Identification and characterization of whole blood gene expression and splicing quantitative trait loci during early to mid-lactation of dairy cattle.

BACKGROUND: Characterization of regulatory variants (e.g., gene expression quantitative trait loci, eQTL; gene splicing QTL, sQTL) is crucial for biologically interpreting molecular mechanisms underlying loci associated with complex traits. However, regulatory variants in dairy cattle, particularly in specific biological contexts (e.g., distinct lactation stages), remain largely unknown. In this study, we explored regulatory variants in whole blood samples collected during early to mid-lactation (22-150 days after calving) of 101 Holstein cows and analyzed them to decipher the regulatory mechanisms underlying complex traits in dairy cattle. RESULTS: We identified 14,303 genes and 227,705 intron clusters expressed in the white blood cells of 101 cattle. The average heritability of gene expression and intron excision ratio explained by cis-SNPs is 0.28 ± 0.13 and 0.25 ± 0.13, respectively. We identified 23,485 SNP-gene expression pairs and 18,166 SNP-intron cluster pairs in dairy cattle during early to mid-lactation. Compared with the 2,380,457 cis-eQTLs reported to be present in blood in the Cattle Genotype-Tissue Expression atlas (CattleGTEx), only 6,114 cis-eQTLs (P < 0.05) were detected in the present study. By conducting colocalization analysis between cis-e/sQTL and the results of genome-wide association studies (GWAS) from four traits, we identified a cis-e/sQTL (rs109421300) of the DGAT1 gene that might be a key marker in early to mid-lactation for milk yield, fat yield, protein yield, and somatic cell score (PP4 > 0.6). Finally, transcriptome-wide association studies (TWAS) revealed certain genes (e.g., FAM83H and TBC1D17) whose expression in white blood cells was significantly (P < 0.05) associated with complex traits. CONCLUSIONS: This study investigated the genetic regulation of gene expression and alternative splicing in dairy cows during early to mid-lactation and provided new insights into the regulatory mechanisms underlying complex traits of economic importance.

Gut microbiota-derived trimethylamine N-Oxide: a novel target for the treatment of preeclampsia.

Pre-eclampsia (PE) is the most common complication of pregnancy and seriously threatens the health and safety of the mother and child. Studies have shown that an imbalance in gut microbiota can affect the progression of PE. Trimethylamine N-oxide (TMAO) is an intestinal microbiota-derived metabolite that is thought to be involved in the occurrence of PE; however, its causal relationship and mechanism remain unclear. In this clinical cohort study, including 28 patients with eclampsia and 39 matched healthy controls, fecal samples were collected for 16S rRNA gene sequencing, and serum was collected for targeted metabolomics research. The results showed that the level of TMAO and the abundance of its source bacteria had significantly increased in patients with PE, and were positively correlated with the clinical progression of PE. Fecal microbiota transplantation (FMT) was applied to an antibiotic-depleted-treated mouse model and targeted inhibition of TMAO. The results of the FMT experiment revealed that mice that received fecal microbiota transplantation from patients with PE developed typical PE symptoms and increased oxidative stress and inflammatory damage, both of which were reversed by 3,3-Dimethyl-1-butanol (DMB), a TMAO inhibitor, which also improved pregnancy outcomes in the model mice. Similar results were obtained in the classical NG-Nitroarginine methyl ester (L-NAME) induced PE mouse model. Mechanistically, TMAO promotes the progression of PE by regulating inflammatory and oxidative stress-related signaling pathways, affecting the migration and angiogenesis of vascular endothelial cells, as well as the migration and invasion of trophoblast cells. Our results reveal the role and mechanism of gut microbiota and TMAO in the progression of PE, provides new ideas for exploring the pathogenesis and therapeutic targets of PE, and determines the potential application value of TMAO as a target for PE intervention.

Cross-Species Comparative DNA Methylation Reveals Novel Insights into Complex Trait Genetics among Cattle, Sheep, and Goats.

The cross-species characterization of evolutionary changes in the functional genome can facilitate the translation of genetic findings across species and the interpretation of the evolutionary basis underlying complex phenotypes. Yet, this has not been fully explored between cattle, sheep, goats, and other mammals. Here, we systematically characterized the evolutionary dynamics of DNA methylation and gene expression in 3 somatic tissues (i.e. brain, liver, and skeletal muscle) and sperm across 7 mammalian species, including 3 ruminant livestock species (cattle, sheep, and goats), humans, pigs, mice, and dogs, by generating and integrating 160 DNA methylation and transcriptomic data sets. We demonstrate dynamic changes of DNA hypomethylated regions and hypermethylated regions in tissue-type manner across cattle, sheep, and goats. Specifically, based on the phylo-epigenetic model of DNA methylome, we identified a total of 25,074 hypomethylated region extension events specific to cattle, which participated in rewiring tissue-specific regulatory network. Furthermore, by integrating genome-wide association studies of 50 cattle traits, we provided novel insights into the genetic and evolutionary basis of complex phenotypes in cattle. Overall, our study provides a valuable resource for exploring the evolutionary dynamics of the functional genome and highlights the importance of cross-species characterization of multiomics data sets for the evolutionary interpretation of complex phenotypes in cattle livestock.

The role of RNA epigenetic modification-related genes in the immune response of cattle to mastitis induced by Staphylococcus aureus.

Objective: RNA epigenetic modifications play an important role in regulating immune response of mammals. Bovine mastitis induced by Staphylococcus aureus (S. aureus) is a threat to the health of dairy cattle. There are numerous RNA modifications, and how these modification-associated enzymes systematically coordinate their immunomodulatory effects during bovine mastitis is not well reported. Therefore, the role of common RNA modification-related genes (RMRGs) in bovine S. aureus mastitis was investigated in this study. Methods: In total, 80 RMRGs were selected for this study. Four public RNA-seq data sets about bovine S. aureus mastitis were collected and one additional RNA-seq data set was generated by this study. Firstly, quantitative trait locus (QTL) database, transcriptome-wide association studies (TWAS) database and differential expression analyses were employed to characterize the potential functions of selected enzyme genes in bovine S. aureus mastitis. Correlation analysis and weighted gene co-expression network analysis (WGCNA) were used to further investigate the relationships of RMRGs from different types at the mRNA expression level. Interference experiments targeting the m6A demethylase FTO and utilizing public MeRIP-seq dataset from bovine Mac-T cells were used to investigate the potential interaction mechanisms among various RNA modifications. Results: Bovine QTL and TWAS database in cattle revealed associations between RMRGs and immune-related complex traits. S. aureus challenged and control groups were effectively distinguished by principal component analysis (PCA) based on the expression of selected RMRGs. WGCNA and correlation analysis identified modules grouping different RMRGs, with highly correlated mRNA expression. The m6A modification gene FTO showed significant effects on the expression of m6A and other RMRGs (such as NSUN2, CPSF2, and METTLE), indicating complex co-expression relationships among different RNA modifications in the regulation of bovine S. aureus mastitis. Conclusion: RNA epigenetic modification genes play important immunoregulatory roles in bovine S. aureus mastitis, and there are extensive interactions of mRNA expression among different RMRGs. It is necessary to investigate the interactions between RNA modification genes regulating complex traits in the future.

Mechanical properties and wound healing potential of bacterial cellulose-xyloglucan-dextran hydrogels.

Bacterial cellulose (BC) is a promising material for use as an artificial skin in wound healing application, however, its applications are limited due to its poor malleability. Incorporating non-cellulosic polysaccharides such as dextran and xyloglucan (XG) may enhance its respective wound healing and malleability. This study presents a novel in situ biopreparation method to produce BC-based hybrid hydrogels containing dextran (BC-D) and xyloglucan-dextran (BC-XG-D) with unique mechanical and rheological properties. Structural analysis revealed that dextran of different sizes (10 k, 70 k and 2 M of Mw) form micron-sized particles by loosely binding to cellulosic fibres. The addition of xyloglucan resulted acts as a lubricant in mechanical testing. The BC-XG-D hybrid hydrogels showed a reduced Young's modulus of 4 MPa and a higher maximum tensile strain of 53 % compared to native BC. Moreover, they displayed less plastic but more viscous behaviour under large shear strain deformation. The wound healing animal model experiments demonstrated that the BC-XG-D hybrid hydrogels promoted wound healing process and skin maturation. Overall, these findings contribute to the development of functional BC-based medical materials with desired mechanical and rheological properties that have the potential to accelerate wound healing.

Integrating sperm cell transcriptome and seminal plasma metabolome to analyze the molecular regulatory mechanism of sperm motility in Holstein stud bulls.

Considering that artificial insemination is the most widely used assisted reproductive technique in the dairy industry, the semen quality of bulls is very important for selecting excellent stud bulls. Sperm motility is one of the important traits of semen quality, and related genes may be regulated by environmental factors. Seminal plasma can affect sperm cell transcriptome and further affect sperm motility through exosome or other processes. However, the molecular regulation mechanism of bull sperm motility has not been studied by combining the sperm cell transcriptome with seminal plasma metabolome. The number of motile sperm per ejaculate (NMSPE) is an integrated indicator for assessing sperm motility in stud bulls. In the present study, we selected 7 bulls with higher NMSPE (5,698.55 million +/- 945.40 million) as group H and 7 bulls with lower NMSPE (2,279.76 million +/- 1,305.69 million) as group L from 53 Holstein stud bulls. The differentially expressed genes (DEGs) in sperm cells were evaluated between the two groups (H vs. L). We conducted gene co-expression network analysis (WGCNA) on H and L groups of bulls, as well as two monozygotic twin Holstein bulls with different NMSPE values, to screen candidate genes for NMSPE. The regulatory effect of seminal plasma metabolome on the candidate genes of NMSPE was also investigated. A total of 1,099 DEGs were identified in the sperm cells of H and L groups. These DEGs were primarily concentrated in energy metabolism and sperm cell transcription. The significantly enriched Kyoto encyclopedia of genes and genomes (KEGG) pathways of the 57 differential metabolites were the aminoacyl-tRNA biosynthesis pathway and vitamin B6 metabolism pathway. Our study discovered 14 genes as the potential candidate markers for sperm motility, including FBXO39. We observed a broad correlation between transcriptome of sperm cells and seminal plasma metabolome, such as three metabolites, namely, mesaconic acid, 2-coumaric acid, and 4-formylaminoantipyrine, might regulate FBXO39 expression through potential pathways. The genes related to seminal plasma metabolites expressed in sperm cells are not only located near the quantitative trait loci of reproductive traits, but also enriched in the genome-wide association study signal of sire conception rate. Collectively, this study was the first to investigate the interplays among transcriptome of sperm cells and seminal plasma metabolome from Holstein stud bulls with different sperm motility.

A Holstein stud bull can produce thousands of doses of frozen semen, which are used to distribute its selected genetics to dairy herds all over the world. The semen quality of stud bulls has an impact on the economics of the breeding centers. Our previous study found that monozygotic twin stud bulls showed different semen quality traits and different transcriptomic profiles in sperm cells. The number of motile sperm per ejaculate (NMSPE) is an integrated trait for assessing sperm motility in stud bulls, which is one of the most important semen quality traits. In the present study, we selected 7 stud bulls that had a high NMSPE (named as H group) and 7 stud bulls with low NMSPE (named as L group) from a Chinese Holstein bull population based on 9 yr of semen quality records. In this study, we investigated the sperm cells transcriptomic differences between the two groups and observed the influences of seminal plasma metabolites on the transcriptomic profiles of the sperm cells. The results showed that the expression level of the differentially expressed genes in the sperm cells is closely related to NMSPE. Our study discovered 14 genes as the potential candidate markers for sperm motility, including FBXO39. Our data provide new insights into the improvement of bovine semen quality traits.

Research progress of Astaxanthin nano-based drug delivery system: Applications, prospects and challenges?

Astaxanthin (ASX) is a kind of carotenoid widely distributed in nature, which has been shown to extremely strong antioxidative effects and significant preventive and therapeutic effects on cancer, diabetes, cardiovascular disease, etc. However, its application in the medical field is greatly limited due to its poor water solubility, unstable chemical properties and other shortcomings. In recent years, the nano-based drug delivery systems such as nanoparticles, liposomes, nanoemulsions, nanodispersions, and polymer micelles, have been used as Astaxanthin delivery carriers with great potential for clinical applications, which have been proved that they can enhance the stability and efficacy of Astaxanthin and achieve targeted delivery of Astaxanthin. Herein, based on the pharmacological effects of Astaxanthin, we reviewed the characteristics of various drug delivery carriers, which is of great significance for improving the bioavailability of Astaxanthin.

Heat-induced amorphous aggregates assembly of soy protein modulate in vitro digestibility of potato starch.

This research focused on the characteristics of amorphous aggregates derived from soy protein (SPAA), and their effects on the structural, physicochemical, and digestive properties of potato starch (PS). The SPAA induced by different heating temperatures at pH 7.0 formed an inhomogeneous spherical structure. The presence of SPAA could improve the degree of short-range order of starch, increase thermal stability, reduce pasting viscosity and breakdown, and setback viscosity values of PS. For the PS complexed with SPAAs under simulated cooking conditions, the fraction of digested starch at 300 min (C300) decreased by 6-14 %, and rapid digestible starch content (RDS) decreased by 18-25 %, while the slowly digestible starch (SDS) and resistant starch (RS) increased by 0.4-3 % and 15-23 %, respectively. The SPAA at higher temperature treatment (SPAA130) reduced digestive rate coefficient (k) values more significantly than SPAA at a lower temperature (SPAA70, SPAA90, SPAA110). And the SPAA had no inhibitory effect on α-amylase. The results of this study would significantly contribute to expanding the theoretical information about protein regulation in starch digestion and promoting the development of healthy foods with digestion-resistant properties.

Comparative epigenomics reveals the impact of ruminant-specific regulatory elements on complex traits.

BACKGROUND: Insights into the genetic basis of complex traits and disease in both human and livestock species have been achieved over the past decade through detection of genetic variants in genome-wide association studies (GWAS). A majority of such variants were found located in noncoding genomic regions, and though the involvement of numerous regulatory elements (REs) has been predicted across multiple tissues in domesticated animals, their evolutionary conservation and effects on complex traits have not been fully elucidated, particularly in ruminants. Here, we systematically analyzed 137 epigenomic and transcriptomic datasets of six mammals, including cattle, sheep, goats, pigs, mice, and humans, and then integrated them with large-scale GWAS of complex traits. RESULTS: Using 40 ChIP-seq datasets of H3K4me3 and H3K27ac, we detected 68,479, 58,562, 63,273, 97,244, 111,881, and 87,049 REs in the liver of cattle, sheep, goats, pigs, humans and mice, respectively. We then systematically characterized the dynamic functional landscapes of these REs by integrating multi-omics datasets, including gene expression, chromatin accessibility, and DNA methylation. We identified a core set (n = 6359) of ruminant-specific REs that are involved in liver development, metabolism, and immune processes. Genes with more complex cis-REs exhibited higher gene expression levels and stronger conservation across species. Furthermore, we integrated expression quantitative trait loci (eQTLs) and GWAS from 44 and 52 complex traits/diseases in cattle and humans, respectively. These results demonstrated that REs with different degrees of evolutionary conservation across species exhibited distinct enrichments for GWAS signals of complex traits. CONCLUSIONS: We systematically annotated genome-wide functional REs in liver across six mammals and demonstrated the evolution of REs and their associations with transcriptional output and conservation. Detecting lineage-specific REs allows us to decipher the evolutionary and genetic basis of complex phenotypes in livestock and humans, which may benefit the discovery of potential biomedical models for functional variants and genes of specific human diseases.

Comparative immune-relevant transcriptome reveals the evolutionary basis of complex traits.

Comparing transcriptome can help us reveal the genetic and evolutionary architecture underlying complex phenotypes within and between species. Here, by analyzing 386 publicly available RNA sequencing samples using a uniform bioinformatics pipeline, we systematically compared expression profiles of 10 immune-relevant tissues across humans, mice, pigs, cattle, sheep, and chickens. In general, we demonstrated that gene expression of orthologous genes was conserved within tissues across species. By integrating our findings with results of genome-wide association studies (GWAS) from 17 health-relevant traits in humans and 16,539 health-relevant quantitative trait loci (QTLs) in animals, we found that transcriptionally conserved genes were significantly enriched for more heritability of complex traits, compared to species-specific genes. In conclusion, our results advanced the knowledge of the transcriptome evolution of immune tissues and demonstrated that multi-species transcriptome comparison is highly informative for understanding the genetics of complex traits/disease.

Adaptation of diabetes prevention program for Chinese Americans - a qualitative study.

BACKGROUND: Studies have demonstrated that a culturally and linguistically tailored Diabetes Prevention Program (DPP) can be effective in reducing diabetes risk in Chinese Americans. The purpose of this study was to explore the cultural and linguistic acceptability of the Centers for Disease Control and Prevention's Prevent T2 curriculum in an online format in the Chinese American community in New York City (NYC). METHODS: Three focus groups among a total of 24 Chinese Americans with prediabetes and one community advisory board (CAB) meeting with 10 key stakeholders with expertise in diabetes care and lifestyle interventions were conducted. Each focus group lasted approximately 1 to 1.5 h. All groups were moderated by a bilingual moderator in Chinese. The sessions were audiotaped, transcribed and translated to English for analysis. Using Atlas.ti software and open coding techniques, two researchers analyzed transcripts for thematic analysis. RESULTS: Five key themes were identified: barriers to behavioral changes, feedback on curriculum content and suggestions, web-based intervention acceptability, web-based intervention feasibility, and web-based intervention implementation and modifications. Participants with prediabetes were found to have high acceptability of web-based DPP interventions. Suggestions for the curriculum included incorporating Chinese American cultural foods and replacing photos of non-Asians with photos of Asians. Barriers included lack of access to the internet, different learning styles and low technology self-efficacy for older adults. CONCLUSION: Although the acceptability of web-based DPP in the Chinese American community in NYC is high, our focus group findings indicated that the major concern is lack of internet access and technical support. Providing support, such as creating an orientation manual for easy online program access for future participants, is important.

Hsa_circ_0008726 regulates the proliferation, migration, and invasion of trophoblast cells in preeclampsia through modulating the miR-1290-LHX6 signaling pathway.

BACKGROUND: Preeclampsia (PE) is a serious complication of pregnancy, with a global incidence of about 2%-8%. It is one of the important causes of morbidity and mortality among the pregnant women and perinatal infants. Circular RNA (circRNA) has been confirmed to play an important regulatory role in PE. This study aimed to evaluate the role of hsa_circ_0008726 in the occurrence and development of PE. METHODS: The expression of hsa_circ_0008726 in PE placental tissue and blood was detected by qRT-PCR. CCK-8, wound closure, and Transwell assay were used to measure cell proliferation, migration, and invasion. Bioinformatics prediction, Western blotting, and dual-luciferase reporter gene detection were used to explore the mechanism of hsa_circ_0008726 in HTR8/SVneo cells. RESULTS: The expression level of circ_0008726 in the placental tissue and blood samples of PE patients was significantly higher than that of normal controls. The overexpression of circ_0008726 can significantly inhibit the proliferation, migration, and invasion ability of HTR-8/SVneo cells. While the silence of circ_0008726 showed an opposite effect. Furthermore, hsa_circ_0008726 can modulate the expression of LHX6 by adsorbing miR-1290. CONCLUSION: Hsa_circ_000872 can regulate LHX6 by adsorbing miR-1290 to inhibit PE progression, thus establishing hsa_circ_000872 as a potential target for predicting and treating PE.

The Diagnostic Potential of Gut Microbiota-Derived Short-Chain Fatty Acids in Preeclampsia.

Preeclampsia (PE) is a complex pregnancy-related hypertensive disorder leading to multiorgan dysfunction. It has high maternal, fetal, and neonatal morbidity and mortality rates. The study of gut microbiota and its metabolites in PE deserves further exploration. Thirty-eight pregnant women with PE and 29 healthy pregnant women in the third trimester of their pregnancy were recruited in this study. We used a targeted metabolomics approach to evaluate the short-chain fatty acids (SCFAs) in serum samples. The correlation between SCFAs and clinical characteristics was also explored. The results of mass spectrometry (MS) showed significant differences at the metabolomics level of SCFAs between the PE and healthy control. The metabolic levels of acetate, propionate, isobutyrate, and valerate were significantly increased in the PE group than in the healthy control group. In contrast, caproic acid and butyrate levels were significantly reduced. The correlation analysis showed that urea, systolic, and diastolic blood pressure levels were positively correlated with four types of SCFAs (acetic acid, propionic acid, isobutyric acid, and valeric acid) which increased in the PE group. Furthermore, the neutrophil percentage and the fetal birth weight were negatively correlated with isobutyric acid and valeric acid. In addition, the receiver operating characteristic (ROC) analysis using a generalized linear model showed that multiple SCFAs would be potential diagnostic markers for PE, with high specificity, sensitivity, and area under the curve (AUC). Among them, isobutyric acid (sensitivity: 97.4%, specificity: 100%, AUC = 1.00), propionic acid (sensitivity: 86.8%, specificity: 93.3%, AUC = 0.954) and acetic acid (sensitivity: 86.8%, specificity: 83.3%, AUC = 0.891) depicted significantly higher diagnostic value and potential clinical applications. In summary, the results of this study indicate that SCFAs have the potential to become effective biomarkers for early screening of PE.

Modelling and assessment of plasticizer migration and structure changes in hydrophobic starch-based films.

The structures of starch and starch-based materials determine additives migration from material matrix. Propionylated starch derived from waxy, normal, G50 and G80 starch were selected as the matrix, the amylose effect on plasticizer (triacetin) migration as well as structural changes in hydrophobic starch-based films were discussed. The constant (k1) of first-order rate and initial release rate (V0) of triacetin migration were consistent with the increment of amylose content. Meanwhile, diffusion model disclosed that Fick's second law was apposite to characterize the short-term migration of triacetin, and larger diffusion coefficient (D) values of short- and long-term migration were also found in films with higher amylose content, indicating that amylose-formed structures were in favor of triacetin migration. In comparison of propionylated amylopectin, Van der Waals's interactions between propionylated amylose and triacetin were easier to be weakened with the migration of triacetin, which promoted the decrease of wavenumber of C-O-C, and enlarged the inter-planner spacing of crystalline structures, promoting the formation of amorphous structures and wrinkles and embossments in films with higher amylose content. This work confirmed that regulating the structures of starch were effective to control the migration behavior of additives from starch-based films.

Expression and clinical significance of short-chain fatty acids in pregnancy complications.

Objective: To investigate the expression of short-chain fatty acids (SCFAs)-metabolites of intestinal flora-in gestational complications of gestational diabetes mellitus (GDM), preeclampsia (PE), and intrahepatic cholestasis of pregnancy (ICP), and its clinical significance. Methods: Targeted metabonomics was used to detect SCFAs in the serum of 28 GDM pregnant women, 28 PE pregnant women, 29 ICP pregnant women, and 27 healthy pregnant women (NP); their expression changes were observed; the correlation between SCFAs and clinical characteristics was studied; and their potential as biomarkers for clinical diagnosis was evaluated. Results: There were significant differences in the SCFA metabolic spectrum between the GDM, PE, ICP, and NP groups. Quantitative analysis showed that the content of isobutyric acid in the three pregnancy complications groups (the GDM, PE, and ICP groups) was significantly higher than that in the NP group (p < 0.05), and other SCFAs also showed significant differences in the three pregnancy complications groups compared with the NP group (p < 0.05). Receiver operating characteristic (ROC) curve analysis of the generalized linear model showed that multiple SCFAs were highly sensitive and specific as diagnostic markers in the pregnancy complications groups, where isobutyric acid was highly predictive in GDM (area under the ROC curve (AUC) = 0.764) and PE (AUC = 1), and caproic acid was highly predictive in ICP (AUC = 0.968), with potential clinical application. Conclusion: The metabolic products of intestinal flora, SCFAs, during pregnancy are closely related to pregnancy complications (GDM, PE, and ICP), and SCFAs can be used as potential markers of pregnancy complications.

The comparison of microbial communities in thyroid tissues from thyroid carcinoma patients.

Thyroid carcinoma is a common endocrine organ cancer associated with abnormal hormone secretion, leading to the disorder of metabolism. The intestinal microbiota is vital to maintain digestive and immunologic homeostasis. The relevant information of the microbial community in the gut and thyroid, including composition, structure, and relationship, is unclear in thyroid carcinoma patients. A total of 93 samples from 25 patients were included in this study. The results showed that microbial communities existed in thyroid tissue; gut and thyroid had high abundance of facultative anaerobes from the Proteobacteria phyla. The microbial metabolism from the thyroid and gut may be affected by the thyroid carcinoma cells. The cooccurrence network showed that the margins of different thyroid tissues were unique areas with more competition; the stabilization of microcommunities from tissue and stool may be maintained by several clusters of species that may execute different vital metabolism processes dominantly that are attributed to the microenvironment of cancer.

Comparative Analyses of Sperm DNA Methylomes Among Three Commercial Pig Breeds Reveal Vital Hypomethylated Regions Associated With Spermatogenesis and Embryonic Development.

Identifying epigenetic changes is essential for an in-depth understanding of phenotypic diversity and pigs as the human medical model for anatomizing complex diseases. Abnormal sperm DNA methylation can lead to male infertility, fetal development failure, and affect the phenotypic traits of offspring. However, the whole genome epigenome map in pig sperm is lacking to date. In this study, we profiled methylation levels of cytosine in three commercial pig breeds, Landrace, Duroc, and Large White using whole-genome bisulfite sequencing (WGBS). The results showed that the correlation of methylation levels between Landrace and Large White pigs was higher. We found that 1,040-1,666 breed-specific hypomethylated regions (HMRs) were associated with embryonic developmental and economically complex traits for each breed. By integrating reduced representation bisulfite sequencing (RRBS) public data of pig testis, 1743 conservated HMRs between sperm and testis were defined, which may play a role in spermatogenesis. In addition, we found that the DNA methylation patterns of human and pig sperm showed high similarity by integrating public data from WGBS and chromatin immunoprecipitation sequencing (ChIP-seq) in other mammals, such as human and mouse. We identified 2,733 conserved HMRs between human and pig involved in organ development and brain-related traits, such as NLGN1 (neuroligin 1) containing a conserved-HMR between human and pig. Our results revealed the similarities and diversity of sperm methylation patterns among three commercial pig breeds and between human and pig. These findings are beneficial for elucidating the mechanism of male fertility, and the changes in commercial traits that undergo strong selection.

Controlling plasticizer migration based on crystal structure and micromorphology in propionylated starch-based food packaging nanocomposites.

Migration of additives is an important issue for proper application in food packaging. In this work, propionylated waxy and normal starch-based nanocomposites (PW-N and PN-N) with two different amylopectin content were immersed in distilled water, and structural changes and migration mechanism of plasticizer (triacetin) were discussed in detail. Results showed that when immersion time was prolonged to 150 h, small crystals of PN-N disappeared, and amorphous structures formed gradually in PW-N and PN-N. Exfoliated structures still remained in PW-N with prolonged immersion time, while exfoliated structures gradually formed from intercalated ones in PN-N, and the peak representing d001 (d-spacing) at q = 1.70 nm-1 faded. The migration mechanism of triacetin obeyed the first-order kinetic model and Fick's law; furthermore, in comparison with PW-N, PN-N showed a larger diffusion coefficient (D2 = 12.13 µm2·h-1). These results contributed to expanding the application of starch-based nanocomposites in future environmentally friendly food packaging.

Comprehensive transcriptome and methylome analysis delineates the biological basis of hair follicle development and wool-related traits in Merino sheep.

BACKGROUND: Characterization of the molecular mechanisms underlying hair follicle development is of paramount importance in the genetic improvement of wool-related traits in sheep and skin-related traits in humans. The Merino is the most important breed of fine-wooled sheep in the world. In this study, we systematically investigated the complexity of sheep hair follicle development by integrating transcriptome and methylome datasets from Merino sheep skin. RESULTS: We analysed 72 sequence datasets, including DNA methylome and the whole transcriptome of four gene types, i.e. protein-coding genes (PCGs), lncRNAs, circRNAs, and miRNAs, across four embryonic days (E65, E85, E105, and E135) and two postnatal days (P7 and P30) from the skin tissue of 18 Merino sheep. We revealed distinct expression profiles of these four gene types across six hair follicle developmental stages, and demonstrated their complex interactions with DNA methylation. PCGs with stage-specific expression or regulated by stage-specific lncRNAs, circRNAs, and miRNAs were significantly enriched in epithelial differentiation and hair follicle morphogenesis. Regulatory network and gene co-expression analyses identified key transcripts controlling hair follicle development. We further predicted transcriptional factors (e.g. KLF4, LEF1, HOXC13, RBPJ, VDR, RARA, and STAT3) with stage-specific involvement in hair follicle morphogenesis. Through integrating these stage-specific genomic features with results from genome-wide association studies (GWAS) of five wool-related traits in 7135 Merino sheep, we detected developmental stages and genes that were relevant with wool-related traits in sheep. For instance, genes that were specifically upregulated at E105 were significantly associated with most of wool-related traits. A phenome-wide association study (PheWAS) demonstrated that candidate genes of wool-related traits (e.g. SPHK1, GHR, PPP1R27, CSRP2, EEF1A2, and PTPN1) in sheep were also significantly associated with dermatological, metabolic, and immune traits in humans. CONCLUSIONS: Our study provides novel insights into the molecular basis of hair follicle morphogenesis and will serve as a foundation to improve breeding for wool traits in sheep. It also indicates the importance of studying gene expression in the normal development of organs in understanding the genetic architecture of economically important traits in livestock. The datasets generated here are useful resources for functionally annotating the sheep genome, and for elucidating early skin development in mammals, including humans.