Artificial intelligence used in genome analysis studies

Next Generation Sequencing (NGS) or deep sequencing technology enables parallel reading of multiple individual DNA fragments, thereby enabling the identification of millions of base pairs in several hours. Recent research has clearly shown that machine learning technologies can efficiently analyse large sets of genomic data and help to identify novel gene functions and regulation regions. A deep artificial neural network consists of a group of artificial neurons that mimic the properties of living neurons. These mathematical models, termed Artificial Neural Networks (ANN), can be used to solve artificial intelligence engineering problems in several different technological fields (e.g., biology, genomics, proteomics, and metabolomics). In practical terms, neural networks are non-linear statistical structures that are organized as modelling tools and are used to simulate complex genomic relationships between inputs and outputs. To date, Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNN) have been demonstrated to be the best tools for improving performance in problem solving tasks within the genomic field

Effects of dietary energy content on the voluntary feed intake and blood parameters of sea bass (Dicentrarchus labrax L.)

Energy and protein requirements of sea bass for maximum growth and fasting energy requirements were determined byusing three diets containing increasing DE levels and two fish weights.Five hundred and sixteen sea bass were divided in two body weight (BW) classes (A: 67.7 ± 0.85g and B: 128.6 ± 0.88g,mean ± SD live weight) and randomly distributed among 24 tanks. They were fed for 12 weeks on three isoproteic dietscharacterized by different levels of digestible energy (DE): low energy (LE), 18.6; medium energy (ME), 19.7; and highenergy (HE), 22.6 MJ kg-1 dry matter (DM). The entire trial lasted 113 d and was divided into two periods: a feeding trialof 83 d and a fasting trial of 30 d. Specific growth rates decreased in fish fed on the HE diet (P < 0.05), but only in fishweighing 68 g. Voluntary feed intakes and feed conversion ratios were inversely related to dietary energy contents in bothweight classes. During the starvation trial, body depletion increased (P<0.05) in fish fed on high-energy diets during thefeeding experiment. The gross energy requirements (per day) for maximum growth were 320 and 221 kJ kg-1 BW for fishweighing 68 g and 128 g, respectively. Fasting metabolisms were 60.6 and 54.1 kJ kg–0.83 BW per day for fish weighing 68gand 128g, respectively.It is concluded that growth performance of sea bass appear to be dependent on digestible dietary energy. Gross energyintake, net energy (production) and maintenance requirements of fish were not influenced by dietary treatments

Numerical simulation of electro-fishing in seawater

We evaluated the feasibility of an electro-fishing system using numerical simulations for laboratory tanks and the open sea. A non-homogeneous bi-dimensional electric-field model for water and fish based on discrete formulation of electro-magnetic field equations was developed using GAME (geometric approach for Maxwell equations) software. Current densities (μA/cm2) and voltage differences (V/m) were calculated for a fixed shape and spatial geometry of electrodes (one circular anode central to two symmetric linear cathodes 10 m distant from each other). Voltage gradients inside the fish and close to the body (head–tail potential difference and mean, maximum and minimum field modules) were determined. Tank and open sea environments were numerically described for single fish 10 cm or 30 cm long and for groups of 30 fish 10 cm long. In the open sea, a tension of 90 V at the electrodes and a water conductibility of 5 S/m resulted in an area of fish attraction (voltage gradient >10 V/m) of about 30 m2. Fish in the open sea and in groups had greater internal voltage differences than did fish in tanks and single fish

alternative plant protein sources in sea bass diets

A control diet (C) containing animal protein (mainly fish meal) was compared with 6 experimental diets containing different plant proteins (soybean meal, SM; rapeseed meal, RM; potato protein concentrate, PPC and a mix of the three vegetable protein sources, M). The plant protein replaced either 25 (1) or 50 (2)% of the animal protein with the exception of diet RM2 where the substitution rate was lowered to 35%, and in diet M where 55% of the total protein given was replaced in equal amounts by the three plant proteins. For the growth trial, which lasted 97 days, 528 European sea bass (initial live weight 107 ± 0,06g), distributed among 24 fibreglass tanks with three replicates per treatment, were used. The pelleted feed was distributed 5 times per day using an automatic dispenser. Energy, crude protein and crude fat digestibility values for fish meal and soybean meal were similar and not statistically different while the values for rapeseed meal and potato protein concentrate were significantly lower. Digestive utilization for NFE was higher in fish meal and decreased significant- ly in soybean meal, rapeseed meal and even more noticeably in potato protein concentrate. Diet digestibility values showed a similar trend with a clear worsening effect at the higher inclusion rates used. Diet M gave digestibility coefficients lower than those observed with diets C, SM1, SM2, RS1and RS2and higher than those of diets PPC1and PPC2. Fish fed a diet in which 25% of the total protein was replaced by soybean had similar performances to those of the control group. On the other hand, sea bass fed diets SM2, RS1, RS2and M had lower growth rates and worse feed utilization than those observed with the control. Finally, specific growth rates and food conversion efficiency in sea bass fed diets containing potato protein concentrate were poor because of the low palatability. These results show that soybean meal can substitute up to 25% of the total protein of the diet without any negative effect on sea bass performance

Effects of electro-fishing on galvano-taxis and carcass quality characteristics in sea bass (Dicentrarchus labrax)

The aim of this study was to investigate the effects of electro-fishing in sea water. We evaluated the feasibility of an electro-fishing system using numerical simulations for laboratory tanks and the open sea and performing a laboratory experiment. A non-homogeneous bi-dimensional electric-field model for marine water and fish based on discrete formulation of electro-magnetic field equations was developed using GAME (geometric approach for Maxwell equations) software. Voltage gradients inside the fish and close to the body were determined. Re- sults showed that fish in the open sea and in groups had greater internal voltage differences than did fish in tanks and single fish. Sea bass (length:10 and 30 cm) were exposed in laboratory tanks to pulsed direct current (PDC), 25-125 Hz and duty cycle (5-40%). We measured the electro-taxis and tetanus thresholds after electrical exposure. It is significant that these values decreased with increasing the size of fish. No differences were found after electro-fishing on overall appearance, internal and external haemorrhage, standard freshness scoring techniques and carcass quality characteristic

Growth parameters in European sea bass (Dicentrarchus labraxL.): effects of live weight and water temperature

The voluntary feed intake (VFI) and growth rate of sea bass were studied for 147 days, based on different starting live weights, under natural photoperiods and varied water temperatures. Sea bass (n = 720) were divided into five weight classes (60-70, 90-110, 130-150, 160-180 and 230-250 g) and distributed among 20 tanks. Seven different water tem- peratures were compared: 13, 16, 19, 22, 25, 28 and 31 °C. A commercial extruded diet (N x 6.25, 43.7% DM; crude fat, 25.7% DM) was used. The trial was performed in a closed-circuit plant, with a daily water turnover rate of 10%. Each tank was fitted with an apparatus for collecting the uneaten food. Automatic feeders distributed equal amounts of food for ten meals per day. The daily food allowance was adjusted, based on fish biomass, to permit ad libitum feeding and to leave approximately 20% uneaten. Fish were exposed to natural photoperiod (March-July). Non-linear regression equations were used to calculate the best-fitting curves for the data