The constitutively active pSMAD2/3 relatively improves the proliferation of chicken primordial germ cells.

In many multicellular organisms, mature gametes originate from primordial germ cells (PGCs). Improvements in the culture of PGCs are important not only for developmental biology research, but also for preserving endangered species, and for genome editing and transgenic animal technologies. SMAD2/3 appear to be powerful regulators of gene expression; however, their potential positive impact on the regulation of PGC proliferation has not been taken into consideration. Here, the effect of TGF-ß signaling as the upstream activator of SMAD2/3 transcription factors was evaluated on chicken PGCs' proliferation. For this, chicken PGCs at stages 26-28 Hamburger-Hamilton were obtained from the embryonic gonadal regions and cultured on different feeders or feeder-free substrates. The results showed that TGF-ß signaling agonists (IDE1 and Activin-A) improved PGC proliferation to some extent while treatment with SB431542, the antagonist of TGF-ß, disrupted PGCs' proliferation. However, the transfection of PGCs with constitutively active SMAD2/3 (SMAD2/3CA) resulted in improved PGC proliferation for more than 5 weeks. The results confirmed the interactions between overexpressed SMAD2/3CA and pluripotency-associated genes NANOG, OCT4, and SOX2. According to the results, the application of SMAD2/3CA could represent a step toward achieving an efficient expansion of avian PGCs.

Bioinformatics and pathway enrichment analysis identified hub genes and potential biomarker for gastric cancer prognosis.

Introduction: Gastric cancer is one of the most common cancers in the world. This study aimed to identify genes, biomarkers, and metabolic pathways affecting gastric cancer using bioinformatic analysis and meta-analysis. Methods: Datasets containing gene expression profiles of tumor lesions and adjacent non-tumor mucosa samples were downloaded. Common differentially expressed genes between data sets were selected to identify hub genes and further analysis. Gene Expression Profiling and Interactive Analyses (GEPIA) and the Kaplan-Meier method were used to further validate the expression level of genes and plot the overall survivalcurve, respectively. Results and disscussion: KEGG pathway analysis showed that the most important pathway was enriched in ECM-receptor interaction. Hub genes includingCOL1A2, FN1, BGN, THBS2, COL5A2, COL6A3, SPARC and COL12A1 wereidentified. The top interactive miRNAs including miR-29a-3p, miR-101-3p,miR-183-5p, and miR-15a-5p targeted the most hub genes. The survival chart showed an increase in mortality in patients with gastric cancer, which shows the importance of the role of these genes in the development of the disease and can be considered candidate genes in the prevention and early diagnosis of gastric cancer.

Runs of homozygosity and cross-generational inbreeding of Iranian fat-tailed sheep.

The Lori-Bakhtiari fat-tailed sheep is one of the most important heavyweight native breeds of Iran. The breed is robust and well-adapted to semi-arid regions and an important resource for smallholder farms. An established nucleus-based breeding scheme is used to improve their production traits but there is an indication of inbreeding depression and loss of genetic diversity due to selection. Here, we estimated the inbreeding levels and the distribution of runs of homozygosity (ROH) islands in 122 multi-generational female Lori-Bakhtiari from different half-sib families selected from a breeding station that were genotyped on the 50k array. A total of 2404 ROH islands were identified. On average, there were 19.70 ± 1.4 ROH per individual ranging between 6 and 41. The mean length of the ROH was 4.1 ± 0.14 Mb. There were 1999 short ROH of length 1-6 Mb and another 300 in the 6-12 Mb range. Additionally long ROH indicative of inbreeding were found in the ranges of 12-24 Mb (95) and 24-48 Mb (10). The average inbreeding coefficient (FROH) was 0.031 ± 0.003 with estimates varying from 0.006 to 0.083. Across generations, FROH increased from 0.019 ± 0.012 to 0.036 ± 0.007. Signatures of selection were identified on chromosomes 2, 6, and 10, encompassing 55 genes and 23 QTL associated with production traits. Inbreeding coefficients are currently within acceptable levels but across generations, inbreeding is increasing due to selection. The breeding program needs to actively monitor future inbreeding rates and ensure that the breed maintains or improves on its current levels of environmental adaptation.

Identification of Key Genes and Potential Pathways Associated with Mastitis Induced by E. coli.

Mastitis is one of the most important diseases of dairy cattle. It is an infectious disease leading to an inflammatory reaction in the cow's mammary gland. Escherichia coli is one of the common bacteria which induce mastitis in cows. The aim of this study was to identify key genes and potential pathways associated with mastitis induced by E. coli in dairy cattle using bioinformatics analysis. The gene expression profile of ten samples including five adjacent tissues from a quarter infected with Escherichia coli and five tissues from a healthy quarter of dairy cattle was assessed using GEO2R. Gene ontology and pathway analysis were performed using bioinformatics tools. A total of 156 differentially expressed genes were detected which 95 genes were upregulated and 61 genes were downregulated in adjacent tissue of quarter infected compared with healthy tissue. Cellular oxidant detoxification and oxidation-reduction process were the most significant biological process terms in gene ontology analysis. The most important pathways of DEGs were the biosynthesis of amino acids, p53 signaling pathway, and Metabolic pathways. Three important modules were identified and their path enrichment analysis was performed. There are 10 core genes, among which SOD2, COL1A2, COL3A1, POSTN, ALDH18A1, and CBS may be the main genes associated with mastitis, which can be considered as candidate genes in the prevention and carly diagnosis program of mastitis.

Transcriptome Analysis of Breast Muscle Reveals Pathways Related to Protein Deposition in High Feed Efficiency of Native Turkeys.

Feed efficiency is important due to the high cost of food, which accounts for about 70% of the total cost of a turkey breeding system. Native poultry are an important genetic resource in poultry breeding programs. This study aimed to conduct a global transcriptome analysis of native male turkeys which have been phenotyped for high and low feed efficiency. Feed efficiency traits were recorded during the experimental period. After slaughter, the three most efficient and three least efficient male turkeys were selected for RNA-Seq analysis. A total of 365 genes with different expressions in muscle tissue were identified between turkeys with a high feed efficiency compared to turkeys with a low feed efficiency. In the pathway analysis of up-regulated genes, major pathways included the "metabolism of glycine, serine, and threonine"; the "adipocytokine signaling pathway" and the "biosynthesis of amino acids". In the pathway analysis of down-regulated genes, the major pathways included "dorso-ventral axis formation" and "actin cytoskeleton regulation". In addition, gene set enrichment analyses were performed, which showed that high feed efficiency birds exhibit an increased expression of genes related to the biosynthesis of amino acids and low feed efficiency birds an increased expression of genes related to the immune response. Furthermore, functional analysis and protein network interaction analysis revealed that genes including GATM, PSAT1, PSPH, PHGDH, VCAM1, CD44, KRAS, SRC, CAV3, NEDD9, and PTPRQ were key genes for feed efficiency. These key genes may be good potential candidates for biomarkers of feed efficiency in genetic selection in turkeys.

Identification of hub genes involved in apparent metabolizable energy of chickens.

Feed efficiency is one of the most economically significant traits in a breeding program. Apparent metabolizable energy is the most used method to evaluate energy utilization for feed efficiency. The purpose of this study was to identify candidate genes of chickens with divergent apparent metabolizable energy by bioinformatics analysis. The gene expression profile of duodenal of the highest and lowest apparent metabolizable energy-ranked birds were analyzed. Differentially expressed genes were picked out using GEO2R tool. Gene ontology and pathway analysis were performed using bioinformatics tools. Cytoscape software was used to visualize protein-protein network. There were 201 DEGs, including 99 up-regulated genes enriched in metabolic pathways, Cellular senescence and Focal adhesion, and 102 down-regulated genes enriched in metabolic pathways, Regulation of actin cytoskeleton, Neuroactive ligand-receptor interaction, Calcium signaling pathway and Focal adhesion. Two important modules were detected and pathway enrichment analysis showed that they were mainly associated with Focal adhesion, Regulation of actin cytoskeleton and RNA transport. Fifteen hub genes were selected and among them, ITGA8, CDC42 and GSK3B might be the core genes related to apparent metabolizable energy of chickens. These hub genes can be used as biomarkers for apparent metabolizable energy and feed efficiency in breeding program of chickens.

Genome-wide association study for postweaning weight traits in Lori-Bakhtiari sheep.

Marker-assisted selection is an effective method in novel animal breeding programs. This study was conducted to perform a genome-wide association study to detect candidate genes and quantitative trait loci associated with postweaning weight traits in meat-type sheep. Body weight records were collected during 29 years (1989 to 2017) in Lori-Bakhtiari sheep flock of the Shooli Breeding Station in Iran. A total of 132 animals were selected based on estimates of breeding values (EBVs) for body weight, using two-tailed and random selection strategies. Genomic DNA was extracted from whole blood samples. The samples were genotyped using Illumina OvineSNP50 BeadChip. De-regressed EBVs for postweaning body weight traits were used as pseudo-phenotypes in a genome-wide association study. One SNP on chromosome 10 (rs406324209) and two SNPs on chromosome 13 (rs401963094 and rs418761613) were significantly (Bonferroni-adjusted p-values < 0.05) associated with postweaning body weight traits. The significant variants accounted for 0.20% and 0.48% of the total genetic variances for 6- and 9-month body weights, respectively. Genomic heritabilities estimated for 6-, 9- and 12-month weights and postweaning weight gain were 0.28 ± 0.34, 0.35 ± 0.29, 0.37 ± 0.34, and 0.16 ± 0.33, respectively. Two significant SNPs were located within the ATP8A2 and PLXDC2 genes, on chromosomes 10 and 13, respectively. Based on the known gene ontologies, both ATP8A2 and PLXDC2 could be considered as candidate genes for postweaning body weight traits.

Investigating the Polymorphism of Bone Morphogenetic Protein Receptor-1B (BMPR1B) Gene in Markhoz Goat Breed.

Reproductive traits in livestock species are genetically controlled by the action of single genes with a major effect, commonly known as fecundity genes. One of the genes involved in controlling prolificacy is BMPR1B (FecB), a dominant autosomal gene located in chromosome 6 responsible for the fecundity and twinning rate in sheep and goat species. Markhoz goat is a valuable Iranian genetic resource endangered by extinction. Increasing the genetic variability and reproductive performances of Markhoz goat could preserve and enhance its economic value. This study was carried out to detect possible polymorphisms in BMPR1B gene in a sample of 100 Markhoz goats from Iran. DNA samples were screened by PCR-RFLP to assess the presence of the previously reported FecB mutation. Finally, the amplicons from seven goats out of the 100 samples were sequenced. The results showed that all the analyzed individuals did not carry the previously reported FecB mutant allele. However, our findings revealed two novel possible mutations in exon 8 of BMPR1B gene (775A > G and 777G > A) that need further investigations.

A new DNA sequence entropy-based Kullback-Leibler algorithm for gene clustering.

Information theory is a branch of mathematics that overlaps with communications, biology, and medical engineering. Entropy is a measure of uncertainty in the set of information. In this study, for each gene and its exons sets, the entropy was calculated in orders one to four. Based on the relative entropy of genes and exons, Kullback-Leibler divergence was calculated. After obtaining the Kullback-Leibler distance for genes and exons sets, the results were entered as input into 7 clustering algorithms: single, complete, average, weighted, centroid, median, and K-means. To aggregate the results of clustering, the AdaBoost algorithm was used. Finally, the results of the AdaBoost algorithm were investigated by GeneMANIA prediction server to explore the results from gene annotation point of view. All calculations were performed using the MATLAB Engineering Software (2015). Following our findings on investigating the results of genes metabolic pathways based on the gene annotations, it was revealed that our proposed clustering method yielded correct, logical, and fast results. This method at the same that had not had the disadvantages of aligning allowed the genes with actual length and content to be considered and also did not require high memory for large-length sequences. We believe that the performance of the proposed method could be used with other competitive gene clustering methods to group biologically relevant set of genes. Also, the proposed method can be seen as a predictive method for those genes bearing up weak genomic annotations.

Genetic parameters and trends for litter size in Markhoz goats / Parámetros genéticos y tendencias para el tamaño de la camada en cabras Markhoz / Parâmetros genéticos e tendências para o tamanho da ninhada em cabras Markhoz

Abstract Background: Prolificacy has a high economic value and is one of the most important reproduction traits in small ruminants such as Markhoz goats, which is an endangered breed. Objective: To estimate genetic, environmental and phenotypic trends, and genetic parameters for litter size (LS), as a prolificacy trait of Markhoz goat does. Methods: The study was conducted using kidding records of 3,064 Markhoz does from 1992 to 2015. Genetic parameters were estimated with a logit link function using ASReml software, fitting a repeatability animal model, with birth year, kidding year, and kidding age as fixed effects, and direct additive genetic and permanent environmental effects as random effects. Genetic, phenotypic and environmental trends were estimated by using regression of breeding value, phenotypic value and environmental deviation averages on birth year, respectively. Results: Low and negligible heritability (0.002), repeatability (0.054) and coefficient of permanent environment (0.052) were estimated for LS, which indicates low possibility to achieve rapid genetic progress through phenotypic selection. A non-significant -actually, zero- genetic trend (0.00004 heads/kidding/year), and significant negative phenotypic and environmental trends (-0.01097 and -0.01100 heads/kidding/year, respectively) were estimated in this study. Conclusion: Optimizing environmental conditions and application of high-throughput technologies in selection programs could help reducing the extinction risk of Markhoz breed.

Resumen Antecedentes: La prolificidad tiene un alto valor económico y es uno de los rasgos reproductivos más importantes en pequeños rumiantes, tales como la raza caprina Markhoz. que está en peligro de extinción. Objetivo: Estimar las tendencias genéticas, ambientales y fenotípicas, y los parámetros genéticos para el tamaño de la camada (LS), como rasgo de prolificidad de las hembras de cabras Markhoz. Métodos: Se utilizaron registros de partos de 3.064 hembras Markhoz, de 1992 a 2015. Los parámetros genéticos se estimaron con una función de enlace logit utilizando el software ASReml, ajustando un modelo animal de repetibilidad, con el año de nacimiento, el año del parto y la edad al parto como efectos fijos, y genéticos aditivos directos y efectos ambientales permanentes como efectos aleatorios. Las tendencias genéticas, fenotípicas y ambientales se estimaron mediante la regresión del valor de la cría, el valor fenotípico y los promedios de desviación ambiental en el año de nacimiento, respectivamente. Resultados: Se estimó la heredabilidad -baja e insignificante- (0,002), repetibilidad (0,054) y coeficiente de ambiente permanente (0,052) para LS, lo que indica una baja posibilidad de lograr un progreso genético rápido a través de selección fenotípica. Se estimó una tendencia genética no significativa -de hecho, cero- (0,00004 cabezas/parto/año) y se estimaron tendencias fenotípicas y ambientales negativas significativas (-0,01097 y -0,01100 cabezas/parto/año, respectivamente) en el período estudiado. Conclusión: La optimización de las condiciones ambientales y la aplicación de tecnologías de alto rendimiento en los programas de selección podrían reducir el riesgo de extinción de la raza Markhoz.

Resumo Antecedentes: A prolificidade tem um elevado valor económico e é uma das mais importantes características de reprodução nos pequenos ruminantes, como a raça de caprinos Markhoz, que está em perigo de extinção. Objetivo: Estimar tendências genéticas, ambientais e fenotípicas, e parâmetros genéticos para o tamanho da serapilheira (LS), como um traço de proliferação de cabras Markhoz. Métodos: Este estudo foi realizado usando registros de parto de 3.064 Markhoz entre 1992 e 2015. Os parâmetros genéticos foram estimados com uma função logit link utilizando o software ASReml, ajustando um modelo animal de repetibilidade, com o ano de nascimento, o ano de parto ea idade de caçoar como efeitos fixos e efeitos ambientais diretos e genéticos diretos como efeitos aleatórios. As tendências genéticas, fenotípicas e ambientais foram estimadas pela regressão do valor de criação, valor fenotípico e médias de desvio ambiental no ano de nascimento, respectivamente. Resultados: Herdabilidade baixa e negligenciável (0,002), repetibilidade (0,054) e coeficiente de ambiente permanente (0,052) foram estimadas para LS, o que indica baixa possibilidade de alcançar um progresso genético rápido através da seleção fenotípica. Foi estimada uma tendência genética não-significativa e realmente zero (0,00004 cabeças/parto/ano) e tendências fenotípicas e ambientais negativas significativas (-0,01097 e -0,01100 cabeças/parto/ano, respectivamente) no período estudado. Conclusão: Parece que a otimização das condições ambientais ea aplicação de tecnologias de alto rendimento em programas de seleção poderiam reduzir o risco de extinção para a raça Markhoz.

In silico analysis of different signal peptides to discover a panel of appropriate signal peptides for secretory production of Interferon-beta 1b in Escherichia coli.

Signal peptides (SPs) are one of the most important factors for suitable secretion of the recombinant  heterologous proteins in Escherichia coli (E. coli). The objective of this study was to identify a panel of signal peptides (among the 90 biologically active SPs) required for the secretory production of interferon-beta 1b (IFN-beta 1b) recombinant protein into the periplasmic space of E. coli host. In the initial step, after predicting the accurate locations of the cleavage sites of signal peptides and their discrimination scores using SignalP 4.1 server, 31 SPs were eliminated from further analysis because their discrimination scores were less than 0.5 or their cleavage sites were inappropriately located. Therefore, only 59 SPs could be theoretically applied to secrete IFN-beta 1b into the periplasmic space of E. coli. The physico-chemical and the solubility properties, which are necessary parameters for selecting appropriate SPs, were predicted using ProtParam and SOLpro servers using the 59 remaining signal peptides. The final subcellular localization of IFN-beta 1b in combination with different SPs was predicted using ProtComB server. Consequently, according to the ranking of 59  confirmed SPs, the obtained results revealed that SPs Flagellar P-ring protein (flgI), Glucan 1,3-beta-glucosidase I/II (EXG1) and outer membrane protein C (OmpC) were theoretically the most potent and desirable SPs for secretion of recombinant IFN-beta 1b into the periplasmic space of E. coli. For further studies in the future, the experimental investigations on the obtained results will be considered.

Genetic characterization of Markhoz goat breed using microsatellite markers.

The use of molecular markers can support the management of endangered populations and should be combined with appropriate breeding strategies to improve productive traits avoiding the decline of the breed. The genetic variability at 10 microsatellite loci were investigated in a sample of 100 unrelated Markhoz goats (77 females and 23 males). The investigated population was reared at the Sanandaj Markhoz goat Performance Testing Station in Kurdistan, Iran. Markhoz goat, a multipurpose breed, is one of the most valuable genetic resources in Iran. All the studied loci were found to be polymorphic and a total number of 52 alleles were identified with an average number of alleles of 5.2. Moreover, some population genetic indices, such as observed and expected heterozygosity, observed and expected number of alleles, Shannon's index, Nei's expected heterozygosity, and polymorphism information content were also calculated. Despite the decreasing population size, Markhoz goat genetic diversity is still conserved. The breed seems to have a good level of genetic variability and, as a consequence, a potential margin of adaptability to environment and for future genetic improvement.

Effect of cotton cultivar on performance of Aphis gossypii (Homoptera: Aphididae) in Iran.

Cotton aphids, Aphis gossypii Glover (Homoptera: Aphididae), obtained from cotton, Gossypium hirsutum L., fields in the Gorgan region of northern Iran, were colonized on 'Varamin' cotton plants in a growth chamber. The development, survivorship, and life table parameters of the cotton aphid were evaluated at 27.5 +/- 1 degrees C, 65 +/- 10% RH, and aphotoperiod of 14:10 (L:D) h of artificial light on five commonly growing cotton cultivars: Varamin, 'Sealand' (relatively resistant cultivar), 'Bakhtegan', 'Sahel' (both relatively susceptible cultivars), and 'Siokra' [resistant to Bemisia tabaci (Gennadius)]. The developmental times of immature stages ranged from 4.6 d on Bakhtegan and Varamin to 6.3 d on Sealand, whereas the immature survival was 97.5 to 65% on Sahel and Siokra, respectively. On average, there were 28.7, 28.3, 23.5, 20.1, and 16.8 nymphs produced per female on Sahel, Bakhtegan, Varamin, Sealand, and Siokra, respectively. The intrinsic rate of natural increase (r(m)) for cotton aphids on Sahel was the highest, whereas the values for r(m) varied from 0.284 (nymphs per female per d) on Siokra to 0.368 on Sahel. Jackknife estimates of generation times (T), net reproductive rate (R(0)), doubling time (DT), and finite rate of increase (lambda) on these cultivars were as follows: 9.79-10.84 d for T, 9.23-23.81 nymphs per female for R(0), 2.17-3.19 d for DT, and 1.28-1.38 nymphs per female per d for lambda. Cotton aphid performance was at its highest on Sahel and lowest on Siokra.