Recent progresses in the application of machine learning approach for predicting protein functional class independent of sequence similarity

Protein sequence contains clues to its function. Functional prediction from sequence presents a challenge particularly for proteins that have low or no sequence similarity to proteins of known function. Recently, machine learning methods have been explored for predicting functional class of proteins from sequence-derived properties independent of sequence similarity, which showed promising potential for low- and non-homologous proteins. These methods can thus be explored as potential tools to complement alignment- and clustering-based methods for predicting protein function. This article reviews the strategies, current progresses, and underlying difficulties in using machine learning methods for predicting the functional class of proteins. The relevant software and web-servers are described. The reported prediction performances in the application of these methods are also presented, which need to be interpreted with caution as they are dependent on such factors as datasets used and choice of parameters.     

Overexpression of miR-26b-5p regulates the cell cycle by targeting CCND2 in GC-2 cells under exposure to extremely low frequency electromagnetic fields

The increasing prevalence of extremely low frequency electromagnetic fields (ELF-EMFs) exposure has raised considerable public concern regarding the potential hazardous effects of ELF-EMFs on male reproductive function. Increasing evidence indicates that miRNAs are necessary for spermatogenesis and male fertility. However, the regulation of miRNA expression and the roles of miRNAs in response to ELF-EMFs remain unclear. In our study, mouse spermatocyte-derived GC-2 cells were intermittently exposed to a 50 Hz ELF-EMF for 72 h (5 min on/10 min off) at magnetic field intensities of 1 mT, 2 mT and 3 mT. MiR-26b-5p was differentially expressed in response to different magnetic field intensities of ELF-EMFs. The host gene CTDSP1 showed an unmethylation status in GC-2 cells at different magnetic field intensities of ELF-EMF exposure. MiR-26b-5p had no significant, obvious influence on the cell viability, apoptosis or cell cycle of GC-2 cells. However, the overexpression of miR-26b-5p significantly decreased the percentage of G0/G1 phase cells and slightly increased the percentage of S phase cells compared to the sham group that was exposed to a 50 Hz ELF-EMF. Computational algorithms identified Cyclin D2 (CCND2) as a direct target of miR-26b-5p. MiR-26b-5p and a 50 Hz ELF-EMF altered the expression of CCND2 at both the mRNA and protein levels. Overexpressed miR-26b-5p in GC-2 cells can change the mRNA expression of CCND2 following 50 Hz ELF-EMF at 3 mT. These findings demonstrate that miR-26b-5p could serve as a potential biomarker following 50 Hz ELF-EMF exposure, and miR-26b-5p-CCND2-mediated cell cycle regulation might play a pivotal role in the biological effects of ELF-EMFs.     

Plasmon-Enhanced Optical Transmission at Multiple Wavelengths Through an Asymmetric Corrugated Thin Silver Film

Micro- and nanometallic structures that exhibit extraordinary optical transmission (EOT) have attracted much attention for their potential applications in photonic devices. However, most existing reports have only discussed EOT at one specific wavelength, which limits its use in multi-wavelength applications. Here, we experimentally demonstrate EOT at multiple wavelengths through an asymmetric corrugated thin silver film due to simultaneous excitation of multiple plasmonic resonances at both interfaces. A unique method that applies single-pulse nanosecond laser interference lithography is introduced to produce the silver grating, which shows high quality over large area. At oblique incidence, each EOT peak is observed to split into two peaks oppositely shifted towards higher and lower frequencies. At some specific angles of incidence, overlap of these shifted peaks gives rise to distorted transmission spectra. Our method may find applications involving multiple wavelengths such as multi-wavelength bandpass filters, anti-Stokes Raman scattering spectroscopy, enhanced four-wave mixing, and so on.     

Purification of the Specific Plasma Membrane Proteins from the Surface of Sperm Cells of Zea mays

Pollen samples of 6 varieties of Zea mays L. were used to isolate the viable sperm cells. After being probed with N-hydroxysuccinimido-biotin (NHS-biotin), the sperm cell plasma membrane proteins were compared with each other using the method of Western blotting. Results showed that there was no significant difference among varieties. The molecular weights of probed plasma membrane proteins were concentrated on 91,60,43,30 and 17 kD. Immunochemical method was adopted for further purification of sperm plasma membrane protein preparation which was some- what contaminated with cell organelles. After the cell organelles were isolated from etiolated seedlings of Zea mays by sucrose density gradient super centrifugation, the crude membrane proteins of organelles, endoplasm reticulum, mitochondria, Golgi body and plasmolemma were respectively used as antigen to immunize Guinea pig. The antibody was obtained from respective antiserum, then further used to produce immuno-affinity absorbent. After the solution of membrane proteins of sperm cells passed through the column, some proteins probed whth NHS-biotin were identified. Two major proteins probed with NHS-biotin were considered to be sperm cell specific. The size of these proteins in SDS-PAGE was about 65 kD, 22 kD, respectively.     

Apoptotic role of TGF-β mediated by Smad4 mitochondria translocation and cytochrome c oxidase subunit II interaction

Smad4, originally isolated from the human chromosome 18q21, is a key factor in transducing the signals of the TGF-β superfamily of growth hormones and plays a pivotal role in mediating antimitogenic and proapoptotic effects of TGF-β, but the mechanisms by which Smad4 induces apoptosis are elusive. Here we report that Smad4 directly translocates to the mitochondria of apoptotic cells. Smad4 gene silencing by siRNA inhibits TGF-β-induced apoptosis in Hep3B cells and UV-induced apoptosis in PANC-1 cells. Cell fractionation assays demonstrated that a fraction of Smad4 translocates to mitochondria after long time TGF-β treatment or UV exposure, during which the cells were under apoptosis. Smad4 mitochondria translocation during apoptosis was also confirmed by fluorescence observation of Smad4 colocalization with MitoTracker Red. We searched for mitochondria proteins that have physical interactions with Smad4 using yeast two-hybrid screening approach. DNA sequence analysis identified 34 positive clones, five of which encoded subunits in mitochondria complex IV, i.e., one clone encoded cytochrome c oxidase COXII, three clones encoded COXIII and one clone encoded COXVb. Strong interaction between Smad4 with COXII, an important apoptosis regulator, was verified in yeast by β-gal activity assays and in mammalian cells by immunoprecipitation assays. Further, mitochondrial portion of cells was isolated and the interaction between COXII and Smad4 in mitochondria upon TGF-β treatment or UV exposure was confirmed. Importantly, targeting Smad4 to mitochondria using import leader fusions enhanced TGF-β-induced apoptosis. Collectively, the results suggest that Smad4 promote apoptosis of the cells through its mitochondrial translocation and association with mitochondria protein COXII.     

天胡荽属三种药用植物果实的形态组织结构特征

对天胡荽属3种药用植物果实进行了形态组织学方面的研究,发现三者中果皮内侧石细胞的存在情况则随品种的不同而不同,结果可作为这三种植物的品种鉴别特征,同时为伞形科植物学研究提供新的内容.     

Ghrelin inhibits insulin resistance induced by glucotoxicity and lipotoxicity in cardiomyocyte

Ghrelin has wide effects on cardiovascular and endocrine system. The aims of this study are to investigate the direct damage effect of high glucose and high palmitate on cardiomyocyte, and to study the effect of ghrelin on insulin resistance induced by glucotoxicity/lipotoxicity in cardiomyocyte and the possible mechanism underlying the cardioprotective activities of ghrelin. The changes of [³H]-2-deoxy-d-glucose (³H-G) intake rates were detected by isotope tracer method and the gene expressions in insulin signal transduction pathway were detected by real-time PCR and Western blot assay. The ³H-G intake rate significantly reduced in high glucose (25 mmol/l) or high palmitate (0.5 mmol/l) treated primary rat ventricular myocytes. After the treatment of ghrelin (10⁻⁷ mol/l), the ³H-G intake rate recovered to the normal level. In addition, the phosphorylation of AKT occurred in 10 min and was the highest in 30 min after the stimulation with ghrelin, which can be blocked by phosphoinositide 3-kinase (PI3K) inhibitor, LY2940002. Ghrelin also increased the mRNA levels of glucose transporter 4 (GLUT4), peroxisome proliferators (PPARr) and AMP activated protein kinase (AMPK) genes in insulin signal transduction pathway. These results indicate that the direct damage of high glucose and high palmitate on cardiomyocyte might be through insulin resistance (IR). Ghrelin can inhibit gluco/lipotoxicity induced insulin resistance by PI3K/AKT pathway. This may provide a clue for therapy for myocardial disease in diabetes mellitus.