Presence of Actinobacterial and Fungal Communities in Clean and Petroleum Hydrocarbon Contaminated Subsurface Soil

Relatively little is known about the microbial communities adapted to soil environments contaminated with aged complex hydrocarbon mixtures, especially in the subsurface soil layers. In this work we studied the microbial communities in two different soil profiles down to the depth of 7 m which originated from a 30-year-old site contaminated with petroleum hydrocarbons (PHCs) and from a clean site next to the contaminated site. The concentration of oxygen in the contaminated soil profile was strongly reduced in soil layers below 1 m depth but not in the clean soil profile. Total microbial biomass and community composition was analyzed by phospholipid fatty acid (PLFA) measurements. The diversity of fungi and actinobacteria was investigated more in detail by construction of rDNA-based clone libraries. The results revealed that there was a significant and diverse microbial community in subsoils at depth below 2 m, also in conditions where oxygen was limiting. The diversity of actinobacteria was different in the two soil profiles; the contaminated soil profile was dominated by Mycobacterium -related sequences whereas sequences from the clean soil samples were related to other, generally uncultured organisms, some of which may represent two new subclasses of actinobacteria. One dominating fungal sequence which matched with the ascomycotes Acremonium sp. and Paecilomyces sp. was identified both in clean and in contaminated soil profiles. Thus, although the relative amounts of fungi and actinobacteria in these microbial communities were highest in the upper soil layers, many representatives from these groups were found in hydrocarbon contaminated subsoils even under oxygen limited conditions

Inter-annual growth of Arctic charr (Salvelinus alpinus, L.) in relation to climate variation

BACKGROUND: Major changes in climate have been observed in the Arctic and climate models predict further amplification of the enhanced greenhouse effect at high-latitudes leading to increased warming. We propose that warming in the Arctic may affect the annual growth conditions of the cold adapted Arctic charr and that such effects can already be detected retrospectrally using otolith data. RESULTS: Inter-annual growth of the circumpolar Arctic charr (Salvelinus alpinus, L.) was analysed in relation to climatic changes observed in the Arctic during the last two decades. Arctic charr were sampled from six locations at Qeqertarsuaq in West Greenland, where climate data have been recorded since 1990. Two fish populations met the criteria of homogeny and, consequently, only these were used in further analyses. The results demonstrate a complex coupling between annual growth rates and fluctuations in annual mean temperatures and precipitation. Significant changes in temporal patterns of growth were observed between cohorts of 1990 and 2004. CONCLUSION: Differences in pattern of growth appear to be a consequence of climatic changes over the last two decades and we thereby conclude that climatic affects short term and inter-annual growth as well as influencing long term shifts in age-specific growth patterns in population of Arctic charr

Oil degradation potential of microbial communities in water and sediment of Baltic Sea coastal area

Two long-term potentially oil exposed Baltic Sea coastal sites near old oil refineries and harbours were compared to nearby less exposed sites in terms of bacterial, archaeal and fungal microbiomes and oil degradation potential. The bacterial, archaeal and fungal diversities were similar in oil exposed and less exposed sampling sites based on bacterial and archaeal 16S rRNA gene and fungal 5.8S rRNA gene amplicon sequencing from both DNA and RNA fractions. The number of genes participating in alkane degradation (alkB) or PAH-ring hydroxylation (PAH–RHDα) were detected by qPCR in all water and sediment samples. These numbers correlated with the number of bacterial 16S rRNA gene copies in sediment samples but not with the concentration of petroleum hydrocarbons or PAHs. This indicates that both the clean and the more polluted sites at the Baltic Sea coastal areas have a potential for petroleum hydrocarbon degradation. The active community (based on RNA) of the coastal Baltic Sea water differed largely from the total community (based on DNA). The most noticeable difference was seen in the bacterial community in the water samples were the active community was dominated by Cyanobacteria and Proteobacteria whereas in total bacterial community Actinobacteria was the most abundant phylum. The abundance, richness and diversity of Fungi present in water and sediment samples was in general lower than that of Bacteria and Archaea. Furthermore, the sampling location influenced the fungal community composition, whereas the bacterial and archaeal communities were not influenced. This may indicate that the fungal species that are adapted to the Baltic Sea environments are few and that Fungi are potentially more vulnerable to or affected by the Baltic Sea conditions than Bacteria and Archaea

A genetically modified minipig model for Alzheimer's disease with SORL1 haploinsufficiency

The established causal genes in Alzheimer’s disease (AD), APP, PSEN1, and PSEN2, are functionally characterized using biomarkers, capturing an in vivo profile reflecting the disease’s initial preclinical phase. Mutations in SORL1, encoding the endosome recycling receptor SORLA, are found in 2%–3% of individuals with early-onset AD, and SORL1 haploinsufficiency appears to be causal for AD. To test whether SORL1 can function as an AD causal gene, we use CRISPR-Cas9-based gene editing to develop a model of SORL1 haploinsufficiency in Göttingen minipigs, taking advantage of porcine models for biomarker investigations. SORL1 haploinsufficiency in young adult minipigs is found to phenocopy the preclinical in vivo profile of AD observed with APP, PSEN1, and PSEN2, resulting in elevated levels of β-amyloid (Aβ) and tau preceding amyloid plaque formation and neurodegeneration, as observed in humans. Our study provides functional support for the theory that SORL1 haploinsufficiency leads to endosome cytopathology with biofluid hallmarks of autosomal dominant AD

Surfactant-Free Colloidal Syntheses of Gold-Based Nanomaterials in Alkaline Water and Mono-alcohol Mixtures [Dataset]

120 pages. -- SA. Synthesis of Au NPs using ROH. -- SB. Experimental section. -- SC. Effect of mono-alcohol, mono-alcohol content and cation. -- SD. Effect of experimental parameters: HAuCl4 concentration, volume of solution, type of container used, light. -- SE. Effect of the nature of the alcohols. -- SF. Kinetics of the reduction. -- SG. Influence of the temperature. -- SH. Influence of base concentration. -- SI. Influence of gas atmosphere. -- SJ. Influence of the order of addition of the chemicals. -- SK. Discussion of Au NP formation. -- SL. Reproducibility. -- SM. Scalability. -- SN. Mixture of mono-alcohols. -- SO. Cation and surfactant effects . -- SP. Electrochemical characterization of Au NPs. -- SQ. Supported NPs. -- SR. Pd and bimetallic NPs. -- SS. Nanocomposites. -- ST. Electrochemical characterization of AuxPdy NPs and [x Au + y Pd] nanocomposites. -- SU. Outlook into multi-metallic nanomaterials. -- SV. Comparison of different catalysts. -- SW. ReferencesGold nanoparticles (Au NPs) and gold-based nanomaterials combine unique properties relevant for medicine, imaging, optics, sensing, catalysis, and energy conversion. While the Turkevich–Frens and Brust–Schiffrin methods remain the state-of-the-art colloidal syntheses of Au NPs, there is a need for more sustainable and tractable synthetic strategies leading to new model systems. In particular, stabilizers are almost systematically used in colloidal syntheses, but they can be detrimental for fundamental and applied studies. Here, a surfactant-free synthesis of size-controlled colloidal Au NPs stable for months is achieved by the simple reduction of HAuCl4 at room temperature in alkaline solutions of low-viscosity mono-alcohols such as ethanol or methanol and water, without the need for any other additives. Palladium (Pd) and bimetallic AuxPdy NPs, nanocomposites and multimetallic samples, are also obtained and are readily active (electro)­catalysts. The multiple benefits over the state-of-the-art syntheses that this simple synthesis bears for fundamental and applied research are highlighted.Peer reviewe

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes

Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities

Petroleum hydrocarbons reach the deep-sea following natural and anthropogenic factors. The process by which they enter deep-sea microbial food webs and impact the biogeochemical cycling of carbon and other elements is unclear. Hydrostatic pressure (HP) is a distinctive parameter of the deep sea, although rarely investigated. Whether HP alone affects the assembly and activity of oil-degrading communities remains to be resolved. Here we have demonstrated that hydrocarbon degradation in deep-sea microbial communities is lower at native HP (10 MPa, about 1000 m below sea surface level) than at ambient pressure. In long-term enrichments, increased HP selectively inhibited obligate hydrocarbon-degraders and downregulated the expression of beta-oxidation-related proteins (i.e., the main hydrocarbon-degradation pathway) resulting in low cell growth and CO2 production. Short-term experiments with HP-adapted synthetic communities confirmed this data, revealing a HP-dependent accumulation of citrate and dihydroxyacetone. Citrate accumulation suggests rates of aerobic oxidation of fatty acids in the TCA cycle were reduced. Dihydroxyacetone is connected to citrate through glycerol metabolism and glycolysis, both upregulated with increased HP. High degradation rates by obligate hydrocarbon-degraders may thus be unfavourable at increased HP, explaining their selective suppression. Through lab-scale cultivation, the present study is the first to highlight a link between impaired cell metabolism and microbial community assembly in hydrocarbon degradation at high HP. Overall, this data indicate that hydrocarbons fate differs substantially in surface waters as compared to deep-sea environments, with in situ low temperature and limited nutrients availability expected to further prolong hydrocarbons persistence at deep sea