Aspidistra longgangensis sp. nov. (Asparagaceae) from limestone areas in Guangxi,China

Aspidistra longgangensis C. R. Lin, Y. S. Huang & Yan Liu, a new species of Asparagaceae from the limestone areas in Guangxi, China, is described and illustrated. It is similar to A. guangxiensis S. C. Tang & Yan Liu in the shape of the flower, but differs by leaf blade pachyphyllous and bigger; the perianth lobes with appendages at base, appendage oblong, 3–5 mm long, apex incurved; stigma upper surface white, with 4(3) radial, bifurcate lines in the center. The new species is currently known only from Longgang National Natural Reserve, situated in southwestern Guangxi, China, near the border with northern Vietnam.     

海洋真菌Aspergillus sp.SCSGAF 0076与细菌Bacillus sp.MNMCCE001共培养次生代谢产物

【目的】阐明海洋真菌Aspergillus sp.SCSGAF 0076与细菌Bacillus sp.MNMCCE 001在平板上共培养时产生的主要抗菌物质和红色素的化学结构。【方法】在固体淀粉培养基上分别进行Aspergillus sp.SCSGAF 0076纯培养、以及SCSGAF 0076和Bacillus sp.MNMCCE 001共培养,培养3 d后分别对纯培养和共培养的培养基进行萃取浓缩得到浸膏,运用高效液相色谱分析比较纯培养和共培养所得浸膏的化学分成的差异,并采用抗菌活性追踪法,结合硅胶柱层析、凝胶柱层析和高效液相色谱等分离方法从共培养浸膏中分离纯化抗菌物质和红色素,运用波谱解析法鉴定化合物的结构。【结果】通过高效液相色谱分析发现,共培养与纯培养的主要次生代谢产物没明显差异,但抗菌物质和红色素的含量差别明显。从这两株菌共培养的发酵产物中分离鉴定了4个化合物,包括抗菌物质青霉酸(1)、青霉酸类似物5(6)-dihydropenicillic acid(2)和9-chloro-8-hydroxy-8,9-deoxyasperlactone(3)、以及红色素viopurpurin(4)。【结论】初步阐明了Aspergillus sp.SCSGAF 0076与Bacillus sp.MNMCCE 001共培养时由Aspergillus sp.SCSGAF 0076产生的主要抗菌活性化合物是青霉酸,伴随明显增多的主要红色素是viopurpurin,二者产率均比Aspergillus sp.SCSGAF 0076纯培养时高。     

Acaricidal properties of an Ailanthus altissima bark extract against Psoroptes cuniculi and Sarcoptes scabiei var. cuniculi in vitro

The potential acaricidal properties of an Ailanthus altissima bark extract were assessed against two common species of animal ectoparasitic mites, Psoroptes cuniculi and Sarcoptes scabiei var. cuniculi, in vitro. A. altissima bark extract was obtained by ethanol thermal circumfluence and tested at four concentrations (1.0, 0.5, 0.25 and 0.125 g/ml) on mites collected from rabbits. Compared to the fenvalerate treatment group, the A. altissima bark exhibited significant acaricidal properties for both mite species treated. The extract of concentrations of 1.0, 0.5 and 0.25 g/ml killed all tested S. scabiei within 7 h, however, only 1.0 and 0.5 g/ml of extract killed all treated P. cuniculi. The median lethal time (LT₅₀) values at 1, 0.5 and 0.25 g/ml were 0.60, 0.78, 1.48 h for S. scabiei and 0.74, 1.29, 3.33 h for P. cuniculi. The median lethal concentration (LC₅₀) for P. cuniculi was approximately 1.6 times that for S. scabiei var. cuniculi at 4 h. The extract showed stronger toxicity against S. scabiei than against P. cuniculi. Mortality rates increased with increasing concentration of extract administered and with increasing time post-treatment, indicating that the acaricidal activity of A. altissima bark extract is both time-dependent and dose-dependent. This is the first report on acaricidal activity of A. altissima against P. cuniculi and S. scabiei var. cuniculi. It indicates that A. altissima contain potential acaricidal compounds. Our study is the first step to develop potentially novel compounds from A. altissima for the effective control of mites in livestock.     

Comparative genomic analysis of clinical and environmental strains provides insight into the pathogenicity and evolution of Vibrio parahaemolyticus

Background

Vibrio parahaemolyticus is a Gram-negative halophilic bacterium. Infections with the bacterium could become systemic and can be life-threatening to immunocompromised individuals. Genome sequences of a few clinical isolates of V. parahaemolyticus are currently available, but the genome dynamics across the species and virulence potential of environmental strains on a genome-scale have not been described before.

Results

Here we present genome sequences of four V. parahaemolyticus clinical strains from stool samples of patients and five environmental strains in Hong Kong. Phylogenomics analysis based on single nucleotide polymorphisms revealed a clear distinction between the clinical and environmental isolates. A new gene cluster belonging to the biofilm associated proteins of V. parahaemolyticus was found in clincial strains. In addition, a novel small genomic island frequently found among clinical isolates was reported. A few environmental strains were found harboring virulence genes and prophage elements, indicating their virulence potential. A unique biphenyl degradation pathway was also reported. A database for V. parahaemolyticus (http://kwanlab.bio.cuhk.edu.hk/vp) was constructed here as a platform to access and analyze genome sequences and annotations of the bacterium.

Conclusions

We have performed a comparative genomics analysis of clinical and environmental strains of V. parahaemolyticus. Our analyses could facilitate understanding of the phylogenetic diversity and niche adaptation of this bacterium.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1135) contains supplementary material, which is available to authorized users.     

A Systematic Review of Scope and Quality of Health Economic Evaluation Studies in Vietnam

Introduction

The application of health economic evaluation (HEE) evidence can play an important role in strategic planning and policy making. This study aimed to assess the scope and quality of existing research, with the goal of elucidating implications for improving the use of HEE evidence in Vietnam.

Methods

A comprehensive search strategy was developed to search medical online databases (Medline, Google Scholar, and Vietnam Medical Databases) to select all types of HEE studies except cost-only analyses. Two researchers assessed the quality of selected studies using the Quality of Health Economic Studies (QHES) instrument.

Results

We selected 26 studies, including 6 published in Vietnam. The majority of these studies focused on infectious diseases (14 studies), with HIV being the most common topic (5 studies). Most papers were cost-effectiveness studies that measured health outcomes using DALY units. Using QHES, we found that the overall quality of HEE studies published internationally was much higher (mean score 88.7+13.3) than that of those published in Vietnam (mean score 67.3+22.9). Lack of costing perspectives, reliable data sources and sensitivity analysis were the main shortcomings of the reviewed studies.

Conclusion

This review indicates that HEE studies published in Vietnam are limited in scope and number, as well as by several important technical errors or omissions. It is necessary to formalize the process of health economic research in Vietnam and to institutionalize the links between researchers and policy-makers. Additionally, the quality of HEE should be enhanced through education about research techniques, and the implementation of standard HEE guidelines.     

Phylogenetic studies of three sinipercid fishes (Perciformes: Sinipercidae) based on complete mitochondrial DNA sequences

The sinipercids are a group of 12 species of freshwater percoid fish endemic to East Asia and their phylogenetic placements have perplexed generations of taxonomists. We cloned and sequenced the complete mitochondrial DNA (mtDNA) of three sinipercid fishes (Siniperca chuatsi, S. kneri, and S. scherzeri) to characterize and compare their mitochondrial genomes. The mitochondrial genomes of S. chuatsi, S. kneri, and S. scherzeri were 16,496, 17,002, and 16,585?bp in length, respectively. The organization of the three mitochondrial genomes is similar to those reported from other fish mitochondrial genomes, which contains 37 genes (13 protein-coding genes, 2 ribosomal RNAs, and 22 transfer RNAs) and a major non-coding control region. Among the 13 protein-coding genes of all the three sinipercid fishes, three reading-frame overlaps were found on the same strand. There is an 81-bp tandem repeat cluster at the end of CSB-3 in the S. scherzeri control region. The complete mitochondrial genomes of the three sinipercids should be useful for the evolutionary studies of sinipercids and other vertebrate species.     

Profiling cellular protein complexes by proximity ligation with dual tag microarray readout

Patterns of protein interactions provide important insights in basic biology, and their analysis plays an increasing role in drug development and diagnostics of disease. We have established a scalable technique to compare two biological samples for the levels of all pairwise interactions among a set of targeted protein molecules. The technique is a combination of the proximity ligation assay with readout via dual tag microarrays. In the proximity ligation assay protein identities are encoded as DNA sequences by attaching DNA oligonucleotides to antibodies directed against the proteins of interest. Upon binding by pairs of antibodies to proteins present in the same molecular complexes, ligation reactions give rise to reporter DNA molecules that contain the combined sequence information from the two DNA strands. The ligation reactions also serve to incorporate a sample barcode in the reporter molecules to allow for direct comparison between pairs of samples. The samples are evaluated using a dual tag microarray where information is decoded, revealing which pairs of tags that have become joined. As a proof-of-concept we demonstrate that this approach can be used to detect a set of five proteins and their pairwise interactions both in cellular lysates and in fixed tissue culture cells. This paper provides a general strategy to analyze the extent of any pairwise interactions in large sets of molecules by decoding reporter DNA strands that identify the interacting molecules.     

The complete mitochondrial genome of the butterfly <Emphasis Type="Italic">Apatura metis</Emphasis> (Lepidoptera: Nymphalidae)

As an important pest in the Slender Leaved Willow (Salix alba), Apatura metis is called Freyer’s purple emperor, and its mitochondrial genome is 15,236 bp long. The encoded genes for 22 tRNA genes, two ribosomal RNA (rrnL and rrnS) genes, and 13 protein-coding genes (PCGs), and a control region in the A. metis mitochondria are highly homologous to other lepidopteran species. The mitochondrial genome of A. metis is biased toward a high A + T content (A + T = 80.5%). All protein-coding genes, except for COI begins with the CGA codon as observed in other lepidopterans, start with a typical ATN initiation codon. All tRNAs show the classic clover-leaf structure, except that the dihydrouridine (DHU) arm of tRNA ^Ser(AGN) forms a simple loop. The A. metis A + T-rich region contains some conserved structures including a structure combining the motif ‘ATAGA’ and 19 bp poly (T) stretch, which is similar to those found in other lepidopteran mitogenomes. The phylogenetic analyses of lepidopterans based on mitogenomes sequences demonstrate that each of the six superfamilies is monophyletic, and the relationship among them is (((Noctuoidea + (Geometroidea + Bombycoidea)) + Pyraloidea) + Papilionoidea) + Tortricoidea. In Papilionoidea group, our conclusion argues that ((Lycaenidae + Pieridae) + Nymphalidae) + Papilionidae.     

Chimeric piggyBac transposases for genomic targeting in human cells

Integrating vectors such as viruses and transposons insert transgenes semi-randomly and can potentially disrupt or deregulate genes. For these techniques to be of therapeutic value, a method for controlling the precise location of insertion is required. The piggyBac (PB) transposase is an efficient gene transfer vector active in a variety of cell types and proven to be amenable to modification. Here we present the design and validation of chimeric PB proteins fused to the Gal4 DNA binding domain with the ability to target transgenes to pre-determined sites. Upstream activating sequence (UAS) Gal4 recognition sites harbored on recipient plasmids were preferentially targeted by the chimeric Gal4-PB transposase in human cells. To analyze the ability of these PB fusion proteins to target chromosomal locations, UAS sites were randomly integrated throughout the genome using the Sleeping Beauty transposon. Both N- and C-terminal Gal4-PB fusion proteins but not native PB were capable of targeting transposition nearby these introduced sites. A genome-wide integration analysis revealed the ability of our fusion constructs to bias 24% of integrations near endogenous Gal4 recognition sequences. This work provides a powerful approach to enhance the properties of the PB system for applications such as genetic engineering and gene therapy.