Identification and clustering of orthologous genes plays an important role in developing evolutionary models such as validating convergent and divergent phylogeny and predicting functional proteins in newly sequenced species of unverified nucleotide protein mappings. Here, we introduce an application of subspace clustering as applied to orthologous gene sequences and discuss the initial results. The working hypothesis is based upon the concept that genetic changes between nucleotide sequences coding for proteins among selected species and groups may lie within a union of subspaces for clusters of the orthologous groups. Estimates for the subspace dimensions were computed for a small population sample. A series of experiments was performed to cluster randomly selected sequences. The experimental design allows for both false positives and false negatives, and estimates for the statistical significance are provided. The clustering results are consistent with the main hypothesis. A simple random mutation binary tree model is used to simulate speciation events that show the interdependence of the subspace rank versus time and mutation rates. The simple mutation model is found to be largely consistent with the observed subspace clustering singular value results. Our study indicates that the subspace clustering method may be applied in orthology analysis.

Guinea fowl (Numidia meleagris) production as an alternative source of meat and poultry has shown potential for economic viability. However, there has been little progress in characterizing the transcriptome of the guinea fowl. In this study RNA-sequencing and de novo transcriptome assembly of several Guinea fowl tissues (pancreas, hypothalamus, liver, bone marrow and bursa) which play key roles in regulating feed intake, satiety, and immune function was performed using Illumina's Hi-Seq 2000.

Is there a trade-off between children ever born (CEB) and post-reproductive lifespan in humans? Here, we report a comprehensive analysis of reproductive trade-offs in the Framingham Heart Study (FHS) dataset using phenotypic and genotypic correlations and a genome-wide association study (GWAS) to look for single-nucleotide polymorphisms (SNPs) that are related to the association between CEB and lifespan.

Mitochondrial transcription factor A (TFAM), the first well-characterized transcription factor from vertebrate mitochondria, is closely related to mitochondrial DNA (mtDNA) maintenance and repair. Recent evidence has shown that the ratio of mtDNA to nuclearDNA (nDNA) is increased in both human cells and murine tissues after ionizing radiation (IR). However, the underlying mechanism has not as yet been clearly identified. In the present study, we demonstrated that in human lung adenocarcinoma A549 cells, expression of TFAM was upregulated, together with the increase of the relative mtDNA copy number and cytochrome c oxidase (COX) activity after α-particle irradiation. Furthermore, short hairpin RNA (shRNA)-mediated TFAM knockdown inhibited the enhancement of the relative mtDNA copy number and COX activity caused by α-particles. Taken together, our data suggested that TFAM plays a crucial role in regulating mtDNA amplification and mitochondrial biogenesis under IR conditions.

Exposure to crystalline silica is suggested to increase the risk for a variety of lung diseases, including fibrosis and lung cancer. However, epidemiological evidences for the exposure-risk relationship are ambiguous and conflicting, and experimental study from a reliable animal model to explore the relationship is lacking. We reasoned that a mouse model that is sensitive to both lung injury and tumorigenesis would be appropriate to evaluate the exposure-risk relationship. Previously, we showed that, Gprc5a-/- mice are susceptible to both lung tumorigenesis and endotoxin-induced acute lung injury. In this study, we investigated the biological consequences in Gprc5a-/- mouse model following silica exposure. Intra-tracheal administration of fine silica particles in Gprc5a-/- mice resulted in more severe lung injury and pulmonary inflammation than in wild-type mice. Moreover, an enhanced fibrogenic response, including EMT-like characteristics, was induced in the lungs of Gprc5a-/- mice compared to those from wild-type ones. Importantly, increased hyperplasia or neoplasia coincided with silica-induced tissue injury and fibrogenic response in lungs from Gprc5a-/- mice. Consistently, expression of MMP9, TGFβ1 and EGFR was significantly increased in lungs from silica-treated Gprc5a-/- mice compared to those untreated or wild-type ones. These results suggest that, the process of tissue repair coincides with tissue damages; whereas persistent tissue damages leads to abnormal repair or neoplasia. Thus, silica-induced pulmonary inflammation and injury contribute to increased neoplasia development in lungs from Gprc5a-/- mouse model.

We announce the draft genome sequence for Chromobacterium violaceum strain CV017, used as a model and tool to understand acyl-homoserine lactone-dependent quorum sensing. The assembly consists of 4,774,638-bp contained in 211 scaffolds.

Heavy metal pollution in Antarctic is serious by anthropogenic emissions and atmospheric transport. To dissect the heavy metal adaptation mechanisms of sea-ice organisms, a basidiomycetous yeast strain AN5 was isolated and its cellular changes were analyzed. Morphological, physiological, and biochemical characterization indicated that this yeast strain belonged to Rhodotorula mucilaginosa AN5. Heavy metal resistance pattern of Cd > Pb = Mn > Cu > Cr > Hg was observed. Scanning electron microscopic (SEM) results exhibited altered cell surface morphology under the influence of copper metal compared to that with control. The determination of physiological and biochemical changes manifested that progressive copper treatment significantly increased antioxidative reagents content and enzymes activity in the red yeast, which quench the active oxygen species to maintain the intercellular balance of redox state and ensure the cellular fission and growth. Comparative proteomic analysis revealed that, under 2 mM copper stress, 95 protein spots were tested reproducible changes of at least 10-fold in cells. Among 95 protein spots, 43 were elevated and 52 were decreased synthesis. After MALDI TOF MS/MS analysis, 51 differentially expressed proteins were identified successfully and classified into six functional groups, including carbohydrate and energy metabolism, nucleotide and protein metabolism, protein folding, antioxidant system, signaling, and unknown function proteins. Function analysis indicated that carbohydrate and energy metabolism-, nucleotide and protein metabolism-, and protein folding-related proteins played central role to the heavy metal resistance of Antarctic yeast. Generally, the results revealed that the yeast has a great capability to cope with heavy metal stress and activate the physiological and protein mechanisms, which allow more efficient recovery after copper stress. Our studies increase understanding of the molecular resistance mechanism of polar yeast to heavy metal, which will be benefitted for the sea-ice isolates to be a potential candidate for bioremediation of metal-contaminated environments.

Hepatocellular carcinoma (HCC), one of the most common aggressive tumors worldwide has a relatively high mortality rate among malignant tumors. MicroRNAs (miRNAs), acting as tumor suppressors, are involved in the regulation of invasion, metastasis, and angiogenesis of tumor cells. However, a potential role for miR-203a in HCC has not been described yet. In this study, we show that miR-203a markedly suppresses HCC cell migration, invasion, and angiogenesis. In addition, the transcription factor HOXD3 appears to be a direct target of miR-203a. HOXD3 knockdown substantially decreased HCC cell migration, invasion, and angiogenesis, effects similar to those seen for miR-203a expression. Rescuing the function of HOXD3 attenuated the effect of miR-203a overexpression in HCC cells. Furthermore, HOXD3 can directly target the promoter region of VEGFR and increase VEGFR expression. Taken together, our findings indicate that miR-203a inhibits HCC cell invasion, metastasis, and angiogenesis by negatively targeting HOXD3 and suppressing cell signaling through the VEGFR pathway, suggesting that miR-203a might represent a potential therapeutic target for HCC intervention.

Interleukin-22 (IL-22) is a recently identified regulator of inflammation, but little is known about its role in liver transplantation. Therefore, in this study, we explored the roles and the underlying mechanisms of IL-22 in acute allograft rejection by using a rat allogeneic liver transplantation model. Results showed that allograft liver transplantation led to damage of the parent liver and to significantly increased IL-22 expression in the allograft liver and plasma of the recipient rats compared with the rats who received isografts. Moreover, the significantly increased IL-22 expression was accompanied by markedly increased level of phospho-STAT3 in the allogeneic liver tissues after transplantation. Of note, neutralization of the IL-22 protein in recipient rats significantly worsened the function of the allograft liver at 1 day post-transplantation (ischemia-reperfusion injury, IRI) but improved the function at 7 days post-transplantation (acute rejection, AR). At IRI stage, IL-22 protected liver function through the increase of anti-apoptosis and pro-regeneration cytokines. However, IL-22 led to the increase of pro-inflammation factors at AR stage, accompanied by the marked increase of the Th17 and the marked decrease of Treg cells in allograft recipient rats through modulating the expression of chemokines for different cell types, which however were reversed by in vivo IL-22 neutralization. Results indicate the dual roles of IL-22 and suggest the differential potential clinical application of IL-22 at different stage of allograft liver transplantation.

Lung cancer is one of the deadliest malignant tumors with limited treatment options. Although targeted therapy, using tyrosine-kinase inhibitors such as erlotinib (Erlo), has shown therapeutic benefit, only 15 % patients with mutated epidermal growth factor receptor (EGFR) in lung cancer cells are sensitive. Therefore, additional therapeutic strategy should be developed. In this study, we found that metformin (Met), which is widely used for the treatment of type 2 diabetes (T2D), sensitized lung cancer cells bearing wild-type EGFR to Erlo treatment by enriching cancer cells expressing higher levels of EGFR with persistent phosphorylation. As a consequence, combination of Met and Erlo more efficiently inhibited the growth of lung cancer cells both in vitro and in mice with xenografted tumors. Our results suggest a novel approach to treating lung cancer cases which are originally resistant to Erlo.

Nicotinamide adenine dinucleotide (NAD) levels decrease with aging as a result of aging-associated CD38 upregulation. Here, we established a cell model with decreased cellular NAD levels by overexpressing CD38 or treating cells with FK866, an inhibitor of nicotinamide phosphoribosyltransferase. We revealed that decreased NAD triggered reactive oxygen species (ROS)-mediated degradation of 15-hydroxyprostaglandin dehydrogenase (15-PGDH), which drove cells to undergo epithelial-mesenchymal transition (EMT). Moreover, we showed that oxidation of the Cys44 residue to sulfonic acid in 15-PGDH led to its degradation via non-canonical ubiquitination-proteasome and autophagy pathways. Mutation of Cys44 to alanine abolished ROS-induced 15-PGDH degradation. We demonstrated that 15-PGDH silencing promoted EMT, whereas supplementation with NAD precursors increased NAD and 15-PGDH stability, and reversed the EMT process. Taken together, these results suggest that declining NAD levels contribute to age-dependent increases in cancer incidence, and repletion of NAD precursors is beneficial for increasing 15-PGDH expression.

Harvest index (HI) in rice is defined as the ratio of grain yield (GY) to biomass (BM). Although it has been demonstrated that HI is significantly related to yield and is considered as one of the most important traits in high-yielding rice breeding, HI-based high-yielding rice breeding is difficult due to its polygenic nature and insufficient knowledge on the genetic basis of HI. Therefore, searching for rice varieties with high HI and mapping genes associated with high HI can facilitate marker-assisted breeding for high HI in rice.

Staphylococcus epidermidis is one of the most important opportunistic pathogens in nosocomial infections. The main pathogenicity associated with S. epidermidis involves the formation of biofilms on implanted medical devices, biofilms dramatically decrease the efficacy of conventional antibiotics and the host immune system. This emphasizes the urgent need for designing novel anti-staphylococcal biofilm agents. Based on the findings that compound 5, targeting the histidine kinase domain of S. epidermidis YycG, possessed bactericidal activity against staphylococci, 39 derivatives of compound 5 with intact thiazolopyrimidinone core structures were newly designed, 7 derivatives were further screened to explore their anti-bacterial and anti-biofilm activities. The seven derivatives strongly inhibited the growth of S. epidermidis and Staphylococcus aureus in the minimal inhibitory concentration range of 1.56-6.25 μM. All the derivatives reduced the proportion of viable cells in mature biofilms. They all displayed low cytotoxicity on mammalian cells and were not hemolytic to human erythrocytes. The biofilm inhibition activities of four derivatives (H5-32, H5-33, H5-34, and H5-35) were further investigated under shearing forces, they all led to significant decreases in the biofilm formation of S. epidermidis. These results were suggestive that the seven derivatives of compound 5 have the potential to be developed into agents for eradicating biofilm-associated infections.

Identification and cloning of cold-tolerant genes that can stably express under different cold environments are crucial for molecular rice breeding for cold tolerance. In the previous study, we identified a cold-tolerant QTL at the seedling stage, qCTS-9 which could be detected under different cold environments using a recombinant inbred line (RIL) population derived from a cold-tolerant variety Lijiangxintuanheigu (LTH) and a cold-sensitive variety Shanhuangzhan 2 (SHZ-2). In this study, eight candidate genes within the qCTS-9 interval were identified through integrated analysis of QTL mapping with genomewide differential expression profiling of LTH. The qRT-PCR assay showed that only Os09g0410300 exhibited different expression patterns between LTH and SHZ-2 during cold stress, and significantly positive correlation was found between cold induction of Os09g0410300 and seedling cold tolerance in the RI lines. Five SNPs and one InDel in the promoters of Os09g0410300 were detected between LTH and SHZ-2, and the InDel marker ID410300 designed based on the insertion-deletion polymorphism in the promoter was significantly associated with seedling cold tolerance in RIL population. Further, Os09g0410300 over-expression plants exhibited enhanced cold tolerance at the seedling stage compared with the wild-type plants. Thus, our results suggest that Os09g0410300 is the functional gene underlying qCTS-9. To our knowledge, it is a novel gene contributed to enhance cold tolerance at the seedling stage in rice. Identification of the functional gene underlying qCTS-9 and development of the gene-specific marker will facilitate molecular breeding for cold tolerance at the seedling stage in rice through transgenic approach and marker-assisted selection (MAS).

The occurrence of adventitious roots is necessary for the survival of cuttings. In this study, comparative transcriptome analysis between two ramie (Boehmeria nivea L.) varieties with different adventitious root (AR) patterns was performed by mRNA-Seq before rooting (control, CK) and 10 days water-induced adventitious rooting (treatment, T) to reveal the regulatory mechanism of rooting. Characterization of the two ramie cultivars, Zhongzhu No 2 (Z2) and Huazhu No 4 (H4), indicated that Z2 had a high adventitious rooting rate but H4 had a low rooting rate. Twelve cDNA libraries of the two varieties were constructed, and a total of 26,723 genes were expressed. In the non-water culture condition, the number of the distinctive genes in H4 was 2.7 times of that in Z2, while in the water culture condition, the number of the distinctive genes in Z2 was nearly 2 times of that in H4. A total of 4411 and 5195 differentially expressed genes (DEGs) were identified in the comparison of H4CK vs. H4T and Z2CK vs. Z2T, respectively. After the water culture, more DEGs were upregulated in Z2, but more DEGs were downregulated in H4. Gene ontology (GO) functional analysis of the DEGs indicated that the polysaccharide metabolic process, carbohydrate metabolic process, cellular carbohydrate metabolic process, cell wall macromolecule metabolic process, and photosystem GO terms were distinctively significantly enriched in H4. Simultaneously, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis, photosynthesis antenna proteins, and starch and sucrose metabolism pathways were distinctively significantly enriched in H4. Moreover, KEGG analysis showed that jasmonic acid (JA) could interact with ethylene to regulate the occurrence and number of AR in Z2. This study reveals the transcriptomic divergence of two ramie varieties with high and low adventitious rooting rates, and provides insights into the molecular regulatory mechanism of AR formation in ramie.

BACKGROUND Novel hybrid surgical techniques that incorporate anterior cervical discectomy and fusion with total disc replacement are widely used. Based on the number of implanted discs, 3-level hybrid surgery can be classified as single fusion combined with double replacement and single replacement combined with double fusion. Few studies to date have directly compared these hybrid techniques. The present study compared the clinical and radiological outcomes of these methods and assessed their characteristics and benefits. MATERIAL AND METHODS Clinical and radiological outcomes were retrospectively evaluated in 64 consecutive patients who underwent 3-level hybrid surgery by single fusion combined with double replacement or single replacement combined with double fusion. RESULTS Significant differences between the 2 groups were observed in postoperative range of motion of C2-C7. C2-C7 cervical lordosis assessed preoperatively and at final follow-up differed significantly in patients who underwent single replacement combined with double fusion. This group showed a higher incidence of heterotopic ossification than patients who underwent double replacement combined with single fusion. CONCLUSIONS Both types of hybrid surgery are safe and effective in treating 3-level cervical degenerative disc diseases. Single replacement combined with double fusion showed greater accuracy in correcting cervical lordosis, but was associated with a higher incidence of heterotopic ossification. In contrast, single fusion combined with double replacement was superior in maintaining cervical range of motion.

Water and N are the most important factors affecting ramie (Boehmeria nivea (L.) Gaudich) growth. In this study, de novo transcriptome assembly and Tandem Mass Tags (TMT) based quantitative proteome analysis of ramie under nitrogen and water co-limitation conditions were performed, and exposed to treatments, including drought and N-deficit (WdNd), proper water but N-deficit (WNd), proper N but drought (WdN), and proper N and water (CK), respectively. A total of 64,848 unigenes (41.92% of total unigenes) were annotated in at least one database, including NCBI non-redundant protein sequences (Nr), Swiss-Prot, Protein family (Pfam), Gene Ontology (GO) and KEGG Orthology (KO), and 4268 protein groups were identified. Most significant changes in transcript levels happened under water-limited conditions, but most significant changes in protein level happened under water-limited conditions only with proper N. Poor correlation between differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) was observed in ramie responding to the treatments. DEG/DEP regulation patterns related to major metabolic processes responding to water and N deficiency were analyzed, including photosynthesis, ethylene responding, glycolysis, and nitrogen metabolism. Moreover, 41 DEGs and 61 DEPs involved in regulating adaptation of ramie under water and N stresses were provided in the study, including DEGs/DEPs related to UDP-glucuronosyhransferase (UGT), ATP synthase, and carbonate dehydratase. The strong dependency of N-response of ramie on water conditions at the gene and protein levels was highlighted. Advices for simultaneously improving water and N efficiency in ramie were also provided, especially in breeding N efficient varieties with drought resistance. This study provided extensive new information on the transcriptome, proteome, their correlation, and diversification in ramie responding to water and N co-limitation.

Myocardial ischaemia reperfusion injury (MIRI) is a difficult problem in clinical practice, and it may involve various microRNAs. This study investigated the role that endogenous microRNA-146a plays in myocardial ischaemia reperfusion and explored the possible target genes.

Cell division cycle-associated 2 (CDCA2) plays an important role in regulating chromosome structure during mitosis. It is highly expressed in oral squamous cell carcinoma, neuroblastoma and lung adenocarcinoma, and its upregulation is positively associated with tumor progression. However, the expression, biological function and underlying mechanisms of the role of CDCA2 in clear cell renal cell carcinoma (ccRCC) remain poorly understood. In the present study, CDCA2 was demonstrated to be upregulated in ccRCC tissues compared with normal kidney tissue, where higher expression was generally associated with the degree of malignancy. Small interfering RNA-mediated knockdown of CDCA2 expression inhibited the viability and proliferation of 786-O and CAKI-1 cells, as measured by an MTT assay, colony formation assay and flow cytometry. Furthermore, western blot analysis suggested that CDCA2 regulates cell proliferation through the cell cycle-associated proteins cyclin D1 and cyclin dependent kinase 4, and the apoptotic protein Bcl-2. In conclusion, the present study indicated that CDCA2 may be an important factor in ccRCC progression and could be a potential therapeutic target in this disease.

Cu-ZSM-5 and Ce-doped Cu-Ce-ZSM-5 samples were prepared by liquid-phase ion exchange method. The two catalysts were subjected to hydrothermal aging treatment in the simulated flue gas of a coal-fired power station at an ageing temperature of 650-850 °C. The denitration experiment found that the activity of the aged Cu-ZSM-5 was 19.6% to 41% lower than that of the fresh Cu-ZSM-5 at the optimal decomposition temperature of NO at 550 °C, while the aged Cu-Ce-ZSM-5 had only a 14.8% to 31.5% reduction in activity than the fresh Cu-Ce-ZSM-5. The samples were characterized by XRD, BET, H2-TPR, XPS, NO-TPD, etc. The results showed that hydrothermal aging treatment leads to the dealumination of the ZSM-5 framework and reduces the specific surface area and pore volume of the micropore in the sample. It also exacerbates the isolated Cu2+, and the active center {Cu2+-O2--Cu2+}2+ dimers migrate towards the sample surface and form inactive CuO. Doping with Ce can promote the dispersion of Cu(OH)+, which was the precursor of {Cu2+-O2--Cu2+}2+. Ce3+ can preferentially occupy the less active bridged hydroxyl exchange sites, so that copper ions occupy the more active aluminum hydroxyl sites, thereby inhibiting the migration of active centers.