Binding of synthetic peptides by a human monoclonal IgM with an unusual combining site structure

Using X-ray crystallography, a human monoclonal IgM cryoglobulin (Mez) was found to have an unusual combining site topography. Analysis of the unliganded Fv at 2.6 A resolution revealed that the HCDR3 had partitioned the active site into two compartments [Ramsland PA et al. 2000. Mol. Immunol. 37: 295-310]. The two cavities had dimensions and chemical properties that were compatible with the binding of peptides. In this study, libraries of peptides were prepared using solid-phase synthesis. Binding of the intact Mez IgM to these peptides was tested by enzyme-linked immunoassays. Screening of 400 dipeptides revealed that binding was markedly skewed toward amino acids with aromatic side-chains (Phe and Trp), especially when located in the second position. Preferential recognition of aromatic side-chains by Mez IgM was confirmed with larger peptides of three to five residues, but C-terminal positioning was not favored in these peptides. Mez IgM also showed binding propensities for acidic residues (Asp and Glu) as well as several other side-chains with different chemical properties, including His, Pro, Asn and Gln. Mez IgM recognized sets of overlapping octapeptides representing the sequences of the constant domains of human IgG1 heavy chains. These peptides represented similar stretches of polypeptide on the three-dimensional structures of all three constant domains (CH1, CH2 and CH3). Thus, Mez IgM may recognize structurally homologous regions of immunoglobulin domains, which were conserved during the evolution of the immune system.     

Genital Chlamydia Prevalence in Europe and Non-European High Income Countries: Systematic Review and Meta-Analysis

Background

Accurate information about the prevalence of Chlamydia trachomatis is needed to assess national prevention and control measures.

Methods

We systematically reviewed population-based cross-sectional studies that estimated chlamydia prevalence in European Union/European Economic Area (EU/EEA) Member States and non-European high income countries from January 1990 to August 2012. We examined results in forest plots, explored heterogeneity using the I² statistic, and conducted random effects meta-analysis if appropriate. Meta-regression was used to examine the relationship between study characteristics and chlamydia prevalence estimates.

Results

We included 25 population-based studies from 11 EU/EEA countries and 14 studies from five other high income countries. Four EU/EEA Member States reported on nationally representative surveys of sexually experienced adults aged 18–26 years (response rates 52–71%). In women, chlamydia point prevalence estimates ranged from 3.0–5.3%; the pooled average of these estimates was 3.6% (95% CI 2.4, 4.8, I² 0%). In men, estimates ranged from 2.4–7.3% (pooled average 3.5%; 95% CI 1.9, 5.2, I² 27%). Estimates in EU/EEA Member States were statistically consistent with those in other high income countries (I² 0% for women, 6% for men). There was statistical evidence of an association between survey response rate and estimated chlamydia prevalence; estimates were higher in surveys with lower response rates, (p = 0.003 in women, 0.018 in men).

Conclusions

Population-based surveys that estimate chlamydia prevalence are at risk of participation bias owing to low response rates. Estimates obtained in nationally representative samples of the general population of EU/EEA Member States are similar to estimates from other high income countries.     

Combined genetic and metabolic manipulation of lipids in Rhodobacter sphaeroides reveals non-phospholipid substitutions in fully active cytochrome c oxidase

A specific requirement for lipids, particularly cardiolipin (CL), in cytochrome c oxidase (CcO) has been reported in many previous studies using mainly in vitro lipid removal approaches in mammalian systems. Our accompanying paper shows that CcO produced in markedly CL-depleted Rhodobacter sphaeroides displays wild-type properties in all respects, likely allowed by quantitative substitution with other negatively charged lipids. To further examine the structural basis for the lipid requirements of R. sphaeroides CcO and the extent of interchangeability between lipids, we employed a metabolic approach to enhance the alteration of the lipid profiles of the CcO-expressing strains of R. sphaeroides in vivo using a phosphate-limiting growth medium in addition to the CL-deficient mutation. Strikingly, the purified CcO produced under these conditions still maintained wild-type function and characteristics, in spite of even greater depletion of cardiolipin compared to that of the CL-deficient mutant alone (undetectable by MS) and drastically altered profiles of all the phospholipids and non-phospholipids. The lipids in the membrane and in the purified CcO were identified and quantified by ESI and MALDI mass spectrometry and tandem mass spectrometry. Comparison between the molecular structures of those lipids that showed major changes provides new insight into the structural rationale for the flexible lipid requirements of CcO from R. sphaeroides and reveals a more comprehensive interchangeability network between different phospholipids and non-phospholipids.     

Anthraquinone-based bird repellent for sunflower crops

Non-lethal alternatives are needed to manage bird damage to confectionery and oilseed sunflower crops (Helianthus annuus). Ring-necked pheasants (Phasianus colchicus) can cause localized damage to newly planted sunflower, and blackbirds (Icterids) damage ripening sunflower annually in the United States of America. We conducted seed germination experiments, a repellent efficacy study with ring-necked pheasants and Avipel^® repellent (a.i. 50% 9,10-anthraquinone), and laboratory and field efficacy studies with common grackles (Quiscalus quiscula) and Avipel^®-treated confectionery sunflower. Compared to the germination of seeds not treated with anthraquinone, we observed no negative effects of up to 12,223 ppm, 14,104 ppm, and 11,569 ppm anthraquinone seed treatments for germination of confectionery sunflower, oilseed sunflower, and canola seeds, respectively. Pheasants avoided emergent sunflower seedlings (12 days post-planting) from 15,800 ppm anthraquinone seed treatments during a caged preference test (P = 0.045). We observed a positive concentration–response relationship (P = 0.001) and predicted a threshold concentration (i.e., 80% repellency) of 9200 ppm anthraquinone for common grackles offered Avipel^®-treated confectionery sunflower seeds. Grackles also reliably discriminated between untreated sunflower and seeds treated with 1300 ppm anthraquinone in captivity (P < 0.001). During our field efficacy study for ripening confectionery sunflower, we observed 18% damage among anthraquinone-treated enclosures and 64% damage among untreated enclosures populated with common grackles (P < 0.001). Harvested seed mass averaged 2.54 kg (dry weight) among treated enclosures and 1.24 kg among untreated enclosures (P < 0.001). Our laboratory and field efficacy data provide a reliable basis for planning future field applications of anthraquinone-based repellents for protection of sunflower crops. Supplemental field efficacy studies are necessary for development of an effective avian repellent and management of avian depredation of ripening agricultural crops, including oilseed sunflower.     

Changes in respiratory control and cytochromes in liver mitochondria during hibernation

Liver mitochondria from the ground squirrel, Citellus lateralis, were compared during states of hibernation and non-hibernation. During hibernation a decreased total amount of mitochondrial cytochrome was noted. In addition changes in the relative amounts of cytochromes b and c and a pronounced decrease in cytochrome a–a₃ was shown by difference spectra. The rate of oxygen uptake with succinate and ADP was less in the hibernator. However, addition of the uncoupler, salicylanilide XIII, stimulated oxygen consumption of the hibernator to a rate greater than that observed in the non-hibernating animal indicating that oxygen uptake was not limited by the cytochrome concentration. It is postulated that the sluggish rate of oxygen uptake under phosphorylating conditions by liver mitochondria of the hibernator may be caused by a change in the penetration of ADP and/or P_i, or an alternation in some parameter of the mechanism of coupled phosphorylation.     

DNA methylation affects nuclear organization, histone modifications, and linker histone binding but not chromatin compaction

DNA methylation has been implicated in chromatin condensation and nuclear organization, especially at sites of constitutive heterochromatin. How this is mediated has not been clear. In this study, using mutant mouse embryonic stem cells completely lacking in DNA methylation, we show that DNA methylation affects nuclear organization and nucleosome structure but not chromatin compaction. In the absence of DNA methylation, there is increased nuclear clustering of pericentric heterochromatin and extensive changes in primary chromatin structure. Global levels of histone H3 methylation and acetylation are altered, and there is a decrease in the mobility of linker histones. However, the compaction of both bulk chromatin and heterochromatin, as assayed by nuclease digestion and sucrose gradient sedimentation, is unaltered by the loss of DNA methylation. This study shows how the complete loss of a major epigenetic mark can have an impact on unexpected levels of chromatin structure and nuclear organization and provides evidence for a novel link between DNA methylation and linker histones in the regulation of chromatin structure.     

Crystallographic location and mutational analysis of Zn and Cd inhibitory sites and role of lipidic carboxylates in rescuing proton path mutants in cytochrome c oxidase

Cytochrome c oxidase (CcO) transfers protons from the inner surface of the enzyme to the buried O2 reduction site through two different pathways, termed K and D, and from the outer surface via an undefined route. These proton paths can be inhibited by metals such as zinc or cadmium, but the sites of inhibition have not been established. Anomalous difference Fourier analyses of Rhodobacter sphaeroides CcO crystals, with cadmium added, reveal metal binding sites that include the proposed initial proton donor/acceptor of the K pathway, Glu-101 of subunit II. Mutant forms of CcO that lack Glu-101II (E101A and E101A/H96A) exhibit low activity and eliminate metal binding at this site. Significant activity is restored to E101A and E101A/H96A by adding the lipophilic carboxylic compounds, arachidonic acid and cholic acid, but not by their non-carboxylic analogues. These amphipathic acids likely provide their carboxylic groups as substitute proton donors/acceptors in the absence of Glu-101II, as previously observed for arachidonic acid in mutants that alter Asp-132I of the D pathway. The activity of E101A/H96A is still inhibited by zinc, but this remaining inhibition is nearly eliminated by removal of subunit III, which is known to alter the D pathway. The results identify the Glu-101/His-96 site of subunit II as the site of metal binding that inhibits the uptake of protons into the K pathway and indicate that subunit III contributes to zinc binding and/or inhibition of the D pathway. By removing subunit III from E101A/H96A, thereby eliminating zinc inhibition of the uptake of protons from the inner surface of CcO, we confirm that an external zinc binding site is involved in inhibiting the backflow of protons to the active site.     

Topoisomerase II binds importin alpha isoforms and exportin/CRM1 but does not shuttle between the nucleus and cytoplasm in proliferating cells

Resistance to anticancer drugs that target DNA topoisomerase II (topo II) isoforms alpha and/or beta is associated with decreased nuclear and increased cytoplasmic topo IIalpha. Earlier studies have confirmed that functional nuclear localization and export signal sequences (NLS and NES) are present in both isoforms. In this study, we show that topo II alpha and beta bind and are imported into the nucleus by importin alpha1, alpha3, and alpha5 in conjunction with importin beta. Topo IIalpha also binds exportin/CRM1 in vitro. However, wild-type topo IIalpha has only been observed in the cytoplasm of cells that are entering plateau phase growth. This suggests that topo IIalpha may shuttle between the nucleus and the cytoplasm with the equilibrium towards the nucleus in proliferating cells but towards the cytoplasm in plateau phase cells. The CRM1 inhibitor Leptomycin B increases the nuclear localization of GFP-tagged topo IIalpha with a mutant NLS, suggesting that its export is being inhibited. However, homokaryon shuttling experiments indicate that fluorescence-tagged wild-type topo II alpha and beta proteins do not shuttle in proliferating Cos-1 or HeLa cells. We conclude that topo II alpha and beta nuclear export is inhibited in proliferating cells so that these proteins do not shuttle.     

Ocean Warming,More than Acidification,Reduces Shell Strength in a Commercial Shellfish Species during Food Limitation

Ocean surface pH levels are predicted to fall by 0.3–0.4 pH units by the end of the century and are likely to coincide with an increase in sea surface temperature of 2–4°C. The combined effect of ocean acidification and warming on the functional properties of bivalve shells is largely unknown and of growing concern as the shell provides protection from mechanical and environmental challenges. We examined the effects of near-future pH (ambient pH –0.4 pH units) and warming (ambient temperature +4°C) on the shells of the commercially important bivalve, Mytilus edulis when fed for a limited period (4–6 h day⁻¹). After six months exposure, warming, but not acidification, significantly reduced shell strength determined as reductions in the maximum load endured by the shells. However, acidification resulted in a reduction in shell flex before failure. Reductions in shell strength with warming could not be explained by alterations in morphology, or shell composition but were accompanied by reductions in shell surface area, and by a fall in whole-body condition index. It appears that warming has an indirect effect on shell strength by re-allocating energy from shell formation to support temperature-related increases in maintenance costs, especially as food supply was limited and the mussels were probably relying on internal energy reserves. The maintenance of shell strength despite seawater acidification suggests that biomineralisation processes are unaffected by the associated changes in CaCO₃ saturation levels. We conclude that under near-future climate change conditions, ocean warming will pose a greater risk to shell integrity in M. edulis than ocean acidification when food availability is limited.