Bnip3 functions as a mitochondrial sensor of oxidative stress during myocardial ischemia and reperfusion

Bcl-2/adenovirus E1B 19-kDa protein-interacting protein 3 (Bnip3) is a member of the Bcl-2 homology domain 3-only subfamily of proapoptotic Bcl-2 proteins and is associated with cell death in the myocardium. In this study, we investigated the potential mechanism(s) by which Bnip3 activity is regulated. We found that Bnip3 forms a DTT-sensitive homodimer that increased after myocardial ischemia-reperfusion (I/R). The presence of the antioxidant N-acetylcysteine reduced I/R-induced homodimerization of Bnip3. Overexpression of Bnip3 in cells revealed that most of exogenous Bnip3 exists as a DTT-sensitive homodimer that correlated with increased cell death. In contrast, endogenous Bnip3 existed mainly as a monomer under normal conditions in the heart. Screening of the Bnip3 protein sequence revealed a single conserved cysteine residue at position 64. Mutation of this cysteine to alanine (Bnip3C64A) or deletion of the NH2-terminus (amino acids 1-64) resulted in reduced cell death activity of Bnip3. Moreover, mutation of a histidine residue in the COOH-terminal transmembrane domain to alanine (Bnip3H173A) almost completely inhibited the cell death activity of Bnip3. Bnip3C64A had a reduced ability to interact with Bnip3, whereas Bnip3H173A was completely unable to interact with Bnip3, suggesting that homodimerization is important for Bnip3 function. A consequence of I/R is the production of reactive oxygen species and oxidation of proteins, which promotes the formation of disulfide bonds between proteins. Thus, these experiments suggest that Bnip3 functions as a redox sensor where increased oxidative stress induces homodimerization and activation of Bnip3 via cooperation of the NH2-terminal cysteine residue and the COOH-terminal transmembrane domain.     

The protozoa dinoflagellate Oxyrrhis marina contains selenoproteins and the relevant translation apparatus

In the phylogenetic tree, selenoproteins and the corresponding translation machinery are found in Archaea, Eubacteria, and animals, but not in fungi and higher plants. As very little is known about Protozoa, we searched for the presence of selenoproteins in the primitive dinoflagellate Oxyrrhis marina, belonging to the Protoctista kingdom. Four selenoproteins could be obtained from O. marina cells cultured in the presence of 75Se. Using O. marina or bovine liver cytosolic extracts, we could serylate and selenylate in vitro total O. marina tRNAs. Moreover, the existence of a tRNA(Sec) could be deduced from in vivo experiments. Lastly, an anti-serum against the specialized mammalian translation elongation factor mSelB reacted with a protein of 48-kDa molecular mass. Altogether, our data showed that O. marina contains selenoproteins and suggests that the corresponding translation machinery is related to that found in animals.     

Monoclonal Antibodies against Aβ42 Fibrils Distinguish Multiple Aggregation State Polymorphisms in Vitro and in Alzheimer Disease Brain

Amyloidogenic proteins generally form intermolecularly hydrogen-bonded β-sheet aggregates, including parallel, in-register β-sheets (recognized by antiserum OC) or antiparallel β-sheets, β-solenoids, β-barrels, and β-cylindrins (recognized by antiserum A11). Although these groups share many common properties, some amyloid sequences have been reported to form polymorphic structural variants or strains. We investigated the humoral immune response to Aβ42 fibrils and produced 23 OC-type monoclonal antibodies recognizing distinct epitopes differentially associated with polymorphic structural variants. These mOC antibodies define at least 18 different immunological profiles represented in aggregates of amyloid-β (Aβ). All of the antibodies strongly prefer amyloid aggregates over monomer, indicating that they recognize conformational epitopes. Most of the antibodies react with N-terminal linear segments of Aβ, although many recognize a discontinuous epitope consisting of an N-terminal domain and a central domain. Several of the antibodies that recognize linear Aβ segments also react with fibrils formed from unrelated amyloid sequences, indicating that reactivity with linear segments of Aβ does not mean the antibody is sequence-specific. The antibodies display strikingly different patterns of immunoreactivity in Alzheimer disease and transgenic mouse brain and identify spatially and temporally unique amyloid deposits. Our results indicate that the immune response to Aβ42 fibrils is diverse and reflects the structural polymorphisms in fibrillar amyloid structures. These polymorphisms may contribute to differences in toxicity and consequent effects on pathological processes. Thus, a single therapeutic monoclonal antibody may not be able to target all of the pathological aggregates necessary to make an impact on the overall disease process.     

A Hip1R-cortactin complex negatively regulates actin assembly associated with endocytosis

Actin polymerization plays a critical role in clathrin-mediated endocytosis in many cell types, but how polymerization is regulated is not known. Hip1R may negatively regulate actin assembly during endocytosis because its depletion increases actin assembly at endocytic sites. Here, we show that the C-terminal proline-rich domain of Hip1R binds to the SH3 domain of cortactin, a protein that binds to dynamin, actin filaments and the Arp2/3 complex. We demonstrate that Hip1R deleted for the cortactin-binding site loses its ability to rescue fully the formation of abnormal actin structures at endocytic sites induced by Hip1R siRNA. To determine when this complex might function during endocytosis, we performed live cell imaging. The maximum in vivo recruitment of Hip1R, clathrin and cortactin to endocytic sites was coincident, and all three proteins disappeared together upon formation of a clathrin-coated vesicle. Finally, we showed that Hip1R inhibits actin assembly by forming a complex with cortactin that blocks actin filament barbed end elongation.     

Relationship of inbreeding with sperm quality and reproductive success in Mexican gray wolves

The ultimate goal of the Mexican gray wolf Canis lupus baileyi captive management program is reintroduction of healthy individuals into wild habitats. To this end, zoo population managers work to provide not only for the physical well-being but also for the genetic health of these animals. However, the very limited genetic founder base, exacerbated by breeding within three distinct lineages, resulted in very high coefficients of inbreeding. Because support for measurable levels of inbreeding depression in the captive wolf population, as defined by reductions in common fitness measures such as juvenile survival or reproductive success, has been weak, we investigated the potential effects on male reproductive capacity. We analyzed semen samples from wolves from all three lineages and compared them with samples from subsequent lineage crosses and from generic gray wolves. We not only found a significant effect of inbreeding on sperm quality but we related both inbreeding and sperm quality to reproductive success. Samples from male offspring of lineage crosses, with inbreeding coefficients of zero were similar in quality to those from generic gray wolves. However, samples from a limited number of offspring from back-crosses were of extremely poor quality. Although it is reassuring that sperm quality was so much improved in male offspring of lineage crosses, the concomitant reduction in inbreeding coefficient does not eliminate the potentially deleterious alleles. Our results demonstrate that sperm quality is an important indicator of fertility and reproductive success in Mexican wolves. In addition, our data lend further support to the presence of inbreeding depression in this taxon.     

Delayed stigma receptivity in Collinsia heterophylla (Plantaginaceae): genetic variation and adaptive significance in relation to pollen competition, delayed self-pollination, and mating-system evolution

To increase our knowledge about mating-system evolution, we need to understand the relationship between specific floral traits and mating system. Species of Collinsia (Plantaginaceae) vary extensively in mating system; this variation is associated with variation in floral morphology and development and with the timing of self-pollination. Counterintuitively, large-flowered, more outcrossing species tend to have delayed stigma receptivity, reducing the amount of time that the stigma is receptive to cross-pollination before autonomous self-pollination. To understand how the timing of stigma receptivity is related to mating-system evolution, we studied in detail the timing of both stigma receptivity and self-pollination (anther-stigma contact) in two greenhouse-grown populations of large-flowered Collinsia heterophylla. Crosses on emasculated flowers at different stages of floral development always produced seeds, suggesting that cross-fertilization can be effected by pollen arriving prior to physiological receptivity. Phenotypic and genetic variation within populations in the timing of stigma receptivity and anther-stigma contact was substantial, although slightly less for the contact. Despite strong interspecific and interpopulation correlations, we did not find an among-genet phenotypic correlation between the traits. This indicates that each trait may respond independently to selection, and the trait association may be the result of correlational selection.     

Oxylipin profiling of the hypersensitive response in Arabidopsis thaliana. Formation of a novel oxo-phytodienoic acid-containing galactolipid, arabidopside E

Oxidation products of unsaturated fatty acids, collectively known as oxylipins, function as signaling molecules in plants during development, wounding, and insect and pathogen attack. Certain oxylipins are also known to have direct cytotoxic effects on pathogens. We used inducible expression of bacterial avirulence proteins in planta to study the involvement of oxylipins in race-specific defense against bacterial pathogens. We demonstrate that recognition of the Pseudomonas syringae avirulence protein AvrRpm1 induces 9- and 13-lipoxygenase-dependent oxylipin synthesis in Arabidopsis thaliana. The major oxylipins accumulated were jasmonic acid, 12-oxo-phytodienoic acid, and dinor-oxo-phytodienoic acid. The majority of the newly formed oxylipins (>90%) was found to be esterified to glycerolipids, whereby 12-oxo-phytodienoic acid and dinor-oxo-phytodienoic acid were found to be esterified to a novel galactolipid. The structure of the substance was determined as a monogalactosyldiacylglycerol containing two 12-oxo-phytodienoic acids and one dinor-oxo-phytodienoic acid acyl chain and was given the trivial name arabidopside E. This substance accumulated to surprisingly high levels, 7-8% of total lipid content, and was shown to inhibit growth of a bacterial pathogen in vitro. Arabidopside E was formed also after recognition of the avirulence protein AvrRpt2, suggesting that this could be a conserved feature of defense reactions against bacterial pathogens. In conclusion, the data presented suggest a role of enzymatically formed oxylipins, especially the octadecanoids and arabidopside E in race-specific resistance against bacterial pathogens.     

Choosing negative examples for the prediction of protein-protein interactions

The protein-protein interaction networks of even well-studied model organisms are sketchy at best, highlighting the continued need for computational methods to help direct experimentalists in the search for novel interactions. This need has prompted the development of a number of methods for predicting protein-protein interactions based on various sources of data and methodologies. The common method for choosing negative examples for training a predictor of protein-protein interactions is based on annotations of cellular localization, and the observation that pairs of proteins that have different localization patterns are unlikely to interact. While this method leads to high quality sets of non-interacting proteins, we find that this choice can lead to biased estimates of prediction accuracy, because the constraints placed on the distribution of the negative examples makes the task easier. The effects of this bias are demonstrated in the context of both sequence-based and non-sequence based features used for predicting protein-protein interactions.     

Identification of local selective sweeps in human populations since the exodus from Africa

Selection on the human genome has been studied using comparative genomics and SNP architecture in the lineage leading to modern humans. In connection with the African exodus and colonization of other continents, human populations have adapted to a range of different environmental conditions. Using a new method that jointly analyses haplotype block length and allele frequency variation (F(ST)) within and between populations, we have identified chromosomal regions that are candidates for having been affected by local selection. Based on 1.6 million SNPs typed in 71 individuals of African American, European American and Han Chinese descent, we have identified a number of genes and non-coding regions that are candidates for having been subjected to local positive selection during the last 100 000 years. Among these genes are those involved in skin pigmentation (SLC24A5) and diet adaptation (LCT). The list of genes implicated in these local selective sweeps overlap partly with those implicated in other studies of human populations using other methods, but show little overlap with those postulated to have been under selection in the 5-7 myr since the divergence of the ancestors of human and chimpanzee. Our analysis provides focal points in the genome for detailed studies of evolutionary events that have shaped human populations as they explored different regions of the world.