Using Blood-Informative Transcripts in Geographical Genomics: Impact of Lifestyle on Gene Expression in Fijians
ABSTRACT: This study explores the impact of lifestyle and environment on gene expression through whole transcriptome profiling of peripheral blood samples in Fijian population (native Melanesians and Indians) living in the rural and urban areas. 41 individuals (14 urban Melanesians, 10 rural Melanesians and 17 urban Indians) of both gender were sampled under informed consents. Only healthy individuals aged between 18 and 65 were sampled. RNA from each sample was hybridized to an Illumina array. No replicates were done in this study
Project description:The human transitions from nomadic to agrarian to urban lifestyles are likely to impact physiology and disease susceptibility. In order to estimate the magnitude of the impact of lifestyle on genome function, we profiled gene expression in total leukocytes of Moroccan Amazigh from three distinct localities. Despite great expression heterogeneity in humans, as much as one third of the PBMC transcriptome was found to differ between the localities. Keywords: Population genomic comparison Overall design: Total leukocytes were collected in December 2006 from three Moroccan Amazigh populations having three distinct lifestyles. Expression profiles of 10,173 transcripts were obtained for 46 individuals.
Project description:Understanding the visual discrepancy and heterogeneity of different places is of great interest to architectural design, urban design and tourism planning. However, previous studies have been limited by the lack of adequate data and efficient methods to quantify the visual aspects of a place. This work proposes a data-driven framework to explore the place-informative scenes and objects by employing deep convolutional neural network to learn and measure the visual knowledge of place appearance automatically from a massive dataset of photos and imagery. Based on the proposed framework, we compare the visual similarity and visual distinctiveness of 18 cities worldwide using millions of geo-tagged photos obtained from social media. As a result, we identify the visual cues of each city that distinguish that city from others: other than landmarks, a large number of historical architecture, religious sites, unique urban scenes, along with some unusual natural landscapes have been identified as the most place-informative elements. In terms of the city-informative objects, taking vehicles as an example, we find that the taxis, police cars and ambulances are the most place-informative objects. The results of this work are inspiring for various fields-providing insights on what large-scale geo-tagged data can achieve in understanding place formalization and urban design.
Project description:Introduction: Urbanization is a globally pervasive trend. Although urban settings provide better access to infrastructure and opportunities, urban lifestyles have certain negative consequences on human health. A number of recent studies have found interesting associations between the structure of human gut microbiota and the prevalence of metabolic conditions characterizing urban populations. The present study attempts to expand the footprint of these investigations to an Indian context. The objectives include elucidating specific patterns and gradients based on resident habitat and lifestyles (i.e., tribal and urban) that characterize gut microbial communities. Methods: Available 16S rRNA sequence datasets corresponding to the gut microbiota of urban and tribal populations from multiple regions of India have been rigorously compared. This analysis was carried out to understand the overall community structure, resident taxa, and their (inferred) functional components as well as their correlations with available meta-information. Results: The gut microbiota of urban and tribal communities are observed to have characteristically different signatures with respect to diversity as well as taxonomic and functional composition. Primarily, the gut microbiota in tribal communities is found to harbor significantly higher species diversity and richness as compared to that in urban populations. In spite of geographical segregation and diet-related differences, gut microbial diversity was not found to differ significantly between tribal groups. Furthermore, while the taxonomic profiles of different tribal communities cluster together irrespective of their geographic location, enterotype analysis indicates that samples from urban communities form two distinct clusters. Taxonomic analysis of samples in one of these clusters reveals the presence of microbes that are common to both urban and tribal cohorts, indicating a probable transient evolutionary state. Prevotella, previously reported to be the dominant genus resident in Indian gut microbiota, is found to have distinct OTUs and strain-specific oligotypes characterizing resident habitats and diet patterns. Certain interesting associations between microbial abundances and specific metadata have also been observed. Overall, urban lifestyle and diet appear to impact the structure and function of gut microbial communities, and the results of this study provide further evidence of this likely detrimental association. Conclusion: This study attempts to analyze, in an Indian context, the impact of urbanization on the human gut microbiota. Overall, the analysis elucidates interesting taxonomic and functional signatures characterizing the evolutionary transition in gut microbiota from tribal to urban.
Project description:Recent years have seen the development of numerous methodologies for reconstructing transmission trees in infectious disease outbreaks from densely sampled whole genome sequence data. However, a fundamental and as of yet poorly addressed limitation of such approaches is the requirement for genetic diversity to arise on epidemiological timescales. Specifically, the position of infected individuals in a transmission tree can only be resolved by genetic data if mutations have accumulated between the sampled pathogen genomes. To quantify and compare the useful genetic diversity expected from genetic data in different pathogen outbreaks, we introduce here the concept of 'transmission divergence', defined as the number of mutations separating whole genome sequences sampled from transmission pairs. Using parameter values obtained by literature review, we simulate outbreak scenarios alongside sequence evolution using two models described in the literature to describe transmission divergence of ten major outbreak-causing pathogens. We find that while mean values vary significantly between the pathogens considered, their transmission divergence is generally very low, with many outbreaks characterised by large numbers of genetically identical transmission pairs. We describe the impact of transmission divergence on our ability to reconstruct outbreaks using two outbreak reconstruction tools, the R packages outbreaker and phybreak, and demonstrate that, in agreement with previous observations, genetic sequence data of rapidly evolving pathogens such as RNA viruses can provide valuable information on individual transmission events. Conversely, sequence data of pathogens with lower mean transmission divergence, including Streptococcus pneumoniae, Shigella sonnei and Clostridium difficile, provide little to no information about individual transmission events. Our results highlight the informational limitations of genetic sequence data in certain outbreak scenarios, and demonstrate the need to expand the toolkit of outbreak reconstruction tools to integrate other types of epidemiological data.
Project description:Motivation:Multiple sequence alignments (MSAs) can provide essential input to many bioinformatics applications, including protein structure prediction and functional annotation. However, the optimal selection of sequences to obtain biologically informative MSAs for such purposes is poorly explored, and has traditionally been performed manually. Results:We present Selection of Alignment by Maximal Mutual Information (SAMMI), an automated, sequence-based approach to objectively select an optimal MSA from a large set of alternatives sampled from a general sequence database search. The hypothesis of this approach is that the mutual information among MSA columns will be maximal for those MSAs that contain the most diverse set possible of the most structurally and functionally homogeneous protein sequences. SAMMI was tested to select MSAs for functional site residue prediction by analysis of conservation patterns on a set of 435 proteins obtained from protein-ligand (peptides, nucleic acids and small substrates) and protein-protein interaction databases. Availability and implementation: A freely accessible program, including source code, implementing SAMMI is available at https://github.com/nelsongil92/SAMMI.git. Contact:email@example.com. Supplementary information:Supplementary data are available at Bioinformatics online.
Project description:Surrey, a county in southern England, is a hot spot for angiostrongylosis in domestic dogs but there have been no investigations into the intermediate hosts of Angiostrongylus vasorum in this area. This study aimed to determine the prevalence of A. vasorum in gastropods in Guildford, the most populous town in Surrey, and to ascertain which gastropod species can act as intermediate hosts for A. vasorum. Gastropods (n?=?97) were sampled in six locations, representing urban, suburban and rural environments, and identified to species based on morphological features. A PCR assay was used to detect A. vasorum DNA in gastropod tissue and the species of infected specimens was confirmed by sequencing of mitochondrial genes. 4.1% (4/97) of sampled gastropods and 9.1% (4/44) of sampled slugs were A. vasorum positive. Infected gastropod species were Arion rufus (n?=?3) and Deroceras invadens (n?=?1), the first description of the latter species as a potential intermediate host for A. vasorum. Two infected slugs were sampled in urban environments and two in suburban environments. The results demonstrate that there is a risk of transmission of A. vasorum to domestic dogs from the gastropod population in urban and suburban areas of Guildford.
Project description:Rodents are the most prominent animal host of Bartonella spp., which are associated with an increasing number of human diseases worldwide. Many rodent species thrive in urban environments and live in close contact with people, which can lead to an increased human risk of infection from rodent-borne pathogens. In this study, we explored the prevalence and distribution of Bartonella spp. in rodents in urban, developing, and rural environments surrounding a growing city in Sarawak, Malaysian Borneo. We found that although Bartonella spp. infection was pervasive in most rodent species sampled, prevalence was highest in urban areas and infection was most commonly detected in the predominant indigenous rodent species sampled (Sundamys muelleri). Within the urban environment, parks and remnant green patches were significantly associated with the presence of both S. muelleri and Bartonella spp., indicating higher localized risk of infection for people using these environments for farming, foraging, or recreation.
Project description:Human-use pharmaceuticals in urban streams link aquatic-ecosystem health to human health. Pharmaceutical mixtures have been widely reported in larger streams due to historical emphasis on wastewater-treatment plant (WWTP) sources, with limited investigation of pharmaceutical exposures and potential effects in smaller headwater streams. In 2014-2017, the United States Geological Survey measured 111 pharmaceutical compounds in 308 headwater streams (261 urban-gradient sites sampled 3-5 times, 47 putative low-impact sites sampled once) in 4 regions across the US. Simultaneous exposures to multiple pharmaceutical compounds (pharmaceutical mixtures) were observed in 91% of streams (248 urban-gradient, 32 low-impact), with 88 analytes detected across all sites and cumulative maximum concentrations up to 36,142 ng/L per site. Cumulative detections and concentrations correlated to urban land use and presence/absence of permitted WWTP discharges, but pharmaceutical mixtures also were common in the 75% of sampled streams without WWTP. Cumulative exposure-activity ratios (EAR) indicated widespread transient exposures with high probability of molecular effects to vertebrates. Considering the potential individual and interactive effects of the detected pharmaceuticals and the recognized analytical underestimation of the pharmaceutical-contaminant (unassessed parent compounds, metabolites, degradates) space, these results demonstrate a nation-wide environmental concern and the need for watershed-scale mitigation of in-stream pharmaceutical contamination.
Project description:Whole peripheral blood samples collected into Tempus tubes from 189 adult participants in the Center for Health Discovery and Well Being study of Emory University and Georgia Tech, in Midtown Atlanta. The sample is of mixed ethnicity, and is part of a survey of the impact of genetics and lifestyle on gene expression and clinical attributes. Sample annotations include gender, self-reported ethnicity, zipcode of current address, and percent body fat, as well as technical features of the study (Sentrix plate ID, date of hybridization, and RNA quality RIN score. 189 individuals in the Center for Health Discovery and Well Being study of Emory University and Georgia Tech, in Midtown Atlanta., 65 men and 124 women. The age of individulas were between 26 and 79 (mean 51). 140 Caucasian (CAU), 37 African American (AFR), 11 Asian (ASN), 1 American Indian (AMI).
Project description:Background:Federal agencies have encouraged the use of central institutional review boards (CIRBs) for multi-site clinical trials. There is limited evidence supporting the use of CIRBs. Our aim is to evaluate how SPRINT sites regulated by CIRBs performed regarding informed consent readability and participant trial adherence compared to those regulated by local IRBs. Methods:We conducted a cohort study using the SPRINT clinical trial. We collected the IRB of record from the stamped and approved 2012 informed consents from each of the sites. We defined CIRB as an IRB for more than one SPRINT site. Our outcomes were informed consent readability measured using the Flesch-Kincaid readability scale and trial adherence defined as a loss to follow-up, consent withdrawal, and missed last 3-month visit. Results:Sixty-one percent of all SPRINT sites used a CIRB as their IRB of record. The adjusted mean grade reading level for CIRB consents was 13.4 (95% CI 12.6-13.8) compared to 12.3 (95% CI 12.1-13.1) for non CIRB consents (p = 0.07). CIRB sites had similar rates of withdrawal of consent and loss to follow-up as non-CIRB sites; subjects missing the last appointment of the study were more likely to come from sites regulated by a CIRB. The Veterans Affairs CIRB had the lowest rate of withdrawal of consent (1.9%) and the lowest rate of missed appointments (1.9%) among CIRBs. Conclusions:Niether CIRB-regulated sites nor IRB regulated sites enforce the recommended readability level of the informed consent documents. Sites regulated by both IRBs had similar participant trial adherence.