Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “sanger sequencing”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

744 records · Page 42Linked to original sources
PubMed2025

Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics.

BACKGROUND: Early-life gut microbiota affects immune system development, including the lung immune response (gut-lung axis). We aimed to investigate whether gut microbiota composition in neonates in the first week of life is associated with hospital admissions for viral lower respiratory tract infections (vLRTIs). METHODS: The Baby Biome Study (BBS) is a prospective birth cohort, which enrolled mother-baby pairs between Jan 1, 2016, and Dec 31, 2017, at three UK hospitals. In the present study, we only included BBS babies with a sequenced first-week stool sample and successful data linkage. Stool was collected in the first week of life for shotgun-metagenomic sequencing. We examined the following microbiota features: alpha diversity (Chao1, Shannon, and Simpson indices) and community structures (cluster-partitioning against medoids method). The participants were followed up through linkage to the Hospital Episode Statistics-Admitted Patient Care (HES-APC) database to determine vLRTI hospital admission incidence in the first 2 years of life. We used Poisson mixed-effects models for univariable and multivariable analyses to evaluate the association between microbiota features and vLRTI hospital admission incidence, adjusting for confounders identified through direct acyclic graphs. FINDINGS: 3305 (95%) of the 3476 BBS-enrolled babies for whom consent to data linkage was obtained were included in the present study. 1111 (34%) babies had a first-week sequenced stool sample, of whom 1082 (97%; 564 born vaginally and 518 born by caesarean section) were successfully linked to HES-APC, and had median follow-up of 2·0 years (IQR 1·4-2·9). Most babies were born at term (996 [92%] ≥37 weeks gestational age and 1070 [99%] >35 weeks gestational age) and healthy (1050 [97%] had no comorbidities), and 520 (48%) were female and 562 (52%) were male. Higher first-week gut microbiota alpha diversity was associated with reduced rates of vLRTI hospital admission (Chao1 Index adjusted hazard ratio [HR] 0·92 [95% CI 0·85-0·99]; Shannon Index adjusted HR 0·57 [0·33-0·98]; and Simpson Index adjusted HR 0·36 [0·11-1·20]). Three microbiota clusters were identified. Cluster 1 had a mixed composition and cluster 2 was dominated by Bifidobacterium breve, with both clusters observed in babies born vaginally and by caesarean section. Cluster 3 was found only in vaginally born babies and was dominated by Bifidobacterium longum. Having cluster 1 (mixed) or cluster 2 (B breve dominated) was independently associated with increased rates of vLRTI hospital admission compared with cluster 3 (B longum dominated; cluster 1 [mixed] 3·05 [1·25-7·41] and cluster 2 [B breve dominated] 2·80 [1·06-7·44]). INTERPRETATION: We report observational evidence that first-week gut microbiota differences are associated with clinically severe vLRTI in young children. This study identified bacterial species that could be of interest for vLRTI prevention. This finding has important implications for the design of future research and intervention strategies. FUNDING: The Wellcome Trust and Wellcome Sanger Institute core funding.

Humans↗
PubMed2000

Identification of differentially expressed genes in dorsal root ganglia following partial sciatic nerve injury.

Partial sciatic nerve injury, a model of neuropathic pain, elicits a variety of neurochemical, electrophysiological and neuroanatomical changes in primary sensory neurons. We have used the technique of messenger RNA differential display to identify genes with altered expression in these neurons which may contribute to the development of aberrant sensation following such peripheral nerve damage. This approach identified 14 distinct complementary DNA clones, representing transcripts with increased ipsilateral expression in L4/5 dorsal root ganglia, two weeks after unilateral partial ligation of the rat sciatic nerve. Both Zucker diabetic fatty rats and their lean counterparts were used in this study but none of the transcripts identified showed an induction that was confined to one of the two groups. The majority of the clones did not show significant sequence similarity to previously reported genes and therefore may represent novel messenger RNA sequences or, alternatively, unknown regions of partially characterised messenger RNAs. Two of the clones represented transcripts for the known proteins muscle LIM protein and acidic epididymal glycoprotein, neither of which had previously been associated with expression in the nervous system. Reverse transcriptase-polymerase chain reaction analysis and in situ hybridization confirmed that the messenger RNA expression of both muscle LIM protein and acidic epididymal glycoprotein was induced in an ipsilateral-specific manner. Their localisations, examined with in situ hybridization in L5 dorsal root ganglia, were limited in each case to a sub-population of neuronal profiles. Those neuronal profiles that demonstrated muscle LIM protein hybridization were distributed across the profile size range, whereas the distribution of acidic epididymal glycoprotein-positive profiles appeared to be skewed towards smaller profiles. The induction of muscle LIM protein and acidic epididymal glycoprotein in dorsal root ganglia may play an important functional role in the adaptive response of primary sensory neurons following partial sciatic nerve injury.

Animals↗
PubMed1997

Zeugmatin is part of the Z-band targeting region of titin.

Originally, zeugmatin was identified as a 600-800 kD muscle specific protein in Z-bands of cardiac and skeletal muscles by Maher et al. (1985). In this presentation we review our work on myofibrillogenesis and present evidence that zeugmatin is actually part of the Z-Band region of titin and that this region of titin plays an important role in the assembly of the Z-bands and myofibrils. Rhee et al. (1994) reported that during myofibrillogenesis, zeugmatin antibody localization is detected in fully formed Z-bands in the mature myofibrils, in the Z-bodies of the nascent myofibrils, but not in the Z-bodies of the premyofibrils. These observations lead to the suggestion that zeugmatin might be responsible for the fusion of the Z-bodies to form the solid Z-bands of the mature myofibrils (Rhee et al. 1994). As part of a study to test aspects of this model of myofibrillogenesis, we isolated a 1.8 kb cDNA from a chicken cardiac expression library using an anti-zeugmatin antibody (Turnacioglu et al., 1996). We found this chicken cDNA to be 60% identical at the amino acid level to a segment of the Z-band region of human cardiac titin (connectin) sequenced by Labeit and Kolmerer (1995). This homology along with Western blot analysis with purified titin, suggested that zeugmatin is in fact part of the N-terminal region of chicken titin. When expressed in non-muscle cells, Z1.1 product colocalized with the alpha-actinin in stress fiber dense bodies and focal adhesions. Cultures of non-muscle cells, skeletal myotubes and cardiomyocytes were also transfected with a fusion construct (Z1.1GFP) consisting of the Z1.1 kb cDNA linked to the cDNA for green fluorescent protein (GFP). The Z1.1 kb cDNA encodes only 362 of the approximately 2,000 amino acids which comprise the Z-band region of titin; nevertheless, the Z1.1GFP fusion protein targets in vivo to the alpha-actinin rich Z-bands of contracting myofibrils. A dominant negative phenotype was observed in living cells expressing high levels of this Z1.1GFP fusion protein with inhibition of myofibrillogenesis as well as the disassembly of preexisting myofibrils in these cells. These data indicate that the Z-band region of titin (connectin) plays an important role in organizing and maintaining the structure of the myofibril.

Animals↗
PubMed2004

Identification & characterisation of the two novel streptococcal pyrogenic exotoxins SPE-L & SPE-M.

BACKGROUND & OBJECTIVES: The streptococcal pyrogenic exotoxins (SPEs) are produced by Streptococcus pyogenes and belong to the family of bacterial superantigens, a group of highly mitogenic proteins. The aim of this study was to search unfinished streptococcal genomes for novel superantigens, to generate recombinant proteins from potential open reading frames (ORFs) and to analyse them for superantigen activity. METHODS: The microbial genome database was searched using a TBLASTN search programme. Genotyping of S. equi and S. pyogenes isolates was done using the specific primer pairs. The spe-l and spe-m genes were amplified by PCR. RESULTS: Two novel streptococcal superantigen genes (sepe-l and sepe-m) were identified from the Streptococcus equi genomic database at the Sanger Centre. Genotyping of S. pyogenes isolates resulted in the detection of the orthologous genes spe-l and spe-m in a restricted number of S. pyogenes isolates and revealed a link of spe-l to the M89 serotype. Recombinant SPE-L and rSPE-M were highly mitogenic for human peripheral blood lymphocytes with half maximum responses at 1 pg/ml and 10 pg/ml, respectively. The results from competitive binding experiments suggest that both proteins bind MHC class II at the beta-chain, but not at the alpha-chain. The most common target for both toxins were human Vbetal.1 expressing T cells. Seroconversion against SPE-L and SPE-M was observed in healthy blood donors. INTERPRETATION & CONCLUSION: The two novel ORFs identified in both, S. equi and S. pyogenes, code for proteins that show typical superantigen features. The seroconversion seen in some blood donors suggest that the proteins are indeed produced by the bacteria. Interestingly, the spe-l gene is highly associated with S. pyogenes M89, which is linked to acute rheumatic fever in New Zealand.

Bacterial Proteins↗
PubMed1994

Symptom severity of beet western yellows virus strain ST9 is conferred by the ST9-associated RNA and is not associated with virus release from the phloem.

The ST9 strain of beet western yellows virus (BWYV ST9) is unique among BWYV strains because it encapsidates not only its 5.6-kb genomic RNA but also a 2.8-kb RNA of distinct nucleotide sequence, designated as the ST9-associated RNA. We obtained isolates of BWYV ST9 that are free of the associated RNA by transfecting Nicotiana tabacum protoplasts with transcripts of an ST9 genomic cDNA clone. Aphids were fed on extracts of infected protoplasts and were transferred to young Shepherd's Purse (Capsella bursa-pastoris) plants. When the protoplast inoculum was ST9 genomic transcript or virion RNA of the L-1 strain of BWYV (free of the associated RNA), symptoms were mild and characteristic of BWYV L-1. When ST9-associated RNA was included in the inoculum with genomic RNA of either source, subsequently infected Shepherd's Purse plants showed the severe symptoms that are characteristic of BWYV ST9. Inclusion of ST9-associated RNA in the inoculum with ST9 genomic RNA increased the accumulation of capsid antigen and ST9 genomic RNA, relative to infections initiated with ST9 genomic RNA alone. Using gold-labeled antibody and electron microscopy, we assessed the distribution of virions in Shepherd's Purse plants. Regardless of whether the associated RNA was present, sites showing immunoreactivity above background levels were restricted to the phloem, suggesting that the increased BWYV ST9 titer and symptom severity that are correlated with the presence of the ST9-associated RNA are not due to escape of the infection from phloem limitation.

Animals↗
PubMed2003

Two novel superantigens found in both group A and group C Streptococcus.

Two novel streptococcal superantigen genes (speL(Se) and speM(Se)) were identified from the Streptococcus equi genome database at the Sanger Center. Genotyping of 8 S. equi isolates and 40 Streptococcus pyogenes isolates resulted in the detection of the orthologous genes speL and speM in a restricted number of S. pyogenes isolates (15 and 5%, respectively). Surprisingly, the novel superantigen genes could not be found in any of the analyzed S. equi isolates. The results suggest that both genes are located on a mobile element that enables gene transfer between individual isolates and between streptococci from different Lancefield groups. S. equi pyrogenic exotoxin L (SPE-L(Se))/streptococcal pyrogenic exotoxin L (SPE-L) and SPE-M(Se)/SPE-M are most closely related to SMEZ, SPE-C, SPE-G, and SPE-J, but build a separate branch within this group. Recombinant SPE-L (rSPE-L) and rSPE-M were highly mitogenic for human peripheral blood lymphocytes, with half-maximum responses at 1 and 10 pg/ml, respectively. The results from competitive binding experiments suggest that both proteins bind major histocompatibility complex class II at the beta-chain, but not at the alpha-chain. The most common targets for both toxins were human Vbeta1.1 expressing T cells. Seroconversion against SPE-L and SPE-M was observed in healthy blood donors, suggesting that the toxins are expressed in vivo. Interestingly, the speL gene is highly associated with S. pyogenes M89, a serotype that is linked to acute rheumatic fever in New Zealand.

Amino Acid Sequence↗