Bizhan Mahmoudi; Hedayatollah Roshanfekr; Mohsen Sari; Mohammad Reza Bakhtiarizadeh
Volume 22, Issue 3 , September 2020, , Pages 337-348
Abstract
The objective of this study was to identify known intergenic lncRNAs related to biological pathways of acidosis in Holstein calves using ruminaltissue. Two groups of healthy calves (N=3) and affected by acidosis (N=3) were compared. Paired-end sequencing method was performed using theHiseq2500 illumine ...
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The objective of this study was to identify known intergenic lncRNAs related to biological pathways of acidosis in Holstein calves using ruminaltissue. Two groups of healthy calves (N=3) and affected by acidosis (N=3) were compared. Paired-end sequencing method was performed using theHiseq2500 illumine platform. Hisat2 software was used to align reads to the bovine reference genome and StringTie software package was used toassemble read files into transcripts. Using next generation sequencing, 1636 genes belonging to known intergenic lncRNAs were identified, of which56 genes showed significant differential expression (P≤0.05). Neighbor genes of known intergenic lncRNAs were determined on bovine genome.Analysis of biological pathways and molecular function showed that five biological pathways were significantly (P≤0.05) enriched. These pathwayswere Apelin signaling pathway, Gap junction, Glucagon signaling pathway, Renin secretion, and AGE-RAGE signaling pathway. Moreover, twomolecular functions including gap junction channel activity, and phosphatidyl inositol phospholipase C activity were significantly (P≤0.05) enriched.Some lncRNAs have different expression in healthy and acidosis samples, and the decreased pH acts as a stimulus to activate some biologicalsignaling pathways. In conclusion, it was indicated that lncRNAs with differential expression between the control group and the group affected byacidosis are associated with pathways related to rumen energy metabolism and signaling. Identified differentially expressed lncRNAs could be used asprognostic in acidosis and biomarkers or promising candidates in animal breeding.
sara Ataei Nazari; abdollah mohammadi sang cheshmeh; Mohammad Reza Bakhtiarizadeh; ali assadi-alamouti; Ali Fouladi Nashta
Volume 22, Issue 3 , September 2020, , Pages 491-500
Abstract
This study was conducted to evaluate the effect of various concentrations of lipopolysaccharide (LPS) in maritaruta medium on oocyte maturation, oocyte developmental competence and metabolites related to maturation medium including glucose, pyruvate, lactate and glutamine. The experimental ...
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This study was conducted to evaluate the effect of various concentrations of lipopolysaccharide (LPS) in maritaruta medium on oocyte maturation, oocyte developmental competence and metabolites related to maturation medium including glucose, pyruvate, lactate and glutamine. The experimental treatments were 0 (control), 0.01, 0.1, 1 and 10 μg/ml of LPS in oocyte maturation medium. The cumulus oocytes complex (COC) were cultured with various concentrations of lipopolysaccharide. After 24 h of oocyte maturation, the medium was collected and the rates of oocyte maturation, cleaved oocyte and oocytes reached to blastocyst stage were analyzed. Oocyte maturation rate was lowest in the treatment with 10 μg/ml of LPS (P<0.05). Among the measured metabolites, only glucose concentration was linearlydecreased in response to increasing levels of LPS in the maturation medium (P<0.05) as treatment with 10 μg/ml of LPS had lower glucose concentration comparing to other treatments. The percentage of oocyte cleavage was significantly lower in treatment with highest level of LPS compared to other treatments (P<0.05). In addition, the treatment with 1 and 10 μg/ml of LPS significantly reduced blastocyst rate compared to control group (P<0.05). According to results of this study, lipopolysaccharide could have detrimental effects on oocyte development and these influences seems to be mediated through pathways related to energy metabolism. Acquiring managerial approaches to control LPS enhancing agents during reproductive season could prevent animal's reproductive failure.
Seyed Nader Albooshoke; Mohammad Reza Bakhtiarizadeh
Volume 21, Issue 2 , July 2019, , Pages 165-180
Abstract
This experiment was carried out to identify lncRNAs associated with skeletal muscle of the Isfahan native chicken and the Ross 708 commercial broiler chicken. To do this, after extraction of RNA from the breast muscle samples at the age of 28 days, paired-end sequencing was performed using the Illume ...
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This experiment was carried out to identify lncRNAs associated with skeletal muscle of the Isfahan native chicken and the Ross 708 commercial broiler chicken. To do this, after extraction of RNA from the breast muscle samples at the age of 28 days, paired-end sequencing was performed using the Illume Hiseq 2000 platform. Hisat2 software was used to align the clean reads to the chicken reference genome and the Stringtie software was used to assemble the transcripts. A total of 1097 lncRNAs were identified as 925 of which were intergenic and 172 were intronic. Also, the number of novel LncRNAs in intergenic and intronic groups were 432 and 128, respectively. Differential gene expression analysis led to the identification of 19 genes and 20 transcripts differentially expressed lncRNAs between two groups. Syntenic analysis showed that differentially expressed lncRNAs are located near by 45 protein encoding genes. Of these, the expression of five gene coding proteins (SCD gene in commercial chickens and GALNT15, KLHDC4, USP7 and ASB1 genes in native chicken) - whose expression was consistent with the expression of their lncRNA - were significantly expressed between two breeds. Functional enrichment analysis of these genes showed that all of them are involved in the skeletal muscle growth. The results of this study showed that the identified lncRNAs probably have the potential to regulate the genes involved in skeletal muscle growth. In this regard, they possibly cause the differences in growth rates between the two chicken breeds.
reza khalkhali ivriq; seyed hassan hafezian; nemat hedayat evrigh; ayoub farhadi; mohammad reza bakhtiarizadeh
Volume 20, Issue 1 , May 2018, , Pages 109-120
Abstract
This study was carried out for identification of deletions, insertions (INDELs) and assessment of their related functional groups in two Iranian dromedary camels (Yazdi camel and Trodi camel) using whole genome sequencing data. In this study, two powerful variant callers (GATK and SAMtools) were used ...
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This study was carried out for identification of deletions, insertions (INDELs) and assessment of their related functional groups in two Iranian dromedary camels (Yazdi camel and Trodi camel) using whole genome sequencing data. In this study, two powerful variant callers (GATK and SAMtools) were used to increase precision and accuracy of detected INDELs. Finally, common identified variants between two programs, after quality filtration, were considered as final INDELs. The present study led to identification of 351429 INDELs for Yazdi camel and 341479 INDELs for Trodi camel. Annotated INDELs that classified as high impact INDELs, were used for further analysis. The numbers of high impact INDELs were 3424 and 3506 for Yazdi and Trodi camels, respectively. To compare Iranian camels with non-Iranian camels, we used whole genome sequencing data of one African origin camel. Comparison of high impact INDELs between three samples showed that 1595 INDELs were common between them. Assessment of gene ontology’s results showed that many of significant terms are related to the ability of camels to withstand serve desert conditions.
Volume 18, Issue 4 , December 2016, , Pages 647-659
Abstract
Bovine mastitis is an inflammation disease of the mammary gland that impose considerable costs to the dairy industry. Regulatory mechanisms of this disease is complex and controlled by various gene regulatory elements and more studies are needed to better understand this disease. In the present study ...
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Bovine mastitis is an inflammation disease of the mammary gland that impose considerable costs to the dairy industry. Regulatory mechanisms of this disease is complex and controlled by various gene regulatory elements and more studies are needed to better understand this disease. In the present study aimed to better understand of regulatory elements involved in mastitis, milk samples of two groups of healthy and infected cows during time series of 0, 12, 24, 36 and 48 hours after contamination were collected. The miRNA-seq data obtained from the milk samples and using the advanced bioinformatics, novel miRNAs, their targets and probability functions, isomirs and novel miRNAs* were identified. The results led to the identification of 92 novel miRNA including 26 miRNAs with homologous and 66 miRNAs without homologous genes in other species. Investigation of the functional groups of predicted targets genes, confirmed the roles of new miRNAs in response to internal and external stimulations, apoptosis and production of immunoglobulin. Furthermore, 135 novel miRNAs were identified. Also, 493 novel isomeric sibling miRNAs (isomers) were discovered that immune related functions of these isomirs were demonstrated in some species like human and mouse. Identification of miRNAs target genes with associated functions in mastitis, including safety, apoptosis and inflammation, can indicated the possible regulatory roles of the identified miRNAs in mastitis.
Zohreh Mozduri; Mohammad Reza Bakhtiarizadeh
Volume 18, Issue 1 , April 2016, , Pages 13-26
Abstract
This study was done to gain insights into transcriptional regulation of negative energy balance (NEB) assoctiated genes. Overexpressed genes in NEB were identified using microarray and RNA-seq data and promoter analysis of these overexpressed genes was applied to identify novel transcription factors. ...
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This study was done to gain insights into transcriptional regulation of negative energy balance (NEB) assoctiated genes. Overexpressed genes in NEB were identified using microarray and RNA-seq data and promoter analysis of these overexpressed genes was applied to identify novel transcription factors. Moreever, STRING database was used to construct a regulatory network of identified transcription factors. The results of the gene expression analysis revealed that eight genes in severe NEB are more frequent and significant (P<0.05) in comparison to the mild NEB. Promoter analysis showed that promoters of overexpressed genes are enriched in putative binding sites for 19 transcription factors. This group included known NEB-associated transcription factor (NF-κB), and a number of transcription factors (such as SP1, ZBP89, NFI, Zf9, MYC, ZBTB7A, FOXF2 and KLF6) that had not been previously reported to be associated with NEB. Based on the present results, 18 new effective candidate trsnacription factors introduced in this study can provide new information to gain a better understanding of the regulatory network involved in NEB.
Raana Jahanbin; Parisa Yazdanshenas; Mehdi Amin Afshar; Abdollah Mohammadi Sangcheshmeh; Hamid Varnaseri; Mohammad Chamani; Mohammad Hasan Nazaran; Mohammad Reza Bakhtiyarizadeh
Volume 17, Issue 2 , October 2015, , Pages 371-380
Abstract
The effect of zinc Nano-particles (Zn- nano- complex) on bull sperm quality after freeze-thawing process studied. Ejaculates collected from four Holstein bulls twice a week. On the day of semen collection, four ejaculates were pooled and diluted with Bioxcell extender containing 0, 10-6, 10-5, 10-4, ...
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The effect of zinc Nano-particles (Zn- nano- complex) on bull sperm quality after freeze-thawing process studied. Ejaculates collected from four Holstein bulls twice a week. On the day of semen collection, four ejaculates were pooled and diluted with Bioxcell extender containing 0, 10-6, 10-5, 10-4, 10-3, 10-2 molar of zinc Nano-complex and frozen. After thawing, sperm motility and motion parameters, plasma membrane integrity, abnormal morphology, plasma membrane functionality and mitochondrial activity were determined. The proportion of the total and progressive motile sperm, the plasma membrane integrity and proportion of the spermatozoa with abnormal morphology was not different among groups. Zinc Nano-complex groups represented a higher plasma membrane functionality than that of control group. Moreover, our flowcytometric data suggested that spermatozoa in the groups of zinc Nano-complex possessed higher mitochondrial activity as compared with the control group. Mitochondrial activity in 10-2 was higher than the 10-6 group. In conclusion, supplementation of zn Nano-complex, can improve the plasma membrane functionality and mitochondrial activity of bull spermatozoa in a dose dependent manner without any deleterious effect on motility parameters.