Quantifying the Detection Sensitivity and Precision of qPCR and ddPCR Mechanisms for eDNA Samples.

Environmental DNA (eDNA) detection employing quantitative PCR (qPCR) and droplet digital PCR (ddPCR) offers a non-invasive and efficient approach for monitoring aquatic organisms. Accurate and sensitive quantification of eDNA is crucial for tracking rare and invasive species and understanding the biodiversity abundance and distribution of aquatic organisms. This study compares the sensitivity and quantification precision of qPCR and ddPCR for eDNA surveys through Bayesian inference using latent parameters from both known concentration (standards) and environmental samples across three teleost fish species assays.

Estrogen contributes to sex differences in M2a macrophages during multi-walled carbon nanotube-induced respiratory inflammation.

Lung diseases characterized by type 2 inflammation are reported to occur with a female bias in prevalence/severity in both humans and mice. This includes previous work examining multi-walled carbon nanotube (MWCNT)-induced eosinophilic inflammation, in which a more exaggerated M2a phenotype was observed in female alveolar macrophages (AMs) compared to males. The mechanisms responsible for this sex difference in AM phenotype are still unclear, but estrogen receptor (ER) signaling is a likely contributor.

Self-replicating murine ex vivo cultured alveolar macrophages as a model for toxicological studies of particle-induced inflammation.

Alveolar macrophages (AM) are integral to maintaining homeostasis within the lungs following exposure to inhaled particles. However, due to the high animal number requirements for in vitro research with primary AM, there remains a need for validated cell models that replicate alveolar macrophages in form and function to better understand the mechanisms that contribute to particle-induced inflammation and disease. A novel, easily adaptable, culture model that facilitates the continued expansion of murine alveolar macrophages for several months, termed murine ex vivo cultured AM (mexAM) has been recently described.

Nanoparticle-Induced Airway Eosinophilia Is Independent of ILC2 Signaling but Associated With Sex Differences in Macrophage Phenotype Development.

The majority of lung diseases occur with a sex bias in terms of prevalence and/or severity. Previous studies demonstrated that, compared with males, female mice develop greater eosinophilic inflammation in the airways after multiwalled carbon nanotube (MWCNT) exposure. However, the mechanism by which this sex bias occurs is unknown.

Going to extremes - a metagenomic journey into the dark matter of life.

The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms.

Quantitative molecular detection of larval Atlantic herring (Clupea harengus) in stomach contents of Atlantic mackerel (Scomber scombrus) marks regions of predation pressure.

Mortality rates in the early life-history stages of fishes are generally high yet identifying the causes remain unclear. Faltering recruitment rates of Atlantic herring (Clupea harengus) in the Norwegian Sea indicate a need to identify which mortality factors influence larval herring survival. Previous research suggests that increased predation pressure by Atlantic mackerel (Scomber scombrus) may contribute to the disconnect between spawning stock biomass and recruitment.

The role of sex in particle-induced inflammation and injury.

The use of engineered nanomaterials within various applications such as medicine, electronics, and cosmetics has been steadily increasing; therefore, the rate of occupational and environmental exposures has also increased. Inhalation is an important route of exposure to nanomaterials and has been shown to cause various respiratory diseases in animal models. Human lung disease frequently presents with a sex/gender-bias in prevalence or severity, but investigation of potential sex-differences in the adverse health outcomes associated with nanoparticle inhalation is greatly lacking.

Sex differences in the inflammatory immune response to multi-walled carbon nanotubes and crystalline silica.

Respiratory disease is a leading cause of death and disability worldwide. These diseases frequently present with a sex bias in occurrence and severity, yet the mechanisms responsible for these sex biases is a critically understudied area of basic research. Male and female C57BL/6 mice were exposed to multi-walled carbon nanotubes (MWCNTs) or crystalline silica (cSiO) via oropharyngeal aspiration.

Multiwalled Carbon Nanotubes of Varying Size Lead to DNA Methylation Changes That Correspond to Lung Inflammation and Injury in a Mouse Model.

Diversity in physicochemical properties of engineered multiwalled carbon nanotubes (MWCNTs) increases the complexity involved in interpreting toxicity studies of these materials. Studies indicate that epigenetic changes could be at least partially involved in MWCNTs-induced pro-inflammatory and fibrotic lung pathology. Therefore, we examined distinct methylation changes in response to MWCNTs of varied sizes to identify potential epigenetic biomarkers of MWCNTs exposure and disease progression.

The potential of sedimentary ancient DNA for reconstructing past sea ice evolution.

Sea ice is a crucial component of the Arctic climate system, yet the tools to document the evolution of sea ice conditions on historical and geological time scales are few and have limitations. Such records are essential for documenting and understanding the natural variations in Arctic sea ice extent. Here we explore sedimentary ancient DNA (aDNA), as a novel tool that unlocks and exploits the genetic (eukaryote) biodiversity preserved in marine sediments specifically for past sea ice reconstructions.

Seasonality Drives Microbial Community Structure, Shaping both Eukaryotic and Prokaryotic Host⁻Viral Relationships in an Arctic Marine Ecosystem.

The Arctic marine environment experiences dramatic seasonal changes in light and nutrient availability. To investigate the influence of seasonality on Arctic marine virus communities, five research cruises to the west and north of Svalbard were conducted across one calendar year, collecting water from the surface to 1000 m in depth. We employed metabarcoding analysis of major capsid protein and genes in order to investigate T4-like myoviruses and large dsDNA viruses infecting prokaryotic and eukaryotic picophytoplankton, respectively.

Von Willebrand factor deficiency reduces liver fibrosis in mice.

Liver diseases are associated with complex changes in the hemostatic system and elevated levels of the platelet-adhesive protein Von Willebrand factor (VWF) are reported in patients with acute and chronic liver damage. Although elevated levels of VWF are associated with fibrosis in the general population, the role of VWF in acute and chronic liver injury has not been examined in depth in experimental settings. We tested the hypothesis that VWF deficiency inhibits experimental liver injury and fibrosis.

Trichloroethylene Exposure Reduces Liver Injury in a Mouse Model of Primary Biliary Cholangitis.

Trichloroethylene (TCE) is a persistent environmental contaminant proposed to contribute to autoimmune disease. Experimental studies in lupus-prone MRL+/+ mice have suggested that TCE exposure can trigger autoimmune hepatitis. The vast majority of studies examining the connection between TCE and autoimmunity utilize this model, and the impact of TCE exposure in other established models of autoimmune liver disease is not known.

Fibrin(ogen) drives repair after acetaminophen-induced liver injury via leukocyte αβ integrin-dependent upregulation of Mmp12.

Background & Aims: Acetaminophen (APAP)-induced liver injury is coupled with activation of the blood coagulation cascade and fibrin(ogen) accumulation within APAP-injured livers of experimental mice. We sought to define the role of fibrin(ogen) deposition in APAP-induced liver injury and repair.

Methods: Wild-type, fibrinogen-deficient mice, mutant mice with fibrin(ogen) incapable of binding leukocyte αβ integrin (Fibγ mice) and matrix metalloproteinase 12 (Mmp12)-deficient mice were fasted, injected with 300mg/kg APAP i.

Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities.

In order to characterize copepod feeding in relation to microbial plankton community dynamics, we combined metabarcoding and metabolome analyses during a 22-day seawater mesocosm experiment. Nutrient amendment of mesocosms promoted the development of haptophyte (Phaeocystis pouchetii)- and diatom (Skeletonema marinoi)-dominated plankton communities in mesocosms, in which Calanus sp. copepods were incubated for 24 h in flow-through chambers to allow access to prey particles (<500 μm).

Dose-dependent effects of alpha-naphthylisothiocyanate disconnect biliary fibrosis from hepatocellular necrosis.

Exposure of rodents to the xenobiotic α-naphthylisothiocyanate (ANIT) is an established model of experimental intrahepatic bile duct injury. Administration of ANIT to mice causes neutrophil-mediated hepatocellular necrosis. Prolonged exposure of mice to ANIT also produces bile duct hyperplasia and liver fibrosis.

Inhibition of PAR-4 and P2Y12 receptor-mediated platelet activation produces distinct hepatic pathologies in experimental xenobiotic-induced cholestatic liver disease.

Emerging evidence supports a protective effect of platelets in experimental cholestatic liver injury and cholangiofibrosis. Coagulation-mediated platelet activation has been shown to inhibit experimental chronic cholestatic liver necrosis and biliary fibrosis. This occurs through thrombin-mediated activation of protease activated receptor-4 (PAR-4) in mice.

Fibrin deposition following bile duct injury limits fibrosis through an αMβ2-dependent mechanism.

Coagulation cascade activation and fibrin deposits have been implicated or observed in diverse forms of liver damage. Given that fibrin amplifies pathological inflammation in several diseases through the integrin receptor αMβ2, we tested the hypothesis that disruption of the fibrin(ogen)-αMβ2 interaction in Fibγ(390-396A) mice would reduce hepatic inflammation and fibrosis in an experimental setting of chemical liver injury. Contrary to our hypothesis, α-naphthylisothiocyanate (ANIT)-induced liver fibrosis increased in Fibγ(390-396A) mice, whereas inflammatory cytokine expression and hepatic necrosis were similar to ANIT-challenged wild-type (WT) mice.

Top-down and bottom-up control on bacterial diversity in a western Norwegian deep-silled fjord.

We investigated the relationship between viruses and co-occurring bacterial communities in the Sognefjord, a deep-silled fjord in Western Norway. A combination of flow cytometry and automated ribosomal intergenic spacer analysis (ARISA) was used to assess prokaryote and viral abundances, and bacterial diversity and community composition, respectively, in depth profiles and at two different sampling seasons (November and May). With one exception, bacterial diversity did not vary between samples regardless of depth or season.

Virus infection of and implicates evolutionary conservation of programmed cell death induction in marine haptophyte-virus interactions.

The mechanisms by which phytoplankton cope with stressors in the marine environment are neither fully characterized nor understood. As viruses are the most abundant entities in the global ocean and represent a strong top-down regulator of phytoplankton abundance and diversity, we sought to characterize the cellular response of two marine haptophytes to virus infection in order to gain more knowledge about the nature and diversity of microalgal responses to this chronic biotic stressor. We infected laboratory cultures of the haptophytes and with CeV-01B or PpV-01B dsDNA viruses, respectively, and assessed the extent to which host cellular responses resemble programmed cell death (PCD) through the activation of diagnostic molecular and biochemical markers.

Norwegian deep-water coral reefs: cultivation and molecular analysis of planktonic microbial communities.

Deep-sea coral reefs do not receive sunlight and depend on plankton. Little is known about the plankton composition at such reefs, even though they constitute habitats for many invertebrates and fish. We investigated plankton communities from three reefs at 260-350 m depth at hydrocarbon fields off the mid-Norwegian coast using a combination of cultivation and small subunit (SSU) rRNA gene and transcript sequencing.

Effect of increased pCO(2) on bacterial assemblage shifts in response to glucose addition in Fram Strait seawater mesocosms.

Ocean acidification may stimulate primary production through increased availability of inorganic carbon in the photic zone, which may in turn change the biogenic flux of dissolved organic carbon (DOC) and the growth potential of heterotrophic bacteria. To investigate the effects of ocean acidification on marine bacterial assemblages, a two-by-three factorial mescosom experiment was conducted using surface sea water from the East Greenland Current in Fram Strait. Pyrosequencing of the V1-V2 region of bacterial 16S ribosomal RNA genes was used to investigate differences in the endpoint (Day 9) composition of bacterial assemblages in mineral nutrient-replete mesocosms amended with glucose (0 μM, 5.

Sexual isolation in Acinetobacter baylyi is locus-specific and varies 10,000-fold over the genome.

Naturally transformable bacteria acquire chromosomal DNA from related species at lower frequencies than from cognate DNA sources. To determine how genome location affects heterogamic transformation in bacteria, we inserted an nptI marker into random chromosome locations in 19 different strains of the Acinetobacter genus (>24% divergent at the mutS/trpE loci). DNA from a total of 95 nptI-tagged isolates was used to transform the recipient Acinetobacter baylyi strain ADP1.

An assessment of the potential of herbivorous insect gut bacteria to develop competence for natural transformation.

Whereas the capability of DNA uptake has been well established for numerous species and strains of bacteria grown in vitro, the broader distribution of natural transformability within bacterial communities remains largely unexplored. Here, we investigate the ability of bacterial isolates from the gut of grass grub larvae (Costelytra zealandica (White); Coleoptera: Scarabaeidae) to develop natural genetic competence in vitro. A total of 37 mostly species-divergent strains isolated from the gut of grass grub larvae were selected for spontaneous rifampicin-resistance.

Experimental methods for assaying natural transformation and inferring horizontal gene transfer.

The observation of frequent lateral acquisitions of genes in sequenced bacterial genomes has spurred experimental investigations to elucidate the factors governing ongoing gene transfer processes in bacteria. The uptake of naked DNA by natural transformation is known to occur in a wide range of bacterial species and in some archaea. We describe a series of protocols designed to dissect the natural genetic transformability of individual bacterial strains under conditions that progress from standard in vitro conditions to purely in situ, or natural, conditions.