Genome-Wide Identification of Specific Genetic Loci Common to Sheep and Goat.

Sheep and goat may become carriers of some zoonotic diseases. They are important livestock and experimental model animals for human beings. The fast and accurate identification of genetic materials originating from sheep and goat can prevent and inhibit the spread of some zoonotic diseases, monitor market product quality, and maintain the stability of animal husbandry and food industries. This study proposed a methodology for identifying sheep and goat common specific sites from a genome-wide perspective. A total of 150 specific sites were selected from three data sources, including the coding sequences of single copy genes from nine species (sheep, goat, cow, pig, dog, horse, human, mouse, and chicken), the dbSNPs for these species, and human 100-way alignment data. These 150 sites exhibited low intraspecific heterogeneity in the resequencing data of 1450 samples from five species (sheep, goat, cow, pig, and chicken) and high interspecific divergence in the human 100-way alignment data after quality control. The results were proven to be reliable at the data level. Using the process proposed in this study, specific sites of other species can be screened, and genome-level species identification can be performed using the screened sites.

Development and uniqueness test of highly selective atomic topological indices based on the number of attached hydrogen atoms.

On the basis of the atomic graph-theoretical index - aEAID (atomic Extended Adjacency matrix IDentification) and molecular adjacent topological index - ATID (Adjacent Topological IDentification) suggested by one of the authors (Zhang Q), a highly selective atomic topological index - aATID (atomic Adjacent Topological IDentification) index was suggested to identify the equivalent atoms in this study. The aATID index of an atom was derived from the number of the attached hydrogen atoms of the atom but omitting bond types. In this case, the suggested index can be used to identify equivalent atoms in chemistry but perhaps not equivalent in the molecular graph. To test the uniqueness of aATID indices, the virtual atomic data sets were derived from alkanes containing 15-20 carbon atoms and the isomers of Octogen, as well as a real data set was derived from the NCI database. Only four pairs of atoms from alkanes containing 20 carbons can't be discriminated by aATID, that is, four pairs of degenerates were found for this data set. To solve this problem, the aATID index was modified by introducing distance factors between atoms, and the 2-aATID index was suggested. Its uniqueness was examined by 5,939,902 atoms derived from alkanes containing 20 carbons and further 16,166,984 atoms from alkanes of 21 carbons, and no degenerates were found. In addition, another large real data set of 16,650,688 atoms derived from the PubChem database was also used to test the uniqueness of both aATID and 2-aATID. As a result, each atom was successfully discriminated by any of the two indices. Finally, the suggested aATID index was applied to the identification of duplicate atoms as data pretreatment for QSPR (Quantitative Structure-Property Relationships) studies.

Taraxacum mongolicum polysaccharide promotes white adipocyte browning by regulating miR-134-3p via Akt/GSK-3ß signalling.

In recent years, the incidence of obesity has gradually increased due to high calorie diets and lack of exercise. Reducing energy intake or increasing energy expenditure is the most effective way to promote weight loss and reduce lipid levels. Activated beige adipocytes can increase energy consumption in the body, and inducing conversion of white adipocytes to brown can prevent and treat obesity. Taraxacum mongolicum polysaccharide (TMP) is a plant polysaccharide that has been widely used for its anti-tumour and antioxidant properties. However, little is known about the role of TMP in the browning of sheep white adipose tissue. The aim of this study was to explore the potential mechanism of TMP and miR-134-3p in regulating the browning of sheep white adipocytes, as well as the regulatory relationship between TMP and miR-134-3p. Our results showed that TMP had a positive regulatory effect on the proliferation and browning of sheep white adipocytes. In addition, miR-134-3p significantly inhibited browning activity and AKT/GSK-3ß signalling. Importantly, we found that TMP function required miR-134-3p mediation in the browning of sheep white adipocytes. Overall, our results suggested that TMP recruited beige adipocytes by regulating AKT/GSK-3ß signalling via miR-134-3p.

Guided self-help mindfulness-based intervention for increasing psychological resilience and reducing job burnout in psychiatric nurses: A randomized controlled trial.

AIMS: The present study aimed to explore the effects of a guided self-help mindfulness intervention on psychological resilience and job burnout among psychiatric nurses. BACKGROUND: Psychiatric nurses work in challenging and potentially high stress settings. Mindfulness interventions can improve psychological resilience and reduce job burnout of nurses. However, face-to-face delivery of mindfulness interventions may be inconvenient for individuals. Guided self-help interventions may be more accessible. METHODS: This randomized controlled trial was conducted from January to August 2022. One hundred and eighteen psychiatric nurses were randomized into the intervention and control groups. The individuals in the intervention group received an 8-week guided self-help mindfulness intervention, while the individuals in the control group received a psycho-educational brochure. The Five Facet Mindfulness Questionnaire, the Connor-Davidson Resilience Scale and the Maslach Burnout Inventory-Human Services Survey were used to evaluate the levels of mindfulness, psychological resilience and job burnout, respectively. RESULTS: After an 8-week intervention, compared with the control group, the levels of mindfulness and psychological resilience were higher, while the level of job burnout was lower in the intervention group. CONCLUSIONS: The guided self-help mindfulness intervention can improve psychological resilience and reduce job burnout among psychiatric nurses.

Machine Learning to Predict Homolytic Dissociation Energies of C-H Bonds: Calibration of DFT-based Models with Experimental Data.

Random Forest (RF) QSPR models were developed with a data set of homolytic bond dissociation energies (BDE) previously calculated by B3LYP/6-311++G(d,p)//DFTB for 2263 sp3C-H covalent bonds. The best set of attributes consisted in 114 descriptors of the carbon atom (counts of atom types in 5 spheres around the kernel atom and ring descriptors). The optimized model predicted the DFT-calculated BDE of an independent test set of 224 bonds with MAE=2.86 kcal/mol. A new data set of 409 bonds from the iBonD database (http://ibond.nankai.edu.cn) was predicted by the RF with a modest MAE (5.36 kcal/mol) but a relatively high R2 (0.75) against experimental energies. A prediction scheme was explored that corrects the RF prediction with the average deviation observed for the k nearest neighbours (KNN) in an additional memory of experimental data. The corrected predictions achieved MAE=2.22 kcal/mol for an independent test set of 145 bonds and the corresponding experimental bond energies.

The Role of Chitooligosaccharidolytic ß-N-Acetylglucosamindase in the Molting and Wing Development of the Silkworm Bombyx mori.

The insect glycoside hydrolase family 20 ß-N-acetylhexosaminidases (HEXs) are key enzymes involved in chitin degradation. In this study, nine HEX genes in Bombyx mori were identified by genome-wide analysis. Bioinformatic analysis based on the transcriptome database indicated that each gene had a distinct expression pattern. qRT-PCR was performed to detect the expression pattern of the chitooligosaccharidolytic ß-N-acetylglucosaminidase (BmChiNAG). BmChiNAG was highly expressed in chitin-rich tissues, such as the epidermis. In the wing disc and epidermis, BmChiNAG has the highest expression level during the wandering stage. CRISPR/Cas9-mediated BmChiNAG deletion was used to study the function. In the BmChiNAG-knockout line, 39.2% of female heterozygotes had small and curly wings. The ultrastructure of a cross-section showed that the lack of BmChiNAG affected the stratification of the wing membrane and the formation of the correct wing vein structure. The molting process of the homozygotes was severely hindered during the larva to pupa transition. Epidermal sections showed that the endocuticle of the pupa was not degraded in the mutant. These results indicate that BmChiNAG is involved in chitin catabolism and plays an important role in the molting and wing development of the silkworm, which highlights the potential of BmChiNAG as a pest control target.

Selenium inhibits ferroptosis and ameliorates autistic-like behaviors of BTBR mice by regulating the Nrf2/GPx4 pathway.

BACKGROUND: Autism spectrum disorder (ASD) is a group of extensive neurodevelopmental disorders for which few efficacious drugs are available. Sodium selenite (Se), the most common inorganic form of selenium given to humans and animals, has antioxidant, anti-inflammatory, and neuroprotective effects in several psychiatric and neurological disorders. However, the effect of Se on ASD is unclear. METHODS: Using the BTBR T + tf/J (BTBR) mouse model of ASD, we investigated the therapeutic effects and underlying mechanism of action of Se on ASD. BTBR mice were randomly divided into four groups: BTBR, BTBR+Se, BTBR+Se+ML385, and BTBR+Se+RSL3. The normal control group was composed of C57BL/6 (B6) mice. Se, Nuclear factor erythroid 2-related factor 2 (Nrf2), and glutathione peroxidase 4 (GPx4) inhibitors were administered separately for 28 days using oral gavage. After 28 days, social behavior, ferroptosis indices, and gene and protein expression levels for components of the Nrf2/GPx4 pathway were assessed to explore the correlation between Se levels and ASD. RESULTS: We demonstrated that Se significantly mitigated impairments in learning and memory, improved social functions, reduced repetitive behaviors, and inhibited ferroptosis in the CA1 area of the hippocampus. We also found that the Nrf2/GPX4 pathway was a target for Se. Treatment with Se increased levels of Nrf2 and GPX4. The Nrf2 inhibitor ML385 reduced the effect of Se on ferroptosis and abnormal behaviors in BTBR mice. In addition, the GPx4 inhibitor RSL3 revealed similar efficacy to ML385 CONCLUSION: We determined that Se exhibited a beneficial effect on autism-relevant behaviors and inhibited ferroptosis in the BTBR mouse model of ASD, possibly through modulation of the Nrf2/GPX4 signaling pathway.

An Unsupervised Video Stabilization Algorithm Based on Key Point Detection.

In recent years, video stabilization has improved significantly in simple scenes, but is not as effective as it could be in complex scenes. In this study, we built an unsupervised video stabilization model. In order to improve the accurate distribution of key points in the full frame, a DNN-based key-point detector was introduced to generate rich key points and optimize the key points and the optical flow in the largest area of the untextured region. Furthermore, for complex scenes with moving foreground targets, we used a foreground and background separation-based approach to obtain unstable motion trajectories, which were then smoothed. For the generated frames, adaptive cropping was conducted to completely remove the black edges while maintaining the maximum detail of the original frame. The results of public benchmark tests showed that this method resulted in less visual distortion than current state-of-the-art video stabilization methods, while retaining greater detail in the original stable frames and completely removing black edges. It also outperformed current stabilization models in terms of both quantitative and operational speed.

Whole-genome resequencing reveals loci under selection during silkworm improvement.

Breeding or genetic improvement refers to the process of artificial selection following domestication; as such, it has had a major influence on modern agriculture and animal production. Improvement generally focuses on traits that greatly affect the economic performance. Therefore, understanding the genetic basis underlying improvement will contribute to the identification of genes controlling economic traits and will facilitate future crop and animal breeding. However, genome-wide study of the molecular basis underlying improvement remains rare. The silkworm is a unique, entirely domesticated economically important invertebrate; genetic improvement has had a huge effect on the silkworm regarding silk-related traits. Herein, we performed whole-genomic sequencing on local and genetically improved silkworm lines to identify the genomic regions under strong selection in silkworm breeding/improvement. By genomic-wide selective sweeping analysis, we identified 24 genomic regions with strong selection signals, eight of which contained 13 candidate genes underlying silkworm breeding. Interestingly, six of these genes were annotated with functions related to neural signal response. Among the six genes, BGIBMGA004050 encodes silkworm CREB-regulated_transcription_coactivator_1 (BmCRTC1), which was reported to be involved in energy-sensing pathways. These results suggested that improvement may have affected the nervous system of the silkworm. This research will provide new insights into the genetic basis underlying the genetic improvement of silkworms and possibly of other species.

Identification, expression, and artificial selection of silkworm epigenetic modification enzymes.

BACKGROUND: Understanding the genetic basis of phenotype variations during domestication and breeding is of great interest. Epigenetics and epigenetic modification enzymes (EMEs) may play a role in phenotypic variations; however, no comprehensive study has been performed to date. Domesticated silkworm (Bombyx mori) may be utilized as a model in determining how EMEs influence domestication traits. RESULTS: We identified 44 EMEs in the genome of silkworm (Bombyx mori) using homology searching. Phylogenetic analysis showed that genes in a subfamily among different animals were well clustered, and the expression pattern of EMEs is constant among Bombyx mori, Drosophila melanogaster, and Mus musculus. These are most highly expressed in brain, early embryo, and internal genitalia. By gene-related selective sweeping, we identified five BmEMEs under artificial selection during the domestication and breeding of silkworm. Among these selected genes, BmSuv4-20 and BmDNMT2 harbor selective mutations in their upstream regions that alter transcription factor-binding sites. Furthermore, these two genes are expressed higher in the testis and ovary of domesticated silkworm compared to wild silkworms, and correlations between their expression pattern and meiosis of the sperm and ova were observed. CONCLUSIONS: The domestication of silkworm has induced artificial selection on epigenetic modification markers that may have led to phenotypic changes during domestication. We present a novel perspective to understand the genetic basis underlying animal domestication and breeding.

Identification and effect of Zf-AD-containing C2H2 zinc finger genes on BmNPV replication in the silkworm (Bombyx mori).

Zf-AD-containing C2H2 zinc -finger genes (ZAD) are uniquely present and have lineage-specific expansion in arthropods. Arthropods are also the hosts of Baculoviruses. We studied the possible relationship between the lineage-specific expansion of ZAD genes and arthropod-Baculovirus co-evolution. We used the silkworm (Bombyx mori) as a model. We identified 73 ZAD genes (BmZAD) in the silkworm. Sequence-based similarity analysis showed that nine clusters involving 28 BmZADs may have undergone species-specific expansion in the silkworm. Expression pattern analysis showed that the BmZADs were divided into five groups. Group I comprised 10 genes with high expression in multiple tissues, suggesting that BmZADs may play roles in the development of various tissues. We identified six BmZADs that could be induced by the Nucleopolyhedrovirus (BmNPV). Among them, BmZAD69 expression is capable of responding to BmNPV infection, and the ZAD domain is indispensable for the function of BmZAD69 in BmNPV replication. We also detected a 3 bp deletion at 1.7 kb upstream of BmZAD69, which may make it more sensitive to BmNPV infection, and thus elevate the BmNPV resistance in Qiufeng_N, a strain with strong virus resistance. These data suggest that BmZADs may be involved in BmNPV infection and that ZAD genes may play a role in arthropod-Baculovirus co-evolution.

The beta-1, 4-N-acetylglucosaminidase 1 gene, selected by domestication and breeding, is involved in cocoon construction of Bombyx mori.

Holometabolous insects have distinct larval, pupal, and adult stages. The pupal stage is typically immobile and can be subject to predation, but cocoon offers pupal protection for many insect species. The cocoon provides a space in which the pupa to adult metamorphosis occurs. It also protects the pupa from weather, predators and parasitoids. Silk protein is a precursor of the silk used in cocoon construction. We used the silkworm as a model species to identify genes affecting silk protein synthesis and cocoon construction. We used quantitative genetic analysis to demonstrate that ß-1,4-N-acetylglucosaminidase 1 (BmGlcNase1) is associated with synthesis of sericin, the main composite of cocoon. BmGlcNase1 has an expression pattern coupled with silk gland development and cocoon shell weight (CSW) variation, and CSW is an index of the ability to synthesize silk protein. Up-regulated expression of BmGlcNase1 increased sericin content by 13.9% and 22.5% while down-regulation reduced sericin content by 41.2% and 27.3% in the cocoons of females and males, respectively. Genomic sequencing revealed that sequence variation upstream of the BmGlcNase1 transcriptional start site (TSS) is associated with the expression of BmGlcNase1 and CSW. Selective pressure analysis showed that GlcNase1 was differentially selected in insects with and without cocoons (ω1 = 0.044 vs. ω2 = 0.154). This indicates that this gene has a conserved function in the cocooning process of insects. BmGlcNase1 appears to be involved in sericin synthesis and silkworm cocooning.

[Cloning and function analysis of elongase of very long chain fatty acid gene Bmelo424 in silkworm].

Genes belonging to the elongases of very long chain fatty acid (ELOVL) family affect many physiological functions in organism. In this paper, Bmelo424 gene, a member of the ELOVL family in silkworm, was cloned and its ORF was 558 bp. Its protein sequence was predicted to have four transmembrane domains, six serine phosphorylation sites, eight threonine phosphorylation sites and four tyrosine phosphorylation sites, and its subcellular localization was in the endoplasmic reticulum. Secondary structure analysis showed that the percentage of alpha-helix and beta-strand was 26.7% and 20% respectively. The results of fluorescence quantitative PCR showed that Bmelo424 gene was expressed in all tissues of silkworm, especially with the highest expression in head. By heterologous expression of Bmelo424 gene in Saccharomyces cerevisiae, the effect of Bmelo424 gene on fatty acid elongation was studied. GC-MS results indicated that the fatty acid content of C16:1n-7 in S. cerevisiae with pYES2-Bmelo424 recombinant plasmid increased significantly, whereas the content of C16:0, C18:0 and C18:1n-9 decreased. The results of temperature stress revealed that Bmelo424 gene could improve the low temperature adaptability of S. cerevisiae, but its high temperature adaptability decreased. This provides a reference for exploring the function of Bmelo424 gene in silkworm.

Identification of Genes that Control Silk Yield by RNA Sequencing Analysis of Silkworm (Bombyx mori) Strains of Variable Silk Yield.

Silk is an important natural fiber of high economic value, and thus genetic study of the silkworm is a major area of research. Transcriptome analysis can provide guidance for genetic studies of silk yield traits. In this study, we performed a transcriptome comparison using multiple silkworms with different silk yields. A total of 22 common differentially expressed genes (DEGs) were identified in multiple strains and were mainly involved in metabolic pathways. Among these, seven significant common DEGs were verified by quantitative reverse transcription polymerase chain reaction, and the results coincided with the findings generated by RNA sequencing. Association analysis showed that BGIBMGA003330 and BGIBMGA005780 are significantly associated with cocoon shell weight and encode uridine nucleosidase and small heat shock protein, respectively. Functional annotation of these genes suggest that these play a role in silkworm silk gland development or silk protein synthesis. In addition, we performed principal component analysis (PCA) in combination with wild silkworm analysis, which indicates that modern breeding has a stronger selection effect on silk yield traits than domestication, and imply that silkworm breeding induces aggregation of genes related to silk yield.

Genome-wide identification and analysis of elongase of very long chain fatty acid genes in the silkworm, Bombyx mori.

Very long chain fatty acids (VLCFAs), such as sphingolipids, are components of cellular lipids, which are essential for cell proliferation. Mutations in the genes that encode proteins participating in VLCFA biosynthesis may cause inherited diseases, such as macular degeneration. Elongases of very long chain fatty acid (ELOVL) are enzymes that are involved in the biosynthesis of VLCFAs. Here, a total of 13 ELOVL genes, distributed across three chromosomes, were identified in the silkworm genome; all the ELOVL members contain a distinct ELO domain and a conserved HXXHH motif. Phylogenetic reconstruction was performed to analyze the evolutionary relationships among different species and to predict gene functions. The 13 ELOVL genes were assigned to the ELOVL3/6, ELOVL1/7, and ELOVL4 clades. Microarray and semiquantitative PCR analyses indicated that these genes are differentially expressed among various tissues, in turn suggesting functional divergence in the growth and development of each tissue. Further investigation showed that the expression level of the BGIBMGA000424 gene is significantly negatively correlated with the cocoon-shell weight among different silkworm strains. Taken together, the present study is the first comprehensive analysis of ELOVL genes in silkworm, and the results may serve as a foundation for further analysis of the physiological functions of ELOVL genes in silkworm.

QTL analysis of cocoon shell weight identifies BmRPL18 associated with silk protein synthesis in silkworm by pooling sequencing.

Mechanisms that regulate silk protein synthesis provide the basis for silkworm variety breeding and silk gland bioreactor optimization. Here, using the pooling sequencing-based methodology, we deciphered the genetic basis for the varied silk production in different silkworm strains. We identified 8 SNPs, with 6 on chromosome 11 and 1 each on chromosomes 22 and 23, that were linked with silk production. After conducting an association analysis between gene expression pattern, silk gland development and cocoon shell weight (CSW), BMGN011620 was found to be regulating silk production. BMGN011620 encodes the 60S ribosomal protein, L18, which is an indispensable component of the 60S ribosomal subunit; therefore we named it BmRPL18. Moreover, the clustering of linked SNPs on chromosome 11 and the analysis of differentially expressed genes reported in previous Omics studies indicated that the genes regulating silk protein synthesis may exhibit a clustering distribution in the silkworm genome. These results collectively advance our understanding of the regulation of silk production, including the role of ribosomal proteins and the clustered distribution of genes involved in silk protein synthesis.