Spatially resolved transcriptomics in immersive environments

Spatially resolved transcriptomics is an emerging class of high-throughput technologies that enable biologists to systematically investigate the expression of genes along with spatial information. Upon data acquisition, one major hurdle is the subsequent interpretation and visualization of the datasets acquired. To address this challenge, VR-Cardiomicsis presented, which is a novel data visualization system with interactive functionalities designed to help biologists interpret spatially resolved transcriptomic datasets. By implementing the system in two separate immersive environments, fish tank virtual reality (FTVR) and head-mounted display virtual reality (HMD-VR), biologists can interact with the data in novel ways not previously possible, such as visually exploring the gene expression patterns of an organ, and comparing genes based on their 3D expression profiles. Further, a biologist-driven use-case is presented, in which immersive environments facilitate biologists to explore and compare the heart expression profiles of different genes.

Fish hydrolysate supplemented diet improved feed efficiency and growth of coral trout (Plectropomus leopardus)

Fish hydrolysate contains hydrolyzed protein which comprised of peptides and free amino acids that are easily digested and absorbed by fish. This study aimed to determine the effectiveness of fish hydrolysate in improving feed efficiency and growth of coral trout. Five experimental diets were formulated to contain 47% protein and 12% lipid with different sources and levels of fish hydrolysate. Diet-1 and diet-2 were added with crustacean hydrolysate at 2% and 4% levels, respectively. Whereas diet-3 and diet-4 were supplemented with 2% and 4% of tuna hydrolysate. Diet-5 was formulated without fish hydrolysate supplementation (control). The diets were prepared as dry pellet with 3 mm diameter. Coral trout juveniles were produced in the hatchery of Institute for Mariculture Research and Fisheries Extension (IMRAFE), Gondol-Bali with the average body weight of 7.6 ± 0.9 g. The juveniles were maintained in 15 fiber tanks, 400L in volume, with a density of 40 fish/tank. The experiment was designed with a completely randomized design (CRD) with 5 treatments (different diets) and 3 replications for each treatment. The fish were fed the experimantal diets three times every day at satiation level for 84 days of feeding experiment. Results of the experiment showed that increased supplementation of fish hydrolysate from 2% to 4% in diet tended to improve fish growth performance. However, the best growth performance, in term of weight gain (WG) and specific growth rate (SGR), was obtained in fish fed diet supplemented with 4% crustacean hydrolysate. This growth performance was significantly higher than of the other treatments (P<0.05). The best feed efficiency (FE) and protein efficiency ratio (PER) were also obtained in fish fed diet supplemented with 4% crustacean hydrolysate. The results of the present study showed that supplementation of 4% crustacean hydrolysate in diet effectively improved the growth and feed efficiency of coral trout.

Inclusions of probiotics and prebiotics in diet for coral trout, Plectropomus leopardus nursery

Coral trout is one of marine fishery commodities with high economic value. This grouper fish has limited ability in the utilization of artificial feed. The aim of this study was to obtain information on the effectiveness of probiotics and prebiotics inclusions in diet to increase growth of coral trout. Fish was reared in fiber tanks 300-L with a density of 30 fish/tank. Fish weight and length were 3.7±0.1 g and 6.3±0.1 cm, respectively. Each tank was equipped with a flowing water system and aeration as a source of oxygen supply. The feed was formulated with 48% protein and 9% lipid. Treatments were inclusion of probiotics in diet (diet A), inclusion of mannan oligosaccharide/MOS (diet B), inclusion of probiotic + mannan oligosaccharide/MOS (diet C), and diet D as control. The study was conducted in a complete randomized design (CRD) with 4 treatments and 4 replications. Fish fed trial diets with a frequency of 3 times a day at satiation. The parameters observed were growth, feed efficiency, feed digestibility, bacteria density and immunity. The data obtained were analysed with anova followed by LSD. The results showed that diet with the probiotic content promoted better growth and feed efficiency of coral trout compared to the other treatments. The highest growth of coral trout fingerlings was obtained by fish fed diet A (added with probiotics) with a weight gain of 794.86%. While fish fed diet containing probiotics and prebiotic (diet C) showed a lower growth response (weight gain 641.26%) than those fed diet with probiotics and prebiotics (MOS) separately. Survival during the study for all treatments ranged from 90.00% to 93.33%.

Effects of a single-phase fasting period and subsequent re-feeding on compensatory growth, digestive enzyme activities, and antioxidant capacity of Sobaity (Sparidentex hasta) and Yellowfin seabream (Acanthopagrus latus)

An eight-week research was carried out to examine the influence of fasting (FA) and refeeding (RF) episodes on the compensatory growth responses (CGR) in sobaity (Sparidentex hasta, 10 g) and yellowfin seabreams (Acanthopagrus latus, 4.3 g) juveniles. Fish were fed with a commercial feed (contained 500 g kg−1 crude protein and 150 g kg−1 crude lipid) as following regimes: control (C, fish were fed three times every day), T1 (two weeks of feeding, one week of FA, and five weeks of RF), T2 (one week of feeding, two weeks of FA and five weeks of RF) and T3 (three weeks of FA and five weeks of RF). Two hundred and forty S. hasta juveniles were stocked into twelve 300-L tanks (20 fish tank−1), and 360 A. latus juveniles were allocated into other 12 tanks (30 fish tank−1). Each treatment was carried out in triplicates for each species, and each tank held only one of the species. The experiment was carried out for both species simultaneously. The weight and length of fish from the four groups were measured individually after the third week (after FA episode) and after eight weeks (after RF episode). After finishing the RF episode (eighth week), six fish of each tank were sacrificed with an overdose of 2-phenoxyethanol (1000 mg L−1), and the liver and the whole gut of the sacrificed fish were sampled, dissected, and then kept in a freezer (−80 °C) until further analyses. Survival rate was decreased in S. hasta juveniles with increasing the FA period mainly due to their cannibalistic behavior, which was triggered by starvation, but it was not affected in A. latus. The fasted groups in both species were significantly lost their weight after FA episodes. After five weeks of RF, S. hasta showed full compensatory growth response; meanwhile A. latus had a partial compensatory response (P<0.05). Hepatosomatic index value decreased after the FA period in both species, but it was restored to the normal level after RF phase. The activities of liver catalase, superoxide dismutase, glutathione-S-transferase, and glutathione peroxidase were increased in T2 group in S. hasta, but liver antioxidant enzymes were not affected in A. latus. In both species, the amount of the lipid peroxidation was significantly increased in the liver of fish groups subjected to T2 or T3 compared to T1 and control groups (P < 0.05). Liver alanine aminotransferase (ALT) and alkaline phosphatase (ALP) in S. hasta fasted for two weeks were higher than the other groups. The activities of trypsin, chymotrypsin, α-amylase, and lipase in S. hasta fasted for a week (T1) were higher than control. In addition, the activities of trypsin and chymotrypsin in A. latus fasted for two or three weeks were lower than C and T1 groups. The activity of ALP was increased with increasing FA period in both species. The findings of the present study showed that single-phase FA episodes reduce survival and induce oxidative stress in S. hasta juveniles; meanwhile A. latus juveniles did not show complete compensatory growth after RF episode.

Identification of bacteria species in aquaponics system using RapID system and 16S rRNA sequencing

Aquaponics is an integrated production system of aquaculture and hydroponics. Beneficial bacteria convert the ammonia and solid wastes produced by fish in the aquaculture component into essential nutrients for plant growth in hydroponics. The objective of the present study was to identify the bacteria community in the aquaponics system. This study was set by using barb fish and basils as organisms of cultivation. The fish tank (aquaculture) water was pumped into the treatment tank containing bio-ring functions as nitrifying bacteria by converting ammonia to nitrates. The nutrient-rich water from the treatment tank was then pumped into the hydroponics containing lightweight expanded clay aggregate (LECA) and plants. Water samples from the treatment tank and hydroponics were pipetted and transferred onto different agar plates for colony growth. Another set of soil growth plant was used for comparison in bacteria community between aquaponics and conventional land agriculture. RapID system and 16S rRNA gene were used to identify gram-negative and gram-positive bacteria respectively. The identified bacteria species from the hydroponics (LECA) and treatment tank (Bio-ring) were Moellerella wisconsensis, Achromobacter xylosoxidans, Bacillus cereus, Burkholderia pseudomallei and Bacillus sp. respectively whereas the bacteria species isolated from soil were Bacillus sp. and Bacillus pumilus.

Ammonia Monitoring in Aquarium for Fish Protection and Alert Generation

Fish is an important species that benefits human life in several ways. Fisheries are the best food provider and also aquarium is used at home and public places which becomes decoration cum mind relaxing item. There are lot of attack to fish which goes unnoticed. Large number fish die due to the ammonia (NH3) produced as a by product of protea metabolism and is the most common waste product of fish. There is a given level of ammonia that becomes dangerous and leads to death of the fish. One of the solutions to this issue is to monitor ammonia in aquarium for fish protection and alert generation. A prototype is developed for monitoring the ammonia in the fish tank using Intern is used for protection and alert generation. Ammonia is monitored by measuring pH values. In this project a prototype model is developed that is connected through Internet of Things (IoT) such that it can be monitored in a remote station through mobile app. The prototype model includes an LCD display for local readout. The project will reach the benefit to many engaged in fisheries industry and also who are using Aquarium.

Evaluation of anaerobic and anoxic reactors installed in serial to treat fish tank effluent

Effluent from a fish tank with Nile tilapia (Oreochromis niloticus) was treated in a system of two parallel fixed-bed anaerobic reactors followed by a suspended stirred, anoxic reactor for solids, organic matter and nitrogen removal. Microbial community structure was compared between the reactors and an enriched anammox culture originated from anaerobic sludge by using the PCR (Polymerase Chain Reaction) and DGGE (Denaturing Gradient Gel Electrophoresis) techniques. DGGE analysis revealed three large microbial clusters, namely, the biomass in the inoculum, the biomass growing in the reactors, and the enriched anammox culture. The similarity between the microbial community recovered from the anaerobic reactors and the anammox community was considered low (32.7%), suggesting differentiation of the bacterial community as a function of the selection of specific anammox groups. The last step in the anoxic reactor had worsened the effluent quality. The potential of organic matter and ammonia removal in a single anaerobic reactor was demonstrated.