Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 17 de 17
Filter
Add more filters










Publication year range
1.
IEEE/ACM Trans Comput Biol Bioinform ; 16(6): 2078-2088, 2019.
Article in English | MEDLINE | ID: mdl-29994028

ABSTRACT

Inflammatory Bowel Disease (IBD) is an umbrella term for a group of inflammatory diseases of the gastrointestinal tract, including Crohn's Disease and ulcerative colitis. Changes to the intestinal microbiome, the community of micro-organisms that resides in the human gut, have been shown to contribute to the pathogenesis of IBD. IBD diagnosis is often delayed due to its non-specific symptoms and because an invasive colonoscopy is required for confirmation, which leads to poor growth in children and worse treatment outcomes. Feature selection algorithms are often applied to microbial communities to identify bacterial groups that drive disease. It has been shown that aggregating Ensemble Feature Selection (EFS) can improve the robustness of feature selection algorithms, which is defined as the variation of feature selector output caused by small changes to the dataset. In this work, we apply a two-step filter and an EFS process to generate robust feature subsets that can non-invasively predict IBD subtypes from high-resolution microbiome data. The predictive power of the robust feature subsets is the highest reported in literature to date. Furthermore, we identify five biologically plausible bacterial species that have not previously been implicated in IBD aetiology.


Subject(s)
Colitis, Ulcerative/diagnosis , Colitis, Ulcerative/microbiology , Computational Biology/methods , Crohn Disease/diagnosis , Crohn Disease/microbiology , Gastrointestinal Microbiome , Actinomyces , Adolescent , Algorithms , Biomarkers , Child , Clostridiales , Cluster Analysis , Colonoscopy , Epigenesis, Genetic , Firmicutes , Humans , Machine Learning , Models, Statistical , Polymerase Chain Reaction , RNA, Ribosomal, 16S/genetics , Sensitivity and Specificity , Software
2.
Mol Cell Endocrinol ; 420: 37-45, 2016 Jan 15.
Article in English | MEDLINE | ID: mdl-26607806

ABSTRACT

The purpose of the present study was to examine if a stable glucose-dependent insulinotropic polypeptide (GIP) agonist could exert beneficial metabolic control in diabetic mice which had been pre-treated with sodium-glucose-cotransporter-2 (SGLT2) inhibitor dapagliflozin (DAPA). High fat fed mice administered low dose streptozotocin (STZ) received vehicle, DAPA once-daily over 28 days, or DAPA once-daily for 14 days followed by (DAla(2))GIP once-daily for 14 days. Energy intake, body weight, glucose and insulin concentrations were measured at regular intervals. Glucose tolerance, insulin tolerance test, dual-energy X-ray absorptiometry (DEXA) and pancreatic histology were examined. Once-daily administration of (DAla(2))GIP for 14 days in high fat fed diabetic mice pre-treated with DAPA demonstrated significant decrease in body weight, blood glucose and increased insulin concentrations which were independent of changes in energy intake. Similarly, glucose tolerance, glucose-stimulated insulin secretion, insulin sensitivity and HOMA-ß were significantly enhanced in (DAla(2))GIP-treated mice. DEXA analysis revealed sustained percentage body fat loss with no changes in lean mass, bone mineral content and density. Pancreatic immunohistochemical analysis revealed decreased islet number and increases in islet area, beta cell area and pancreatic insulin content. The DAPA-induced increase in alpha cell area was also reversed. Additional acute in vitro and in vivo experiments confirmed that the impaired action of (DAla(2))GIP under hyperglycaemic-induced conditions was significantly reversed by DAPA treatment. These data demonstrate that (DAla(2))GIP can exert beneficial metabolic control in high fat fed diabetic mice pre-treated with DAPA. The results highlight possibility of a targeted and personalized approach using a GIP agonist and SGLT2 inhibitor for the treatment of type 2 diabetes.


Subject(s)
Diabetes Mellitus, Experimental/drug therapy , Diabetes Mellitus, Experimental/metabolism , Gastric Inhibitory Polypeptide/agonists , Sodium-Glucose Transporter 2 Inhibitors , Animals , Benzhydryl Compounds/administration & dosage , Benzhydryl Compounds/pharmacology , Benzhydryl Compounds/therapeutic use , Blood Glucose/metabolism , Body Composition/drug effects , Body Weight/drug effects , Bone Density/drug effects , Diabetes Mellitus, Experimental/blood , Diet, High-Fat , Energy Metabolism/drug effects , Fasting/blood , Gastric Inhibitory Polypeptide/administration & dosage , Gastric Inhibitory Polypeptide/pharmacology , Gastric Inhibitory Polypeptide/therapeutic use , Glucosides/administration & dosage , Glucosides/pharmacology , Glucosides/therapeutic use , Homeostasis/drug effects , Insulin/blood , Islets of Langerhans/drug effects , Islets of Langerhans/metabolism , Islets of Langerhans/pathology , Male , Mice , RNA, Messenger/genetics , RNA, Messenger/metabolism , Sodium-Glucose Transporter 2/genetics , Sodium-Glucose Transporter 2/metabolism
3.
J Plant Physiol ; 164(6): 794-806, 2007 Jun.
Article in English | MEDLINE | ID: mdl-16887234

ABSTRACT

Interactions between legumes and rhizobia are controlled by the sequential exchange of symbiotic signals. Two different techniques, 2D-PAGE electrophoresis and differential display were used to study the effects of rhizobial signals on legume development. Application of variously substituted lipo-oligo-saccharidic Nod-factors to roots of Vigna unguiculata resulted in changes in the phosphorylation patterns of microsomal proteins. Reliable amino-acid sequences were obtained for one Nod-factor enhanced protein which was highly homologous to the 57-kDa subunit from Arabidopsis thaliana vacuolar membrane H(+)-ATPase. Immuno-blotting techniques demonstrated that Nod-factors cause rapid and massive increases of this enzyme in treated roots, suggesting that H(+)-ATPases play symbiotic roles. Concomitantly, we used differential display (DD) techniques on mRNA isolated from root-hairs to analyse early root responses to NGR234. Significant matches of several DD clones to known sequences were found. Clone D2.62 was homologous to a multitude of receptor kinases including S receptor-like kinases of A. thaliana and clone D4.1 showed similarities to Lotus japonicus phosphatidylinositol transfer-like protein III and late nodulin 16. Independent confirmatory analyses of these differentially expressed clones indicated expression at very low levels.


Subject(s)
Fabaceae/microbiology , Rhizobium/physiology , Cell Fractionation/methods , Cell Membrane/metabolism , Cloning, Molecular , Electrophoresis, Gel, Two-Dimensional , Fabaceae/genetics , Fabaceae/metabolism , Gene Expression Profiling , Immunoblotting , Plant Roots/genetics , Plant Roots/metabolism , Plant Roots/microbiology , Proteomics , RNA, Messenger/metabolism , Sequence Analysis, Protein , Sequence Analysis, RNA , Signal Transduction , Symbiosis
4.
Int J Syst Evol Microbiol ; 51(Pt 5): 1681-1685, 2001 Sep.
Article in English | MEDLINE | ID: mdl-11594595

ABSTRACT

An azo-dye-reducing, endospore-forming bacterium isolated from textile industry wastewater has been taxonomically studied. Particularly interesting was the ability of this organism to decolorize the azo dye Remazol Black B by 98% within 24 h. Levels of 16S rRNA similarity between the isolate and Paenibacillus species ranged from 92.1 to 95.0%. The DNA G+C content was 46.8 mol % and anteiso-branched C15:0 was the major fatty acid. Based upon the phenotypic properties and the phylogenetic inference, it is proposed that the bacterium should be designated Paenibacillus azoreducens sp. nov. The type strain of Paenibacillus azoreducens is CM1T (= DSM 13822T = NCIMB 13761T).


Subject(s)
Azo Compounds/metabolism , Bacillus/classification , Industrial Waste , Water Microbiology , Water Purification/methods , Bacillus/genetics , Bacillus/metabolism , Base Composition , Biodegradation, Environmental , Coloring Agents/metabolism , DNA, Ribosomal/analysis , Fatty Acids/analysis , Molecular Sequence Data , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
5.
Mol Biochem Parasitol ; 116(2): 199-208, 2001 Sep 03.
Article in English | MEDLINE | ID: mdl-11522352

ABSTRACT

This study presents data demonstrating the presence of FMRFamide-related peptides (FaRPs) in potato cyst nematodes (PCN). Five transcripts of FaRP encoding genes, designated gpflp-1 to gpflp-5, were characterised using RACE. In terms of ORFs, gpflp-1 was 444 base pairs (bp) long and coded for four copies of the FaRP, PF3 (KSAYMRFamide) whilst gpflp-2 was 309 bp long and encoded one copy of the peptide, KNKFEFIRFamide. gpflp-3 (420 bp) Encoded two copies of KHEYLRFamide (AF2) and the genes gpflp-4 and gpflp-5 encoded a total of 11 FaRPs, most of which are novel to PCN. FMRFamide-related peptide (FaRP)-like immunoreactivity was observed in both PCN species, Globodera pallida and Globodera rostochiensis, using an antiserum raised against the invertebrate peptide, FMRFamide. Immunopositive neurones were found throughout the central nervous system in the ventral and dorsal nerve cords and the circumpharyngeal and perianal nerve rings. Reactive neurones were also present peripherally, innervating the highly muscular pharynx with a nerve net and ring-like structures. Positive immunostaining was also observed in neurones running toward the stylet protractor muscles and/or the anterior sensory apparatus. This study implicates a role for FaRPs in feeding, host penetration and sensory function of PCN. This is the first study to characterise FaRP encoding genes from a plant-parasitic nematode using a targeted PCR based RACE approach and further underlines the importance and diversity of this neuropeptide group in the phylum Nematoda.


Subject(s)
FMRFamide/analysis , Helminth Proteins/analysis , Nematoda/chemistry , Solanum tuberosum/parasitology , Amino Acid Sequence , Animals , Cloning, Molecular , FMRFamide/genetics , Helminth Proteins/genetics , Immunohistochemistry , Molecular Sequence Data , Nematoda/genetics , Open Reading Frames
6.
Mol Plant Microbe Interact ; 12(9): 825-8, 1999 Sep.
Article in English | MEDLINE | ID: mdl-10494634

ABSTRACT

Temporal reverse transcription-polymerase chain reaction (RT-PCR) expression analyses were performed on Trprx2, a new white clover peroxidase, with roots challenged with homologous rhizobia, heterologous rhizobia, and a pathogen, Pseudomonas syringae. Low levels of Trprx2 expression were evident in all rhizobial treatments but in P.syringae-treated clover background expression was dramatically reduced within 1 h and was undetectable in treatments inoculated for more than 3 h. Spraying 4 mM salicylic acid onto seedlings increased Trprx2 expression. These data suggest a defensive role for Trprx2 in white clover and indicate active defense suppression by the pathogen.


Subject(s)
DNA, Complementary/genetics , DNA, Plant/genetics , Fabaceae/enzymology , Fabaceae/genetics , Peroxidase/genetics , Plants, Medicinal , Amino Acid Sequence , Fabaceae/microbiology , Gene Expression , Genes, Plant , Molecular Sequence Data , Plant Roots/enzymology , Plant Roots/microbiology , Pseudomonas/physiology , Rhizobium/physiology , Sequence Homology, Amino Acid , Symbiosis
7.
FEMS Microbiol Lett ; 171(1): 17-25, 1999 Feb 01.
Article in English | MEDLINE | ID: mdl-9987837

ABSTRACT

Enzootic abortion in ewes (EAE) is caused by strains of Chlamydia psittaci which have the ability to invade and colonise the placenta of sheep. In an attempt to improve diagnostic methods for the detection of EAE, subtraction hybridisation was used to isolate unique fragments of the genome of an abortifacient strain (S26/3) of C. psittaci. One S26/3 strain-specific sequence identified was shown to encode a putative helicase which is repeated throughout the EAE genome. The labelled strain-specific helicase gene fragment was used in the dot-blot hybridisation test for the detection of EAE DNA in ovine placental samples. We report the identification of C. psittaci S26/3 strain-specific sequence with potential as diagnostic probes for the detection of EAE.


Subject(s)
Abortion, Veterinary/microbiology , Chlamydophila psittaci/genetics , Nucleic Acid Hybridization/methods , Sheep Diseases/microbiology , Amino Acid Sequence , Animals , Base Sequence , Blotting, Southern , Chick Embryo , Chlamydophila psittaci/isolation & purification , DNA Helicases/analysis , DNA, Bacterial/genetics , DNA, Bacterial/isolation & purification , Female , Molecular Sequence Data , Placenta/microbiology , Pregnancy , Sequence Analysis , Sheep , Species Specificity
8.
J Endocrinol ; 159(3): 381-7, 1998 Dec.
Article in English | MEDLINE | ID: mdl-9834455

ABSTRACT

Insulin is as integral and important to the management of metabolism in ruminants as it is in non-ruminants. The suggestion of a lowered ruminant sensitivity and/or responsivity to insulin may relate more to the insulin receptor than to the hormone itself. We screened an ovine cDNA library using degenerate primers and polymerase chain reaction (PCR) to detect and sequence a cDNA portion corresponding to exons 10, 11 and 12 of the human insulin receptor gene in which a 36 base pair (bp) segment (exon 11) is alternatively spliced to produce two distinct receptor isoforms differing in functional characteristics including binding affinity for insulin. The ovine cDNA segment (nucleotides 671 to 770) displayed 84, 84, and 78% nucleotide homology to equivalent segments from the human, rhesus monkey and rat respectively. Reverse transcription PCR (RT-PCR) of selected tissues (liver, m. longissimus dorsi, m. rectus capitis and omental, perirenal and subcutaneous fats) taken at slaughter from three male, pure Dutch Texel lambs (experiment 1) and five male Texel-Greyface crossbred lambs (experiment 2) revealed two mRNA products in each tissue (including spleen; experiment 2 only) corresponding to cDNAs of molecular sizes 161 and 197 bp -- a difference of 36 bp. Sequence alignment showed the 36 bp segment to be homologous to the alternatively spliced exon 11 region of the human insulin receptor gene and to be highly conserved with that from other species. The abundance of the exon 11(+) isoform in the purebred Texel genotype was significantly higher in liver than in perirenal fat and rectus capitis and longissimus dorsi skeletal muscles (P<0.05) and higher also than in subcutaneous and omental fats (P<0.01). There was, however, no difference in the abundance of the exon 11(+) isoform between the individual muscle and fat depots in this sheep genotype. The abundance of the exon 11(+) isoform in the crossbred Texel genotype was significantly higher in liver (P<0. 05) than in the muscles (rectus capitis, P<0.05; longissimus dorsi, P<0.001), all three fats (P<0.001) and spleen (P<0.001). In the crossbred genotype, the abundance of the exon 11(+) isoform was higher in skeletal muscle than in all three fat depots (P<0.001), in which the isoform abundance was similar. Altered ratios of expression of the two products of this alternative splicing event could determine tissue sensitivity and/or responsivity to insulin and provide a mechanism for the management of nutrient partitioning and nutrient utilisation between tissues which is fundamental to the growth of tissues and manipulation of carcass characteristics in meat-producing animals.


Subject(s)
Alternative Splicing , Gene Expression Regulation/physiology , Liver/metabolism , Receptor, Insulin/genetics , Sheep/genetics , Adipose Tissue/metabolism , Amino Acid Sequence , Animals , Base Sequence , DNA, Complementary/analysis , Exons , Humans , Macaca mulatta , Male , Molecular Sequence Data , Muscle, Skeletal/metabolism , Protein Isoforms , Rats , Reverse Transcriptase Polymerase Chain Reaction/methods , Sequence Homology, Nucleic Acid
9.
Microbiology (Reading) ; 144 ( Pt 8): 2367-2372, 1998 Aug.
Article in English | MEDLINE | ID: mdl-9720059

ABSTRACT

PCR amplification of the small subunit (SSU) rDNA gene of 40 isolates of Nectria galligena revealed four length polymorphisms. PCR-RFLP analysis of the SSU rDNA gene divided the isolates into four categories similar, but not identical, to categories identified by Southern-RFLP analysis. Nucleotide sequence analysis revealed that isolates in three of the four SSU rDNA (18S) categories possess an intron of 363 bp, 1185 bp or 1423 bp at the NS 7 priming site. Isolates in the fourth category do not possess an intron. The nucleotide sequences of these introns did not contain the core elements characteristic of typical group I introns, nor did they exhibit a group I intron secondary structure. Homology between the introns indicates a common lineage, all three possibly having come from a larger intron and having been formed by subsequent deletions. PCR primers upstream of the SSU rDNA intron region and from within the internal transcribed spacer 1 region amplify a product specific to N. galligena, which will confirm the identity of the pathogen and reveal its 18S category in a single reaction.


Subject(s)
DNA, Fungal/genetics , DNA, Ribosomal/genetics , Introns/genetics , Polymorphism, Restriction Fragment Length , Deoxyribonuclease EcoRI , Gene Amplification , Hypocreales , Molecular Sequence Data , Polymerase Chain Reaction , RNA, Ribosomal, 18S/genetics
10.
Nature ; 387(6632 Suppl): 81-4, 1997 May 29.
Article in English | MEDLINE | ID: mdl-9169869

ABSTRACT

The complete nucleotide sequence of Saccharomyces cerevisiae chromosome VII has 572 predicted open reading frames (ORFs), of which 341 are new. No correlation was found between G+C content and gene density along the chromosome, and their variations are random. Of the ORFs, 17% show high similarity to human proteins. Almost half of the ORFs could be classified in functional categories, and there is a slight increase in the number of transcription (7.0%) and translation (5.2%) factors when compared with the complete S. cerevisiae genome. Accurate verification procedures demonstrate that there are less than two errors per 10,000 base pairs in the published sequence.


Subject(s)
Chromosomes, Fungal , Saccharomyces cerevisiae/genetics , Base Sequence , DNA, Fungal , Fungal Proteins/genetics , Humans , Open Reading Frames , Sequence Homology, Amino Acid
12.
Int J Food Microbiol ; 22(1): 43-54, 1994 Apr.
Article in English | MEDLINE | ID: mdl-8060792

ABSTRACT

A digoxygenin-labelled total genomic DNA probe was used to identify Staphylococcus aureus. Isolation and identification of organisms was possible in less than 4 days. Identification alone could be completed in less than 2 days, compared with over 5 days for identification of isolates by multipoint inoculation. The probe showed excellent discrimination of S. aureus from other staphylococci and from a wide range of bacteria commonly associated with milk and meat. The effectiveness of this probe was tested against cultural isolation of staphylococci in milk using Baird-Parker agar followed by identification using multipoint inoculation and API Staph. The probe gave comparable results to the conventional methods and, for large sample numbers, offered lower cost and greater ease of use.


Subject(s)
DNA, Bacterial/analysis , Food Microbiology , Milk/microbiology , Nucleic Acid Hybridization/methods , Staphylococcus aureus/isolation & purification , Animals , DNA Probes , Time Factors
13.
Nucleic Acids Res ; 22(8): 1335-41, 1994 Apr 25.
Article in English | MEDLINE | ID: mdl-8190622

ABSTRACT

Traditionally, new loci involved in the Rhizobium-legume symbiosis have been identified by transposon mutagenesis and/or complementation. Wide dispersal of the symbiotic loci in Rhizobium species NGR234, as well as the large number of potential host-plants to be screened, greatly reduces the efficiency of these techniques. As an alternate strategy designed to identify new NGR234 genes involved in the early stages of the symbiosis, we combined data from competitive RNA hybridisation, subtractive DNA hybridisation and shot-gun sequencing. On the assumption that the expression of most nodulation genes is triggered by compounds released by the host-plant, we identified, in the ordered cosmid library of the large symbiotic plasmid pNGR234a, restriction fragments that carry transcripts induced by flavonoids. To target genes not present in the closely related strain R. fredii USDA257, we selected fragments that also carried sequences purified by subtractive DNA hybridisation. Shot-gun sequencing of this subset of fragments lead to the identification of sequences with strong homology to diverse prokaryotic genes/proteins. Amongst these, a symbiotically active ORF from pNGR234a, is highly homologous to the leucine responsive regulatory protein of Escherichia coli (Lrp), is induced by flavonoids, and is not present in USDA257.


Subject(s)
DNA, Bacterial/analysis , Fabaceae/genetics , Nucleic Acid Hybridization , Plants, Medicinal , Rhizobium/genetics , Sequence Analysis, DNA , Symbiosis/genetics , Amino Acid Sequence , Base Sequence , Cloning, Molecular , Escherichia coli/genetics , Fabaceae/microbiology , Genetic Complementation Test , Molecular Sequence Data , Mutagenesis, Insertional , Open Reading Frames , Phenotype , Pseudomonas putida/genetics , Restriction Mapping , Rhizobium/physiology , Sequence Analysis, DNA/methods , Sequence Homology, Amino Acid
15.
Appl Environ Microbiol ; 58(7): 2296-301, 1992 Jul.
Article in English | MEDLINE | ID: mdl-1637166

ABSTRACT

A novel subtraction hybridization procedure, incorporating a combination of four separation strategies, was developed to isolate unique DNA sequences from a strain of Rhizobium leguminosarum bv. trifolii. Sau3A-digested DNA from this strain, i.e., the probe strain, was ligated to a linker and hybridized in solution with an excess of pooled subtracter DNA from seven other strains of the same biovar which had been restricted, ligated to a different, biotinylated, subtracter-specific linker, and amplified by polymerase chain reaction to incorporate dUTP. Subtracter DNA and subtracter-probe hybrids were removed by phenol-chloroform extraction of a streptavidin-biotin-DNA complex. NENSORB chromatography of the sequences remaining in the aqueous layer captured biotinylated subtracter DNA which may have escaped removal by phenol-chloroform treatment. Any traces of contaminating subtracter DNA were removed by digestion with uracil DNA glycosylase. Finally, remaining sequences were amplified by polymerase chain reaction with a probe strain-specific primer, labelled with 32P, and tested for specificity in dot blot hybridizations against total genomic target DNA from each strain in the subtracter pool. Two rounds of subtraction-amplification were sufficient to remove cross-hybridizing sequences and to give a probe which hybridized only with homologous target DNA. The method is applicable to the isolation of DNA and RNA sequences from both procaryotic and eucaryotic cells.


Subject(s)
DNA, Bacterial/genetics , Polymerase Chain Reaction/methods , Rhizobium leguminosarum/genetics , Base Sequence , DNA Probes , DNA, Bacterial/isolation & purification , Evaluation Studies as Topic , Gene Amplification , Molecular Sequence Data , Nucleic Acid Hybridization , Species Specificity
16.
Appl Environ Microbiol ; 54(11): 2852-5, 1988 Nov.
Article in English | MEDLINE | ID: mdl-16347782

ABSTRACT

Mixed-phase (heterogeneous) and single-phase (homogeneous) DNA subtraction-hybridization methods were used to isolate specific DNA probes for closely related Rhizobium loti strains. In the heterogeneous method, DNA from the prospective probe strain was repeatedly hybridized to a mixture of DNA from cross-hybridizing strains (subtracter DNA) which was immobilized on an epoxy-activated cellulose matrix. Probe strain sequences which shared homology with the matrix-bound subtracter DNA hybridized to it, leaving unique probe strain sequences in the mobile phase. In the homogeneous method, probe strain sequences were hybridized in solution to biotinylated, mercurated subtracter DNA. Biotinylated, mercurated subtracer DNA and probe strain sequences hybridized to it were removed by two-step affinity chromatography on streptavidin-agarose and thiol-Sepharose. The specificity of the sequences remaining after subtraction hybridization by both methods was assessed and compared by colony hybridization with R. loti strains. Both methods allowed the rapid isolation of strain-specific DNA fragments which were suitable for use as probes.

17.
Appl Environ Microbiol ; 53(7): 1705-7, 1987 Jul.
Article in English | MEDLINE | ID: mdl-16347400

ABSTRACT

Hybridization of crushed Lotus pedunculatus root nodules with P-labeled total genomic DNA probes was used to identify Rhizobium loti and Bradyrhizobium sp. (Lotus rhizobia). Probes always hybridized with homologous target DNA and frequently with DNAs of other strains from the same genus. Intergeneric hybridization did not occur. Results were comparable to those from colony hybridization.

SELECTION OF CITATIONS
SEARCH DETAIL
...