Genome-wide analysis of population structure, effective population size and inbreeding in Iranian and exotic horses

Population structure and genetic diversity are the key parameters to study the breeding history of animals. This research aimed to provide a characterization of the population structure and to compare the effective population size (Ne), LD decay, genetic diversity, and genomic inbreeding in Iranian native Caspian (n = 38), Turkmen (n = 24) and Kurdish (n = 29) breeds and some other exotic horses consisting of Arabian (n = 24), Fell pony (n = 21) and Akhal-Teke (n = 20). A variety of statistical population analysis techniques, such as principal component analysis (PCA), discriminant analysis of principal component (DAPC) and model-based method (STRUCTURE) were employed. The results of the population analysis clearly demonstrated a distinct separation of native and exotic horse breeds and clarified the relationships between studied breeds. The effective population size (Ne) for the last six generations was estimated 54, 49, 37, 35, 27 and 26 for the Caspian, Kurdish, Arabian, Turkmen, Akhal-Teke and Fell pony breeds, respectively. The Caspian breed showed the lowest LD with an average r2 value of 0.079, while the highest was observed in Fell pony (0.148). The highest and lowest average observed heterozygosity were found in the Kurdish breeds (0.346) and Fell pony (0.290) breeds, respectively. The lowest genomic inbreeding coefficient based on run of homozygosity (FROH) and excess of homozygosity (FHOM) was in the Caspian and Kurdish breeds, respectively, while based on genomic relationship matrix) FGRM) and correlation between uniting gametes) FUNI) the lowest genomic inbreeding coefficient was found in the Kurdish breed. The estimation of genomic inbreeding rates in the six breeds revealed that FROH yielded lower estimates compared to the other three methods. Additionally, the Iranian breeds displayed lower levels of inbreeding compared to the exotic breeds. Overall, the findings of this study provide valuable insights for the development of effective breeding management strategies aimed at preserving these horse breeds.

Genital stones: Radiological, histopathological, ultrastructural, and molecular analysis in rooster

Epididymal lithiasis, characterized by the formation of stones in the epididymis, has been associated with a decline in fertility in roosters. This study aimed to investigate the reproductive performance, ultrastructural characteristics, and expression of aromatase cytochrome P450 (CYP19) and aquaporin 9 (AQP9) in aged broiler breeder roosters affected by epididymal lithiasis. X-ray analysis confirmed the presence of genital stones in both the epididymis and testicular tissue regions. While there was a significant decrease in sperm concentration in the affected roosters compared to non-affected roosters, no significant differences were observed in total and progressive sperm motility between the two groups. Furthermore, the affected roosters exhibited significant abnormalities in semen parameters, except for sperm concentration and morphology. Transmission electron microscopy (TEM) revealed the depletion and deciliation of ciliated cells in the distal efferent ductules of the epididymis in affected roosters. Additionally, the expression of CYP19 and AQP9 was found to be increased in the epididymal region of affected roosters. Notably, we report the presence of testicular stones for the first time in this study, in addition to epididymal stones. Considering the male reproductive tract lesions observed, we propose the term "genital stones" to describe these conditions. Moreover, our findings suggest that the overexpression of AQP9, which is associated with a high copy number of the CYP19 gene in the epididymal region of affected aged roosters, may contribute to the formation of genital stones by promoting increased reabsorption of fluids in the epididymis. The condensation of epididymal duct contents and reduction in the population of ciliated cells further impairs semen movement and can lead to the blockage of extra-testicular ducts, resulting in the low fertility syndrome observed in aged roosters.

Genetic diversity and signatures of selection in four indigenous horse breeds of Iran

Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52) populations, using genomewide genotyping data. The contemporary effective population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian Arabian, and Kurdish breeds, respectively. By analysis of the population genetic structure, we classified the north breeds (Caspian and Turkmen) and west/southwest breeds (Persian Arabian and Kurdish) into two phylogeographic clades reflecting their geographic origin. Using the de-correlated composite of multiple selection signal statistics based on pairwise comparisons, we detected a different number of significant SNPs under putative selection from 13 to 28 for the six pairwise comparisons (FDR < 0.05). The identified SNPs under putative selection coincided with genes previously associated with known QTLs for morphological, adaptation, and fitness traits. Our results showed HMGA2 and LLPH as strong candidate genes for height variation between Caspian horses with a small size and the other studied breeds with a medium size. Using the results of studies on human height retrieved from the GWAS catalog, we suggested 38 new putative candidate genes under selection. These results provide a genomewide map of selection signatures in the studied breeds, which represent valuable information for formulating genetic conservation and improved breeding strategies for the breeds.

Effects of Antifreeze Protein Type I and Glycerol in Diluents on Cryopreserved Goat Epididymal Sperm

The effect of antifreeze protein (AFP) as a cryoprotectant used in different concentrations of glycerol on post-thaw quality of epididymal sperm was investigated. Sperm were isolated from 50 testicles, obtained from 25 healthy mature goat bucks, with progressive motility >80%, and total morphological abnormalities <10% were pooled in each replication. The semen samples were diluted with Tris-citrate-fructose-soybean lecithin extender containing different concentration of AFP [0 μg/mL (A0), 5 μg/mL (A5), 10 μg/mL (A10)]. Each concentration of AFP was added in an extender containing either 7% (G7) or 5% (G5) glycerol. Post-thaw total and progressive motility were found to be higher (p < 0.05) in groups A5G5 and A5G7. Plasma membrane integrity, sperm acrosome integrity, DNA integrity, acrosome intact sperm, and mitochondrial membrane potential were found to be higher (p < 0.05) in groups A5G5 and A10G5. Sperm viability was found to be higher (p < 0.05) in group A5G5, while lipid peroxidation was recorded lower (p < 0.05) in groups A5G5 and A5G7. Regarding the apoptosis occurrence, the results demonstrate higher (p < 0.05) live post-thawed spermatozoa for groups containing 5 μg/mL AFP with 5% and 7% glycerol in addition to the lowest (p < 0.05) value for groups containing 0 μg/mL AFP with 5% and 7% glycerol. Based on these results, the present study concludes that the addition of 5 μg/mL AFP in combination with 5% glycerol in freezing extender improves the post-thaw quality, structure, and function parameters for buck spermatozoa.

Genome-wide association study reveals novel candidate genes for litter size in Markhoz goats

Introduction

The Markhoz goat is the only breed that can produce high-quality fiber called mohair in Iran; however, the size of its population has faced a dramatic decline during the last decades, mainly due to the reluctance of farmers to rear Markhoz goats caused by a reduction in goat production income. Litter size at birth (LSB) and weaning (LSW) are two economically important reproductive traits for local goat breeders and have the potential of increasing the population growth rate. The present study was aimed to identify possible genomic regions that are associated with LSB and LSW in Markhoz goats using a genome-wide association study (GWAS).

Methods

To this end, 136 Markhoz goats with record(s) of kidding were selected for GWAS using the Illumina Caprine 50K bead chip. The individual breeding values (BV) of available LSB and LSW records estimated under an animal mixed model were used as the dependent variable in the GWAS, thereby incorporating repeated categorical variables of litter size.

Results

Four SNPs on chromosomes 2, 20 and 21 were identified to be significantly associated (FDR p < 0.05) with LSB after multiple testing correction under a Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model. Least-square analysis was performed to investigate the effects of detected genotypes on LSB. Ultimately, the GWAS results introduced six candidate genes, including GABRA5, AKAP13, SV2B, PPP1R1C, SSFA2 and TRNAS-GCU in a 100 kb adjacent region of the identified SNPs. Previous studies proposed functional roles of GABRA5 and AKAP13 genes in reproductive processes; however, the role of other candidate genes in reproduction is not clear.

Conclusion

These findings warrant further investigation for use in marker-assisted selection programs in Markhoz goats.

Meta-analysis of association between c.963A>G single-nucleotide polymorphism on BMP15 gene and litter size in goats

Litter size is an important economic trait in the goat industry. Previous studies on the bone morphogenetic protein 15 (BMP15) gene detected some single-nucleotide polymorphisms (SNPs) such as c.963A > G that were associated with an increase in ovulation rate and litter size. The aim of this study was to conduct a meta-analysis on the effect of this polymorphism on litter size. We gathered and pooled data from five eligible published studies. To investigate the effect of c.963A > G on litter size, we utilized four different genetic models assuming dominant (GG  +  GA vs. AA), recessive (GG vs. GA  +  AA), additive (GG vs. AA) and co-dominant (GG  +  AA vs. GA) model of inheritance. Data were analyzed under random-effects models based on the I 2 value. Furthermore, sensitivity analysis was carried out to validate the stability of results. The results showed that the c.963A > G polymorphism is associated with litter size when applying a dominant model (standardized mean difference (SMD) is 0.815, 95 % CI [0.170, 1.461], P  value  =  0.013) and also with an additive model (SMD  =  0.755, 95 % CI [0.111, 1.400], P  value  =  0.022). However, the effect of c.963A > G polymorphism was not significant under recessive (SMD  =  0.186, 95 % CI [ - 0.195, 4.259], P  value  =  0.339) and co-dominant (SMD  =   - 0.119, 95 % CI [ - 0.525, 0.288], P  value  =  0.568) models. Sensitivity analysis demonstrated that dropping studies with wide confidence intervals affects overall results under the assumption of an additive model. The meta-analysis results revealed that the AA genotype could be positively connected with litter size in goats.

Use of Purslane (Portulaca oleracea) Extracts and Cysteine in Diluents to Improve the Cryopreserved Quality of Goat Sperm

Highlights Using cysteine and purslane extracts in extenders improved significantly the post-thaw sperm characteristics. Sperm viability, DNA integrity, and mitochondrial activity demonstrate an improvement in post-thaw sperm. Malondialdehyde production was decreased based on the positive effects of treated extenders. The obtained results demonstrate that supplementation of 50 μg/mL of purslane methanolic extract with cysteine to freezing extenders was significantly superior compared with other treatments.

Characterization of Arsenic-Resistant Endophytic Bacteria From Alfalfa and Chickpea Plants

The present investigation was carried out to isolate arsenic (As)-resistant endophytic bacteria from the roots of alfalfa and chickpea plants grown in arsenic-contamination soil, characterize their As tolerance ability, plant growth-promoting characteristics, and their role to induce As resistance by the plant. A total of four root endophytic bacteria were isolated from plants grown in As-contaminated soil (160-260-mg As kg^-1 of soil). These isolates were studied for plant growth-promoting (PGP) characteristics through siderophore, phosphate solubilization, nitrogen fixation, protease, and lipase production, and the presence of the arsenate reductase (arsC) gene. Based on 16S rDNA sequence analysis, these isolates belong to the genera Acinetobacter, Pseudomonas, and Rahnella. All isolates were found As tolerant, of which one isolate, Pseudomonas sp. QNC1, showed the highest tolerance up to 350-mM concentration in the LB medium. All isolates exhibited phosphate solubilization activity. Siderophore production activity was shown by only Pseudomonas sp. QNC1, while nitrogen fixation activity was shown by only Rahnella sp. QNC2 isolate. Acinetobacter sp. QNA1, QNA2, and Rahnella sp. QNC2 exhibited lipase production, while only Pseudomonas sp. QNC1 was able to produce protease. The presence of the arsC gene was detected in all isolates. The effect of endophytic bacteria on biomass production of alfalfa and chickpea in five levels of arsenic concentrations (0-, 10-, 50-, 75-, and 100-mg kg^-1 soil) was evaluated. The fresh and dry weights of roots of alfalfa and chickpea plants were decreased as the arsenic concentration of the soil was increased. Results indicate that the fresh and dry root weights of alfalfa and chickpea plants were significantly higher in endophytic bacteria-treated plants compared with non-treated plants. Inoculation of chickpea plants with Pseudomonas sp. QNC1 and Rahnella sp. QNC2 induced lower NPR3 gene expression in chickpea roots grown in soil with the final concentration of 100-mg kg^-1 sodium arsenate compared with the non-endophyte-treated control. The same results were obtained in Acinetobacter sp. QNA2-treated alfalfa plants grown in the soil plus 50-mg kg^-1 sodium arsenate. These results demonstrated that arsenic-resistant endophytic bacteria are potential candidates to enhance plant-growth promotion in As contamination soils. Characterization of bacterial endophytes with plant growth potential can help us apply them to improve plant yield under stress conditions.

Effect of orally administrated letrozole on reproduction performance and gene expression of FOXJ1, LPR2 and PVRL3 in reproductive tract in aged roosters

letrozole is an aromatase inhibitor that stops the production of estrogen through interrupting the entrance of hormone androgen into a small amount of estrogen. Therefore, the current study was developed to estimate orally administrated Letrozole on the reproductive performance and relative abundance of Foxj1, PVRL3, and LPR2 mRNA in aged roosters. Fifty-five-week old ROSS 308 breeder roosters (n = 18) were orally treated using letrozole. Primarily, the body weight of the animals was recorded, and they were randomly classified into three groups (n = 6 birds/group) receiving different doses of Letrozole, including 0, 0.015, and 0.03 mg/kg body weight/day for three weeks. At the end of the trial, seminal traits, plasma, testicular hormone levels (testosterone, estradiol, and FSH), histopathological studies, in vitro fertility, and relative abundance of testis PVRL3, epidydimal Foxj1, and LPR2 mRNA were evaluated. Based on the results, the sperm quality variables were statistically higher in the 0.03 group compared to the controls. Greater histologic parameters, such as diameter of seminiferous tubules, thickness of seminiferous epithelium, categorized epididymal region, and in vitro fertility rates were estimated for the treated groups(p < 0.001). Plasma and testicular testosterone, estradiol concentrations, and plasma FSH levels were significantly influenced by letrozll treatment (p < 0.001). Relative mRNA transcript abundance increased for PVRL3 and decreased for Foxj1 and LPR2 in treated groups. Overall, aromatase inhibitors can enhance the reproductive performance of aged commercial broiler breeder roosters. However, it can impact endocytosis and ciliogenesis events via reducing estradiol.

Protective effects of Tribulus terrestris and Cinnamomum zeylanicum extracts and trehalose added to diluents on goat epididymal sperm freezability

This study investigates the effect of adding Tribulus terrestris ethanol extract (TEE) and Cinnamomum zeylanicum ethanol extract (CEE) and trehalose on freezability of goat epididymal spermatozoa. In Experiment 1, the treatments consist of basic extender containing 25, 50 or 100 μg/ml of TEE or CEE. The control contained no additives. Experiment 2 was carried out to compare the effect of best concentrations resulted in the first experiment with 150 mM trehalose added to basic extender. The results of experiment 1 showed that supplementation of 50 μg/ml TEE and 50 μg/ml CEE increased significantly the percentages of motility, progressive motility and viability of cryopreserved spermatozoa, while the level of malondialdehyde concentration was decreased. Moreover, the 50 μg/ml TEE treatment indicate significantly) P < 0.05) the lowest DNA fragmentation among the other treatments. The data obtained from experiment 2 show that all treatments increased significantly) P < 0.05) the percentages of total motility, viability and membrane integrity, and concurrently decreased the rate of MDA compared to control. In addition, the rates of viability and progressive motility were significantly (P < 0.05) higher in diluents contained herb extracts and trehalose. Regarding DNA fragmentation, the results demonstrate that using the extracts and trehalose in diluents decreased the DNA damages and thereby improved the rate of intact sperm heads. In conclusion, the results of this study indicate that 50 μg/ml of Tribulus terrestris and Cinnamomum zeylanicum ethanolic extracts alone and plus trehalose improved the spermatozoa quality and could be used for cryopreservation.

A novel variant in the promoter region of miR-9 gene strongly affects litter size in Markhoz goats

This study aimed to identify and evaluate the effects of single nucleotide polymorphisms (SNPs) within miR-9 and miR-27a genes and their promoters, as well as 3'UTR regions of KITLG and IGF1 genes on litter size in Markhoz goats. PCR-SSCP analysis revealed different band patterns and sequencing results confirmed four SNPs including a C/A, a A/G, a C/T and a A/G substitution located in the promoter region of miR-9 gene, 48 bp upstream of miR-9 seed region within the 3'UTR of KITLG gene, 37 bp downstream of miR-27a gene and 39 bp upstream of miR-9 seed region within the 3'UTR of IGF1 gene, respectively. The results of the least-square analyses indicated that AA genotype of miR-9 gene strongly and positively affects litter size in Markhoz goats (P < 0.01). Furthermore, the results of the logistic regression analyses confirmed that the A allele of miR-9 gene has a tremendous impact on litter size in Markhoz goats (P < 0.01). Scanning the promoter region of miR-9 gene showed that changing C allele to A may prevent HES1, HES2, NRF1 and TCFL5 transcription factors (TFs) from binding to the promoter, which can reduce the expression of miR-9 gene. Principle component analysis (PCA) showed that approximately 60% of the variation of the data set was explained by two of four SNPs. Also, the biplot from the PCA showed a strong association between litter size and C/A polymorphism of miR-9 promoter. Linkage disequilibrium analysis revealed a very slight linkage among investigated loci.

Evaluation of pentoxifylline and Basal Medium Eagle supplemented to diluent on cryopreserved goat spermatozoa

This study investigated the effect of pentoxifylline (PTX) and Basal Medium Eagle (BME) on frozen-thawed goat spermatozoa. Immediately after initial examination of ejaculated semen, samples were pooled and reexamined for quality. Then, samples were divided into eight equal aliquots and diluted with a basic tris-extender containing PTX (3, 6, 9 mM) and BME (5 mM) to reach a final concentration of 25 × 10⁹ and frozen. After 24 hr, the samples were individually thawed at 37°C for 30 s and evaluated for different characteristics. Obtained post-thaw results from Computer-Assisted Sperm Analysis indicate using of 3 and 6 mM PTX led significantly to an improvement in total motility, progressive motility and velocity characteristics of spermatozoa, except the beat/cross frequency (BCF) which indicated statistically no differences (p > .05) among control and treatments. Diluents prepared with BME (5 mM) and PTX alone (3 and 6 mM) improved significantly the membrane integrity-functionality, acrosome integrity and also hyaluronidase activity. Regarding recovery rate, the results showed significantly (p < .05) higher values for diluents containing 3 and 6 mM PTX compared to other groups. Malondialdehyde concentration exhibited also a significant difference (p < .05) in diluents supplemented with 5 mM BME, 3, 6 and 9 mM PTX, and mixture of 3 mM PTX and 5 mM BME which illustrate a similarity for active mitochondria, apoptotic-like and dead spermatozoa. Finally, the ratio of sperm chromatin dispersion stained spermatozoa presented significant differences (p < .05) among treatments in which the diluents added PTX alone demonstrated significantly lower values than control and extenders containing the mixtures of BME and PTX. In conclusion, the observation in this study indicates using of 3 and 6 mM PTX and BME alone may improve significantly (p < .05) the quality of cryopreserved goat spermatozoa.

A meta-analysis on association between CSN3 gene variants and milk yield and composition in cattle

A meta-analysis on the effects of A and B alleles, the most frequent alleles of CSN3 gene, on milk yield and composition traits was conducted by pooling a large dataset consisting of 30 471 genotyped cattle. Four genetic models, comprising dominant (AA + AB vs. BB), recessive (AA vs. AB + BB), additive (AA vs. BB) and co-dominant (AA + BB vs. AB), were employed to analyze data. Standardized mean difference (SMD) was used to measure the size of the effects of A and B alleles of CSN3 on studied traits. Effect sizes of 0.2, 0.5 and 0.8 represent small, medium and large effects, respectively. The results indicate that B allele, in the form of BB genotype, has a significant, but medium effect on lactation yield under dominant (SMD = 0.259, P-value = 0.006) and additive (SMD = 0.279, P-value = 0.035) models. Moreover, a small decrease in the fat percentage occurred in cows having A allele under dominant (SMD = -0.077, P-value = 0.006) and additive (SMD = -0.106, P-value = 0.035) models. Furthermore, CSN3 variants significantly but slightly affect protein percentage under dominant (SMD = -0.146, P-value = 0.000), recessive (SMD = -0.077, P-value = 0.000) and additive (SMD = -0.219, P-value = 0.000) models, showing the negative effect of A allele on this trait. Meta-analysis results reveal that daily milk yield is slightly affected by CSN3 variants under recessive (SMD = 0.056, P-value = 0.033) and additive (SMD = 0.061, P-value = 0.013) genetic models. There is no effect of CSN3 variants on either protein or fat yield. In addition, the effects of CSN3 variants on milk-related traits were not observed under the co-dominant model. Sensitivity and publication bias analyses were carried out to confirm the stability of meta-analyses results.

Effect of a high dose of exogenous phytase and supplementary myo-inositol on mineral solubility of broiler digesta and diets subjected to in vitro digestion assay

This study was conducted to evaluate the effect of microbial phytase and myo-inositol supplementation in low non-phytate phosphorus (nPP) diets on pH and the solubility of minerals in an in vitro digestion procedure (IVDP) and to compare this with digesta from birds fed different diets (grower diets) compared to the in vitro test (starter diets). A total of 660 1-day-old broilers were randomly allotted into 11 dietary treatments and fed a corn-soybean-meal-based diet with recommended nPP (positive control; PC), an nPP-deficient diet (negative control; NC), NC diets supplemented with phytase (500; 1,000; 2,000; 3,000; 4,000; 5,000; and 6,000 FTU/kg), an NC diet plus 0.15% myo-inositol, and an NC diet with reduced Ca level (Ca: nPP ratio same as PC) from 1 to 23 D of age. The pH and Ca solubility of the NC diet was increased compared with the PC when subjected to IVDP (P < 0.05). P solubility in the gizzard and jejunal digesta was reduced in the NC compared with the PC diet and this was also reflected in the IVDP. Phytase addition to the NC diets linearly increased (P < 0.05) the pH value and Ca and P solubilities in both digesta and diets subjected to IVDP. Higher doses of microbial phytase increased (P < 0.05) Zn and Fe solubilities in both digesta and IVDP. Myo-inositol supplementation of the NC diet had no effect on mineral solubility, but decreased (P < 0.05) the pH of the IVDP. Lowering the Ca content of the NC diet decreased (P < 0.05) the pH of the in vitro digested diets and Ca solubility in both broiler digesta and IVDP and also increased (P < 0.05) P solubility in both the jejunal digesta and IVDP. Correlations were noted between the solubility of P in the in vitro assay and that in the gizzard and jejunal digesta, and also with bird performance, confirms the usefulness of in vitro assay.

Association between c.1189G>A single nucleotide polymorphism of GDF9 gene and litter size in goats: A meta-analysis

Litter size is one of the most important traits in goat production and breeding. The most common and presumed single nucleotide polymorphism (SNP) detected in the Growth Differentiation Factor 9 gene is c.1189G>A (rs637044681, Ensembl) which results in an altered sequence of the encoded protein. In some studies, there was no effect of this SNP on litter size, while in other studies there was an effect. In the present study there was a meta-analysis conducted by pooling results from 11 eligible published studies to investigate effects of c.1189G>A polymorphism on litter size using four different genetic models including dominant (AA + AG compared with GG), recessive (AA compared with AG + GG), additive (AA compared with GG) and co-dominant (AA + GG compared with AG). Data were analyzed using fixed and random-effect models based on the I-squared value. Results indicate the c.1189G>A polymorphism is positively associated with litter size with use of the dominant model (SMD = 0.093, 95% CI = 0.028 to 0.158, P-Value = 0.005). There, however, was no effect of the c.1189G>A polymorphism using the recessive (SMD = 0.065, 95% CI = -0.164 to 0.295, P-Value = 0.577), additive (SMD = 0.172, 95% CI = -0.169 to 0.513, P-Value = 0.324) and co-dominant (SMD = -0.083, 95% CI = -0.200 to 0.034, P-Value = 0.164) genetic models. Results from use of the sensitivity analysis indicate the GG genotype affect litter size with use of the additive model (P < 0.01). The results from this meta-analysis indicate the GG genotype is associated with litter size in goats.

Generation of Fam83h knockout mice by CRISPR/Cas9-mediated gene engineering

Family with sequence similarity 83 member H (FAM83H) protein-coding geneplay an essential role in the structural organization, calcification of developing enamel, and keratin cytoskeleton disassembly by recruiting Casein kinase 1 alpha (CSNK1A1) to keratin filaments. In this study, we have applied CRISPR Cas9 nickase (D10A) to knockout (KO) the Fam83h gene in NMRI outbred mice. We generated homozygous Fam83h KO mice ( Fam83h ^Ko/Ko ) through a premature termination codon, which was validated by Sanger sequencing in F0 generation. Next, we also bred the FAM83H KO for two generations. Reverse-transcription polymerase chain reaction and Western blot analysis approved the Fam83h KO mice. The Fam83h KO mice had evidence of normal morphology at the cervical loops, secretory and maturation stages, and mandibular molars. In comparison with the normal wild-type mice ( Fam83h ^W/W ), the F2 homozygous KO ( Fam83h ^Ko/Ko ) had sparse, scruffy coats with small body size and decreased general activity. Also, they had the natural reproductive ability and natural lifespan. In addition, delay in opening the eyes and dry eyes among infant mice were seen. The F1 heterozygous mice looked comparable to the normal wild-type mice ( Fam83h ^W/W ), which showed autosomal recessive inheritance of these phenotypes. The KO of FAM83H had controversial effects on the development of teeth and the formation of enamel. The phenotype defect in dental development and the enamel formation were seen in three mice among four generations. It can be concluded that null FAM83H in outbred mice not only showed the reported phenotypes in null inbred mouse but also showed normal lifespan and reproductive ability; dental deficiency in three homozygous mice; and the symptoms that were similar to the symptoms of dry eye syndrome and curly coat dog syndrome in all four evaluated KO generations.

Association of morphine-induced analgesic tolerance with changes in gene expression of GluN1 and MOR1 in rat spinal cord and midbrain

OBJECTIVES

We aimed to examine association of gene expression of MOR1 and GluN1 at mRNA level in the lumbosacral cord and midbrain with morphine tolerance in male Wistar rats.

MATERIALS AND METHODS

Analgesic effects of morphine administrated intraperitoneally at doses of 0.1, 1, 5 and 10 mg/kg were examined using a hot plate test in rats with and without a history of 15 days morphine (10 mg/kg) treatment. Morphine-induced analgesic tolerance was also assessed on days 1, 5, 10 and 15 of chronic morphine injections. Two groups with history of 15 days injections of saline or morphine (10 mg/kg) were decapitated on day 15 and their lumbosacral cord and midbrain were dissected for evaluating MOR1 and GluN1 gene expression.

RESULTS

The results of the hot plate test showed that morphine (5 and 10 mg/kg) induced significant analgesia in naïve rats but its analgesic effects in rats receiving 15 days injections of morphine (10 mg/kg) was decreased, indicating tolerance to morphine analgesia. The results also showed that the GluN1 gene expression in tolerant rats was decreased by 71% in the lumbosacral cord but increased by 110 % in the midbrain compared to the control group. However, no significant change was observed for the MOR1 gene expression in both areas.

CONCLUSION

It can be concluded that tolerance following administration of morphine (10 mg/kg) for 15 days is associated with site specific changes in the GluN1 gene expression in the spinal cord and midbrain but the MOR1 gene expression is not affected.

Morphine-Induced Analgesic Tolerance Effect on Gene Expression of the NMDA Receptor Subunit 1 in Rat Striatum and Prefrontal Cortex

Introduction:

Morphine is a potent analgesic but its continual use results in analgesic tolerance. Mechanisms of this tolerance remain to be clarified. However, changes in the functions of μ-opioid and N-Methyl-D-aspartate (NMDA) receptors have been proposed in morphine tolerance. We examined changes in gene expression of the NMDA receptor subunit 1 (NR1) at mRNA levels in rat striatum and prefrontal cortex (PFC) after induction of morphine tolerance.

Methods:

Morphine (10 mg/kg, IP) was injected in male Wistar rats for 7 consecutive days (intervention group), but control rats received just normal saline (1 mL/kg, IP). We used a hotplate test of analgesia to assess induction of tolerance to analgesic effects of morphine on days 1 and 8 of injections. Later, two groups of rats were sacrificed one day after 7 days of injections, their whole brains removed, and the striatum and PFC immediately dissected. Then, the NR1 gene expression was examined with a semi-quantitative RT-PCR method.

Results:

The results showed that long-term morphine a administration induces tolerance to analgesic effect of the opioid, as revealed by a significant decrease in morphine-induced analgesia on day 8 compared to day 1 of the injections (P<0.001). The results also showed that the NR1 gene expression at mRNA level in rats tolerant to morphine was significantly increased in the striatum (P<0.01) but decreased in the PFC (P<0.001).

Conclusion:

Therefore, changes in the NR1 gene expression in rat striatum and PFC have a region-specific association with morphine-induced analgesic tolerance.

Forced expression of Hnf4a induces hepatic gene activation through directed differentiation

Embryonic stem (ES) cells are capable of unlimited self-renewal and have a diverse differentiation potential. These unique features make ES cells as an attractive source for developmental biology studies. Having the mature hepatocyte in the lab with functional activities is valuable in drug discovery studies. Overexpression of hepatocyte lineage-specific transcription factors (TFs) becomes a promising approach in pluripotent cell differentiation toward liver cells. Many studies generate transgenic ES cell lines to examine the effects of specific TFs overexpression in cell differentiation. In the present report, we have addressed whether a suspension or adherent model of differentiation is an appropriate way to study the role of Hnf4a overexpression. We generated ES cells that carried a doxycycline (Dox)-inducible Hnf4a using lentiviral vectors. The transduced cells were subjected to induced Hnf4a overexpression through both spontaneous and directed differentiation methods. Gene expression analysis showed substantially increased expression of hepatic gene markers, particularly Ttr and endogenous Hnf4a, in transduced cells differentiated by the directed approach. These results demonstrated that forced expression of TFs during directed differentiation would be an appropriate way to study relevant gene activation and the effects of overexpression in the context of hepatic differentiation.

Hepatic encephalopathy induces site-specific changes in gene expression of GluN1 subunit of NMDA receptor in rat brain

We investigate changes in gene expression of GluN1 subunit of N-Methyl-D-Aspartate (NMDA) receptor in the prefrontal cortex (PFC), hippocampus and striatum in a rat model of hepatic encephalopathy (HE). We used male Wistar rats in which HE was induced after a common bile duct ligation (BDL). The animals were divided into three sets, and each set included three groups of control, sham operated and BDL. In the first set of animals, blood samples collected for biochemical analysis on day 21 of BDL. In the second set, changes in nociception threshold was assessed on day 21 of BDL using a hotplate test. In the third set, whole brain extracted, and the PFC, the hippocampus and the striatum in each rat were immediately dissected. We used a semi-quantitative RT-PCR method for evaluating the GluN1 gene expression. The biochemical analyses showed that plasma levels of ammonia and bilirubin in BDL rats were significantly increased compared to the sham control group on day 21 of BDL (P < 0.01). Nociception threshold was also increased in rats with BDL compared to sham group (P < 0.001). The results revealed that the GluN1 gene expression at mRNA levels in BDL group was decreased by 19 % in the PFC (P < 0.05) but increased by 82 % in the hippocampus (P < 0.01) compared to the sham control group; however, no significant change was observed in the striatum. It can be concluded that HE affects the GluN1 gene expression in rat brain with a site-specific pattern, and the PFC and hippocampus are more sensitive areas than striatum.

Association of Two Polymorphic Codons in P53 and ABCC1 Promoter with Prostate Cancer

BACKGROUND

In prostate cancer, mutated p53 alleles typically contain missense single-base substitution in codon 72 that resides within exons 5-8. Stable p53 proteins in tumor cell nuclei have been associated with malignancy. A role of p53 is the regulation of drug transporters like ABCC1 (MRP1) by an effect on promoter region.

OBJECTIVES

The objective of this study was to identify association of mutations of p53 at codon 72 and 282 and promoter region of ABCC1 with increased risks of prostate cancer.

MATERIALS AND METHODS

Formalin fixed, paraffin-embedded malignant tissues of 45 patients and 45 control samples were evaluated. PCR-RFLP using BstUI for codon 72 and HpaII restriction enzyme for codon 282 p53 gene, and G-1666A promoter region of ABCC1 gene was performed. To assess the frequency of these mutations and to detect new mutations in cancerous samples, PCR-SSCP analysis was performed.

RESULTS

The frequencies of CC, GC and GG genotypes of codon 72 of p53 were 33.33%, 46.67% and 20.00% in patients with cancer and 15.56%, 48.89% and 35.55% in controls, respectively. The relative allele frequencies of ABCC1 promoter polymorphism were 60.00% A and 40.00% G in patients as opposed to 37.78% for A and 62.22% for G in controls. Genotypic frequencies of p53 codon 72 and G1666A of ABCC1 in patients vs. Controls were statistically significant(p<0.05). The study of these samples with PCR-SSCP displayed some new banding patterns.

CONCLUSIONS

The present findings suggest that CC homozygosity in codon 72 of p53 gene and AA genotype in G-1666A of ABCC1 gene may play a role in combination in prostate cancer and increased susceptibility for this malignancy in the Iranian Kurdish population.

Association of CTLA-4 gene 49A/G polymorphism with the incidence of type 1 diabetes mellitus in the Iranian Kurdish population

Cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4) has an inhibitory function on T cells and is critical for the induction of peripheral tolerance. CTLA-4 +49 G allele affects the CTLA-4 function and has been reported to be correlated with a higher risk of various autoimmune diseases including type 1 diabetes (T1D). The present study was conducted to investigate the association between the polymorphism of the CTLA-4 exon 1+49 A/G and susceptibility to TID and type 2 diabetes (T2D) in Kurds living in Iranian Kurdistan. The+49 A/G polymorphism was analyzed in 60 patients with T1D, 56 patients with T2D and 107 control subjects using PCR Single-strand Conformation Polymorphism (SSCP) and restriction fragment length polymorphism methods. All studied populations (T1D, T2D and Controls) were in Hardy-Weinberg equilibrium (p, 0.39, 0.94 and 0.89, respectively). Both+49 G allele (p = 0. 015, OR = 1.86) and +49 A/G genotype frequencies (p = 0. 012, OR = 2.31) were significantly higher in T1D patients than control. There was significant over-representation of the G allele in female T1D patients. No significant differences in +49 G allele and +49 A/G genotype frequencies were found between T2D and control subjects. SSCP analysis did not show new mutation in the amplified segment. The results of this study indicate that CTLA-4+49 A/G gene polymorphism confers genetic susceptibility to T1D but not T2D in the Kurdish population living in Iranian Kurdistan and women carrying the +49 G allele are at greater risk of getting T1D than men having the G allele.

Gene Expression Profile of Calcium/Calmodulin-Dependent Protein Kinase IIα in Rat's Hippocampus during Morphine Withdrawal

INTRODUCTION

Calcium/calmodulin-dependent protein kinase II (CaMKII) which is highly expressed in the hippocampus is known to play a pivotal role in reward-related memories and morphine dependence.

METHODS

In the present study, repeated morphine injections once daily for 7 days was done to induce morphine tolerance in male Wistar rats, after which gene expression profile of α-isoform of CaMKII (CaMKIIα) in the hippocampus was evaluated upon discontinuation of morphine injection over 21 days of morphine withdrawal. Control groups received saline for 7 consecutive days. For gene expression study, rats' brains were removed and the hippocampus was dissected in separate groups on days 1, 3, 7, 14, and 21 since discontinuation of of morphine injection. A semi-quantitative RT-PCR method was used to evaluate the gene expression profile.

RESULTS

Tolerance to morphine was verified by a significant decrease in morphine analgesia in a hotplate test on day 8 (one day after the final repeated morphine injections). Results showed that gene expression of CaMKIIα at mRNA level on day 1, 3, 7, 14 and 21 of morphine withdrawal was significantly altered as compared to the saline control group. Post hoc Tukey's test revealed a significantly enhanced CaMKIIα gene expression on day 14.

DISCUSSION

It can be concluded that CaMKIIα gene expression during repeated injections of morphine is increased and this increase continues up to 14 days of withdrawal then settles at a new set point. Therefore, the strong morphine reward-related memory in morphine abstinent animals may, at least partly be attributed to, the up-regulation of CaMKIIα in the hippocampus over 14 days of morphine withdrawal.

Genetic diversity in mazandaranian native cattle: a comparison with Holstein cattle, using ISSR marker

This study was carried out to investigate genetic diversity in Mazandaranian native cattle population comparised to the Holstein breed, using Inter Simple Sequence Repeats (ISSR) marker. A total of 175 animals, including 71 native and 104 cattle of Holstein breed were screened. The extraction of DNA samples were carried out, using modified salting out method. A 19-mer oligonucleotide, (GA)9C, was used as primer in PCR reactions. The PCR products showed 15 different fragments with length ranged from 120 to 1600 bp in the two breeds.. Genetic variation indexes, including effective number of alleles, Shannon index, Nei's gene diversity and standard genetic distance were estimated, using POPGene software. Generally, the estimated genetic variation indexes showed low levels of diversity in the two breeds. However, Nei's gene diversity and Shannon index estimation was observed almost two folds in native cattle compared to Holstein breed. Less levels of diversity in Holstein cattle may be because of applying intensive selection programs. Conversely, native cattle have been less affected by selection. Therefore, it seems that Mazandaranian native cattle probably are better for breeding programs than Holstein cattle. Results showed that ISSR Markers are reliable and can be used in genetic diversity investigations.

[Allelic polymorphism of kappa-casein gene (CSN3) in Russian cattle breeds and its informative value as a genetic marker]

The frequencies of the kappa-casein gene (CSN3) alleles and genotypes have been determined in five Russian cattle breeds (Bestuzhev, Kalmyk, Russian Black Pied, Yaroslavl, and Yakut breeds) by means of PCR-RFLP analysis using two independent restriction nucleases (HinfI and TaqI) and by allele-specific PCR. Typing alleles A and B of CSN3 is of practical importance, because allele B is correlated with commercially valuable parameters of milk productivity (protein content and milk yield) and improves the cheese yielding capacity. The frequencies of the B allele of CSN3 in the breeds studied vary from 0.16 to 0.50; and those of the AB and BB genotypes, from 0.27 to 0.60 and from 0.02 to 0.23, respectively. The Yaroslavl breed had the highest frequencies of CSN3 allele B and genotype BB (0.50 and 0.23, respectively). The frequencies of the B allele and BB genotype in other breeds studied varied from 0.25 to 0.32 and from 0.03 to 0.09, respectively. In none of the breeds studied have the observed and expected heterozygosities been found to differ from each other significantly. However, the observed genotype distributions significantly differ from the expected one in some herds (in most such cases, an excess of heterozygotes is observed). Two herds of the Yaroslavl breed dramatically differ from each other in the heterozygosity level: a deficit (D = -0.14) and an excess (D = 0.20) of heterozygotes have been observed at the Mikhailovskoe and Gorshikha farms, respectively. In general, however, the heterozygosity of the Yaroslavl breed corresponds to the expected level (D = 0.04). Analysis of breeds for homogeneity with the use of Kulback's test has shown that all cattle breeds studied are heterogeneous, the CSN3 diversity within breeds being higher than that among different breeds, which is confirmed by low Fst values (0.0025-0.0431). Thus, a DNA marker based on CSN3 gene polymorphism is extremely important for breeding practice as a marker of milk quality; however, it is inapplicable to marking differences between breeds or phylogenetic relationships between cattle breeds because of the high diversity with respect to this locus within breeds.