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PubMed2004

Identification and quantitation of mucosal and faecal desulfovibrios using real time polymerase chain reaction.

BACKGROUND: Desulfovibrios produce sulphide, which is toxic to colonic epithelial cells. These bacteria have previously been linked to ulcerative colitis. Traditional methods of culturing these organisms are slow, and often unreliable, while molecular approaches are either non-quantitative or lack sensitivity. AIMS: To develop a sensitive method for quantitating desulfovibrios in stools and biopsy tissue, and to investigate the effects of age and disease on these bacteria. METHODS: Rectal biopsies were taken from 10 colitis patients and 10 healthy controls. Stool samples were obtained from 10 healthy infants (mean age 1.01 (0.18) years), 10 healthy young adults (26.7 (1.2) years), and 10 healthy elderly people (71.7 (1.2) years). Primers were designed and developed for analysing Desulfovibrio populations in the bowel using real time polymerase chain reaction (PCR). RESULTS: The PCR primers were highly specific for desulfovibrios. Large numbers (approximately 10(6)-10(7)/g) occurred in biopsies in colitis patients and healthy subjects, and no disease related differences were observed. Measurements of mucosal desulfovibrios over 12 months showed marked changes in some patients. Infants (10(6)-10(7)/g) and elderly people (10(7)-10(8)/g) had significantly higher numbers of desulfovibrios in stools compared with young adults (10(5)/g). CONCLUSIONS: Real time PCR analysis of desulfovibrios was an efficient and accurate method for studying these potentially harmful microorganisms. Desulfovibrios were ubiquitous in the bowel, irrespective of age. As rectal mucosae were heavily colonised in health and disease, if these bacteria play a role in colitis, some host defect, possibly in sulphide detoxication pathways or in bacterial antigen handling, is required for manifestations of pathogenicity.

Adult↗

PubMed2005

Differential identification of Ascogregarina species (Apicomplexa: Lecudinidae) in Aedes aegypti and Aedes albopictus (Diptera: Culicidae) by polymerase chain reaction.

We report 2 polymerase chain reaction (PCR)-based methods for distinguishing morphologically similar gregarine species based on amplification of variable regions of the internal transcribed spacer region of ribosomal DNA. The gregarines we investigated were Ascogregarina barretti (Vavra), A. culicis (Ross), and A. taiwanensis (Lien and Levine), parasites of the mosquitoes Ochlerotatus triseriatus (Say), Aedes aegypti (Linnaeus), and Ae. albopictus (Skuse), respectively. These 3 important vector mosquitoes often utilize the same container habitats, where larval development and infection by the parasite occurs, leaving ample opportunity for cross-species gregarine infection. Because previous studies have shown that the parasites A. culicis and A. taiwanensis variably affect fitness in both normal and abnormal mosquito hosts, distinguishing parasite infection and species is important. The task is complicated by the fact that these 2 parasite species are virtually identical in morphology, whereas A. barretti is morphologically distinct. Of the 2 PCR-based assays reported here, the first provides a rapid, sensitive, and straight-forward means of general ascogregarine detection based on a single PCR amplification. The second method provides a means of differentiation between A. culicis and A. taiwanensis based on a species-specific PCR assay. Together, these assays allow whole mosquitoes to be tested for the presence of Ascogregarina species as well as identification of both A. culicis and A. taiwanensis singly or in dual infections.

Aedes↗

PubMed1993

The Onchocerca volvulus mRNAs for a hsp70, a collagen-like protein and a ribosomal protein possess a 5' spliced leader sequence.

To detect and analyse Onchocerca volvulus mRNAs possessing a spliced leader (SL) sequence, a SL cDNA library was constructed from O. volvulus RNA using a PCR method. Three of the sixty cDNAs analysed displayed significant homology to a known sequence. These cDNAs encode a hsp70, a collagen-like protein and a 60S ribosomal protein. The remaining cDNAs analysed either encoded proteins with no apparent homology to known sequences or they appeared to be generated from RNAs with an internal SL and did not possess an open reading frame.

Amino Acid Sequence↗

PubMed1975

Studies on monotreme proteins. VI. Amino acid sequence of the beta-chain of haemoglobin from the platypus, Ornithorhynchus anatinus.

The amino acid sequence of the 146 residues of the beta-chain of the major haemoglobin from the platypus has been determined. The soluble peptides derived from the chain by tryptic digestion were isolated by paper ionophoresis and chromatography. The amino acid sequences were determined by the dansyl-Edman procedure or by further digestion with other enzymes. The tryptic peptides were aligned by homology with other beta-globins. There were 14 changes in sequence compared with echidna beta-chain. The number of changes in sequence compared with human beta-chain is 34 which is less than the 39 changes between human and platypus alpha-chains. Generally there are more changes between beta-chains; there are only three other examples reported where there are more changes between alpha-chains than beta-chains, these are of echidna, rabbit and dog globins. By comparison with the 'contact sites' in horse haemoglobin there is one change in beta-haem contacts, three changes in beta1-alpha1 contacts and no changes in beta2-alpha1 contacts. The date of divergence of the monotremes from the other mammals was estimated at 132 +/- 33 million years, based on the number of amino acid differences between species and allowing for multiple mutations during the evolutionary period. This estimate differs widely from the estimate given by similar treatment of the alpha-chain sequences and the significance of this discrepancy to the validity of the method is discussed.

Amino Acid Sequence↗

PubMed1997

Cloning, sequence, and expression of kynureninase from Pseudomonas fluorescens.

We have cloned the gene encoding kynureninase from Pseudomonas fluorescens using a restriction site polymerase chain reaction technique (RS-PCR) (G. Sarkar, R. T. Turner, and M. E. Bolander PCR Methods Appl. 2, 318-322, 1993) and expressed the enzyme in Escherichia coli DH5a F'. The kynureninase gene has an open reading frame (ORF) of 1251 base pairs that codes for a protein of 416 amino acids with a calculated molecular weight of 45,906. The protein purified from P. fluorescens has N-terminal threonine and an observed molecular weight of 45,787 by electrospray mass spectrometry, suggesting that the N-terminal methionine is removed by posttranslational processing. The complete gene was obtained by PCR and inserted into pTZ18U. The resultant plasmid was used to transform E. coli DH5alpha F', and these cells overexpressed kynureninase to about 37% of total soluble protein. The isolated recombinant protein has molecular weight and Km values identical to those of the native protein from P. fluorescens. The amino acid sequence exhibits 29% identity with those of rat and human kynureninases and 32% identity with the amino acid sequence translated from a Saccharomyces cerevisiae ORF. Alignment of the four sequences shows a highly conserved region which corresponds to the pyridoxal-5'-phosphate (PLP) binding site of rat kynureninase. Based on this alignment, we predict that Lys227 and Asp212 in P. fluorescens kynureninase are involved in pyridoxal-5'-phosphate binding. P. fluorescens kynureninase also exhibits significant homology to the nifS gene product, cysteine desulfurase, and to eucaryotic serine/pyruvate aminotransferases, suggesting that it is a member of subgroup IV of the aminotransferase family of PLP-dependent enzymes.

Amino Acid Sequence↗

PubMed2026

Development of a Blockchain-Based Platform to Enable Indigenous Data Sovereignty and Shared Research Participation With Indigenous Communities: Technology Prototyping and Community Engagement Study.

BACKGROUND: Historic and ongoing problematic practices regarding the collection, storage, and use of Indigenous health data have led to the need to ensure principles of Indigenous Data Sovereignty (IDS) are followed in research practices and technology development. OBJECTIVE: This project, a partnership between UC San Diego and the Native BioData Consortium (NativeBio), sought to explore the practical application of blockchain technology and its potential to facilitate Indigenous-led research collaboration. METHODS: This project first undertook purposeful relationship building with NativeBio to form a Community Advisory Board (CAB) for identifying community and technology needs for a blockchain research collaboration platform with an initial focus on genomic data. Over a 2-year project period, a series of public meetings and presentations at Indigenous-led conferences introduced the concept of exploring compatibility between blockchain and IDS principles, followed by iterative prototyping and co-design of a blockchain platform with NativeBio, using Ethereum as the underlying protocol. RESULTS: Direct engagement with NativeBio and the CAB informed the initial design and development of a "b-IDS" proof-of-concept (POC) blockchain platform. The POC consists of three main components: (1) the web front-end layer, (2) the Ethereum network that executes the smart contract and blockchain storage aspects of the framework, and (3) the back-end database that stores off-chain interactions and data for future use with external genomic data repositories. After refinement of the POC, a community-based participatory research (CBPR) use case aligned with IDS principles was identified as a practical workflow and incorporated into the design of the POC for implementation. CONCLUSIONS: The findings from this project demonstrated the potential use of operationalizing IDS through blockchain technology with proactive and sustained engagement with Indigenous partners. Blockchain technology may have certain advantages over other data governance approaches and systems, facilitating timely oversight, shared decision-making and consent structures, and direct involvement of Indigenous communities in technology design, respecting the core principles of IDS and CBPR. Future development of the blockchain-IDS POC will need to incorporate other research practices and ethics frameworks to expand its use to other public health and biomedical research use cases.

Blockchain↗

PubMed2005

MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes.

BACKGROUND: Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. The ability to identify them in a genome-wide manner depends on the availability of accurate models and of search methods able to detect putative regulatory elements with enhanced sensitivity and specificity. RESULTS: We describe the implementation of a search method for putative transcription factor binding sites (TFBSs) based on hidden Markov models built from alignments of known sites. We built 1,079 models of TFBSs using experimentally determined sequence alignments of sites provided by the TRANSFAC and JASPAR databases and used them to scan sequences of the human, mouse, fly, worm and yeast genomes. In several cases tested the method identified correctly experimentally characterized sites, with better specificity and sensitivity than other similar computational methods. Moreover, a large-scale comparison using synthetic data showed that in the majority of cases our method performed significantly better than a nucleotide weight matrix-based method. CONCLUSION: The search engine, available at http://mapper.chip.org, allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, fly, worm and yeast genomes. In addition it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. Due to its extensive database of models, powerful search engine and flexible interface, MAPPER represents an effective resource for the large-scale computational analysis of transcriptional regulation.

Algorithms↗

PubMed2004

Molecular characterization of echovirus 11 isolates from India.

BACKGROUND & OBJECTIVES: Echovirus 11 (ECV11) is one of the most frequent non-polio enteroviruses isolated from stool samples of children with acute flaccid paralysis in north India. The present work was undertaken to study the sequence variability in the 440 bp of 5'-non-translated region of ECV11 genome using heteroduplex mobility assay (HMA). METHODS: Twelve ECV11 isolates were studied for sequence variability in the 5'-non-translated region (5'NTR) using the HMA followed by nucleotide sequencing. HMA was used to determine sequence diversity between Indian ECV11 isolates and prototype Gregory strain. HMA results were confirmed by 5'NTR nucleotide sequencing of five Indian ECV11 isolates. RESULTS: HMA results showed high genomic diversity between the prototype Gregory strain and Indian ECV11 isolates. All isolates were grouped into five different types of heteroduplex mobility patterns with respect to Gregory strain. A 440 bp 5'NTR fragment of five ECV11 isolates representing different heteroduplex patterns, was sequenced. The sequence alignment showed that 5'NTR of Indian isolates was different from prototype Gregory strain and identical to the ECV11 isolates of Finland and Hungary. Phylogenetic analysis including ECV11 isolate sequences from different parts of the world showed that Indian ECV11 isolates represented a different subgroup. INTERPRETATION & CONCLUSION: The results of the present study suggested that the HMA could be successfully used as a preliminary screening method for sequence variability determination of enterovirus field isolates. The sequence data generated on ECV11 isolates from India will be useful for future studies of endemic genotypes of echovirus.

5' Untranslated Regions↗

PubMedDate not supplied

Ultrastructural findings in feline corneal sequestra.

OBJECTIVES: (1) To describe the ultrastructural features of corneal sequestra in cats; and (2) to enhance our understanding regarding the pathogenesis of feline corneal sequestration. METHODS: Nine corneal sequestra were harvested via keratectomy from globes of nine cats. The sequestra were routinely fixed then postfixed for high resolution light and transmission electron microscopy (HR-LM and TEM, respectively). The tissues were embedded in Epon/Araldite. Sections of 0.5-microm thickness were cut and stained with 1% toluidine blue in 1% sodium tetraborate solution for HR-LM. Ultrathin sections were collected on copper grids and stained with uranyl acetate and Sato's lead stain for TEM. Ultrathin sections were examined and the images were captured on an Advantage HR CCD camera using a Hitachi 7500 electron microscope operated at 80 kV. Two healthy corneas from two cats were harvested immediately following euthanasia. These corneal tissues (control samples) were processed in the same manner as the corneal sequestra for HR-LM and TEM. A portion of each sequestrum was also submitted for polymerase chain reaction (PCR) testing for infectious agents including feline herpesvirus-1 (FHV-1), Toxoplasma gondii, Chlamydophila felis and Mycoplasma spp. RESULTS: Ultrastructure of healthy corneal tissues revealed basal corneal epithelial cells aligned adjacent to a thin acellular layer similar to Bowman's layer with underlying tightly packed, regularly arranged, collagen fibrils oriented in different planes. Keratocytes were elongated and had long and irregularly shaped nuclei, and cytoplasm contained rough endoplasmic reticulum and abundant membrane-bound vesicles. In contrast, corneal sequestra contained varying amounts of an amorphous, electron-dense substance, continuous with intact basal epithelial basement membranes peripherally, and overlying corneal ulceration and loosely packed collagen fibrils. Remnants of necrotic keratocytes were seen in spaces between disarranged collagen layers. In all samples, occasional keratocytes exhibited morphology indicative of apoptosis including clumping and margination of chromatin, and shrunken cytoplasm. Varying degrees of inflammation were noted on HR-LM and TEM of affected corneas including peri- and intralesional neutrophils, lymphocytes, plasma cells, and macrophages. Corneal sequestra were FHV-1-positive (n = 3), FHV-1- and T. gondii-positive (n = 1), T. gondii-positive (n = 3), or negative for DNA of these infectious agents (n = 2) using PCR. All corneal sequestra were negative for DNA of Chlamydophila felis and Mycoplasma spp. using PCR. CONCLUSIONS: Apoptosis may play a role in the pathogenesis of feline corneal sequestration independent of the presence of DNA of these infectious organisms. Prospective clinical studies are warranted to further understand the significance of T. gondii in relation to feline corneal sequestration.

Animals↗

PubMed1993

The sheep erythropoietin gene: molecular cloning and effect of hemorrhage on plasma erythropoietin and renal/liver messenger RNA in adult sheep.

Erythropoietin (Epo) production was studied in adult sheep. Nine ewes, body weight (BW) 39 +/- 1.3 kg, were hemorrhaged a volume of blood equivalent to 1.6% BW, and sampled at 0, 2, 4, 6, 24 h. Oxygen content (O2 CT) decreased by 2.7 +/- 0.6 ml/dl at 2 h. Plasma immunoreactive (IR) Epo was only significantly increased at 24 h, from 18.5 +/- 3.5 to 40 +/- 10.7 mU/ml (mean +/- SEM). A further 5 ewes were bled extensively (2793 +/- 82 ml) over 54 h, and killed for Epo mRNA determination. The O2 CT decreased from 12.3 +/- 1.6 to 4.1 +/- 0.6 ml/dl, and plasma Epo increased from 15 +/- 4 to 1675 +/- 287 mU/ml. The sequence of ovine Epo cDNA was derived from the kidney RNA of a severely bled sheep using reverse transcription/polymerase chain reaction (RT/PCR), and from an ovine Epo genomic clone. The cDNA encodes a peptide of 194 amino acids, including a 27 amino acid signal peptide. The deduced amino acid sequence of sheep Epo shows 82%, 78% and 80% homology with mature Epos of human, mouse and monkey, respectively. The gene structure resembles closely those of human and mouse, with 5 exons and 4 introns. The expression of the ovine Epo gene in tissues from normal and hemorrhaged sheep was analysed by a competitive RT/PCR method. Epo mRNA was difficult to detect in liver from normal sheep, but was detectable at 0.01-0.04 amol/microgram total RNA in kidney from normal sheep. In the kidneys of severely bled sheep, the Epo mRNA levels (per micrograms total RNA) increased 400-1500-fold compared to that of normal kidneys, and were approximately 60-fold greater than those in the livers of the hemorrhaged sheep.

Amino Acid Sequence↗

PubMed1997

Polymerase chain reaction for detection of guinea pig adenovirus.

Lack of in vitro cultivation methods has inhibited the development of rapid, reliable diagnostic procedures for adenovirus-associated necrotizing bronchopneumonia in guinea pigs. Because polymerase chain reaction (PCR) techniques are well established for human adenoviruses, primers for the amplification of guinea pig adenovirus DNA were evaluated. The DNA for PCR was purified from the lung tissue of spontaneously infected and healthy guinea pigs. Adenovirus DNA could only be detected in the lungs of the infected animals. Subsequent sequence analysis of PCR products revealed that the guinea pig adenovirus is a distinct adenovirus.

Adenoviridae↗

PubMed2000

A rapid PCR based method to distinguish between Lactococcus and Enterococcus.

Phenotypic characterisation of Lactococcus and Enterococcus species remains unreliable as strains of both genera have been isolated which do not conform to the traditional criteria for separation of these genera. A bank of 131 isolates was phenotypically characterised by three methods: (a) traditional broth tests, (b) API Rapid ID 32 Strep and (c) BBL Crystal ID kits. Differences in genus designation between commercial kits were evident for 12 strains (9%), while 7 strains (5%) remained unidentified by either kit. Published 16S rRNA sequences were aligned and used to design genus-specific primers which, when used in separate PCR reactions, were capable of distinguishing all type strains of Lactococcus and Enterococcus. These primers did not react with known species of Streptococcus, Pediococcus, Lactobacillus, Leuconostoc or Tetragenococcus. Isolates which could not be identified by phenotype were assigned to either genus on the basis of the gene primers.

DNA Primers↗

PubMed2004

Cellulose membrane supported peptide arrays for deciphering protein-protein interaction sites: the case of PIN, a protein with multiple natural partners.

Cellulose membrane supported peptide arrays, prepared according to the Spot method, allow the rapid identification and characterization of protein-protein interaction sites. Here, the method was used to screen reactive peptides from different proteins that bind to a single molecule, the PIN protein. PIN possesses two binding grooves, that have been shown to interact with several targets, including neuronal NO synthase, dynein intermediate chain, myosin V, the proapoptotic protein Bim, the scaffolding proteins DAP1alpha and gephyrin, and the transcription factor NRF-1. Arrays of peptides representing sequences of these targets were probed for reactivity with GST-tagged PIN, enabling the precise identification of binding motifs. Binding motifs were then minimized to seven or eight amino acid long peptides: YSKETQT for dynein IC, CDKSTQT for Bim, KDTGIQVD for nNOS, QSVGVQV for DAP1alpha and EDKNTMTD for myosin V. Alascan and substitution analysis provided proof that the Gln residue is critical for the interaction and cannot be easily replaced. Positions -1 and +1, just flanking the pivotal Gln, are also important; they consist of hydrophobic residues (Thr, Val) that could only be replaced by hydrophobic or aromatic amino acids. Position -4 is also critical for binding, with its Asp or Ser being replaceable to some extent. Alignment of sequences of proteins known to bind PIN shows that the most frequent amino acids in the motif are DKGTQT, consistent with the Spot results. We postulate that the degenerate character of binding to PIN is based on the propensity of several sequences to adopt a beta-strand conformation that allows the Gln residue to position itself in the PIN channel and on the conformational breathing of the PIN binding groove.

Amino Acid Sequence↗

PubMed2005

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

A central problem in the bioinformatics of gene regulation is to find the binding sites for regulatory proteins. One of the most promising approaches toward identifying these short and fuzzy sequence patterns is the comparative analysis of orthologous intergenic regions of related species. This analysis is complicated by various factors. First, one needs to take the phylogenetic relationship between the species into account in order to distinguish conservation that is due to the occurrence of functional sites from spurious conservation that is due to evolutionary proximity. Second, one has to deal with the complexities of multiple alignments of orthologous intergenic regions, and one has to consider the possibility that functional sites may occur outside of conserved segments. Here we present a new motif sampling algorithm, PhyloGibbs, that runs on arbitrary collections of multiple local sequence alignments of orthologous sequences. The algorithm searches over all ways in which an arbitrary number of binding sites for an arbitrary number of transcription factors (TFs) can be assigned to the multiple sequence alignments. These binding site configurations are scored by a Bayesian probabilistic model that treats aligned sequences by a model for the evolution of binding sites and "background" intergenic DNA. This model takes the phylogenetic relationship between the species in the alignment explicitly into account. The algorithm uses simulated annealing and Monte Carlo Markov-chain sampling to rigorously assign posterior probabilities to all the binding sites that it reports. In tests on synthetic data and real data from five Saccharomyces species our algorithm performs significantly better than four other motif-finding algorithms, including algorithms that also take phylogeny into account. Our results also show that, in contrast to the other algorithms, PhyloGibbs can make realistic estimates of the reliability of its predictions. Our tests suggest that, running on the five-species multiple alignment of a single gene's upstream region, PhyloGibbs on average recovers over 50% of all binding sites in S. cerevisiae at a specificity of about 50%, and 33% of all binding sites at a specificity of about 85%. We also tested PhyloGibbs on collections of multiple alignments of intergenic regions that were recently annotated, based on ChIP-on-chip data, to contain binding sites for the same TF. We compared PhyloGibbs's results with the previous analysis of these data using six other motif-finding algorithms. For 16 of 21 TFs for which all other motif-finding methods failed to find a significant motif, PhyloGibbs did recover a motif that matches the literature consensus. In 11 cases where there was disagreement in the results we compiled lists of known target genes from the literature, and found that running PhyloGibbs on their regulatory regions yielded a binding motif matching the literature consensus in all but one of the cases. Interestingly, these literature gene lists had little overlap with the targets annotated based on the ChIP-on-chip data. The PhyloGibbs code can be downloaded from http://www.biozentrum.unibas.ch/~nimwegen/cgi-bin/phylogibbs.cgi or http://www.imsc.res.in/~rsidd/phylogibbs. The full set of predicted sites from our tests on yeast are available at http://www.swissregulon.unibas.ch.

Algorithms↗

PubMedDate not supplied

Phylogenetic relationships of Bacteria based on comparative sequence analysis of elongation factor Tu and ATP-synthase beta-subunit genes.

Comparative sequence analyses were performed on 14 genes encoding bacterial elongation factors EF-Tu and 7 genes encoding the beta-subunit of bacterial F1F0 type ATP-synthases. The corresponding predicted amino acid sequences were compared with published primary structures of homologous molecules. Phylogenetic trees were reconstructed from both data sets of aligned protein sequences and from an equivalent selection of 16S rRNA sequences by applying distance matrix and maximum parsimony methods. The EF-Tu data were in very good agreement with the rRNA data, although the resolution within the EF-Tu tree was reduced at certain phylogenetic levels. The resolution power of the ATPase beta-subunit sequence data were more reduced than those of the EF-Tu data. In comparison with the 16S rRNA tree there are minor differences in the order of adjacent branchings within the ATPase beta-subunit tree.

Amino Acid Sequence↗

PubMed1991

Rapid detection of maize DNA sequence variation.

The allele-specific polymerase chain reaction (ASPCR) has been used to determine the genotype of maize lines at two loci, wx and NPI288. The ASPCR method uses allele-specific oligonucleotide primers in PCR amplifications to amplify and discriminate simultaneously between polymorphic alleles. The success of this technique relies on the specific failure of PCR to amplify with primers that do not perfectly match the DNA sequence of one of the allelic variants. Amplification results were evaluated by dot-blot hybridization using an alkaline-phosphatase-coupled probe. The technique's speed, accuracy, sensitivity, and high throughput make it valuable for plant-breeding applications.

Base Sequence↗

PubMed2005

Rapid differential diagnosis of Mycoplasma agalactiae and Mycoplasma bovis based on a multiplex-PCR and a PCR-RFLP.

The membrane-protein 81 gene (mb-mp81) of Mycoplasma bovis was cloned, sequenced and compared to membrane-protein 81 gene (ma-mp81) of Mycoplasma agalactiae. After alignment of both sequences, specific primers pairs were designed from variable or unchanging nucleotide segments. In this study, we describe the development and optimization of a multiplex-PCR (MPCR) for the rapid detection of M. agalactiae and M. bovis strains. In addition, a simple and rapid PCR-restriction fragment length polymorphism (RFLP) assay, using the restriction enzymes AluI, DraI, RsaI and XbaI, is described to distinguish between both species. The results suggest that MPCR and PCR-RFLP assays could be used as an alternative method in routine diagnosis for rapid and specific simultaneous detection of M. agalactiae and M. bovis.

Bacterial Proteins↗

PubMed2004

Mesomorphous structure and properties of non-equimolar complexes of poly(ethylenimine) and perfluorooctanoic acid.

A series of solid complexes, PEI-PFAO, made of poly(ethylenimine) (PEI) and perfluorooctanoic acid (PFOA) with different compositions were prepared through a "starving addition" method, where PFOA was fed into PEI solution at the molar ratio, phi(feed), of acid group to the amino group of PEI, never beyond unity. Wide-angle X-ray diffraction diagrams confirmed amorphous structure of these complexes. Small-angle X-ray scattering indicated two ordered mesomorphous structures of alpha and beta lamellar phases, with respective long periods of 2.29 and 1.15 nm in the complexes. By increasing the actual molar ratio, phi, of PFOA to the amino group of PEI, the complex structure was altered from alpha-phase dominant to beta-phase dominant. All complexes exhibited two thermal degradation processes induced by decomposition of the bound PFOA below 230 degrees C and PEI backbone at about 350 degrees C. The initiating degradation temperature, Tid, decreases with increasing phi due to the preferential degradation of the PFOA chain bound to the tertiary amino groups. The glass transition temperature, Tg, of the complex increases with phi up to the degradation of the complex of phi = 1. This increase in Tg with phi also supports an ordered alignment of the bound PFOA chains, which greatly restricts the PEI mobility. The solid surface tension, gammaS, and critical surface tension, gammac, of the complex are between 15.4 and 16.8 mN/m and between 13.5 and 15.4 mN/m, respectively. The latter is very close to or even smaller than gammac of PTFE (15 mN/m), suggesting the enrichment of CF2 and CF3 groups at the complex surfaces. The fact that the PEI-POFA complex combines high hydrophobicity with selective thermal degradation of bound fluorinated chains promises a potential of selective change and local functionalization of the surface in a well-controlled manner.

Caprylates↗