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Public Databases (public + databases)
Selected AbstractsAn automated in situ hybridization screen in the medaka to identify unknown neural genesDEVELOPMENTAL DYNAMICS, Issue 3 2005Carole Deyts Abstract Despite the fact that a large body of factors that play important roles in development are known, there are still large gaps in understanding the genetic pathways that govern these processes. To find previously unknown genes that are expressed during embryonic development, we optimized and performed an automated whole-mount in situ hybridization screen on medaka embryos at the end of somitogenesis. Partial cDNA sequences were compared against public databases and identified according to similarities found to other genes and gene products. Among 321 isolated genes showing specific expression in the central nervous system in at least one of five stages of development, 55.14% represented genes whose functions are already documented (in fish or other model organisms). Additionally, 16.51% were identified as conserved unknown genes or genes with unknown function. We provide new data on eight of these genes that presented a restricted expression pattern that allowed for formulating testable hypotheses on their developmental roles, and that were homologous to mammalian molecules of unknown function. Thus, gene expression screening in medaka is an efficient tool for isolating new regulators of embryonic development, and can complement genome-sequencing projects that are producing a high number of genes without ascribed functions. Developmental Dynamics 234:698,708, 2005. © 2005 Wiley-Liss, Inc. [source] Prediction of metabolite identity from accurate mass, migration time prediction and isotopic pattern information in CE-TOFMS dataELECTROPHORESIS, Issue 14 2010Masahiro Sugimoto Abstract CE-TOFMS is a powerful method for profiling charged metabolites. However, the limited availability of metabolite standards hinders the process of identifying compounds from detected features in CE-TOFMS data sets. To overcome this problem, we developed a method to identify unknown peaks based on the predicted migration time (tm) and accurate m/z values. We developed a predictive model using 375 standard cationic metabolites and support vector regression. The model yielded good correlations between the predicted and measured tm (R=0.952 and 0.905 using complete and cross-validation data sets, respectively). Using the trained model, we subsequently predicted the tm for 2938 metabolites available from the public databases and assigned tentative identities to noise-filtered features in human urine samples. While 38.9% of the peaks were assigned metabolite names by matching with the standard library alone, the proportion increased to 52.2%. The proposed methodology increases the value of metabolomic data sets obtained from CE-TOFMS profiling. [source] Genomic BLAST: custom-defined virtual databases for complete and unfinished genomesFEMS MICROBIOLOGY LETTERS, Issue 2 2002Leda Cummings Abstract BLAST (Basic Local Alignment Search Tool) searches against DNA and protein sequence databases have become an indispensable tool for biomedical research. The proliferation of the genome sequencing projects is steadily increasing the fraction of genome-derived sequences in the public databases and their importance as a public resource. We report here the availability of Genomic BLAST, a novel graphical tool for simplifying BLAST searches against complete and unfinished genome sequences. This tool allows the user to compare the query sequence against a virtual database of DNA and/or protein sequences from a selected group of organisms with finished or unfinished genomes. The organisms for such a database can be selected using either a graphic taxonomy-based tree or an alphabetical list of organism-specific sequences. The first option is designed to help explore the evolutionary relationships among organisms within a certain taxonomy group when performing BLAST searches. The use of an alphabetical list allows the user to perform a more elaborate set of selections, assembling any given number of organism-specific databases from unfinished or complete genomes. This tool, available at the NCBI web site http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi, currently provides access to over 170 bacterial and archaeal genomes and over 40 eukaryotic genomes. [source] Toll-like receptor-1, -2, and -6 polymorphisms influence disease extension in inflammatory bowel diseasesINFLAMMATORY BOWEL DISEASES, Issue 1 2006Marie Pierik MD Abstract Background: Evidence that a deficient innate immune response toward the bacterial flora of the gut plays a role in the pathogenesis of inflammatory bowel disease (IBD) is growing. This is underscored by the finding of the association between CARD15 variants and Crohn's disease (CD) and D299G in Toll-like receptor (TLR) 4 and IBD. Our aims were to study nonsynonymous polymorphisms in other TLR genes in IBD. Methods: Thirty-five single nucleotide polymorphisms (SNP) in TLR1-10 were identified from public databases. 284 IBD parent-child trios and a second independent cohort of 285 IBD patients and 191 healthy controls were genotyped with polymerase chain reaction-restriction fragment length polymorphisms. Patients were pooled for genotype-phenotype analyses. Results: Although none of the SNPs was involved in disease susceptibility, a number of variants influenced the disease phenotype. A positive association between TLR1 R80T and pancolitis in UC (P = .045, OR [95% CI] 2.844 [1.026-7.844]) was found. The TLR2 R753G SNP was also associated with pancolitis (P = .027, OR [95% CI] 4.741 [1.197-18.773]). The relative risks for heterozygous patients to develop pancolitis were 5.8 and 3.3 for R80T and R753G, respectively. There was a negative association between TLR6 S249P and ulcerative colitis with proctitis only (P = .026, OR [95% CI] 0.223 [0.096-0.705]). In CD, we found a negative association between ileal disease involvement and TLR1 S602I (P = .03, OR [95% CI] 0.522 [0.286-0.950]). Conclusion:TLR2 and its cofactors TLR1 and TLR6 are involved in the initial immune response to bacteria by recognizing peptidoglycan. An association between nonsynonymous variants in the TLR1, - 2, and - 6 genes and extensive colonic disease in UC and CD was found. Our findings further highlight the role of an abnormal innate immune response in the pathogenesis of IBD. [source] Genes encoding a group of related small secreted proteins from the gut of Hessian fly larvae [Mayetiola destructor (Say)]INSECT SCIENCE, Issue 5 2006MING-SHUN CHEN Abstract A group of related genes has been isolated and characterized from the gut of Hessian fly larvae [Mayetiola destructor (Say)]. Members in this group appear to encode proteins with secretary signal pep tides at the N-terminals. The mature putative proteins are small, acidic proteins with calculated molecular masses of 14.5 to 15.3 kDa, and isoelectric points from 4.56 to 4.88. Northern blot analysis revealed that these genes are expressed predominantly in the gut of Hessian fly larvae and pupae. Two related genes, G10K1 and G10K2, were isolated as tandem repeats. Both genes contain three exons and two introns. The intron/exon boundaries were conserved in terms of amino acid encoding, suggesting that they arose by gene duplication. The fact that the frequency of this group of clones in a gut cDNA library higher than that of total cDNA clones encoding digestive enzymes suggested that this group of proteins may perform an important function in the gut physiology of this insect. However, the exact functions of these proteins are as yet known since no sequence similarity could be identified between these proteins and any known sequences in public databases using standard methods. [source] Expression profile of genes identified in human spermatogonial stem cell-like cells using suppression subtractive hybridizationJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 3 2010Jung Ki Yoo Abstract Spermatogenesis is the process by which testicular spermatogonial stem cells (SSCs) self-renew and differentiate into mature sperm in the testis. Maintaining healthy spermatogenesis requires proper proliferation of SSCs. In this study, we sought to identify factors that regulate the proliferation of SSCs. Human SSC (hSSC)-like cells were isolated from azoospermic patients by a modified culture method and propagated in vitro. After four to five passages, the SSC-like cells spontaneously ceased proliferating in vitro, so we collected proliferating (P)-hSSC-like cells at passage two and senescent (S)-hSSC-like cells at passage five. Suppression subtractive hybridization (SSH) was used to identify genes that were differentially expressed between the P-hSSC-like and S-hSSC-like cells. We selected positive clones up-regulated in P-hSSC-like cells using SSH and functionally characterized them by reference to public databases using NCBI BLAST tools. Expression levels of genes corresponding to subtracted clones were analyzed using RT-PCR. Finally, we confirmed the differential expression of 128 genes in positive clones of P-hSSC-like cells compared with S-hSSC-like cells and selected 23 known and 39 unknown clones for further study. Known genes were associated with diverse functions; 22% were related to metabolism. Fifteen of the known genes and two of the unknown genes were down-regulated after senescence of hSSC-like cells. A comparison with previous reports further suggests that known genes selected, SPP1, may be related to germ cell biogenesis and cellular proliferation. Our findings identify several potential novel candidate biomarkers of proliferating- and senescencet-hSSCs, and they provide potentially important insights into the function and characteristics of human SSCs. J. Cell. Biochem. 110: 752,762, 2010. © 2010 Wiley-Liss, Inc. [source] DNA-based identification of preys from non-destructive, total DNA extractions of predators using arthropod universal primersMOLECULAR ECOLOGY RESOURCES, Issue 3 2006JOAN PONS Abstract Here, I show that prey sequences can be detected from DNA of tiger beetles of the genus Rivacindela using whole specimens, nondestructive methods, and universal cytochrome b primers for arthropods. BLAST searches of the obtained sequences against public databases revealed that the diet of Rivacindela is mostly composed of flies but also termites and other beetles. Accurate determination of order, family and even genus was achieved in most cases but rarely to species level. Results suggest that stored DNA samples extracted from whole predatory specimens could be an alternative to dissected gut contents as starting source for DNA-based dietary studies. [source] Acrylamide: An Update on Current Knowledge in Analysis, Levels in Food, Mechanisms of Formation, and Potential Strategies of ControlNUTRITION REVIEWS, Issue 12 2004Richard H. Stadler PhD This review summarizes the research to date on acrylamide levels in food, analytical methods, main sources of dietary exposure, mechanisms of formation, and mitigation research in the major food categories. Significant progress in the research has been made over the past 18 months, as reflected by the numerous publications and national and international workshops on the subject. This rapid pace of developments is mainly attributable to the coordinated and collaborative efforts of all of those concerned: the food industry, academia, private/enforcement laboratories, and national authorities. Most of the information gaps identified since the findings in early 2002 on the occurrence of acrylamide in foods and exposure assessments have been addressed, and public databases have been established by several authorities. Today, the performance of analytical methods, particularly for "difficult" food matrices, is adequate, and any modifications made over the past 12 to 18 months in analytical procedures did not significantly impact the initial exposure calculations. Several avenues into mitigation have been explored in the different food categories, with much emphasis being placed on potato-based products, and empirical trials (mostly pilot studies) have provided better knowledge of the key parameters that influence acrylamide formation. However, despite these intensive efforts, only marginal reductions have been achieved by the food industry, and any further progress will entail long-term studies at the primary production level. Any measures devised to reduce exposure to acrylamide in commercial foods must be carefully assessed in terms of food safety and quality. A hitherto poorly addressed concern is the formation of acrylamide in foods prepared by consumers in the home, and more guidance on this by national authorities is warranted. [source] Cytochrome b gene structure and consequences for resistance to Qo inhibitor fungicides in plant pathogensPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 6 2006Valeria Grasso Abstract The cytochrome b (cyt b) gene structure was characterized for different agronomically important plant pathogens, such as Puccinia recondita f sp tritici (Erikss) CO Johnston, P graminis f sp tritici Erikss and Hennings, P striiformis f sp tritici Erikss, P coronata f sp avenae P Syd & Syd, P hordei GH Otth, P recondita f sp secalis Roberge, P sorghi Schwein, P horiana Henn, Uromyces appendiculatus (Pers) Unger, Phakopsora pachyrhizi Syd & P Syd, Hemileia vastatrix Berk & Broome, Alternaria solani Sorauer, A alternata (Fr) Keissl and Plasmopara viticola (Berk & Curt) Berlese & de Toni. The sequenced fragment included the two hot spot regions in which mutations conferring resistance to QoI fungicides may occur. The cyt b gene structure of these pathogens was compared with that of other species from public databases, including the strobilurin-producing fungus Mycena galopoda (Pers) P Kumm, Saccharomyces cerevisiae Meyer ex Hansen, Venturia inaequalis (Cooke) Winter and Mycosphaerella fijiensis Morelet. In all rust species, as well as in A solani, resistance to QoI fungicides caused by the mutation G143A has never been reported. A type I intron was observed directly after the codon for glycine at position 143 in these species. This intron was absent in pathogens such as A alternata, Blumeria graminis (DC) Speer, Pyricularia grisea Sacc, Mycosphaerella graminicola (Fuckel) J Schröt, M fijiensis, V inaequalis and P viticola, in which resistance to QoI fungicides has occurred and the glycine is replaced by alanine at position 143 in the resistant genotype. The present authors predict that a nucleotide substitution in codon 143 would prevent splicing of the intron, leading to a deficient cytochrome b, which is lethal. As a consequence, the evolution of resistance to QoI fungicides based on G143A is not likely to evolve in pathogens carrying an intron directly after this codon. Copyright © 2006 Society of Chemical Industry [source] Poplar Genomics is Getting Popular: The Impact of the Poplar Genome Project on Tree ResearchPLANT BIOLOGY, Issue 1 2004G. A. Tuskan Abstract: Trees, due to their long life-span, have characteristics that distinguish them from annual, herbaceous plants. It is likely that many of these properties are based on a tree-specific genetic foundation. The U.S. Department of Energy initiated a genome-sequencing project for Populus, a model perennial plant. Through international collaboration and input to the sequencing effort, the annotated whole genome sequence of Populus trichocarpa will be released to the public in early 2004. This genomic resource will, for the first time, allow comparison between a perennial and an annual plant on a whole genome basis and therefore provide clues for molecular research on tree-specific questions like dormancy, development of a secondary cambium, juvenile-mature phase change, or long-term host-pest interactions. The approximately 520 Mbp of annotated genomic sequence will complement and expand the knowledge provided so far by the 125 000 ESTs from poplar that are available in public databases. This article introduces the international poplar research programmes and points out the significance of the poplar genome project for plant research. [source] The secreted and surface proteomes of the adult stage of the carcinogenic human liver fluke Opisthorchis viverriniPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 5 2010Jason Mulvenna Abstract Infection with the human liver fluke, Opisthorchis viverrini, is a serious public health problem in Thailand, Laos and nearby locations in Southeast Asia. Both experimental and epidemiological evidence strongly implicate liver fluke infection in the etiology of one of the liver cancer subtypes, cholangiocarcinoma (CCA). To identify parasite proteins critical for liver fluke survival and the etiology of CCA, OFFGEL electrophoresis and multiple reaction monitoring were employed to characterize 300 parasite proteins from the O. viverrini excretory/secretory products and, utilizing selective labeling and sequential solubilization, from the host-exposed tegument. The excretory/secretory included a complex mixture of proteins that have been associated with cancers, including proteases of different mechanistic classes and orthologues of mammalian growth factors and anti-apoptotic proteins. Also identified was a cysteine protease inhibitor which, in other helminth pathogens, induces nitric oxide production by macrophages, and, hence may contribute to malignant transformation of inflamed cells. More than 160 tegumental proteins were identified using sequential solubilization of isolated teguments, and a subset of these was localized to the surface membrane of the tegument by labeling living flukes with biotin and confirming surface localization with fluorescence microscopy. These included annexins, which are potential immuno-modulators, and orthologues of the schistosomiasis vaccine antigens Sm29 and tetraspanin-2. Novel roles in pathogenesis were suggested for the tegument,host interface since more than ten surface proteins had no homologues in the public databases. The O. viverrini proteins identified here provide an extensive catalogue of novel leads for research on the pathogenesis of opisthorchiasis and the development of novel interventions for this disease and CCA, as well as providing a scaffold for sequencing the genome of this fluke. [source] The secretome of Pleurotus sapidusPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 18 2005Holger Zorn Dr. Abstract Due to their unique capability to attack lignified biopolymers, extracellular enzymes of white-rot fungi enjoy an increasing interest in various fields of white biotechnology. The edible fungus Pleurotus sapidus was selected as a model organism for the analysis of the secretome by means of 2-DE. For enzyme production, the fungus was grown in submerged cultures either on peanut shells or on glass wool as a carrier material. Identification of the secreted enzymes was performed by tryptic digestion, ESI-MS/MS ab initio sequencing, and homology searches against public databases. The spectrum of secreted enzymes comprised various types of hydrolases and lignolytic enzymes of the manganese peroxidase/versatile peroxidase family. While peptidases were secreted mainly by the cultures grown on peanut shells, versatile peroxidase type enzymes dominated in the cultures grown on glass wool. [source] Analysis of phosphatase and tensin homolog tumor suppressor interacting proteins by in vitro and in silico proteomicsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 5 2005David K. Crockett Abstract The phosphatase and tensin homolog (PTEN) tumor suppressor is a multifunctional protein deregulated in many types of cancer. To date, a comprehensive documentation of PTEN interacting proteins has not been performed. The goal of our study was to characterize the PTEN interactome using affinity pull-down and tandem mass spectrometry (MS/MS). Wild-type PTEN cDNA was inserted into pTRC-His2 vector to create a 6-His tagged protein, which was expressed in Escherichia coli. Lysate from a human lymphoma cell line was used in pull-down assays, utilizing affinity for nickel-agarose beads. Bound proteins were eluted with imidazole, digested and analyzed on an LCQ DecaXP ion trap mass spectrometer. The nickel affinity pull-down efficiency was evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analysis. Acquired data were searched against the NCBI nr.fasta nonredundant protein database using the SEQUEST algorithm and screened using INTERACT and ProteinProphet. All experiments were performed in duplicate with 6-His- lacZ serving as control. A total of 79 proteins were identified in the wild-type 6-His-PTEN pull-down by MS/MS. We further validated a subset of the proteins present in the PTEN interactome by performing immunoprecipitation using an anti-PTEN antibody and establishing the presence of the proteins in the immunocomplex by Western blot analysis. A search of published PTEN interactions was also performed using Online Mendelian Inheritance in Man, Human Protein Reference Database, the IntAct Project database, and PubMed. This in silico analysis confirmed 42 out of 79 (53%) of the proteins identified by MS/MS. The remaining 37 proteins represent probable PTEN interactions not previously documented in public databases or reported in the literature. These results highlight the value of combining both in vitro biochemical approaches with in silico analyses for a comprehensive study of protein-protein interactions. [source] The bovine fatty acid binding protein 4 gene is significantly associated with marbling and subcutaneous fat depth in Wagyu x Limousin F2 crossesANIMAL GENETICS, Issue 4 2006J. J. Michal Summary Fatty acid binding protein 4 (FABP4), which is expressed in adipose tissue, interacts with peroxisome proliferator-activated receptors and binds to hormone-sensitive lipase and therefore, plays an important role in lipid metabolism and homeostasis in adipocytes. The objective of this study was to investigate associations of the bovine FABP4 gene with fat deposition. Both cDNA and genomic DNA sequences of the bovine gene were retrieved from the public databases and aligned to determine its genomic organization. Primers targeting two regions of the FABP4 gene were designed: from nucleotides 5433,6106 and from nucleotides 7417,7868 (AAFC01136716). Direct sequencing of polymerase chain reaction (PCR) products on two DNA pools from high- and low-marbling animals revealed two single nucleotide polymorphisms (SNPs): AAFC01136716.1:g.7516G>C and g.7713G>C. The former SNP, detected by PCR-restriction fragment length polymorphism using restriction enzyme MspA1I, was genotyped on 246 F2 animals in a Waygu × Limousin F2 reference population. Statistical analysis showed that the FABP4 genotype significantly affected marbling score (P = 0.0398) and subcutaneous fat depth (P = 0.0246). The FABP4 gene falls into a suggestive/significant quantitative trait loci interval for beef marbling that was previously reported on bovine chromosome 14 in three other populations. [source] Characterization of single-nucleotide polymorphism markers in the Mediterranean mussel, Mytilus galloprovincialisAQUACULTURE RESEARCH, Issue 10 2010Manuel Vera Abstract The Mediterranean mussel, Mytilus galloprovincialis, is one of the most important aquaculture species in Europe. Appropriate molecular markers are required to evaluate genetic resources and to trace genealogies in breeding programmes for improving mussel culture. Microsatellites have been commonly applied to this purpose in other species. However, Mediterranean mussel microsatellites have demonstrated high frequencies of null alleles that hamper accurate estimates of population parameters and confident parentage inferences. As alternative markers, we have characterized in silico 25 potential single-nucleotide polymorphism (SNP) markers in the Mediterranean mussel from expressed sequence tag (EST) public databases. The genotyping of SNPs was performed using a single-base extension approach. Their polymorphism was evaluated in 47 individuals from an Atlantic population. Out of the 25 potential SNPs tested, 12 were technically feasible (producing a single amplicon) and polymorphic. All were biallelic and had an unbiased heterozygosity ranging from 0.160 to 0.504. One SNP was from a mitochondrial gene. The combined potential of nuclear SNPs for parentage assignment gave an exclusion probability of a false couple of parents of 0.9471. These markers will be useful for evaluating resources and tracing genealogies in genetic breeding programmes implemented to solve the main problems of mussel culture. [source] In this issue: Biotechnology Journal 9/2010BIOTECHNOLOGY JOURNAL, Issue 9 2010Article first published online: 10 SEP 2010 Linking obesity and colorectal cancer Sung and Bae, Biotechnol. J. 2010, 5, 930,941 Obesity is known as one of the most closely related risk factors of colorectal cancer (CRC). However, due to the complicated nature of the diet, it has been very difficult to provide clear explanations and molecular mechanisms for the role of dietary components in carcinogenesis. Nutrigenomics has become a powerful tool to study the relationships between food components and genes. It includes nutrigenetics (dealing with genetic variations related to phenotypic changes in response to diet), nutritional epigenomics and nutritional transcriptomics/proteomics/metabolomics. This review summarizes data on genes, proteins and metabolites that are related to either obesity or CRC and candidate molecules that may link obesity and CRC. The application of bioinformatics helps to perform large-scale network analysis to study cause-effect relationships between dietary components and CRC in the future. Hepatoprotective effects of oleuropein Kim et al., Biotechnol. J. 2010, 5, 950,960 Oleuropein, an active constituent of olive leaf, has a variety of pharmacological activities associated with its capacity to scavenge reactive oxygen species and has a protective effect against non-alcoholic fatty liver disease (NAFLD) in vivo. To gain insights into the molecular mechanisms of its hepatoprotective action the group of Taesun Park (Seoul, Korea) fed mice with a high fat diet supplemented with oleuropein. Then, liver tissue was subjected to DNA microarray analysis. Oleuropein in high fat diet reduced the mRNA level of regulators of hepatic fatty acid uptake and transport. The expression of a number of genes involved in oxidative stress responses, detoxification of lipid peroxidation products and proinflammatory cytokine genes were reduced, while highly regulated transcription factors were implicated in the lipogenesis, inflammation, insulin resistance and fibrosis, underlying the multifactorial effect of oleuropein on NAFLD. Genetic variations in obesity and diabetes Varma et al., Biotechnol. J. 2010, 5, 942,949 Obesity is a state of metabolic deregulation and a leading cause for development of type 2 diabetes, which are complex polygenic diseases. Here, authors from the National Centre of Toxicological Research at the FDA (Jefferson, Arizona, USA) used a data mining approach to evaluate the role of carbohydrate metabolic pathway genes in the development of obesity and type 2 diabetes. Data from public databases were used to map the position of these genes to known quantitative trait loci (QTL) and to find sequence and structural genetic variants such as single nucleotide polymorphisms (SNPs). The results demonstrated that a majority of carbohydrate metabolic pathways genes are associated with QTL for obesity and many for type 2 diabetes. This data mining approach can establish a strategy for interpreting an individual's risk factor for disease development, instead of population attributable risks. [source] Carbohydrate metabolic pathway genes associated with quantitative trait loci (QTL) for obesity and type 2 diabetes: Identification by data miningBIOTECHNOLOGY JOURNAL, Issue 9 2010Dr. Vijayalakshmi Varma Abstract Increasing consumption of refined carbohydrates is now being recognized as a primary contributor to the development of nutritionally related chronic diseases such as obesity and type 2 diabetes mellitus (T2DM). A data mining approach was used to evaluate the role of carbohydrate metabolic pathway genes in the development of obesity and T2DM. Data from public databases were used to map the position of the carbohydrate metabolic pathway genes to known quantitative trait loci (QTL) for obesity and T2DM and for examining the pathway genes for the presence of sequence and structural genetic variants such as single nucleotide polymorphisms (SNPs) and copy number variants (CNS), respectively. The results demonstrated that a majority of the genes of the carbohydrate metabolic pathways are associated with QTL for obesity and many for T2DM. In addition, some key genes of the pathways also encode non-synonymous SNPs that exhibit significant differences in population frequencies. This study emphasizes the significance of the metabolic pathways genes in the development of disease phenotypes, its differential occurrence across populations and between individuals, and a strategy for interpreting an individuals' risk for disease. [source] Re-analysis of 178 previously unidentifiable Mycobacterium isolates in the Netherlands in 1999,2007CLINICAL MICROBIOLOGY AND INFECTION, Issue 9 2010J. Van Ingen Clin Microbiol Infect 2010; 16: 1470,1474 Abstract Nontuberculous mycobacteria (NTM) that cannot be identified to the species level by reverse line blot hybridization assays and sequencing of the 16S rRNA gene comprise a challenge for reference laboratories. However, the number of 16S rRNA gene sequences added to online public databases is growing rapidly, as is the number of Mycobacterium species. Therefore, we re-analysed 178 Mycobacterium isolates with 53 previously unmatched 16S rRNA gene sequences, submitted to our national reference laboratory in 1999,2007. All sequences were again compared with the GenBank database sequences and the isolates were re-identified using two commercially available identification kits, targeting separate genetic loci. Ninety-three out of 178 isolates (52%) with 20 different 16S rRNA gene sequences could be assigned to validly published species. The two reverse line blot assays provided false identifications for three recently described species and 22 discrepancies were recorded in the identification results between the two reverse line blot assays. Identification by reverse line blot assays underestimates the genetic heterogeneity among NTM. This heterogeneity can be clinically relevant because particular sub-groupings of species can cause specific disease types. Therefore, sequence-based identification is preferable, at least at the reference laboratory level, although the exact targets needed for clinically useful results remain to be established. The number of NTM species in the environment is probably so high that unidentifiable clinical isolates should be given a separate species status only if this is clinically meaningful. [source] | ||||||||||||||||