bluuebunny/crossref_metadata_2025 huggingface dataset:
An ILP solution for the gene duplication problem
Authors: Chang Wen-Chieh , Burleigh Gordon J , Fernández-Baca David F , Eulenstein Oliver
Published: February 2011

Background

The gene duplication (GD) problem seeks a species tree that implies the fewest gene duplication events across a given collection of gene trees. Solving this problem makes it possible to use large gene families with complex histories of duplication and loss to infer phylogenetic trees. However, the GD problem is NP-hard, and therefore, most analyses use heuristics that lack any performance guarantee.

Results

We describe the first integer linear programming (ILP) formulation to solve instances of the gene duplication problem exactly. With simulations, we demonstrate that the ILP solution can solve problem instances with up to 14 taxa. Furthermore, we apply the new ILP solution to solve the gene duplication problem for the seed plant phylogeny using a 12-taxon, 6, 084-gene data set. The unique, optimal solution, which places Gnetales sister to the conifers, represents a new, large-scale genomic perspective on one of the most puzzling questions in plant systematics.

Conclusions

Although the GD problem is NP-hard, our novel ILP solution for it can solve instances with data sets consisting of as many as 14 taxa and 1, 000 genes in a few hours. These are the largest instances that have been solved to optimally to date. Thus, this work can provide large-scale genomic perspectives on phylogenetic questions that previously could only be addressed by heuristic estimates.
The G protein-coupled receptors in the pufferfish Takifugu rubripes
Authors: Sarkar Anita , Kumar Sonu , Sundar Durai
Published: February 2011

Background

Guanine protein-coupled receptors (GPCRs) constitute a eukaryotic transmembrane protein family and function as “molecular switches” in the second messenger cascades and are found in all organisms between yeast and humans. They form the single, biggest drug-target family due to their versatility of action and their role in several physiological functions, being active players in detecting the presence of light, a variety of smells and tastes, amino acids, nucleotides, lipids, chemicals etc. in the environment of the cell. Comparative genomic studies on model organisms provide information on target receptors in humans and their function. The Japanese teleost Fugu has been identified as one of the smallest vertebrate genomes and a compact model to study the human genome, owing to the great similarity in its gene repertoire with that of human and other vertebrates. Thus the characterization of the GPCRs of Fugu would provide insights to the evolution of the vertebrate genome.

Results

We classified the GPCRs in the Fugu genome and our analysis of its 316 membrane-bound receptors, available on the public databases as well as from literature, detected 298 GPCRs that were grouped into five main families according to the GRAFS classification system (namely, Glutamate, Rhodopsin, Adhesion, Frizzled and Secretin). We also identified 18 other GPCRs that could not be grouped under the GRAFS family and hence were classified as ‘Other 7TM’ receptors. On comparison of the GPCR information from the Fugu genome with those in the human and chicken genomes, we detected 96.83% (306/316) and 96.51% (305/316) orthology in GPCRs among the Fugu-human genomes and Fugu-chicken genomes, respectively.

Conclusions

This study reveals the position of pisces in vertebrate evolution from the GPCR perspective. Fugu can act as a reference model for the human genome for other protein families as well, going by the high orthology observed for GPCRs between Fugu and human. The evolutionary comparison of GPCR sequences between key vertebrate classes of mammals, birds and fish will help in identifying key functional residues and motifs so as to fill in the blanks in the evolution of GPCRs in vertebrates.
A study on the flexibility of enzyme active sites
Authors: Weng Yi-Zhong , Chang Darby Tien-Hao , Huang Yu-Feng , Lin Chih-Wei
Published: February 2011

Background

A common assumption about enzyme active sites is that their structures are highly conserved to specifically distinguish between closely similar compounds. However, with the discovery of distinct enzymes with similar reaction chemistries, more and more studies discussing the structural flexibility of the active site have been conducted.

Results

Most of the existing works on the flexibility of active sites focuses on a set of pre-selected active sites that were already known to be flexible. This study, on the other hand, proposes an analysis framework composed of a new data collecting strategy, a local structure alignment tool and several physicochemical measures derived from the alignments. The method proposed to identify flexible active sites is highly automated and robust so that more extensive studies will be feasible in the future. The experimental results show the proposed method is (a) consistent with previous works based on manually identified flexible active sites and (b) capable of identifying potentially new flexible active sites.

Conclusions

This proposed analysis framework and the former analyses on flexibility have their own advantages and disadvantage, depending on the cause of the flexibility. In this regard, this study proposes an alternative that complements previous studies and helps to construct a more comprehensive view of the flexibility of enzyme active sites.
iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis
Authors: Hsu Kai-Cheng , Chen Yen-Fu , Lin Shen-Rong , Yang Jinn-Moon
Published: February 2011

Background

Pharmacological interactions are useful for understanding ligand binding mechanisms of a therapeutic target. These interactions are often inferred from a set of active compounds that were acquired experimentally. Moreover, most docking programs loosely coupled the stages (binding-site and ligand preparations, virtual screening, and post-screening analysis) of structure-based virtual screening (VS). An integrated VS environment, which provides the friendly interface to seamlessly combine these VS stages and to identify the pharmacological interactions directly from screening compounds, is valuable for drug discovery.

Results

We developed an easy-to-use graphic environment, i GEMDOCK, integrating VS stages (from preparations to post-screening analysis). For post-screening analysis, i GEMDOCK provides biological insights by deriving the pharmacological interactions from screening compounds without relying on the experimental data of active compounds. The pharmacological interactions represent conserved interacting residues, which often form binding pockets with specific physico-chemical properties, to play the essential functions of a target protein. Our experimental results show that the pharmacological interactions derived by i GEMDOCK are often hot spots involving in the biological functions. In addition, i GEMDOCK provides the visualizations of the protein-compound interaction profiles and the hierarchical clustering dendrogram of the compounds for post-screening analysis.

Conclusions

We have developed i GEMDOCK to facilitate steps from preparations of target proteins and ligand libraries toward post-screening analysis. i GEMDOCK is especially useful for post-screening analysis and inferring pharmacological interactions from screening compounds. We believe that i GEMDOCK is useful for understanding the ligand binding mechanisms and discovering lead compounds. i GEMDOCK is available at http://gemdock.life.nctu.edu.tw/dock/igemdock.php.
Query-based biclustering of gene expression data using Probabilistic Relational Models
Authors: Zhao Hui , Cloots Lore , Van den Bulcke Tim , Wu Yan , De Smet Riet , Storms Valerie , Meysman Pieter , Engelen Kristof , Marchal Kathleen
Published: February 2011

Background

With the availability of large scale expression compendia it is now possible to view own findings in the light of what is already available and retrieve genes with an expression profile similar to a set of genes of interest (i.e., a query or seed set) for a subset of conditions. To that end, a query-based strategy is needed that maximally exploits the coexpression behaviour of the seed genes to guide the biclustering, but that at the same time is robust against the presence of noisy genes in the seed set as seed genes are often assumed, but not guaranteed to be coexpressed in the queried compendium. Therefore, we developedProBic, a query-based biclustering strategy based on Probabilistic Relational Models (PRMs) that exploits the use of prior distributions to extract the information contained within the seed set.

Results

We appliedProBic on a large scaleEscherichia colicompendium to extend partially described regulons with potentially novel members. We comparedProBic's performance with previously published query-based biclustering algorithms, namely ISA and QDB, from the perspective of bicluster expression quality, robustness of the outcome against noisy seed sets and biological relevance.

This comparison learns thatProBic is able to retrieve biologically relevant, high quality biclusters that retain their seed genes and that it is particularly strong in handling noisy seeds.

Conclusions

ProBic is a query-based biclustering algorithm developed in a flexible framework, designed to detect biologically relevant, high quality biclusters that retain relevant seed genes even in the presence of noise or when dealing with low quality seed sets.
Coregulation of transcription factors and microRNAs in human transcriptional regulatory network
Authors: Chen Cho-Yi , Chen Shui-Tein , Fuh Chiou-Shann , Juan Hsueh-Fen , Huang Hsuan-Cheng
Published: February 2011

Background

MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression at the post-transcriptional level. Recent studies have suggested that miRNAs and transcription factors are primary metazoan gene regulators; however, the crosstalk between them still remains unclear.

Methods

We proposed a novel model utilizing functional annotation information to identify significant coregulation between transcriptional and post-transcriptional layers. Based on this model, function-enriched coregulation relationships were discovered and combined into different kinds of functional coregulation networks.

Results

We found that miRNAs may engage in a wider diversity of biological processes by coordinating with transcription factors, and this kind of cross-layer coregulation may have higher specificity than intra-layer coregulation. In addition, the coregulation networks reveal several types of network motifs, including feed-forward loops and massive upstream crosstalk. Finally, the expression patterns of these coregulation pairs in normal and tumour tissues were analyzed. Different coregulation types show unique expression correlation trends. More importantly, the disruption of coregulation may be associated with cancers.

Conclusion

Our findings elucidate the combinatorial and cooperative properties of transcription factors and miRNAs regulation, and we proposes that the coordinated regulation may play an important role in many biological processes.
Semantically enabled and statistically supported biological hypothesis testing with tissue microarray databases
Authors: Song Young Soo , Park Chan Hee , Chung Hee-Joon , Shin Hyunjung , Kim Jihun , Kim Ju Han
Published: February 2011

Background

Although many biological databases are applying semantic web technologies, meaningful biological hypothesis testing cannot be easily achieved. Database-driven high throughput genomic hypothesis testing requires both of the capabilities of obtaining semantically relevant experimental data and of performing relevant statistical testing for the retrieved data. Tissue Microarray (TMA) data are semantically rich and contains many biologically important hypotheses waiting for high throughput conclusions.

Methods

An application-specific ontology was developed for managing TMA and DNA microarray databases by semantic web technologies. Data were represented as Resource Description Framework (RDF) according to the framework of the ontology. Applications for hypothesis testing (Xperanto-RDF) for TMA data were designed and implemented by (1) formulating the syntactic and semantic structures of the hypotheses derived from TMA experiments, (2) formulating SPARQLs to reflect the semantic structures of the hypotheses, and (3) performing statistical test with the result sets returned by the SPARQLs.

Results

When a user designs a hypothesis in Xperanto-RDF and submits it, the hypothesis can be tested against TMA experimental data stored in Xperanto-RDF. When we evaluated four previously validated hypotheses as an illustration, all the hypotheses were supported by Xperanto-RDF.

Conclusions

We demonstrated the utility of high throughput biological hypothesis testing. We believe that preliminary investigation before performing highly controlled experiment can be benefited.
Repeat-aware modeling and correction of short read errors
Authors: Yang Xiao , Aluru Srinivas , Dorman Karin S
Published: February 2011

Background

High-throughput short read sequencing is revolutionizing genomics and systems biology research by enabling cost-effective deep coverage sequencing of genomes and transcriptomes. Error detection and correction are crucial to many short read sequencing applications including de novo genome sequencing, genome resequencing, and digital gene expression analysis. Short read error detection is typically carried out by counting the observed frequencies of k mers in reads and validating those with frequencies exceeding a threshold. In case of genomes with high repeat content, an erroneous k mer may be frequently observed if it has few nucleotide differences with valid k mers with multiple occurrences in the genome. Error detection and correction were mostly applied to genomes with low repeat content and this remains a challenging problem for genomes with high repeat content.

Results

We develop a statistical model and a computational method for error detection and correction in the presence of genomic repeats. We propose a method to infer genomic frequencies of k mers from their observed frequencies by analyzing the misread relationships among observed k mers. We also propose a method to estimate the threshold useful for validating k mers whose estimated genomic frequency exceeds the threshold. We demonstrate that superior error detection is achieved using these methods. Furthermore, we break away from the common assumption of uniformly distributed errors within a read, and provide a framework to model position-dependent error occurrence frequencies common to many short read platforms. Lastly, we achieve better error correction in genomes with high repeat content. Availability: The software is implemented in C++ and is freely available under GNU GPL3 license and Boost Software V1.0 license at “http://aluru-sun.ece.iastate.edu/doku.php?id=redeem”.

Conclusions

We introduce a statistical framework to model sequencing errors in next-generation reads, which led to promising results in detecting and correcting errors for genomes with high repeat content.
Ontology-based instance data validation for high-quality curated biological pathways
Authors: Jeong Euna , Nagasaki Masao , Ueno Kazuko , Miyano Satoru
Published: February 2011

Background

Modeling in systems biology is vital for understanding the complexity of biological systems across scales and predicting system-level behaviors. To obtain high-quality pathway databases, it is essential to improve the efficiency of model validation and model update based on appropriate feedback.

Results

We have developed a new method to guide creating novel high-quality biological pathways, using a rule-based validation. Rules are defined to correct models against biological semantics and improve models for dynamic simulation. In this work, we have defined 40 rules which constrain event-specific participants and the related features and adding missing processes based on biological events. This approach is applied to data in Cell System Ontology which is a comprehensive ontology that represents complex biological pathways with dynamics and visualization. The experimental results show that the relatively simple rules can efficiently detect errors made during curation, such as misassignment and misuse of ontology concepts and terms in curated models.

Conclusions

A new rule-based approach has been developed to facilitate model validation and model complementation. Our rule-based validation embedding biological semantics enables us to provide high-quality curated biological pathways. This approach can serve as a preprocessing step for model integration, exchange and extraction data, and simulation.
UMARS: Un-MAppable Reads Solution
Authors: Li Sung-Chou , Chan Wen-Ching , Lai Chun-Hung , Tsai Kuo-Wang , Hsu Chun-Nan , Jou Yuh-Shan , Chen Hua-Chien , Chen Chun-Hong , Lin Wen-chang
Published: February 2011

Background

Un-MAppable Reads Solution (UMARS) is a user-friendly web service focusing on retrieving valuable information from sequence reads that cannot be mapped back to reference genomes. Recently, next-generation sequencing (NGS) technology has emerged as a powerful tool for generating high-throughput sequencing data and has been applied to many kinds of biological research. In a typical analysis, adaptor-trimmed NGS reads were first mapped back to reference sequences, including genomes or transcripts. However, a fraction of NGS reads failed to be mapped back to the reference sequences. Such un-mappable reads are usually imputed to sequencing errors and discarded without further consideration.

Methods

We are investigating possible biological relevance and possible sources of un-mappable reads. Therefore, we developed UMARS to scan for virus genomic fragments or exon-exon junctions of novel alternative splicing isoforms from un-mappable reads. For mapping un-mappable reads, we first collected viral genomes and sequences of exon-exon junctions. Then, we constructed UMARS pipeline as an automatic alignment interface.

Results

By demonstrating the results of two UMARS alignment cases, we show the applicability of UMARS. We first showed that the expected EBV genomic fragments can be detected by UMARS. Second, we also detected exon-exon junctions from un-mappable reads. Further experimental validation also ensured the authenticity of the UMARS pipeline. The UMARS service is freely available to the academic community and can be accessed via http://musk.ibms.sinica.edu.tw/UMARS/.

Conclusions

In this study, we have shown that some un-mappable reads are not caused by sequencing errors. They can originate from viral infection or transcript splicing. Our UMARS pipeline provides another way to examine and recycle the un-mappable reads that are commonly discarded as garbage.
Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics
Authors: Anderson-Carpenter Lynn L , McLachlan Jason S , Jackson Stephen T , Kuch Melanie , Lumibao Candice Y , Poinar Hendrik N
Published: February 2011

Background

Quaternary plant ecology in much of the world has historically relied on morphological identification of macro- and microfossils from sediments of small freshwater lakes. Here, we report new protocols that reliably yield DNA sequence data from Holocene plant macrofossils and bulk lake sediment used to infer ecological change. This will allow changes in census populations, estimated from fossils and associated sediment, to be directly associated with population genetic changes.

Results

We successfully sequenced DNA from 64 samples (out of 126) comprised of bulk sediment and seeds, leaf fragments, budscales, and samaras extracted from Holocene lake sediments in the western Great Lakes region of North America. Overall, DNA yields were low. However, we were able to reliably amplify samples with as few as 10 copies of a short cpDNA fragment with little detectable PCR inhibition. Our success rate was highest for sediments < 2000 years old, but we were able to successfully amplify DNA from samples up to 4600 years old. DNA sequences matched the taxonomic identity of the macrofossil from which they were extracted 79% of the time. Exceptions suggest that DNA molecules from surrounding nearby sediments may permeate or adhere to macrofossils in sediments.

Conclusions

An ability to extract ancient DNA from Holocene sediments potentially allows exciting new insights into the genetic consequences of long-term environmental change. The low DNA copy numbers we found in fossil material and the discovery of multiple sequence variants from single macrofossil extractions highlight the need for careful experimental and laboratory protocols. Further application of these protocols should lead to better understanding of the ecological and evolutionary consequences of environmental change.
Fused eco29kIR- and Mgenes coding for a fully functional hybrid polypeptide as a model of molecular evolution of restriction-modification systems
Authors: Mokrishcheva Marina L , Solonin Alexander S , Nikitin Dmitri V
Published: February 2011

Background

The discovery of restriction endonucleases and modification DNA methyltransferases, key instruments of genetic engineering, opened a new era of molecular biology through development of the recombinant DNA technology. Today, the number of potential proteins assigned to type II restriction enzymes alone is beyond 6000, which probably reflects the high diversity of evolutionary pathways. Here we present experimental evidence that a new type IIC restriction and modification enzymes carrying both activities in a single polypeptide could result from fusion of the appropriate genes from preexisting bipartite restriction-modification systems.

Results

Fusion of eco29kIR and M ORFs gave a novel gene encoding for a fully functional hybrid polypeptide that carried both restriction endonuclease and DNA methyltransferase activities. It has been placed into a subclass of type II restriction and modification enzymes - type IIC. Its MTase activity, 80% that of the M.Eco29kI enzyme, remained almost unchanged, while its REase activity decreased by three times, concurrently with changed reaction optima, which presumably can be caused by increased steric hindrance in interaction with the substrate. In vitro the enzyme preferentially cuts DNA, with only a low level of DNA modification detected. In vivo new RMS can provide a 102-fold less protection of host cells against phage invasion.

Conclusions

We propose a molecular mechanism of appearing of type IIC restriction-modification and M.SsoII-related enzymes, as well as other multifunctional proteins. As shown, gene fusion could play an important role in evolution of restriction-modification systems and be responsible for the enzyme subclass interconversion. Based on the proposed approach, hundreds of new type IIC enzymes can be generated using head-to-tail oriented type I, II, and III restriction and modification genes. These bifunctional polypeptides can serve a basis for enzymes with altered recognition specificities. Lastly, this study demonstrates that protein fusion may change biochemical properties of the involved enzymes, thus giving a starting point for their further evolutionary divergence.
Southeast Asian diversity: first insights into the complex mtDNA structure of Laos
Authors: Bodner Martin , Zimmermann Bettina , Röck Alexander , Kloss-Brandstätter Anita , Horst David , Horst Basil , Sengchanh Sourideth , Sanguansermsri Torpong , Horst Jürgen , Krämer Tanja , Schneider Peter M , Parson Walther
Published: February 2011

Background

Vast migrations and subsequent assimilation processes have shaped the genetic composition of Southeast Asia, an area of close contact between several major ethnic groups. To better characterize the genetic variation of this region, we analyzed the entire mtDNA control region of 214 unrelated donors from Laos according to highest forensic quality standards. To detail the phylogeny, we inspected selected SNPs from the mtDNA coding region. For a posteriori data quality control, quasi-median network constructions and autosomal STR typing were performed. In order to describe the mtDNA setup of Laos more thoroughly, the data were subjected to population genetic comparisons with 16 East Asian groups.

Results

The Laos sample exhibited ample mtDNA diversity, reflecting the huge number of ethnic groups listed. We found several new, so far undescribed mtDNA lineages in this dataset and surrounding populations. The Laos population was characteristic in terms of haplotype composition and genetic structure, however, genetic comparisons with other Southeast Asian populations revealed limited, but significant genetic differentiation. Notable differences in the maternal relationship to the major indigenous Southeast Asian ethnolinguistic groups were detected.

Conclusions

In this study, we portray the great mtDNA variety of Laos for the first time. Our findings will contribute to clarify the migration history of the region. They encourage setting up regional and subpopulation databases, especially for forensic applications. The Laotian sequences will be incorporated into the collaborative EMPOP mtDNA database http://www.empop.org upon publication and will be available as the first mtDNA reference data for this country.
Applicability of RNA standards for evaluating RT-qPCR assays and platforms
Authors: Devonshire Alison S , Elaswarapu Ramnath , Foy Carole A
Published: February 2011

The availability of diverse RT-qPCR assay formats and technologies hinder comparability of data between platforms. Reference standards to facilitate platform evaluation and comparability are needed. We have explored using universal RNA standards for comparing the performance of a novel qPCR platform (Fluidigm® BioMark™) against the widely used ABI 7900HT system. Our results show that such standards may form part of a toolkit to evaluate the key performance characteristics of platforms.
Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology
Authors: Oliver Rebekah E , Lazo Gerard R , Lutz Joseph D , Rubenfield Marc J , Tinker Nicholas A , Anderson Joseph M , Wisniewski Morehead Nicole H , Adhikary Dinesh , Jellen Eric N , Maughan P Jeffrey , Brown Guedira Gina L , Chao Shiaoman , Beattie Aaron D , Carson Martin L , Rines Howard W , Obert Donald E , Bonman J Michael , Jackson Eric W
Published: February 2011

Background

Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST) information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat.

Results

Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subgenome homology, and 96 in silico SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM) analysis. Of these, 52 (54%) were polymorphic between parents of the Ogle1040 × TAM O-301 (OT) mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, deletions, and heterozygotes in secondary oat germplasm pools, generating multiple alleles at some primer targets. To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. Dendrogram clusters corresponded generally to known genome composition and genetic ancestry.

Conclusions

The high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. The current-generation HRM system is a simple and highly-informative platform for SNP genotyping. These techniques provide a model for SNP discovery and genotyping in other species with complex and poorly-characterized genomes.
Ethidium bromide transport across Mycobacterium smegmatiscell-wall: correlation with antibiotic resistance
Authors: Rodrigues Liliana , Ramos Jorge , Couto Isabel , Amaral Leonard , Viveiros Miguel
Published: February 2011

Background

Active efflux systems and reduced cell-wall permeability are considered to be the main causes of mycobacterial intrinsic resistance to many antimicrobials. In this study, we have compared the Mycobacterium smegmatis wild-type strain mc2155 with knockout mutants for porins MspA (the main porin of M. smegmatis) and MspC, the efflux pump LfrA (the main efflux pump system of M. smegmatis) and its repressor LfrR for their ability to transport ethidium bromide (EtBr) on a real-time basis. This information was then correlated with minimum inhibitory concentrations (MICs) of several antibiotics in the presence or absence of the efflux inhibitors chlorpromazine, thioridazine and verapamil.

Results

In the absence of porins MspA and MspC, accumulation of ethidium bromide decreased and the cells became more resistant to several antibiotics, whereas the knockout mutant for the LfrA pump showed increased accumulation of EtBr and increased susceptibility to EtBr, rifampicin, ethambutol and ciprofloxacin. Moreover, the efflux inhibitors caused a reduction of the MICs of streptomycin, rifampicin, amikacin, ciprofloxacin, clarithromycin and erythromycin in most of the strains tested.

Conclusions

The methodology used in this study demonstrated that porin MspA plays an important role in the influx of quaternary ammonium compounds and antibiotics and that efflux via the LfrA pump is involved in low-level resistance to several antimicrobial drugs in M. smegmatis. The results obtained with this non-pathogenic mycobacterium will be used in future studies as a model for the evaluation of the activity of the same efflux inhibitors on the susceptibility of multidrug resistant strains of Mycobacterium tuberculosis to isoniazid and rifampicin.
Incidence of Hepatitis-C among HIV infected men who have sex with men (MSM) attending a sexual health service: a cohort study
Authors: Gamage Deepa G , Read Tim RH , Bradshaw Catriona S , Hocking Jane S , Howley Kerry , Chen Marcus Y , Fairley Christopher K
Published: February 2011

Background

We aimed to determine the incidence of Hepatitis C (HCV) infection among HIV-infected men who have sex with men (MSM) attending a Sexual Health Centre.

Methods

A retrospective cohort study was carried out among HIV-infected MSM seen at least once between February 2002 and March 2010. The analysis was restricted to MSM who had had a negative HCV antibody test at least 6 months after their diagnosis for HIV. Duration of follow up was taken from the date of HIV diagnosis to the first positive or last negative HCV antibody test.

Results

During the time 1445 HIV-infected men attended the clinic of whom 1065 (74%) were MSM. Of these, 869 (82%) were tested for HCV at any time after HIV diagnosis. Of these 869, 69% (620) tested HCV negative at least 6 months after their HIV diagnosis. These 620 men had a mean age of 34 years (range 17-72) at HIV diagnosis and a total of 4,359 person years (PY) of follow up. There were 40 incident cases of HCV, of which 16 were in injecting drug users (IDU) and 24 in non-IDU. The overall incidence of HCV among HIV-infected MSM was 0.9/100 PY (95% CI 0.6-1.2). The incidence among HIV-infected IDU was 4.7/100 PY (95% CI 2.7-7.5) while the incidence among HIV-infected non-IDU was 0.6/100 PY (95% CI 0.4-0.8) (hazard ratio of 8.7 and 95% CI 4.6-16.6, P < 0.001).

The majority (78%) were tested for HCV because they developed abnormal liver transaminases (n = 31) or hepatitis symptoms (n = 2), while others (n = 7) were identified through routine HCV testing.

Conclusion

A considerable proportion of HIV-positive MSM who did not inject drugs contracted HCV, presumably via sexual transmission and the main trigger for investigation was abnormal liver transaminases.
Serum antibodies against genitourinary infectious agents in prostate cancer and benign prostate hyperplasia patients: a case-control study
Authors: Hrbacek Jan , Urban Michael , Hamsikova Eva , Tachezy Ruth , Eis Vaclav , Brabec Marek , Heracek Jiri
Published: February 2011

Background

Infection plays a role in the pathogenesis of many human malignancies. Whether prostate cancer (PCa) - an important health issue in the aging male population in the Western world - belongs to these conditions has been a matter of research since the 1970 s. Persistent serum antibodies are a proof of present or past infection. The aim of this study was to compare serum antibodies against genitourinary infectious agents between PCa patients and controls with benign prostate hyperplasia (BPH). We hypothesized that elevated serum antibody levels or higher seroprevalence in PCa patients would suggest an association of genitourinary infection in patient history and elevated PCa risk.

Methods

A total of 434 males who had undergone open prostate surgery in a single institution were included in the study: 329 PCa patients and 105 controls with BPH. The subjects' serum samples were analysed by means of enzyme-linked immunosorbent assay, complement fixation test and indirect immunofluorescence for the presence of antibodies against common genitourinary infectious agents: human papillomavirus (HPV) 6, 11, 16, 18, 31 and 33, herpes simplex virus (HSV) 1 and 2, human cytomegalovirus (CMV), Chlamydia trachomatis, Mycoplasma hominis, Ureaplasma urealyticum, Neisseria gonorrhoeae and Treponema pallidum. Antibody seroprevalence and mean serum antibody levels were compared between cases and controls. Tumour grade and stage were correlated with serological findings.

Results

PCa patients were more likely to harbour antibodies against Ureaplasma urealyticum (odds ratio (OR) 2.06; 95% confidence interval (CI) 1.08-4.28). Men with BPH were more often seropositive for HPV 18 and Chlamydia trachomatis (OR 0.23; 95% CI 0.09-0.61 and OR 0.45; 95% CI 0.21-0.99, respectively) and had higher mean serum CMV antibody levels than PCa patients (p = 0.0004). Among PCa patients, antibodies against HPV 6 were associated with a higher Gleason score (p = 0.0305).

Conclusions

Antibody seropositivity against the analyzed pathogens with the exception of Ureaplasma does not seem to be a risk factor for PCa pathogenesis. The presence or higher levels of serum antibodies against the genitourinary pathogens studied were not consistently associated with PCa. Serostatus was not a predictor of disease stage in the studied population.
Evaluation of a single round polymerase chain reaction assay using dried blood spots for diagnosis of HIV-1 infection in infants in an African setting
Authors: Chohan Bhavna H , Emery Sandra , Wamalwa Dalton , John-Stewart Grace , Majiwa Maxwel , Ng'ayo Musa , Froggett Steve , Overbaugh Julie
Published: February 2011

Background

The aim of this study was to develop an economical 'in-house' single round polymerase chain reaction (PCR) assay using filter paper-dried blood spots (FP-DBS) for early infant HIV-1 diagnosis and to evaluate its performance in an African setting.

Methods

An 'in-house' single round PCR assay that targets conserved regions in the HIV-1 polymerase (pol) gene was validated for use with FP-DBS; first we validated this assay using FP-DBS spiked with cell standards of known HIV-1 copy numbers. Next, we validated the assay by testing the archived FP-DBS (N = 115) from infants of known HIV-1 infection status. Subsequently this 'in-house' HIV-1polPCR FP-DBS assay was then established in Nairobi, Kenya for further evaluation on freshly collected FP-DBS (N = 186) from infants, and compared with findings from a reference laboratory using the Roche Amplicor®HIV-1 DNA Test, version 1.5 assay.

Results

The HIV-1polPCR FP-DBS assay could detect one HIV-1 proviral copy in 38.7% of tests, 2 copies in 46.9% of tests, 5 copies in 72.5% of tests and 10 copies in 98.1% of tests performed with spiked samples. Using the archived FP-DBS samples from infants of known infection status, this assay was 92.8% sensitive and 98.3% specific for HIV-1 infant diagnosis. Using 186 FP-DBS collected from infants recently defined as HIV-1 positive using the commercially available Roche Amplicor v1.5 assay, 178 FP-DBS tested positive by this 'in-house' single-round HIV-1polPCR FP-DBS PCR assay. Upon subsequent retesting, the 8 infant FP-DBS samples that were discordant were confirmed as HIV-1 negative by both assays using a second blood sample.

Conclusions

HIV-1 was detected with high sensitivity and specificity using both archived and more recently collected samples. This suggests that this 'in-house' HIV-1polFP-DBS PCR assay can provide an alternative cost-effective, reliable and rapid method for early detection of HIV-1 infection in infants.
The Happy Life Club™ study protocol: A cluster randomised controlled trial of a type 2 diabetes health coach intervention
Authors: Browning Colette , Chapman Anna , Cowlishaw Sean , Li Zhixin , Thomas Shane A , Yang Hui , Zhang Tuohong
Published: February 2011

Background

The Happy Life Club™ is an intervention that utilises health coaches trained in behavioural change and motivational interviewing techniques to assist with the management of type 2 diabetes mellitus (T2DM) in primary care settings in China. Health coaches will support participants to improve modifiable risk factors and adhere to effective self-management treatments associated with T2DM.

Methods/Design

A cluster randomised controlled trial involving 22 Community Health Centres (CHCs) in Fengtai District of Beijing, China. CHCs will be randomised into a control or intervention group, facilitating recruitment of at least 1320 individual participants with T2DM into the study. Participants in the intervention group will receive a combination of both telephone and face-to-face health coaching over 18 months, in addition to usual care received by the control group. Health coaching will be performed by CHC doctors and nurses certified in coach-assisted chronic disease management. Outcomes will be assessed at baseline and again at 6, 12 and 18 months by means of a clinical health check and self-administered questionnaire. The primary outcome measure is HbA1c level. Secondary outcomes include metabolic, physiological and psychological variables.

Discussion

This cluster RCT has been developed to suit the Chinese health care system and will contribute to the evidence base for the management of patients with T2DM. With a strong focus on self-management and health coach support, the study has the potential to be adapted to other chronic diseases, as well as other regions of China.

Trial Registration

Current Controlled Trials ISRCTN01010526
Ethnic disparity in 21-hydroxylase gene mutations identified in Pakistani congenital adrenal hyperplasia patients
Authors: Khan Aysha H , Aban Muniba , Raza Jamal , ul Haq Naeem , Jabbar Abdul , Moatter Tariq
Published: February 2011

Background

Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorders caused by defects in the steroid 21 hydroxylase gene (CYP21A2). We studied the spectrum of mutations in CYP21A2 gene in a multi-ethnic population in Pakistan to explore the genetics of CAH.

Methods

A cross sectional study was conducted for the identification of mutations CYP21A2 and their phenotypic associations in CAH using ARMS-PCR assay.

Results

Overall, 29 patients were analyzed for nine different mutations. The group consisted of two major forms of CAH including 17 salt wasters and 12 simple virilizers. There were 14 phenotypic males and 15 females representing all the major ethnic groups of Pakistan. Parental consanguinity was reported in 65% cases and was equally distributed in the major ethnic groups. Among 58 chromosomes analyzed, mutations were identified in 45 (78.6%) chromosomes. The most frequent mutation was I2 splice (27%) followed by Ile173Asn (26%), Arg 357 Trp (19%), Gln319stop, 16% and Leu308InsT (12%), whereas Val282Leu was not observed in this study. Homozygosity was seen in 44% and heterozygosity in 34% cases. I2 splice mutation was found to be associated with SW in the homozygous. The Ile173Asn mutation was identified in both SW and SV forms. Moreover, Arg357Trp manifested SW in compound heterozygous state.

Conclusion

Our study showed that CAH exists in our population with ethnic difference in the prevalence of mutations examined.
Spatio-temporal analysis of mortality among children under the age of five in Manhiça (Mozambique) during the period 1997-2005
Authors: Escaramís Geòrgia , Carrasco Josep L , Aponte John J , Nhalungo Delino , Nhacolo Ariel , Alonso Pedro , Ascaso Carlos
Published: February 2011

Background

Reducing childhood mortality is the fourth goal of the Millennium Development Goals agreed at the United Nations Millennium Summit in September 2000. However, childhood mortality in developing countries remains high. Providing an accurate picture of space and time-trend variations in child mortality in a region might generate further ideas for health planning actions to achieve such a reduction. The purpose of this study was to examine the spatio-temporal variation for child mortality rates in Manhiça, a district within the Maputo province of southern rural Mozambique during the period 1997-2005 using a proper generalized linear mixed model.

Results

The results showed that childhood mortality in all the area was modified from year to year describing a convex time-trend but the spatial pattern described by the neighbourhood-specific underlying mortality rates did not change during the entire period from 1997 to 2005, where neighbourhoods with highest risks are situated in the peripheral side of the district. The spatial distribution, though more blurred here, was similar to the spatial distribution of child malaria incidence in the same area. The peak in mortality rates observed in 2001 could have been caused by the precipitation system that started in early February 2000, following which heavy rains flooded parts of Mozambique's southern provinces. However, the mortality rates at the end of the period returned to initial values.

Conclusions

The results of this study suggest that the health intervention programmes established in Manhiça to alleviate the effects of flooding on child mortality should cover a period of around five years and that special attention might be focused on eradicating malaria transmission. These outcomes also suggest the utility of suitably modelling space-time trend variations in a region when a point effect of an environmental factor affects all the study area.
In vivo observation of gold nanoparticles in the central nervous system of Blaberus discoidalis
Authors: Rocha Aracely , Zhou Yan , Kundu Subrata , González Jorge M , BradleighVinson S , Liang Hong
Published: February 2011

Background

Nanoparticles (NPs) are widely studied for biomedical applications. Understanding interactions between NPs and biomolecules or cells has yet to be achieved. Here we present a novel in vivo method to study interactions between NPs and the nervous system of the discoid or false dead-head roach, Blaberus discoidalis. The aims of this study were to present a new and effective method to observe NPs in vivo that opens the door to new methods of study to observe the interactions between NPs and biological systems and to present an inexpensive and easy-to-handle biological system.

Results

Negatively charged gold nanoparticles (nAuNPs) of 50 nm in diameter were injected into the central nervous system (CNS) of the insect. By using such a cost effective method, we were able to characterize nAuNPs and to analyze their interactions with a biological system. It showed that the charged particles affected the insect's locomotion. The nAuNPs affected the insect's behavior but had no major impacts on the life expectancy of the cockroach after two months of observation. This was apparently due to the encapsulation of nAuNPs inside the insect's brain. Based on cockroach's daily activity, we believed that the encapsulation occurred in the first 17 days.

Conclusions

The method proposed here is an inexpensive and reliable way of observing the response of biological systems to nanoparticles in-vivo. It opens new windows to further understand how nanoparticles affect neural communication by monitoring insect activity and locomotion.
Epidermal growth factor receptor mutation in combination with expression of MIG6 alters gefitinib sensitivity
Authors: Naruo Yoshimi , Nagashima Takeshi , Ushikoshi-Nakayama Ryoko , Saeki Yuko , Nakakuki Takashi , Naka Takashi , Tanaka Hiroshi , Tsai Shih-Feng , Okada-Hatakeyama Mariko
Published: February 2011

Background

Epidermal growth factor receptor (EGFR) signaling plays an important role in the regulation of cell proliferation, survival, metastasis, and invasion in various tumors. Earlier studies showed that the EGFR is frequently overexpressed in non-small-cell lung cancer (NSCLC) and EGFR mutations at specific amino acid residues in the kinase domain induce altered responsiveness to gefitinib, a small molecule EGFR tyrosine kinase inhibitor. However, the mechanism underlying the drug response modulated by EGFR mutation is still largely unknown. To elucidate drug response in EGFR signal transduction pathway in which complex dynamics of multiple molecules involved, a systematic approach is necessary. In this paper, we performed experimental and computational analyses to clarify the underlying mechanism of EGFR signaling and cell-specific gefitinib responsiveness in three H1299-derived NSCLC cell lines; H1299 wild type (H1299WT), H1299 with an overexpressed wild type EGFR (H1299EGFR-WT), and H1299 with an overexpressed mutant EGFR L858R (H1299L858R; gefitinib sensitive mutant).

Results

We predicted and experimentally verified that Mig6, which is a known negative regulator of EGFR and specifically expressed in H1299L858R cells, synergized with gefitinib to suppress cellular growth. Computational analyses indicated that this inhibitory effect is amplified at the phosphorylation/dephosphorylation steps of MEK and ERK.

Conclusions

Thus, we showed that L858R receptor mutation in combination with expression of its negative regulator, Mig6, alters signaling outcomes and results in variable drug sensitivity.
Ovarian cryopreservation after laparoscopic ovariectomy using the Endo-GIA stapling device and LAPRO-clip absorbable ligating clip in a woman: a case report
Authors: Roux Isabelle , Grynberg Michaël , Linehan Jenna , Messner Alexandra , Deffieux Xavier
Published: February 2011

Introduction

Several options are available for preserving fertility before cytotoxic treatment, including ovarian tissue cryopreservation. Most reported surgical techniques include electrocoagulation. Our hypothesis is that avoidance of electrocoagulation may decrease ovarian cortex injury during cryopreservation procedures.

Case presentation

We report a laparoscopic technique of whole-ovary removal without coagulation using Endo-GIA forceps and clips. Laparoscopic ovariectomy was performed for cryopreservation in a 37-year-old Caucasian woman with breast cancer and for whom chemotherapy was planned. The procedure was completed quickly and without complication. This Endo-GIA procedure was of short duration with a short period of ischemia before freezing.

Conclusion

Laparoscopic ovariectomy using the Endo-GIA stapling device procedure without coagulation may diminish ovary injury before ovarian cryopreservation.