Comparative Transcriptome Analysis Research Articles

Structural and functional analysis of aquaporins in Bombus terrestris

Bombus terrestris are efficient pollinators in forestry and agriculture, with higher cold tolerance than other bees. Yet, their cold tolerance mechanism remains unclear. Aquaporins (AQPs) function as cell membrane proteins facilitating rapid water flow, aiding in osmoregulation. Recent studies highlight the importance of insect AQPs in dehydration and cold stress. Comparative transcriptome analysis of B. terrestris under cold stress revealed up-regulation of four AQPs, indicating their potential role in cold tolerance. Seven AQPs—Eglp1, Eglp2, Eglp3, DRIP, PRIP, Bib, and AQP12L—have been identified in B. terrestris. These are widely expressed in various tissues, particularly in the alimentary canal and Malpighian tubules. Functional analysis of BterAQPs in the Xenopus laevis oocytes expressing system showed distinct water and glycerol selectivity, with BterDrip exhibiting the highest water permeability. Molecular modeling of BterDrip revealed six transmembrane domains, two NPA motifs, and an ar/R constriction region (Phe131, His256, Ser265, and Arg271), likely contributing to its water selectivity. Silencing BterDRIP accelerated mortality in B. terrestris under cold stress, highlighting the crucial role of BterDRIP in their cold tolerance and providing a molecular mechanism for their cold adaptation.

Transcriptomic analysis reveals PC4's participation in thermotolerance of scallop Argopecten irradians irradians by regulating myocardial bioelectric activity

Rising ocean temperatures due to global warming pose a significant threat to the bay scallop aquaculture industry. Understanding the mechanisms of thermotolerance in bay scallops is crucial for developing thermotolerant breeds. Our prior research identified Arg0230340.1, part of the positive cofactor 4 (PC4) family, as a key gene associated with the thermotolerance index Arrhenius break temperature (ABT) in bay scallops. Further validation through RNA interference (RNAi) reinforced PC4's role in thermotolerance, offering a solid basis for investigating thermal response mechanisms in these scallops. In this study, we performed a comparative transcriptomic analysis on the temperature-sensitive hearts of bay scallops after siRNA-mediated RNAi targeting Arg0230340.1, to delve into the detailed molecular mechanism of PC4's participation in thermotolerance regulation. The analysis revealed that silencing Arg0230340.1 significantly reduced the expression of mitochondrial tRNA and rRNA, potentially affecting mitochondrial function and the heart's blood supply capacity. Conversely, the up-regulation of genes involved in energy metabolism, RNA polymerase II (RNAPII)-mediated basal transcription, and aminoacyl-tRNA synthesis pathways points to an intrinsic protective response, providing energy and substrates for damage repair and maintenance of essential functions under stress. GO and KEGG enrichment analyses indicated that the up-regulated genes were primarily associated with energy metabolism and spliceosome pathways, likely contributing to myocardial remodeling post-Arg0230340.1 knockdown. Down-regulated genes were enriched in ion channel pathways, particularly those for Na+, K+, and Ca2+ channels, whose dysfunction could disrupt normal myocardial bioelectric activity. The impaired cardiac performance resulting from RNAi targeting Arg0230340.1 reduced the cardiac workload in scallop hearts, thus affecting myocardial oxygen consumption and thermotolerance. We propose a hypothetical mechanism where PC4 down-regulation impairs cardiac bioelectric activity, leading to decreased thermotolerance in bay scallops, providing theoretical guidance for breeding thermotolerant scallop varieties and developing strategies for sustainable aquaculture in the face of long-term environmental changes.

Methyl jasmonate-induced bHLH42 mediates tissue-specific accumulation of anthocyanins via regulating flavonoid metabolism-related pathways in Caitai.

Anthocyanin is a type of plant secondary metabolite beneficial to human health. The anthocyanin content of vegetable and fruit crops signifies their nutritional quality. However, the molecular mechanism of anthocyanin accumulation, especially tissue-specific accumulation, in Caitai, as well as in other Brassica rapa varieties, remains elusive. In the present study, taking advantage of three kinds of Caitai cultivars with diverse colour traits between leaves and stems, we conducted a comparative transcriptome analysis and identified the molecular pathway of anthocyanin biosynthesis in Caitai leaves and stems, respectively. Our further investigations demonstrate that bHLH42, which is robustly induced by MeJA, closely correlates with tissue-specific accumulation of anthocyanins in Caitai; bHLH42 upregulates the expression of flavonoid/anthocyanin biosynthetic pathway genes to activate anthocyanin biosynthesis pathway, importantly, overexpression of bHLH42 significantly improves the anthocyanin content of Caitai. Our analysis convincingly suggests that bHLH42 induced by jasmonic acid signalling plays a crucial role in tissue-specific accumulation of anthocyanins in Caitai.

Comparative transcriptome analysis of acne vulgaris, rosacea, and hidradenitis suppurativa supports high-dose dietary zinc as a therapeutic agent.

Acne vulgaris, rosacea, and hidradenitis suppurativa are enduring inflammatory skin conditions that frequently manifest with akin clinical attributes, posing a considerable challenge for their distinctive diagnosis. While these conditions do exhibit certain resemblances, they also demonstrate distinct underlying pathophysiological mechanisms and treatment modalities. Delving into both the molecular parallels and disparities among these three disorders can yield invaluable insights for refined diagnostics, effective management, and targeted therapeutic interventions. In this report, we present a comparative analysis of transcriptomic data across these three diseases, elucidating differentially expressed genes and enriched pathways specific to each ailment, as well as those shared among them. Specifically, we identified multiple zinc-binding proteins (SERPINA1, S100A7, S100A8, S100A9 and KRT16) as consistently highly upregulated genes across all three diseases. Our hypothesis suggests that these proteins could bind and sequester zinc, potentially leading to localized zinc deficiency and heightened inflammation. We identified high-dose dietary zinc as a promising therapeutic approach and confirmed its effectiveness through validation in an acne mouse model.

Hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors.

Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce hybridexpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). hybridexpress provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of hybridexpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. hybridexpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. hybridexpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).

Comparative Phenotypic and Transcriptomic Analyses Provide Novel Insights into the Molecular Mechanism of Seed Germination in Response to Low Temperature Stress in Alfalfa.

Low temperature is the most common abiotic factor that usually occurs during the seed germination of alfalfa (Medicago sativa L.). However, the potential regulatory mechanisms involved in alfalfa seed germination under low temperature stress are still ambiguous. Therefore, to determine the relevant key genes and pathways, the phenotypic and transcriptomic analyses of low-temperature sensitive (Instict) and low-temperature tolerant (Sardi10) alfalfa were conducted at 6 and 15 h of seed germination under normal (20 °C) and low (10 °C) temperature conditions. Germination phenotypic results showed that Sardi10 had the strongest germination ability under low temperatures, which was manifested by the higher germination-related indicators. Further transcriptome analysis indicated that differentially expressed genes were mainly enriched in galactose metabolism and carbon metabolism pathways, which were the most commonly enriched in two alfalfa genotypes. Additionally, fatty acid metabolism and glutathione metabolism pathways were preferably enriched in Sardi10 alfalfa. The Weighted Gene Co-Expression Network Analysis (WGCNA) suggested that genes were closely related to galactose metabolism, fatty acid metabolism, and glutathione metabolism in Sardi10 alfalfa at the module with the highest correlation (6 h of germination under low temperature). Finally, qRT-PCR analysis further validated the related genes involved in the above pathways, which might play crucial roles in regulating seed germination of alfalfa under low temperature conditions. These findings provide new insights into the molecular mechanisms of seed germination underlying the low temperature stress in alfalfa.

Assessing marine ecosystem health using multi-omic analysis of blue mussel liquid biopsies: A case study within a national marine park

Marine ecosystems are under escalating threats from myriad environmental stressors, necessitating a deeper understanding of their impact on biodiversity and the health of sentinel organisms. In this study, we carried out a spatiotemporal multi-omic analysis of liquid biopsies collected from mussels (Mytilus spp.) in marine ecosystems of a national park. We delved into the epigenomic, transcriptomic, glycomic, proteomic, and microbiomic profiles to unravel the intricate interplay between ecosystem biodiversity and mussels' biological response to their environments. Our analysis revealed temporal fluctuations in the alpha diversity of the circulating microbiome associated with human activities. Analysis of the hemolymphatic circulating cell-free DNA (ccfDNA) provided information on the biodiversity and the presence of potential pathogens. Epigenomic analysis revealed widespread hypomethylation sites within the mitochondrial (mtDNA). Comparative transcriptomic and glycomic analyses highlighted differences in metabolic pathways and genes associated with immune and wound healing functions. This study demonstrates the potential of multi-omic analysis of liquid biopsy in sentinel to provide a holistic view of human activities' environmental impacts on marine coastal ecosystems. Overall, this approach has the potential to enhance the effectiveness and efficiency of various conservation efforts, leading to more informed decision-making and better outcomes for biodiversity and ecosystem conservation.

Studies on Human Cultured Fibroblasts and Cutaneous Squamous Cell Carcinomas Suggest That Overexpression of Histone Variant H2A.J Promotes Radioresistance and Oncogenic Transformation.

Background: Cellular senescence in response to ionizing radiation (IR) limits the replication of damaged cells by causing permanent cell cycle arrest. However, IR can induce pro-survival signaling pathways that reduce the extent of radiation-induced cytotoxicity and promote the development of radioresistance. The differential incorporation of histone variant H2A.J has profound effects on higher-order chromatin organization and on establishing the epigenetic state of radiation-induced senescence. However, the precise epigenetic mechanism and function of H2A.J overexpression in response to IR exposure still needs to be elucidated. Methods: Primary (no target, NT) and genetically modified fibroblasts overexpressing H2A.J (H2A.J-OE) were exposed to 20 Gy and analyzed 2 weeks post-IR for radiation-induced senescence by immunohistochemistry and immunofluorescence microscopy. Transcriptome signatures were analyzed in (non-)irradiated NT and H2A.J-OE fibroblasts by RNA sequencing. Since H2A.J plays an important role in the epidermal homeostasis of human skin, the oncogenic potential of H2A.J was investigated in cutaneous squamous cell carcinoma (cSCC). The tissue microarrays of cSCC were analyzed for H2A.J protein expression pattern by automated image analysis. Results: In response to radiation-induced DNA damage, the overexpression of H2A.J impairs the formation of senescence-associated heterochromatin foci (SAHF), thereby inhibiting the SAHF-mediated silencing of proliferation-promoting genes. The dysregulated activation of cyclins and cyclin-dependent kinases disturbs cell cycle arrest in irradiated H2A.J-OE fibroblasts, thereby overcoming radiation-induced senescence. Comparative transcriptome analysis revealed significantly increased WNT16 signaling in H2A.J OE fibroblasts after IR exposure, promoting the fundamental mechanisms of tumor development and progression, including the activation of the epithelial-mesenchymal transition. The quantitative analysis of cSCCs revealed that undifferentiated tumors are associated with high nuclear H2A.J expression, related with greater oncogenic potential. Conclusion: H2A.J overexpression induces radioresistance and promotes oncogenic transformation through the activation of WNT16 signaling pathway functions. H2A.J-associated signatures may improve risk stratification by identifying patients with more aggressive cSCC who may require radiotherapy with increased doses.

Comparative transcriptomics analysis on Senecavirus A-infected and non-infected cells.

Senecavirus A (SVA) is an emerging virus that causes the vesicular disease in pigs, clinically indistinguishable from other high consequence vesicular diseases. This virus belongs to the genus Senecavirus in the family Picornaviridae. Its genome is a positive-sense, single-stranded RNA, approximately 7,300 nt in length, with a 3' poly(A) tail but without 5'-end capped structure. SVA can efficiently propagate in different cells, including some non-pig-derived cell lines. A wild-type SVA was previously rescued from its cDNA clone using reverse genetics in our laboratory. In the present study, the BSR-T7/5 cell line was inoculated with the passage-5 SVA. At 12 h post-inoculation, SVA-infected and non-infected cells were independently collected for the analysis on comparative transcriptomics. The results totally showed 628 differentially expressed genes, including 565 upregulated and 63 downregulated ones, suggesting that SVA infection significantly stimulated the transcription initiation in cells. GO and KEGG enrichment analyses demonstrated that SVA exerted multiple effects on immunity-related pathways in cells. Furthermore, the RNA sequencing data were subjected to other in-depth analyses, such as the single-nucleotide polymorphism, transcription factors, and protein-protein interactions. The present study, along with our previous proteomics and metabolomics researches, provides a multi-omics insight into the interaction between SVA and its hosts.

Comparative Transcriptome Analysis Reveals Key Functions of MiMYB Gene Family in Macadamia Nut Pericarp Formation.

Macadamia nuts are one of the most important economic food items in the world. Pericarp thickness and flavonoid composition are the key quality traits of Macadamia nuts, but the underlying mechanism of pericarp formation is still unknown. In this study, three varieties with significantly different pericarp thicknesses, namely, A38, Guire No.1, and HAES 900, at the same stage of maturity, were used for transcriptome analysis, and the results showed that there were significant differences in their gene expression profile. A total of 3837 new genes were discovered, of which 1532 were functionally annotated. The GO, COG, and KEGG analysis showed that the main categories in which there were significant differences were flavonoid biosynthesis, phenylpropanoid biosynthesis, and the cutin, suberine, and wax biosynthesis pathways. Furthermore, 63 MiMYB transcription factors were identified, and 56 R2R3-MYB transcription factors were clustered into different subgroups compared with those in Arabidopsis R2R3-MYB. Among them, the S4, S6, and S7 subgroups were involved in flavonoid biosynthesis and pericarp formation. A total of 14 MiMYBs' gene expression were verified by RT-qPCR analysis. These results provide fundamental knowledge of the pericarp formation regulatory mechanism in macadamia nuts.

Comparative transcriptome analysis reveals genes involved in trichome development and metabolism in tobacco

BackgroundThe glandular trichomes of tobacco (Nicotiana tabacum) can efficiently produce secondary metabolites. They act as natural bioreactors, and their natural products function to protect plants against insect-pests and pathogens and are also components of industrial chemicals. To clarify the molecular mechanisms of tobacco glandular trichome development and secondary metabolic regulation, glandular trichomes and glandless trichomes, as well as other different developmental tissues, were used for RNA sequencing and analysis.ResultsBy comparing glandless and glandular trichomes with other tissues, we obtained differentially expressed genes. They were obviously enriched in KEGG pathways, such as cutin, suberine, and wax biosynthesis, flavonoid and isoflavonoid biosynthesis, terpenoid biosynthesis, and plant–pathogen interaction. In particular, the expression levels of genes related to the terpenoid, flavonoid, and wax biosynthesis pathway mainly showed down-regulation in glandless trichomes, implying that they lack the capability to synthesize certain exudate compounds. Among the differentially expressed genes, 234 transcription factors were found, including AP2-ERFs, MYBs, bHLHs, WRKYs, Homeoboxes (HD-ZIP), and C2H2-ZFs. These transcription factor and genes that highly expressed in trichomes or specially expressed in GT or GLT. Following the overexpression of R2R3-MYB transcription factor Nitab4.5_0011760g0030.1 in tobacco, an increase in the number of branched glandular trichomes was observed.ConclusionsOur data provide comprehensive gene expression information at the transcriptional level and an understanding of the regulatory pathways involved in glandular trichome development and secondary metabolism.

Comparative Analysis of Transcriptomes to Identify Genes during Bud Dormancy of Pyrus pyrifolia ‘Huanghua’

The study of pear dormancy mechanisms is currently a major research area in pear production and has high economic significance for agricultural production. We selected the southern sand pear cultivar Pyrus pyrifolia ‘Huanghua’ as the test material to study the pear dormancy process through microscopic observation of pear flower buds. The endodormancy period is abbreviated as D_bud. Similarly, the endodormancy release initiation period and the ecodormancy period are referred to as DB_bud and G_bud, respectively. Meanwhile, RNA sequencing was used to obtain the gene expression profile of Pyrus pyrifolia ‘Huanghua’ flower buds. The RNA sequencing results indicated that there were 224 differentially expressed genes (DEGs) in endodormancy (D) vs. endodormancy release initiation period (DB), while 975 were identified between endodormancy and ecodormancy (G). Finally, a total of 868 DEGs were found in the DB vs. G comparison. The expression levels of the genes Pbr009498.1 (LAX1-1), Pbr012348.1 (LAX1-2), Pbr021158.1 (GH35), and Pbr031621.1 (LAX2) encoding IAA were significantly higher during the DB_bud than during the D_bud. The expression level of Pbr025864.2 (IAA13) during the D_bud was significantly higher than the DB_bud and G_bud. The Pbr041942.1 (GID1B) gene also showed a significant increase during ecodormancy. Taken together, these results suggest that these genes, annotated as LAX1, GH35, LAX2, IAA13, and GID1C, are involved in endodormancy maintenance and in the transition from endodormancy to ecodormancy in Pyrus pyrifolia ‘Huanghua’.

Impact of activated charcoal on the progression of somatic embryogenesis in grape cells: Histological and transcriptomic perspectives

Somatic embryogenesis is a crucial genetic transformation method in plants. Despite numerous studies being conducted for acquiring embryogenic competence in plant cells, somatic embryo (SE) induction from embryogenic cells (ECs) has attracted relatively limited research attention. In grapes, somatic cell induction is impeded by unidentified inhibitors, which hinders the progression of globular embryo (GE) formation and subsequently embryo development. We found that addition of activated charcoal (AC) to the grape SE induction medium augmented the speed, consistency, and synchronization of embryogenesis. Cell samples cultured in the induction medium with and without AC were thoroughly evaluated through histological anatomy analysis, subcellular structure observation, and comparative transcriptomic analysis. The histological observation revealed the specific timeline of SE formation. An intermediate developmental state, referred to as the globular embryo precursor (PGE), was observed during the induction of GE formation from EC. Members of transcription factor families such as WRKY, MYB, MADS, AP2/ERF, HB-KNOX, HB-HD-ZIP, HB-WOX, NAC, and GRF were identified in the early and middle stages of GE formation. Additionally, we explored the key roles of reactive oxygen species (ROS)-, starch-, cell wall-, and hormone-related genes. The cell wall-related genes were highly enriched in differentially expressed gene sets. Several amyloplasts in EC disappeared, potentially because of hydrolysis, and numerous mitochondria were observed. In AC-added samples, starch was consumed more, and cellulose hydrolysis-related genes were downregulated, whereas cellulose synthesis-related genes had higher expression than AC-free samples. ROS response-related genes were induced when GE induction was initiated. When applied, an optimal concentration of external H2O2 promoted SE initiation in grapes, whereas a high concentration caused delayed GE formation. This study suggests that, by absorbing and releasing substances, the added AC can create a stable buffer environment for cell survival, protect against excessive ROS- or inhibitor-induced cell damage, and support uninterrupted progress of somatic embryogenesis.

Comparative metabolomics and transcriptomics analyses provide insights into branching changes induced by heterografting in Pinus massoniana seedlings

The investigation of dwarfing rootstocks for the establishment of high-generation seed orchards is a prospective avenue of research. In this investigation, Pinus massoniana, Pinus yunnanensis var. pygmaea (P. pygmaea), and P. elliottii seedlings were used as rootstocks for grafting with P. massoniana scions. Grafting P. massoniana onto P. pygmaea rootstock resulted in observable phenotypic alterations in lateral branches, apical buds, and needle length. Certain characteristic metabolites of rootstocks, such as fatty acyls, pregnenolones, steroids, and steroid derivatives, were found to be highly expressed in scions after grafting. RNA-seq analysis revealed MYB-related, SBP, and bHLH demonstrating a significant positive correlation, while C2H2 and Orphans exhibited negative correlations with the differential intensity of metabolites related to lipids and lipid-like molecules. This study offers valuable insights for the establishment of rootstock breeding programs.

Comparative analysis of liver transcriptomes associated with hypoxia tolerance in the improve blunt snout bream (Megalobrama amblycephala)

The blunt snout bream (Megalobrama amblycephala, BSB) is one of important freshwater fish of value in China, but it has poor tolerance to hypoxia environment. To improve this disadvantage, we cultivate an improved blunt snout bream (BTBB) from a hybrid lineage of Megalobrama amblycephala (♀) × Culter alburnus (♂). In this study, we found that the BTBB had higher tolerance hypoxia than BSB. Moreover, in order to take a deep insight into the molecular mechanisms of higher hypoxia tolerance in BTBB, we analyzed the liver transcriptomes of BTBB and BSB under normoxic and hypoxia conditions comparatively and found out several differentially expressed genes (DEGs). Among the GO functional categories, negative regulation of response to stimulus (GO: 0048585), oxidation-reduction process (GO: 0055114), and response to oxidative stress (GO: 0006979) in biological processes were observed. In addition, according to Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, the results indicated that many DEGs participated in FoxO signaling pathway, MAPK signaling pathway, VEGF signaling pathway, PPAR signaling pathway and p53 signaling pathway, and other processes. This study provides important clues about the potential molecular mechanisms explaining the higher hypoxia tolerance in BTBB. It also presents further evidence for the enhanced ability to resist hypoxia in BTBB, which is significant for fish genetic breeding.

Comparative transcriptome analysis of vegetable soybean grain discloses genes essential for grain quality

BackgroundVegetable soybean is an important vegetable crop in world. Seed size and soluble sugar content are considered crucial indicators of quality in vegetable soybean, and there is a lack of clarity on the molecular basis of grain quality in vegetable soybean.ResultsIn this context, we performed a comprehensive comparative transcriptome analysis of seeds between a high-sucrose content and large-grain variety (Zhenong 6, ZN6) and a low-sucrose content and small-grain variety (Williams 82, W82) at three developmental stages, i.e. stage R5 (Beginning Seed), stage R6 (Full Seed), and stage R7 (Beginning Maturity). The transcriptome analysis showed that 17,107 and 13,571 differentially expressed genes (DEGs) were identified in ZN6 at R6 (vs. R5) and R7 (vs. R6), respectively, whereas 16,203 and 16,032 were detected in W82. Gene expression pattern and DEGs functional enrichment proposed genotype-specific biological processes during seed development. The genes participating in soluble sugar biosynthesis such as FKGP were overexpressed in ZN6, whereas those responsible for lipid and protein metabolism such as ALDH3 were more enhanced in W82, exhibiting different dry material accumulation between two genotypes. Furthermore, hormone-associated transcriptional factors involved in seed size regulation such as BEH4 were overrepresented in ZN6, exhibiting different seed size regulation processes between two genotypes.ConclusionsHerein, we not only discovered the differential expression of genes encoding metabolic enzymes involved in seed composition, but also identified a type of hormone-associated transcriptional factors overexpressed in ZN6, which may regulate seed size and soluble content. This study provides new insights into the underlying causes of differences in the soybean metabolites and appearance, and suggests that genetic data can be used to improve its appearance and textural quality.

Comparative Analysis of Transcriptome at Different Growth and Development Stages of Camellia oleifera

Comparative Analysis of Transcriptome at Different Growth and Development Stages of Camellia oleifera

Comparative Analysis of Transcriptome at Different Growth and Development Stages of Camellia oleifera

Comparative Analysis of Transcriptome at Different Growth and Development Stages of Camellia oleifera

Comparative transcriptome analysis of doramectin-producing Streptomyces avermitilis N72 and its mutant strains.

Doramectin, an essential animal anthelmintic, is synthesized through the fermentation process of Streptomyces avermitilis. This study delves into the transcriptomic profiles of two strains, namely the doramectin-producing wild-type S. avermitilis N72 and its highly doramectin-producing mutant counterpart, S. avermitilis XY-62. Comparative analysis revealed 860 up-regulated genes and 762 down-regulated genes in the mutant strain, notably impacting the expression of key genes pivotal in doramectin biosynthesis, including aveA1, aveA2, aveA3, aveA4, aveE, and aveBI. These findings shed light on the molecular mechanisms underpinning the heightened doramectin production in S. avermitilis XY-62, presenting promising avenues for optimizing doramectin production processes.

Unraveling the Genetic Landscape of Pulmonary Arterial Hypertension in Indian Patients: A Transcriptome Study

BackgroundPulmonary hypertension (PH) is the abnormal elevation of pressure in the pulmonary vascular system, with various underlying causes. A specific type of PH is pulmonary arterial hypertension (PAH), a severe condition characterized by high pulmonary arterial pressure resulting from structural changes in distal pulmonary vessels, altered arterial tone, and inflammation. This leads to right ventricular hypertrophy and heart failure. The molecular mechanisms behind PAH are not well understood. This manuscript aims to elucidate these mechanisms using the genetic tool, aiding in diagnosis and treatment selection. MethodIn our present study, we have obtained blood samples from both patients with pulmonary arterial hypertension (PAH) and healthy individuals. We conducted a comparative transcriptome analysis to identify genes that are either upregulated or downregulated in PAH patients when compared to the control group. Subsequently, we carried out a validation study focusing on the log2-fold downregulated genes in PAH, employing Quantitative Real-Time PCR for confirmation. Additionally, we quantified the proteins encoded by the validated genes using the ELISA technique. ResultsThe results of the transcriptome analysis revealed that 97 genes were significantly upregulated, and 6 genes were significantly downregulated. Among these, we chose to focus on and validate only four of the downregulated genes, as they were directly or indirectly associated with the hypertension pathway. We also conducted validation studies for the proteins encoded by these genes, and the results were consistent with those obtained in the transcriptome analysis. ConclusionIn conclusion, the findings of this study indicate that the four validated genes identified in the context of PAH can be further explored as potential targets for both diagnostic and therapeutic applications.