Structural Insight of a Trimodular Halophilic Cellulase with a Family 46 Carbohydrate-Binding Module

Cellulases are the key enzymes used in the biofuel industry. A typical cellulase contains a catalytic domain connected to a carbohydrate-binding module (CBM) through a flexible linker. Here we report the structure of an atypical trimodular cellulase which harbors a catalytic domain, a CBM46 domain and a rigid CBM_X domain between them. The catalytic domain shows the features of GH5 family, while the CBM46 domain has a sandwich-like structure. The catalytic domain and the CBM46 domain form an extended substrate binding cleft, within which several tryptophan residues are well exposed. Mutagenesis assays indicate that these residues are essential for the enzymatic activities. Gel affinity electrophoresis shows that these tryptophan residues are involved in the polysaccharide substrate binding. Also, electrostatic potential analysis indicates that almost the entire solvent accessible surface of CelB is negatively charged, which is consistent with the halophilic nature of this enzyme.     

Phylogenetic diversity and mutational analysis of New Delhi Metallo-β-lactamase (NDM) producing E. coli strains from pediatric patients in Pakistan

The evolution of NDM genes (bla_NDM) in E. coli is accounted for expansive multidrug resistance (MDR), causing severe infections and morbidities in the pediatric population. This study aimed to analyze the phylogeny and mutations in NDM variants of E. coli recovered from the pediatric population. Carbapenem-resistant clinical strains of E. coli were identified using microbiological phenotypic techniques. PCR technique used to amplify the bla_NDM genes, identified on agarose gel, and analyzed by DNA sequencing. The amino acid substitutions were examined for mutations after aligning with wild types. Mutational and phylogenetic analysis was performed using Lasergene, NCBI blastn, Clustal Omega, and MEGA software, whereas PHYRE2 software was used for the protein structure predictions. PCR amplification of the bla_NDM genes detected 113 clinical strains of E. coli with the contribution of bla_NDM-1 (46%), bla_NDM-4 (3.5%), and bla_NDM-5 (50%) variants. DNA sequencing of bla_NDM variants showed homology to the previously described bla_NDM-1, bla_NDM-4, and bla_NDM-5 genes available at GenBank and NCBI database. In addition, the mutational analysis revealed in frame substitutions of Pro60Ala and Pro59Ala in bla_NDM-4 and bla_NDM-5, respectively. The bla_NDM-1 was ortholog with related sequences of E. coli available at GenBank. The phylogenetic analysis indicated that the NDM gene variants resemble other microbes reported globally with some new mutational sites.     

Differences in Reporting of Violence and Deliberate Self Harm Related Injuries to Health and Police Authorities,Rawalpindi, Pakistan

Background

The aim of study was to assess differences in reporting of violence and deliberate self harm (DSH) related injuries to police and emergency department (ED) in an urban town of Pakistan.

Methods/Principal Findings

Study setting was Rawalpindi city of 1.6 million inhabitants. Incidences of violence and DSH related injuries and deaths were estimated from record linkage of police and ED data. These were then compared to reported figures in both datasets. All persons reporting violence and DSH related injury to the police station, the public hospital''s ED, or both in Rawalpindi city from July 1, 2007 to June 30, 2008 were included. In Rawalpindi city, 1 016 intentional injury victims reported to police whereas 3 012 reported to ED. Comparing violence related fatality estimates (N = 56, 95% CI: 46–64), police reported 75.0% and ED reported 42.8% of them. Comparing violence related injury estimates (N = 7 990, 95% CI: 7 322–8 565), police reported 12.1% and ED reported 33.2% of them. Comparing DSH related fatality estimates (N = 17, 95% CI: 4–30), police reported 17.7% and ED reported 47.1% of them. Comparing DSH related injury estimates (N = 809, 95% CI: 101–1 516), police reported 0.5% and ED reported 39.9% of them.

Conclusion

In Rawalpindi city, police records were more likely to be complete for violence related deaths as compared to injuries due to same mechanism. As compared to ED, police reported DSH related injuries and deaths far less than those due to other types of violence.     

κ-卡拉胶琥珀酰基化衍生物的抗氧化活性研究

对κ-卡拉胶进行酸降解得到三种卡拉胶低聚糖,并进一步琥珀酰基化得到分子量分别为2720、4000和5960的κ-卡拉胶琥珀酰衍生物(A、B和C)。对产物进行FT-IR表征,并测得其琥珀酰基取代度(DS)分别为0.61、0.29和0.83。检测了三种κ-卡拉胶琥珀酰衍生物对超氧阴离子自由基O2.-、DPPH自由基、羟基自由基.OH以及过氧化氢的清除活性。结果表明:随着取代度的增加,其清除超氧阴离子自由基O2.-和DPPH自由基的能力增强;随着分子量的增加,其清除羟基自由基.OH和过氧化氢的能力增强。这可能与衍生物的羟基含量、取代基团的性质以及取代度等因素有关。     

锌对铅染毒新生大鼠成骨细胞增殖分化的影响

目的:探讨铅锌联合染毒对乳鼠颅骨成骨细胞增殖分化的影响。方法:分离并培养原代成骨细胞,加入不同浓度铅、锌培养48h,检测其对成骨细胞增殖的作用;用碱性磷酸酶试剂盒检测ALP活力。结果:在染铅48h后,当铅浓度≥10μmol/L时,细胞增殖功能下降(P<0.05);加锌干预48h后,铅+锌组细胞增殖功能均高于各自单独染铅组,其中铅(1μmol/L、10μmol/L)+锌(50μmol/L)组、铅(10)+锌(100)组与对照组间的差异具有统计学意义(P<0.05)。铅干预48h后,100μmol/L铅组的ALP活力显著下(P<0.05),给予锌干预的铅锌联合染毒组,各组ALP活力均有增加,其中铅(1μmol/L、10μmol/L)+锌(50μmol/L)组ALP活力均高于对照组,而铅(100μmol/L)+锌(50μmol/L)组ALP活力低于对照组,差异均有统计学意义(P<0.05)。结论:铅对成骨细胞有毒性作用,影响其增殖和分化功能;50μmol/L锌在一定程度上可以拮抗铅对成骨细胞增殖和分化功能的损伤,且对ALP活力的作用更显著,为铅中毒骨病的防治提供一定的科学依据。     

A unified framework for the restoration of Southeast Asian mangroves—bridging ecology, society and economics

The effect of intensive human intervention, poor socio-economic conditions and little knowledge on mangrove ecology pose enormous challenges for mangrove restoration in Southeast Asia. We present a framework for tropical mangrove restoration. Our proposed restoration framework addresses the ecology, economy and social issues simultaneously by considering the causes of mangrove degradation. We provide a step by step guideline for its restoration. We argue that although, ecological issues are of prime importance, economic and social issues must be considered in the restoration plan in order for it to be successful. Since mangrove ecology is not adequately studied in this region, local ecological knowledge can be used to fill the baseline information gaps. Unwanted human disturbance can be minimized by encouraging community participation. This can be ensured and sustained by facilitating the livelihood of the coastal community. We translated the restoration paradigm into a readily available practical guideline for the executors of the plans. We provide an example of mangrove restoration project that is closely related to our proposed framework. We are optimistic that this framework has the potential for universal application with necessary adjustments.     

A new tool for prioritization of sequence variants from whole exome sequencing data

Background

Whole exome sequencing (WES) has provided a means for researchers to gain access to a highly enriched subset of the human genome in which to search for variants that are likely to be pathogenic and possibly provide important insights into disease mechanisms. In developing countries, bioinformatics capacity and expertise is severely limited and wet bench scientists are required to take on the challenging task of understanding and implementing the barrage of bioinformatics tools that are available to them.

Results

We designed a novel method for the filtration of WES data called TAPER? (Tool for Automated selection and Prioritization for Efficient Retrieval of sequence variants).

Conclusions

TAPER? implements a set of logical steps by which to prioritize candidate variants that could be associated with disease and this is aimed for implementation in biomedical laboratories with limited bioinformatics capacity. TAPER? is free, can be setup on a Windows operating system (from Windows 7 and above) and does not require any programming knowledge. In summary, we have developed a freely available tool that simplifies variant prioritization from WES data in order to facilitate discovery of disease-causing genes.

     

Amblyomma sculptum: genetic diversity and rickettsias in the Brazilian Cerrado biome

Amblyomma sculptum (Ixodida: Ixodidae) Berlese, 1888 is the most important tick vector in Brazil, transmitting the bioagent of the most severe form of spotted fever (SF) in part of the Cerrado (in the states of Minas Gerais and São Paulo). In another part of the Cerrado (Central‐West region of Brazil), a milder form of SF has been recorded. However, neither the rickettsia nor the vector involved have been characterized. The aim of the current study was to analyse genetic variation and the presence of rickettsia in A. sculptum in Cerrado, from silent areas and with the milder form of SF. Samples were subjected to DNA extraction, amplification and sequencing of 12S rDNA, cytochrome oxidase subunit II and D‐loop mitochondrial genes (for tick population analyses), and gltA, htrA, ompA and gene D (sca4) genes for rickettsia researches. Exclusive haplotypes with low frequencies, high haplotype diversity and low nucleotide diversity, star‐shaped networks and significant results in neutrality tests indicate A. sculptum population expansions in some areas. Rickettsia amblyommatis, Candidatus Rickettsia andeanae and Rickettsia felis were detected. The A. sculptum diversity is not geographically, or biome delimited, pointing to a different potential in vector capacity, possibly associated with differing tick genetic profiles.