| 1. |
- Arif, Muhammad, et al.
(author)
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INetModels 2.0: An interactive visualization and database of multi-omics data
- 2021
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 49:W1, s. W271-W276
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Journal article (peer-reviewed)abstract
- It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics, plasma metabolomics, as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and disease research. iNetModels can be accessed freely at https://inetmodels.com without any limitation.
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| 2. |
- Bhattacharya, Prosun, et al.
(author)
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Distribution and mobility of arsenic in the Rio Dulce alluvial aquifers in Santiago del Estero Province, Argentina
- 2006
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In: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 358:1-3, s. 97-120
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Journal article (peer-reviewed)abstract
- Factors controlling arsenic (As) mobilization in the aquifers of the Rio Dulce alluvial cone were investigated. Groundwater analyses show severe As contamination (average concentration of 743 mu g/L) from geogenic sources, but spatial variability of As concentration is considerable. Sequential leaching of sediment samples from unsaturated zone using de-ionised water, bicarbonate, acetate, and oxalate extracted As to different extents. Sediment oxalate extraction showed that Al and Mn oxide and hydroxides are more abundant than Fe oxides and hydroxides, in spite of similar total Fe, Mn, and Al concentrations in the sediment. Speciation calculations performed for saturated zone samples indicated that Fe and Al oxides and hydroxides are stable in groundwater, suggesting that As adsorption processes may be to some extent controlled by the presence of Fe and Al mineral phases. Principal Component Analysis (PCA) showed that As is related to F, V, Mo, B, Si, most likely due to their common origin in volcanic ash. This suggests the volcanic ash as the probable source of groundwater As. Locally, elevated pH values linked to carbonate dissolution, cation exchange, and dissolution of silicates promote release of adsorbed As. Another factor contributing to the release of As locally may be the input of organic matter from excessive irrigation. The conceptual model of As release includes: i) As influx from dissolution of volcanic glass in volcanic ash, ii) adsorption of As on the surface of Fe and Al mineral phases in relatively low pH zones, and iii) high mobility of As in high pH zones. Future work should be focused on the determination of mineralogical forms of As in volcanic ash and on detailed investigation on factors controlling As mobility.
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| 3. |
- Bhattacharya, Prosun, et al.
(author)
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Natural arsenic in the groundwater of the alluvial aquifers of Santiago del Estero Province, Argentina
- 2005
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In: Natural Arsenic in Groundwater. - London : Balkema. - 041536700X ; , s. 57-65
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Conference paper (peer-reviewed)abstract
- Natural occurrences of arsenic has been documented in groundwater of the shallow aquifers of the Chaco-Pampean Plain, Argentina. The distribution of arsenic and mechanisms of its mobilization in the shallow alluvial aquifers was investigated around the city of Santiago del Estero in Northwestern Argentina in order to provide an insight into the complex hydrological and geochemical conditions that yields high As concentrations in groundwater. Significant spatial variations of total arsenic (As-tot) concentrations were observed with an average value of 743 mu g/L. Arsenate was a dominant species in most samples. Average concentrations of Al, Mn, and Fe were 360 mu g/L, 574 mu g/L, and 459 mu g/L, respectively. The 7M HNO3 extraction of sediments and volcanic ash-layer indicated AS(N03) concentrations ranging between 2.5-7.1 mg/kg. AS(N03) indicated a significant positive correlation with Mn-N03, Al-N03, and Fe-N03. Oxalate extractions revealed significant fractions of As (Aso(ox)) in the sediments (0.4-1.4mg/kg) and a dominance of oxalate extractable Al- and Mn. Speciation calculations indicate that Al oxide and hydroxides have the potential to precipitate in the groundwater, suggesting that As adsorption processes may be to some extent controlled by Al oxides and hydroxides. Mobility of As at local scale seems to depend on high pH values, related to the dissolution of carbonates driven by cation exchange, and dissolution of silicates. There is a clear relationship of As with F, V, B and Si, suggesting their common origin in volcanic ash layer. Preliminary conceptual model of arsenic input includes release of As and Al from dissolution of volcanic ash layer, precipitation of Al oxides and hydroxides followed by adsorption of As on Al and Fe phases in sediments, and release of As under high pH conditions.
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| 4. |
- Fagerberg, Linn, et al.
(author)
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Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics
- 2014
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In: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 13:2, s. 397-406
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Journal article (peer-reviewed)abstract
- Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody- based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to 80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body.
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| 5. |
- Hu, Yue O. O., et al.
(author)
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Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems
- 2018
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In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 8
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Journal article (peer-reviewed)abstract
- Urban sewer systems consist of wastewater and stormwater sewers, of which only wastewater is processed before being discharged. Occasionally, misconnections or damages in the network occur, resulting in untreated wastewater entering natural water bodies via the stormwater system. Cultivation of faecal indicator bacteria (e.g. Escherichia coli; E. coli) is the current standard for tracing wastewater contamination. This method is cheap but has limited specificity and mobility. Here, we compared the E. coli culturing approach with two sequencing-based methodologies (Illumina MiSeq 16S rRNA gene amplicon sequencing and Oxford Nanopore MinION shotgun metagenomic sequencing), analysing 73 stormwater samples collected in Stockholm. High correlations were obtained between E. coli culturing counts and frequencies of human gut microbiome amplicon sequences, indicating E. coli is indeed a good indicator of faecal contamination. However, the amplicon data further holds information on contamination source or alternatively how much time has elapsed since the faecal matter has entered the system. Shotgun metagenomic sequencing on a subset of the samples using a portable real-time sequencer, MinION, correlated well with the amplicon sequencing data. This study demonstrates the use of DNA sequencing to detect human faecal contamination in stormwater systems and the potential of tracing faecal contamination directly in the field.
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| 6. |
- Hu, Yue, 1987-, et al.
(author)
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Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems
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Other publication (other academic/artistic)abstract
- Urban sewer systems consist of wastewater and stormwater sewers, of which typically onlythe wastewater is processed before being discharged. Occasionally, misconnections ordamages in the network occur, resulting in wastewater entering the stormwater system andbeing discharged without prior processing. Cultivation of faecal indicator bacteria, such asEscherichia coli (E. coli), is the current standard for tracing wastewater contamination. Thismethod is cheap but cannot be employed in the field and is characterised by its limitedspecificity. Here, we compared the E. coli culturing approach with two different DNAsequencing-based methodologies (i.e., 16S rRNA amplicon sequencing on the IlluminaMiSeq platform and shotgun metagenomic sequencing on an Oxford Nanopore MinIOndevice), analysing 73 stormwater samples collected throughout the Stockholm city areas.High correlations were obtained between E. coli culturing counts and frequencies of humangut microbiome sequencing reads (via amplicon sequencing), indicating that E. coli is indeeda good indicator of faecal contamination. In contrast to E.coli culturing, amplicon sequencingcould, however, further distinguish between two different sources of contamination in anarea, where misconnections in the stormwater system were later on detected. Shotgunmetagenomic sequencing on a subset of the samples using the portable Oxford NanoporeMinION real-time sequencing device correlated well with the amplicon sequencing data. Insummary, this study shows that DNA sequencing allows distinguishing differentcontamination sources in stormwater systems and demonstrates the potential of using aportable sequencing device in the field for tracking faecal contamination.
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| 7. |
- Kampf, Caroline, et al.
(author)
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Defining the human gallbladder proteome by transcriptomics and affinity proteomics
- 2014
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In: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 14:21-22, s. 2498-2507
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Journal article (peer-reviewed)abstract
- Global protein analysis of human gallbladder tissue is vital for identification of molecular regulators and effectors of its physiological activity. Here, we employed a genome-wide deep RNA sequencing analysis in 28 human tissues to identify the genes overrepresented in the gallbladder and complemented it with antibody-based immunohistochemistry in 48 human tissues. We characterized human gallbladder proteins and identified 140 gallbladder-specific proteins with an elevated expression in the gallbladder as compared to the other analyzed tissues. Five genes were categorized as enriched, with at least fivefold higher levels in gallbladder, 60 genes were categorized as group enriched with elevated transcript levels in gallbladder shared with at least one other tissue and 75 genes were categorized as enhanced with higher expression than the average expression in other tissues. We explored the localization of the genes within the gallbladder through cell-type specific antibody-based protein profiling and the subcellular localization of the genes through immunofluorescent-based profiling. Finally, we revealed the biological processes and metabolic functions carried out by these genes through the use of GO, KEGG Pathway, and HMR2.0 that is compilation of the human metabolic reactions. We demonstrated the results of the combined analysis of the transcriptomics and affinity proteomics.
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| 8. |
- Kampf, Caroline, et al.
(author)
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The human liver-specific proteome defined by transcriptomics and antibody-based profiling
- 2014
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In: FASEB Journal. - : Wiley. - 1530-6860 .- 0892-6638. ; 28:7, s. 2901-2914
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Journal article (peer-reviewed)abstract
- Human liver physiology and the genetic etiology of the liver diseases can potentially be elucidated through the identification of proteins with enriched expression in the liver. Here, we combined data from RNA sequencing (RNA-Seq) and antibody-based immunohistochemistry across all major human tissues to explore the human liver proteome with enriched expression, as well as the cell type-enriched expression in hepatocyte and bile duct cells. We identified in total 477 protein-coding genes with elevated expression in the liver: 179 genes have higher expression as compared to all the other analyzed tissues; 164 genes have elevated transcript levels in the liver shared with at least one other tissue type; and an additional 134 genes have a mild level of increased expression in the liver. We identified the precise localization of these proteins through antibody-based protein profiling and the subcellular localization of these proteins through immunofluorescent-based profiling. We also identified the biological processes and metabolic functions associated with these proteins, investigated their contribution in the occurrence of liver diseases, and identified potential targets for their treatment. Our study demonstrates the use of RNA-Seq and antibody-based immunohistochemistry for characterizing the human liver proteome, as well as the use of tissue-specific proteins in identification of novel drug targets and discovery of biomarkers.
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| 9. |
- Karlsson, Fredrik, 1984, et al.
(author)
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Gut metagenome in European women with normal, impaired and diabetic glucose control
- 2013
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 498:7452, s. 99-103
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Journal article (peer-reviewed)abstract
- Type 2 diabetes (T2D) is a result of complex gene-environment interactions, and several risk factors have been identified, including age, family history, diet, sedentary lifestyle and obesity. Statistical models that combine known risk factors for T2D can partly identify individuals at high risk of developing the disease. However, these studies have so far indicated that human genetics contributes little to the models, whereas socio-demographic and environmental factors have greater influence(1). Recent evidence suggests the importance of the gut microbiota as an environmental factor, and an altered gut microbiota has been linked to metabolic diseases including obesity(2,3), diabetes(4) and cardiovascular disease(5). Here we use shotgun sequencing to characterize the faecal metagenome of 145 European women with normal, impaired or diabetic glucose control. We observe compositional and functional alterations in the metagenomes of women with T2D, and develop a mathematical model based on metagenomic profiles that identified T2D with high accuracy. We applied this model to women with impaired glucose tolerance, and show that it can identify women who have a diabetes-like metabolism. Furthermore, glucose control and medication were unlikely to have major confounding effects. We also applied our model to a recently described Chinese cohort(4) and show that the discriminant metagenomicmarkers for T2D differ between the European and Chinese cohorts. Therefore, metagenomic predictive tools for T2D should be specific for the age and geographical location of the populations studied.
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| 10. |
- Karlsson, Fredrik, 1984, et al.
(author)
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Symptomatic atherosclerosis is associated with an altered gut metagenome
- 2012
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 3
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Journal article (peer-reviewed)abstract
- Recent findings have implicated the gut microbiota as a contributor of metabolic diseases through the modulation of host metabolism and inflammation. Atherosclerosis is associated with lipid accumulation and inflammation in the arterial wall, and bacteria have been suggested as a causative agent of this disease. Here we use shotgun sequencing of the gut metagenome to demonstrate that the genus Collinsella was enriched in patients with symptomatic atherosclerosis, defined as stenotic atherosclerotic plaques in the carotid artery leading to cerebrovascular events, whereas Roseburia and Eubacterium were enriched in healthy controls. Further characterization of the functional capacity of the metagenomes revealed that patient gut metagenomes were enriched in genes encoding peptidoglycan synthesis and depleted in phytoene dehydrogenase; patients also had reduced serum levels of β-carotene. Our findings suggest that the gut metagenome is associated with the inflammatory status of the host and patients with symptomatic atherosclerosis harbor characteristic changes in the gut metagenome.
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