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2010-02-09
Annotation and classification of the bovine T cell receptor delta genes
BioMed Central - Latest articles
Background:Gamma delta T cells differ from alpha beta T cells with regard to the types of antigen with which their T cell receptors interact; gamma delta T cell antigens are not necessarily peptides nor are they presented on MHC. Cattle are considered a "gamma delta T cell high" species indicating they have an increased proportion of gamma delta T cells in circulation relative to that in "gamma delta T cell low" species such as humans and mice. Prior to the onset of the studies described here, there was limited information regarding the genes that code for the T cell receptor delta chains of this gamma delta T cell high species.Results:By annotating the bovine (Bos taurus) genome Btau_3.1 assembly the presence of 56 distinct T cell receptor delta (TRD) variable (V) genes were found, 52 of which belong to the TRDV1 subgroup and were co-mingled with the T cell receptor alpha variable (TRAV) genes. In addition, two genes belonging to the TRDV2 subgroup and single TRDV3 and TRDV4 genes were found. We confirmed the presence of five diversity (D) genes, three junctional (J) genes and a single constant (C) gene and describe the organization of the TRD locus. The TRDV4 gene is found downstream of the C gene and in an inverted orientation of transcription, consistent with its orthologs in humans and mice. cDNA evidence was assessed to validate expression of the variable genes and showed that one to five D genes could be incorporated into a single transcript. Finally, we grouped the bovine and ovine TRDV1 genes into sets based on their relatedness.Conclusions:The bovine genome contains a large and diverse repertoire of TRD genes when compared to the genomes of "gamma delta T cell low" species. This suggests that in cattle gamma delta T cells play a more important role in immune function since they would be predicted to bind a greater variety of antigens.
Keywords:
Bos taurus
2010-02-07
Mopane worm allergy in a 36-year-old woman: a case report
BioMed Central - Latest articles
IntroductionThe increasing incidence of new diseases as well as changing features of known diseases has partly been attributed to the impact of environmental changes. As a result, there have been calls from health experts for proper surveillance and monitoring of these changes.This is a report of mopane worm allergy in a 36 year old lady from the Tswana tribe in Botswana. Mopane worm, the caterpillar stage of Gonimbrasia belina moths, is a seasonal delicacy of people in many communities in southern Africa. As a result, by adulthood, many residents of these communities have had substantial exposure to the worm. Gonimbrasia belina moths belong to the Lepidoptera order of insects. Though some members of this order are known to induce contact allergy, there is no reported incidence of ingestion allergy from mopane worm. Therefore, it is important to track this case for its epidemiological significance and to alert both clinicians and the vulnerable public on this incidence of mopane worm allergy in this region.Case presentationThis is a case of a 36 year old female nurse from Tswana ethnic group in Botswana, who was diagnosed of food allergy. She presented with itchy skin rash, facial swelling, and mild hypotension after eating mopane worm. She had no previous history of allergic reaction following contact or ingestion of mopane worm. She has no atopic illness in the past. She was treated and her symptoms resolved after 4 days.Conclusion:The proper management of allergy involves patients' avoidance and clinicians' predictability. Though hypothetical, this report is expected to sensitize clinicians to anticipate and properly manage subsequent occurrence, as well as educate the public in these communities. In addition, tracking new disease patterns, with remote relationship to environmental changes, will complement existing evidence in validating the importance of proper environmental surveillance and management.
Keywords:
Gonimbrasia belina, Lepidoptera
2010-02-06
Bacteria under SOS evolve anticancer phenotypes
BioMed Central - Latest articles
Background:The anticancer drugs, such as DNA replication inhibitors, stimulate bacterial adhesion and induce the bacterial SOS response. As a variety of bacterial mutants can be generated during SOS, novel phenotypes are likely to be selected under the drug pressure.Presentation of the hypothesisBacteria growing with cancer cells in the presence of the replication inhibitors undergo the SOS response and evolve advantageous phenotypes for the bacteria to invade the cancer cells in order to evade the drug attack. This hypothesis predicts that bacteria produce the proteins that mediate bacterial capture and invasion of cancer cells - the advantageous phenotypes. Generation of the phenotypes may be facilitated during the SOS response induced by anticancer drugs.Testing the hypothesisExperimental design: 1) Examine attachment and invasion of bacterium Pseudomonas aeruginosa and the SOS mutant control to cancer cells in the presence of the anticancer drugs that inhibit DNA replication enzymes and trigger the SOS response. 2) Reveal the bacterial proteins that exhibit changes in expression. 3) Identify the genes encoding cancer adhesion and invasion. 4) Construct the mutants for the genes, clone and express these genes. 5) Examine the bacterial capture and invasion of cancer cells in contrast to non-cancer control.Expected results: 1) The bacterial proteins will be differentially induced during bacteria-cancer interaction under the SOS response to the anticancer drugs. 2) Knocking out the bacterial cancer-adhesion-invasion genes will disrupt the adhesion-invasion phenotypes of the bacteria. 3) Expressing these genes will direct the bacterial capture and invasion of cancer cells.Implications of the hypothesisBacteria can evolve anticancer phenotypes targeting metastatic cells. If this hypothesis is true, the outcomes will contribute to development of a novel bacterial anti-metastasis regimen.
Keywords:
Pseudomonas aeruginosa
2010-02-04
Whole-genome sequencing of a laboratory-evolved yeast strain
BioMed Central - Latest articles
Background:Experimental evolution of microbial populations provides a unique opportunity to study evolutionary adaptation in response to controlled selective pressures. However, until recently it has been difficult to identify the precise genetic changes underlying adaptation at a genome-wide scale. New DNA sequencing technologies now allow the genome of parental and evolved strains of microorganisms to be rapidly determined.Results:We sequenced >93.5% of the genome of a laboratory-evolved strain of the yeast Saccharomyces cerevisiae and its ancestor at >28x depth. Both single nucleotide polymorphisms and copy number amplifications were found, with specific gains over array-based methodologies previously used to analyze these genomes. Applying a segmentation algorithm to quantify structural changes, we determined the approximate genomic boundaries of a 5x gene amplification. These boundaries guided the recovery of breakpoint sequences, which provide insights into the nature of a complex genomic rearrangement.Conclusions:This study suggests that whole-genome sequencing can provide a rapid approach to uncover the genetic basis of evolutionary adaptations, with further applications in the study of laboratory selections and mutagenesis screens. In addition, we show how single-end, short read sequencing data can provide detailed information about structural rearrangements, and generate predictions about the genomic features and processes that underlie genome plasticity.
Keywords:
Saccharomyces cerevisiae
2010-02-04
Escherichia coli genes that reduce the lethal effects of stress
BioMed Central - Latest articles
Background:The continuing emergence of antimicrobial resistance requires the development of new compounds and/or enhancers of existing compounds. Genes that protect against the lethal effects of antibiotic stress are potential targets of enhancers. To distinguish such genes from those involved in drug uptake and efflux, a new susceptibility screen is required.Results:Transposon (Tn5)-mediated mutagenesis was used to create a library of Escherichia coli mutants that was screened for hypersensitivity to the lethal action of quinolones and counter-screened to have wild-type bacteriostatic susceptibility. Mutants with this novel "hyperlethal" phenotype were found. The phenotype was transferable to other E. coli strains by P1-mediated transduction, and for a subset of the mutants the phenotype was complemented by the corresponding wild-type gene cloned into a plasmid. Thus, the inactivation of these genes was responsible for hyperlethality. Nucleotide sequence analysis identified 14 genes, mostly of unknown function, as potential factors protecting from lethal effects of stress. The 14 mutants were killed more readily than wild-type cells by mitomycin C and hydrogen peroxide; nine were also more readily killed by UV irradiation, and several exhibited increased susceptibility to killing by sodium dodecyl sulfate. No mutant was more readily killed by high temperature.Conclusions:A new screening strategy identified a diverse set of E. coli genes involved in the response to lethal antimicrobial and environmental stress, with some genes being involved in the response to multiple stressors. The gene set, which differed from sets previously identified with bacteriostatic assays, provides an entry point for obtaining small-molecule enhancers that will affect multiple antimicrobial agents.
Keywords:
Escherichia coli
2010-02-01
Dextran sulfate sodium and 2,4,6-trinitrobenzene sulfonic acid induce lipid peroxidation by the proliferation of intestinal gram-negative bacteria in mice
BioMed Central - Latest articles
Background:To understand whether TLR-4-linked NF-kB activation negatively correlates with lipid peroxidation in colitic animal models, we caused colitis by the treatment with dextran sulfate sodium (DSS) or 2,4,6-trinitrobenzenesulfonic acid (TNBS) to C3H/HeJ (TLR-4-defective) and C3H/HeN (wild type) mice, investigated inflammatory markers, lipid peroxidation, proinflammatory cytokines and TLR-4-linked NF-kappaB activation, in colon and intestinal bacterial composition in vivo.Methods:Orally administered DSS and intrarectally injected TNBS all caused severe inflammation, manifested by shortened colons in both mice. These agents increased intestinal myeloperoxidase activity and the expression of the pro-inflammatory cytokines, IL-1beta, TNF-alpha and IL-6, in the colon.Results:DSS and TNBS induced the protein expression of TLR-4 and activated transcription factor NF-kappaB. However, these colitic agents did not express TLR-4 in C3H/HeJ mice. Of proinflammatory cytokines, IL-1beta was most potently expressed in C3H/HeN mice. IL-1beta potently induced NF-kappaB activation in CaCo-2 cells, but did not induce TLR-4 expression. DSS and TNBS increased lipid peroxide (malondialdehyde) and 4-hydroxy-2-nonenal content in the colon, but reduced glutathione content and superoxide dismutase and catalase activities. These colitic inducers increased the number of Enterobacteriaceae grown in DHL agar plates in both mice, although the number of anaerobes and bifidobacteria grown in GAM and BL agar plates was reduced. E. coli, K. pneumoniae and Proteus mirabilis isolated in DHL agar plates increased lipid peroxidation in liposomes prepared by L-alpha-phosphatidylcholine, but B. animalis and B. cholerium isolated from BL agar plates inhibited it.DiscussionThese findings suggest that DSS and TNBS may cause colitis by inducing lipid peroxidation and enterobacterial proliferation, which may deteriorate the colitis by regulating proinflammatory cytokines via TLR-4-linked NF-kappaB activation pathway.
Keywords:
Enterobacteriaceae, Proteus mirabilis
2010-01-31
A temporal precedence based clustering method for geneexpression microarray data
BioMed Central - Latest articles
Background:Time-course microarray experiments can produce useful data which can help in understanding the underlying dynamics of the system. Clustering is an important stage in microarray data analysis where the data is grouped together according to certain characteristics. The majority of clustering techniques are based on distance or visual similarity measures which may not be suitable for clustering of temporal microarray data where the sequential nature of time is important. We present a Granger causality based technique to cluster temporal microarray gene expression data, which measures the interdependence between two time-series by statistically testing if one time-series can be used for forecasting the other time-series or not.Results:A gene-association matrix is constructed by testing temporal relationships between pairs of genes using the Granger causality test. The association matrix is further analyzed using a graph-theoretic technique to detect highly connected components representing interesting biological modules. We test our approach on synthesized datasets and real biological datasets obtained for Arabidopsis thaliana. We show the effectiveness of our approach by analyzing the results using the existing biological literature. We also report interesting structural properties of the association network commonly desired in any biological system.Conclusions:Our experiments on synthesized and real microarray datasets show that our approach produces encouraging results. The method is simple in implementation and is statistically traceable at each step. The method can produce sets of functionally related genes which can be further used for reverse engineering of gene circuits.
Keywords:
Arabidopsis thaliana
2010-01-31
Staphylococcus aureus sigma B-dependent emergence of small-colony variants and biofilm production following exposure toPseudomonas aeruginosa 4-hydroxy-2-heptylquinoline-N-oxide
BioMed Central - Latest articles
Background:Staphylococcus aureus and Pseudomonas aeruginosa are often found together in the airways of cystic fibrosis (CF) patients. It was previously shown that the P. aeruginosa exoproduct 4-hydroxy-2-heptylquinoline-N-oxide (HQNO) suppresses the growth of S. aureus and provokes the emergence of small-colony variants (SCVs). The presence of S. aureus SCVs as well as biofilms have both been associated with chronic infections in CF.Results:We demonstrated that HQNO stimulates S. aureus to form a biofilm in association with the formation of SCVs. The emergence of SCVs and biofilm production under HQNO exposure was shown to be dependent on the activity of the stress- and colonization-related alternative sigma factor B (SigB). Analysis of gene expression revealed that exposure of a prototypical S. aureus strain to HQNO activates SigB, which was leading to an increase in the expression of the fibronectin-binding protein A and the biofilm-associated sarA genes. Conversely, the quorum sensing accessory gene regulator (agr) system and the alpha-hemolysin gene were repressed by HQNO. Experiments using culture supernatants from P. aeruginosa PAO1 and a double chamber co-culture model confirmed that P. aeruginosa stimulates biofilm formation and activates SigB in a S. aureus strain isolated from a CF patient. Furthermore, the supernatant from P. aeruginosa mutants unable to produce HQNO induced the production of biofilms by S. aureus to a lesser extent than the wild-type strain only in a S. aureus SigB-functional background.Conclusions:These results suggest that S. aureus responds to HQNO from P. aeruginosa by forming SCVs and biofilms through SigB activation, a phenomenon that may contribute to the establishment of chronic infections in CF patients.
Keywords:
Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus aureus sigma
2010-01-30
Global transcriptomic response of Leptospira interrogans serovar Copenhageni upon exposure to serum
BioMed Central - Latest articles
Background:Leptospirosis is a zoonosis of worldwide distribution caused by infection with pathogenic serovars of Leptospira spp. The most common species, L. interrogans, can survive in the environment for lengthy periods of time in between infection of mammalian hosts. The pathogen then spreads hematogenously, resulting in multi-organ failure and death in severe cases. Previous DNA microarray studies have identified differentially expressed genes required for adaptation to temperature and osmolarity conditions inside the host compared to those of the environment.Results:In order to identify genes involved in survival in the early spirochetemic phase of infection, we performed a transcriptional analysis of L. interrogans serovar Copenhageni upon exposure to serum in comparison with EMJH medium. One hundred and sixty-eight genes were found to be differentially expressed, of which 55 were up-regulated and 113 were down-regulated. Genes of known or predicted function accounted for 54.5 and 45.1% of up- and down-regulated genes, respectively. Most of the differentially expressed genes were predicted to be involved in transcriptional regulation, translational process, two-component signal transduction systems, cell or membrane biogenesis, and metabolic pathways.Conclusions:Our study showed global transcriptional changes of pathogenic Leptospira upon exposure to serum, representing a specific host environmental cue present in the bloodstream. The presence of serum led to a distinct pattern of gene expression in comparison to those of previous single-stimulus microarray studies on the effect of temperature and osmolarity upshift. The results provide insights into the pathogenesis of leptospirosis during the early bacteremic phase of infection.
Keywords:
Leptospira interrogans
2010-01-29
Antibacterial activity of Artemisia nilagirica leaf extracts against clinical and phytopathogenic bacteria.
BioMed Central - Latest articles
Background:The six organic solvent extracts of Artemisia nilagirica were screened for the potential antimicrobial activity against phytopathogens and clinically important standard reference bacterial strains.Methods:The agar disk diffusion method was used to study the antibacterial activity of A. nilagirica extracts against 15 bacterial strains. The Minimum Inhibitory Concentration (MIC) of the plant extracts were tested using two fold agar dilution method at concentrations ranging from 32 to 512 mug/ml. The phytochemical screening of extracts was carried out for major phytochemical derivatives in A. nilagirica.Results:All the extracts showed inhibitory activity for gram-positive and gram-negative bacteria except for Klebsiella pneumonia, Enterococcus faccalis and Staphylococcus aureus. The hexane extract was found to be effective against all phytopathogens with low MIC of 32 mug/ml and the methanol extract exhibited a higher inhibition activity against Escherichia coli, Yersinia enterocolitica, Salmonella typhi, Entrobacter acrogens, Proteus valgaris, Pseudomonas aeruginosa (32 mug/ml), Basillus subtilis (64 mug/ml) and Shigella flaxneri (128 mug/ml). The phytochemical screening of extracts answered for the major derivative of alkaloids, amino acids, flavonoids, phenol, quinines, tannins and terpenoids.Conclusion:All the extracts showed antibacterial activity against the tested strains. However, methanol and hexane extracts showed high inhibition against clinical and phytopathogens, respectively. The results also indicate the presence of major phytochemical derivatives in the A. nilagirica extracts. Hence, the isolation and purification of therapeutic potential compounds from A. nilagirica could be used as an effective source against bacterial diseases in human and plants.
Keywords:
Artemisia nilagirica, Escherichia coli, Klebsiella pneumonia, Proteus valgaris, Pseudomonas aeruginosa, Salmonella typhi, Shigella, Staphylococcus aureus, Yersinia enterocolitica
2010-01-28
Schistosomiasis vaccine discovery using immunomics
BioMed Central - Latest articles
The recent publication of the Schistosoma japonicum and S. mansoni genomes has expanded greatly the opportunities for post-genomic schistosomiasis vaccine research. Immunomics protein microarrays provide an excellent application of this new schistosome sequence information, having been utilised successfully for vaccine antigen discovery with a range of bacterial and viral pathogens, and malaria. Accordingly, we have designed and manufactured a Schistosoma immunomics protein microarray as a vaccine discovery tool. The microarray protein selection combined previously published data and in silico screening of available sequences for potential immunogens based on protein location, homology to known protective antigens, and high specificity to schistosome species. Following cloning, selected sequences were expressed cell-free and contact-printed onto nitrocellulose microarrays. The reactivity of microarray proteins with antisera from schistosomiasis-exposed/resistant animals or human patients can be measured with labelled secondary antibodies and a laser microarray scanner; highly reactive proteins can be further assessed as putative vaccines. This highly innovative technology has the potential to transform vaccine research for schistosomiasis and other parasitic diseases of humans and animals.
Keywords:
Schistosoma japonicum, Schistosoma mansoni
2010-01-22
Prevalence of Coxiella burnetii antibodies in Danish dairy herds
BioMed Central - Latest articles
During recent years in Denmark higher rates of antibodies to Coxiella burnetii have been detected in animals and humans than previously reported. A study based on bulk tank milk samples from 100 randomly selected dairy herds was performed to estimate the prevalence and geographical distribution of antibody positive dairy herds. Using the CHEKIT Q-Fever Antibody ELISA Test Kit (IDEXX), the study demonstrated a prevalence of 59% antibody positive herds, 11% antibody intermediate herds and 30% antibody negative herds based on the instructions provided by the manufacturer. The geographical distribution does not indicate a relationship between the regional density of dairy farms and the prevalence of antibody positive dairy farms. The result supports the hypothesis of an increase in the prevalence of positive dairy herds compared to previous years.
Keywords:
Coxiella burnetii
2010-01-21
Ecological niche model of Phlebotomus alexandri and P. papatasi (Diptera: Psychodidae) in the Middle East
BioMed Central - Latest articles
Background:The purpose of this study is to create distribution models of two sand fly species, Phlebotomus papatasi (Scopoli) and P. alexandri (Sinton), across the Middle East. Phlebotomus alexandri is a vector of visceral leishmaniasis, while P. papatasi is a vector of cutaneous leishmaniasis and sand fly fever. Collection records were obtained from literature reports from 1950 through 2007 and unpublished field collection records. Environmental layers considered in the model were elevation, precipitation, land cover, and WorldClim bioclimatic variables. Models were evaluated using the threshold-independent area under the curve (AUC) receiver operating characteristic analysis and the threshold-dependent minimum training presence.Results:For both species, land cover was the most influential environmental layer in model development. The bioclimatic and altitude variables all contributed to model development; however, none influenced the model as strongly as land cover.Conclusion:While not perfect representations of the absolute distribution of P. papatasi and P. alexandri, these models indicate areas with a higher probability of presence of these species. This information could be used to help guide future research efforts into the ecology of these species and epidemiology of the pathogens that they transmit.
Keywords:
Diptera, Phlebotomus alexandri, Phlebotomus papatasi, Psychodidae
2010-01-17
Detection of myxoma viruses encoding a defective M135R gene from clinical cases of myxomatosis; possible implications for the role of the M135R protein as a virulence factor
BioMed Central - Latest articles
Background:Myxoma virus is a member of the Poxviridae and causes disease in European rabbits. Laboratory confirmation of the clinical disease, which occurs in the autumn of most years in Denmark, has been achieved previously using antigen ELISA and electron microscopy.Results:An unusually large number of clinically suspected cases of myxomatosis were observed in Denmark during 2007. Myxoma virus DNA was detected, using a new real time PCR assay which targets the M029L gene, in over 70% of the clinical samples submitted for laboratory confirmation. Unexpectedly, further analysis revealed that a high proportion of these viral DNA preparations contained a frame-shift mutation within the M135R gene that has previously been identified as a virulence factor. This frame-shift mutation results in expression of a greatly truncated product. The same frame-shift mutation has also been found recently within an avirulent strain of myxoma virus (6918). However, three other frame-shift mutations found in this strain (in the genes M009L, M036L and M148R) were not shared with the Danish viruses but a single nucleotide deletion in the M138R/M139R intergenic region was a common feature.Conclusions:It appears that expression of the full-length myxoma virus M135R protein is not required for virulence in rabbits. Hence, the frame-shift mutation in the M135R gene in the nonpathogenic 6918 virus strain is not sufficient to explain the attenuation of this myxoma virus but one/some of the other frame-shift mutations alone or in conjunction with one/some of the thirty two amino acid substitutions must also contribute. The real time PCR assay for myxoma virus is a useful diagnostic tool for laboratory confirmation of suspected cases of myxomatosis.
Keywords:
Poxviridae
2010-01-08
Evaluating clinical periodontal measures as surrogates for bacterial exposure: The Oral Infections and Vascular Disease Epidemiology Study (INVEST)
BioMed Central - Latest articles
Background:Epidemiologic studies of periodontal infection as a risk factor for cardiovascular disease often use clinical periodontal measures as a surrogate for the underlying bacterial exposure of interest. There are currently no methodological studies evaluating which clinical periodontal measures best reflect the levels of subgingival bacterial colonization in population-based settings. We investigated the characteristics of clinical periodontal definitions that were most representative of exposure to bacterial species that are believed to be either markers, or themselves etiologic, of periodontal disease.Methods:706 men and women aged >=55 years, residing in northern Manhattan were enrolled. Using DNA-DNA checkerboard hybridization in subgingival biofilms, standardized values for Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia were averaged within mouth and summed to define "bacterial burden". Correlations of bacterial burden with clinical periodontal constructs defined by the severity and extent of attachment loss (AL), pocket depth (PD) and bleeding on probing (BOP) were assessed.Results:Clinical periodontal constructs demonstrating the highest correlations with bacterial burden were: i) percent of sites with BOP (r=0.62); ii) percent of sites with PD>=3 mm (r=0.61); and iii) number of sites with BOP (r=0.59). Increasing PD or AL severity thresholds consistently attenuated correlations, i.e., the correlation of bacterial burden with the percent of sites with PD>=8 mm was only r=0.16.Conclusions:Clinical exposure definitions of periodontal disease should incorporate relatively shallow pockets to best reflect whole mouth exposure to bacterial burden.
Keywords:
Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola
2010-01-04
Cloning and characterization of Escherichia coli DUF299: a bifunctional ADP-dependent kinase - phosphate-dependent pyrophosphorylase from bacteria.
BioMed Central - Latest articles
Background:Phosphoenolpyruvate synthetase (PEPS; EC 2.7.9.2) catalyzes the synthesis of phosphoenolpyruvate from pyruvate in Escherichia coli when cells are grown on a three carbon source. It also catalyses the anabolic conversion of pyruvate to phosphoenolpyruvate in gluconeogenesis. A bioinformatics search conducted following the successful cloning and expression of maize leaf pyruvate, orthophosphate dikinase regulatory protein (PDRP) revealed the presence of PDRP homologs in more than 300 bacterial species; the PDRP homolog was identified as DUF299.Results:This paper describes the cloning and expression of both PEPS and DUF299 from E. coli and establishes that E. coli DUF299 catalyzes both the ADP-dependent inactivation and the Pi-dependent activation of PEPS.Conclusion:This paper represents the first report of a bifunctional regulatory enzyme catalysing an ADP-dependent phosphorylation and a Pi-dependent pyrophosphorylation reaction in bacteria.
Keywords:
Escherichia coli
2010-01-01
Clostridium septicum infection of hepatic metastases following alcohol injection: a case report
BioMed Central - Latest articles
Clostridium septicum infections are generally associated with gastrointestinal or hematologic malignancies. We report the first case of hepatic metastases infection with Clostridium septicum that followed alcohol injection of liver lesion. Clinicians should consider this possibility in patients with underlying malignancy who present with hepatic abscess, as prompt surgical drainage and empiric antibiotics may be life saving.
Keywords:
Clostridium septicum
2009-12-31
The roles of EGF and Wnt signaling during patterning of the C. elegans Bgamma/delta Equivalence Group
BioMed Central - Latest articles
Background:During development, different signaling pathways interact to specify cell fate by regulating transcription factors necessary for fate specification and morphogenesis. In Caenorhabditis elegans, the EGF-Ras and Wnt signaling pathways have been shown to interact to specify cell fate in three equivalence groups: the vulval precursor cells (VPCs), the hook competence group (HCG) and P11/12. In the VPCs, HCG and P11/12 pair, EGF and Wnt signaling positively regulate different Hox genes, each of which also functions during fate specification. In the male, EGF-Ras signaling is required to specify the Bgamma fate within the Bgamma/delta equivalence pair, while Notch signaling is required for Bdelta fate specification. In addition, TGF-beta signaling by dbl-1/dpp controls ceh-13/labial/Hox1 expression in Bgamma.Results:We show that EGF-Ras signaling is required for Bgamma expression of ceh-13/labial/Hox1. The transcription factors lin-1/ETS and lin-31/Forkhead, functioning downstream of the EGF pathway, as well as sur-2/MED23 (a component of the Mediator complex) also control ceh-13 expression in Bgamma. In addition, our results indicate that lin-44/Wnt, mom-2/Wnt and lin-17/Fz are necessary to maintain the division of Bgamma along a longitudinal axis. We also show that dbl-1/dpp acts either in parallel or downstream of EGF pathway to regulate ceh-13/Hox1 expression in Bgamma. Lastly, we find that a dbl-1/dpp null mutation did not cause any vulval or P12 defects and did not enhance vulval and P12 defects of reduction-of-function mutations of components of the EGF pathway.Conclusions:ceh-13/labial/Hox1 expression in Bgamma is regulated by the EGF pathway and downstream factors lin-1/ETS lin-31/Forkhead and sur-2/MED23. Wnt signaling is required for proper Bgamma division, perhaps to orient the Bgamma mitotic spindle. Our results suggest that dbl-1/dpp is not required for VPC and P12 specification, highlighting another difference among these EGF-dependent equivalence groups.
Keywords:
Caenorhabditis elegans, Cyclamen elegans
2009-12-26
Flux Design: In silico design of cell factories based on correlation of pathway fluxes to desired properties
BioMed Central - Latest articles
Background:The identification of genetic target genes is a key step for rational engineering of production strains towards bio-based chemicals, fuels or therapeutics. This is often a difficult task, because superior production performance typically requires a combination of multiple targets, whereby the complex metabolic networks complicate straightforward identification. Recent attempts towards target prediction mainly focus on the prediction of gene deletion targets and therefore can cover only a part of genetic modifications proven valuable in metabolic engineering. Efficient in silico methods for simultaneous genome-scale identification of targets to be amplified or deleted are still lacking.Results:Here we propose the identification of targets via flux correlation to a chosen objective flux as approach towards improved biotechnological production strains with optimally designed fluxes. The approach, we name Flux Design, computes elementary modes and, by search through the modes, identifies targets to be amplified (positive correlation) or down-regulated (negative correlation). Supported by statistical evaluation, a target potential is attributed to the identified reactions in a quantitative manner. Based on systems-wide models of the industrial microorganisms Corynebacterium glutamicum and Aspergillus niger, up to more than 20,000 modes were obtained for each case, differing strongly in production performance and intracellular fluxes. For lysine production in C. glutamicum the identified targets nicely matched with reported successful metabolic engineering strategies. In addition, simulations revealed insights, e.g. into the flexibility of energy metabolism. For enzyme production in A. niger flux correlation analysis suggested a number of targets, including non-obvious ones. Hereby, the relevance of most targets depended on the metabolic state of the cell and also on the carbon source.Conclusions:Objective flux correlation analysis provided a detailed insight into the metabolic networks of industrially relevant prokaryotic and eukaryotic microorganisms. It was shown that capacity, pathway usage, and relevant genetic targets for optimal production partly depend on the network structure and the metabolic state of the cell which should be considered in future metabolic engineering strategies. The presented strategy can be generally used to identify priority sorted amplification and deletion targets for metabolic engineering purposes under various conditions and thus displays a useful strategy to be incorporated into efficient strain and bioprocess optimization.
Keywords:
Aspergillus niger, Corynebacterium glutamicum
2009-12-24
Downregulation of protein kinase C-alpha enhances intracellular survival of Mycobacteria: role of PknG
BioMed Central - Latest articles
Background:Intracellular trafficking of mycobacteria is comprehensively dependent on the unusual regulation of host proteins. Recently, we have reported that infection of macrophages by Mycobacterium tuberculosis H37Rv (Rv) selectively downregulates the expression of PKCalpha while infection by Mycobacterium smegmatis (MS) does not.Results:Based on our earlier study, we have extrapolated for the first time that knockdown of PKCalpha, impairs phagocytosis of mycobacteria by macrophages while their intracellular survival is drastically increased. Mycobacterium bovis BCG (BCG) and Mycobacterium tuberculosis H37Ra (Ra) have also been shown to downregulate the expression of PKCalpha during the infection. Since PknG is uniquely expressed in BCG, Ra, Rv but not in MS and has been reported to promote intracellular survival of mycobacteria, led us to believe that PknG may be involved in such downregulation of PKCalpha. THP-1 cells infected with recombinant MS expressing PknG (MS-G), showed significant reduction in PKCalpha expression. In normal THP-1 cells survival of MS-G was enhanced as compared to MS, while their behavior in PKCalpha deficient cells could not be distinguished. The results strongly demonstrate that pathogenic mycobacteria recognize and then inhibit PKCalpha to circumvent phagocytosis and the hostile environment of macrophages. We emphasize that, this inhibition is controlled by PknG.Conclusions:All together, our data reveal a mechanism that shows substantial interdependence of PKCalpha with PknG, in sustaining mycobacterial infection.
Keywords:
Mycobacteria, Mycobacterium bovis, Mycobacterium smegmatis, Mycobacterium tuberculosis
2009-12-23
Scale-up from microtiter plate to laboratory fermenter: evaluation by online monitoring techniques of growth and protein expression in Escherichia coli and Hansenula polymorpha fermentations
BioMed Central - Latest articles
Background:In the past decade, an enormous number of new bioprocesses have evolved in the biotechnology industry. These bioprocesses have to be developed fast and at a maximum productivity. Up to now, only few microbioreactors were developed to fulfill these demands and to facilitate sample processing. One predominant reaction platform is the shaken microtiter plate (MTP), which provides high-throughput at minimal expenses in time, money and work effort. By taking advantage of this simple and efficient microbioreactor array, a new online monitoring technique for biomass and fluorescence, called BioLector, has been recently developed. The combination of high-throughput and high information content makes the BioLector a very powerful tool in bioprocess development. Nevertheless, the scalability of results from the micro-scale to laboratory or even larger scales is very important for short development times. Therefore, engineering parameters regarding the reactor design and its operation conditions play an important role even on a micro-scale. In order to evaluate the scale-up from a microtiter plate scale (200 uL) to a stirred tank fermenter scale (1.4 L), two standard microbial expression systems, Escherichia coli and Hansenula polymorpha, were fermented in parallel at both scales and compared with regard to the biomass and protein formation.Results:Volumetric mass transfer coefficients (kLa) ranging from 100 to 350 1/h were obtained in 96-well microtiter plates. Even with a suboptimal mass transfer condition in the microtiter plate compared to the stirred tank fermenter (kLa= 370-600 1/h), identical growth and protein expression kinetics were attained in bacteria and yeast fermentations. The bioprocess kinetics were evaluated by optical online measurements of biomass and protein concentrations exhibiting the same fermentation times and maximum signal deviations below 10% between the scales. In the experiments, the widely applied green fluorescent protein (GFP) served as an online reporter of protein expression for both strains.Conclusions:The successful 7000-fold scale-up from a shaken microtiter plate to a stirred tank fermenter was demonstrated in parallel fermentations for standard microbial expression systems. This confirms that the very economical and time efficient platform of microtiter plates can be very easily scaled up to larger stirred tank fermenters under defined engineering conditions. New online monitoring techniques for microtiter plates, such as the BioLector, provide even more real-time kinetic data from fermentations than ever before and at an affordable price. This paves the way for a better understanding of the bioprocess and a more rational process design.
Keywords:
Escherichia coli, Hansenula polymorpha
2009-12-23
Habitat suitability and ecological niche profile of major malaria vectors in Cameroon
BioMed Central - Latest articles
Background:Suitability of environmental conditions determines a species distribution in space and time. Understanding and modelling the ecological niche of mosquito disease vectors can, therefore, be a powerful predictor of the risk of exposure to the pathogens they transmit. In Africa, five anophelines are responsible for over 95% of total malaria transmission. However, detailed knowledge of the geographic distribution and ecological requirements of these species is to date still inadequate.Methods:Indoor-resting mosquitoes were sampled from 386 villages covering the full range of ecological settings available in Cameroon, Central Africa. Using a predictive species distribution modeling approach based only on presence records, habitat suitability maps were constructed for the five major malaria vectors Anopheles gambiae, Anopheles funestus, Anopheles arabiensis, Anopheles nili and Anopheles moucheti. The influence of 17 climatic, topographic, and land use variables on mosquito geographic distribution was assessed by multivariate regression and ordination techniques.Results:Twenty-four anopheline species were collected, of which 17 are known to transmit malaria in Africa. Ecological Niche Factor Analysis, Habitat Suitability modeling and Canonical Correspondence Analysis revealed marked differences among the five major malaria vector species, both in terms of ecological requirements and niche breadth. Eco-geographical variables (EGVs) related to human activity had the highest impact on habitat suitability for the five major malaria vectors, with areas of low population density being of marginal or unsuitable habitat quality. Sunlight exposure, rainfall, evapo-transpiration, relative humidity, and wind speed were among the most discriminative EGVs separating "forest" from "savanna" species.Conclusions:The distribution of major malaria vectors in Cameroon is strongly affected by the impact of humans on the environment, with variables related to proximity to human settings being among the best predictors of habitat suitability. The ecologically more tolerant species An. gambiae and An. funestus were recorded in a wide range of eco-climatic settings. The other three major vectors, An. arabiensis, An. moucheti, and An. nili, were more specialized. Ecological niche and species distribution modelling should help improve malaria vector control interventions by targeting places and times where the impact on vector populations and disease transmission can be optimized.
Keywords:
Anopheles arabiensis, Anopheles funestus, Anopheles gambiae, Anopheles moucheti, Anopheles nili
2009-12-21
Investigation of a community outbreak of typhoid fever associated with drinking water
BioMed Central - Latest articles
Background:This report is about the investigation of an outbreak of typhoid fever claimed three human lives and left more than 300 people suffered within one week. The aim of this report is to draw the attention of global health community towards the areas that are still far from basic human essentialities.Methods:A total of 250 suspected cases of typhoid fever were interviewed, out of which 100 were selected for sample collection on the basis of criteria included temperature > 38oC since the onset of outbreak, abdominal discomfort, diarrhea, vomiting and weakness. Food and water samples were also collected and analyzed microbiologically.Results:Inhabitants of village lived in poor and unhygienic with no proper water supply or sewage disposal facilities and other basic necessities of life. They consumed water from a nearby well which was the only available source of drinking water. Epidemiological evidences revealed the gross contamination of well with dead and decaying animal bodies, their fecal material and garbage. Microbiological analysis of household and well water samples revealed the presence of heavy bacterial load with an average total aerobic count 106-109 CFU/ ml. A number of Gram positive and Gram negative bacteria including Escherichia coli, Klebseilla, Bacillus species, Staphylococcus species, Enterobacter species, and Pseudomonas aeruginosa were isolated. Lab investigations confirmed the presence of multidrug resistant strain of Salmonella enterica serovar Typhi in 100% well water, 65% household water samples and 2% food items. 22% of clinical stool samples were tested positive with Salmonella enterica serover TyphiConclusions:This study indicated the possible involvement of well water in outbreak. In order to avoid such outbreaks in future, we contacted the local health authorities and urged them to immediately make arrangements for safe drinking water supply
Keywords:
Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica
2009-12-21
Genome-wide profiling of Populus small RNAs
BioMed Central - Latest articles
Background:Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale.We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced Populus trichocarpa using a concatenation strategy in combination with 454 sequencing.Results:The most abundant size class of sRNAs were 24 nt. Long Terminal Repeats were particularly associated with 24 nt sRNAs. Additionally, some repetitive elements were associated with 22 nt sRNAs. We identified a sRNA hot-spot on chromosome 19, overlapping a region containing both the sex-determining loci and a major cluster of NBS-LRR genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and NBS-LRR disease resistance genes, classes of genes that have been significantly expanded in Populus. Additional loci enriched for sRNA production were characterised. 15 novel microRNAs (miRNAs) were predicted, including miRNA* sequences, including a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs).Conclusions:The short RNA population of P. trichocarpa is at least as complex as that of Arabidopsis thaliana. We provide a first genome-wide view of short RNA production for P. trichocarpa and identify new, non-conserved miRNAs.
Keywords:
Arabidopsis thaliana, Populus trichocarpa
2009-12-21
Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken
BioMed Central - Latest articles
Background:The chicken (Gallus gallus), like most avian species, has a very distinct karyotype consisting of many micro- and a few macrochromosomes. While it is known that recombination frequencies are much higher for micro- as compared to macrochromosomes, there is limited information on differences in linkage disequilibrium (LD) and haplotype diversity between these two classes of chromosomes. In this study, LD and haplotype diversity were systematically characterized in 371 birds from eight chicken populations (commercial lines, fancy breeds, and red jungle fowl) across macro- and microchromosomes. To this end we sampled four regions of ~1cM each on macrochromosomes (GGA1 and GGA2), and four 1.5 -2cM regions on microchromosomes (GGA26 and GGA27) at a high density of 1 SNP every 2kb (total of 889 SNPs).Results:At a similar physical distance, LD, haplotype homozygosity, haploblock structure, and haplotype sharing were all lower for the micro- as compared to the macrochromosomes. These differences were consistent across populations. Heterozygosity, genetic differentiation, and derived allele frequencies were also higher for the microchromosomes. Differences in LD, haplotype variation, and haplotype sharing between populations were largely in line with known demographic history of the commercial chicken. Despite very low levels of LD, as measured by r2 for most populations, some haploblock structure was observed, particularly in the macrochromosomes, but the haploblock sizes were typically less than 10kb.Conclusion:Differences in LD between micro- and macrochromosomes were almost completely explained by differences in recombination rate. Differences in haplotype diversity and haplotype sharing between micro- and macrochromosomes were explained by differences in recombination rate and genotype variation. Haploblock structure was consistent with demography of the chicken populations, and differences in recombination rates between micro- and macrochromosomes. The limited haploblock structure and LD suggests that future whole-genome marker assays will need 100+K SNPs to exploit haplotype information. Interpretation and transferability of genetic parameters will need to take into account the size of chromosomes in chicken, and, since most birds have microchromosomes, in other avian species as well.
Keywords:
Gallus gallus
2009-12-20
Virulence potential of five major pathogenicity islands (SPI-1 to SPI-5) of Salmonella enterica serovar Enteritidis for chickens
BioMed Central - Latest articles
Background:Salmonella is a highly successful parasite of reptiles, birds and mammals. Its ability to infect and colonise such a broad range of hosts coincided with the introduction of new genetic determinants, among them 5 major pathogenicity islands (SPI1-5), into the Salmonella genome. However, only limited information is available on how each of these pathogenicity islands influences the ability of Salmonella to infect chickens. In this study, we therefore constructed Salmonella Enteritidis mutants with each SPI deleted separately, with single individual SPIs (i.e. with the remaining four deleted) and a mutant with all 5 SPIs deleted, and assessed their virulence in one-day-old chickens, together with the innate immune response of this host.Results:The mutant lacking all 5 major SPIs was still capable of colonising the caecum while colonisation of the liver and spleen was dependent on the presence of both SPI-1 and SPI-2. In contrast, the absence of SPI-3, SPI-4 or SPI-5 individually did not influence virulence of S. Enteritidis for chickens, but collectively they contributed to the colonisation of the spleen. Proinflammatory signalling and heterophil infiltration was dependent on intact SPI-1 only and not on other SPIs.Conclusions:SPI-1 and SPI-2 are the two most important pathogenicity islands of Salmonella Enteritidis required for the colonisation of systemic sites in chickens.
Keywords:
Salmonella, Salmonella enterica
2009-12-19
Mucosa-associated lymphoid tissue lymphoma of the duodenum together with multiple intra-abdominal thromboses and hepatitis C virus infection: a case report
BioMed Central - Latest articles
Mucosa associated lymphoid tissue MALT lymphoma is a low grade malignancy that arises most commonly from the gastric mucosa. Small intestinal involvement is very rare. The causative relationship between Helicobacter pylori and the gastric MALT lymphoma is a well known issue, but recently there are several data suggesting the role of hepatitis C virus (HCV) infection in the pathogenesis of lymphoma including MALT lymphoma. Herein we present a rare case of duodenal MALT lymphoma with multiple intra-abdominal thromboses together with HCV infection that was confirmed by real-time polymerase chain reaction detecting HCV-RNA within the peripheral blood mononuclear cells.
Keywords:
Helicobacter pylori
2009-12-18
Clonal dissemination of the multi-drug resistant Salmonella enterica serovar Braenderup, but not the serovar Bareilly, of prevalent serogroup C1 Salmonella from Taiwan
BioMed Central - Latest articles
Background:Nontyphoidal Salmonella is the main cause of human salmonellosis. In order to study the prevalent serogroups and serovars of clinical isolates in Taiwan, 8931 Salmonellae isolates were collected from 19 medical centers and district hospitals throughout the country from 2004 to 2007. The pulsed-field eletrophoresis types (PFGE) and antibiotic resistance profiles of Salmonella enterica serovars Bareilly (S. Bareilly) and Braenderup (S. Braenderup) were compared, and multi-drug resistance (MDR) plasmids were characterized. Results: Over 95% of human salmonellosis in Taiwan were caused by five Salmonella serogroups: B, C1, C2-C3, D1, and E1. S. Typhymurium, S. Enteritidis, S. Stanley and S. Newport were the four most prevalent serovars, accounting for about 64% of isolates. While only one or two major serovars from four of the most prevalent serogroups were represented, four predominant serovars were found in serogroup C1 Salmonellae. The prevalence was decreasing for S. Choleraeuis and S. Braenderup, and S. Virchow and increasing for S. Bareilly. S. Braenderup mainly caused gastroenteritis in children; in contrast, S. Bareiley infected children and elderly people. Both serovars differed by XbaI-PFGE patterns. Almost all S. Bareilly isolates were susceptible to antibiotics of interest, while all lacked plasmids and belonged to one clone. Two distinct major clones in S. Braenderup were cluster A, mainly including MDR isolates with large MDR plasmid from North Taiwan, and cluster B, mainly containing susceptible isolates without R plasmid from South Taiwan. In cluster A, there were two types of conjugative R plasmids with sizes ranging from 75 to 130 kb. Type 1 plasmids consisted of replicons F1A/F1B, blaTEM, IS26, and a class 1 integron with the genes dfrA12-orfF-aadA2-qacEDelta1-sulI. Type 2 plasmids belonged to incompatibility group IncI, contained tnpA-blaCMY-2-blc-sugE genetic structures and lacked both IS26 and class 1 integrons. Although type 2 plasmids showed higher conjugation capability, type 1 plasmids were the predominant plasmid. Conclusions: Serogroups B, C1, C2-C3, D1, and E1 of Salmonella caused over 95% of human salmonellosis. Two prevalent serovars within serogroup C1, S. Bareilly and cluster B of S. Braenderup, were clonal and drug-susceptible. However, cluster A of S. Braenderup was MDR and probably derived from susceptible isolates by acquiring one of two distinct conjugative R plasmids.
Keywords:
Salmonella, Salmonella enterica
2009-12-18
Compound K, a metabolite of ginseng saponin, induces apoptosis via caspase-8-dependent pathway in HL-60 human leukemia cells
BioMed Central - Latest articles
Background:Compound K [20-O-beta-(D-glucopyranosyl)-20(S)-protopanaxadiol], a metabolite of the protopanaxadiol-type saponins of Panax ginseng C.A. Meyer, has been reported to possess anti-tumor properties to inhibit angiogenesis and to induce tumor apoptosis. In the present study, we investigated the effect of compound K on apoptosis and explored the underlying mechanisms involved in HL-60 human leukemia cells.Methods:We examined the effect of compound K on the viabilities of various cancer cell lines using MTT assays. DAPI assay, Annexin V and PI double staining, western blot assay and immunoprecipitation were used to determine the effect of compound K on the induction of apoptosis.Results:Compound K was found to inhibit the viability of HL-60 cells in a dose- and time-dependent manner with an IC50 of 14 muM. Moreover, this cell death had typical features of apoptosis, that is, DNA fragmentation, DNA ladder formation, and the externalization of Annexin V targeted phosphatidylserine residues in HL-60 cells. In addition, compound-K induced a series of intracellular events associated with both the mitochondrial- and death receptor-dependent apoptotic pathways, namely, (1) the activations of caspases-3, -8, and -9; (2) the loss of mitochondrial membrane potential; (3) the release of cytochrome c and Smac/DIABLO to the cytosol; (4) the translocation of Bid and Bax to mitochondria; and (5) the downregulations of Bcl-2 and Bcl-xL. Furthermore, a caspase-8 inhibitor completely abolished caspase-3 activation, Bid cleavage, and subsequent DNA fragmentation by compound K. Interestingly, the activations of caspase-3 and -8 and DNA fragmentation were significantly prevented in the presence of cycloheximide, suggesting that compound K-induced apoptosis is dependent on de novo protein synthesis.Conclusions:The results indicate that caspase-8 plays a key role in compound K-stimulated apoptosis via the activation of caspase-3 directly or indirectly through Bid cleavage, cytochrome c release, and caspase-9 activation.
Keywords:
Panax ginseng
2009-12-15
EEVD motif of heat shock cognate protein 70 contributes to bacterial uptake by trophoblast giant cells
BioMed Central - Latest articles
Background:The uptake of abortion-inducing pathogens by trophoblast giant (TG) cells is a key event in infectious abortion. However, little is known about phagocytic functions of TG cells against the pathogens. Here we show that heat shock cognate protein 70 (Hsc70) contributes to bacterial uptake by TG cells and the EEVD motif of Hsc70 plays an important role in this.Methods:Brucella abortus and Listeria monocytogenes were used as the bacterial antigen in this study. Recombinant proteins containing tetratricopeptide repeat (TPR) domains were constructed and confirmation of the binding capacity to Hsc70 was assessed by ELISA. The recombinant TPR proteins were used for investigation of the effect of TPR proteins on bacterial uptake by TG cells and on pregnancy in mice.Results:The monoclonal antibody that inhibits bacterial uptake by TG cells reacted with the EEVD motif of Hsc70. Bacterial TPR proteins bound to the C-terminal of Hsc70 through its EEVD motif and this binding inhibited bacterial uptake by TG cells. Infectious abortion was also prevented by blocking the EEVD motif of Hsc70.Conclusions:Our results demonstrate that surface located Hsc70 on TG cells mediates the uptake of pathogenic bacteria and proteins containing the TPR domain inhibit the function of Hsc70 by binding to its EEVD motif. These molecules may be useful in the development of methods for preventing infectious abortion.
Keywords:
Brucella abortus, Listeria monocytogenes
2009-12-14
Proteomic analysis during larval development and metamorphosis of the spionid polychaete Pseudopolydora vexillosa
BioMed Central - Latest articles
Background:While the larval-juvenile transition (metamorphosis) in the spionid polychaete Pseudopolydora vexillosa involves gradual morphological changes and does not require substantial development of juvenile organs, the opposite occurs in the barnacle Balanus amphitrite. We hypothesized that the proteome changes during metamorphosis in the spionids are less drastic than that in the barnacles. To test this, proteomes of pre-competent larvae, competent larvae (ready to metamorphose), and juveniles of P. vexillosa were compared using 2-dimensional gel electrophoresis (2-DE), and they were then compared to those of the barnacle.Results:Unlike the significant changes found during barnacle metamorphosis, proteomes of competent P. vexillosa larvae were more similar to those of their juveniles. Pre-competent larvae had significantly fewer protein spots (384 spots), while both competent larvae and juveniles expressed about 660 protein spots each. Proteins up-regulated during competence identified by MALDI-TOF/TOF analysis included a molecular chaperon (calreticulin), a signal transduction regulator (tyrosin activation protein), and a tissue-remodeling enzyme (metallopeptidase).Conclusions:This was the first time to study the protein expression patterns during the metamorphosis of a marine polychaete and to compare the proteomes of marine invertebrates that have different levels of morphological changes during metamorphosis. The findings provide promising initial steps towards the development of a proteome database for marine invertebrate metamorphosis, thus deciphering the possible mechanisms underlying larval metamorphosis in non-model marine organisms.
Keywords:
Balanus amphitrite, Pseudopolydora vexillosa
2009-12-11
Evidence for an association of HLA-DRB1*15 and DRB1*09 with leprosy and the impact of DRB1*09 on disease onset in a Chinese Han population
BioMed Central - Latest articles
Background:Human leukocyte antigens (HLAs) have been proposed to modulate the immune response to Mycobacterium leprae. The association of HLA-DRB1 with leprosy has been reported in several populations, but not in a Chinese population.Methods:The polymerase chain reaction-sequence-specific oligonucleotide probe with Luminex100 (PCR-SSOP-Luminex) method was used to genotype HLA-DRB1 alleles in 305 leprosy patients and 527 healthy control individuals.Results:The HLA-DRB1*15 allele was significantly more prevalent among leprosy patients than healthy controls, whereas the frequency of the HLA-DRB1*09 allele was lower among leprosy patients, especially those with early-onset disease.Conclusions:HLA-DRB1 alleles are associated with leprosy susceptibility in a Chinese population. The HLA-DRB1*09 allele was found to be protective exclusively in a subset of early-onset leprosy patients.
Keywords:
Mycobacterium leprae
2009-12-10
Identifying sexual differentiation genes that affect Drosophila life span
BioMed Central - Latest articles
Background:Sexual differentiation often has significant effects on life span and aging phenotypes. For example, males and females of several species have different life spans, and genetic and environmental manipulations that affect life span often have different magnitude of effect in males versus females. Moreover, the presence of a differentiated germ-line has been shown to affect life span in several species, including Drosophila and C. elegans.Methods:Experiments were conducted to determine how alterations in sexual differentiation gene activity might affect the life span of Drosophila melanogaster. Drosophila females heterozygous for the tudor[1] mutation produce normal offspring, while their homozygous sisters produce offspring that lack a germ line. To identify additional sexual differentiation genes that might affect life span, the conditional transgenic system Geneswitch was employed, whereby feeding adult flies or developing larvae the drug RU486 causes the over-expression of selected UAS-transgenes.Results:In this study germ-line ablation caused by the maternal tudor[1] mutation was examined in a long-lived genetic background, and was found to increase life span in males but not in females, consistent with previous reports. Fitting the data to a Gompertz-Makeham model indicated that the maternal tudor[1] mutation increases the life span of male progeny by decreasing age-independent mortality. The Geneswitch system was used to screen through several UAS-type and EP-type P element mutations in genes that regulate sexual differentiation, to determine if additional sex-specific effects on life span would be obtained. Conditional over-expression of transformer female isoform (traF) during development produced male adults with inhibited sexual differentiation, however this caused no significant change in life span. Over-expression of doublesex female isoform (dsxF) during development was lethal to males, and produced a limited number of female escapers, whereas over-expression of dsxF specifically in adults greatly reduced both male and female life span. Similarly, over-expression of fruitless male isoform A (fru-MA) during development was lethal to both males and females, whereas over-expression of fru-MA in adults greatly reduced both male and female life span.Conclusions:Manipulation of sexual differentiation gene expression specifically in the adult, after morphological sexual differentiation is complete, was still able to affect life span. In addition, by manipulating gene expression during development, it was possible to significantly alter morphological sexual differentiation without a significant effect on adult life span. The data demonstrate that manipulation of sexual differentiation pathway genes either during development or in adults can affect adult life span.
Keywords:
Drosophila melanogaster
2009-12-10
Towards a comprehensive barcode library for arctic life-Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada
BioMed Central - Latest articles
Background:This study reports progress in assembling a DNA barcode reference library for Ephemeroptera, Plecoptera, and Trichoptera ("EPTs") from a Canadian subartic site, which is the focus of a comprehensive biodiversity inventory using DNA barcoding. These three groups of aquatic insects exhibit a moderate level of species diversity, making them ideal for testing the feasibility of DNA barcoding for routine biotic surveys. We explore the correlation between the morphological species delineations, DNA barcode-based haplotype clusters delimited by a sequence threshold (2%), and a threshold-free approach to biodiversity quantification-phylogenetic diversity.Results:A DNA barcode reference library is built for 112 EPT species from the focal region, consisting of 2272 COI sequences. Close correspondence was found between EPT morphospecies and haplotype clusters as designated using a standard threshold value. Similarly, the shapes of taxon accumulation curves based upon haplotype clusters were very similar to those generated using phylogenetic diversity accumulation curves, but were much more computationally efficient.Conclusion:The results of this study will facilitate other lines of research on northern EPTs and also bode well for rapidly conducting initial biodiversity assessments in unknown EPT faunas.
Keywords:
Ephemeroptera, Plecoptera, Trichoptera
2009-12-07
Uncovering transcriptional interactions via an adaptive fuzzy logic approach
BioMed Central - Latest articles
Background:To date, only a limited number of transcriptional regulatory interactions have been uncovered. In a pilot study integrating sequence data with microarray data, a position weight matrix (PWM) performed poorly in inferring transcriptional interactions (TIs), which represent physical interactions between transcription factors (TF) and upstream sequences of target genes. Inferring a TI means that the promoter sequence of a target is inferred to match the consensus sequence motifs of a potential TF, and their interaction type such as AT or RT is also predicted. Thus, a robust PWM (rPWM) was developed to search for consensus sequence motifs. In addition to rPWM, one feature extracted from ChIP-chip data was incorporated to identify potential TIs under specific conditions. An interaction type classifier was assembled to predict activation/repression of potential TIs using microarray data. This approach, combining an adaptive (learning) fuzzy inference system and an interaction type classifier to predict transcriptional regulatory networks, was named AdaFuzzy.Results:AdaFuzzy was applied to predict TIs using real genomics data from Saccharomyces cerevisiae. Following one of the latest advances in predicting TIs, constrained probabilistic sparse matrix factorization (cPSMF), and using 19 transcription factors (TFs), we compared AdaFuzzy to four well-known approaches using over-representation analysis and gene set enrichment analysis. AdaFuzzy outperformed these four algorithms. Furthermore, AdaFuzzy was shown to perform comparably to `ChIP-experimental method' in inferring TIs identified by two sets of large scale ChIP-chip data, respectively. AdaFuzzy was also able to classify all predicted TIs into one or more of the four promoter architectures. The results coincided with known promoter architectures in yeast and provided insights into transcriptional regulatory mechanisms.Conclusions:AdaFuzzy successfully integrates multiple types of data (sequence, ChIP, and microarray) to predict transcriptional regulatory networks. The validated success in the prediction results implies that AdaFuzzy can be applied to uncover TIs in yeast.
Keywords:
Saccharomyces cerevisiae
2009-12-06
A pooling-based genome-wide analysis identifies new potential candidate genes for atopy in the European Community Respiratory Health Survey (ECRHS)
BioMed Central - Latest articles
Background:Asthma and atopy are complex phenotypes with shared genetic component. In this study we attempt to identify genes related to these traits performing a two-stage DNA pooling genome-wide analysis in order to reduce costs. First, we assessed all markers in a subset of subjects using DNA pooling, and in a second stage we evaluated the most promising markers at an individual level.Methods:For the genome-wide analysis, we constructed DNA pools from 75 subjects with atopy and asthma, 75 subjects with atopy and without asthma and 75 control subjects without atopy or asthma. In a second stage, the most promising regions surrounding significant markers after correction for false discovery rate were replicated with individual genotyping of samples included in the pools and an additional set of 429 atopic subjects and 222 controls from the same study centres.Results:Homo sapiens protein kinase-like protein SgK493 (SGK493) was found to be associated with atopy. To lesser extent mitogen-activated protein kinase 5 (MAP3K5), collagen type XVIII alpha 1 (COL18A1) and collagen type XXIX alpha 1 (COL29A1) were also found to be associated with atopy. Functional evidences points out a role for MAP3K5, COL18A1 and COL29A1 but the function of SGK493 is unknown.Conclusions:In this analysis we have identified new candidate regions related to atopy and suggest SGK493 as an atopy locus, although these results need further replication.
Keywords:
Homo sapiens, Mariona
2009-12-06
Molecular characterization and phylogenetic analysis of the complete genome of a porcine sapovirus from Chinese swine
BioMed Central - Latest articles
Background:Porcine sapovirus was first identified in the United States in 1980, hitherto, several Asian countries have detected this virus. In 2008, the first outbreak of gastroenteritis in piglets caused by porcine sapovirus in China was reported. The complete genome of the identified SaV strain Ch-sw-sav1 was sequenced and analyzed to provide gene profile for this outbreak.Methods:The whole genome of Ch-sw-sav1 was amplified by RT-PCR and was sequenced. Sequence alignment of the complete genome or RNA dependent RNA polymerase (RdRp) gene was done. 3' end of ORF2 with 21-nt nucleotide insertion was further analyzed using software.Results:Sequence analysis indicated that the genome of Ch-sw-sav1 was 7541 nucleotide long with two ORFs, excluding the 17 nucleotides ploy (A) at the 3' end. Phylogenetic analysis based on part of RdRp gene of this strain showed that it was classified into subgroup GIII. Sequence alignment indicated that there was an inserted 21-nt long nucleotide sequence at the 3' end of ORF2. The insertion showed high antigenicity index comparing to other regions in ORF2.Conclusions:Ch-sw-sav1 shared similar genetic profile with an American PEC strain except the 21-nt nucleotide at the 3' end of ORF2. The insert sequence shared high identity with part gene of Sus scrofa clone RP44-484M10.
Keywords:
Sus scrofa
2009-11-29
Go contributes to olfactory reception in Drosophila melanogaster
BioMed Central - Latest articles
Background:Seven-transmembrane receptors typically mediate olfactory signal transduction by coupling to G-proteins. Although insect odorant receptors have seven transmembrane domains like G-protein coupled receptors, they have an inverted membrane topology and function as ligand-gated cation channels. Consequently, the involvement of cyclic nucleotides and G proteins in insect odor reception is controversial. Since the heterotrimeric Goalpha subunit is expressed in Drosophila olfactory receptor neurons, we reasoned that Go acts together with insect odorant receptor cation channels to mediate odor-induced physiological responses.Results:To test whether Go dependent signaling is involved in mediating olfactory responses in Drosophila, we analyzed electroantennogram and single-sensillum recordings from flies that conditionally express pertussis toxin, a specific inhibitor of Go in Drosophila. Pertussis toxin expression in olfactory receptor neurons reversibly reduced the amplitude and hastened the termination of electroantennogram responses induced by ethyl acetate. The frequency of odor-induced spike firing from individual sensory neurons was also reduced by pertussis toxin. These results demonstrate that Go signaling is involved in increasing sensitivity of olfactory physiology in Drosophila. The effect of pertussis toxin was independent of odorant identity and intensity, indicating a generalized involvement of Go in olfactory reception.Conclusion:These results demonstrate that Go is required for maximal physiological responses to multiple odorants in Drosophila, and suggest that OR channel function and G-protein signaling are required for optimal physiological responses to odors.
Keywords:
Drosophila melanogaster
2009-11-29
Computational prediction of essential genes in an unculturable endosymbiotic bacterium, Wolbachia of Brugia malayi
BioMed Central - Latest articles
Background:Wolbachia (wBm) is an obligate endosymbiotic bacterium of Brugia malayi, a parasitic filarial nematode of humans and one of the causative agents of lymphatic filariasis. There is a pressing need for new drugs against filarial parasites, such as Brugia malayi. As wBm is required for Brugia malayi development and fertility, targeting wBm is a promising approach. However, the lifecycle of neither Brugia malayi nor wBm can be maintained in vitro. To facilitate selection of potential drug targets, we computationally ranked the wBm genome based on confidence that a particular gene is essential for the survival of the bacteria.Results:wBm protein sequences were aligned using BLAST to the Database of Essential Genes (DEG) version 5.2, a collection of 5,260 experimentally identified essential genes in 15 bacterial strains. A confidence score, the Multiple Hit Score (MHS), was developed to predict each wBm gene's essentiality based on the top alignments to essential genes in each bacterial strain. This method was validated using a jackknife methodology to test the ability to recover known essential genes in a control genome. A second estimation of essentiality, the Gene Conservation Score (GCS), was calculated on the basis of phyletic conservation of genes across Wolbachia's parent order Rickettsiales. Clusters of orthologous genes were predicted within the 27 currently available complete genomes. Druggability of wBm proteins was predicted by alignment to a database of protein targets of known compounds.Conclusions:Ranking wBm genes by either MHS or GCS predicts and prioritizes potentially essential genes. Comparison of the MHS to GCS produces quadrants representing four types of predictions: those with high confidence of essentiality by both methods (245 genes), those highly conserved across Rickettsiales (299 genes), those similar to distant essential genes (8 genes), and those with low confidence of essentiality (253 genes). These data facilitate selection of wBm genes for entry into drug design pipelines.
Keywords:
Brugia malayi, Rickettsiales
2009-11-28
An evaluation of minimal cellular functions to sustain a bacterial cell
BioMed Central - Latest articles
Background:Both computational and experimental approaches have been used to determine the minimal gene set required to sustain a bacterial cell. Such studies have provided clues to the minimal cellular-function set needed for life. We evaluate a minimal cellular-function set directly, instead of a gene set.Results:We estimated the essentialities of KEGG pathway maps as the entities of cellular functions, based on comparative genomics and metabolic network analyses. The former examined the evolutionary conservation of each pathway map by homology searches, and detected "conserved pathway maps". The latter identified "organism-specific pathway maps" that supply compounds required for the conserved pathway maps. We defined both pathway maps as "autonomous pathway maps". Among the set of autonomous pathway maps, the one that could synthesize all of the biomass components (the essential constituents for the cellular component of Escherichia coli / Bacillus subtilis), and that was composed of a minimal number of pathway maps, was determined for each of E. coli and B. subtilis, as "minimal pathway maps". We consider that they correspond to a minimal cellular-function set. The network of minimal pathway maps, composed of 20 conserved pathway maps and 21 organism-specific pathway maps for E. coli, starts a sequence of catabolic processes from carbohydrate metabolism. The catabolized compounds are used for anabolism, thus creating materials for cell components and for genetic information processing.Conclusions:Our analyses of these pathway maps revealed that those functioning in "genetic information processing" are likely to be conserved, but those for catabolism are not, reflecting an evolutionary aspect of cellular functions. Minimal pathway maps were compared with systematic gene knockout experiments, other computational results and parasitic genomes, and showed qualitative agreement, with some reasonable exceptions due to the experimental conditions or differences of computational methods. Our method provides an alternative way to explore the minimal cellular function set.
Keywords:
Bacillus subtilis, Escherichia coli
2009-11-27
Natural selection drives the fine-scale divergence of a coevolutionary arms race involving a long-mouthed weevil and its obligate host plant
BioMed Central - Latest articles
Background:One of the major recent advances in evolutionary biology is the recognition that evolutionary interactions between species are substantially differentiated among geographic populations. To date, several authors have revealed natural selection pressures mediating the geographically-divergent processes of coevolution. How local, then, is the geographic structuring of natural selection in coevolutionary systems?Results:I examined the spatial scale of a "geographic selection mosaic," focusing on a system involving a seed-predatory insect, the camellia weevil (Curculio camelliae), and its host plant, the Japanese camellia (Camellia japonica). In this system, female weevils excavate camellia fruits with their extremely-long mouthparts to lay eggs into seeds, while camellia seeds are protected by thick pericarps. Selection gradient analyses demonstrated that thicker camellia pericarps are significantly favored in some, but not all, populations within a small island (Yakushima Island, Japan; diameter ca. 30 km). At the extreme, camellia populations separated by only several kilometers were subject to different selection pressures. Interestingly, in a population with the thickest pericarps, camellia individuals with intermediate pericarp thickness had relatively high fitness when the potential costs of producing thick pericarps were considered. Also importantly, some parameters of the weevilcamellia interaction such as the severity of seed infestation showed clines along temperature, suggesting the effects of climate on the fine-scale geographic differentiation of the coevolutionary processes.Conclusion:These results show that natural selection can drive the geographic differentiation of interspecific interactions at surprisingly small spatial scales. Future studies should reveal the evolutionary/ecological outcomes of the "fine scale geographic mosaics" in biological communities.
Keywords:
Camellia japonica, Curculio camelliae
2009-11-25
Functional analysis of conserved aromatic amino acids in the discoidin domain of Paenibacillus beta-1,3-glucanase
BioMed Central - Latest articles
The 190-kDa Paenibacillus beta-1,3-glucanase (LamA) contains a catalytic module of the glycoside hydrolase family 16 (GH16) and several auxiliary domains. Of these, a discoidin domain (DS domain), present in both eukaryotic and prokaryotic proteins with a wide variety of functions, exists at the carboxyl-terminus. To better understand the bacterial DS domain in terms of its structure and function, this domain alone was expressed in Escherichia coli and characterized. The results indicate that the DS domain binds various polysaccharides and enhances the biological activity of the GH16 module on composite substrates. We also investigated the importance of several conserved aromatic residues in the domain's stability and substrate-binding affinity. Both were affected by mutations of these residues; however, the effect on protein stability was more notable. In particular, the forces contributed by a sandwiched triad (W1688, R1756, and W1729) were critical for the presumable beta-sandwich fold.
Keywords:
Escherichia coli
2009-11-25
Neuropsychiatric manifestation of confusional psychosis due to Cryptococcus neoformans var. grubii in an apparently immunocompetent host: a case report
BioMed Central - Latest articles
Cognitive disorders like dementia, delirium, depression, anxiety, psychosis and mania are the commonest neuropsychiatric manifestations. We discuss here a case of an adult women presenting with neuropsychiatric manifestations of confusional psychosis owing to Cryptococcosis. The principal cause was consequently established by culturing Cryptococcus neoformans from the cerebrospinal fluid confirmed as C. neoformans var. grubii (Serotype A) by genotypic methods. Antifungal therapy with IV Amphotericin B lead to sustained improvement and recovery of the patient from behavioural disorders. The case discussed here invokes the need for the vigilance it demands in delineating organic brain syndromes for a favourable treatment outcome.
Keywords:
Cryptococcus neoformans, Cryptococcus neoformans grubii
2009-11-24
Neurogenesis suggests independent evolution of opercula in serpulid polychaetes
BioMed Central - Latest articles
Background:The internal phylogenetic relationships of Annelida, one of the key lophotrochozoan lineages, are still heavily debated. Recent molecular analyses suggest that morphologically distinct groups, such as the polychaetes, are paraphyletic assemblages, thus questioning the homology of a number of polychaete morphological characters. Serpulid polychaetes are typically recognized by having fused anterior ends bearing a tentacular crown and an operculum. The latter is commonly viewed as a modified tentacle (= radiole) and is often used as an important diagnostic character in serpulid systematics.Results:By reconstructing the developmental neuroanatomy of the serpulid polychaete Spirorbis cf. spirorbis (Spirorbinae), we found striking differences in the overall neural architecture, the innervation pattern, and the ontogenetic establishment of the nervous supply of the operculum and the radioles in this species. Accordingly, the spirorbin operculum might not be homologous to the radioles or to the opercula of other serpulid taxa such as Serpula and Pomatoceros and is thus probably not a part of the tentacular crown.Conclusions:We demonstrate that common morphological traits such as the prostomial appendages may have evolved independently in respective serpulid sublineages and therefore require reassessment before being used in phylogenetic analyses. Our findings corroborate recent molecular studies that argue for a revision of serpulid systematics. In addition, our data on Spirorbis neurogenesis provide a novel set of characters that highlight the developmental plasticity of the segmented annelid nervous system.
Keywords:
Annelida, Spirorbinae
2009-11-24
Annotation and expression of carboxylesterases in the silkworm, Bombyx mori
BioMed Central - Latest articles
Background:Carboxylesterase is a multifunctional superfamily and ubiquitous in all living organisms, including animals, plants, insects, and microbes. It plays important roles in xenobiotic detoxification, and pheromone degradation, neurogenesis and regulating development. Previous studies mainly used Dipteran Drosophila and mosquitoes as model organisms to investigate the roles of the insect COEs in insecticide resistance. However, genome-wide characterization of COEs in phytophagous insects and comparative analysis remain to be performed.Results:Based on the newly assembled genome sequence, 76 putative COEs were identified in Bombyx mori. Relative to other Dipteran and Hymenopteran insects, alpha-esterases were significantly expanded in the silkworm. Genomics analysis suggested that BmCOEs showed chromosome preferable distribution and 55% of which were tandem arranged. Sixty-one BmCOEs were transcribed based on cDNA/ESTs and microarray data. Generally, most of the COEs showed tissue specific expressions and expression level between male and female did not display obvious differences. Three main patterns could be classified, i.e. midgut-, head and integument-, and silk gland-specific expressions. Midgut is the first barrier of xenobiotics peroral toxicity, in which COEs may be involved in eliminating secondary metabolites of mulberry leaves and contaminants of insecticides in diet. For head and integument-class, most of the members were homologous to odorant-degrading enzyme (ODE) and antennal esterase. RT-PCR verified that the ODE-like esterases were also highly expressed in larvae antenna and maxilla, and thus they may play important roles in degradation of plant volatiles or other xenobiotics.Conclusion:B. mori has the largest number of insect COE genes characterized to date. Comparative genomic analysis suggested that the gene expansion mainly occurred in silkworm alpha-esterases. Expression evidence indicated that the expanded genes were specifically expressed in midgut, integument and head, implying that these genes may have important roles in detoxifying secondary metabolites of mulberry leaves, contaminants in diet, and odorants. Our results provide some new insights into functions and evolutionary characteristics of COEs in phytophagous insects.
Keywords:
Bombyx mori
2009-11-21
Silencing of a putative immunophilin gene in the cattle tick Rhipicephalus (Boophilus) microplus increases the infection rate of Babesia bovis in larval progeny
BioMed Central - Latest articles
Background:The cattle tick Rhipicephalus (Boophilus) microplus is involved in the transmission of the protozoan Babesia bovis, the etiological agent of bovine babesiosis. Interactions between ticks and protozoa are poorly understood and the investigation of tick genes that affect tick fitness and protozoan infection can set the stage for dissecting the molecular interactions between the two species.Results:In this study, RNA interference was used to silence R. microplus genes that had been previously shown to be up-regulated in response to B. bovis infection. The silencing of a putative immunophilin gene (Imnp) in female ticks fed on a calf acutely infected with B. bovis decreased the hatching rate and survival of larval progeny. Interestingly, Imnp was up-regulated significantly in ovaries of R. microplus in response to B. bovis infection and its silencing in female ticks significantly increased the infection rate of the protozoan in larval progeny. The results also showed that the silencing of a putative Kunitz-type serine protease inhibitor (Spi) gene and a putative lipocalin (Lpc) gene decreased the fitness of R. microplus females, but had no significant effect on the infection rate of B. bovis in larval progeny.Conclusion:The silencing of the Imnp, Spi or Lpc genes decreased the fitness of R. microplus females fed on a calf during acute B. bovis infection. The Imnp gene data suggest that this putative immunophilin gene is involved in the defense system of R. microplus against B. bovis and may play a role in controlling the protozoan infection in tick ovaries and larval progeny.
Keywords:
Babesia bovis, Rhipicephalus microplus
2009-11-20
Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis
BioMed Central - Latest articles
Background:Spermatogenesis is a late developmental process that involves a coordinated expression program in germ cells and a permanent communication between the testicular somatic cells and the germ-line. Current knowledge regarding molecular factors driving male germ cell proliferation and differentiation in vertebrates is still limited and mainly based on existing data from rodents and human. Fish with a marked reproductive cycle and a germ cell development in synchronous cysts have proven to be choice models to study precise stages of the spermatogenetic development and the germ cell-somatic cell communication network. In this study we used 9K cDNA microarrays to investigate the expression profiles underlying testis maturation during the male reproductive cycle of the trout, Oncorhynchus mykiss.Results:Using total testis samples at various developmental stages and isolated spermatogonia, spermatocytes and spermatids, 3379 differentially expressed trout cDNAs were identified and their gene activation or repression patterns throughout the reproductive cycle were reported. We also performed a tissue-profiling analysis and highlighted many genes for which expression signals were restricted to the testes or gonads from both sexes. The search for orthologous genes in genome-sequenced fish species and the use of their mammalian orthologs allowed us to provide accurate annotations for trout cDNAs. The analysis of the GeneOntology terms therefore validated and broadened our interpretation of expression clusters by highlighting enriched functions that are consistent with known sequential events during male gametogenesis. Furthermore, we compared expression profiles of trout and mouse orthologs and identified a complement of genes for which expression during spermatogenesis was maintained throughout evolution.Conclusion:A comprehensive study of gene expression and associated functions during testis maturation and germ cell differentiation in the rainbow trout is presented. The study identifies new pathways involved during spermatogonia self-renewal or rapid proliferation, meiosis and gamete differentiation, in fish and potentially in all vertebrates. It also provides the necessary basis to further investigate the hormonal and molecular networks that trigger puberty and annual testicular recrudescence in seasonally breeding species.
Keywords:
Oncorhynchus mykiss
2009-11-19
Cryptococcus neoformans meningitis in a diabetic patient - the perils of an overzealous immune response: a case report
BioMed Central - Latest articles
Uncontrolled diabetics are prone to infections due to numerous factors as the glucose-rich blood serves as an excellent media for growth. Cryptococcus neoformans is an opportunistic fungus that is an important cause of CNS infections among immunocompromised patients, but it has only sporadically been reported in non-HIV-positive persons. The presence of elevated pro-inflammatory cytokines and abnormalities in numerous systemic indicators of inflammation in diabetics makes it conceivable that diabetics mount an exaggerated immune response to C.neoformans (paradoxical to their defective immune state) leading to grave outcomes. We present a fatal case of C.neoformans meningitis in a diabetic patient which emphasizes the perils of an overzealous immune response.
Keywords:
Cryptococcus neoformans
2009-11-19
Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia
BioMed Central - Latest articles
Background:Anopheles albimanus is an important malaria vector in some areas throughout its distribution in the Caribbean and the Pacific regions of Colombia, covering three biogeographic zones of the neotropical region, Maracaibo, Magdalena and Choco.Methods:This study was conducted to estimate intra-population genetic diversity, genetic differentiation and demographic history of An. albimanus populations because knowledge of vector population structure is a useful tool to guide malaria control programmes. Analyses were based on mtDNA COI gene sequences and four microsatellite loci of individuals collected in eight populations from the Caribbean and the Pacific regions of Colombia.Results:Two distinctive groups were consistently detected corresponding to COI haplotypes from each region. A star-shaped statistical parsimony network, significant and unimodal mismatch distribution, and significant negative neutrality tests together suggest a past demographic expansion or a selective sweep in An. albimanus from the Caribbean coast approximately 21,994 years ago during the late Pleistocene. Overall moderate to low genetic differentiation was observed between populations within each region. However, a significant level of differentiation among the populations closer to Buenaventura in the Pacific region was observed. The isolation by distance model best explained genetic differentiation among the Caribbean region localities: Los Achiotes, Santa Rosa de Lima and Monitos, but it could not explain the genetic differentiation observed between Turbo (Magdalena providence), and the Pacific region localities (Nuqui, Buenaventura, Tumaco). The patterns of differentiation in the populations from the different biogeographic provinces could not be entirely attributed to isolation by distance.Conclusions:The data provide evidence for limited past gene flow between the Caribbean and the Pacific regions, as estimated by mtDNA sequences and current gene flow patterns among An. albimanus populations as measured by MS loci which may be mainly influenced by semi-permeable natural barriers in each biogeographical region that lead to the genetic differences and effective population sizes detected. The relatively high genetic differentiation in the port city of Buenaventura may be the result of specific ecological conditions, human migration and activities and/or differences in effective population sizes. This knowledge could serve to evaluate and coordinate vector control strategies in these regions of Colombia.
Keywords:
Anopheles albimanus
2009-11-18
Genome scale transcriptome analysis of shoot organogenesis in Populus
BioMed Central - Latest articles
Background:Our aim is to improve knowledge of gene regulatory circuits important to dedifferentiation, redifferentiation, and adventitious meristem organization during in vitro regeneration of plants. Regeneration of transgenic cells remains a major obstacle to research and commercial deployment of most taxa of transgenic plants, and woody species are particularly recalcitrant. The model woody species Populus, due to its genome sequence and amenability to in vitro manipulation, is an excellent species for study in this area. The genes recognized will help to identify useful tools for improving the efficiency of plant regeneration and transformation.Results:We analyzed gene expression during poplar in vitro dedifferentiation and shoot regeneration using an Affymetrix array representing over 56,000 poplar transcripts. We focused on callus induction and shoot formation, thus we sampled RNAs from tissues: prior to callus induction, 3 days and 15 days after callus induction, and 3 days and 8 days after the start of shoot induction. We used a female hybrid white poplar clone (INRA 717-1 B4, Populus tremula x P. alba) that is used widely as a model transgenic genotype. Approximately 15% of the monitored genes were significantly up-or down-regulated when controlling the false discovery rate (FDR) at 0.01; over 3,000 genes had a 5-fold or greater change in expression. We found a large initial change in expression after the beginning of hormone treatment (at the earliest stage of callus induction), and then a much smaller number of additional differentially expressed genes at subsequent regeneration stages. A total of 588 transcription factors that were distributed in 45 gene families were differentially regulated. Genes that showed strong differential expression included components of auxin and cytokinin signaling, selected cell division genes, and genes related to plastid development and photosynthesis. When compared with data on in vitro callogenesis in Arabidopsis, 25% (1,260) of up-regulated and 22% (748) of down-regulated genes were in common with the genes regulated in poplar during callus induction.Conclusions:The major regulatory events during plant cell organogenesis occur at early stages of dedifferentiation. The regulatory circuits reflect the combinational effects of transcriptional control and hormone signaling, and associated changes in light environment imposed during dedifferentiation.
Keywords:
Populus alba, Populus tremula
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