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The goal of this study was to evaluate the effects of Tenebrio molitor (TM) larvae meal on the growth performance, serum biochemical parameters and caecal metabolome of broiler chickens. A total of 600 1-d-old male Liangfenghua broilers were randomly assigned to five equal groups with 5 replicates and 24 birds in each replicate. The dietary treatments were as follows: the control group (TM0 group) was fed a basal diet, and the experimental groups were fed experimental diets in which 3% (TM3 group), 5% (TM5 group), 7% (TM7 group) and 9% (TM9 group) TM larvae meal included in the basal diet, respectively. The feeding period was 70 d. The results showed that body weight (BW) and average daily gain (ADG) significantly increased (p 1.5) and the relative contents of 27 metabolites like prostaglandin F2α, glucocorticoids and prostaglandin E2 were significantly down-regulated (FC < 0.667) in the TM3 group. The main altered pathways were clustered into arachidonic acid metabolism, primary bile acid metabolism and propionic acid metabolism. In conclusion, the results indicated that supplementation of 3% TM larvae meal can improve growth performance, reduce the activity of serum AST and the content of TG, and regulation of the pathways of lipid, amino acid, and sugar metabolism in the caecum of broilers by improving nutrient digestion and absorption.

ABSTRACT: Chickens exhibit extensive genetic diversity and are distributed worldwide. Different chicken breeds have evolved to thrive in diverse environmental conditions. However, research on the genetic mechanisms underlying chicken adaptation to extreme environments, such as tropical, frigid and drought-prone regions, remains limited. In this study, we conducted whole-genome sequencing of 240 individuals from six native chicken breeds in Xinjiang, China, as well as 4 publicly available chicken breeds inhabiting regions with varying annual precipitations, temperatures, and altitudes. Our analysis revealed several genetic variants among the examined breeds. Furthermore, we investigated the genetic diversity and population structure of breeds residing in extreme drought and temperature environments by comparing them. Notably, native chicken breeds exhibited different genetic diversity and population structures. Moreover, we identified candidate genes associated with chicken adaptability to the environment, such as CORO2A, CTNNA3, AGMO, GRID2, BBOX1, COL3A1, INSR, SOX5, MAP2 and PLPPR1. Additionally, pathways such as lysosome, cysteine and methionine metabolism, glycosaminoglycan degradation, and Wnt signaling may be play crucial roles in regulating chicken adaptation to drought environments. Overall, these findings contribute to our understanding of the genetic mechanisms governing chicken adaptation to extreme environments, and also offer insights for enhancing the resilience of chicken breeds to different climatic conditions.

Abstract Background The study was conducted to find out the candidate microRNA (miRNA) and genes that associated with sperm motility of Yili goose through small RNA sequencing of testicular tissue of Yili goose, and provide a theoretical basis for the study of the regulation mechanism of sperm motility of Yili goose gander. Results In this study, five male geese with high sperm motility and five male geese with low sperm motility were slaughtered to obtain their testis tissues for small RNA sequencing, and biological information methods were used for data analysis. The results showed that a total of 1575 known miRNAs and 68 novel miRNAs were identified in the testis tissue of Yili goose, and 71 differentially expressed miRNAs and 660 differentially expressed genes were screened. GO functional analysis showed that miRNAs target genes were mainly involved in the binding, kinase activity, structural constituent of cytoskeleton and intermediate filament cytoskeleton. KEGG functional analysis showed that miRNAs target genes were significantly enriched in arginine and proline metabolism, glycolysis / gluconeogenesis, fructose and mannose metabolism and beta-Alanine metabolism and other pathways. miRNAs-mRNAs interaction network suggests miR-140/miR-140-3p/miR-140-3p-NKAIN3, let-7d-BTG1 and miR-145-5p/miR -145a-5p-CLEC2E may play an important role in testis development and spermatogenesis. Conclusions The results of this study suggest that the sperm motility of Yili goose may be regulated by different miRNAs, and the target genes are significantly enriched in pathways related to sperm metabolism, indicating that miRNAs affect the sperm motility of Yili goose by regulating the metabolic process of sperm and the expression of related genes. This study can provide a reference for revealing the regulation mechanism of Yili goose sperm motility at the molecular level.

ABSTRACT: In poultries, muscle growth is a quantitative trait controlled by multiple genes. The regulatory mechanisms governing muscle tissue growth and development in poultry, particularly during the early stages of growth, are intricate. Through the examination of leg muscle transcripts from Yili geese during various stages of development, this study offers valuable insights into the molecular mechanisms underlying the growth and development of Yili geese. This study aimed to perform a comparative analysis of the histological characteristics of leg muscles and the mRNA expression profiles of leg muscles in Yili geese at different ages (2, 4, 6, 8, and 10 wk). The objective was to identify differentially expressed genes related to muscle development in Yili geese and utilize bioinformatics to predict the potential biological functions of these genes. Through histological studies on leg muscle tissues, it was discerned that male geese at 4 wk exhibit a significantly reduced muscle fiber density in comparison to females (P < 0.01). In contrast, by the time they reach 6, 8, and 10 wk, their muscle fiber diameter and cross-sectional dimensions significantly outpace the females (P < 0.01). With the advancement in age, muscle fiber density tends to decrease. It is worth noting that 4- and 6-wk-old male geese have a substantially elevated muscle fiber density when matched against females (P < 0.01). Conversely, at the age of 10 wk, their muscle fiber density is notably inferior to the females (P < 0.01). Furthermore, male geese exhibit the most rapid increase in muscle fiber diameter and cross-sectional area between 4 and 6 wk of age. The density of muscle fibers in these geese significantly decreases from 4 to 8 wk. In contrast, female geese show the most pronounced growth in muscle fiber diameter and cross-sectional area between 2 and 6 wk, with a swift decline in density following the 6-wk mark, accompanied by a gradual reduction in the rate of muscle fiber growth. A comprehensive analysis of the leg muscle mRNA expression profiles from 12 Yili geese generated a cumulative total of 502,065,268 valid sequence reads, corresponding to a data volume of 75.30 Gb. In a comparative analysis between 4-wk-old and 2-wk-old groups (T4 vs. T2), 8-wk-old and 2-wk-old groups (T8 vs. T2), and 8-wk-old and 4-wk-old groups (T8 vs. T4), we identified 1,700, 1,583, and 221 differentially expressed genes (DEGs), respectively. Differentially expressed genes were significantly enriched in Gene Ontology (GO) terms such as organelle organization, cytoskeletal protein binding, cation transport, myosin complex, and actin cytoskeleton. Among the significantly enriched signaling pathways, 5 pathways were found to be significantly related to growth and development: adhesion patch, extracellular matrix receptor interaction, tight junction, TGF-β signaling pathway, and MAPK signaling pathway, with a total of 38 differentially differentiated genes contained in these 5 pathways, and it was hypothesized that the above pathways as well as the DEGs in the pathways played an important role in the regulation of early growth and development of the Yili goose. This investigation serves as a foundational reference for elucidating the molecular regulatory mechanisms involved in the development of goose muscle. Furthermore, it contributes to the expansion of the theoretical framework concerning the genetic regulation of muscle growth in geese.

Abstract Background The development of the ovaries is an important factor that affects egg production performance in geese. Ovarian development is regulated by genes that are expressed dynamically and stage-specifically. The transcriptome profile analysis on ovarian tissues of goose at different egg laying stages could provide an important basis for screening and identifying key genes regulating ovarian development. Results In this study, 4 ovary tissues at each breeding period of pre-laying (PP), laying (LP), and ceased-laying period (CP), respectively, with significant morphology difference, were used for RNA extraction and mRNAs, lncRNAs, and miRNAs comparison in Yili geese. CeRNA regulatory network was constructed for key genes screening. A total of 337, 1136, and 525 differentially expressed DE mRNAs, 466, 925, and 742 DE lncRNAs and 258, 1131 and 909 DE miRNAs were identified between PP and LP, between CP and LP, and between CP and PP groups, respectively. Functional enrichment analysis showed that the differentially expressed mRNAs and non-coding RNA target genes were mainly involved in the cell process, cytokine-cytokine receptor interaction, phagosome, calcium signaling pathway, steroid biosynthesis and ECM-receptor interaction. Differential genes and non-coding RNAs, PDGFRB, ERBB4, LHCGR, MSTRG.129094.34, MSTRG.3524.1 and gga-miR-145–5p, related to reproduction and ovarian development were highly enriched. Furthermore, lncRNA-miRNA-mRNA regulatory networks related to ovary development were constructed. Conclusions Our study found dramatic transcriptomic differences in ovaries of Yili geese at different egg-laying stages, and a differential lncRNA-miRNA-mRNA regulatory network related to cell proliferation, differentiation and apoptosis and involved in stromal follicle development were established and preliminarily validated, which could be regarded as a key regulatory pathway of ovarian development in Yili geese.

ABSTRACT: The development of follicles in the ovaries is a critical determinant of poultry egg production. There are existing studies on the follicular development patterns in poultry, but the specific regulatory mechanisms still need further study. In a previous study, we identified long non-coding RNA (lncRNA) MSTRG.5970.28, anosmin 1 (ANOS1), and its predicted target miR-133a-3p that may be associated with goose ovary development. However, the function of MSTRG.5970.28 in goose granulosa cells and its regulatory mechanisms affecting granulosa cell proliferation and apoptosis have not been reported. In the present study, MSTRG.5970.28 and miR-133a-3p overexpression and interference vectors were constructed. Combined with reverse-transcription real-time quantitative PCR (RT-qPCR), a dual luciferase activity assay, Cell Counting Kit-8 (CCK-8), and flow cytometric analysis, we investigated the role of the MSTRG.5970.28-miR-133a-3p-ANOS1 axis in goose follicular granulosa cells and the associated regulatory mechanisms. MSTRG.5970.28 was found to be localized in the cytoplasm and its expression was influenced by reproductive hormones. The targeting relationship among MSTRG.5970.28, ANOS1, and miR-133a-3p were verified by a dual luciferase activity assay. CCK-8 and apoptosis assays showed that MSTRG.5970.28 inhibited the proliferation and promoted apoptosis of goose granulosa cells. The regulatory role of miR-133a-3p on granulosa cell proliferation and apoptosis was opposite to MSTRG.5970.28. We found that the proliferative and apoptotic effects of granulosa cells caused by MSTRG.5970.28 overexpression were attenuated by miR-133a-3p. MSTRG.5970.28 functions as a competitive endogenous RNA that regulates ANOS1 expression by sponging miR-133a-3p and thus exerts regulatory functions in granulosa cells. In sum, the present study identified lncRNA MSTRG.5970.28 as associated with goose ovary development, which affects the expression of ANOS1 by targeting miR-133a-3p, thereby influencing the proliferation and apoptosis of goose granulosa cells.

The aim of this study was to explore the potential biological function of circular RNAs (circRNAs) in the sperm motility traits of Xinjiang Yili geese, and to provide a reference for analyzing the mechanism of regulation of Yili geese sperm motility. The 10 selected Xinjiang Yili Geese with high or low sperm motility (five for each group) were 3 years old, in good health, and were kept in the same feeding conditions. Yili geese were slaughtered for the collection of testicular tissue and high-throughput sequencing technology was used to screen differentially expressed circRNAs for bioinformatics analysis. Combined with the previously screened miRNAs related to the sperm motility of Yili geese, the circRNAs miRNAs regulatory network was constructed. The results showed that a total of 26,311 circRNAs were obtained from testicular tissues with high and low sperm motility, and 173 DECs were screened between the two groups (p < 0.05, |log2Foldchange|>0), of which 82 were up-regulated and 91 were down-regulated. Functional analysis of the source genes of these DECs showed that the source genes were mainly involved in biological processes. KEGG enrichment analysis showed that the source genes of DECs were mainly enriched in autophagy-animal, ubiquinone and other terpenoid-quinone biosynthesis, progesterone-mediated oocyte maturation, regulation of the actin cytoskeleton and other pathways. Furthermore, the visual regulatory network of differential circRNA-miRNA-mRNA was constructed, including 20 circRNAs, 18 miRNAs and 177 mRNAs, and nine core regulatory circRNAs were screened, including novell_circ_0045314, novel_circ_0019994 and novel_circ_0020422, etc., targeting ppy-mir-16, hsa-mir-221–3p, gga-mir-499–5p, etc. The results suggest that circRNAs may interact with miRNAs to further regulate mRNA to regulate sperm motility in Yili geese, so as to provide a reference for analyzing the molecular mechanism of sperm motility regulation.

Hepatitis B virus (HBV) infection is a public health threat worldwide, and there is no direct treatment yet available. In the event of infection, patients may present liver cirrhosis and cancer, which threaten the patients’ health globally, especially in the Asia-Pacific region and China. In 2019, Chinese hepatopathologists updated the 2015 Guidelines for the Prevention and Treatment of Chronic Hepatitis B as the clinical reference. The other versions formulated by the American Association for the Study of Liver Diseases (2018 AASLD guidelines) (AASLD, 2018), European Association for the Study of the Liver (2017 EASL guidelines) (EASL, 2017), and Asian-Pacific Association for the Study of the Liver (2015 APASL guidelines) (APASL, 2015) also provide clinical guidance. However, there are still some issues that need to be addressed. In the present study, the following aspects will be introduced successively: (1) Who should be treated in the general population according to the guidelines; (2) Treatment of specific populations infected with HBV; (3) Controversial issues in clinical practice; (4) Perspective.

Abstract To conquer the worldwide outbreak of COVID-19 virus, a large number of studies have been carried out on COVID-19 infection, transmission and treatment. However, few studies have been conducted from the perspectives of circRNA and lncRNA, which are known to be involved in regulating many life activities, such as immune tolerance and immune escapes, and hence may provide invaluable information in the emerging COVID-19 infection and recurrence. Moreover, exosomes has been reported to play an important role in COVID-19 recurrence, and thus may interact with the expression of circRNA and lncRNA. In this work, we sequenced circRNA, lncRNA and mRNA from recurrent COVID-19 patients and healthy people, and compared the differences. GO and KEGG enrichment analysis show that differentially expressed circRNA and lncRNA are mainly involved in the regulation of host cell cycle, apoptosis, immune inflammation, signaling pathway and other processes. The comparison to exosomes related databases shows that there are 114 differentially expressed circRNA, and 10 differentially expressed lncRNA related to exosomes. These studies provide reference for exploring circRNA and lncRNA to study the infection mechanism of COVID-19, their diagnostic and therapeutic values, as well as the possibility to employ them as biomarkers.

BackgroundRecently, more patients who recovered from the novel coronavirus disease 2019 (COVID-19) may later test positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) again using reverse transcription-polymerase chain reaction (RT-PCR) testing. Even though it is still controversial about the possible explanation for clinical cases of long-term viral shedding, it remains unclear whether the persistent viral shedding means re-infection or recurrence.MethodsSpecimens were collected from three COVID-19-confirmed patients, and whole-genome sequencing was performed on these clinical specimens during their first hospital admission with a high viral load of SARS-CoV-2. Laboratory tests were examined and analyzed throughout the whole course of the disease. Phylogenetic analysis was carried out for SARS-CoV-2 haplotypes.ResultsWe found haplotypes of SARS-CoV-2 co-infection in two COVID-19 patients (YW01 and YW03) with a long period of hospitalization. However, only one haplotype was observed in the other patient with chronic lymphocytic leukemia (YW02), which was verified as one kind of viral haplotype. Patients YW01 and YW02 were admitted to the hospital after being infected with COVID-19 as members of a family cluster, but they had different haplotype characteristics in the early stage of infection; YW01 and YW03 were from different infection sources; however, similar haplotypes were found together.ConclusionThese findings show that haplotype diversity of SARS-CoV-2 may result in viral adaptation for persistent shedding in multiple recurrences of COVID-19 patients, who met the discharge requirement. However, the correlation between haplotype diversity of SARS-CoV-2 virus and immune status is not absolute. It showed important implications for the clinical management strategies for COVID-19 patients with long-term hospitalization or cases of recurrence.

Hepatitis B virus (HBV) specifically infects liver cells, leading to progressive liver cirrhosis and significantly increasing the risk of hepatocellular carcinoma (HCC). The maturity of sequencing technology, improvement in bioinformatics data analysis and progress of omics technologies had improved research efficiency. The occurrence and progression of HCC are affected by multisystem and multilevel pathological changes. With the application of single-omics technologies, including genomics, transcriptomics, metabolomics and proteomics in tissue and body fluid samples, and even the novel development of multi-omics analysis on a single-cell platform, HBV-associated HCC changes can be better analyzed. The review summarizes the application of single omics and combined analysis of multi-omics data in HBV-associated HCC and proposes the importance of multi-omics analysis in the type of HCC, which provide the possibility for the precise diagnosis and therapy of HBV-associated HCC.

Background: Hepatitis B surface antigen (HBsAg) and viral load are important clinical indicators for antiviral therapy. Few studies have evaluated viral sequence biomarkers predicting the risk of hepatocellular carcinoma (HCC) in the stage, which show a low serological response (HBsAg < 100 IU/ml) and high viral levels (HBV DNA > 2,000 IU/ml). This study aims to determine the trend of the biological prevalence within the pre-S/S regions of special model of inactive CHB infection.Methods: We used Sanger sequencing, quantitative HBV serology (HBeAg and HBsAg), and liver function index to identify whether HBV genome sequences are associated with long-term risk of further HCC progression in special inactive CHB infection.Results: HBV sequencing analysis of 28 CHB patients with special infectious pattern showed higher genetic diversity among four opening reading frames (ORFs) (p < 0.001). However, dN/dS ratios of HBsAg and pre-C/C regions in the experimental group showed no significantly different from those in the HCC group (p = 0.06), while significantly lower in polymerase and HBxAg regions of the experimental group (p < 0.001). In addition, seven positively selected sites were identified in pre-S1, five in pre-S2, and four in S, in which five sites (128H/135Q/135R/139L/141P) were among “α” determinant.Conclusions: These mutations in the pre-S/S region might be associated with the HCC phenotype of low HBsAg expression, with the P region possibly impacting high viral loads. Increased viral diversity across the HBV genome is also associated with low levels of HBsAg. The cumulative evolutionary changes in the HBV pre-S/S regions shows that facilitate immune evasion should be monitored individually. Due to the similarity of evolutionary characteristics in HCC, low serological responses and high viremia may be associated with the risk of further disease progression.

The study was conducted to investigate the transcriptomic differences of the hypothalamic-pituitary-gonadal axis between Xinjiang Yili geese with high and low egg production and to find candidate genes regulating the egg production of Xinjiang Yili geese. The 8 selected Xinjiang Yili Geese with high or low egg production (4 for each group) were 3 years old, with good health, and under the same feeding condition. High-throughput sequencing technology was used to sequence cDNA libraries of the hypothalami, pituitary glands, and ovaries. The sequencing data were compared and analyzed, and the transcripts with significant differences were identified and analyzed with bioinformatics. The study showed that the transcriptome sequencing data of the 24 samples contained a total of 1,176,496,146 valid reads and 176.47 gigabase data. Differential expression analyses identified 135, 56, and 331 genes in the hypothalami, pituitary glands, and ovaries of Xinjiang Yili geese with high and low egg production. Further annotation of these differentially expressed genes in the non-redundant protein sequence database (Nr) revealed that 98, 52, and 309 genes were annotated, respectively. Through the annotations of GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases, 30 candidate genes related to the egg production of Xinjiang Yili geese were preliminarily selected. The gap junction, focal adhesion, and ECM-receptor interaction signaling pathways were enriched with the hypothalamic, pituitary, and ovarian differentially expressed genes, and the calcium signaling pathway was enriched with the pituitary and ovarian differentially expressed genes. Thus, these pathways in the hypothalamic-pituitary-gonadal axis may play an important role in regulating egg production of Xinjiang Yili geese. The results provided the transcriptomic information of the hypothalamic-pituitary-gonadal axis of Xinjiang Yili geese and laid the theoretical basis for revealing the molecular mechanisms regulating the egg-laying traits of Xinjiang Yili geese.

Background: As an emerging infectious disease, coronavirus disease 2019 (COVID-19) exhibits occult infection, which might cause difficulties in controlling disease spread. The possibility of aerosol transmission in a relatively closed environment contributes to the high infectivity of severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) in hospitals. This study presents an environmental surveillance system for SARS-CoV-2 that is suitable for a clinical laboratory and may also lead to further assessment of infection prevention programs in different departments in hospitals. Methods: The study was performed in a SARS-CoV-2 RNA laboratory involved in the diagnosis of COVID-19 in China. Reverse transcription-polymerase chain reaction (RT-PCR) assays were used to detect viral pathogens. Standard operating procedures (SOPs) for monitoring infectious pathogens were developed in this study. Results: In total, more than 180 air and surface samples were tested for SARS-CoV-2 to determine whether the virus was present at the airborne and particle level. The employed molecular method effectively identified environmental contamination. Conclusions: Our study suggests that regular environmental surveillance is critical in a clinical PCR laboratory. The presented strategy could also be used for monitoring and surveillance in negative pressure wards and clinics in hospitals to prevent hospital-acquired infections. [ABSTRACT FROM AUTHOR]