Spatial variability in nutrient concentration and biofilm nutrient limitation in an urban watershed

Nutrient enrichment threatens river ecosystem health in urban watersheds, but the influence of urbanization on spatial variation in nutrient concentrations and nutrient limitation of biofilm activity are infrequently measured simultaneously. In summer 2009, we used synoptic sampling to measure spatial patterns of nitrate (NO₃ ⁻), ammonium (NH₄ ⁺), and soluble reactive phosphorus (SRP) concentration, flux, and instantaneous yield throughout the Bronx River watershed within New York City and adjacent suburbs. We also quantified biofilm response to addition of NO₃ ⁻, phosphate (PO₄ ³⁻), and NO₃ ⁻ + PO₄ ³⁻ on organic and inorganic surfaces in the river mainstem and tributaries. Longitudinal variation in NO₃ ⁻ was low and related to impervious surface cover across sub-watersheds, but spatial variation in NH₄ ⁺ and SRP was higher and unrelated to sub-watershed land-use. Biofilm respiration on organic surfaces was frequently limited by PO₄ ³⁻ or NO₃ ⁻ + PO₄ ³⁻, while primary production on organic and inorganic surfaces was nutrient-limited at just one site. Infrequent NO₃ ⁻ limitation and low spatial variability of NO₃ ⁻ throughout the watershed suggested saturation of biological N demand. For P, both higher biological demand and point-sources contributed to greater spatial variability. Finally, a comparison of our data to synoptic studies of forested, temperate watersheds showed lower spatial variation of N and P in urban watersheds. Reduced spatial variation in nutrients as a result of biological saturation may represent an overlooked effect of urbanization on watershed ecology, and may influence urban stream biota and downstream environments.     

Roles of carboxyl groups in the transmembrane insertion of peptides

We have used pHLIP® [pH (low) insertion peptide] to study the roles of carboxyl groups in transmembrane (TM) peptide insertion. pHLIP binds to the surface of a lipid bilayer as a disordered peptide at neutral pH; when the pH is lowered, it inserts across the membrane to form a TM helix. Peptide insertion is reversed when the pH is raised above the characteristic pK_a (6.0). A key event that facilitates membrane insertion is the protonation of aspartic acid (Asp) and/or glutamic acid (Glu) residues, since their negatively charged side chains hinder membrane insertion at neutral pH. In order to gain mechanistic understanding, we studied the membrane insertion and exit of a series of pHLIP variants where the four Asp residues were sequentially mutated to nonacidic residues, including histidine (His). Our results show that the presence of His residues does not prevent the pH-dependent peptide membrane insertion at ∼ pH 4 driven by the protonation of carboxyl groups at the inserting end of the peptide. A further pH drop leads to the protonation of His residues in the TM part of the peptide, which induces peptide exit from the bilayer. We also find that the number of ionizable residues that undergo a change in protonation during membrane insertion correlates with the pH-dependent insertion into the lipid bilayer and exit from the lipid bilayer, and that cooperativity increases with their number. We expect that our understanding will be used to improve the targeting of acidic diseased tissue by pHLIP.     

Function‐based assessment of structural similarity measurements using metal co‐factor orientation

Structure comparison is widely used to quantify protein relationships. Although there are several approaches to calculate structural similarity, specifying significance thresholds for similarity metrics is difficult due to the inherent likeness of common secondary structure elements. In this study, metal co‐factor location is used to assess the biological relevance of structural alignments. The distance between the centroids of bound co‐factors adds a chemical and function‐relevant constraint to the structural superimposition of two proteins. This additional dimension can be used to define cut‐off values for discriminating valid and spurious alignments in large alignment sets. The hypothesis underlying our approach is that metal coordination sites constrain structural evolution, thus revealing functional relationships between distantly related proteins. A comparison of three related nitrogenases shows the sequence and fold constraints imposed on the protein structures up to 18 Å away from the centers of their bound metal clusters. Proteins 2014; 82:648–656. © 2013 Wiley Periodicals, Inc.     

Motility and Chemotaxis Mediate the Preferential Colonization of Gastric Injury Sites by Helicobacter pylori

Helicobacter pylori (H. pylori) is a pathogen contributing to peptic inflammation, ulceration, and cancer. A crucial step in the pathogenic sequence is when the bacterium first interacts with gastric tissue, an event that is poorly understood in vivo. We have shown that the luminal space adjacent to gastric epithelial damage is a microenvironment, and we hypothesized that this microenvironment might enhance H. pylori colonization. Inoculation with 10⁶ H. pylori (wild-type Sydney Strain 1, SS1) significantly delayed healing of acetic-acid induced ulcers at Day 1, 7 and 30 post-inoculation, and wild-type SS1 preferentially colonized the ulcerated area compared to uninjured gastric tissue in the same animal at all time points. Gastric resident Lactobacillus spp. did not preferentially colonize ulcerated tissue. To determine whether bacterial motility and chemotaxis are important to ulcer healing and colonization, we analyzed isogenic H. pylori mutants defective in motility (ΔmotB) or chemotaxis (ΔcheY). ΔmotB (10⁶) failed to colonize ulcerated or healthy stomach tissue. ΔcheY (10⁶) colonized both tissues, but without preferential colonization of ulcerated tissue. However, ΔcheY did modestly delay ulcer healing, suggesting that chemotaxis is not required for this process. We used two-photon microscopy to induce microscopic epithelial lesions in vivo, and evaluated accumulation of fluorescently labeled H. pylori at gastric damage sites in the time frame of minutes instead of days. By 5 min after inducing damage, H. pylori SS1 preferentially accumulated at the site of damage and inhibited gastric epithelial restitution. H. pylori ΔcheY modestly accumulated at the gastric surface and inhibited restitution, but did not preferentially accumulate at the injury site. H. pylori ΔmotB neither accumulated at the surface nor inhibited restitution. We conclude that bacterial chemosensing and motility rapidly promote H. pylori colonization of injury sites, and thereby biases the injured tissue towards sustained gastric damage.     

The Influence of Nanocrystal Aggregates on Photovoltaic Performance in Nanocrystal–Polymer Bulk Heterojunction Solar Cells

CdSe nanocrystals (NCs) can be used as an electron acceptor in solar cells, employing organic ligands to passivate their surface and make them processable from solution. The nature and abundance of impurities present after NC ligand exchange from oleic acid to n‐butylamine are identified. A further purification step using hexane as a selective solvent is described, which excludes NC aggregates from solution. The influence of NC aggregates on photovoltaic device performance is studied in a CdSe:poly[2‐methoxy‐5‐(3′,7′‐dimethyloctyloxy)‐1,4‐phenylene vinylene] (MDMO‐PPV) bulk heterojunction solar cell. The exclusion of NC aggregates leads to a four‐fold increase in device power conversion efficiency (PCE) in optimized devices. A superior blend morphology leading to improved charge generation and a better NC percolation network is identified as the main causes of this increased solar cell performance.     

Prevalence and Trends in Obesity among China’s Children and Adolescents, 1985–2010

Objectives

We examined the prevalence of and trends in obesity among children and adolescents in China (1985–2010).

Methods

We used data from the 1985, 1991, 1995, 2000, 2005, and 2010 Chinese National Surveys on Students’ Constitution and Health (CNSSCH). The CNSSCH is a national survey of physical fitness and health status in Chinese students that uses multistage stratified sampling of 31 provinces and municipalities. A subject was considered obese or overweight if weight-for-height exceeded the 20% or 10% of standard weight-for-height. The standard weight-for-height was the 80th percentile for sex- and age-specific growth charts.

Results

The age-adjusted prevalence of obesity and of overweight and obesity combined was 8.1% (95% CI, 8.0–8.3%) and 19.2% (95% CI, 19.1–19.4%) among children and adolescents 7–18 years in age. Obesity was more likely to be present among children or adolescents who were male (RR, 1.93; 95% CI, 1.90–1.97), urban (RR, 1.99; 95% CI, 1.95–2.02), or 10–12 years (RR, 1.43; 95% CI, 1.40–1.46). Trend analyses of the 25-year period revealed a significant increasing trend in males (RR, 1.59; 95% CI, 1.58–1.60) and in females (RR, 1.49; 95% CI, 1.48–1.50). The rate of increase in obese or overweight prevalence was highest in boys from rural areas (9% annual increase).

Conclusions

During 1985–2010, there was a significant and continuous increase in the prevalence of obesity in children and adolescents. Obesity is epidemic in China, but may be reduced with evidence-based interventions (e.g., school intervention programs).     

Herp coordinates compartmentalization and recruitment of HRD1 and misfolded proteins for ERAD

A functional unfolded protein response (UPR) is essential for endoplasmic reticulum (ER)-associated degradation (ERAD) of misfolded secretory proteins, reflecting the fact that some level of UPR activation must exist under normal physiological conditions. A coordinator of the UPR and ERAD processes has long been sought. We previously showed that the PKR-like, ER-localized eukaryotic translation initiation factor 2α kinase branch of the UPR is required for the recruitment of misfolded proteins and the ubiquitin ligase HRD1 to the ER-derived quality control compartment (ERQC), a staging ground for ERAD. Here we show that homocysteine-induced ER protein (Herp), a protein highly upregulated by this UPR branch, is responsible for this compartmentalization. Herp localizes to the ERQC, and our results suggest that it recruits HRD1, which targets to ERAD the substrate presented by the OS-9 lectin at the ERQC. Predicted overall structural similarity of Herp to the ubiquitin-proteasome shuttle hHR23, but including a transmembrane hairpin, suggests that Herp may function as a hub for membrane association of ERAD machinery components, a key organizer of the ERAD complex.     

Rad21l1 cohesin subunit is dispensable for spermatogenesis but not oogenesis in zebrafish

During meiosis I, ring-shaped cohesin complexes play important roles in aiding the proper segregation of homologous chromosomes. RAD21L is a meiosis-specific vertebrate cohesin that is required for spermatogenesis in mice but is dispensable for oogenesis in young animals. The role of this cohesin in other vertebrate models has not been explored. Here, we tested if the zebrafish homolog Rad21l1 is required for meiotic chromosome dynamics during spermatogenesis and oogenesis. We found that Rad21l1 localizes to unsynapsed chromosome axes. It is also found between the axes of the mature tripartite synaptonemal complex (SC) in both sexes. We knocked out rad21l1 and found that nearly all rad21l1^-/- mutants develop as fertile males, suggesting that the mutation causes a defect in juvenile oogenesis, since insufficient oocyte production triggers female to male sex reversal in zebrafish. Sex reversal was partially suppressed by mutation of the checkpoint gene tp53, suggesting that the rad21l1 mutation activates Tp53-mediated apoptosis or arrest in females. This response, however, is not linked to a defect in repairing Spo11-induced double-strand breaks since deletion of spo11 does not suppress the sex reversal phenotype. Compared to tp53 single mutant controls, rad21l1^-/- tp53^-/- double mutant females produce poor quality eggs that often die or develop into malformed embryos. Overall, these results indicate that the absence of rad21l1^-/- females is due to a checkpoint-mediated response and highlight a role for a meiotic-specific cohesin subunit in oogenesis but not spermatogenesis.     

A comparative study on the heparin‐binding proteomes of Toxoplasma gondii and Plasmodium falciparum

Toxoplasma gondii is an obligatory intracellular apicomplexan parasite which exploits host cell surface components in cell invasion and intracellular parasitization. Sulfated glycans such as heparin and heparan sulfate have been reported to inhibit cell invasion by T. gondii and other apicomplexan parasites such as Plasmodium falciparum. The aim of this study was to investigate the heparin‐binding proteome of T. gondii. The parasite‐derived components were affinity‐purified on the heparin moiety followed by MS fingerprinting of the proteins. The heparin‐binding proteins of T. gondii and P. falciparum were compared based on functionality and affinity to heparin. Among the proteins identified, the invasion‐related parasite ligands derived from tachyzoite/merozoite surface and the secretory organelles were prominent. However, the profiles of the proteins were different in terms of affinity to heparin. In T. gondii, the proteins with highest affinity to heparin were the intracellular components with functions of parasite development contrasted to that of P. falciparum, of which the rhoptry‐derived proteins were prominently identified. The profiling of the heparin‐binding proteins of the two apicomplexan parasites not only explained the mechanism of heparin‐mediated host cell invasion inhibition, but also, to a certain extent, revealed that the action of heparin on the parasite extended after endocytosis.