Search

Ion binding proteins (IBPs) can selectively and non-covalently interact with ions. IBPs in phages also play an important role in biological processes. Therefore, accurate identification of IBPs is necessary for understanding their biological functions and molecular mechanisms that involve binding to ions. Since molecular biology experimental methods are still labor-intensive and cost-ineffective in identifying IBPs, it is helpful to develop computational methods to identify IBPs quickly and efficiently. In this work, a random forest (RF)-based model was constructed to quickly identify IBPs. Based on the protein sequence information and residues’ physicochemical properties, the dipeptide composition combined with the physicochemical correlation between two residues were proposed for the extraction of features. A feature selection technique called analysis of variance (ANOVA) was used to exclude redundant information. By comparing with other classified methods, we demonstrated that our method could identify IBPs accurately. Based on the model, a Python package named IBPred was built with the source code which can be accessed at https://github.com/ShishiYuan/IBPred.

BACKGROUND: With market-oriented economic and health-care reform, public hospitals in China have received unprecedented pressures from governmental regulations, public opinions, and financial demands. To adapt the changing environment and keep pace of modernizing healthcare delivery system, public hospitals in China are expanding clinical services and improving delivery efficiency, while controlling costs. Recent experiences are valuable lessons for guiding future healthcare reform. Here we carefully study three teaching hospitals, to exemplify their experiences during this period. METHODS: We performed a systematic analysis on hospitalization costs, health-care quality and delivery efficiencies from 2006 to 2010 in three teaching hospitals in Beijing, China. The analysis measured temporal changes of inpatient cost per stay (CPS), cost per day (CPD), inpatient mortality rate (IMR), and length of stay (LOS), using a generalized additive model. FINDINGS: There were 651,559 hospitalizations during the period analyzed. Averaged CPS was stable over time, while averaged CPD steadily increased by 41.7% (P

The biocontrol potential of entomopathogenic fungi against arthropod pests depends on not only their virulence to target pests but tolerance to outdoor high temperature and solar UV irradiation. Two Beauveria bassiana superoxide dismutases (SODs), BbSod2 and BbSod3, were characterized as cytosolic and mitochondrial manganese-cored isoenzymes (MnSODs) dominating the total SOD activity of the fungal entomopathogen under normal growth conditions. To probe their effects on the biocontrol potential of B. bassiana, ΔBbSod2, ΔBbSod3, and three hairpin RNA-interfered (RNAi) mutants with the transcripts of both BbSod2 and BbSod3 being suppressed by 91-97% were constructed and assayed for various phenotypic parameters in conjunction with ΔBbSod2/BbSod2, ΔBbSod3/BbSod3 and wild-type (control strains). In normal cultures, the knockout and RNAi mutants showed significant phenotypic alterations, including delayed sporulation, reduced conidial yields, and impaired conidial quality, but little change in colony morphology. Their mycelia or conidia became much more sensitive to menadione or H(2)O(2)-induced oxidative stress but had little change in sensitivity to the hyperosmolarity of NaCl and the high temperature of 45°C. Accompanied with the decreased antioxidative capability, conidial tolerances to UV-A and UV-B irradiations were reduced by 16.8% and 45.4% for ΔBbSod2, 18.7% and 44.7% for ΔBbSod3, and ∼33.7% and ∼63.8% for the RNAi mutants, respectively. Their median lethal times (LT(50)s) against Myzus persicae apterae, which were topically inoculated under a standardized spray, were delayed by 18.8%, 14.5% and 37.1%, respectively. Remarkably, the effects of cytosolic BbSod2 and mitochondrial BbSod3 on the phenotypic parameters important for the fungal bioncontrol potential were additive, well in accordance with the decreased SOD activities and the increased superoxide levels in the knockout and RNAi mutants. Our findings highlight for the first time that the two MnSODs co-contribute to the biocontrol potential of B. bassiana by mediating cellular antioxidative response.

Metarhizium spp. are being used as environmentally friendly alternatives to chemical insecticides, as model systems for studying insect-fungus interactions, and as a resource of genes for biotechnology. We present a comparative analysis of the genome sequences of the broad-spectrum insect pathogen Metarhizium anisopliae and the acridid-specific M. acridum. Whole-genome analyses indicate that the genome structures of these two species are highly syntenic and suggest that the genus Metarhizium evolved from plant endophytes or pathogens. Both M. anisopliae and M. acridum have a strikingly larger proportion of genes encoding secreted proteins than other fungi, while ~30% of these have no functionally characterized homologs, suggesting hitherto unsuspected interactions between fungal pathogens and insects. The analysis of transposase genes provided evidence of repeat-induced point mutations occurring in M. acridum but not in M. anisopliae. With the help of pathogen-host interaction gene database, ~16% of Metarhizium genes were identified that are similar to experimentally verified genes involved in pathogenicity in other fungi, particularly plant pathogens. However, relative to M. acridum, M. anisopliae has evolved with many expanded gene families of proteases, chitinases, cytochrome P450s, polyketide synthases, and nonribosomal peptide synthetases for cuticle-degradation, detoxification, and toxin biosynthesis that may facilitate its ability to adapt to heterogeneous environments. Transcriptional analysis of both fungi during early infection processes provided further insights into the genes and pathways involved in infectivity and specificity. Of particular note, M. acridum transcribed distinct G-protein coupled receptors on cuticles from locusts (the natural hosts) and cockroaches, whereas M. anisopliae transcribed the same receptor on both hosts. This study will facilitate the identification of virulence genes and the development of improved biocontrol strains with customized properties.

Tripartite motif (TRIM)38 is an E3 ubiquitin ligase that was reported to regulate signaling in innate immune and inflammatory responses in certain cell lines. In this study, we show that Trim38 deficiency markedly increased TLR3- and TLR4-mediated induction of type I IFNs and proinflammatory cytokines, such as TNF-α, IL-1β, and IL-6, in immune cells and in vivo. Trim38 deficiency also caused the mice to be more susceptible to death triggered by polyinosinic-polycytidylic acid, LPS, and Salmonella typhimurium. Mechanistically, TRIM38 catalyzed K48-linked polyubiquitination of the TLR3/4 adapter protein TIR domain-containing adapter-inducing IFN-β at K228 and promoted its proteasomal degradation in immune cells. Moreover, Trim38 was highly induced by type I IFNs, which then negatively regulated TNF-α/IL-1β signaling in IFN-β-primed immune cells, but not unprimed immune cells, by mediating degradation of Tab2 in a lysosomal-dependent process. These results suggest that Trim38 negatively regulates TLR3/4-mediated innate immune and inflammatory responses by two sequential and distinct mechanisms. This study increases our understanding of how the innate immune response is initiated during the early phase of infection to defend against microbial invasion and is efficiently terminated during the late phase to prevent excessive and harmful inflammatory responses. [ABSTRACT FROM AUTHOR]

A superoxide dismutase (SOD) was characterized from Beauveria bassiana, a fungal entomopathogen widely applied to insect control. This 209-aa enzyme (BbSod2) showed no more than 71% sequence identity to other fungal Mn-SODs, sharing all conserved residues with the Mn-SOD family and lacking a mitochondrial signal. The SOD activity of purified BbSod2 was significantly elevated by Mn2+, suppressed by Cu2+ and Zn2+ but inhibited by Fe3+. Overexpressing the enzyme in a BbSod2-absent B. bassiana strain enhanced its SOD activity (107.2 ± 6.1 U mg−1 protein) by 4–10-fold in different transformants analyzed. The best BbSod2-transformed strain with the SOD activity of 1,157.9 ± 74.7 U mg−1 was 93% and 61% more tolerant to superoxide-generating menadione in both colony growth (EC50 = 2.41 ± 0.03 versus 1.25 ± 0.01 mM) and conidial germination (EC50 = 0.89 ± 0.06 versus 0.55 ± 0.07 mM), and 23% more tolerant to UV-B irradiation (LD50 = 0.49 ± 0.02 versus 0.39 ± 0.01 J cm−2). Its virulence to Spodoptera litura larvae was enhanced by 26% [LT50 = 4.5 (4.2–4.8) versus 5.7 (5.2–6.4) days]. Our study highlights for the first time that the Mn2+-cofactored, cytosolic BbSod2 contributes significantly to the virulence and stress tolerance of B. bassiana and reveals possible means to improving field persistence and efficacy of a fungal formulation by manipulating the antioxidant enzymes of a candidate strain. [ABSTRACT FROM AUTHOR]

Objective To summarize lessons learned from an outbreak of severe acute respiratory syndrome (SARS) in China during the spring of 2004. Methods Data of SARS cases were officially reported by Beijing Municipal Center for Disease Control and Prevention (BCDC) and Anhui Provincial Center for Disease Control and Prevention (APCDC) and results of epidemiological investigations were collected and analyzed. Results Three generations of 11 cases of SARS were identified during the outbreak. Initial two cases were most likely to be infected in Diarrhea Virus Laboratory of National Institute of Virology, China Centers for Disease Control and Prevention and main mode of transmission was direct contact with SARS patients. Delay in detecting initial case resulted in spread of the illness at hospitals and Communities with two generations of secondary cases. Conclusions SARS outbreak in 2004 has yielded following lessons for public health globally. (1) Lab bio-safety programs should be made and should be strictly abided by. Studies in highly pathogenic viruses such as SARS coronavirus should be utmost cautious. (2) Management systems of occupational exposure to virus and disease surveillance need to be strengthened to take all risk factors into account so as to detect potential patients with infectious disease as early as possible. [ABSTRACT FROM AUTHOR]

Objective To study the potential risk factors for severe acute respiratory syndromes (SARS)-related deaths in Beijing. Methods Epidemiological data were collected among the confirmed SARS patients officially reported by Beijing Centers for Disease Control and Prevention (BCDC), and information was also supplemented by a follow-up case survey. Chi-square test and multivariate stepwise logistic regression analysis were performed. Results Old age (over 60 years) was found to be significantly associated with SARS-related deaths in the univariate analysis. Also, history of contacting SARS patients within 2 weeks prior to the onset of illness, health occupation, and inferior hospital ranking as well as longer interval of clinic consulting (longer than 1 day) were the risk factors for SARS-related deaths. Multivariate stepwise logistic regression analysis found four risk factors for SARS-related deaths. Conclusion Old age (over 60 years) is the major risk factor for SARS-related deaths. Moreover, hospital health workers, the designated hospitals for SARS clinical services and the interval of consulting doctors (less than 1 day) are protective factors for surviving from SARS. [ABSTRACT FROM AUTHOR]

Objective To describe the case fatality rate of SARS in Beijing. Methods Data of SARS cases notified from Beijing Center for Disease Control and Prevention (BCDC) and supplemented by other channels were collected. The data were analyzed by rate calculation. Results The case fatality rate of SARS in Beijing was 7.66%, and had an ascending trend while the age of cases was getting older, and a descending trend while the epidemic development. The case fatality rate in Beijing was lower than that in other main epidemic countries or regions. Conclusions The risk of death increases with the increment of age of SARS patients. Beijing is successful in controlling and treating SARS. [ABSTRACT FROM AUTHOR]

Objectives To assess the impacts of public health interventions on the outbreak of SARS in Beijing by analyzing the intervals between symptom onset, hospital admission and notification of its cases. Methods Data of SARS cases reported from the Beijing Municipal Centers for Disease Prevention and Control (BCDC) were collected and analyzed by descriptive epidemiology. Results in the early epidemic period, the intervals between the disease onset and the hospital admission seemed irregular, so was the intervals between the hospital admission and the notification. After the middle ten days of April, the intervals turned out to be more regular, and the disordered situation in terms of the hospital admission and the case notification was gradually brought under control. Conclusions Public health interventions against SARS has revealed positive impacts on SARS control program in Beijing. The timing and sensitivity of epidemic information reporting Systems has been greatly improved in Beijing as a result of successful fight against this disease. [ABSTRACT FROM AUTHOR]

Objective To describe the specific features of the contact history of probable cases of severe acute respiratory syndrome (SARS) in Beijing. Methods Data of SARS cases notified from the Beijing Municipal Center for Disease Control and Prevention (BCDC) and supplemented by other channels were collected. All the data were analyzed by descriptive epidemiology. Results 1) The number of probable cases with contact history was significantly higher than the excluded cases. 2) The proportion of probable cases with contact history descended with epidemic development, but this situation did not occur in health care workers (HCWs). 3) The fatality rate of probable cases with contact history was significantly higher than the cases without contact history (OR= 1.489). 4) The proportion of probable cases with contact history was 85.86% among health care workers, which was significantly higher than that of non-health care workers (85.86% v.s. 56.44%, OR=4.69). Conclusions 1) The susceptible persons with contact history may not get infected, and the contact history is just a sufficient condition of infecting SARS; 2) There are 3 conceivable reasons for the descending trend of the proportion in probable cases with contact history; 3) The contact history is one of the risk factors of the death of SARS cases; 4) The risk of contacting with SARS among health care workers is approximately 5 times higher than that of non-HCWs. [ABSTRACT FROM AUTHOR]

Eleven isolates within four species of the entomogenous fungus Aschersonia from China, the USA, Japan, the Philippines, Malaysia and Columbia were characterized using 17 RAPD primers. Genetic diversity among these strains of Aschersonia was found. The clustering results showed that the genetic variability among interspecies was more than that among intraspecies of Aschersonia. In the constructed phylogenetic tree, these isolates were not clustered according to their geographic origins or hosts. Furthermore, sequences of the divergent domain at the 5′-end of the large subunit (LSU) in nuclear rRNA from the mitosporic entomogenous fungi were employed to analyse the phylogenetic relationships of 11 Aschersonia isolates. The relationships of interspecies or intraspecies shown in the phylogenetic tree were almost consistent with the results of the morphological study. Different species isolated from different geographic origins could be clearly distinguished in the tree. But there were no close relationships among species isolated from the same family or order of insect hosts. The tree indicated that isolate Aa, belonging to A. aleyrodis, was the same as Aa992 and Aa3.4485. Moreover, results of RAPD analyses were consistent with those of LSU nuclear rDNA analysis for the same isolates tested, which consequently indicates that both methods can be independently applied for classification and identification of Aschersonia. [ABSTRACT FROM PUBLISHER]