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PubMed2004

Significance of the genetic relationships deduced from partial nucleotide sequencing of infectious bursal disease virus genome segments A or B.

The rapid genomic characterization of infectious bursal disease virus (IBDV) requires determining which partial nucleotide (nt) sequences derived from IBDV segments A or B would produce phylogenetic information as significant as sequencing the whole corresponding segments. Long nt coding sequences of 27 IBDV segments A (aa 20-991) and 21 segments B (aa 7-stop codon) were retrieved from databanks and used to compute reference phylogenetic trees using Neighbor Joining (NJ) and Parsimony (P): clusters appearing in the NJ and P reference trees with a bootstrap value greater than 80% were considered as significant (Whole Segment Clusters, WSC). The sequences were then cut into overlapping regions. These were used to compute phylogenetic trees which were compared with reference ones. Of the partial sequences, the VP2 gene best represented IBDV segment A (10 out of 13 WSC were conserved), and the 5' two thirds of segment B best represented segment B (5 to 6 conserved WSC out of 6). Implementation of the Plato programme finally demonstrated that the region encoding VP2 variable domain (vVP2, segment A) is the only region of IBDV genome with a significantly different evolution rate, which result is consistent with vVP2 being subjected to a high selection pressure.

Databases, Genetic↗
PubMedDate not supplied

[Changes in selenium levels in epilepsy].

INTRODUCTION: It has been suggested that antiepileptic drug therapies deplete total body selenium stores and failure to give appropriate selenium supplementation, especially to patients receiving valproic acid during pregnancy may increase the risk of neural tube defects or other free radical mediated damage. Selenium is essential for the synthesis of selenoproteins, including glutathione peroxidase. AIMS: To review the present state of knowledge about selenium behaviour in people with epilepsy taking antiepileptic drugs and to develop guidelines for the appropriate use of selenium supplements. DEVELOPMENT: Databases such as Medline, Embase, Scisearch and Lilacs were consulted to have access to literature. A search in said databases was performed in order to find articles published from January 1966 to August 2004. All articles published in English and Spanish were considered. A manual review of the references present in each produced article was done in order to identify the articles that the electronic search may have not found itself. The title and abstract of the potential articles were analyzed before asking for the complete article. However, articles which seemed ambiguous were completely analyzed later to establish their relevance. CONCLUSIONS: There is insufficient evidence to fully evaluate the effect of selenium supplementation. The possible beneficial effects on pregnancy need to be evaluated in further studies.

Anticonvulsants↗
PubMed2003

The phylogenetic diversity of eukaryotic transcription.

Eukaryotic transcription is a highly regulated process involving interactions between large numbers of proteins. To analyse the phylogenetic distribution of the components of this process, six crown eukaryote group genomes were queried with a reference set of transcription-associated (TA) proteins. On average, one in 10 proteins encoded by these genomes were found to be homologous to sequences in the reference set. Analysis of families identified using an accurate sequence clustering algorithm and containing both TA proteins and eukaryotic sequences showed that in two-thirds of the families the homologues originate from a single kingdom. Furthermore, in only 15% of the fungal-specific clusters are the homologues present in both budding and fission yeast, as compared with the metazoan-specific clusters where 53% of the homologues originate from two or more species. Families whose members comprise general transcription factor or RNA polymerase subunits exhibit a low degree of taxon specificity, suggesting that the transcription initiation complex is highly conserved. This contrasts with transcriptional regulator families, that are primarily taxon-specific, indicating proteins controlling gene activation exhibit considerable sequence diversity across the eukaryotic domain.

Animals↗
PubMed1996

cDNA cloning and characterization of a novel nucleolar protein.

In an initial study of anti-nuclear antibodies in the chronic inflammatory bladder disease interstitial cystitis, we reported that 7% of interstitial cystitis patients studied had autoantibodies to the nucleolus. We now report that, using an autoimmune serum from a patient with interstitial cystitis, we have identified and partially characterized a novel protein with an M(r) of approximately 55 kDa (hereafter referred to as No55) localized to the granular component of the nucleolus. No55 was initially characterized by diffuse nucleolar immunofluorescence staining in interphase cells and by Western blotting as a 55-kDa doublet on whole-cell extracts. During mitosis, No55 was associated with chromosomes and appeared in prenucleolar bodies during telophase, but it did not colocalize with p80-coilin in coiled bodies. Immunoelectron microscopy revealed that No55 was localized uniformly throughout the granular component of the nucleolus compared with a more peripheral localization of nucleolar granular component protein B23. On segregation of the nucleolus with actinomycin D, No55 remained with the granular component of the segregated nucleolus, whereas protein B23 was found predominantly in the nucleoplasm. Finally, a cDNA expression library was screened with the human autoantibody against No55, and a 2.4-kb insert was isolated, subcloned to homogeneity, and then sequenced. Analysis of this sequence showed an open reading frame of approximately 1.3 kb coding for 437 amino acids with a predicted molecular weight of 50 kDa. A search of the gene sequence database indicated homology with SC65, a rat synaptonemal complex protein. Therefore, on the basis of molecular weight, nucleolar sublocalization, response to actinomycin D, and cDNA sequence determination, No55 is a novel protein of the interphase nucleolus.

Amino Acid Sequence↗
PubMed1998

Objective interpretation of bovine clinical biochemistry data: application of Bayes law to a database model.

With the advent of animal-side biochemistry analysers in veterinary practice, the requirement for ready access to reliable means for interpretation of the results is of increasing importance. At the University of Glasgow Veterinary School (GUVS), a large computerised hospital database containing extensive clinical, laboratory, and pathological information has been maintained. A retrospective study was undertaken to investigate plasma biochemistry results and corresponding post mortem diagnosis data from 754 unwell cattle which had presented to GUVS over the study period. Initial analysis of the clinical biochemistry data from this unwell population revealed that the parameters did not follow a normal distribution. This finding suggested that the accepted reference range method for the interpretation of clinical biochemistry data may provide limited information about the unwell animal. By applying a combination of percentile analysis and conditional probability techniques to the hospital data, the development of a means of clinical biochemistry interpretation was developed whereby a clinician could determine whether a value was abnormal, the degree of abnormality, and the most likely associated diseases. For example, a urea value of 30 mmol/l lay within the top 5% of results, and one of the most common diseases associated with this urea value was pyelonephritis. Furthermore, a Bayesian approach allowed the quantification of the relationship between any plasma biochemistry value and disease through the generation of a ratio termed the 'biochemical factor'. Using the same example, given a urea value of 30 mmol/l, pyelonephritis was eight times more likely than before any biochemistry information was known. The results from the study were used to form the basis of a software system which may ultimately be used by the clinical to aid in the recognition, treatment and prevention of disease in the veterinary domain.

Animals↗
PubMed1989

The conformations and electrostatic potential maps of phorbol esters, teleocidins and ingenols.

Phorbol esters and the structurally dissimilar teleocidins and ingenols bind to and activate protein kinase C (PKC) during the course of tumour promotion. These compounds are referred to as TPA-like tumour promoters (from 12-O-tetradencanoyl phorbol-13-acetate, the most active of the class) and are amongst the most potent tumour promoters known. Despite their structural dissimilarity, all three groups of molecules have been shown to bind to the diacylglycerol site of PKC with high affinity. It is thought that this binding to and consequent activation of PKC is the crucial step in tumour promotion by these compounds. The aim of this work was to provide a description of the binding site by comparing structural features (in particular the electrostatic potential) with the activity of numerous derivatives of the three classes. Initially the description was obtained by consideration of the phorbol derivatives, and then refined using the teleocidins and ingenols. The activity data were collected from a variety of sources and the structures calculated using the semi-empirical MNDO approximation embodied in the MOPAC program. Where possible, the crystal structure was obtained from the Cambridge Crystallographic Database, and used as a starting point for the calculation. In other cases, a preliminary calculation was carried out using the molecular mechanics program AMBER. Electrostatic potentials were calculated and displayed using an in-house program 3D2, while superpositions of molecules were carried out using CHEM-X.

Diterpenes↗
PubMed2005

MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.

The annotation of newly sequenced bacterial genomes begins with running several automatic analysis methods, with major emphasis on the identification of protein-coding genes. DNA sequences are heterogeneous in local nucleotide composition and this leads sometimes to sequences being annotated as authentic genes when they are not protein-coding genes or are true but uncharacterized protein-coding genes. This first annotation step is generally followed by an expert manual annotation of the predicted genes. The genomic data (sequence and annotations) organized in an appropriate databank file format is subsequently submitted to an entry point of the International Nucleotide Sequence Database. These procedures are inevitably subject to mistakes, and this can lead to unintentional syntactic annotation errors being stored in public databanks. Here, we present a new web program, MICheck (MIcrobial genome Checker), that enables rapid verification of sets of annotated genes and frameshifts in previously published bacterial genomes. The web interface allows one easily to investigate the MICheck results, i.e. inaccurate or missed gene annotations: a graphical representation is drawn, in which the genomic context of a unique coding DNA sequence annotation or a predicted frameshift is given, using information on the coding potential (curves) and annotation of the neighbouring genes. We illustrate some capabilities of the MICheck site through the analysis of 20 bacterial genomes, 9 of which were selected for their 'Reviewed' status in the National Center for Biotechnology Information (NCBI) Reference Sequence Project (RefSeq). In the context of the numerous re-annotation projects for microbial genomes, this tool can be seen as a preliminary step before the functional re-annotation step to check quickly for missing or wrongly annotated genes. The MICheck website is accessible at the following address: http://www.genoscope.cns.fr/agc/tools/micheck.

Computer Graphics↗
PubMed2005

Identification of genomic features using microsyntenies of domains: domain teams.

The detection, across several genomes, of local conservation of gene content and proximity considerably helps the prediction of features of interest, such as gene fusions or physical and functional interactions. Here, we want to process realistic models of chromosomes, in which genes (or genomic segments of several genes) can be duplicated within a chromosome, or be absent from some other chromosome(s). Our approach adopts the technique of temporarily forgetting genes and working directly with protein "domains" such as those found in Pfam. This allows the detection of strings of domains that are conserved in their content, but not necessarily in their order, which we refer to as domain teams. The prominent feature of the method is that it relaxes the rigidity of the orthology criterion and avoids many of the pitfalls of gene-families identification methods, often hampered by multidomain proteins or low levels of sequence similarity. This approach, that allows both inter- and intrachromosomal comparisons, proves to be more sensitive than the classical methods based on pairwise sequence comparisons, particularly in the simultaneous treatment of many species. The automated and fast detection of domain teams, together with its increased sensitivity at identifying segments of identical (protein-coding) gene contents as well as gene fusions, should prove a useful complement to other existing methods.

Bacterial Proteins↗
PubMed2004

PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation.

PhosphoSite is a curated, web-based bioinformatics resource dedicated to physiologic sites of protein phosphorylation in human and mouse. PhosphoSite is populated with information derived from published literature as well as high-throughput discovery programs. PhosphoSite provides information about the phosphorylated residue and its surrounding sequence, orthologous sites in other species, location of the site within known domains and motifs, and relevant literature references. Links are also provided to a number of external resources for protein sequences, structure, post-translational modifications and signaling pathways, as well as sources of phospho-specific antibodies and probes. As the amount of information in the underlying knowledgebase expands, users will be able to systematically search for the kinases, phosphatases, ligands, treatments, and receptors that have been shown to regulate the phosphorylation status of the sites, and pathways in which the phosphorylation sites function. As it develops into a comprehensive resource of known in vivo phosphorylation sites, we expect that PhosphoSite will be a valuable tool for researchers seeking to understand the role of intracellular signaling pathways in a wide variety of biological processes.

Animals↗
PubMed2005

Proteomic expression analysis of colorectal cancer by two-dimensional differential gel electrophoresis.

The identification of specific protein markers for colorectal cancer would provide the basis for early diagnosis and detection, as well as clues for understanding the molecular mechanisms governing cancer progression. In this report, we describe the proteomic analysis of the samples of colorectal cancer corresponding to seven patients. We have used the highly sensitive two-dimensional differential gel electrophoresis (2-D DIGE) coupled with mass spectrometry (MS) for the identification of proteins differentially expressed in tumoral and neighboring normal mucosa. We have detected differences in abundance of 52 proteins with statistical variance of the tumor versus normal spot volume ratio within the 95th confidence level (Student's t-test; p < 0.05). Forty-one out of 52 analyzed proteins were unambiguously identified by matrix-assisted laser desorption/ionization-time of flight MS coupled with database interrogation as being differentially expressed in colorectal cancer. An ontology analysis of these proteins revealed that they were mainly involved in regulation of transcription (synovial sarcoma X5 protein, metastasis-associated protein 1), cellular reorganization and cytoskeleton (cytokeratins, vimentin, beta actin), cell communication and signal transduction (annexins IV and V, relaxin, APC), and protein synthesis and folding (heat shock protein 60, calreticulin, cathepsin D, RSP4) among others. Preliminary studies demonstrated that the differentially expressed proteins found by 2-D DIGE could be confirmed and validated by immunoblotting and immunohistochemistry analyses in those few cases where antibodies were available. We believe that the incorporation of more samples and new datasets will permit the definition of a collection of proteins with a potential interest as biomarkers for colorectal cancer.

Biopsy↗
PubMed1999

Novel matrix descriptor for secondary structure segments in proteins: demonstration of predictability from circular dichroism spectra.

An extension to standard protein secondary structure predictions using optical spectra that encompasses the number and average lengths of segments of uniform secondary structure in the sequence is demonstrated. The connectivity and numbers of segments can be described by a matrix descriptor [sij] (i, j representing segment types such as helix and beta-sheet strands). Independent knowledge of the fractional concentration of each secondary structure type and of the total number of residues in the protein then with [sij] yields the average segment length of each type. The physical background for prediction of this extended structural descriptor from spectral data is summarized, rules for its generation from reference X-ray structures are defined, and formal variants of its form are discussed. Using a novel neural network approach to analyze a training set of electronic circular dichroism (ECD) and vibrational circular dichroism (VCD) spectra for 23 proteins, matrix descriptors encompassing helix, sheet, and other forms are predicted. The results show that the matrix descriptor can be predicted to an accuracy comparable to that of conventionally predicted average fractional secondary structures. In this respect the ECD predictions of [sij] were significantly more accurate than the VCD ones, which may result from the longer range length dependence of the ECD bandshape and intensity. Summary results for a parallel analysis using Fourier transform infrared spectra indicate somewhat lower reliability than those for VCD.

Circular Dichroism↗
PubMed2004

[Correction of five different types of errors of model REFSEQs appeared in NCBI human gene database only by using two novel human genes C17orf32 and ZNF362].

Found that there exist many mistakes in the REFSEQ issued in the genome annotation project of NCBI, the result of which indicates that people be cautious in using REFSEQ database in NCBI. By adopting the technical route combining bioinformatics analysis and experimental verification, through the comparison of the cloned genes in the non-redundant database, we found that there were many mistakes in the computer annotation human genome coding sequences that were issued on the internet. First we quoted nine wrong types of novel human genes anticipated by NCBI GENOME Annotation Project. Here we give one example in detail: (1) Comparison of the sequences between novel human gene C17orf32 and hypothetical human gene LOC124919. LOC123722 is a modified sequence of C17orf32 cDNA with an inserted G between 406 -407 nucleotides. The base G in the 401 position of LOC123722 cDNA is a redundant insert, which causes a reading frame shift in the translation of an alternative protein. This inserted G has not been found in our experimental clone, and is fully rejected by human EST alignment, and is shown as a redundance by genomic GT/AG organization analysis. (2) Comparison of the sequences between novel human gene C17orf32 and hypothetical human gene LOC147007. C17orf32 gene (ORF from 31 to 657 nucleotides) is located on human chromosome 17(Accession No. NT_010808.7), and is only linked with a hypothetical human gene LOC147007 (ORF from 55 to 435 nucleotides) at present. This hypothetical human gene sequence has not been verified by experiment, and is a wrong form of our verified C17orf32 gene. The full-length 1 679 bp cDNA sequence of C17orf32 exhibits overall homology to that of LOC147007 of 625 bp mRNA, with matching percentage of 37% in 36% of total window over the full-length nucleotide, especially 121 approximately 366 bp of LOC147007 is just the same as 316 approximately 561 bp of C17orf32. Thus, the 126 aa protein encoded by XP_097165 of LOC147007 exhibits overall homology to the 208 aa protein encoded by C17orf32, with matching percentage of 50% in 48% of total window over the full-length protein, especially 23 approximately 104 aa of XP_097165 is just the same as 96 approximately 177 aa of C17orf32 protein. Both flanking regions of LOC147007 outside the same ORF central part are wrong assembly of non-relative cDNA. In addition, we have in silico cloned a novel mouse gene, ORF32 (open reading frame 32) with TPA accession number of BK000258, which is the mouse ortholog of human C17orf32. Our strategy is helpful in both finding out more novel human genes and correcting the mistakes in the REFSEQs issued by NCBI genome annnotation project. For example, we adopted the gene anticipating method, through automatic calculation and analysis, anticipated two modes reference sequences (LOC124919 and LOC147007) from NCBI contig NT_ 010808. Both of them should be C17orf32, but the fact is that both of them are various wrong forms of C17orf32, respectively are the first type and second type of mistakes. Another example, we adopted gene anticipation method, through automatic calculation and analysis, anticipated three modes reference sequences (LOC14907, LOC200084 and LOC91126) from NCBI contig NT_004511 which really are one type of gene of ZNF362, but submitted three different wrong forms of ZNF362, respectively are: the fourth, fifth, and seventh type of mistakes. We can correct or avoid the currently wrong human genome coding sequence by using in silico clone and combining experimental verification. People should be cautious in treating the computer's annotation which may exist all type of wrong human genome coding sequences. The correct identification and annotation of the novel human genes still remain to be a long and arduous task.

Amino Acid Sequence↗
PubMedDate not supplied

Attributable testing for abnormal prion protein, database linkage, and blood-borne vCJD risks.

CONTEXT: National prospective collection of tonsillar tissue to be tested anonymously for abnormal lymphoreticular accumulation of prion protein (PrP) was approved to begin in the UK in 2004. The UK is not, however, testing autopsy specimens attributably for abnormal PrP (PrP(SC)) so that recipients at risk after a blood transfusion from, or exposed to surgical instruments from, a deceased carrier of variant Creutzfeldt-Jakob disease (vCJD) can be followed up to quantify transmission risks. In Switzerland, surveillance for subclinical vCJD includes unconsented testing in autopsies: consented testing of tonsillar tissue is potentially attributable to interrupt human-to-human vCJD transmission or treat it. STARTING POINT: The UK announced its first case of probable blood-borne vCJD transmission in December, 2003, and first detected a case of probable blood-borne subclinical vCJD in July, 2004. To reduce the possible risk of onward transmission to other people, UK patients who had received vCJD-implicated plasma products are being contacted. They, and their general practitioner, are asked to inform anyone giving them medical, surgical, or dental treatment, and the patients must refrain from donating blood, tissues, or organs. WHERE NEXT? Prudent additional surveillance options for human PrP(SC)--particularly at autopsy or to sanction the release of quarantined operation sets pending effective decontamination--can be costed by reference to results for cattle and sheep. Some ethical or legal impediments to the UK's potentially-attributable testing for PrP(SC) may yet be rued.

Animals↗
PubMed1991

cDNA cloning of the B cell membrane protein CD22: a mediator of B-B cell interactions.

We have cloned a full-length cDNA for the B cell membrane protein CD22, which is referred to as B lymphocyte cell adhesion molecule (BL-CAM). Using subtractive hybridization techniques, several B lymphocyte-specific cDNAs were isolated. Northern blot analysis with one of the clones, clone 66, revealed expression in normal activated B cells and a variety of B cell lines, but not in normal activated T cells, T cell lines, Hela cells, or several tissues, including brain and placenta. One major transcript of approximately 3.3 kb was found in B cells although several smaller transcripts were also present in low amounts (approximately 2.6, 2.3, and 1.6 kb). Sequence analysis of a full-length cDNA clone revealed an open reading frame of 2,541 bases coding for a predicted protein of 847 amino acids with a molecular mass of 95 kD. The BL-CAM cDNA is nearly identical to a recently isolated cDNA clone for CD22, with the exception of an additional 531 bases in the coding region of BL-CAM. BL-CAM has a predicted transmembrane spanning region and a 140-amino acid intracytoplasmic domain. Search of the National Biological Research Foundation protein database revealed that this protein is a member of the immunoglobulin super family and that it had significant homology with three homotypic cell adhesion proteins: carcinoembryonic antigen (29% identity over 460 amino acids), myelin-associated glycoprotein (27% identity over 425 amino acids), and neural cell adhesion molecule (21.5% over 274 amino acids). Northern blot analysis revealed low-level BL-CAM mRNA expression in unactivated tonsillar B cells, which was rapidly increased after B cell activation with Staphylococcus aureus Cowan strain 1 and phorbol myristate acetate, but not by various cytokines, including interleukin 4 (IL-4), IL-6, and gamma interferon. In situ hybridization with an antisense BL-CAM RNA probe revealed expression in B cell-rich areas in tonsil and lymph node, although the most striking hybridization was in the germinal centers. COS cells transfected with a BL-CAM expression vector were immunofluorescently stained positively with two different CD22 antibodies, each of which recognizes a different epitope. Additionally, both normal tonsil B cells and a B cell line were found to adhere to COS transfected with BL-CAM in the sense but not the antisense direction.(ABSTRACT TRUNCATED AT 400 WORDS)

Adolescent↗
PubMed2003

Safety and anti-inflammatory activity of curcumin: a component of tumeric (Curcuma longa).

INTRODUCTION: Tumeric is a spice that comes from the root Curcuma longa, a member of the ginger family, Zingaberaceae. In Ayurveda (Indian traditional medicine), tumeric has been used for its medicinal properties for various indications and through different routes of administration, including topically, orally, and by inhalation. Curcuminoids are components of tumeric, which include mainly curcumin (diferuloyl methane), demethoxycurcumin, and bisdemethoxycurcmin. OBJECTIVES: The goal of this systematic review of the literature was to summarize the literature on the safety and anti-inflammatory activity of curcumin. METHODS: A search of the computerized database MEDLINE (1966 to January 2002), a manual search of bibliographies of papers identified through MEDLINE, and an Internet search using multiple search engines for references on this topic was conducted. The PDR for Herbal Medicines, and four textbooks on herbal medicine and their bibliographies were also searched. RESULTS: A large number of studies on curcumin were identified. These included studies on the antioxidant, anti-inflammatory, antiviral, and antifungal properties of curcuminoids. Studies on the toxicity and anti-inflammatory properties of curcumin have included in vitro, animal, and human studies. A phase 1 human trial with 25 subjects using up to 8000 mg of curcumin per day for 3 months found no toxicity from curcumin. Five other human trials using 1125-2500 mg of curcumin per day have also found it to be safe. These human studies have found some evidence of anti-inflammatory activity of curcumin. The laboratory studies have identified a number of different molecules involved in inflammation that are inhibited by curcumin including phospholipase, lipooxygenase, cyclooxygenase 2, leukotrienes, thromboxane, prostaglandins, nitric oxide, collagenase, elastase, hyaluronidase, monocyte chemoattractant protein-1 (MCP-1), interferon-inducible protein, tumor necrosis factor (TNF), and interleukin-12 (IL-12). CONCLUSIONS: Curcumin has been demonstrated to be safe in six human trials and has demonstrated anti-inflammatory activity. It may exert its anti-inflammatory activity by inhibition of a number of different molecules that play a role in inflammation.

Anti-Inflammatory Agents, Non-Steroidal↗
PubMed2006

Expanding the protein catalogue in the proteome reference map of human breast cancer cells.

In this report we present a catalogue of 162 proteins (including isoforms and variants) identified in a prototype of proteomic map of breast cancer cells. This work represents the prosecution of previous studies describing the protein complement of breast cancer cells of the line 8701-BC, which has been well characterized for several parameters, providing to be a useful model for the study of breast cancer-associated candidate biomarkers. In particular, 110 spots were identified ex novo by PMF, or validated following previous gel matching identification method; 30 were identified by N-terminal microsequencing and the remaining by gel matching with maps available from our former work. As a consequence of the expanded number of proteins, we have updated our previous classification extending the number of protein groups from 4 to 13. In order to facilitate comparative proteome studies of different kinds of breast cancers, in this report we provide the whole complement of proteins so far identified and grouped into the new classification. A consistent number of them were not described before in other proteomic maps of breast cancer cells or tissues, and therefore they represent a valuable contribution for breast cancer protein databases and for future application in basic and clinical researches.

Biomarkers, Tumor↗
PubMed1997

Characterization of Borrelia lusitaniae sp. nov. by 16S ribosomal DNA sequence analysis.

We determined the complete sequence of the rrs gene from five strains of genomic species PotiB2. Both distance and parsimony methods were used to infer the evolutionary relationships of the rrs gene sequence of this genomic species in comparison with the rrs gene sequence of Borrelia valaisiana and the rrs gene sequences of Borrelia burgdorferi sensu lato species obtained from sequence databases. The phylogenetic analysis revealed that the genomic species PotiB2 strains clustered in a separate lineage, which was consistent with data from previous DNA-DNA hybridization experiments (D. Postic, M. V. Assous, P. A. D. Grimont, and G. Baranton, Int. J. Syst. Bacteriol. 44:743-752, 1994). A PCR-restriction fragment length polymorphism analysis was used to identify genomic species PotiB2 and to differentiate it from B. burgdorferi sensu lato species. Moreover, signature nucleotide positions were identified for each B. burgdorferi sensu lato species. In accordance with DNA relatedness values, our findings suggest that genomic species PotiB2 can be more clearly defined and identified, and we propose that it should be referred to as a new species, Borrelia lusitaniae. The type strain is PotiB2.

Bacterial Proteins↗
PubMedDate not supplied

Precision parameters of methods of analysis required for nutrition labeling. Part I. Major nutrients.

Major components of foods and feeds are fat, protein, and carbohydrates. Fat and protein are determined by direct measurements that are interpreted as the quantity of the constituent. Carbohydrates are usually calculated by difference. For this calculation, values for moisture/solids, ash, and "fiber" are also needed. The readily available collaborative studies for the determination of these major components are reviewed in an attempt to assign precision parameters to validated methods of analysis. When a number of studies for the same analyte, in the same food, by the same method are available, it is seen that the precision parameters among laboratories (standard deviations, SR; relative standard deviations, RSDR) and the ISO maximum tolerable difference functions (repeatability value, r; reproducibility value, R) are not characterized by any conventional distribution. The precision data are best summarized as a median or average parameter and the interval containing the centermost 90% of reported values. Typically, the precision of methods of analysis can be expressed as a function of concentration only, independent of analyte, matrix, and method. The average RSDR value from each collaborative data set can then be used as the numerator in a ratio containing, as the denominator, the value calculated from the Horwitz equation: RSDR = 2 exp (1 - 0.5 log C) where C is the concentration as a decimal fraction. A series of ratios consistently above 1, and especially above 2, probably indicates that a method is unacceptable with respect to precision. By this criterion, only the protein (Kjeldahl) determination is unqualifiedly acceptable with a 90% interval for RSDR of 1 to 3% at C values above about 0.01 (1 g/100 g). Fat, moisture/solids, and ash are acceptable down to limiting concentrations in the region of 1 to 5 g/100 g, if a test portion large enough to provide at least 50 mg of weighable residue or volatiles is specified. Measurements of individual carbohydrates and fiber-related analytes have unexpectedly poor precisions among laboratories. The variability, although high, may still be suitable for nutrition labeling. Reliability of analyses for the control of labeling of the primary nutrients must be achieved through quality assurance programs that require strict adherence to the directions of empirical methods and the use of suitable reference materials for absolute methods.

Databases, Bibliographic↗