Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces

Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with the physicochemical complementarity features based on the non-covalent interaction data derived from protein interiors.     

Glycolate oxidase isozymes are coordinately controlled by GLO1 and GLO4 in rice

Glycolate oxidase (GLO) is a key enzyme in photorespiratory metabolism. Four putative GLO genes were identified in the rice genome, but how each gene member contributes to GLO activities, particularly to its isozyme profile, is not well understood. In this study, we analyzed how each gene plays a role in isozyme formation and enzymatic activities in both yeast cells and rice tissues. Five GLO isozymes were detected in rice leaves. GLO1 and GLO4 are predominately expressed in rice leaves, while GLO3 and GLO5 are mainly expressed in the root. Enzymatic assays showed that all yeast-expressed GLO members except GLO5 have enzymatic activities. Further analyses suggested that GLO1, GLO3 and GLO4 interacted with each other, but no interactions were observed for GLO5. GLO1/GLO4 co-expressed in yeast exhibited the same isozyme pattern as that from rice leaves. When either GLO1 or GLO4 was silenced, expressions of both genes were simultaneously suppressed and most of the GLO activities were lost, and consistent with this observation, little GLO isozyme protein was detected in the silenced plants. In contrast, no observable effect was detected when GLO3 was suppressed. Comparative analyses between the GLO isoforms expressed in yeast and the isozymes from rice leaves indicated that two of the five isozymes are homo-oligomers composed of either GLO1 or GLO4, and the other three are hetero-oligomers composed of both GLO1 and GLO4. Our current data suggest that GLO isozymes are coordinately controlled by GLO1 and GLO4 in rice, and the existence of GLO isozymes and GLO molecular and compositional complexities implicate potential novel roles for GLO in plants.     

Role of IKK/NF-κB signaling in extinction of conditioned place aversion memory in rats

The inhibitor κB protein kinase/nuclear factor κB (IKK/NF-κB) signaling pathway is critical for synaptic plasticity. However, the role of IKK/NF-κB in drug withdrawal-associated conditioned place aversion (CPA) memory is unknown. Here, we showed that inhibition of IKK/NF-κB by sulphasalazine (SSZ; 10 mM, i.c.v.) selectively blocked the extinction but not acquisition or expression of morphine-induced CPA in rats. The blockade of CPA extinction induced by SSZ was abolished by sodium butyrate, an inhibitor of histone deacetylase. Thus, the IKK/NF-κB signaling pathway might play a critical role in the extinction of morphine-induced CPA in rats and might be a potential pharmacotherapy target for opiate addiction.     

DNA binding and nucleolytic properties of Cu(ii) complexes of salicylaldehyde semicarbazones

The copper(ii) complexes of two salicylaldehyde semicarbazones, HOC(6)H(4)CH[double bond, length as m-dash]N-NHCONR(2) [H(2)Bnz(2) (R = CH(2)Ph) and H(2)Bu(2) (R = Bu)], were evaluated for their DNA binding and cleavage properties by spectrophotometric DNA titration, ethidium bromide displacement assay and electrophoretic mobility shift assay. Results showed that the Cu(ii) complexes can bind to DNA via a partial intercalation mode with binding constants of 1.1 × 10(4) and 9.5 × 10(3) M(-1) for [Cu(HBnz(2))Cl] and [Cu(HBu(2))Cl], respectively. These complexes also cleave DNA in the presence of ascorbic acid, most likely through hydroxyl radicals that are generated via the reduction of a Cu(ii) to a Cu(i) species. The complexes show similar DNA cleavage activity, which is reflected in the similarity of their frontier molecular orbital energies calculated by density functional theory. These results are discussed in relation to the anticancer properties of the complexes.     

Evidence for the persistence of wild Ginkgo biloba (Ginkgoaceae) populations in the Dalou Mountains, southwestern China

?Premise of the study: The possible persistence of wild Ginkgo biloba populations in China has long been debated but never scientifically confirmed. We test our hypothesis that the extant Ginkgo populations in the Dalou Mountains (SW China) represent fragments of the original natural Ginkgo range and offer a range of pertinent perspectives on the living fossil Ginkgo's history, prehistory, ecology, and place in human culture-all important aspects of this highly valued species. ?Methods: We analyzed the vegetation of the study area, determined the population age structure of Ginkgo, and compared it to existing fossil records. For supporting material, we also examined records of the lack of human presence before the mid-17th century in the area, the local people's beliefs regarding preservation of the forests and existing genetic studies. ?Key results: Current species composition of Ginkgo forests in the Dalou Mountains agrees closely with floristic assemblages from fossil records bearing G. biloba. Current populations are found in habitats similar to those of fossil Ginkgo, which, as today, favored rock crevices. Female to male ratios are 3:2. Estimated ages for many of the trees show that Ginkgo was present in this area prior to human settlement and indigenous peoples of this area are unlikely to have planted Ginkgo because of traditional beliefs. Our results agree with existing genetic studies that show that these mountains were glacial refugia for G. biloba. ?Conclusions: The corroborative evidence confirms the finding that these populations represent fragments of the original natural Ginkgo in the valley and lower mountain slopes of the Dalou Mountains.     

Alterations of protein complexes and pathways in genetic information flow and response to stimulus contribute to Escherichia coli resistance to balofloxacin

Protein-protein interactions are important biological processes and essential for a global understanding of cell functions. To date, little is known about the protein interactions and roles of the protein interacting networks and protein complexes in bacterial resistance to antibiotics. In the present study, we investigated protein complexes in Escherichia coli exposed to an antibiotic balofloxacin (BLFX). One homomeric and eight heteromeric protein complexes involved in BLFX resistance were detected. Potential roles of these complexes that are played in BLFX resistance were characterized and categorized into four functional areas: information streams, monosaccharide metabolism, response to stimulus and amino acid metabolic processes. Protein complexes involved in information streams and response to stimulus played more significant roles in the resistance. These results are consistent with previously published mechanisms on the acquired quinolone-resistance through the GyrA-GyrB complex, and two novel antibiotic-resistant pathways were identified: upregulation of genetic information flow and alteration of the response to a stimulus. The balance of the two pathways will be a viable means of reducing BLFX-resistance.     

Molecular cloning, expression profile, polymorphism and the genetic effects of the dopamine D1 receptor gene on duck reproductive traits

The dopamine D1 receptor (DRD1), a member of the dopamine receptor (DR) gene family, participates in the regulation of reproductive behaviors in birds. In this study, a 1,390 bp fragment covering the complete coding region (CDS) of duck DRD1 gene was obtained. The cDNA (GenBank: JQ346726) contains a 1,353 bp CDS and a 37 bp 3'- UTR including a TGA termination codon (nucleotides 1,354-1,356 bp). The duck DRD1 shares about 76-96 % nucleic acid identity and 82-98 % amino acid identity with their counterparts in other species. A phylogenetic tree based on amino acid sequences displays that duck DRD1 protein is closely related with those of chicken and zebra finch. The quantitative real-time PCR analysis indicates that the DRD1 mRNA is widely expressed in all examined tissues. Five single nucleotide polymorphisms (SNPs) (c.189A > T, c.507C > T, c.681C > T, c.765A > T, c.1044A > G) in the CDS of duck DRD1 gene were indentified, c.681C > T and c.765A > T were genotyped and analyzed in a two generations duck population by using of PCR-RFLP. Association analysis demonstrated that the c.681C > T genotypes were significantly associated with body weight at sexual maturity (when laying their first egg) (P < 0.01), egg production within 360 days (P < 0.05) and 420 days (P < 0.01); the c.765A > T genotypes were significantly associated with egg shape index and egg shell strength (P < 0.05). Those results suggest that the DRD1 gene may be a potential genetic marker to improve some reproductive traits in ducks.     

Medium optimization of α-glucosidase inhibitors production by response surface analysis

[目的]采用响应面法对戈壁三素链霉菌PW409发酵合成α-糖苷酶抑制剂的培养基进行优化.[方法]采用Plackett-Burman法筛选影响α-糖苷酶抑制剂产生的关键因素,用最陡爬坡试验逼近关键因素的最大响应区域,采用Box-Behnken设计以及响应面分析法,得到各因素的最佳浓度,通过液相色谱-串联质谱法(LC-MS/MS)对发酵液中α-糖苷酶抑制剂进行定量分析.[结果]发酵培养基中可溶性淀粉、KNO3和K2HPO4的浓度对α-糖苷酶抑制剂的产量影响较大.优化后的培养基组成为:可溶性淀粉9.01 g/L,KNO311.0 g/L,K2HPO4 0.32 g/L,MgSO4·7H2O 0.50 g/L,FeSO4·7H2O 0.01 g/L,pH 7.5.[结论]在此优化条件下,链霉菌PW409发酵液对麦芽糖苷酶的半数抑制浓度IC50为22 mg/L,抑制活性较优化前提高了近10倍.发酵液中的1-脱氧野尻霉素含量可达7.84 mg/L,较优化前提高了668倍,米格列醇的含量可达0.94 mg/L,较优化前提高了10倍.     

MicroRNA-451 regulates p38 MAPK signaling by targeting of Ywhaz and suppresses the mesangial hypertrophy in early diabetic nephropathy

Diabetic nephropathy (DN) is a major diabetic complication. However, the initiating molecular events triggering DN are unknown. In this study we focused on microRNA-451 (miR-451), which is downregulated during early DN. We found that miR-451 negatively regulated the expression of Ywhaz through Ywhaz 3'UTR and that Ywhaz was required for the miR-451-mediated downregulation of p38 MAPK signalling. Moreover, over-expression of miR-451 inhibits glomerular mesangial cell proliferation in vitro and in vivo. These findings suggest that the growth-inhibitory effect of miR-451 may be explained in part by miR-451-induced suppression of Ywhaz and p38 MAPK signalling, providing evidence for the potential role of miR-451 in early DN.     

Care Needs and Clinical Outcomes of Older People with Dementia: A Population-Based Propensity Score-Matched Cohort Study

Objective

To explore the healthcare resource utilization, psychotropic drug use and mortality of older people with dementia.

Design

A nationwide propensity score-matched cohort study.

Setting

National Health Insurance Research database.

Participants

A total of 32,649 elderly people with dementia and their propensity-score matched controls (n=32,649).

Measurements

Outpatient visits, inpatient care, psychotropic drug use, in-hospital mortality and all-cause mortality at 90 and 365 days.

Results

Compared to the non-dementia group, a higher proportion of patients with dementia used inpatient services (1 year after index date: 20.91% vs. 9.55%), and the dementia group had more outpatient visits (median [standard deviation]: 7.00 [8.87] vs. 3.00 [8.30]). Furthermore, dementia cases with acute admission had the highest psychotropic drug utilization both at baseline and at the post-index dates (difference-in-differences: all <0.001). Dementia was associated with an increased risk of all-cause mortality (90 days, Odds ratio (OR)=1.85 [95%CI 1.67-2.05], p<0.001; 365 days, OR=1.59 [1.50-1.69], p<0.001) and in-hospital mortality (90 days, OR=1.97 [1.71-2.27], p<0.001; 365 days, OR=1.82 [1.61-2.05], p<0.001) compared to matched controls.

Conclusions

When older people with dementia are admitted for acute illnesses, they may increase their use of psychotropic agents and their risk of death, particularly in-hospital mortality.