Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth

Immediately after birth, newborn babies experience rapid colonization by microorganisms from their mothers and the surrounding environment1. Diseases in childhood and later in life are potentially mediated by the perturbation of the colonization of the infant gut microbiota2. However, the effects of delivery via caesarean section on the earliest stages of the acquisition and development of the gut microbiota, during the neonatal period (≤1 month), remain controversial3,4. Here we report the disrupted transmission of maternal Bacteroides strains, and high-level colonization by opportunistic pathogens associated with the hospital environment (including Enterococcus, Enterobacter and Klebsiella species), in babies delivered by caesarean section. These effects were also seen, to a lesser extent, in vaginally delivered babies whose mothers underwent antibiotic prophylaxis and in babies who were not breastfed during the neonatal period. We applied longitudinal sampling and whole-genome shotgun metagenomic analysis to 1,679 gut microbiota samples (taken at several time points during the neonatal period, and in infancy) from 596 full-term babies born in UK hospitals; for a subset of these babies, we collected additional matched samples from mothers (175 mothers paired with 178 babies). This analysis demonstrates that the mode of delivery is a significant factor that affects the composition of the gut microbiota throughout the neonatal period, and into infancy. Matched large-scale culturing and whole-genome sequencing of over 800 bacterial strains from these babies identified virulence factors and clinically relevant antimicrobial resistance in opportunistic pathogens that may predispose individuals to opportunistic infections. Our findings highlight the critical role of the local environment in establishing the gut microbiota in very early life, and identify colonization with antimicrobial-resistance-containing opportunistic pathogens as a previously underappreciated risk factor in hospital births

Measurement of the cardiac time intervals of the fetal ECG utilising a computerised algorithm: A retrospective observational study

.ObjectiveEstablish whether the reliable measurement of cardiac time intervals of the fetal ECG can be automated and to address whether this approach could be used to investigate large datasets.DesignRetrospective observational study.SettingTeaching hospitals in London UK, Nottingham UK and New York USA.ParticipantsSingleton pregnancies with no known fetal abnormality.MethodsArchived fetal ECG's performed using the MonicaAN24 monitor. A single ECG (PQRST) complex was generated from 5000 signal-averaged beats and electrical cardiac time intervals measured in an automated way and manually.Main Outcome measureValidation of a newly developed algorithm to measure the cardiac time intervals of the fetal ECG.Results188/236 (79.7%) subjects with fECGs of suitable signal:noise ratio were included for analysis comparing manual with automated measurement. PR interval was measured in 173/188 (92%), QRS complex in 170/188 (90%) and QT interval in 123/188 (65.4%). PR interval was 107.6 (12.07) ms [mean(SD)] manual vs 109.11 (14.7) ms algorithm. QRS duration was 54.72(6.35) ms manual vs 58.34(5.73) ms algorithm. QT-interval was 268.93 (21.59) ms manual vs 261.63 (36.16) ms algorithm. QTc was 407.5(32.71) ms manual vs 396.4 (54.78) ms algorithm. The QRS-duration increased with gestational age in both manual and algorithm measurements.ConclusionAccurate measurement of fetal ECG cardiac time intervals can be automated with potential application to interpretation of larger datasets

Hyaluronan turnover and hypoxic brown adipocytic differentiation are co-localized with ossification in calcified human aortic valves

The calcification process in aortic stenosis has garnered considerable interest but only limited investigation into selected signaling pathways. This study investigated mechanisms related to hypoxia, hyaluronan homeostasis, brown adipocytic differentiation, and ossification within calcified valves. Surgically explanted calcified aortic valves (nﾠ=ﾠ14) were immunostained for markers relevant to these mechanisms and evaluated in the center (NodCtr) and edge (NodEdge) of the calcified nodule (NodCtr), tissue directly surrounding nodule (NodSurr); center and tissue surrounding small ﾓprenodulesﾔ (PreNod, PreNodSurr); and normal fibrosa layer (CollFibr). Pearson correlations were determined between staining intensities of markers within regions. Ossification markers primarily localized to NodCtr and NodEdge, along with markers related to hyaluronan turnover and hypoxia. Markers of brown adipocytic differentiation were frequently co-localized with markers of hypoxia. In NodCtr and NodSurr, brown fat and ossification markers correlated with hyaluronidase-1, whereas these markers, as well as hypoxia, correlated with hyaluronan synthases in NodEdge. The protein product of tumor necrosis factor-? stimulated gene-6 strongly correlated with ossification markers and hyaluronidase in the regions surrounding the nodules (NodSurr, PreNodSurr). In conclusion, this study suggests roles for hyaluronan homeostasis and the promotion of hypoxia by cells demonstrating brown fat markers in calcific aortic valve disease

Life satisfaction, ethnicity and neighbourhoods: Is there an effect of neighbourhood ethnic composition on life satisfaction?

Immigrants and ethnic minorities tend to have lower life satisfaction than majority populations. However, current understanding of the drivers of these gaps is limited. Using a rich, nationally representative data set with a large sample of ethnic minorities and matched neighbourhood characteristics, we test whether first and second generation minorities experience lower life satisfaction once accounting for compositional differences and whether, specifically, neighbourhood deprivation impacts their wellbeing. We further investigate whether a larger proportion of own ethnic group in the neighbourhood improves satisfaction. We find life satisfaction is lower among ethnic minorities, and especially for the second generation, even controlling for individual and area characteristics. Neighbourhood concentration of own ethnic group is, however, associated with higher life satisfaction for Black Africans and UK born Indians and Pakistanis. The effect for Black Africans may stem from selection into areas, but findings for Indians and Pakistanis are robust to sensitivity tests

A pilot study for channel catfish whole genome sequencing and de novo assembly

<p>Abstract</p> <p>Background</p> <p>Recent advances in next-generation sequencing technologies have drastically increased throughput and significantly reduced sequencing costs. However, the average read lengths in next-generation sequencing technologies are short as compared with that of traditional Sanger sequencing. The short sequence reads pose great challenges for <it>de novo </it>sequence assembly. As a pilot project for whole genome sequencing of the catfish genome, here we attempt to determine the proper sequence coverage, the proper software for assembly, and various parameters used for the assembly of a BAC physical map contig spanning approximately a million of base pairs.</p> <p>Results</p> <p>A combination of low sequence coverage of 454 and Illumina sequencing appeared to provide effective assembly as reflected by a high N50 value. Using 454 sequencing alone, a sequencing depth of 18 X was sufficient to obtain the good quality assembly, whereas a 70 X Illumina appeared to be sufficient for a good quality assembly. Additional sequencing coverage after 18 X of 454 or after 70 X of Illumina sequencing does not provide significant improvement of the assembly. Considering the cost of sequencing, a 2 X 454 sequencing, when coupled to 70 X Illumina sequencing, provided an assembly of reasonably good quality. With several software tested, Newbler with a seed length of 16 and ABySS with a K-value of 60 appear to be appropriate for the assembly of 454 reads alone and Illumina paired-end reads alone, respectively. Using both 454 and Illumina paired-end reads, a hybrid assembly strategy using Newbler for initial 454 sequence assembly, Velvet for initial Illumina sequence assembly, followed by a second step assembly using MIRA provided the best assembly of the physical map contig, resulting in 193 contigs with a N50 value of 13,123 bp.</p> <p>Conclusions</p> <p>A hybrid sequencing strategy using low sequencing depth of 454 and high sequencing depth of Illumina provided the good quality assembly with high N50 value and relatively low cost. A combination of Newbler, Velvet, and MIRA can be used to assemble the 454 sequence reads and the Illumina reads effectively. The assembled sequence can serve as a resource for comparative genome analysis. Additional long reads using the third generation sequencing platforms are needed to sequence through repetitive genome regions that should further enhance the sequence assembly.</p

Metabolic inactivation of estrogens in breast tissue by UDP-glucuronosyltransferase enzymes: an overview

The breast tissue is the site of major metabolic conversions of estradiol (E(2)) mediated by specific cytochromes P450 hydroxylations and methylation by catechol-O-methytransferase. In addition to E(2 )itself, recent findings highlight the significance of 4-hydroxylated estrogen metabolites as chemical mediators and their link to breast cancer development and progression, whereas, in opposition, 2-methoxylated estrogens appear to be protective. Recent data also indicate that breast tissue possesses enzymatic machinery to inactivate and eliminate E(2 )and its oxidized and methoxylated metabolites through conjugation catalyzed by UDP-glucuronosyltransferases (UGTs), which involves the covalent addition of glucuronic acid. In opposition to other metabolic pathways of estrogen, the UGT-mediated process leads to the formation of glucuronides that are devoid of biologic activity and are readily excreted from the tissue into the circulation. This review addresses the most recent findings on the identification of UGT enzymes that are responsible for the glucuronidation of E(2 )and its metabolites, and evidence regarding their potential role in breast cancer

Introduced deer and their potential role in disease transmission to livestock in Australia

1. The transmission of pathogens between wildlife and livestock is a globally recognised threat to the livestock industry, as well as to human and wildlife health. Wild cervids are susceptible to many diseases affecting livestock. This presents a challenge for wildlife and domestic animal disease management because the frequent use of agricultural areas by wild cervids may hamper the effectiveness of disease control strategies. 2. Six deer species have established wild populations in Australia and are expanding in range and abundance. A comprehensive literature review of diseases impacting deer and livestock was undertaken, resulting in consideration of 38 pathogens. A qualitative risk assessment was then carried out to assess the overall risk posed by the pathogens to the livestock industry. 3. Five diseases (bovine tuberculosis, foot and mouth disease, malignant catarrhal fever, surra, and screw‐worm fly infestation) ranked highly in our risk assessment. Of these five diseases, only one (malignant catarrhal fever) is currently present in Australia, but all five are notifiable diseases at a national level. Data on these diseases in deer are limited, especially for one of the most abundant species, the sambar deer Rusa unicolor, highlighting a further potential risk attributable to a lack of understanding of disease epidemiology. 4. This paper provides a detailed review of the pathogens affecting both cervids and livestock in Australia, and applies a qualitative framework for assessing the risk posed by deer to the livestock industry. The qualitative framework used here could easily be adapted to assess disease risk in other contexts, making this work relevant to scientists and wildlife managers, as well as to livestock industry workers, worldwide

Interactions between Type 1 Interferons and the Th17 Response in Tuberculosis: Lessons Learned from Autoimmune Diseases

textabstractThe classical paradigm of tuberculosis (TB) immunity, with a central protective role for Th1 responses and IFN-γ-stimulated cellular responses, has been challenged by unsatisfactory results of vaccine strategies aimed at enhancing Th1 immunity. Moreover, preclinical TB models have shown that increasing IFN-γ responses in the lungs is more damaging to the host than to the pathogen. Type 1 interferon signaling and altered Th17 responses have also been associated with active TB, but their functional roles in TB pathogenesis remain to be established. These two host responses have been studied in more detail in autoimmune diseases (AID) and show functional interactions that are of potential interest in TB immunity. In this review, we first identify the role of type 1 interferons and Th17 immunity in TB, followed by an overview of interactions between these responses observed in systemic AID. We discuss (i) the effects of GM-CSF-secreting Th17.1 cells and type 1 interferons on CCR2+ monocytes; (ii) convergence of IL-17 and type 1 interferon signaling on stimulating B-cell activating factor production and the central role of neutrophils in this process; and (iii) synergy between IL-17 and type 1 interferons in the generation and function of tertiary lymphoid structures and the associated follicular helper T-cell responses. Evaluation of these autoimmune-related pathways in TB pathogenesis provides a new perspective on recent developments in TB research

Ethnicity and ethnic group measures in social survey research

This article is a review of issues associated with measuring ethnicity and using ethnicity measures in social science research. The review is oriented towards researchers who undertake secondary analyses of large-scale multipurpose social science datasets. The article begins with an outline of two main approaches used in social surveys to measure ethnicity, the ‘mutually exclusive category’ approach and the ‘multiple characteristics’ approach. We also describe approaches to the use of ethnicity measures in cross-national comparative research. We emphasise the value of sensitivity analyses. We also encourage researchers to carefully consider the possible relationships between ethnicity and other important variables in order to avoid spurious interpretations of the effects of ethnicity