Earticle

Background: This study explores the potential of discarded male layer embryos as a sustainable and non-GMO cell source for cultivated chicken meat production. The research aims to identify efficient methods for isolating muscle progenitor cells (MPCs) with high proliferative potential by conducting transcriptome analysis on thigh muscle tissues from both male and female chick embryos. Methods: Transcriptome analysis was performed on the thigh muscle tissues of male and female chick embryos, aged 12-13 days, (n = 4 each), to investigate the gene expression profiles and identify strategies for efficiently isolating MPCs. This approach aims to pinpoint techniques that would allow for the selection of MPCs with optimal growth and proliferation capabilities. Results: Using heatmap, hierarchical clustering, and multidimensional scaling (MDS), we found no significant sex-based differences in gene expression, except for the overexpression of the female-specific gene LIPBLL. The expression of muscle stem cell factors, including PAX3, PAX7, and other myogenic regulatory genes, showed no significant variation. However, to recover MPC-rich cells isolated from male thigh muscle, we found that by the pre-plating 7 stage, myogenesis-related genes, MYHs and MUSTN1 were minimally expressed, while the cell cycle arrest gene CDKN1A sharply increased. Conclusions: Our findings suggest that simple cell isolation directly from tissue is a more scalable and efficient approach for cultivated meat production, compared to labor-intensive pre-plating methods, making it a viable solution for sustainable research and resource recycling.

Wheat gluten is an increasingly common ingredient in poultry diets but its impact on the small intestine in chicken is not fully understood. This study aimed to identify effects of high-gluten diets on chicken small intestines and the variation of their associated transcriptional responses by age. A total of 120 broilers (Ross Strain) were used to perform two animal experiments consisting of two gluten inclusion levels (0% or 25%) by bird’s age (1 week or 4 weeks). Transcriptomics and histochemical techniques were employed to study the effect of gluten on their duodenal mucosa using randomly selected 12 broilers (3 chicks per group). A reduction in feed intake and body weight gain was found in the broilers fed a high-gluten containing diet at both ages. Histochemical photomicrographs showed a reduced villus height to crypt depth ratio in the duodenum of gluten-fed broilers at 1 week. We found mainly a significant effect on the gene expression of duodenal mucosa in gluten-fed broilers at 1 week (289 differentially expressed genes [DEGs]). Pathway analyses revealed that the significant DEGs were mainly involved in ribosome, oxidative phosphorylation, and peroxisome proliferator-activated receptor (PPAR) signaling pathways. These pathways are involved in ribosome protein biogenesis, oxidative phosphorylation and fatty acid metabolism, respectively. Our results suggest a pattern of differential gene expression in these pathways that can be linked to chronic inflammation, suppression of cell proliferation, cell cycle arrest and apoptosis. And via such a mode of action, high-gluten inclusion levels in poultry diets could lead to the observed retardation of villi development in the duodenal mucosa of young broiler chicken.

After pubertal, cohort of small antral follicles enters to gonadotrophin-sensitive development, called recruited follicles. This study was aimed to identify candidate genes in follicular cyclic recruitment via analysis of protein-protein interaction (PPI) network. Differentially expressed genes (DEGs) in ovine granulosa cells of small antral follicles between follicular and luteal phases were accumulated among gene/protein symbols of the Ensembl annotation. Following directed graphs, PTPN6 and FYN have the highest indegree and outdegree, respectively. Since, these hubs being up-regulated in ovine granulosa cells of small antral follicles during the follicular phase, it represents an accumulation of blood immune cells in follicular phase in comparison with luteal phase. By contrast, the up-regulated hubs in the luteal phase including CDK1, INSRR and TOP2A which stimulated DNA replication and proliferation of granulosa cells, they known as candidate genes of the cyclic recruitment.

The color of the Pleurotus ostreatus pileus is black, gray to yellow, and pink to yellow, etc. the transcriptomes of the white Pleurotus ostreatus "Baekseon" and the black Pleurotus ostreatus "Heuktari" with different shades were analyzed to confirm the difference between the color of the Pleurotus ostreatus and the amount of gene expression. The results are as follows. As a result of the analysis of oyster transcripts, 12,460 genes were expressed, and 1080 genes were identified with an expression level of 2-fold change or more. Among them, 536 genes were up-regulated and 544 were down-regulated. Among the up-regulated genes, carbohydrate esterase family 1 protein, glycosyltransferase family 58 protein, cora superfamily, and copper-amine-oxidase superfamily were identified. Among the down-regulated genes, polysaccharide lyase family 3 protein, cytochrome C1 protein, pleurotolysin B precursor Etc. were confirmed.

The range of possible growth temperature of the Lentinula edodes mycelium is 5~32℃, and the appropriate temperature is 22~26℃, which is generally known as medium and high temperature. In order to check the expression level of the gene according to the temperature during growth, the temperature was divided into three treatments of 10, 20, and 30℃ to grow the altitude, and 20℃ was used as a control. The result is as follows. a total of 32,706 genes were identified, and 1319 genes were identified at 10℃ compared to the control for those with a more than 2-fold change expression level. among them, 591 genes were up-regulated at 10℃ compared to the control. it was confirmed that 728 genes were down-regulated, and those grown at 30°C were 6,977 genes that expressed more than 2 fold change compared to the control, and the number of up-regulated genes was 3,703 down-regulated. 3,274 genes were identified. among the upregulated genes, cytochrome P450, Alpha beta hydrolase fold protein, chondroitin AC alginate lyase, and proline-specific peptidase were identified. Among the downregulated genes, farnesyl-diphosphate synthase, zinc finger transcription factor 1, and glycolytic enzyme family 79 proteins were identified.

In this study, we extracted RNA of Pleurotus ostreatus fruiting body treated 10, 100ppm Mepiquat chloride dry weight of sawdust medium. Result of fruiting body’s mRNA-seq, 12460 genes are fold changed and contrast 2-fold-change 149 genes including tRNA-His, tRNA-Thr, tRNA-pro, carbohydrate esterase family 16 protein, etc. are up-regulated and 64 genes including QCR9, subunit of the ubiquinol cytochrome-c reductase complex, glycoside hydrolase family 17 protein, carbohydrate-binding module family 13 protein etc. are down-regulated at 10, 100ppm

The ascomycete fungus Cordyceps militaris infects lepidopteran insect pupae, forming characteristic fruiting bodies called “Dong Chung Ha Cho” in Korean. They have been used as medicines owing to their anti-allergic, anti-inflammatory, and immune-enhancing effects. This fungus can be grown on the geminated soybeans Rhynchosia nulubilis, which also contains several novel isoflavones. We performed a comparative transcriptome analysis to determine core gene sets or pathways contributing to biologically active products such as isoflavone. Initially, we sequenced 2-week-old fungal cultures on different soybean agar media, where different amounts of water agar were implemented to show different surface topology. We selected 830 upregulated and 188 downregulated genes by comparing linear models of the samples (two-fold change threshold). Gene ontology analysis identified that the “IMP biosynthesis” term was significantly found in the upregulated gene sets. The pathway is involved in the synthesis of cordycepin, the reference chemical for C. militaris. This finding in the transcriptome data is consistent with the previous observation: increased cordycepin concentrations in the C. militaris cultured on germinated soybean.

Cinnamomum camphora (Lauraceae) is an evergreen broad-leaved tree and distributed in the south of China and Japan. This species has been widely cultivated in many countries because of its aromatic oils, insect-repellent effects and ornamental value. Despite its vast utilization and cultivation, little is known about its genetic diversity and population genetics. To date, only a few genomic simple sequence repeat (SSR) markers were developed in C. camphora and no genic-SSR primers were available yet. Thus, it is necessary to develop more genic-SSR markers, which will facilitate the genetic studies of Cinanamomum. In this study, a total of 74,289 simple sequence repeats (SSRs) were found in 56,124 unigenes, of which 14,225 unigenes contained more than one SSR locus. Among these SSR loci, the mono-nucleotide repeats were the most frequent, with a frequency of 61.14%, followed by 24.87% di-nucleotide repeats and 12.87% tri-nucleotide repeats. Twenty-one polymorphic SSR markers were developed and validated in 45 camphor trees. The 21 loci were further examined for genetic diversity of 38 provenances, 190 individuals in the whole natural distribution area of camphor tree in China. The results showed that 74 polymorphic sites were detected with average 2.74 polymorphic were detected for each prime. The means of observed and expected heterozygosities were 0.4446 and 0.4419, respectively. Nei's and Shannon’s information index for these populations were 0.4400 and 0.7193, respectively. The genetic similarity coefficient of 38 provenances was between 0.05 and 0.95, with an average of 0.17.The smallest genetic distance is JXWY and JXRJ and the genetic distance between JXTG and GZDZ was the largest. Cluster analysis in 0.88 genetic distance can divide into five groups. Jiangxi provenances clustered into two groups, of which JXAY grouped into one group and other provenances grouped into another group. Other provenances of China grouped three small branches: CQYY and HNHH, GZDZ and SCLZ, and other provenances. The clustering results showed that the genetic components of camphor tree in China had obvious regional features. The analysis of molecular variance exhibited that 77% of genetic variation was observed within the populations. The novel genic-SSR markers will not only benefit genetic diversity analysis and wild resources conservation of C. camphora, but also contribute to exploring the further evolutionary history and genetic differentiation pattern of Cinnamomum.

The thermotolerant methylotrophic yeast Hansenula polymorpha has been shown to metabolize and ferment ethanol from glucose, xylose, cellobiose, starch, and xylan substrates which makes it an ideal candidate for lignocellulosic biomass-based ethanol fermentation. In addition to biomass, crude glycerol, a co-product of biodiesel transesterification, has become a valuable substance for ethanol production due to its high abundance, low cost, and high reducibility. However, ethanol production from glycerol by H. polymorpha has not been investigated thoroughly. In this study, we compared the transcriptome profiles of H. polymorpha grown on glycerol with those of glucose-grown cells both under aerobic and microaerobic conditions. About two percent of the 5.848 H. polymorpha genes were either up- or down-regulated more than two-fold during growth on glycerol. As expected the majority of the up-regulated genes was involved in metabolism including some of glycerol metabolic genes. On the other hand, the majority of the down-regulated genes was involved in central metabolism and cellular transport. Our results will allow us to understand and engineer the glycerol metabolism in H. polymorpha.

A strain of Mannheimia succiniciproducens, a gram-negative rumen bacterium producing succinic acid, was adapted to environment of high-concentration of succinic acid and showed increased acid tolerance. Responses of the adapted M. succiniciproducens strain to succinic acid were studied based on transcriptome analysis, by investigating genetic expression levels of cells after 30 minute and 300 minute of succinic acid shock. During the investigations, gene expression levels of the adapted M. succiniciproducens strain were compared with a parent strain and the expression patterns after acid shock are classified refer to function of genes. Genes related to chaperones, Energy production, metabolism of Amino acid and inorganic ion are increased metabolism generally increase their expression levels. Expression levels of genes for carbohydrate transport and metabolism are decreased in both strains. There are significantly different fold-changes in gene expression levels between both strains in data after 300 minute of succinic acid shock though only small differences were exhibited in 30 minute after data. Standing on the transcriptome data, specific genes of M. succiniciproducens were selected as targets of genetic manipulations and it would contribute to improvement of succinic acid tolerance. [This work was supported by the Genome-Based Integrated Bioprocess Development Project of the Ministry of Education, Science and Technology (MEST). Further supports by the LG Chem Chair Professorship, Microsoft, IBM SUR, WCU (World Class University) program through the National Research Foundation of Korea funded by MEST (R32-2008-000-10142-0) are appreciated.]

Escherichia coli L-valine production strain was constructed by rational design. L-valine production strain was constructed by releasing two regulatory mechanisms, feedback inhibition and attenuation. Two amino acids alterations were introduced into ilvH which is subject to feedback inhibition by using site-directed mutagenesis. The leader region of ilvGMEDA and ilvBN operon which is involved in attenuation was changed with the strong tac promoter by homologous recombination. Further improvement of the L-valine production strain was achieved by knocking out ilvA, leuA and panB genes thus making more substrate available for L-valine biosynthesis. L-valine production strain also contains plasmid to overexpress the ilvBNCED genes. Transcriptome analysis was used to identify the physiology at mRNA level during the biosynthesis of L-valine. And we also achieved improvement of L-valine production strain based on transcriptome profiling.[This work was supported by the Korea Science and Engineering Foundation (KOSEF) grant funded by the Korea government (MOST) (No. M10309020000-03B5002-00000). Further supports by LG Chem Chair Professorship, Microsoft and IBM SUR program are appreciated.]

Mannheimia succiniciproducens, a gram-negative rumen bacterium producing succinic acid, was adapted to medium with high-concentration of succinic acid for acid tolerance. Responses of the adapted M. succiniciproducens strain to succinic acid shock were investigated based on transcriptome analysis. During the investigations, gene expression levels of the adapted M. succiniciproducens strain were compared with a parent strain and the expression patterns after acid shock are classified refer to function of genes. Standing on the transcriptome data, specific genes of M. succiniciproducens are selected as targets of genetic manipulations. To improve tolerance for succinic acid, It was tried that overexpression or knock-out experiments of target genes and finding global regulators for acid resistance. [This work was supported by the Genome-Based Integrated Bioprocess Development Project from the Korean Ministry of Education, Science and Technology (No. 2005-01304). Further supports by LG Chem Chair Professorship, and WCU (World Class University) program through the National Research Foundation of Korea are greatly appreciated.]

wblA (SCO3579) is a pleiotropic down-regulator of antibiotic biosynthesis in Streptomyces species, as well as modulates morphological differentiation (Kang et al. 2007). Although wblA is notable pleiotropic down-regulator in valuable secondary metabolite production, these regulatory networks are still largely unknown. In this study, total cosmid DNA library screening in doxorubicin (DXR)-producing S. peucetius resulted in the isolation of S. peucetius wblA gene (named wblA-spe). To examine biological significance of the wblA-spe on DXR production, the wblA-spe was disrupted from the chromosome of DXRoverproducing S. peucetius strain by PCR-targeting system, followed by quantitative DXR HPLC analysis. After the wblA-spe gene disruption, biosynthesis of DXR and DXR intermediate aklavinone were slightly enhanced. Furthermore, using Streptomyces interspecies DNA microarray analysis between the DXR high-producer S. peucetius strain and wblA-spe disruption mutant strain, several putative wblA-dependent genes were identified. To verify the biological significance of this comparative transcriptomics-guided targets, the five putative wblA-dependent target genes were individually cloned under the strong-and constitutive promoter(PermE*) of the Streptomyces integrative expression vector, followed by conjugation into S. coelicolor. Among the putative wblA-dependent genes tested, the overexpression of NADH dehydrogenase subunit, (SCO4571) conserved hypothetical protein (SCO4967), and putative oxidoreductase beta-subunit (SCO6569) in S. coelicolor enhanced biosynthesis of actinorhodin about 1.5-2-fold relative to that of S.coelicolor exconjugant harboring the empty vector alone. More detailed results will be discussed.

The efficacy of plant breeding has been enhanced by application of molecular markers in population screening and selection. Pepper (Capsicum annuum L.) is a major staple crop that is economically important with worldwide distribution. It is valued for its spicy taste and medicinal effect. The aim of this study was to discover single nucleotide polymorphisms (SNPs), microsatellite markers information, and percentage sharing through orthologous analysis of pepper-specific pungency-related genes. Here, we report the results of transcriptome analysis and microsatellite markers for four pepper varieties that possess a pungency-related gene. Orthologous analyses was performed to identify species-specific pungency-related genes in pepper, Arabidopsis thaliana L., potato (Solanum tuberosum L.), and tomato (Solanum lycopersicum L.). Advancements in next-generation sequencing technologies enabled us to quickly and cost-effectively assemble and characterize genes to select molecular markers in various organisms, including pepper. We identified a total of 9762, 7302, 8596, and 6886 SNPs for the four pepper cultivars Blackcluster, Mandarine, Saengryeg 211, and Saengryeg 213, respectively. We used 454 GS-FLX pyrosequencing to identify microsatellite markers and tri-nucleotide repeats (54.4%), the most common repeats, followed by di-, hexa-, tetra-, and penta-nucleotide repeats. A total of 5156 (15.9%) pepper-specific pungency-related genes were discovered as a result of orthologous analysis.

Dry age-related macular degeneration (AMD) is a type of progressive blindness that is primarily due to dysfunction and the loss of retinal pigment epithelium (RPE). The accumulation of N-retinylidene-N-retinylethanolamine (A2E), a by-product of the visual cycle, causes RPE and photoreceptor degeneration that impairs vision. Genes associated with dry AMD have been identified using a blue light model of A2E accumulation in the retinal pigment epithelium and transcriptomic studies of retinal tissue from patients with AMD. However, dry macular degeneration progresses slowly, and current approaches cannot reveal changes in gene transcription according to stages of AMD progression. Thus, they are limited in terms of identifying genes responsible for pathogenesis. Here, we created a model of long-term exposure to identify temporally-dependent changes in gene expression induced in human retinal pigment epithelial cells (ARPE-19) exposed to blue light and a non-cytotoxic dose of A2E for 120 days. We identified stage-specific genes at 40, 100, and 120 days, respectively. The expression of genes corresponding to epithelial-mesenchymal transition (EMT) during the early stage, glycolysis and angiogenesis during the middle stage, and apoptosis and inflammation pathways during the late stage was significantly altered by A2E and blue light. Changes in the expression of genes at the late stages of the EMT were similar to those found in human eyes with late-stage AMD. Our results provide further insight into the pathogenesis of dry AMD induced by blue light and a novel model in vitro with which relevant genes can be identified in the future.

The amino acids found in plants play important roles in protein biosynthesis, signaling processes, and stress responses, and as components in other biosynthesis pathways. Amino acid degradation helps maintain plant cells' energy states under certain carbon starvation conditions. Branched-chain amino acid transferases (BCATs) play an essential role in the metabolism of branched-chain amino acids (BCAAs) such as isoleucine, leucine and valine. In this paper, we performed genome-wide RNA-seq analysis using CsBCAT7-overexpressing Arabidopsis plants. We observed significant changes in genes related to flowering time and genes that are germination-responsive in transgenic plants. RNA-seq and RT-qPCR analyses revealed that the expression levels of some BCAA catabolic genes were upregulated in these same transgenic plants, and that this correlated with a delay in their senescence phenotype when the plants were placed in extended darkness conditions. These results suggest a connection between BCAT and the genes implicated in BCAA catabolism.

Morchella is a genus of fungi with the ability to concentrate Cd both in the fruit-body and mycelium. However, the molecular mechanisms conferring resistance to Cd stress in Morchella are unknown. Here, RNA-based transcriptomic sequencing was used to identify the genes and pathways involved in Cd tolerance in Morchella spongiola. 7444 differentially expressed genes (DEGs) were identified by cultivating M. spongiola in media containing 0.15, 0.90, or 1.50 mg/L Cd²⁺. The DEGs were divided into six sub-clusters based on their global expression profiles. GO enrichment analysis indicated that numerous DEGs were associated with catalytic activity, cell cycle control, and the ribosome. KEGG enrichment analysis showed that the main pathways under Cd stress were MAPK signaling, oxidative phosphorylation, pyruvate metabolism, and propanoate metabolism. In addition, several DEGs encoding ion transporters, enzymatic/non-enzymatic antioxidants, and transcription factors were identified. Based on these results, a preliminary gene regulatory network was firstly proposed to illustrate the molecular mechanisms of Cd detoxification in M. spongiola. These results provide valuable insights into the Cd tolerance mechanism of M. spongiola and constitute a robust foundation for further studies on detoxification mechanisms in macrofungi that could potentially lead to the development of new and improved fungal bioremediation strategies.