Molecular cloning, bioinformatics analysis and expression of insulin-like growth factor 2 from Tianzhu white yak, Bos grunniens

Age-dependent changes in the expression and localization of LYZL4, LYZL6 and PCNA during testicular development in the Ashidan yak

Lysozyme like 4 (LYZL4), lysozyme like 6 (LYZL6) and proliferating cell nuclear antigen (PCNA) are implicated in the regulation of testicular function, but there was no research reported available on the expression patterns of LYZL4, LYZL6 and PCNA genes at different developmental stages of yak testes. In this study, we used the qRT-PCR, western blotting and immunohistochemistry estimated the LYZL4, LYZL6 and PCNA gene expression and protein lo-calization at different developmental stages of yak testes. The qPCR results showed that the mRNA expression of LYZL4, LYZL6 and PCNA genes significantly increased with age in the testes of yaks. Western blot results showed that the protein abundance of LYZL4, LYZL6 and PCNA in yak testes was significantly higher after puberty than before puberty. Furthermore, the results of immunohistochemistry indicated that LYZL4, LYZL6 and PCNA may be involved in the regulation of spermatogonia proliferation and Leydig cell function in immature testis. In adult yak testes, LYZL4, LYZL6 and PCNA may involve in the development of round spermatids and primary spermatocytes during testicular development. Our results indicated that LYZL4, LYZL6 and PCNA may be involved in the development of Sertoli cells, Leydig cells and gonocytes in yak testes.

Quantitative Proteomic Analysis Reveals Key Proteins Involved in Testicular Development of Yaks

Male reproductive health is largely determined already in the early development of the testis. Although much work has been carried out to study the mechanisms of testicular development and spermatogenesis, there was previously no information on the differences in the protein composition of yak testicles during early development. In this study, the protein profiles in the testicles of 6- (M6), 18- (M18), and 30-month-old (M30) yaks were comparatively analyzed using TMT proteomics. A total of 5521 proteins were identified, with 13, 1295, and 1397 differentially expressed proteins (DEPs) in 30- vs. 18-, 18- vs. 6-, and 30- vs. 6-month-old testes, respectively. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that DEPs were mainly involved in signaling pathways related to testicular development and spermatogenesis, including the MAPK, PI3K-Akt, Wnt, mTOR, TGF-β, and AMPK signaling pathways. Furthermore, we also identified eight potential proteins (TEX101, PDCL2, SYCP2, SYCP3, COL1A1, COL1A2, ADAM10, and ATF1) that may be related to the testicular development and spermatogenesis of yaks. This study may provide new insights into the molecular mechanisms of the testicular development and spermatogenesis of yaks.

Screening and Identification of Differential Ovarian Proteins before and after Induced Ovulation via Seminal Plasma in Bactrian Camels

Simple Summary

Camelidae are induced ovulators whose ovulation is tightly regulated by multiple factors. Understanding the biological mechanisms underlying follicular development, hormone secretion, and ovulation requires investigating the potential molecular pathways involved in these mechanisms. However, little is known about these molecular pathways in Bactrian camels. To screen and identify candidate biomarkers after seminal plasma (SP)-induced ovulation in the ovaries, we performed comprehensive proteomic and molecular biological analyses of the ovaries from camels that were intramuscularly injected with either seminal plasma or phosphate-buffered saline. Identification of these candidate biomarkers will enable a better understanding of reproduction in Bactrian camels. Our findings suggest candidate proteins for further studies on the molecular mechanisms of induced ovulation.

Abstract

Camelidae are induced ovulators whose ovulation is tightly regulated by multiple factors. Understanding the biological mechanisms underlying follicular development, hormone secretion, and ovulation requires investigating the potential molecular pathways involved. However, little is known about these pathways in Bactrian camels. To screen and identify candidate biomarkers after inducing ovulation, this study performed comprehensive proteomic and molecular biological analyses of the ovaries from two camel groups (n = 6). We identified 5075 expressed ovarian proteins, of which 404 were differentially expressed (264 upregulated, 140 downregulated) (p < 0.05 or p < 0.01), in samples from plasma-induced versus control camels. Gene ontology annotation identified the potential functions of the differentially expressed proteins (DEPs). These results validated the differential expression for a subset of these proteins using Western blot (p < 0.05) and immunofluorescence staining. Three DEPs (FST, NR5A1, and PRL) were involved in neurochemical signal transduction, as well as endocrine and reproductive hormone regulatory processes. The Kyoto Encyclopedia of Genes and Genomes analysis indicated the involvement of several pathways, including the calcium, cAMP, gonadotropin-releasing hormone, MAPK, and neuroactive ligand–receptor signaling pathways, suggesting that induced ovulation depends on the hypothalamic–pituitary–ovarian axis. Identifying these candidate biomarkers enables a better understanding of Bactrian camel reproduction. Ovarian proteomic profiling and the measurement of selected proteins using more targeted methods is a promising approach for studying induced-ovulation mechanisms.

Histological Analysis, Bioinformatics Profile, and Expression of Methylenetetrahydrofolate Reductase (MTHFR) in Bovine Testes

Simple Summary

To date, several genes have been sequenced but their corresponding protein characteristics remain unknown. This study highlights the histological structure of bovine (yellow-cattle and yak) testes as a build-up to exploring the bioinformatics profile and expression characteristics of methylenetetrahydrofolate reductase (MTHFR) in bovine testes. Our findings suggest that yellow-cattle testis have similar anatomical characteristics with that of yak, except for the weight or size, for which that of yellow-cattle is significantly higher or greater than yak. We also found that the secondary and 3D protein structures of MTHFR were similar to that of humans, with differences in the number of nucleotides, amino acids, and some physico-chemical characteristics. Moreover, MTHFR mRNA expression was higher in adult yellow-cattle and yak compared to their juvenile ones, however, its protein expression was higher but not statistically significant in adult yellow-cattle and yak compared to the juvenile ones. This provides a basis for further investigations into the regulatory function of MTHFR in bovine testes.

Abstract

Methylenetetrahydrofolate reductase (MTHFR), an enzyme expressed in mammalian testes, exerts a direct effect on spermatogenesis; however, its protein characteristics in bovine testes remain unknown. Here, we analysed bovine testicular structure, MTHFR bioinformatics profile, mRNA, and protein expression characteristics in yellow-cattle (y-c) and yak testis using histological procedures, bioinformatics analysis, qRT-PCR, and western blot. Testes from 13 bovines, ≤2 years juvenile (y-c, n = 3; yak, n = 3) and ≥3 years adult (y-c, n = 3; yak, n = 4) were collected and analysed. Anatomical characteristics of testis in y-c and yak were similar except the weight or size for which that of y-c was significantly higher or greater than yak. In y-c, an open reading frame (ORF) for 2600 nucleotides sequence, encoding 655 amino acids showed high homology with zebu cattle (99.51%) and wild yak (98.68%). Secondary and 3D protein structures were similar to that of humans with differences in the number of nucleotides, amino acids, and some physico-chemical characteristics. MTHFR mRNA expression in y-c and yak were significantly higher in adult testes compared with juvenile ones. However, its protein expression was higher, but not statistically significant, in adult y-c and yak compared to the juvenile ones. The highlights and inferences of these and other findings are discussed.

Comparative analysis of Longissimus dorsi tissue from two sheep groups identifies differentially expressed genes related to growth, development and meat quality

From a genetic perspective, the advantages of crossbreeding in sheep are unclear. In the present study, a comparative transcriptomic analysis was performed using Longissimus dorsi tissues from two sheep groups in order to identify differentially expressed genes (DEGs) related to growth, development and meat quality. Compared to Small Tail Han sheep, a total of 874 DEGs were identified in the crossbred sheep. Among these DEGs, 30, 116 and 32 DEGs were related to growth, development and meat quality, respectively. Seven DEGs highlighted by functional analysis as playing crucial roles in growth, development and meat quality were validated by the gene-act-network and co-expression-network. The expression levels of DEG mRNAs and proteins were further confirmed using RT-qPCR and western blot analyses. The results were consistent with the comparative transcriptome data. The data from this transcriptomic analysis will help to understand genetic heterosis and molecular-assisted breeding in sheep.

An Untargeted Metabolomics Investigation of Jiulong Yak (Bos grunniens) Meat by 1H-NMR

Yak represents the main meat source for Tibetan people. This work aimed to investigate the metabolome of raw meat from Jiulong yaks, focusing on specimens farmed and harvested locally through traditional procedures. Untargeted nuclear magnetic resonance spectroscopy (¹H-NMR) was selected as the analytical platform. Samples from longissimus thoracis, trapezius, triceps brachii and biceps femoris muscles, with different prevalences of red and white fibers, were selected. Among the fifty-three metabolites quantified in each of them, carnitine, carnosine, creatine and taurine are known for their bioactive properties. Twelve molecules were found to be differently concentrated in relation to muscle type. Longissimus thoracis, compared to biceps femoris, had higher concentrations of carnosine and formate and lower concentrations of mannose, inosine, threonine, IMP, alanine, valine, isoleucine, tyrosine, phenylalanine and leucine. A metabolic pathway analysis suggested that the main pathways differing among the muscles were connected to the turnover of amino acids. These results contribute to a deeper understanding of yak raw meat metabolism and muscle type differences, which can be used as an initial reference for the meat industry to set up muscle-specific investigations. The possibility of simultaneously quantifying several bioactive compounds suggests that these investigations could revolve around meat’s nutritional value.

Yak FOXO1 and FOXO3 SNPs and association with production traits, and their promotes cells apoptosis via RNAi

FOXOs transcription factors not only play key roles in glucose metabolism, muscle atrophy and energy homeostasis but also play crucial transcriptional regulatory roles in the cell's metabolism, orchestrating programs of gene expression that regulate cell apoptosis, cell-cycle progression and oxidative stress resistance. However, the specific function of FOXOs promoting fibroblasts proliferation and apoptosis are still unknown. Thus, we used the High-Resolution Melting (HRM) and RNA interference methods to detect SNPs and function. We found one SNP in the exon of FOXO1, three SNPs were identified in the exon of FOXO3, and three SNPs and production traits were significantly different. The siRNA sequence of yak FOXO1 and FOXO3 were transfected into the yak fibroblasts, and effects were detected by a series of assays to reveal the function in yak fibroblasts. The results demonstrated that down-regulated expression of FOXO1 and FOXO3 resulted in up-regulated the expression of BAX, Caspase9 and Caspase3, and down-regulated the expression level of anti-apoptotic gene of BCL2. The apoptotic situation was consistent with results of the flow cytometry and Tunel test cell cycle and cell vitality results revealed that knockdown FOXO1 and FOXO3 resulted in increased P27 expression level and decreased CyclinD1. Meanwhile, cell vitality was also decreased. These results demonstrated that FOXO1 and FOXO3 are two novel regulatory factors to suppress cells proliferation and promote cells apoptosis. Furthermore, these results provide evidence that FOXO1 and FOXO3 play a functional role in cell apoptosis.

Comparative Transcriptome Analysis Identifying the Different Molecular Genetic Markers Related to Production Performance and Meat Quality in Longissimus Dorsi Tissues of MG × STH and STH Sheep

Crossbred sheep have many prominent traits, such as excellent production performance and high-quality meat, when compared to local sheep breeds. However, the genetic molecular markers related to these characteristics remain unclear. The crossbred MG × STH (small-tailed Han sheep (STH) × Mongolian sheep (MG)) breed and the STH breed were selected to measure production performance and meat quality. We used 14 indexes of production performance and meat quality, which in the MG × STH population showed significant differences compared to the STH breed. Subsequently, the longissimusdorsi from the two sheep were subjected to comparative transcriptomic analyses to identify differentially expressed genes (DEGs) related to production performance and meat quality. A total of 874 DEGs were identified between the two sheep groups. A total of 110 unique DEGs related to sheep production performance and meat quality were selected as the candidate DEGs. We found 6 production-performance-related and 30 meat-quality-related DEGs through a correlation analysis, including SPARC, ACVRL1, FNDC5 and FREM1. The expression levels of 11 DEGs were validated by real-time PCR, and the results were in accordance with the results of the comparative transcriptomic and correlation analyses. These results will assist in understanding sheep heterosis and molecular marker-assisted selection.

Characterization of Yak Common Biofluids Metabolome by Means of Proton Nuclear Magnetic Resonance Spectroscopy

The aim of this study was to evaluate the metabolic profiles of yak (Bos grunniens) serum, feces, and urine by using proton nuclear magnetic resonance (¹H-NMR), to serve as a reference guide for the healthy yak milieu. A total of 108 metabolites, giving information about diet, protein digestion, and energy generation or gut-microbial co-metabolism, were assigned across the three biological matrices. A core metabolome of 15 metabolites was ubiquitous across all biofluids. Lactate, acetate, and creatinine could be regarded as the most abundant metabolites in the metabolome of serum, feces, and urine, respectively. Metabolic pathway analysis showed that the molecules identified could be able to give thorough information about four main metabolic pathways, namely valine, leucine, and isoleucine biosynthesis; phenylalanine, tyrosine, and tryptophan biosynthesis; glutamine and glutamate metabolism; and taurine and hypotaurine metabolism.

Yak OXGR1 promotes fibroblast proliferation via the PI3K/AKT pathways

Oxoglutarate receptor 1 (OXGR1), as one of the intermediates in G protein-coupled receptors (GPCRs), plays a crucial role in the citric acid cycle receptor of α-ketoglutarate and metabolism. GPCR can control the cell proliferation by regulating the downstream signaling of G protein signaling pathways. The PI3K/AKT pathway transmits the downstream signals of GPCRs and receptor tyrosine kinases. However, the specific role of OXGR1 promoting cell proliferation and differentiation are still unknown. In current study, the over-expression vector and knockdown sequence of yak OXGR1 were transfected into yak fibroblasts, and the effects were detected by a series of assays. The results revealed that OXGR1 expression in yak lung parenchyma tissue was significantly higher than that of other tissues. In yak fibroblasts, the upregulated expression of OXGR1 resulted in activating the PIK3CG (downstream signal) of the PI3K/AKT1 pathway that can upregulated the expression of proliferation genes ( CDK1, PCNA, and CyclinD1) and promote cell proliferation. Conversely, the downregulated expression of OXGR1 inhibited cell proliferation via PI3K/AKT1 pathway. Cell cycle and cell proliferation assays demonstrated that over-expression of OXGR1 can enhanced the DNA synthesis and promoted yak fibroblasts proliferation. While the conversely, knockdown of OXGR1 can decreased DNA synthesis and inhibited cell proliferation. These results illustrated that changes of OXGR1 expression can trigger the fibroblasts proliferation via PI3K/AKT signaling pathway, which indicating that OXGR1 is a novel regulator for cell proliferation and differentiation. Furthermore, these results provide evidence supporting the functional role of GPCRs-PI3K-AKT1 and OXGR1 in cell proliferation.

Comprehensive Analysis of MicroRNA⁻Messenger RNA from White Yak Testis Reveals the Differentially Expressed Molecules Involved in Development and Reproduction

Testis development is a vital and tightly regulated process in mammals. Understanding the biological mechanisms underlying testis development will benefit the animal reproduction industry. Expression changes in microRNA and messenger RNA in response to dynamic regulation effects have been associated with this process. However, very little is known about the roles of these molecules in yak development. Using whole-genome small RNA and messenger RNA sequencing, we performed a comprehensive analysis of the microRNA–messenger RNA interaction network expression in the testicles of Tianzhu white yaks during three developmental stages. Using Short Time-series Expression Miner analysis we identified 589 differentially expressed microRNAs (DERs) and 3383 differentially expressed messenger RNAs (DEGs) in the three age groups. A total of 93 unique DEGs are primarily involved in reproduction and testis development. Subsequently, four integration networks were constructed according to the DEGs and DERs in three biological processes. Nineteen DEGs were potentially regulated by 60 DERs, of which miR-574 and target gene AURKA played a crucial role in yak testis development and reproduction. The results of this study provide a basis for further exploration of the microRNA–messenger RNA interactions in testis development and reproduction and aid in uncovering the molecular mechanisms of spermatogenesis in male mammals.

Yak IGF2 Promotes Fibroblast Proliferation Via Suppression of IGF1R and PI3KCG Expression

Insulin-like growth factor 2 (IGF2) recapitulates many of the activities of insulin and promotes differentiation of myoblasts and osteoblasts, which likely contribute to genetic variations of growth potential. However, little is known about the functions and signaling properties of IGF2 variants in yaks. The over-expression vector and knockdown sequence of yak IGF2 were transfected into yak fibroblasts, and the effects were detected by a series of assays. IGF2 expression in yak muscle tissues was significantly lower than that of other tissues. In yak fibroblasts, the up-regulated expression of IGF2 inhibits expression of IGF1 and insulin-like growth factor 2 receptor (IGF2R) and significantly up-regulates expression of IGF1R. Inhibition of IGF2 expression caused the up-regulates expression of IGF1, IGF1R and IGF2R. Both over-expression and knockdown of IGF2 resulted in up-regulation of threonine protein kinase 1 (Akt1) expression and down-regulation of phosphatidylinositol 3-kinase, catalytic subunit gamma (PIK3CG). Cell cycle and cell proliferation assays revealed that over-expression of IGF2 enhanced the DNA synthesis phase and promoted yak fibroblasts proliferation. Conversely, knockdown of IGF2 decreased DNA synthesis and inhibited proliferation. These results suggested that IGF2 was negatively correlated with IGF1R and PIK3CG and demonstrated an association with the IGFs-PI3K-Akt (IGFs-phosphatidylinositol 3-kinase- threonine protein kinase) pathway in cell proliferation and provided evidence supporting the functional role of IGF2 for use in improving the production performance of yaks.

Chicoric Acid Improves Heart and Blood Responses to Hypobaric Hypoxia in Tibetan Yaks

Yak is a wild bovine species living on the Qinghai Tibet Plateau that demonstrates good adaptability to the hypoxic environment. Chicoric acid, a natural phenolic compound, is known as having anti-oxidant, antiviral, anti-inflammatory and analgesic properties. However, its effect on hypoxia adaptability of yak is still unclear. In this study 40 yaks were selected that were of similar age, parity and weight, and divided into the control group and experimental groups 1, 2, 3, randomly. Results showed that chicoric acid significantly improved RBC, HGB, and WBC. There are significantly beneficial effects to increasing total protein contents ([Formula: see text]): all treatments increased HDL-C contents, and supplementations 100[Formula: see text]mg/h significantly decreased the content of TG on the 60th day ([Formula: see text]). Contents of the serum related enzymes like ALP, GOP and GPT showed varying degrees of change, but no significant differences and the indexes of anti-oxidant capacity (T-AOC and GSH-Px) were significantly improved ([Formula: see text]), but MDA was decreased ([Formula: see text]) under the action of the chicoric acid. Hypoxia-inducible factor in serum such as HIF-2[Formula: see text], EPO, ROS, Fe[Formula: see text] and Tf are all significantly decreased ([Formula: see text]). The myocardial mitochondrial parameters mtDNA, UCP2, PGC1-[Formula: see text], NRF1 and mitochondrial complexes were altered remarkably. Some indicators of glucose metabolism presented variation trends. Taken together, chicoric acid has shown a positive effect on the adaptive ability of yak in high altitude, hypoxic environment in plateau areas. Our findings reported a new potential means to enhance immunity and inflammatory response and improve the anti-oxidant capacity.

Identification and verification of potential piRNAs from domesticated yak testis

PIWI-interacting RNAs (piRNA) are small non-coding RNA molecules expressed in animal germ cells that interact with PIWI family proteins to form RNA–protein complexes involved in epigenetic and post-transcriptional gene silencing of retrotransposons and other genetic elements in germ line cells, including reproductive stem cell self-sustainment, differentiation, meiosis and spermatogenesis. In the present study, we performed high-throughput sequencing of piRNAs in testis samples from yaks in different stages of sexual maturity. Deep sequencing of the small RNAs (18–40 nt in length) yielded 4,900,538 unique reads from a total of 53,035,635 reads. We identified yak small RNAs (18–30 nt) and performed functional characterization. Yak small RNAs showed a bimodal length distribution, with two peaks at 22 nt and >28 nt. More than 80% of the 3,106,033 putative piRNAs were mapped to 4637 piRNA-producing genomic clusters using RPKM. 6388 candidate piRNAs were identified from clean reads and the annotations were compared with the yak reference genome repeat region. Integrated network analysis suggested that some differentially expressed genes were involved in spermatogenesis through ECM–receptor interaction and PI3K-Akt signaling pathways. Our data provide novel insights into the molecular expression and regulation similarities and diversities in spermatogenesis and testicular development in yaks at different stages of sexual maturity.

Insulin-like growth factor I (IGF-I) in Chinese alligator, Alligator sinensis: Molecular characterization, tissue distribution and mRNA expression changes during the active and hibernating periods

The Chinese alligator Alligator sinensis is an endangered species endemic to China, up to date, little is known about the regulation of its growth and development. Insulin-like growth factor I (IGF-I) plays a vital role in regulating vertebrate growth and development. In this study, the full-length cDNA of IGF-I in Chinese alligator (caIGF-I) was obtained for the first time, it contains 890-bp nucleotides encoding a 153-amino acid precursor, the mature caIGF-I consists of 70 amino acids by cleaving the signal peptide and C-terminal extension (E domain). The caIGF-I contains all the features of IGF-I peptide with B, C, A, and D domains and the six conservative cysteine residues involved in the stable tertiary structure. Multiple alignment analysis showed that the amino acid sequence of caIGF-I shares high identity with American alligator Alligator mississippiensis (100%) and birds (95-97%). Phylogenetic tree analysis of the IGF-I amino acid sequences indicated that alligators cluster into the bird branch. Real-time quantitative PCR technique showed that caIGF-I is widely expressed in all the examined tissues with the highest expression level in liver, higher in pancreas and oviduct while lower in heart, spleen, lung, kidney, stomach, intestines, ovary and muscles. During hibernation, the caIGF-I expression level decreased significantly in liver, pancreas, oviduct and kidney, while did not significantly change in heart, spleen, lung, stomach, small intestine, ovary and muscles. The mRNA expression changes during the two periods implicate that caIGF-I might play an important role in the regulation of feeding and growth in the Chinese alligator.

Dynamic transcriptome profiles of skeletal muscle tissue across 11 developmental stages for both Tongcheng and Yorkshire pigs

Background

The growth and development of skeletal muscle directly impacts the quantity and quality of pork production. Chinese indigenous pig breeds and exotic species vary greatly in terms of muscle production and performance traits. We present transcriptome profiles of 110 skeletal muscle samples from Tongcheng (TC) and Yorkshire (YK) pigs at 11 developmental periods (30, 40, 55, 63, 70, 90, and 105 days of gestation, and 0, 1, 3, and 5 weeks of age) using digital gene expression on Solexa/Illumina’s Genome Analyzer platform to investigate the differences in prenatal and postnatal skeletal muscle between the two breeds.

Results

Muscle morphological changes indicate the importance of primary fiber formation from 30 to 40 dpc (days post coitus), and secondary fiber formation from 55 to 70 dpc. We screened 4,331 differentially expressed genes in TC and 2,259 in YK (log₂ ratio >1 and probability >0.7). Cluster analysis showed different gene expression patterns between TC and YK pigs. The transcripts were annotated in terms of Gene Ontology related to muscle development. We found that the genes CXCL10, EIF2B5, PSMA6, FBXO32, and LOC100622249 played vital roles in the muscle regulatory networks in the TC breed, whereas the genes SGCD, ENG, THBD, AQP4, and BTG2 played dominant roles in the YK breed. These genes showed breed-specific and development-dependent differential expression patterns. Furthermore, 984 genes were identified in myogenesis. A heat map showed that significantly enriched pathways (FDR <0.05) had stage-specific functional regulatory mechanisms. Finally, the differentially expressed genes from our sequencing results were confirmed by real-time quantitative polymerase chain reaction.

Conclusions

This study detected many functional genes and showed differences in the molecular mechanisms of skeletal muscle development between TC and YK pigs. TC pigs showed slower muscle growth and more complicated genetic regulation than YK pigs. Many differentially expressed genes showed breed-specific expression patterns. Our data provide a better understanding of skeletal muscle developmental differences and valuable information for improving pork quality.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1580-7) contains supplementary material, which is available to authorized users.