Digital PCR-based evaluation of nucleic acid extraction kit performance for the co-purification of cell-free DNA and RNA.

Background: Blood plasma, one of the most studied liquid biopsies, contains various molecules that have biomarker potential for cancer detection, including cell-free DNA (cfDNA) and cell-free RNA (cfRNA). As the vast majority of cell-free nucleic acids in circulation are non-cancerous, a laboratory workflow with a high detection sensitivity of tumor-derived nucleic acids is a prerequisite for precision oncology. One way to meet this requirement is by the combined analysis of cfDNA and cfRNA from the same liquid biopsy sample.

mRNA Capture Sequencing and RT-qPCR for the Detection of Pathognomonic, Novel, and Secondary Fusion Transcripts in FFPE Tissue: A Sarcoma Showcase.

We assess the performance of mRNA capture sequencing to identify fusion transcripts in FFPE tissue of different sarcoma types, followed by RT-qPCR confirmation. To validate our workflow, six positive control tumors with a specific chromosomal rearrangement were analyzed using the TruSight RNA Pan-Cancer Panel. Fusion transcript calling by FusionCatcher confirmed these aberrations and enabled the identification of both fusion gene partners and breakpoints.

Freshwater fish biodiversity restoration in floodplain rivers requires connectivity and habitat heterogeneity at multiple spatial scales.

With a sixth mass extinction looming and freshwater biodiversity declining at unprecedented rates, evaluating ecological efficacy of river restoration efforts is critical in combatting global biodiversity loss. Here, we present a comprehensive study of the functioning for fishes of 46 river restoration projects in the river Rhine, one of the world's most heavily engineered lowland rivers. Floodplains with permanent, either one- or two-sided lateral connectivity to the main channel, favour total fish abundance, and are essential as nursery areas for riverine fishes.

30 years of large river restoration: How long do restored floodplain channels remain suitable for targeted rheophilic fishes in the lower river Rhine?

The ecological efficacy of river restoration projects may change over time, resulting in the loss of their ecological function for targeted species. The goal of this study was to evaluate the rheophilic nursery function of restored floodplain channels over time, by analysing 30 years of monitoring data from 12 restoration projects in the lower river Rhine. We hypothesised that the nursery function would change over time, caused by the combined effects of decreasing flow conditions and succession processes affecting habitat heterogeneity.

Integration of Algae to Improve Nitrogenous Waste Management in Recirculating Aquaculture Systems: A Review.

This review investigates the performance and the feasibility of the integration of an algal reactor in recirculating aquaculture systems (RAS). The number of studies related to this topic is limited, despite the apparent benefit of algae that can assimilate part of the inorganic waste in RAS. We identified two major challenges related to algal integration in RAS: first, the practical feasibility for improving nitrogen removal performance by algae in RAS; second, the economic feasibility of integrating an algal reactor in RAS.

Resistance and resilience of small-scale recirculating aquaculture systems (RAS) with or without algae to pH perturbation.

The experimental set-up of this study mimicked recirculating aquaculture systems (RAS) where water quality parameters such as dissolved oxygen, pH, temperature, and turbidity were controlled and wastes produced by fish and feeding were converted to inorganic forms. A key process in the RAS was the conversion of ammonia to nitrite and nitrite to nitrate through nitrification. It was hypothesized that algae inclusion in RAS would improve the ammonia removal from the water; thereby improving RAS water quality and stability.

Interactive effects of oxygen, carbon dioxide and flow on photosynthesis and respiration in the scleractinian coral .

Rates of dark respiration and net photosynthesis were measured for six replicate clonal fragments of the stony coral (Linnaeus 1767), which were incubated under 12 different combinations of dissolved oxygen (20%, 100% and 150% saturation), dissolved carbon dioxide (9.5 and 19.1 µmol l) and water flow (1-1.

The impact of rearing environment on the development of gut microbiota in tilapia larvae.

This study explores the effect of rearing environment on water bacterial communities (BC) and the association with those present in the gut of Nile tilapia larvae (Oreochromis niloticus, Linnaeus) grown in either recirculating or active suspension systems. 454 pyrosequencing of PCR-amplified 16S rRNA gene fragments was applied to characterize the composition of water, feed and gut bacteria communities. Observed changes in water BC over time and differences in water BCs between systems were highly correlated with corresponding water physico-chemical properties.

Exploring the climate change concerns of striped catfish producers in the Mekong Delta, Vietnam.

This study investigated the perceptions on and adaptations to climate change impacts of 235 pangasius farmers in the Mekong Delta, Vietnam. Data were collected using semi-structured household surveys in six provinces, from three regions along the Mekong river branches. A Chi-Square test was used to determine the association between variables, and a logit regression model was employed to identify factors correlated with farmer's perception and adaptation.

Horizontal transmission dynamics of White spot syndrome virus by cohabitation trials in juvenile Penaeus monodon and P. vannamei.

White spot syndrome virus (WSSV), a rod-shaped double-stranded DNA virus, is an infectious agent causing fatal disease in shrimp farming around the globe. Within shrimp populations WSSV is transmitted very fast, however, the modes and dynamics of transmission of this virus are not well understood. In the current study the dynamics of disease transmission of WSSV were investigated in small, closed populations of Penaeus monodon and Penaeus vannamei.

The colonization dynamics of the gut microbiota in tilapia larvae.

The gut microbiota of fish larvae evolves fast towards a complex community. Both host and environment affect the development of the gut microbiota; however, the relative importance of both is poorly understood. Determining specific changes in gut microbial populations in response to a change in an environmental factor is very complicated.

Transmission of white spot syndrome virus (WSSV) from Dendronereis spp. (Peters) (Nereididae) to penaeid shrimp.

Dendronereis spp. (Peters) (Nereididae) is a common polychaete in shrimp ponds built on intertidal land and is natural food for shrimp in traditionally managed ponds in Indonesia. White spot syndrome virus (WSSV), an important viral pathogen of the shrimp, can replicate in this polychaete (Desrina et al.

Simulated impacts of climate change on current farming locations of striped catfish (Pangasianodon hypophthalmus; Sauvage) in the Mekong Delta, Vietnam.

In Vietnam, culturing striped catfish makes an important contribution to the Mekong Delta's economy. Water level rise during rainy season and salt intrusion during dry season affect the water exchange and quality for this culture. Sea level rise as a consequence of climate change will worsen these influences.

Oxygen consumption constrains food intake in fish fed diets varying in essential amino acid composition.

Compromisation of food intake when confronted with diets deficient in essential amino acids is a common response of fish and other animals, but the underlying physiological factors are poorly understood. We hypothesize that oxygen consumption of fish is a possible physiological factor constraining food intake. To verify, we assessed the food intake and oxygen consumption of rainbow trout fed to satiation with diets which differed in essential amino acid (methionine and lysine) compositions: a balanced vs.

Replication of white spot syndrome virus (WSSV) in the polychaete Dendronereis spp.

This study investigated whether WSSV replicates in naturally infected Dendronereis spp., a common polychaete (Nereididae) species in shrimp ponds in Indonesia. To detect WSSV replication, (i) immunohistochemistry (IHC) using a monoclonal antibody against WSSV VP28 protein and (ii) nested RT-PCR using specific primers set for the vp28 gene to detect WSSV-specific mRNA were applied.

Dietary electrolyte balance affects the nutrient digestibility and maintenance energy expenditure of Nile tilapia.

Acid-base disturbances caused by environmental factors and physiological events including feeding have been well documented in several fish species, but little is known about the impact of dietary electrolyte balance (dEB). In the present study, we investigated the effect of feeding diets differing in dEB (-100, 200, 500 or 800 mEq/kg diet) on the growth, nutrient digestibility and energy balance of Nile tilapia. After 5 weeks on the test diet, the growth of the fish was linearly affected by the dEB levels (P< 0·001), with the lowest growth being observed in the fish fed the 800 dEB diet.

Voluntary feed intake in rainbow trout is regulated by diet-induced differences in oxygen use.

This study investigated the hypothesis that the voluntary feed intake in fish is regulated by diet-induced differences in oxygen use. Four diets were prepared with a similar digestible protein:digestible energy ratio (18 mg/kJ), but which differed in the composition of nonprotein energy source. This replacement of fat (F) by starch (S) was intended to create a diet-induced difference in oxygen use (per unit of feed): diets F30-S70, F50-S50, F65-S35, and F80-S20 with digestible fat providing 28, 49, 65, and 81% of the nonprotein digestible energy (NPDE), respectively.

Survival of heterophyid metacercaria in common carp (Cyprinus carpio).

Heterophyidae are small intestinal trematodes that infect vertebrates worldwide. Common carp (Cyprinus carpio) is one of the most preferred freshwater fish species by consumers in Asia, the region where fish-borne trematodes like Heterophyidae are most prevalent. How long Heterophyidae survive in common carp is unknown.

Isoenergetic replacement of fat by starch in diets for African catfish (Clarias gariepinus): effect on water fluxes in the gastro intestinal tract.

The effect of an isoenergetic replacement of dietary fat by starch, on chyme characteristics and water fluxes in the gastro intestinal tract (GIT) was assessed. Adult African catfish (Clarias gariepinus) were fed a starch (SD) or fat (FD) diet and groups of fish were dissected at 2, 5 and 8 h after the consumption of a single meal. Chyme was collected quantitatively and was analysed for osmolality and dry matter (DM) content.

Transmission of fish-borne zoonotic trematodes (Heterophyidae) to common carp (Cyprinus carpio) is independent of density of fish and trematodes.

Fish-borne zoonotic trematodes (FZTs) can cause major human health problems. The aim of this study was to quantify the transmission of parapleurolophocercous cercariae to common carp (Cyprinus carpio) and to study the effect of the density of cercariae and the density of fish on transmission with respect to the volume of water and surface area of the bottom. Fish were kept individually either as controls (n= 91) or were exposed to 250 cercariae in tubes with a volume of 25, 50, 100, 250 or 500 ml water (n= 190) with a surface area of 4, 12, 21, 30 or 49 cm2 (n= 195).

Epizoic acoelomorph flatworms impair zooplankton feeding by the scleractinian coral Galaxea fascicularis.

Many scleractinian coral species host epizoic acoelomorph flatworms, both in aquaculture and in situ. These symbiotic flatworms may impair coral growth and health through light-shading, mucus removal and disruption of heterotrophic feeding. To quantify the effect of epizoic flatworms on zooplankton feeding, we conducted video analyses of single polyps of Galaxea fascicularis (Linnaeus 1767) grazing on Artemia nauplii in the presence and absence of symbiotic flatworms.

Oxygen and heterotrophy affect calcification of the scleractinian coral Galaxea fascicularis.

Heterotrophy is known to stimulate calcification of scleractinian corals, possibly through enhanced organic matrix synthesis and photosynthesis, and increased supply of metabolic DIC. In contrast to the positive long-term effects of heterotrophy, inhibition of calcification has been observed during feeding, which may be explained by a temporal oxygen limitation in coral tissue. To test this hypothesis, we measured the short-term effects of zooplankton feeding on light and dark calcification rates of the scleractinian coral Galaxea fascicularis (n=4) at oxygen saturation levels ranging from 13 to 280%.

Constraints on energy intake in fish: the link between diet composition, energy metabolism, and energy intake in rainbow trout.

The hypothesis was tested that fish fed to satiation with iso-energetic diets differing in macronutrient composition will have different digestible energy intakes (DEI) but similar total heat production. Four iso-energetic diets (2 × 2 factorial design) were formulated having a contrast in i) the ratio of protein to energy (P/E): high (H(P/E)) vs. low (L(P/E)) and ii) the type of non-protein energy (NPE) source: fat vs.