DiMo: discovery of microRNA motifs using deep learning and motif embedding.

MicroRNAs are small regulatory RNAs that decrease gene expression after transcription in various biological disciplines. In bioinformatics, identifying microRNAs and predicting their functionalities is critical. Finding motifs is one of the most well-known and important methods for identifying the functionalities of microRNAs. Several motif discovery techniques have been proposed, some of which rely on artificial intelligence-based techniques. However, in the case of few or no training data, their accuracy is low. In this research, we propose a new computational approach, called DiMo, for identifying motifs in microRNAs and generally macromolecules of small length. We employ word embedding techniques and deep learning models to improve the accuracy of motif discovery results. Also, we rely on transfer learning models to pre-train a model and use it in cases of a lack of (enough) training data. We compare our approach with five state-of-the-art works using three real-world datasets. DiMo outperforms the selected related works in terms of precision, recall, accuracy and f1-score.

Trade-off between feed efficiency and immunity in specialized high-performing chickens.

Based on resource allocation theory, ignoring importance of immunity, and focus on growth and feed efficiency (FE) traits in breeding plans may lead to serious weakness in immune system performance. However, in poultry the adverse effects of selection for FE on the immune system are unclear. Therefore, an experiment was conducted to study the trade-off between FE and immunity using a total of 180 high-performing specialized male chickens from a commercial broiler line which were selected over 30 generations for growth (body weight gain, BWG) and FE (residual feed intake, RFI). Birds were reared for 42 d and 5 FE-related traits of the birds in the last week were considered including daily feed intake (DFI), feed conversion ratio (FCR), residual feed intake (RFI), residual BW gain (RG), and residual intake and gain (RIG). For all 180 chickens, immune system performance including humoral immune response, cell-mediated immunity (CMI), and the activity of lysozyme enzyme (L. activity) as innate immunity was measured. After ascending sort of each FE records, 10% of higher records (H-FE: N = 18) and 10% of lower records (L-FE: N = 18) were determined, and immunity between L-FE and H-FE groups were compared. Moreover, L-BWG and H-BWG were analyzed because BWG is one of components in the FE formula. Performance of the immune system was not statistically different for CMI in none of the studied FE groups. Moreover, high and low groups for DFI and BWG were not different regarding the immunity of the birds. Antibody titers against Newcastle disease virus (NDV) were different between low and high groups of FCR, RG, and RIG. Likewise, SRBC-derived antibodies were significantly different between RFI groups. Rather than humoral immunity, RIG had adversely effect on the innate immunity. Results of the present study showed that although RIG is a more appropriate indicator for FE, choosing for high RIG can weaken the performance of the both humoral and innate immune systems, while RFI had fewer adverse effects.

Direct and maternal genetic effects for preinflection point growth traits and humoral immunity in quail.

Early growth traits in quails are considered as the growth performances before the inflection point which are genetically different from body weights (BW) at later stages. Moreover, in addition to growth performance, humoral immunity is moderately heritable and is considered in some breeding programs. However, estimating the direct genetic, particularly the maternal genetic correlations between growth and immunity in quail, are not studied sufficiently, which were the aims of the present study. The quails' BW were recorded at hatch (BW0) to 25 d of age with a 5-d interval and body weight gains (BWG) were measured as average growth performance of the birds in a 5-d period. Antibody titer against Newcastle disease virus (IgN) was measured through the hemagglutination inhibition (HI) test. For titration of anti-SRBC antibodies (IgY and IgM), a hemagglutination microtiter assay was used. In general, growth records in 4,181 birds and humoral immune responses in 1,023 birds were assigned to the study. The genetic parameters were estimated by single-trait analysis via Gibb's sampling. After finding the best model for each trait, multi-trait analysis was done to estimate the direct and maternal genetic correlations. Direct heritabilities (h2) were estimated to be moderate for BW (0.481-0.551) and BWG (0.524-0.557), while h2 for immune responses were low (0.035-0.079). Maternal environmental effect (c2) was only significant for BW0, BW5, and BWG0-5. Maternal heritabilities (m2) for BW and BWG were all lower than corresponding h2, ranging from 0.072 (BW25) to 0.098 (BW0). The m2 for IgN (0.098) was more than 2.5 times greater than h2 (0.040) for this trait. Direct (ra) and maternal (rm) genetic correlations between IgN-BW, IgY-BW, and IgY-BWG were negative, while ra and rm for IgM-BW, IgN-BWG, and IgM-BWG were positive. The ra between humoral immune responses were low to moderate and rm was significant only for IgY-IgM (0.339). Given positive genetic correlations in BWG-IgN and BWG-IgM as well as positive genetic correlations between both IgN and IgM with IgY, it is suggested that including the BWG in the breeding programs would directly result in the improvement of the birds' growth performance. It would also contribute indirectly to the improvement of the birds' humoral immune responses.

Investigation of egg production curve in ostrich using nonlinear functions.

In most countries, ostrich farming is considered a developing branch of the efficient poultry industry. The profitability of ostrich farm requires specific consideration of productions features such as the female fertility, egg production, hatchability, and growth performance. Hence, this study aimed to fit nonlinear functions to describe the ostrich egg production pattern to achieve the most appropriate and recommendable mathematical function for future studies. For this purpose, 14,507 daily records of 184 female ostriches in 5 production seasons (periods) during 2016 to 2021 were used. Five nonlinear functions including Incomplete gamma (Wood function), Corrected gamma (McNally), nonlinear Logistic (Yang), Logistic (Nelder), and Lokhorst were fitted for modeling the egg production curve in ostrich. The goodness of fit criteria's including Mean Square Error (MSE), Likelihood Ratio Test (LRT), Akaike Information Criterion (AIC), and Bayesian Information Criterion (BIC) were used to evaluate and selection of the best function. The results indicated that the Wood and the McNally functions with a slight difference in all fitting criteria were the best-fitted functions and the Yang function with the highest values of MSE, LRT, AIC, BIC, were the most inappropriate function to describe the ostrich egg production curve. The McNally and the Wood can be recommended as appropriate functions to describe egg production during 5 production seasons in the studied ostrich flock.

Study of genetic and non-genetic effects on cumulative survival in a crossbred population of quail.

Minimizing bird mortality in the commercial quail breeding industry is important from an economic and welfare perspective. Genetic and non-genetic factors can influence on the cumulative survival of the birds (CS). Accordingly, this study aimed to investigate non-genetic factors on CSs (cumulative survival of the birds from hatch to 5 (CS1), 10 (CS2), 15 (CS3), 20 (CS4), 25 (CS5), 30 (CS6), 35 (CS7), 40 (CS8), and 45 (CS9) days of age), and estimation of the genetic parameters for CSs in crossbred population of quail. Data set included 1794 records from crossbred chicks hatched from 70 sires and 72 dams. The fixed effects were analyzed using an animal model by ASReml software, and all traits were analyzed using Bayesian method via Gibbs sampling by fitting of 6 threshold animal models including the direct genetic effect, the maternal permanent environmental effect, and the maternal genetic effect. The best fitted model for each trait was selected based on the deviance information criteria. Hatch number, the month of hatch, and combination of chickens showed a significant effect on CSs, but the sex of chickens does not have a significant effect on CSs. However, females have higher survival than males (except for CS1). With the best model, the highest and lowest direct heritability was estimated for CS5 (0.386) and CS3 (0.250), respectively. The maternal genetic effect was significant for CS1, CS2, CS3, and CS4 traits, but the maternal permanent environmental effect was significant only for CS1. The range of maternal heritability for CS1 to CS4 traits was estimated from 0.064 to 0.111, and ratio of the permanent environmental variance to phenotypic variance for CS1 was 0.021. The result showed that increasing of the birds' survival could be performed by correcting non-genetic factors and genetic selection for CSs considering the maternal genetic effects in younger ages. HIGHLIGHTS: • In the commercial quail breeding industry, the bird mortality is important from an economic and welfare perspective. • Improving quail survival can be achieved by controlling the genetic and non-genetic factors affecting on survival, so knowledge of these factors is necessary. • The combination of crossbred chickens had a significant effect on cumulative survival traits. • The Cumulative survival traits in the crossbred population had relatively high genetic diversity, so genetic selection for these traits could be effective.

Scientometric evaluation of 100-year history of Poultry Science (1921-2020).

To have a better contribution to the poultry production community, the Poultry Science Association founded journals including Poultry Science (PS) at 1921. Now, after 100 yr of publishing, PS ranks between the top 10 journals in the category of "agriculture, dairy, and animal science". One hundred years after publishing the first paper in PS, the poultry industry has been completely revolutionized. Hence, it will be interesting to establish scientometrics study of the PS development during the last century. Therefore, based on findings of the current study, among countries/authors' collaborations, future research fronts, and possibility of hot topics in the coming years may be predictable. Accordingly, a total of 22,451 articles were retrieved. For content analyses, according to the PS categorization for subject areas, 14 different subject areas were developed, including "behavior, breeding and quantitative genetics, education and extension, health and welfare, immunology, management and environment, metabolism and nutrition, microbiology and virology, modeling, molecular biology, physiology and anatomy, production, products, processing and marketing, and reproduction". Considering the 100-yr of PS, the most frequent subject area was "nutrition and metabolism" (14,109 articles), and "modeling" (1,114 articles) attracted less scholarly attention. However, considering the last decade (2011-2020), the most important subject area was "molecular biology" (1,420 of 2,466 articles; 57.58%), followed by "modeling" (544 of 1,144 articles; 48.88%). Moreover, the most frequent poultry species/strains were broilers (retrieved in 6,156 articles), followed by laying hens, turkeys, and quail. Considering collaboration of countries and researchers, it can be said that a total number of 108 countries contributed to PS, with the most prolific country being United States (with 9,421 articles; 43.16%), followed by China, Canada, the Netherlands, and Japan. Among the authors, Harms RH (287 articles), and Siegel PB (208) were the most prolific authors, and Siegel PB and Dunnington EA (71 articles) had more collaborations. To study keyword trends, including 3 time periods broilers was the central co-occurrent keyword, while the importance of chickens and turkeys declined during the time. Salmonella spp. was a constant representative of poultry microbiology during 100 yr. While "nutrition and metabolism" was the most important subject area, nutrition-related keywords (major items) were not concentrated and co-occurred with a variety of keywords from different subject areas. While "molecular biology" ranked first over the past decade, the importance of "nutrition and metabolism" should not be ignored. In fact, in recent years, molecular basis of the nutrition has been studied. In big-data era and due to developing the molecular biology technologies, it seems that using mathematical modeling and computational methodologies will increase and probably remains as one of the most attractive research areas for scientists at least in the upcoming future decades.

Fifty years of sheep red blood cells to monitor humoral immunity in poultry: a scientometric evaluation.

Sheep red blood cells (SRBC) are commonly employed by scientists to address humoral immune responses in poultry. While SRBC are closely related to the study of humoral immunity in poultry, the initial purpose of much research did not focus on the mechanisms involved. Here, we provide a qualitative approach and utilize scientometric techniques, including trend analyses, scientific collaborations and mapping, and word co-occurrence evaluations, to summarize the role of SRBC in the poultry studies. First, a search strategy on Web of Science (WoS) was conducted to find publications that included SRBC in the poultry studies. Publications were partitioned into 4 categories: nutrition, genetics, microbiology, and physiology. For scientometric evaluation, scientific maps and networks were produced to clarify the occurrence of SRBC in the poultry studies. Data used included 702 publications over a period of 50 y (1968-2018) that were retrieved from the WoS database. About 95% of the publications were published in English language. Indigenous, experimental, and commercial chickens, quail, and medicinal plants field/topics were the main subjects of publications. In recent years, authors have used SRBC to study humoral immune response as a secondary aim of their research, especially when poultry production/performance was studied. This was especially the case in recent decades for studies in poultry nutrition. Analysis of keywords co-occurrence showed that the phrase SRBC mostly occurred with chickens, immune response, and especially with broilers. Moreover, the "medicinal plants" are becoming important especially for research on broilers and the reduced use of antibiotics in feed. Consequently, in addition to studying the medicinal plants, finding antibiotic replacements, and/or growth performance in the birds, humoral immunity is suggested to be investigated using SRBC. Moreover, interdisciplinary studies with the cooperation of scientists from agriculture, veterinary, immunology, biochemistry and molecular biology, and toxicology will develop in the future.

Prediction and optimization of slaughter weight in meat-type quails using artificial neural network modeling.

Carcass yield of meat-type quails is strongly correlated with the weight of the birds at slaughter (slaughter weight [SW]; body weight at 45 D of age). Moreover, prediction of superior animals for SW at the earlier stages of the rearing period is favorable for producers. Therefore, the aim of the present study was to predict and optimize SW of Japanese quails based on their early growth performances, sex, and egg weight as predictors through artificial neural network (ANN) modeling. To construct the ANN model a feed-forward multilayer perceptron neural network structure was used. Moreover, sensitivity analysis was used to arrange the predictors in the ANN model(s) according to their predictive importance too. In addition, the optimization process was conducted to determine the optimum values for the input variables to yield maximum SW. The best-fitted network on input data to predict SW in Japanese quails was determined with 7 neurons in the input layer, 11 neurons in the hidden layer, and one neuron in the output layer. The coefficient of determination (R2) was 0.9404, 0.9359, and 0.9223 for training, validation, and testing phases, respectively. For the corresponding phases, SEM were also 51.8854, 52.2764, and 55.2572, respectively. According to sensitivity analysis, the most important input variable for prediction of SW was body weight at 20 D of age (BW20), whereas the less important input variables were weight of the birds at hatch and body weight at 5 D of age. The results of the neural network optimization indicated that all the input variables, except for BW20, were very similar but slightly higher than mean values (µ for each input variable). The results of this study suggest that the ANN provides a practical approach to predict the final body weight (SW) of Japanese quails based on early performances. Moreover, phenotypic selection for higher values of early growth traits did not ensure the achievement of maximum SW, except for BW20.

Excess dietary tryptophan mitigates aflatoxicosis in growing quails.

A biological assay was carried out to evaluate the impact of dietary tryptophan (TRP) in aflatoxin B1 -contaminated diets (AFB1 -D) on performance, blood parameters, immunity, meat quality and microbial populations of intestine in Japanese quails. Six experimental diets were formulated to include two levels of dietary TRP; 2.9 (moderate high: MH-TRP) and 4.9 g/kg (excess: Ex-TRP); and three levels of AFB1 (0.0, 2.5, and 5.0 mg/kg). Each experimental diet was fed to the one of the six groups of birds from 7 to 35 days of age in a completely randomized design with 2 × 3 factorial arrangement. Decrease in feed intake, body weight gain and gain:feed in birds fed 5.0 mg/kg AFB1 -D was restored to the control level by 4.9 g TRP/kg of the diet. The hepatic enzymes in blood were elevated in quails fed on AFB1 -D but attenuated by 4.9 g TRP/kg of the diet (Ex-TRP; p ≤ .01). High serum uric acid in birds challenged with AFB1 significantly decreased by Ex-TRP (p ≤ .01). The skin thickness to 2,4-dinitro-1-chlorobenzene challenge suppressed by AFB1 but increased by Ex-TRP diet (p ≤ .02). The AFB1 increased the malondialdehyde in meat, whereas TRP efficiently diminished malondialdehyde production (p ≤ .01). The greatest drip loss and pH in meat were observed in the birds fed 5.0 mg/kg AFB1 -D but Ex-TRP augmented the adverse effects of AFB1 (p ≤ .01). The Ex-TRP reduced the total microbial and Escherichia coli counts (p ≤ .01). The adverse effect of AFB1 on ileal Lactic acid bacteria was completely prevented by Ex-TRP (p ≤ .03). This study showed that tryptophan supplementation could be considered as a powerful nutritional tool to ameliorate the adverse effects of AFB1 in growing quails.

Effect of sex and rearing system on the quality and mineral content of fiber from raeini cashmere goats.

The aim of this study was to compare the quality characteristics and mineral content of the fiber from male and female cashmere goats raised under different management systems. Male and female Raeini cashmere goats (<1.5 years of age, n = 48) were selected from flocks raised at a government breeding station or raised commercially under either rural or nomadic conditions. The staple length, cashmere fiber diameter, coefficient of variation for fiber diameter, percentage of cashmere in a fleece, percentage of guard hair in a fleece and cashmere tenacity averaged 4.6 ±0.1 cm, 18.0 ±0.1 µm, 20.9 ± 0.4%, 66.1 ± 1.5%, 33.8 ± 1.5% and 1.8 ± 0.2 gf/tex, respectively. The sulfur, copper and zinc content of the cashmere averaged 2.8 ± 0.1%, 0.00065 ± 0.00002% and 0.01276 ± 0.00025%, respectively. Rearing method significantly affected staple length, coefficient of variation of fiber diameter, cashmere tenacity and copper content. Males had a higher coefficient of variation of fiber diameter and cashmere tenacity than females (P < 0.05).