Probabilistic protein function prediction from heterogeneous genome-wide data

Dramatic improvements in high throughput sequencing technologies have led to a staggering growth in the number of predicted genes. However, a large fraction of these newly discovered genes do not have a functional assignment. Fortunately, a variety of novel high-throughput genome-wide functional screening technologies provide important clues that shed light on gene function. The integration of heterogeneous data to predict protein function has been shown to improve the accuracy of automated gene annotation systems. In this paper, we propose and evaluate a probabilistic approach for protein function prediction that integrates protein-protein interaction (PPI) data, gene expression data, protein motif information, mutant phenotype data, and protein localization data. First, functional linkage graphs are constructed from PPI data and gene expression data, in which an edge between nodes (proteins) represents evidence for functional similarity. The assumption here is that graph neighbors are more likely to share protein function, compared to proteins that are not neighbors. The functional linkage graph model is then used in concert with protein domain, mutant phenotype and protein localization data to produce a functional prediction. Our method is applied to the functional prediction of Saccharomyces cerevisiae genes, using Gene Ontology (GO) terms as the basis of our annotation. In a cross validation study we show that the integrated model increases recall by 18%, compared to using PPI data alone at the 50% precision. We also show that the integrated predictor is significantly better than each individual predictor. However, the observed improvement vs. PPI depends on both the new source of data and the functional category to be predicted. Surprisingly, in some contexts integration hurts overall prediction accuracy. Lastly, we provide a comprehensive assignment of putative GO terms to 463 proteins that currently have no assigned function.     

Clinical Features and Treatment Modes of Mandibular Fracture at the Department of Oral and Maxillofacial Surgery,Shimane University Hospital,Japan

Background

The number of elderly patients with maxillofacial trauma is rapidly increasing due to active lifestyles and longevity. Shimane prefecture has the fastest growing proportion of elderly individuals in Japan. The aim of this study was to reveal the distinctive features and treatment modes of mandibular fracture treatment mode in patients requiring hospitalization at the Department of Oral and Maxillofacial Surgery, Shimane University Hospital, Japan.

Patients and Methods

Patient age, sex, period between injury and first consultation, years since injury, cause of injury, fracture site, treatment, and duration of hospitalization were evaluated. Univariate Poisson regression, relative risk with 95% confidence interval based on the Wald test, Fisher’s exact test, and Kruskal-Wallis test were used to explore associations among clinical and demographic variables.

Results

In total, 305 patients were diagnosed with and hospitalized for mandibular fracture from 1980 to 2010. Younger age increased the risk for mandibular fracture. Incidence was higher in males than females, particularly in the young, but the male to female ratio decreased with age. The period until first hospital consultation decreased progressively over the study period. Fall was a much more frequent cause in patients aged ≥60 than in those aged <60 years. Mandibular fracture with condyle, symphysis, and angle involvement were most common and were associated with sex, age, and treatment mode. Length of hospitalization has decreased since 1980.

Conclusion

In our department, patients aged ≥60 years accounted for a greater proportion of mandibular fracture cases than in many previous studies, reflecting the greater proportion of elderly residents in Shimane prefecture.     

N-cadherin-mediated cell adhesion determines the plasticity for cell alignment in response to mechanical stretch in cultured cardiomyocytes

Mechanical stretch has been implicated as the growth stimuli in the heart. Physiologically, mechanical stretch is reported to contribute to the orientation of cardiomyocytes, though the molecular mechanism remains to be elucidated. This study was designed to make clear functional significances of N-cadherin in plasticity of cell alignment in response to mechanical stretch. Neonatal rat cardiomyocytes, cultured on silicone dishes, were subjected to artificial uniaxial cyclic stretch. Mechanical stretch was started at certain times (3-75h) after seeding and continued for 24h. Stretch stimulation in 3h after cultivation promoted cell orientation running parallel to tension direction. In contrast, cardiac myocytes fail to align when exposed to stretch 24-75h after cultivation. To address the importance of N-cadherin in the responsiveness to stretch, the expression and distribution of N-cadherin were analyzed. Immediately after seeding, N-cadherin showed dispersed distributions. During cultivation, N-cadherin localized to cell-cell contacts accompanied by the upregulation of its protein. Next, to investigate influence of cell-cell adhesion, cardiomyocytes cultured for 72h were replated by trypsin treatment and exposed to stretch 3h after replating. The cardiomyocytes replated by trypsinization were oriented in parallel to tension direction by mechanical stretch. Finally, adenoviral transfection of dominant-negative N-cadherin recovered the ability to exhibit cell orientation in response to stretch. Our results suggested that N-cadherin was involved in the oriented responses of cardiomyocytes induced by mechanical stretch.     

TGF-beta1 enhances degradation of IFN-gamma-induced iNOS protein via proteasomes in RAW 264.7 cells.

TGF-beta1 is a well-known immunosuppressive cytokine that inhibits inducible nitric oxide synthase (iNOS) gene expression in various cells including macrophages. In this study, we investigated the suppressive mechanisms of TGF-beta1 on IFN-gamma-induced iNOS gene expression using the murine macrophage-like cell line RAW 264.7. TGF-beta1 decreased iNOS protein amount through enhanced degradation, although TGF-beta1 did not affect IFN-gamma-induced iNOS mRNA level or stability. In addition, the enhancement of iNOS protein degradation by TGF-beta1 treatment was almost completely blocked by MG132, a proteasome inhibitor. Furthermore, TGF-beta1 enhanced the trypsin-like activity of proteasomes in the presence of IFN-gamma, although did not enhance the peptidylglutamyl-peptide hydrolyzing and chymotrypsin-like activities of proteasomes. The level of ubiquitinated iNOS protein was not significantly altered by IFN-gamma or IFN-gamma plus TGF-beta1 treatment. Because MG132 inhibited iNOS protein degradation and IFN-gamma plus TGF-beta1 treatment increased the trypsin-like activity of proteasomes, we hypothesized that TGF-beta1 might enhance iNOS protein degradation via the ubiquitin-proteasome pathway in the presence of IFN-gamma. We propose that these mechanisms of TGF-beta1 in the posttranslational regulation of iNOS gene expression may contribute to suppression of excess nitric oxide during inflammatory processes.     

Increase of regulatory T cells in the peripheral blood of dogs with metastatic tumors

It is well known that lymphocytes from patients with advanced-stage cancer have impaired immune responsiveness and that type1 T lymphocyte subsets in tumor bearing hosts are suppressed. Treg have been reported to comprise a subgroup which inhibits T cell mediated immune responses. In the present study, the percentage of Treg, Th1 and Tc1 in the peripheral blood of tumor bearing dogs with or without metastases was evaluated. The percentages of Th1 and Tc1 in dogs with metastatic tumor were significantly less, and that of Treg was significantly greater, than those of dogs without metastatic tumor. The percentage of Treg showed an inverse correlation with that of Th1 and Tc1 in tumor bearing dogs. It was concluded that an increase in Treg in the peripheral blood of dogs with metastatic tumor may induce suppression of tumor surveillance by the Type1 immune response and lead to metastasis of tumor[0][0].[0]     

Immunological effects of recombinant feline interferon-omega (KT-80) administration in the dog

The immunological effects of recombinant feline interferon-omega (rFeIFN-omega ; KT-80, Toray) were examined on administration to healthy dogs. The activities of whole blood cells, macrophages, and natural killer cells were enhanced. Moreover, the whole blood activity was examined when KT-80 was administered to dogs which had been diagnosed as having natural canine parvovirus (CPV) infection. Only some cases in which the activity increased until 3 hr post-administration survived. These results suggest that rFeIFN-omega (KT-80) treatment enhanced the cellular immunity of normal dogs, and could exert significant therapeutic effects on only natural CPV infected dogs with induced continuous immunoenhancement.     

Effects of in vitro culture of mouse fetal gonads on subsequent ovarian development in vivo and oocyte maturation in vitro

Under organ culture, female fetal gonads in mice cannot develop beyond the preantral follicle stage unless the follicles are individually isolated and cultured again. In this study, we investigated the effect of in vitro culture of female fetal gonads before transplantation on subsequent in vivo development. The gonads derived from female fetuses 12.5 days postcoitum were organ-cultured for 0, 7 and 14 days, and then were grafted underneath the kidney capsules of severe combined immunodeficient mice and recovered at 21, 14 and 7 days post-transplantation, respectively. The histological analysis of the grafts showed that the in vitro culture of the fetal gonads restricted follicular development to the antral follicle stage post-transplantation. In the grafts cultured for 14 days, particularly, no antral follicle was observed. However, the oocytes in these follicles had grown to around 65 µm in diameter and had competence to resume meiosis in vitro . When the fetal gonads were grafted after culture for 7 and 14 days, 13.0% and 6.8% of the oocytes progressed to the metaphase II stage, respectively. These data showed significant differences ( P  < 0.05) in comparison with the control group (25.3%). Our results indicate that the in vitro culture of female fetal gonads before transplantation affects the subsequent in vivo development of both follicular cells and oocytes, and in vitro oocyte maturation. However, this effect seems to be more severe in terms of follicular development when compared with oocyte growth and maturation.     

Ebp2p, the yeast homolog of Epstein-Barr virus nuclear antigen 1-binding protein 2, interacts with factors of both the 60 S and the 40 s ribosomal subunit assembly

Ebp2p, the yeast homolog of human Epstein-Barr virus nuclear antigen 1-binding protein 2, is essential for biogenesis of the 60 S ribosomal subunit. Two-hybrid screening exhibited that, in addition to factors necessary for assembly of the 60 S subunit, Ebp2p interacts with Rps16p, ribosomal protein S16, and the 40 S ribosomal subunit assembly factor, Utp11p, as well as Yil019w, the function of which was previously uncharacterized. Depletion of Yil019w resulted in reduction in levels of both of 18 S rRNA and 40 S ribosomal subunit without affecting levels of 25 S rRNA and 60 S ribosomal subunits. 35 S pre-rRNA and aberrant 23 S RNA accumulated, indicating that pre-rRNA processing at sites A(0)-A(2) is inhibited when Yil019w is depleted. Each combination from Yil019w, Utp11p, and Rps16p showed two-hybrid interaction.     

Integration of relational and hierarchical network information for protein function prediction

Background  

In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Most existing technologies pursue this task as a classification problem, on a term-by-term basis, for each term in a database, such as the Gene Ontology (GO) database, a popular rigorous vocabulary for biological functions. However, ontology structures are essentially hierarchies, with certain top to bottom annotation rules which protein function predictions should in principle follow. Currently, the most common approach to imposing these hierarchical constraints on network-based classifiers is through the use of transitive closure to predictions.     

Gene Cloning of Dihydroxyacetone Reductase from a Methylotrophic Yeast,Hansenula ofunaensis,and its Expression in Escherichia coli HB101 for Production of Optically Active 2‐Pentanol

Optically active alcohols are important building blocks as versatile chiral synthons for asymmetric syntheses of pharmaceuticals and agrochemicals. The aim of this paper is to efficiently prepare chiral 2‐pentanol by means of microorganisms. The gene of dihydroxyacetone reductase (EC 1.1.1.6) from a methylotrophic yeast, Hansenula ofunaensis, was cloned and chiral 2‐pentanol was produced by the recombinant Escherichia coli harboring the gene. The gene encoding the enzyme was cloned from an H. ofunaensis genomic library. In the deduced amino acid sequence of 364 residues, the NAD(H) binding motif and the cysteine residues that correspond to the cysteine ligands in the zinc atom were conserved, as they are in alcohol dehydrogenases from other origins. Dihydroxyacetone reductase was similar to alcohol dehydrogenases of prokaryotes. For the production of chiral compounds, an E. coli HB101 strain was transformed. The H. ofunaensis gene product, dihydroxyacetone reductase, catalyzed the NAD⁺‐dependent oxidation of 2‐pentanol to 2‐pentanone as well as the corresponding reverse reactions, showing specificity towards the secondary alcohol in (R)‐configuration. From 100 mM 2‐pentanone, (R)‐2‐pentanol (98 mM, > 99.9 % enantiometric excess, e.e.) was obtained in a 30‐min reaction with resting cells of the E. coli HB101 strain harboring the expression plasmid, pSG‐HOD1, which possesses the genes of both dihydroxyacetone reductase and glucose dehydrogenase as an NADH reproducing system. The stereospecificity changed during the reduction, depending on the pH. E. coli HB101 was also transformed by the expression plasmid, pSE‐HOD4, in which the gene of glucose dehydrogenase was removed from pSG‐HOD1, and designated as E. coli HB101 (pSE‐HOD4). E. coli HB101 (pSE‐HOD4) oxidized only (R)‐2‐pentanol in 100 mM of the racemate (R:S = 52:48), and the reaction medium was enriched with (S)‐2‐pentanol (48 mM, 98 % e.e.) after 30 min of incubation. The reaction was sufficiently promoted without the other additives. E. coli transformants expressing the gene of this enzyme could be particularly advantageous to the production of optically active 2‐pentanol.