Integrated analysis of genomics and transcriptomics revealed the genetic basis for goaty flavor formation in goat milk.

Goat milk exhibits a robust and distinctive "goaty" flavor. However, the underlying genetic basis of goaty flavor remains elusive and requires further elucidation at the genomic level. Through comparative genomics analysis, we identified divergent signatures of certain proteins in goat, sheep, and cow. MMUT has undergone a goat-specific mutation in the B12 binding domain. We observed the goat FASN exhibits nonsynonymous mutations in the acyltransferase domain. Structural variations in these key proteins may enhance the capacity for synthesizing goaty flavor compounds in goat. Integrated omics analysis revealed the catabolism of branched-chain amino acids contributed to the goat milk flavor. Furthermore, we uncovered a regulatory mechanism in which the transcription factor ZNF281 suppresses the expression of the ECHDC1 gene may play a pivotal role in the accumulation of flavor substances in goat milk. These findings provide insights into the genetic basis underlying the formation of goaty flavor in goat milk. STATEMENT OF SIGNIFICANCE: Branched-chain fatty acids (BCFAs) play a crucial role in generating the distinctive "goaty" flavor of goat milk. Whether there is an underlying genetic basis associated with goaty flavor is unknown. To begin deciphering mechanisms of goat milk flavor development, we collected transcriptomic data from mammary tissue of goat, sheep, cow, and buffalo at peak lactation for cross-species transcriptome analysis and downloaded nine publicly available genomes for comparative genomic analysis. Our data indicate that the catabolic pathway of branched-chain amino acids (BCAAs) is under positive selection in the goat genome, and most genes involved in this pathway exhibit significantly higher expression levels in goat mammary tissue compared to other species, which contributes to the development of flavor in goat milk. Furthermore, we have elucidated the regulatory mechanism by which the transcription factor ZNF281 suppresses ECHDC1 gene expression, thereby exerting an important influence on the accumulation of flavor compounds in goat milk. These findings provide insights into the genetic mechanisms underlying flavor formation in goat milk and suggest further research to manipulate the flavor of animal products.

Genome-wide association study provided insights into the polled phenotype and polled intersex syndrome (PIS) in goats.

BACKGROUND: Breeding polled goats is a welfare-friendly approach for horn removal in comparison to invasive methods. To gain a comprehensive understanding of the genetic basis underlying polledness in goats, we conducted whole-genome sequencing of 106 Xinong Saanen dairy goats, including 33 horned individuals, 70 polled individuals, and 3 polled intersexuality syndrome (PIS) individuals. METHODS: The present study employed a genome-wide association study (GWAS) and linkage disequilibrium (LD) analysis to precisely map the genetic locus underlying the polled phenotype in goats. RESULTS: The analysis conducted in our study revealed a total of 320 genome-wide significant single nucleotide polymorphisms (SNPs) associated with the horned/polled phenotype in goats. These SNPs exhibited two distinct peaks on chromosome 1, spanning from 128,817,052 to 133,005,441 bp and from 150,336,143 to 150,808,639 bp. The present study identified three genome-wide significant SNPs, namely Chr1:129789816, Chr1:129791507, and Chr1:129791577, as potential markers of PIS-affected goats. The results of our LD analysis suggested a potential association between MRPS22 and infertile intersex individuals, as well as a potential association between ERG and the polled trait in goats. CONCLUSION: We have successfully identified three marker SNPs closely linked to PIS, as well as several candidate genes associated with the polled trait in goats. These results may contribute to the development of SNP chips for early prediction of PIS in goats, thereby facilitating breeding programs aimed at producing fertile herds with polled traits.

Fatty Acid Desaturation Is Suppressed in Mir-26a/b Knockout Goat Mammary Epithelial Cells by Upregulating INSIG1.

MicroRNA-26 (miR-26a and miR-26b) plays a critical role in lipid metabolism, but its endogenous regulatory mechanism in fatty acid metabolism is not clear in goat mammary epithelial cells (GMECs). GMECs with the simultaneous knockout of miR-26a and miR-26b were obtained using the CRISPR/Cas9 system with four sgRNAs. In knockout GMECs, the contents of triglyceride, cholesterol, lipid droplets, and unsaturated fatty acid (UFA) were significantly reduced, and the expression of genes related to fatty acid metabolism was decreased, but the expression level of miR-26 target insulin-induced gene 1 (INSIG1) was significantly increased. Interestingly, the content of UFA in miR-26a and miR-26b simultaneous knockout GMECs was significantly lower than that in wild-type GMECs and miR-26a- and miR-26b-alone knockout cells. After decreasing INSIG1 expression in knockout cells, the contents of triglycerides, cholesterol, lipid droplets, and UFAs were restored, respectively. Our studies demonstrate that the knockout of miR-26a/b suppressed fatty acid desaturation by upregulating the target INSIG1. This provides reference methods and data for studying the functions of miRNA families and using miRNAs to regulate mammary fatty acid synthesis.

The pomegranate (Punica granatum L.) draft genome dissects genetic divergence between soft- and hard-seeded cultivars.

Complete and highly accurate reference genomes and gene annotations are indispensable for basic biological research and trait improvement of woody tree species. In this study, we integrated single-molecule sequencing and high-throughput chromosome conformation capture techniques to produce a high-quality and long-range contiguity chromosome-scale genome assembly of the soft-seeded pomegranate cultivar 'Tunisia'. The genome covers 320.31 Mb (scaffold N50 = 39.96 Mb; contig N50 = 4.49 Mb) and includes 33 594 protein-coding genes. We also resequenced 26 pomegranate varieties that varied regarding seed hardness. Comparative genomic analyses revealed many genetic differences between soft- and hard-seeded pomegranate varieties. A set of selective loci containing SUC8-like, SUC6, FoxO and MAPK were identified by the selective sweep analysis between hard- and soft-seeded populations. An exceptionally large selective region (26.2 Mb) was identified on chromosome 1. Our assembled pomegranate genome is more complete than other currently available genome assemblies. Our results indicate that genomic variations and selective genes may have contributed to the genetic divergence between soft- and hard-seeded pomegranate varieties.

[Effect of 18-ß Glycyrrhetinic Acid on the Endoplasmic Reticulum of Nasal Epithelial Cells in Allergic Rhinitis Model Rats].

OBJECTIVE: To explore the effect of 18-ß glycyrrhetinic acid (GA) on the endoplasmic reticulum of nasal epithelial cells in allergic rhinitis (AR) model rats. METHODS: Totally 96 Wistar rats were randomly divided into the blank group, the AR model group, the loratadine group, the GA group, 24 in each group. AR models were established by peritoneally injecting ovalbumin (OVA). Morphological scoring was performed. GA at 21. 6 mg/kg was intragastrically administered to rats in the GA group. Nasal mucosal tissues were taken for electron microscopic examinations at the second, fourth, sixth, and tenth week after drug intervention. RESULTS: The overlapping score was 2.10 ± 0.45 in the blank group, 5.10 ± 0.56 in the loratadine group, 5.10 ± 0.56 in the AR model group, 5.20 ± 0.78 in the GA group, showing statistical difference when compared with the blank group (P < 0.01). Results under transmission electron microscope showed that the number of the endoplasmic reticulum increased in the AR model group, with obvious cystic dilatation, a lot of vacuole formation, and degranulation. A large number of free ribosomes could be seen in cytoplasm. With persistent allergen exposure, changes mentioned above was progressively aggravated in the endoplasmic reticulum of nasal mucosal epithelium in the AR model group. But the dilation of endoplasmic reticulum, vacuole formation, and degranulation were relieved in the GA group, and got close to those of the blank group. CONCLUSION: 18-ß GA could improve the expansion, vacuolization, and degranulation of the endoplasmic reticulum of nasal epithelial cells in AR model rats.

[Effects of 18ß-glycyrrhetinic Acid on the Expression of CCL11, AQP1 and EOS in Nasal Mucosa of Allergic Rhinitis Rats].

OBJECTIVE: To investigate the effects of 18ß-glycyrrhetinic acid (GA) on the expression of eotaxin 1 (CCL11), aquaporin protein 1 (AQP1) and eosinophil (EOS) in nasal mucosa of allergic rhinitis (AR) rats. METHODS: Seventy six Wistar rats were randomly divided into 4 groups, normal control (NC) group, AR model (AR) group, loratadine (LOA) group and 18ß-GA group. All the mice in AR, LOA and 18ß-GA groups were sensitized intraperitoneally with OVA and AL(OH), from day 1-14, then induced by intranasal administration with OVA from day 14-21, while the mice in NC group were sensitized with saline. The mice in both LOA and 18ß-GA group were given LOA and 18ß-GA once a day respectively from the 21 d, while the mice in AR and NC groups were administrated with saline. At the end of 1 week, 2 weeks and 3 weeks, the behavioral changes of mice were observed and recorded, the level of CCL11 mRNA was measured by RT-QPCR, and AQP1 expression was investiaged by SP staing. EOS in nasal mucosa was studied with the methods of HE staining. RESULTS: Compared with NC group, AR group showed typical AR symptoms. With the treatments, AR symptom scores and the expression levels of CCL11, AQP1 and EOS in nasal mucosa were improved significantly (P<0. 05). When compared with AR group, the above statistics in LOA group were down-regulated evidently at different points in time (P<. 05). At the end of 1 week, the above detection results in 18ß-GA group were lower than those in AR group (P<0. 05). At the end of 2 weeks, those parameters approached to the levels of LOA and NC group significantly. CONCLUSION: 18ß-GA administration could down-regulate the expression levels of CCL11, AQP1 and EOS in nasal mucosa of allergic rhinitis rats and cast effects on inhibiting the progress of AR.

Knockdown of PROX1 promotes milk fatty acid synthesis by targeting PPARGC1A in dairy goat mammary gland.

Goat milk is rich in various fatty acids that are beneficial to human health. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) and RNA-seq analyses of goat mammary glands at different lactation stages revealed a novel lactation regulatory factor, Prospero homeobox 1 (PROX1). However, the mechanism whereby PROX1 regulates lipid metabolism in dairy goats remains unclear. We found that PROX1 exhibits the highest expression level during peak lactation period. PROX1 knockdown enhanced the expression of genes related to de novo fatty acid synthesis (e.g., SREBP1 and FASN) and triacylglycerol (TAG) synthesis (e.g., DGAT1 and GPAM) in goat mammary epithelial cells (GMECs). Consistently, intracellular TAG and lipid droplet contents were significantly increased in PROX1 knockdown cells and reduced in PROX1 overexpression cells, and we observed similar results in PROX1 knockout mice. Following PROX1 overexpression, RNA-seq showed a significant upregulation of peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PPARGC1A) expression. Further, PPARGC1A knockdown attenuated the inhibitory effects of PROX1 on TAG contents and lipid-droplet formation in GMECs. Moreover, we found that PROX1 promoted PPARGC1A transcription via the PROX1 binding sites (PBSs) located in the PPARGC1A promoter. These results suggest a novel target for manipulating the goat milk-fat composition and improving the quality of goat milk.

Effect of Starch Plasticization on Morphological, Mechanical, Crystalline, Thermal, and Optical Behavior of Poly(butylene adipate-co-terephthalate)/Thermoplastic Starch Composite Films.

Starches plasticized with glycerol/citric acid/stearic acid and tributyl 2-acetylcitrate (ATBC), respectively, were processed with poly (butylene adipate-Co-terephthalate (PBAT) via extrusion and a film-blown process. All the composite films were determined for morphology, mechanical, thermal stability, crystalline, and optical properties. Results show that the most improved morphology was in the 30% glycerol plasticized PBAT/thermoplastic starch (TPS) composite films, characterized by the smallest and narrowest distribution of TPS particle sizes and a more uniform dispersion of TPS particles. However, the water absorption of PBAT/TPS composite films plasticized with glycerol surpassed that observed with ATBC as a plasticizer. Mechanical properties indicated insufficient plasticization of the starch crystal structure when using 10% ATBC, 20% ATBC, and 20% glycerol as plasticizers, leading to poor compatibility between PBAT and TPS. This resulted in stress concentration points under external forces, adversely affecting the mechanical properties of the composites. All PBAT/TPS composite films exhibited a negative impact on the initial thermal decomposition temperature compared to PBAT. Additionally, the haze value of PBAT/TPS composite films exceeded 96%, while pure PBAT had a haze value of 47.42%. Films plasticized with 10% ATBC, 20% ATBC, and 20% glycerol displayed lower transmittance values in the visible light region. The increased transmittance of films plasticized with 30% glycerol further demonstrated their superior plasticizing effect compared to other PBAT/TPS composite films. This study provides a simple and feasible method for preparing low-cost PBAT composites, and their extensions are expected to further replace general-purpose plastics in daily applications.

MiR-103-5p deficiency suppresses lipid accumulation via upregulating PLSCR4 and its host gene PANK3 in goat mammary epithelial cells.

Lipids are intimately related to the unique flavor and nutritional values of goat milk. MicroRNAs (miRNA) participate in the regulation of various biological functions, including the synthesis and degradation of lipids. Several studies have shown that miR-103 is involved in the regulation of lipid metabolism, however, the molecular mechanism by which miR-103 regulates lipid metabolism in goat mammary gland is poorly understood. In this study, miR-103 was knocked out in goat mammary epithelial cells (GMECs) by CRISPR/Cas9, and the accumulation of lipid droplets, triglycerides, and cholesterol in the cells was suppressed subsequently. Overexpression or knockdown of miR-103-5p and miR-103-3p in GMECs revealed that it was miR-103-5p that promoted lipid accumulation but not miR-103-3p. In addition, Pantothenate Kinase 3 (PANK3), the host gene of miR-103, and Phospholipid Scramblase 4 (PLSCR4) were identified as the target genes of miR-103-5p by dual fluorescein and miRNA pulldown. Furthermore, we identified that cellular lipid levels were negatively regulated by PANK3 and PLSCR4. Lastly, in miR-103 knockout GMECs, the knockdown of PANK and PLSCR4 rescued the lipid accumulation. These findings suggest that miR-103-5p promotes lipid accumulation by targeting PLSCR4 and the host gene PANK3 in GMECs, providing new insights for the regulation of goat milk lipids via miRNAs.

Widely Targeted Metabolomic Analysis Revealed the Diversity in Milk from Goats, Sheep, Cows, and Buffaloes and Its Association with Flavor Profiles.

The milk flavor can be attributed to the presence of numerous flavor molecules and precursors. In this study, we employed widely targeted metabolomic analysis techniques to analyze the metabolic profiles of various milk samples obtained from goats, sheep, dairy cows, and buffaloes. A total of 631 metabolites were identified in the milk samples, which were further categorized into 16 distinct classes. Principal component analysis (PCA) suggested that the metabolite profiles of samples from the same species exhibit clustering, while separated patterns of metabolite profiles are observed across goat, sheep, cow, and buffalo species. The differential metabolites between the groups of each species were screened based on fold change and variable importance in projection (VIP) values. Five core differential metabolites were subsequently identified, including 3-(3-hydroxyphenyl)-3-hydroxypropanoic acid, inosine 5'-triphosphate, methylcysteine, N-cinnamylglycine, and small peptide (L-tyrosine-L-aspartate). Through multiple comparisons, we also screened biomarkers of each type of milk. Our metabolomic data showed significant inter-species differences in the composition and concentration of some compounds, such as organic acids, amino acids, sugars, nucleotides, and their derivatives, which may affect the overall flavor properties of the milk sample. These findings provided insights into the molecular basis underlying inter-species variations in milk flavor.

The FoxO1-ATGL axis alters milk lipolysis homeostasis through PI3K/AKT signaling pathway in dairy goat mammary epithelial cells.

Goat milk is enriched in fatty acids which are beneficial to human health. Previous research has revealed that 98% of milk fat is composed of triglycerides. However, the mechanisms regulating milk fat composition remain unclear. Forkhead box protein O1 (FoxO1) is a crucial regulatory factor involved in lipid metabolism across various cell types. Chromatin immunoprecipitation sequencing (ChIP)-seq data) and RNA sequencing (RNA-seq) data revealed that have indicated a close association between FoxO1 was closely related to lipid metabolism during lactation in dairy goats. The objective of this study was to investigate the mechanisms by which FoxO1 regulates lipid metabolism in goat mammary epithelial cells (GMECs). FoxO1 knockdown significantly downregulated the expression of adipose triglyceride lipase (ATGL) and suppressed the activity of the ATGL promoter. Consistently, the number of lipid droplets decreased significantly in FoxO1-overexpressing cells and increased in ATGL-knockdown cells. To further verify the effect of FoxO1 on ATGL promoter activity, cells were transfected with four promoter fragments of different lengths. We found that the core region of the ATGL promoter was located between -882 bp and -524 bp, encompassing two FoxO1 binding sites (FKH1 and FKH2). Mutations in the FoxO1 binding sites significantly downregulated ATGL promoter activity in GMECs. Luciferase reporter assays demonstrated that FoxO1 overexpression markedly enhanced ATGL promoter activity. Furthermore, site-directed mutation confirmed that FKH1 and FKH2 sites were simultaneously mutated significantly attenuated the stimulatory effect of FoxO1 on ATGL promoter activities simultaneous mutation of FKH1 and FKH2 sites significantly attenuated the stimulatory effect of FoxO1 on ATGL promoter activity. ChIP assays showed that FoxO1 directly binds to the FKH2 element located in the ATGL promoter in vivo. Finally, immunofluorescence staining revealed that insulin promotes the translocation of FoxO1 from the nucleus to the cytoplasm, thereby attenuating the FoxO1-induced activation of the ATGL promoter. Collectively, these findings uncover a novel pathway where by FoxO1 may regulate lipid metabolism in GMECs specifically by modulating the transcriptional activity of ATGL.

Forkhead box protein O1(FoxO1) is a key cellular regulatory factor that was involved in lipid metabolism in several cell types. This study was performed to explore the regulatory mechanism of FoxO1 in adipose triglyceride lipase (ATGL) promoter-driven transcription during lactation in dairy goats. Chromatin immunoprecipitation (ChIP)-seq and RNA sequencing (RNA-seq) data revealed that FoxO1 was closely related to lipid metabolism and inflammation during lactation in dairy goats. FoxO1 overexpression significantly decreased cellular triglyceride (TAG) content lipid droplet accumulation in goat mammary epithelial cells (GMECs), while ATGL knockdown attenuated this effect of FoxO1. Furthermore, the relative content of free fatty acid (FFAs) was markedly increased in FoxO1-overexpressed cells. Additionally, site-directed mutation and ChIP assays confirmed that FoxO1 promotes ATGL transcription through FoxO1 binding sites (FKH) located in the ATGL promoter. Moreover, insulin attenuated the FoxO1-induced activation of the ATGL promoter. Our data reveal that FoxO1 regulates the activity of ATGL in GMECs by binding to FKH elements located in the ATGL promoter.

Genome-wide analysis of the acyl-coenzyme A synthetase family and their association with the formation of goat milk flavour.

Goat milk is rich in fat and protein, thus, has high nutritional values and benefits human health. However, goaty flavour is a major concern that interferes with consumer acceptability of goat milk and the 4-alkyl-branched-chain fatty acids (vBCFAs) are the major substances relevant to the goaty flavour in goat milk. Previous research reported that the acyl-coenzyme A synthetases (ACSs) play a key role in the activation of fatty acids, which is a prerequisite for fatty acids entering anabolic and catabolic processes and highly involved in the regulation of vBCFAs metabolism. Although ACS genes have been identified in humans and mice, they have not been systematically characterized in goats. In this research, we performed genome-wide characterization of the ACS genes in goats, identifying that a total of 25 ACS genes (without ACSM2A) were obtained in the Capra hircus and each ACS protein contained the conserved AMP-binding domain. Phylogenetic analysis showed that out of the 25 genes, 21 belonged to the ACSS, ACSM, ACSL, ACSVL, and ACSBG subfamilies. However, AACS, AASDH, ACSF, and ACSF3 genes were not classified in the common evolutionary branch and belonged to the ACS superfamily. The genes in the same clade had similar conserved structures, motifs and protein domains. The expression analysis showed that the majority of ACS genes were expressed in multi tissues. The comparative analysis of expression patterns in non-lactation and lactation mammary glands of goat, sheep and cow indicated that ACSS2 and ACSF3 genes may participate in the formation mechanisms of goaty flavour in goat milk. In conclusion, current research provides important genomic resources and expression information for ACSs in goats, which will support further research on investigating the formation mechanisms of the goaty flavour in goat milk.

How Capital Endowment and Ecological Cognition Affect Environment-Friendly Technology Adoption: A Case of Apple Farmers of Shandong Province, China.

Ever-increasing global environmental issues, land degradation, and groundwater contamination may significantly impact the agricultural sector of any country. The situation worsens while the global agricultural sectors are going through the unsustainable intensification of agricultural production powered by chemical fertilizers and pesticides. This trend leads the sector to exercise environmentally friendly technology (EFT). Capital endowment and ecological cognition may significantly impact fostering farmers' adoption of environmentally friendly technology. The government also tends to change the existing policies to cope with ever-increasing challenges like pollution control, maintaining ecological balance, and supporting agricultural sectors substantially by employing ecological compensation policy. The study's main objective is to explore the impacts of farmer's ecological compensation, capital endowment, and ecological cognition for the adoption of EFT. The empirical setup of the study quantifies with survey data of 471 apple farmers from nine counties of Shandong province. The study used Heckman's two-stage model to craft the findings. The results showed that 52.02% of fruit farmers adopted two environmentally friendly technologies, and 23.99% of fruit farmers adopted three forms of environmentally friendly technologies. At the same time, we have traced that the capital endowment, planting scale, family income, and technical specialization of fruit farmers significantly impact adopting EFT. The study also revealed that understanding ecological compensation policy has a significant positive effect on adopting environmentally friendly technology. Seemingly, ecological compensation policy has a specific regulatory effect on fruit farmers' capital endowment and ecological cognition. Therefore, it is necessary to extend the demonstration facilities, training, and frequently arrange awareness-building campaigns regarding rural non-point source pollution hazards and improve the cognition level of farmers. The agriculture extension department should strengthen the agricultural value chain facilities to make farmers fully realize the importance of EFT. Government should promote and extend the supports for availing new and innovative EFT at a reasonable price. Moreover, cooperative, financial, and credit organizations need to lead for the smooth transition of EFT. The agricultural cooperatives and formal risk-taking networks should act responsibly for shaping the behavioral factors of farmers.

Changes in Chinese Adults' Physical Activity Behavior and Determinants before and during the COVID-19 Pandemic.

PURPOSE: To investigate the changes in Chinese adults' physical activity (PA) behavior and determinants before and during the COVID-19 pandemic. METHOD: A total of 1028 adults (aged 19-59 years) were recruited from 127 urban and rural neighborhoods in China using stratified three-stage probability sampling. Data collection was conducted in December 2019 and July 2020. RESULTS: Compared with the data before the pandemic, individuals' weekly moderate-to-vigorous-intensity PA (MVPA) decreased significantly from 139 min to 120 min, seven months after the outbreak (p = 0.01), with female and rural populations displaying a more significant decrease (p = 0.02). Overall, 13.7% of participants met the PA guidelines (World Health Organization) both before and during the pandemic, while 21.8% met the guidelines only before the pandemic and 18.1% increased their PA and met the PA guidelines during the pandemic. A total of 46.4% did not meet the PA guidelines before or during the pandemic. Determinants of PA behavior change before and during the pandemic included sports skills, self-determined motivation and support from sports organizations. CONCLUSIONS: The Chinese adults' PA levels decreased significantly from before to during the COVID-19 pandemic, particularly among the female population. It is suggested that the enhancement of self-determined motivation, improvement of sport skills, and support from sports organizations might be effective in facilitating individuals' engagement in PA during the pandemic.

Characterization of microRNA profiles in the mammary gland tissue of dairy goats at the late lactation, dry period and late gestation stages.

MicroRNAs (miRNAs) play an important role in regulating mammary gland development and lactation. We previously analyzed miRNA expression profiles in Laoshan dairy goat mammary glands at the early (20 d postpartum), peak (90 d postpartum) and late lactation (210 d postpartum) stages. To further enrich and clarify the miRNA expression profiles during the lactation physiological cycle, we sequenced miRNAs in the mammary gland tissues of Laoshan dairy goats at three newly selected stages: the late lactation (240 d postpartum), dry period (300 d postpartum) and late gestation (140 d after mating) stages. We obtained 4038 miRNAs and 385 important miRNA families, including mir-10, let-7 and mir-9. We also identified 754 differentially expressed miRNAs in the mammary gland tissue at the 3 different stages and 6 groups of miRNA clusters that had unique expression patterns. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that GO terms such as mammary gland development (GO:0030879) and mammary gland morphogenesis (GO:0060443) and important signaling pathways, including the insulin signaling pathway (chx04910), hippo signaling pathway (chx04390) and estrogen signaling pathway (chx04915), were enriched. We screened miRNAs and potential target genes that may be involved in the regulation of lactation, mammary gland growth and differentiation, cell apoptosis, and substance transport and synthesis and detected the expression patterns of important genes at the three stages. These miRNAs and critical target genes may be important factors for mammary gland development and lactation regulation and potentially valuable molecular markers, which may provide a theoretical reference for further investigation of mammary gland physiology.

The comfort of patients with different nasal packings after endoscopic sinus surgery for chronic rhinosinusitis: A protocol for network meta-analysis.

BACKGROUND: Chronic sinusitis (CRS) is a high incidence disease and seriously affects the patients' quality of life, causes tremendous economic burden as well. Endoscopic sinus surgery (ESS) is one of the most common therapies for chronic sinusitis. While whether there is a need for nasal packing and which is the best one is still unclear. METHOD AND ANALYSIS: A systematic search will be performed using PubMed, EMBASE.com, the Cochrane Central Register of Controlled Trials, Chinese Biomedical Literature Database, China National Knowledge Infrastructure and Wanfang database to include randomized controlled trials (RCTs), comparing the efficacy and comfort in patients with nasal packings after ESS who is diagnosed as CRS. The risk of bias of the included RCTs will be assessed by the Cochrane Handbook version 5.1.0. A Bayesian network meta-analysis will be conducted using R-3.3.2 software. RESULTS: This study is ongoing and the results will be published in a peer-reviewed journal. CONCLUSION: The results of this study will be sent to clinicians and healthcare providers in the National Health Service, which is expected to help clinicians make more informed choices on nasal packings. ETHICS AND DISSEMINATION: Ethical approval is not applicable since this study is a network meta-analysis based on published trials. PROTOCOL REGISTRATION NUMBER: CRD42019119233.

Long noncoding RNA HOXD-AS1 in various cancers: a meta-analysis and TCGA data review.

Background and aims: HOXD antisense growth-associated long noncoding RNA (HOXD-AS1) was reported to be upregulated in various cancers, such as gastric cancer, hepatocellular carcinoma, colorectal cancer, and glioma. Here, we conducted a meta-analysis and The Cancer Genome Atlas data review to investigate the clinicopathologic and prognostic value of HOXD-AS1 in patients with malignant tumors. Materials and methods: Systematic literatures were searched from PubMed, Medline, Cochrane Library, Web of Science, EMBASE database, Ovid, Chinese CNKI, and the Chinese WanFang database. The role of HOXD-AS1 in cancers was evaluated by pooled ORs and HRs with 95% CIs. The Cancer Genome Atlas dataset was used to explore the prognostic value of HOXD-AS1 in various cancers. RESULTS: Fifteen studies with 1,678 patients were included in this meta-analysis. The results indicated that HOXD-AS1 was associated with tumor size, differentiation, lymph node metastasis, and TNM stage. Moreover, the high HOXD-AS1 expression indicated a poor overall survival (OS) rate and can be an independent predictive factor for OS. The TCGA dataset, which included 9,502 cancer patients, showed that the expression of HOXD-AS1 was related to poor OS and disease-free survival. We also analyzed the prognostic role in different kinds of cancers such as digestive cancers, female reproductive system cancers, respiratory system cancers, and urinary system cancers. CONCLUSION: This study demonstrated that HOXD-AS1 was closely correlated with tumor size, lymph node metastasis, distant metastasis, and TNM stage, and an increased HOXD-AS1 expression could be a reliable prognostic biomarker in human cancers. However, more studies are needed to confirm this conclusion.

Complementary iTRAQ-based proteomic and RNA sequencing-based transcriptomic analyses reveal a complex network regulating pomegranate (Punica granatum L.) fruit peel colour.

Peel colour is an important factor affecting the marketability of pomegranate fruits. Therefore, elucidating the genetic mechanism of fruit peel colour development may be useful for breeding pomegranate cultivars with enhanced fruit peel colours. In this study, we combined an iTRAQ-based proteome-level analysis with an RNA sequencing-based transcriptome-level analysis to detect the proteins and genes related to fruit peel colour development in pomegranate. We analysed the 'Tunisia' (red fruit) and 'White' (white fruit) pomegranate cultivars at two stages of fruit development. A total of 27 differentially abundant proteins (increased abundance) and 54 differentially expressed genes (16 up-regulated and 38 down-regulated) were identified from our proteomics and transcriptomics data. The identified proteins and genes contribute to pomegranate fruit peel colour by participating in the biosynthesis of anthocyanins, stilbenoids, diarylheptanoids, gingerols, flavonoids, and phenylpropanoids. Several candidate proteins and genes corresponded to enzymes related to general reactions (PAL, 4CL, DFR, LDOX/ANS, CHS, and F3'5'H) and glycosylation (GT1 and UGAT) of compounds and pigments related to the colour of pomegranate fruit peel. Complementary proteome- and transcriptome-level analyses revealed a complex molecular network controlling fruit peel colour. The candidate genes identified in this study may be useful for the marker-based breeding of new pomegranate cultivars.

Integrated microRNA and mRNA expression profiling reveals a complex network regulating pomegranate (Punica granatum L.) seed hardness.

The breeding of new soft-seeded pomegranate cultivars provides new products for the market and increases farmers' incomes, yet the genetic architecture mediating seed hardness is largely unknown. Here, the seed hardness and hundred-seed weights of 26 cultivars were determined in 2 successive years. We conducted miRNA and mRNA sequencing to analyse the seeds of two varieties of Punica granatum: soft-seeded Tunisia and hard-seeded Sanbai, at 60 and 120 d after flowering. Seed hardness was strongly positively correlated with hundred-seed weight. We detected 25 and 12 differentially expressed miRNA-mRNA pairs with negative regulatory relationships between the two genotypes at 60 and 120 d after flowering, respectively. These miRNA-mRNA pairs mainly regulated seed hardness by altering cell wall structure. Transcription factors including NAC1, WRKY and MYC, which are involved in seed hardness, were targeted by differentially expressed mdm-miR164e and mdm-miR172b. Thus, seed hardness is the result of a complex biological process regulated by a miRNA-mRNA network in pomegranate. These results will help us understand the complexity of seed hardness and help to elucidate the miRNA-mediated molecular mechanisms that contribute to seed hardness in pomegranate.

De novo transcriptome assembly and quantification reveal differentially expressed genes between soft-seed and hard-seed pomegranate (Punica granatum L.).

Pomegranate (Punica granatum L.) belongs to Punicaceae, and is valued for its social, ecological, economic, and aesthetic values, as well as more recently for its health benefits. The 'Tunisia' variety has softer seeds and big arils that are easily swallowed. It is a widely popular fruit; however, the molecular mechanisms of the formation of hard and soft seeds is not yet clear. We conducted a de novo assembly of the seed transcriptome in P. granatum L. and revealed differential gene expression between the soft-seed and hard-seed pomegranate varieties. A total of 35.1 Gb of data were acquired in this study, including 280,881,106 raw reads. Additionally, de novo transcriptome assembly generated 132,287 transcripts and 105,743 representative unigenes; approximately 13,805 unigenes (37.7%) were longer than 1,000 bp. Using bioinformatics annotation libraries, a total of 76,806 unigenes were annotated and, among the high-quality reads, 72.63% had at least one significant match to an existing gene model. Gene expression and differentially expressed genes were analyzed. The seed formation of the two pomegranate cultivars involves lignin biosynthesis and metabolism, including some genes encoding laccase and peroxidase, WRKY, MYB, and NAC transcription factors. In the hard-seed pomegranate, lignin-related genes and cellulose synthesis-related genes were highly expressed; in soft-seed pomegranates, expression of genes related to flavonoids and programmed cell death was slightly higher. We validated selection of the identified genes using qRT-PCR. This is the first transcriptome analysis of P. granatum L. This transcription sequencing greatly enriched the pomegranate molecular database, and the high-quality SSRs generated in this study will aid the gene cloning from pomegranate in the future. It provides important insights into the molecular mechanisms underlying the formation of soft seeds in pomegranate.