan stone tools. Peak normal force, pressure, impulse, and the pressure/time integral are significantly lower on the thumb than on digits 2 and/or digit 3 in every subject. Our findings call into question hypotheses linking modern human thumb robusticity specifically to load resistance during stone tool production.     

Food insecurity and increased BMI in young adult women

Food insecurity has been associated with weight status in children and adults although results have been mixed. We aimed to identify whether food insecurity was associated with BMI in young adults and whether this association differed by gender and was modified by food stamp use and the presence of children in the home. Cross-sectional data from wave 4 (2007-2008) of the National Longitudinal Study of Adolescent Health were analyzed. Multiple linear regression was used to investigate the association between food insecurity and BMI in gender stratified models of young adult women (n = 7,116) and men (n = 6,604) controlling for age, race/ethnicity, income, education, physical activity, smoking, alcohol use, the presence of children in the home, and food stamp use in young adulthood and/or adolescence. Food insecurity was more common in young adult women (14%) than young adult men (9%). After controlling for a variety of individual variables, food insecure women had a BMI that was on average 0.9 kg/m(2) units higher than women who were food secure. This difference in BMI persisted after controlling for recent or past food stamp use and was not different among women with or without children in the household. No relationship was found between food insecurity and BMI in young adult men. Providers should inquire about food insecurity, especially when treating obesity, and policy initiatives should address the role of access to healthy food in those facing food insecurity.