Physiological Responses of Synechocystis sp PCC 6803 under Clinorotation

Photosystem efficiency and the characteristic on oxidative stress were examined to elucidate the metabolic responses of Synechocystis sp. PCC 6803 to short-term clinorotation. Results compiled when using clinostat to simulate microgravity for 60 h, showed that clinorotation clearly prohibited the photochemical quantum yield, but promoted the synthesis of chlorophyll and total protein. This may be a compensatory mechanism for the algal cell to maintain its normal metabolism. An increased malondialdehyde (MDA) content of algal cell upon clinorotation, together with an enhanced catalase (CAT) activity was observed during the whole period of clinorotation. One conclusion is that short-term clinorotation acts as a kind of stress, and that these physiological responses may be a special way for an algal cell to adapt itself to a different environment other than earth gravity.Photosystem efficiency and the characteristic on oxidative stress were examined to elucidate the metabolic responses of Synechocystis sp. PCC 6803 to short-term clinorotation. Results compiled when using clinostat to simulate microgravity for 60 h, showed that clinorotation clearly prohibited the photochemical quantum yield, but promoted the synthesis of chlorophyll and total protein. This may be a compensatory mechanism for the algal cell to maintain its normal metabolism. An increased malondialdehyde (MDA) content of algal cell upon clinorotation, together with an enhanced catalase (CAT) activity was observed during the whole period of clinorotation. One conclusion is that short-term clinorotation acts as a kind of stress, and that these physiological responses may be a special way for an algal cell to adapt itself to a different environment other than earth gravity

Detection of Oxidation Products of 5-Methyl-2′-Deoxycytidine in Arabidopsis DNA

Epigenetic regulations play important roles in plant development and adaptation to environmental stress. Recent studies from mammalian systems have demonstrated the involvement of ten-eleven translocation (Tet) family of dioxygenases in the generation of a series of oxidized derivatives of 5-methylcytosine (5-mC) in mammalian DNA. In addition, these oxidized 5-mC nucleobases have important roles in epigenetic remodeling and aberrant levels of 5-hydroxymethyl-29-deoxycytidine (5-HmdC) were found to be associated with different types of human cancers. However, there is a lack of evidence supporting the presence of these modified bases in plant DNA. Here we reported the use of a reversed-phase HPLC coupled with tandem mass spectrometry method and stable isotope-labeled standards for assessing the levels of the oxidized 5-mC nucleosides along with two other oxidatively induced DNA modifications in genomic DNA of Arabidopsis. These included 5- HmdC, 5-formyl-29-deoxycytidine (5-FodC), 5-carboxyl-29-deoxycytidine (5-CadC), 5-hydroxymethyl-29-deoxyuridine (5- HmdU), and the (59S) diastereomer of 8,59-cyclo-29-deoxyguanosine (S-cdG). We found that, in Arabidopsis DNA, the levels of 5-HmdC, 5-FodC, and 5-CadC are approximately 0.8 modifications per 106 nucleosides, with the frequency of 5-HmdC (per 5-mdC) being comparable to that of 5-HmdU (per thymidine). The relatively low levels of the 5-mdC oxidation products suggest that they arise likely from reactive oxygen species present in cells, which is in line with the lack of homologous Tetfamily dioxygenase enzymes in Arabidopsis

Data Imputation in EEG Signals for Brainprint Identification

Electroencephalograms (EEG) signals have very low signal-to-noise ratio, thus can be easily affected and changes over milliseconds. Normally, trials with excessive body movements or other types of artefacts with amplitude more than 100 µV should be discarded to reduce the noise stains. Scrapping the affected features is not advisable. Therefore, missing values imputation is essential to avoid incomplete data that may deteriorate the computational modelling performance. Hence, this paper proposes a similarity matching method to replace the missing values in the EEG trials. The main idea of the missing values imputation is based on the similarity measure between the trials. The trials with the highest similarity is taken to replace the missing values for the related EEG channels. Statistical evaluation and classification evaluation are used to evaluate the reliability of the proposed similarity matching method. The mean, variance and standard deviation are used for statistical evaluation. For the classification evaluation, the dataset is classified for brainprint identification by using the Incremental Fuzzy-Rough Nearest Neighbour (IncFRNN). The statistical evaluation proved that the proposed similarity matching imputation method is promising when the missing values are not come from the same channels. The classification results achieved the excellent performance with 98.19% in accuracy and 0.998 in AUC

Robust estimation of microbial diversity in theory and in practice

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ("Hill diversities"), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.Comment: To be published in The ISME Journal. Main text: 16 pages, 5 figures. Supplement: 16 pages, 4 figure

Molecular Cloning and Sequence Analysis of a Novel P450 Gene Encoding CYP345D3 from the Red Flour Beetle, Tribolium castaneum

A novel cDNA clone encoding a cytochrome P450 gene has been isolated from the insecticide-susceptible strain of the red flour beetle, Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae). The nucleotide sequence of the clone, designated CYP345D3, was determined. The cDNA is 1554 bp in length and contains an open reading frame from base pairs 32 to 1513, encoding a protein of 493 amino acid residues and a predicted molecular weight of 57466 Daltons. The putative protein contains the classic heme-binding sequence motif FxxGxxxCxG (residues 430–439) conserved among all P450 enzymes as well as other characteristic motifs of the cytochrome P450s. Comparison of the deduced amino acid sequence with other CYP members shows that CYP345D3 shares 91% identity with the previously published sequence of CYP345D1 from the T. castaneum genome project and the nucleotide sequence identity between them is less than 80%. Phylogenetic analysis of amino acid sequences from members of various P450 families indicated close phylogenetic relationship of CYP345D3 with CYP6 of other insects than those from mammals and amore distant relationship to P450 from other families. CYP345D3 was submitted to GenBank, accession number EU008544

Effects of Four Host Plants on Biology and Food Utilization of the Cutworm, Spodoptera litura

Effects of four host plants, tobacco, Chinese cabbage, cowpea and sweet potato, on larval and pupal development and survival, and longevity and fecundity of adults of Spodoptera litura (F) (Lepidoptera: Noctuidae), were studied under laboratory conditions (26° C, 60–80% RH), as was the utilization of the four host plants and adaptation on tobacco. All of the biological parameters included in the study were affected by the host plants. In a choice test, S. litura females oviposited most on Chinese cabbage, least on tobacco, and intermediate on cowpea and sweet potato. S. litura larvae developed differently on the four host plants, from shortest to longest in the following order: Chinese cabbage, cowpea, sweet potato, and tobacco. Pupal development was shorter on cowpea than on the other three host plants, and males generally developed longer than females. More females than males were found among emerged adults, and male adults lived 1–2 d longer than females. Larvae survived best on cowpea (81.6%), followed by Chinese cabbage (75.5%), then sweet potato (66.1%), and worst on tobacco (49.2%). Pupal survival rates were relatively high (91.4 – 95.9%) in all four host plant treatments, although that on sweet potato was lower than those on the other three host plants. Pupal weights on tobacco and sweet potato were similar, but both were lower than those on Chinese cabbage and cowpea. Generally, male pupae weighed less than female pupae. Numbers of eggs oviposited by female S. litura were highest on sweet potato, followed by those on cowpea, Chinese cabbage, and lowest on tobacco. Relative food consumption rate was highest on sweet potato, followed by that on cowpea, Chinese cabbage, and lowest on tobacco. In contrast, S. litura larvae that fed on tobacco had higher efficiency of conversion of digested food, highest efficiency of conversion of ingested food, and lowest approximate digestibility as compared with larvae that fed on other host plants. The potential causes for S. litura outbreaks on tobacco are discussed

Disparities and risks of sexually transmissible infections among men who have sex with men in China: a meta-analysis and data synthesis.

BACKGROUND: Sexually transmitted infections (STIs), including Hepatitis B and C virus, are emerging public health risks in China, especially among men who have sex with men (MSM). This study aims to assess the magnitude and risks of STIs among Chinese MSM. METHODS: Chinese and English peer-reviewed articles were searched in five electronic databases from January 2000 to February 2013. Pooled prevalence estimates for each STI infection were calculated using meta-analysis. Infection risks of STIs in MSM, HIV-positive MSM and male sex workers (MSW) were obtained. This review followed the PRISMA guidelines and was registered in PROSPERO. RESULTS: Eighty-eight articles (11 in English and 77 in Chinese) investigating 35,203 MSM in 28 provinces were included in this review. The prevalence levels of STIs among MSM were 6.3% (95% CI: 3.5-11.0%) for chlamydia, 1.5% (0.7-2.9%) for genital wart, 1.9% (1.3-2.7%) for gonorrhoea, 8.9% (7.8-10.2%) for hepatitis B (HBV), 1.2% (1.0-1.6%) for hepatitis C (HCV), 66.3% (57.4-74.1%) for human papillomavirus (HPV), 10.6% (6.2-17.6%) for herpes simplex virus (HSV-2) and 4.3% (3.2-5.8%) for Ureaplasma urealyticum. HIV-positive MSM have consistently higher odds of all these infections than the broader MSM population. As a subgroup of MSM, MSW were 2.5 (1.4-4.7), 5.7 (2.7-12.3), and 2.2 (1.4-3.7) times more likely to be infected with chlamydia, gonorrhoea and HCV than the broader MSM population, respectively. CONCLUSION: Prevalence levels of STIs among MSW were significantly higher than the broader MSM population. Co-infection of HIV and STIs were prevalent among Chinese MSM. Integration of HIV and STIs healthcare and surveillance systems is essential in providing effective HIV/STIs preventive measures and treatments. TRIAL REGISTRATION: PROSPERO NO: CRD42013003721

Presence of qnr gene in Escherichia coli and Klebsiella pneumoniae resistant to ciprofloxacin isolated from pediatric patients in China

<p>Abstract</p> <p>Background</p> <p>Quinolone resistance in <it>Enterobacteriaceae </it>results mainly from mutations in type II DNA topoisomerase genes and/or changes in the expression of outer membrane and efflux pumps. Several recent studies have indicated that plasmid-mediated resistance mechanisms also play a significant role in fluoroquinolone resistance, and its prevalence is increasing worldwide. In China, the presence of the <it>qnr </it>gene in the clinical isolates of <it>Enterobacteriaceae </it>has been reported, but this transmissible quinolone resistance gene has not been detected in strains isolated singly from pediatric patients. Because quinolones associated with a variety of adverse side effects on children, they are not authorized for pediatric use. This study therefore aimed to investigate the presence of the <it>qnr </it>gene in clinical isolates of <it>E. coli </it>and <it>K. pneumoniae </it>from pediatric patients in China.</p> <p>Methods</p> <p>A total 213 of non-repetitive clinical isolates resistant to ciprofloxacin from <it>E. coli </it>and <it>K. pneumoniae </it>were collected from hospitalized patients at five children's hospital in Beijing, Shanghai, Guangzhou, and Chongqing. The isolates were screened for the plasmid-mediated quinolone resistance genes of <it>qnrA</it>, <it>qnrB</it>, and <it>qnrS </it>by PCR. Transferability was examined by conjugation with the sodium azide-resistant <it>E. coli </it>J53. All <it>qnr</it>-positive were analyzed for clonality by enterobacterial repetitive intergenic consensus (ERIC)-PCR.</p> <p>Results</p> <p>The study found that 19 ciprofloxacin-resistant clinical isolates of <it>E. coli </it>and <it>K. pneumoniae </it>were positive for the <it>qnr </it>gene, and most of the <it>qnr </it>positive strains were ESBL producers. Conjugation experiments showed that quinolone resitance could be transferred to recipients. Apart from this, different DNA banding patterns were obtained by ERIC-PCR from positive strains, which means that most of them were not clonally related.</p> <p>Conclusion</p> <p>This report on transferable fluoroquinolone resistance due to the <it>qnr </it>gene among <it>E. coli </it>and <it>K. pneumoniae </it>strains indicated that plasmid-mediated quinolone resistance has emerged in pediatric patients in China.</p