Construction and validation of a mitochondria-associated genes prognostic signature and immune microenvironment characteristic of sepsis.

BACKGROUND: Sepsis is a common critical condition seen in clinical settings, with mitochondrial dysfunction playing an important role in the progression of sepsis. However, a mitochondrial prognosis model related to sepsis has not been established yet, and the relationship between the sepsis immune microenvironment and mitochondria remains unclear. METHODS: Sepsis prognostic mitochondria-associated genes (MiAGs) were screened by univariate Cox, multivariate Cox, and LASSO analysis from the GEO dataset. Consensus Cluster was used to analyze MiAGs-based molecular subtypes for sepsis. The ESTIMATE and ssGSEA algorithms were used to analyze the situation of sepsis immune cell infiltration and its relation to MiAGs. Further, MiAGs score was calculated to construct a sepsis prognosis risk model to predict the prognosis of sepsis patients. Clinical blood samples were used to investigate the expression level of selected MiAGs in sepsis. Single-cell sequencing analysis, mitochondrial membrane potential (MMP), reactive oxygen species (ROS), and ATP detection were used to verify the influence of MiAGs on mitochondrial dysfunction in sepsis. RESULTS: A total of 5 MiAGs of sepsis were screened. Based on MiAGs, sepsis MiAGs subtypes were analyzed, where Cluster A had a better prognosis than Cluster B, and there were significant differences in immune infiltration between the two clusters. The sepsis mitochondrial prognosis model suggested that the high MiAG score group had a shorter survival time compared to the low MiAG score group. Significant differences were also observed in the immune microenvironment between the high and low MiAG score groups. Prognostic analysis and the Nomogram indicated that the MiAG score is an independent prognostic factor in sepsis. Single-cell sequencing analysis exhibited the possible influence of MiAGs on the mitochondrial function of monocytes. Finally, the downregulation of the COX7B could effectively improve mitochondrial function in the LPS-stimulated sepsis model. CONCLUSION: Our findings suggest that MiAGs can be used to predict the prognosis of sepsis and that regulating the mitochondrial prognostic gene COX7B can effectively improve the mitochondrial function of immune cells in sepsis.

Integrated metabolomics and transcriptomics analyses reveal the key genes regulating differential metabolites of longissimus dorsi muscle in castrated South Sichuan black goats (Capra hircus).

The main aim of the current work was to explore the differential metabolites and differentially expressed genes of longissimus dorsi muscle (LDM) between castrated and uncastrated fattening male South Sichuan black goats (Capra hircus). Then, the key genes regulating important differential metabolites (DMs) in castrated male goats were observed by integrated metabolomics and transcriptomics analyses. In addition, we evaluated the effects of castration on blood constituents, dressing percentage, and water holding capacity of LDM in male black goats. The results showed that the concentrations of alkaline phosphatase (ALP), total cholesterol (TC), triglyceride (TG), and low-density lipoprotein cholesterol (LDL-C) were significantly increased and testosterone was significantly decreased in castrated male goats compared with the uncastrated male goats, while dressing percentage of black goats and water holding capacity of longissimus dorsi muscle were not significant differences. Through metabolomics and transcriptomics analyses, 23 important KEGG pathways, 13 important DMs, 32 important differentially expressed genes (DEGs), and 13 key genes related to the "Metabolism" and "Organismal systems" pathways were screened. Lipid accumulation may be elevated in the blood of fattening South Sichuan black goats after castration. Castration might play a positive role in energy provision, intercellular signaling, muscle function, softening of meat, disease reduction, and anti-oxidation of LDM. P4HA2, AKR1B1, GPT2, L2HGDH, ENSCHIG00000021660, ENSCHIG00000023861, DGAT2, ULK1, SLC38A3, PLA2G4A, SLC6A1, ENSCHIG00000026624, and ND2 might be the key genes regulating important DMs in the KEGG pathways related to "Metabolism" and "Organismal systems" of castrated male goats compared with the uncastrated male goats.

Physiological and Molecular Characteristics of Southern Leaf Blight Resistance in Sweet Corn Inbred Lines.

Southern corn leaf blight is one of the most widespread foliar diseases in maize-producing areas worldwide and can seriously reduce the yield and quality of sweet corn. However, the molecular mechanisms underlying the disease in sweet corn have not been widely reported. In this study, two sweet corn inbred lines, resistant K13 (RK13) and susceptible K39 (SK39), were used to explore the disease resistance mechanism of southern leaf blight. We observed morphological characteristics and assessed the changes in protective enzymatic activity in sweet corn leaves after inoculation of C. heterostrophus. RNA-seq was performed to elucidate the transcriptional dynamics and reveal the key pathways involved in southern leaf blight resistance without pathogens (Mock) and at 1 and 3 days post inoculation (1 and 3 dpi). Differentially expressed genes (DEGs) were identified in the SK39 group (including three pairwise combinations: SK39-0d_vs_SK39-1d, SK39-1d_vs_SK39-3d and SK39-1d_vs_SK39-3d), the RK13 group (including three pairwise combinations: RK13-0d_vs_RK13-1d, RK13-1d_vs_RK13-3d and RK13-1d_vs_RK13-3d), and the SK39_vs_RK13 group (including three pairwise combinations: SK39-0d_vs_RK13-0d, SK39-1d_vs_RK13-1d, and SK39-3d_vs_RK13-3d). In our study, 9455 DEGs from the RK13 group, 9626 from the SK39 group, and 9051 DEGs from the SK39_vs_RK13 group were obtained. Furthermore, 2775, 163, and 185 DEGs were co-expressed at SK39_vs_RK13, RK13, and SK39, respectively. A functional analysis of the DEGs revealed that five pathways-i.e., photosynthesis, plant hormone signal transduction, MAPK signaling pathway, phenylpropanoid biosynthesis, and biosynthesis of secondary metabolites-and transcription factor families play crucial roles in disease resistance. The results from the present study enabled the identification of the JA and SA signaling pathways, which are potentially involved in the response to southern leaf blight in maize. Our findings also highlight the significance of ZIM transcription factors and pathogenesis-related (PR) genes during pathogen infection. This study preliminarily explored the molecular mechanisms of the interaction between sweet corn and C. heterostrophus and provides a reference for identifying southern leaf blight resistance genes in the future.

Genome-Wide Identification and Characterization of Actin-Depolymerizing Factor (ADF) Family Genes and Expression Analysis of Responses to Various Stresses in Zea Mays L.

Actin-depolymerizing factor (ADF) is a small class of actin-binding proteins that regulates the dynamics of actin in cells. Moreover, it is well known that the plant ADF family plays key roles in growth, development and defense-related functions. Results: Thirteen maize (Zea mays L., ZmADFs) ADF genes were identified using Hidden Markov Model. Phylogenetic analysis indicated that the 36 identified ADF genes in Physcomitrella patens, Arabidopsis thaliana, Oryza sativa japonica, and Zea mays were clustered into five groups. Four pairs of segmental genes were found in the maize ADF gene family. The tissue-specific expression of ZmADFs and OsADFs was analyzed using microarray data obtained from the Maize and Rice eFP Browsers. Five ZmADFs (ZmADF1/2/7/12/13) from group V exhibited specifically high expression in tassel, pollen, and anther. The expression patterns of 13 ZmADFs in seedlings under five abiotic stresses were analyzed using qRT-PCR, and we found that the ADFs mainly responded to heat, salt, drought, and ABA. Conclusions: In our study, we identified ADF genes in maize and analyzed the gene structure and phylogenetic relationships. The results of expression analysis demonstrated that the expression level of ADF genes was diverse in various tissues and different stimuli, including abiotic and phytohormone stresses, indicating their different roles in plant growth, development, and response to external stimulus. This report extends our knowledge to understand the function of ADF genes in maize.

Genome-wide identification, phylogenetic and expression analysis of the maize HECT E3 ubiquitin ligase genes.

HECT (homologous to the E6AP carboxyl terminus) ubiquitin ligase genes (E3s) are enzymes with diverse functions influencing plant growth, development, and responses to abiotic stresses. However, there is relatively little information available regarding the maize HECT E3 gene family. In the present study, 12 maize HECT E3 genes (ZmUPL1 to ZmUPL12) were identified at the whole-genome level. The phylogenetic relationships, structures, and expression levels of the maize HECT E3 genes were then analyzed. On the basis of the constructed maximum likelihood phylogenetic tree, the HECT E3 genes were divided into six groups. The quantitative real-time polymerase chain reaction assay results revealed that all of the maize ZmUPL genes were expressed in most of the examined tissues and were responsive to three abiotic stresses. Considered together, the study results may provide a useful foundation for future investigations of maize stress-tolerance genes as well as functional analyses of the E3 enzymes in diverse agriculturally important crop species.

Complete sequence and characterization of mitochondrial genome of Jianyang Daer goat (Capra hircus).

This study has presented the complete mitogenome of Jianyang Daer goat (Capra hircus), a crossbreed known for its high growth rate and good-meat quality in China. The mitogenome was 16,643 bp in length, including 33.54% A, 26.07% C, 13.10% G and 27.29% T. It contained a non-coding control region, 2 ribosomal RNA genes, 13 protein-coding genes and 22 transfer RNA genes. Two kinds of inititiation codon and four types of termination codon were identified. Moreover, most of the genes were encoded on H-strand. These information will be useful for further investigation on the genetic divergence among Chinese domestic goats.

Role of microRNA-101a in the regulation of goat skeletal muscle satellite cell proliferation and differentiation.

MicroRNAs are a class of small, non-coding RNAs that participate in the regulation of diverse biological processes including skeletal muscle development. However, the underlying molecular mechanisms are not fully understood, particularly in goat. Here, we identified goat miR-101a as a novel myogenic microRNA mediating myogenic differentiation. The expression of miR-101a was enriched in goat skeletal muscles and up-regulated during satellite cell differentiation. After transfection with a miR-101a mimic and culturing in differentiation medium, satellite cell differentiation was promoted, accompanied by a significant increase in mRNA expression of the myogenic marker, MyoG, and decreased expression of MyoD. In contrast, blocking the function of miR-101a with a 2'-O-methylated antisense oligonucleotide inhibitor repressed satellite cell differentiation. However, both gain- and loss-of-function studies demonstrated that miR-101a had no significant influence on satellite cell proliferation. Therefore, our results provide a new insight on miR-101a in the regulation of goat skeletal muscle satellite cell proliferation and differentiation.

Spontaneous uptake of exogenous DNA by goat spermatozoa and selection of donor bucks for sperm-mediated gene transfer.

Sperm-mediated gene transfer (SMGT) has been long heralded as a faster and cheaper alternative to more commonly used methods of producing transgenic animals. In this study, the capra semen ejaculates were pooled together and then incubated in vitro with DIG-labeled DNA. The binding and internalizing rates were observed by the in situ hybridization methods. We also compared the standard sperm parameters and the efficiencies of interaction with exogenous DNA of 60 individuals to select donor bucks for SMGT. It was showed that labeled exogenous DNA was detected in different localizations in spermatozoa but genuine DNA uptake, in contrast to mere binding, seems to be limited to the postacrosomal region. The removal of seminal plasma increased significantly (P < 0.01) the capability in picking up exogenous DNA. Use of frozen-thawed semen (without cryoprotectant agents) and Triton X-100 treatment also increased significantly (P < 0.01) the DNA-binding capacity, but reduced the sperm viability. The binding rates (the proportion of labeled-DNA positive spermatozoa to all the spermatozoa counted) of 60 buck individuals were in the range of 3.08-73.39%, and the internalizing rates (the proportion of DNaseI-treated labeled-DNA positive spermatozoa to all the spermatozoa counted) were 4.83-70.00%. About 8.34% (5/60) bucks showed high binding, but low internalizing ability. Chi-square test showed that there was significant difference among the breeds (x(2) = 26.515, P < 0.01). Eight individual bucks that demonstrated high DNA uptake were selected for SMGT. It was demonstrated that the goat spermatozoa was capable of spontaneous uptake of exogenous DNA. Seminal fluid inhibits DNA uptake and that membrane disruption increases DNA binding but greatly diminishes uptake.

Association of goat (Capra hircus) CD4 gene exon 6 polymorphisms with ability of sperm internalizing exogenous DNA.

As one of the transport systems on the sperm plasma membrane, CD4 molecule plays a distinct role in the process of sperm/DNA interaction. This makes it possible to explain the mechanism of sperm-mediated gene transfer (SMGT), which at present is still a mystery in this area. In this study, seminal samples of 60 individuals from seven breed bucks were collected to detect the ability of sperm in internalizing exogenous DNA, and genomic DNA from 147 individual blood samples (including 60 bucks referred ahead) were extracted to test the polymorphisms of CD4 genes by using PCR-SSCP technique. Then the correlation between them was evaluated. The results showed that: (1) it was a novel finding that breed-dependence of exogenous DNA binding to goat spermatozoa. There was the most significant difference among the buck breeds of sperm in binding exogenous DNA (F((6, 53)) = 4.811, P = 0.001) and in internalizing them into nuclei (F((6, 53)) = 4.587, P = 0.001). The ability of Lezhi Black goat was the lowest (P < 0.01) among the seven breeds. (2) There was no significant correlation between the ability of sperm in internalizing exogenous DNA and each semen quality parameter (P > 0.05). (3) In particular, three single-nucleotide polymorphisms (SNP) were described and there was one SNP (G/A(700)) of CD4 gene that made G234R substitution in the amino acid sequence of CD4 molecule. Nanjiang Yellow goat and Lezhi Black goat had higher hereditary variation compared with other breeds. (4) CD4 polymorphisms were highly associated with the ability of sperm in internalizing exogenous DNA. The SNP of Caprine CD4 gene exon 6 might be an important molecular marker of the ability to internalize exogenous DNA into sperm.