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- Toft, G., et al.
(author)
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Exposure to perfluorinated compounds and human semen quality in arctic and European populations
- 2012
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In: Human Reproduction. - : Oxford University Press (OUP). - 0268-1161 .- 1460-2350. ; 27:8, s. 2532-2540
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Journal article (peer-reviewed)abstract
- Perfluorinated compounds (PFCs) have been suspected to adversely affect human reproductive health. The aim of this study was to investigate the associations between PFC exposure and male semen quality. PFCs were measured in serum from 588 partners of pregnant women from Greenland, Poland and Ukraine who provided a semen sample, using liquid chromatography tandem mass spectrometry. Perfluorooctane sulfonate (PFOS), perfluorooctanoic acid (PFOA), perfluorohexane sulfonic acid (PFHxS) and perfluorononanoic acid (PFNA) could be detected in 97 of the samples. The associations between levels of these compounds and semen volume, sperm concentration, total sperm count, motility and morphology were assessed. Across countries, sperm concentration, total sperm count and semen volume were not consistently associated with PFOS, PFOA, PFHxS or PFNA levels. The proportion of morphologically normal cells was 35 lower [95 confidence interval (CI): 466) for the third tertile of PFOS exposure as compared with the first. A similar reduction was found in relation to increasing PFHxS levels. At the third PFOA exposure tertile, the percentage of motile spermatozoa was 19 (95 CI: 1 to 39) higher than in the first. The most robust finding in the present study was the negative associations between PFOS exposure and sperm morphology suggesting adverse effects of PFOS on semen quality, possibly due to interference with the endocrine activity or sperm membrane function. It cannot be excluded that this association and the positive association between PFOA and semen motility, which was not consistent across countries, might represent a chance finding due to the multiple statistical tests being performed.
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- Akram, Neelam, et al.
(author)
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Regulation of proteorhodopsin gene expression by nutrient limitation in the marine bacterium Vibrio sp AND4
- 2013
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In: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 15:5, s. 1400-1415
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Journal article (peer-reviewed)abstract
- Proteorhodopsin (PR), a ubiquitous membrane photoprotein in marine environments, acts as a light-driven proton pump and can provide energy for bacterial cellular metabolism. However, knowledge of factors that regulate PR gene expression in different bacteria remains strongly limited. Here, experiments with Vibrio sp. AND4 showed that PR phototrophy promoted survival only in cells from stationary phase and not in actively growing cells. PR gene expression was tightly regulated, with very low values in exponential phase, a pronounced peak at the exponential/stationary phase intersection, and a marked decline in stationary phase. Thus, PR gene expression at the entry into stationary phase preceded, and could therefore largely explain, the stationary phase light-induced survival response in AND4. Further experiments revealed nutrient limitation, not light exposure, regulated this differential PR expression. Screening of available marine vibrios showed that the PR gene, and thus the potential for PR phototrophy, is found in at least three different clusters in the genus Vibrio. In an ecological context, our findings suggest that some PR-containing bacteria adapted to the exploitation of nutrient-rich micro-environments rely on a phase of relatively slowly declining resources to mount a cellular response preparing them for adverse conditions dispersed in the water column.
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- Alneberg, Johannes, et al.
(author)
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Genomes from uncultivated prokaryotes : a comparison of metagenome-assembled and single-amplified genomes
- 2018
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In: Microbiome. - : BioMed Central. - 2049-2618. ; 6
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Journal article (peer-reviewed)abstract
- Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs. Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.
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- Alneberg, Johannes, et al.
(author)
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Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
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Other publication (other academic/artistic)abstract
- Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (>98.7% identity) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs; the metagenome assembly was found to cause incompleteness to a higher degree than the binning procedure.Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.
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- Baltar, Federico, et al.
(author)
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Prokaryotic community structure and respiration during long-term incubations
- 2012
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In: MicrobiologyOpen. - : Wiley. - 2045-8827. ; 1:2, s. 214-224
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Journal article (peer-reviewed)abstract
- Despite the importance of incubation assays for studies inmicrobial ecology that frequentlyrequire long confinement times, few reports are available in which changesin the assemblage structure of aquatic prokaryotes were monitored during longtermincubations.We measured rates of dissolved organic carbon degradation andmicrobial respiration by consumption of dissolved oxygen (DO) in four experimentswith Lake Kinneret near-surface water and, concomitantly, we analyzed thevariability in prokaryotic community structure during long-term dark bottle incubations.During the first 24 h, therewere only minor changes in bacterial communitycomposition. Thereafter there were marked changes in the prokaryotic communitystructure during the incubations. In contrast, oxygen consumption rates (a proxyfor both respiration and dissolved organic carbon degradation rates) remained stablefor up to 10–23 days. This study is one of the first to examine closely the phylogeneticchanges that occur in the microbial community of untreated freshwaterduring long-term (days) incubations in dark, sealed containers. Novel informationon the diversity of the main bacterial phylotypes that may be involved in dissolvedorganic matter degradation in lake Kinneret is also provided. Our results suggestthat, under certain ecological settings, constant community metabolic rates can bemaintained as a result of shifts in community composition.
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