ALBERT

Description: Background: A live foreign body in trachea or bronchus is a very rare as well as life threatening condition. A bigger fish with irregular shape usually impacts at the oropharynx, hypopharynx or inlet of the larynx. But a small or flat, elongated foreign body may cross the glottis and enter into trachea and bronchus. We report a rare type of very long live fish in trachea and bronchus.Case presentationA 16-year-old Bangladeshi boy presented with severe respiratory distress and cyanosis with a history of live fish impaction in the throat. To relieve respiratory distress and secure life an emergency tracheostomy was carried out while a tail fin of a fish was seen through tracheostome directed to the right bronchus which was grasped with an artery forceps and pulled out of the trachea. Respiratory distress was relieved immediately. The fish removed from the trachea was locally known as Guchi Baim Fish (Macrognathus pancalus). It was about 16 cm long and about 2 cm wide at its central region. Conclusion: Live fish lodging in the trachea and bronchus is an acute emergency condition. It is very difficult to diagnose and manage because of its presence in critical anatomical location. So a quick short history from accompanying persons especially about the type of fish is crucial to predicting the site of its lodgement in the airway as well as management plan. Avoidance of the tendency of holding the fish between teeth during fishing can prevent this life threatening condition.

Description: Background: Hyperlipidaemia is a major risk factor for coronary artery disease (CAD) and cholesteryl ester transfer protein (CETP) gene polymorphisms are known to be associated with lipid profiles. Methods: In this study, we investigated the association of two polymorphisms in the CETP, Taq1B (rs708272) and -629C 〉 A (rs1800775), with CAD and lipid levels HDL-C in 662 CAD + cases and 927 controls from the Singapore population comprising Chinese, Malays and Indians. Results: TaqB2 frequency was significantly lowest in the Malays (0.43) followed by Chinese (0.47) and highest in the Indians (0.56) in the controls. The B2 allele frequency was significantly lower in the Chinese CAD + cases compared to the controls (p = 0.002). The absence of the B2 allele was associated with CAD with an OR 2.0 (95% CI 1.2 to 3.4) after adjustment for the confounding effects of age, smoking, BMI, gender, hypertension, dyslipidemia and diabetes mellitus. The B2 allele was significantly associated with higher plasma HDL-C levels in the Chinese men after adjusting for confounders. Associations with plasma apoA1 levels were significant only in the Chinese men for Taq1B and -629C 〉 A. In addition, the Taq1B polymorphism was only associated with plasma Apo B and Lp(a) in the Malay men. Significant associations were only found in non-smoking subjects with BMI A polymorphisms seemed to be weak. Conclusion: The absence the Taq1B2 allele was associated with CAD in the Chinese population only and the minor allele of the Taq1B polymorphism of the CETP gene was significantly associated with higher plasma HDL-C levels in Chinese men.

Description: Plant genomes are populated by different types of repetitive elements including transposable elements (TEs) and simple sequence repeats (SSRs) that can have a strong impact on genome size and dynamic as well a...

Description: Regulation of gene expression by histone-modifying enzymes is essential to control cell fate decisions and developmental processes. Two histone-modifying enzymes, RPD3, a deacetylase, and dKDM5/LID, a demethyl...

Description: Background: Development of Salmonella enterica serovar Typhimurium (S. Typhimurium) live attenuated vaccine carrier strain to prevent enteric infections has been a subject of intensive study. Several mutants of S. Typhimurium have been proposed as an effective live attenuated vaccine strain. Unfortunately, many such mutant strains failed to successfully complete the clinical trials as they were suboptimal in delivering effective safety and immunogenicity. However, it remained unclear, whether the existing live attenuated S. Typhimurium strains can further be attenuated with improved safety and immune efficacy or not. Results: We deleted a specific non-SPI (Salmonella Pathogenicity Island) encoded virulence factor mig-14 (an antimicrobial peptide resistant protein) in ssaV deficient S. Typhimurium strain. The ssaV is an important SPI-II gene involved in Salmonella replication in macrophages and its mutant strain is considered as a potential live attenuated strain. However, fatal systemic infection was previously reported in immunocompromised mice like Nos2-/- and Il-10-/- when infected with ssaV deficient S. Typhimurium. Here we reported that attenuation of S. Typhimurium ssaV mutant in immunocompromised mice can further be improved by introducing additional deletion of gene mig-14. The ssaV, mig-14 double mutant was as efficient as ssaV mutant, with respect to host colonization and eliciting Salmonella-specific mucosal sIgA and serum IgG response in wild-type C57BL/6 mice. Interestingly, this double mutant did not show any systemic infection in immunocompromised mice. Conclusions: This study suggests that ssaV, mig-14 double mutant strain can be effectively used as a potential vaccine candidate even in immunocompromised mice. Such attenuated vaccine strain could possibly used for expression of heterologous antigens and thus for development of a polyvalent vaccine strain.

Description: Background: The Firmicutes often possess three conspicuous genome features: marked Purine Asymmetry (PAS) across two strands of replication, Strand-biased Gene Distribution (SGD) and presence of two isoforms of DNA polymerase III alpha subunit, PolC and DnaE. Despite considerable research efforts, it is not clear whether the co-existence of PAS, PolC and/or SGD is an essential and exclusive characteristic of the Firmicutes. The nature of correlations, if any, between these three features within and beyond the lineages of Firmicutes has also remained elusive. The present study has been designed to address these issues. Results: A large-scale analysis of diverse bacterial genomes indicates that PAS, PolC and SGD are neither essential nor exclusive features of the Firmicutes. PolC prevails in four bacterial phyla: Firmicutes, Fusobacteria, Tenericutes and Thermotogae, while PAS occurs only in subsets of Firmicutes, Fusobacteria and Tenericutes. There are five major compositional trends in Firmicutes: (I) an explicit PAS or G + A-dominance along the entire leading strand (II) only G-dominance in the leading strand, (III) alternate stretches of purine-rich and pyrimidine-rich sequences, (IV) G + T dominance along the leading strand, and (V) no identifiable patterns in base usage. Presence of strong SGD has been observed not only in genomes having PAS, but also in genomes with G-dominance along their leading strands - an observation that defies the notion of co-occurrence of PAS and SGD in Firmicutes. The PolC-containing non-Firmicutes organisms often have alternate stretches of R-dominant and Y-dominant sequences along their genomes and most of them show relatively weak, but significant SGD. Firmicutes having G + A-dominance or G-dominance along LeS usually show distinct base usage patterns in three codon sites of genes. Probable molecular mechanisms that might have incurred such usage patterns have been proposed. Conclusion: Co-occurrence of PAS, strong SGD and PolC should not be regarded as a genome signature of the Firmicutes. Presence of PAS in a species may warrant PolC and strong SGD, but PolC and/or SGD not necessarily implies PAS.

Description: Background: Affinity-Purification Mass-Spectrometry (AP-MS) provides a powerful means of identifyingprotein complexes and interactions. Several important challenges exist in interpreting theresults of AP-MS experiments. First, the reproducibility of AP-MS experimental replicatescan be low, due both to technical variability and the dynamic nature of protein interactions inthe cell. Second, the identification of true protein-protein interactions in AP-MS experimentsis subject to inaccuracy due to high false negative and false positive rates. Severalexperimental approaches can be used to mitigate these drawbacks, including the use ofreplicated and control experiments and relative quantification to sensitively distinguish trueinteracting proteins from false ones. Results: To address the issues of reproducibility and accuracy of protein-protein interactions, weintroduce a two-step method, called ROCS, which makes use of Indicator Proteins to selectreproducible AP-MS experiments, and of Confidence Scores to select specific protein-proteininteractions. The Indicator Proteins account for measures of protein identification as well asprotein reproducibility, effectively allowing removal of outlier experiments that contributenoise and affect downstream inferences. The filtered set of experiments is then used in theProtein-Protein Interaction (PPI) scoring step. Prey protein scoring is done by computing aConfidence Score, which accounts for the probability of occurrence of prey proteins in thebait experiments relative to the control experiment, where the significance cutoff parameter isestimated by simultaneously controlling false positives and false negatives against metrics offalse discovery rate and biological coherence respectively. In summary, the ROCS methodrelies on automatic objective criterions for parameter estimation and error-controlledprocedures. We illustrate the performance of our method by applying it to five previously published AP-MS experiments, each containing well characterized protein interactions,allowing for systematic benchmarking of ROCS. We show that our method may be used onits own to make accurate identification of specific, biologically relevant protein-proteininteractions or in combination with other AP-MS scoring methods to significantly improveinferences. Conclusions: Our method addresses important issues encountered in AP-MS datasets, making ROCS a verypromising tool for this purpose, either on its own or especially in conjunction with other Methods: We anticipate that our methodology may be used more generally in proteomicsstudies and databases, where experimental reproducibility issues arise. The method isimplemented in the R language, and is available as an R package called "ROCS", freelyavailable from the CRAN repository http://cran.r-project.org/.

Description: Background; Single Nucleotide Polymorphisms (SNPs) are sequence variations found in individuals at some spe-cific points in the genomic sequence. As SNPs are highly conserved throughout evolution and withina population, the map of SNPs serves as an excellent genotypic marker. Conventional SNPs analysismechanisms suffer from large run times, inefficient memory usage, and frequent overestimation. Inthis paper, we propose efficient, scalable, and reliable algorithms to select a small subset of SNPsfrom a large set of SNPs which can together be employed to perform phenotypic classification.Methods; Our algorithms exploit the techniques of gene selection and random projections to identify a mean-ingful subset of SNPs. To the best of our knowledge, these techniques have not been employed beforein the context of genotype-phenotype correlations. Random projections are used to project the inputdata into a lower dimensional space (closely preserving distances). Gene selection is then applied onthe projected data to identify a subset of the most relevant SNPs.Results; We have compared the performance of our algorithms with one of the currently known best algorithmscalled Multifactor Dimensionality Reduction (MDR), and Principal Component Analysis (PCA) tech-nique. Experimental results demonstrate that our algorithms are superior in terms of accuracy as wellas run time.Conclusions; In our proposed techniques, random projection is used to map data from a high dimensional space toa lower dimensional space, and thus overcomes the curse of dimensionality problem. From this spaceof reduced dimension, we select the best subset of attributes. It is a unique mechanism in the domainof SNPs analysis, and to the best of our knowledge it is not employed before. As revealed by ourexperimental results, our proposed techniques offer the potential of high accuracies while keeping therun times low.

Description: Among SNP markers that become increasingly valuable in molecular breeding of crop plants are the CAPS and dCAPS markers derived from the genes of interest. To date, the number of such gene-based markers is sma...