Members of the Candidate Division OP10 are spread in a variety of environments

Our planet holds a huge bacterial diversity. Most of these bacteria have only been detected by their 16S rRNA gene sequences remaining to be cultured. Many are classified within Candidate Divisions. One them is the Candidate Division OP10. Analysis of environmental 16S rRNA gene sequences available in public repositories revealed the existence of numerous sequences clustering within the Candidate Division OP10 but currently unclassified or assigned to other bacterial phyla. Newly proposed 16S rRNA sequences multiply several fold the reported sequences for the Candidate Division OP10. This study showed that the Candidate Division OP10 is a diverse and broadly distributed bacterial phylum and represents a stable microbial component in different natural environments.     

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

Taxonomic classification of the thousands–millions of 16S rRNA gene sequences generated in microbiome studies is often achieved using a naïve Bayesian classifier (for example, the Ribosomal Database Project II (RDP) classifier), due to favorable trade-offs among automation, speed and accuracy. The resulting classification depends on the reference sequences and taxonomic hierarchy used to train the model; although the influence of primer sets and classification algorithms have been explored in detail, the influence of training set has not been characterized. We compared classification results obtained using three different publicly available databases as training sets, applied to five different bacterial 16S rRNA gene pyrosequencing data sets generated (from human body, mouse gut, python gut, soil and anaerobic digester samples). We observed numerous advantages to using the largest, most diverse training set available, that we constructed from the Greengenes (GG) bacterial/archaeal 16S rRNA gene sequence database and the latest GG taxonomy. Phylogenetic clusters of previously unclassified experimental sequences were identified with notable improvements (for example, 50% reduction in reads unclassified at the phylum level in mouse gut, soil and anaerobic digester samples), especially for phylotypes belonging to specific phyla (Tenericutes, Chloroflexi, Synergistetes and Candidate phyla TM6, TM7). Trimming the reference sequences to the primer region resulted in systematic improvements in classification depth, and greatest gains at higher confidence thresholds. Phylotypes unclassified at the genus level represented a greater proportion of the total community variation than classified operational taxonomic units in mouse gut and anaerobic digester samples, underscoring the need for greater diversity in existing reference databases.     

The Future Role of the International Atomic Energy Authority (IAEA) in Tissue Banking

The International Atomic Energy Agency, an agency of the United Nations, has supported tissue banking programmes in 28 countries to further extend the use of ionising radiation for medical sterilisation applications. Up to 1998, some 115,000 tissue allografts have been produced and clinically used. A new thematic approach has now been introduced to set strict criteria to govern future developments. The emphasis will be on appropriate training and the introduction of Quality Systems in order to achieve international standards. Countries wishing to gain further support will be required to demonstrate the need and performance. To ensure a training mode appropriate to a global organisation, a multi-media training curriculum has been developed, which can be delivered by distance learning methods. Following its successful launch in the Asia Pacific region, the curriculum is now being translated into Spanish for use in Latin American countries. The Republic of Korea government too has provided resources for translation into their language and to initiate a national programme. In other countries national networks are being set up for improving public and professional awareness, training and tissue distribution. Collaboration with international organisations is another new area of development.     

WHO international reference reagents for human proinsulin and human insulin C-peptide

Candidate preparations for international reference reagents for immunoassays of human proinsulin and human insulin C-peptide were evaluated in an international collaborative study. With the authorization of the Expert Committee on Biological Standardization of WHO, the following preparations were established as international reference reagents: human proinsulin (84/611, nominal ampoule content 6 micrograms) and human insulin C-peptide (84/510, 10 micrograms). Each preparation is intended as a primary reference reagent for the calibration of immunoassays.     

Torsadogenic Risk of Antipsychotics: Combining Adverse Event Reports with Drug Utilization Data across Europe

Background

Antipsychotics (APs) have been associated with risk of torsade de Pointes (TdP). This has important public health implications. Therefore, (a) we exploited the public FDA Adverse Event Reporting System (FAERS) to characterize their torsadogenic profile; (b) we collected drug utilization data from 12 European Countries to assess the population exposure over the 2005-2010 period.

Methods

FAERS data (2004-2010) were analyzed based on the following criteria: (1) ≥4 cases of TdP/QT abnormalities; (2) Significant Reporting Odds Ratio, ROR [Lower Limit of the 95% confidence interval>1], for TdP/QT abnormalities, adjusted and stratified (Arizona CERT drugs as effect modifiers); (3) ≥4 cases of ventricular arrhythmia/sudden cardiac death (VA/SCD); (4) Significant ROR for VA/SCD; (5) Significant ROR, combined by aggregating TdP/QT abnormalities with VA and SCD. Torsadogenic signals were characterized in terms of signal strength: from Group A (very strong torsadogenic signal: all criteria fulfilled) to group E (unclear/uncertain signal: only 2/5 criteria). Consumption data were retrieved from 12 European Countries and expressed as defined daily doses per 1,000 inhabitants per day (DID).

Results

Thirty-five antipsychotics met at least one criterium: 9 agents were classified in Group A (amisulpride, chlorpromazine, clozapine, cyamemazine, haloperidol, olanzapine, quetiapine, risperidone, ziprasidone). In 2010, the overall exposure to antipsychotics varied from 5.94 DID (Estonia) to 13.99 (France, 2009). Considerable increment of Group A agents was found in several Countries (+3.47 in France): the exposure to olanzapine increased across all Countries (+1.84 in France) and peaked 2.96 in Norway; cyamemazine was typically used only in France (2.81 in 2009). Among Group B drugs, levomepromazine peaked 3.78 (Serbia); fluphenazine 1.61 (Slovenia).

Conclusions

This parallel approach through spontaneous reporting and drug utilization analyses highlighted drug- and Country-specific scenarios requiring potential regulatory consideration: levomepromazine (Serbia), fluphenazine (Slovenia), olanzapine (across Europe), cyamemazine (France). This synergy should be encouraged to support future pharmacovigilance activities.     

珠海市海-陆交错带水环境原核生物多样性

采用16S rRNA基因PCR-RFLP分析技术,对珠海市海-陆交错带的海水和地下水进行原核生物多样性分析,并将所得数据与国际基因数据库Genbank进行相似性比较及聚类分析.结果表明：海水细菌以变形菌居多,其次是古菌和芽单胞菌,以及Candidate division OP3、OP8和浮霉菌等;海 陆交错带地下水细菌则以古菌居多,其次是变形菌和鞘脂杆菌,以及Candidate division OP3、放线菌和假单胞菌等.海-陆交错带地下水中大部分优势类群与源于海洋的不可培养细菌具有很高的相似性.地下水样中存在大量能降解有机质和具有净化水体潜力的细菌,说明在长期演化下,海-陆交错带兼备了海洋生态系统和陆地生态系统的特征.     

WHO international reference reagents for bovine and porcine proinsulins

Candidate preparations for International Reference Reagents (IRR) for immunoassays of bovine and porcine proinsulin were evaluated in an international collaborative study. With the authorization of the Expert Committee on Biological Standardization of WHO, the following preparations were established as IRRs: bovine proinsulin (code 84/514, defined ampoule content 25 micrograms) and porcine proinsulin (84/528, 20 micrograms). The content of ampoules of these materials is defined in terms of mass rather than international units of activity, therefore they are IRR rather than International Standards. Both preparations are intended as primary reference reagents for the calibration of immunoassays.     

CPR-C4 is a highly conserved novel protease from the Candidate Phyla Radiation with remote structural homology to human vasohibins

The Candidate Phyla Radiation is a recently uncovered and vast expansion of the bacterial domain of life, made up of largely uncharacterized phyla that lack isolated representatives. This unexplored territory of genetic diversity presents an abundance of novel proteins with potential applications in the life-science sectors. Here, we present the structural and functional elucidation of CPR-C4, a hypothetical protein from the genome of a thermophilic Candidate Phyla Radiation organism, identified through metagenomic sequencing. Our analyses revealed that CPR-C4 is a member of a family of highly conserved proteins within the Candidate Phyla Radiation. The function of CPR-C4 as a cysteine protease was predicted through remote structural similarity to the Homo sapiens vasohibins and subsequently confirmed experimentally with fluorescence-based activity assays. Furthermore, detailed structural and sequence alignment analysis enabled identification of a noncanonical cysteine-histidine-leucine(carbonyl) catalytic triad. The unexpected structural and functional similarities between CPR-C4 and the human vasohibins suggest an evolutionary relationship undetectable at the sequence level alone.     

Review

Book reviewed in this article:
Laasimer, L., Kuusk, V., Tabaka, L., & Lekavicius, L. (eds). A. Flora of the Baltic Countries, Compendium of Vascular Plants vol. I.
Kuusk, V., Tabaka, L., &Jankeviciene, R. (eds). Flora of the Baltic Countries, Compedium of Vascular Plants vol. II.     

Quality of Reporting of Randomised Controlled Trials of Herbal Interventions in ASEAN Plus Six Countries: A Systematic Review

Background

Many randomised controlled trials (RCTs) of herbal interventions have been conducted in the ASEAN Communities. Good quality reporting of RCTs is essential for assessing clinical significance. Given the importance ASEAN placed on herbal medicines, the reporting quality of RCTs of herbal interventions among the ASEAN Communities deserved a special attention.

Objectives

To systematically review the quality of reporting of RCTs of herbal interventions conducted in the ASEAN Plus Six Countries.

Methods

Searches were performed using PubMed, EMBASE, The Cochrane Library, and Allied and Complementary Medicine (AMED), from inception through October 2013. These were limited to studies specific to humans and RCTs. Herbal species search terms were based on those listed in the National List of Essential Medicines [NLEM (Thailand, 2011)]. Studies conducted in the ASEAN Plus Six Countries, published in English were included.

Results

Seventy-one articles were identified. Thirty (42.25%) RCTs were from ASEAN Countries, whereas 41 RCTs (57.75%) were from Plus Six Group. Adherence to the recommended CONSORT checklist items for reporting of RCTs of herbal interventions among ASEAN Plus Six Countries ranged from 0% to 97.18%. Less than a quarter of the RCTs (18.31%) reported information on standardisation of the herbal products. However, the scope of our interventions of interest was limited to those developed from 20 herbal species listed in the NLEM of Thailand.

Conclusions

The present study highlights the need to improve reporting quality of RCTs of herbal interventions across ASEAN Plus Six Communities.     

Genomic analysis of a region encompassing QRfs1 and QRfs2: genes that underlie soybean resistance to sudden death syndrome.

Candidate genes were identified for two loci, QRfs2 providing resistance to the leaf scorch called soybean (Glycine max (L.) Merr.) sudden death syndrome (SDS) and QRfs1 providing resistance to root infection by the causal pathogen Fusarium solani f.sp. glycines. The 7.5 +/- 0.5 cM region of chromosome 18 (linkage group G) was shown to encompass a cluster of resistance loci using recombination events from 4 near-isogenic line populations and 9 DNA markers. The DNA markers anchored 9 physical map contigs (7 are shown on the soybean Gbrowse, 2 are unpublished), 45 BAC end sequences (41 in Gbrowse), and contiguous DNA sequences of 315, 127, and 110 kbp. Gene density was high at 1 gene per 7 kbp only around the already sequenced regions. Three to 4 gene-rich islands were inferred to be distributed across the entire 7.5 cM or 3.5 Mbp showing that genes are clustered in the soybean genome. Candidate resistance genes were identified and a molecular basis for interactions among the disease resistance genes in the cluster inferred.     

The salmon genome (and other issues in bioinformatics)

A report on the fourth annual conference of the Society for Bioinformatics in the Nordic Countries (SOCBIN), Bioinformatics 2002, Bergen, Norway, 4-7 April 2002.     

Structure-based stabilization of an enzyme: the case of penicillin acylase from Alcaligenes faecalis

The modeled structure of penicillin acylase from Alcaligenes faecali (AFPGA) was constructed by comparative modeling with the Modeller program. Candidate positions that could be replaced with cysteine were estimated by scanning the modeled structure of AFPGA with the program MODIP (modeling disulfide bond in protein). The mutant Q3C/P751C had a higher optimum temperature by three degrees than that of the wild type AFPGA. The half life of the double mutant Q3C/P751C at 55 degrees C was increased by 50%. To our knowledge, this was the first structure-based genetic modification of AFPGA.     

From microarrays to genome duplications

A report on the fifth annual conference of the Society for Bioinformatics in the Nordic Countries (SOCBIN), 'Bioinformatics 2003', Helsinki, Finland, 22-24 May 2003.     

Comparative inactivation of enteroviruses and adenovirus 2 by UV light

The doses of UV irradiation necessary to inactivate selected enteric viruses on the U.S. Environmental Protection Agency Contaminant Candidate List were determined. Three-log reductions of echovirus 1, echovirus 11, coxsackievirus B3, coxsackievirus B5, poliovirus 1, and human adenovirus type 2 were effected by doses of 25, 20.5, 24.5, 27, 23, and 119 mW/cm(2), respectively. Human adenovirus type 2 is the most UV light-resistant enteric virus reported to date.     

Italian activities in biomass gasification

The role of ENEA (Italian Commission for Nuclear and Alternative Energy Sources) in supporting and promoting technological research in biomass gasification is illustrated. The main interests are: (a) biomass (wood and agricultural residues) gasificaiton for its application in the Developing Countries and/or in specific industrial applications and (b) RDF gasification as an energy supply for some industrial sectors. The more active Italian firms involved in manufacturing gasifiers are indicated. The performance of several producer gas systems has been examined and experimental tests have been carried out for long-term operation in field trials.Standards and procedures for the evaluation of technical performance and safety requirements of wood gasifiers have been developed and tested.