Structure and dynamics of an acid-denatured protein G mutant

NMR studies of protein denatured states provide insights into potential initiation sites for folding that may be too transient to be observed kinetically. We have characterized the structure and dynamics of the acid-denatured state of protein G by using a F30H mutant of G(B1) which is on the margin of stability. At 5 degrees C, F30H-G(B1) is greater than 95% folded at pH 7.0 and is greater than 95% unfolded at pH 4.0. This range of stability is useful because the denatured state can be examined under relatively mild conditions which are optimal for folding G(B1). We have assigned almost all backbone (15)N, H(N), and H(alpha) resonances in the acid-denatured state. Chemical shift, coupling constant, and NOE data indicate that the denatured state has considerably more residual structure when studied under these mild conditions than in the presence of chemical denaturants. The acid-denatured state populates nativelike conformations with both alpha-helical and beta-hairpin characteristics. To our knowledge, this is the first example of a denatured state with NOE and coupling constant evidence for beta-hairpin character. A number of non-native turn structures are also detected, particularly in the region corresponding to the beta1-beta2 hairpin of the folded state. Steady-state ?(1)H-(15)N? NOE results demonstrate restricted backbone flexibility in more structured regions of the denatured protein. Overall, our studies suggest that regions of the helix, the beta3-beta4 hairpin, and the beta1-beta2 turn may serve as potential initiation sites for folding of G(B). Furthermore, residual structure in acid-denatured F30H-G(B1) is more extensive than in peptide fragments corresponding to the beta1-beta2, alpha-helix, and beta3-beta4 regions, suggesting additional medium-to-long-range interactions in the full-length polypeptide chain.     

The pathological examinations of gastric mucosa in patients with Helicobacter pylori-positive and -negative pernicious anemia

Background. The basic histopathological finding in gastric mucosa is chronic atrophic gastritis in patients with pernicious anemia.
Materials and Methods. We evaluated the frequency of Helicobacter pylori and pathological examinations of gastric mucosa in pernicious anemia (n = 30) by endoscopical findings and biopsy. The results were compared with gastric mucosa specimens of patients with H. pylori –positive nonulcer dyspepsia (n = 36) and H. pylori –negative nonulcer dyspepsia (n = 21).
Results. H. pylori was diagnosed in 12 patients (40%) with pernicious anemia. Fundal biopsy examinations showed atrophic gastritis in 30 patients (100%), intestinal metaplasia in 13 patients (43.3%), lymphoid follicle in 15 patients (50%), and dysplasia in 6 patients (20%). Antral biopsy examinations showed atrophic gastritis in 8 patients (26.6%), intestinal metaplasia in 8 patients (26.6%), lymphoid follicle in 8 patients (26.6%), and dysplasia in 3 patients (10%). The frequency of fundal inflammation, atrophy, intestinal metaplasia, lymphoid follicle, and dysplasia and antral intestinal metaplasia and mild antral dysplasia were found to be higher in those in the pernicious anemia group than in the nonulcer dyspeptic patients. Antral inflammation, atrophy, and moderate and severe antral dysplasia were found to be higher in those in the nonulcer dyspeptic group.
Conclusions. Particularly, fundal precancerous lesions were found to be more frequent in patients with pernicious anemia independent of H. pylori.     

Parentage analysis with incomplete sampling of candidate parents and offspring

Many breeding systems include 'multiple mating' in which males or females mate with multiple partners. We identify two forms of multiple mating: 'single-sex', where the next-generation individuals (NGIs) are the product of multiple mating by one sex; and 'two-sex', where the NGIs are the product of multiple mating by both sexes. For both mating systems we develop models that estimate the proportion of NGIs that is fathered (paternity) or mothered (maternity) by the putative parents. The models only require genetic data from the parent or parents in question and the sample of NGIs, as well as an estimate of population allele frequencies. The models provide unbiased estimates, can accommodate loci with many alleles and are robust to violations of their assumptions. They allow researchers to address intractable problems such as the parentage of seeds found on the ground, juvenile fish in a stream, and nestlings in a communal breeding bird. We demonstrate the models using genetic data from a nest of the bluegill sunfish Lepomis macrochirus, where the NGIs may be from multiple females that have spawned with multiple males from different life histories (cuckolder and parental).     

Production and purification of recombinant human α2C2 adrenergic receptor using Saccharomyces cerevisiae

The objective is to generate milligram quantities of recombinant human ₂C2 adrenergic receptor for X-ray crystallographic studies. It has been cloned in Saccharomyces cerevisiae, and the production level is at best about 13 pmol/mg of membrane protein, as estimated by radio-ligand binding assay. The receptor is solubilized with sucrose monolaurate followed by immunoaffinity purification and reconstitution into phospholipid vesicles. The efficiency of solubilization and immuno-purification are 60% and 91%, respectively.     

The effects of different sugars on motility, morphology and DNA damage during the liquid storage of rat epididymal sperm at 4°C

This study evaluated the protective effects of supplementation with three different sugars on the motility, morphology and DNA integrity of rat epididymal sperm chilled and stored at 4°C Epididymides were obtained from each donor. Rat epididymal sperm was diluted in Ham's F10 plus raffinose, Ham's F10 plus trehalose, Ham's F10 plus fructose, and Ham's F10 medium for control purposes. Thereafter, the extended sperm were chilled and stored in liquid form at 4°C. Sperm motility, morphological abnormalities and DNA damage were determined at 0 and 12h after chilling. No significant difference was observed in any of the parameters evaluated at 0h, before storage (P>0.05). After 12h of storage, all sugar additives led to statistically higher motility, normal sperm morphology and DNA integrity in comparison to the control group. Raffinose gave the best motility percentages (32.86±1.84%) after 12h of storage at 4°C, compared to the other groups (P<0.001). In conclusion, Raffinose, trehalose and fructose provided a better protection of sperm functional parameters against chilling injury, in comparison to the control group.     

Causality and persistence in ecological systems: a nonparametric spectral granger causality approach

Abstract Directionality in coupling, defined as the linkage relating causes to their effects at a later time, can be used to explain the core dynamics of ecological systems by untangling direct and feedback relationships between the different components of the systems. Inferring causality from measured ecological variables sampled through time remains a formidable challenge further made difficult by the action of periodic drivers overlapping the natural dynamics of the system. Periodicity in the drivers can often mask the self-sustained oscillations originating from the autonomous dynamics. While linear and direct causal relationships are commonly addressed in the time domain, using the well-established machinery of Granger causality (G-causality), the presence of periodic forcing requires frequency-based statistics (e.g., the Fourier transform), able to distinguish coupling induced by oscillations in external drivers from genuine endogenous interactions. Recent nonparametric spectral extensions of G-causality to the frequency domain pave the way for the scale-by-scale decomposition of causality, which can improve our ability to link oscillatory behaviors of ecological networks to causal mechanisms. The performance of both spectral G-causality and its conditional extension for multivariate systems is explored in quantifying causal interactions within ecological networks. Through two case studies involving synthetic and actual time series, it is demonstrated that conditional G-causality outperforms standard G-causality in identifying causal links and their concomitant timescales.     

Elevated CO2 affects photosynthetic responses in canopy pine and subcanopy deciduous trees over 10 years: a synthesis from Duke FACE

Leaf responses to elevated atmospheric CO₂ concentration (C_a) are central to models of forest CO₂ exchange with the atmosphere and constrain the magnitude of the future carbon sink. Estimating the magnitude of primary productivity enhancement of forests in elevated C_a requires an understanding of how photosynthesis is regulated by diffusional and biochemical components and up‐scaled to entire canopies. To test the sensitivity of leaf photosynthesis and stomatal conductance to elevated C_a in time and space, we compiled a comprehensive dataset measured over 10 years for a temperate pine forest of Pinus taeda, but also including deciduous species, primarily Liquidambar styraciflua. We combined over one thousand controlled‐response curves of photosynthesis as a function of environmental drivers (light, air C_a and temperature) measured at canopy heights up to 20 m over 11 years (1996–2006) to generate parameterizations for leaf‐scale models for the Duke free‐air CO₂ enrichment (FACE) experiment. The enhancement of leaf net photosynthesis (A_net) in P. taeda by elevated C_a of +200 μmol mol^?1 was 67% for current‐year needles in the upper crown in summer conditions over 10 years. Photosynthetic enhancement of P. taeda at the leaf‐scale increased by two‐fold from the driest to wettest growing seasons. Current‐year pine foliage A_net was sensitive to temporal variation, whereas previous‐year foliage A_net was less responsive and overall showed less enhancement (+30%). Photosynthetic downregulation in overwintering upper canopy pine needles was small at average leaf N (N_area), but statistically significant. In contrast, co‐dominant and subcanopy L. styraciflua trees showed A_net enhancement of 62% and no A_net–N_area adjustments. Various understory deciduous tree species showed an average A_net enhancement of 42%. Differences in photosynthetic responses between overwintering pine needles and subcanopy deciduous leaves suggest that increased C_a has the potential to enhance the mixed‐species composition of planted pine stands and, by extension, naturally regenerating pine‐dominated stands.     

Mechanism of Fcγ Receptor-Mediated Trogocytosis-Based False-Positive Results in Flow Cytometry

The whole blood erythrocyte lysis method is the most common protocol of sample preparation for flow cytometry (FCM). Although this method has many virtues, our recent study has demonstrated false-positive results when surface markers of monocytes were examined by this method due to the phenomenon called Fcγ receptor (FcγR)-mediated trogocytosis. In the present study, similar FcγR-mediated trogocytosis-based false-positive results have been demonstrated when granulocytes were focused on instead of monocytes. These findings indicated that not only monocytes but also granulocytes, the largest population with FcγR expression in peripheral blood, could perform FcγR-mediated trogocytosis. Since the capacity of FcγR-mediated trogocytosis was different among blood samples, identification of factors that could regulate the occurrence of FcγR-mediated trogocytosis should be important for the quality control of FCM. Our studies have suggested that such factors are present in the serum. In order to identify the serum factors, we employed the in vitro model of FcγR-mediated trogocytosis using granulocytes. Investigation with this model determined the serum factors as heat-labile molecules with molecular weight of more than 100 kDa. Complements in the classical pathway were initially assumed as candidates; however, the C1 inhibitor did not yield an obvious influence on FcγR-mediated trogocytosis. On the other hand, although immunoglobulin ought to be resistant to heat inactivation, the inhibitor of human anti-mouse antibodies (HAMA) effectively blocked FcγR-mediated trogocytosis. Moreover, the inhibition rates were significantly higher in HAMA^high serum than HAMA^low serum. The collective findings suggested the involvement of heterophilic antibodies such as HAMA in the mechanism of false-positive results in FCM due to FcγR-mediated trogocytosis.     

A non-mammalian type opsin 5 functions dually in the photoreceptive and non-photoreceptive organs of birds

A mammalian type opsin 5 (neuropsin) is a recently identified ultraviolet (UV)-sensitive pigment of the retina and other photosensitive organs in birds. Two other opsin 5-related molecules have been found in the genomes of non-mammalian vertebrates. However, their functions have not been examined as yet. Here, we identify the molecular properties of a second avian opsin 5, cOpn5L2 (chicken opsin 5-like 2), and its localization in the post-hatch chicken. Spectrophotometric analysis and radionucleotide-binding assay have revealed that cOpn5L2 is a UV-sensitive bistable pigment that couples with the Gi subtype of guanine nucleotide-binding protein (G protein). As a bistable pigment, it also shows the direct binding ability to agonist all-trans-retinal to activate G protein. The absorption maxima of UV-light-absorbing and visible light-absorbing forms were 350 and 521 nm, respectively. Expression analysis showed relatively high expression of cOpn5L2 mRNA in the adrenal gland, which is not photoreceptive but an endocrine organ, while lower expression was found in the brain and retina. At the protein level, cOpn5L2 immunoreactive cells were present in the chromaffin cells of the adrenal gland. In the brain, cOpn5L2 immunoreactive cells were found in the paraventricular and supraoptic nuclei of the anterior hypothalamus, known for photoreceptive deep brain areas. In the retina, cOpn5L2 protein was localized to subsets of cells in the ganglion cell layer and the inner nuclear layer. These results suggest that the non-mammalian type opsin 5 (Opn5L2) functions as a second UV sensor in the photoreceptive organs, while it might function as chemosensor using its direct binding ability to agonist all-trans-retinal in non-photoreceptive organs such as the adrenal gland of birds.     

Genetic Barcodes for Improved Environmental Tracking of an Anthrax Simulant

The development of realistic risk models that predict the dissemination, dispersion and persistence of potential biothreat agents have utilized nonpathogenic surrogate organisms such as Bacillus atrophaeus subsp. globigii or commercial products such as Bacillus thuringiensis subsp. kurstaki. Comparison of results from outdoor tests under different conditions requires the use of genetically identical strains; however, the requirement for isogenic strains limits the ability to compare other desirable properties, such as the behavior in the environment of the same strain prepared using different methods. Finally, current methods do not allow long-term studies of persistence or reaerosolization in test sites where simulants are heavily used or in areas where B. thuringiensis subsp. kurstaki is applied as a biopesticide. To create a set of genetically heterogeneous yet phenotypically indistinguishable strains so that variables intrinsic to simulations (e.g., sample preparation) can be varied and the strains can be tested under otherwise identical conditions, we have developed a strategy of introducing small genetic signatures (“barcodes”) into neutral regions of the genome. The barcodes are stable over 300 generations and do not impact in vitro growth or sporulation. Each barcode contains common and specific tags that allow differentiation of marked strains from wild-type strains and from each other. Each tag is paired with specific real-time PCR assays that facilitate discrimination of barcoded strains from wild-type strains and from each other. These uniquely barcoded strains will be valuable tools for research into the environmental fate of released organisms by providing specific artificial detection signatures.