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Folsomia candida is a tiny soil-living arthropod belonging to the Collembola, which is an outgroup to Insecta. It resembles insects as having a pair of antennae and three pairs of thorax legs, while it also possesses three abdominal appendages: a ventral tube located in the first abdominal segment (A1), a retinaculum in A3, and a furca in A4. Collembolan Ubx and AbdA specify abdominal appendages, but they are unable to repress appendage marker gene Dll. The genetic basis of collembolan appendage formation and the mechanisms by which Ubx and AbdA regulate Dll transcription and appendage development remains unknown. In this study, we analysed the developmental transcriptomes of F. candida and identified candidate appendage formation genes, including Ubx (FcUbx). The expression data revealed the dominance of Dll over Ubx during the embryonic 3.5 and 4.5 days, suggesting that Ubx is deficient in suppressing Dll at early appendage formation stages. Furthermore, via electrophoretic mobility shift assays and dual luciferase assays, we found that the binding and repression capacity of FcUbx on Drosophila Dll resembles those of the longest isoform of Drosophila Ubx (DmUbx_Ib), while the regulatory mechanism of the C-terminus of FcUbx on Dll repression is similar to that of the crustacean Artemia franciscana Ubx (AfUbx), demonstrating that the function of collembolan Ubx is intermediate between that of Insecta and Crustacea. In summary, our study provides novel insights into collembolan appendage formation and sheds light on the functional evolution of Ubx. Additionally, we propose a model that collembolan Ubx regulates abdominal segments in a context-specific manner. [ABSTRACT FROM AUTHOR]

Environmental stresses are responsible for limiting soybean yield. To mitigate the impacts generated by water deficit, molecular biology tools are being used to develop genetically modified plants. Previous studies showed that two independent events (B1 and B3) of soybean transgenic plants expressing a Solanum nigrum osmotin (SnOLP) had an increment in drought tolerance. The present study aims to investigate the modulated pathways that results in the drought tolerance promoted by osmotin overexpression in soybean. Transgenic and non-transgenic (NT) plants in the vegetative stage were submitted to water deficit by irrigation suppression for seven days. Control plants were kept irrigated. Physiological variables were monitored and confirmed that the transgenic plants present better performance when compared to the NT plants. The total RNA extracted from leaves was sequenced and data was normalized by DESeq2. A total of 2044 and 1505 differentially expressed genes (DEGs) were identified in B1 and B3 events, respectively. Regarding the B1 event, 769 genes were upregulated and 1275 downregulated. For B3, 541 genes were upregulated and 964 genes were downregulated. Excluding common differentially expressed genes (DEGs) between transgenic and non-transgenic (NT) plants yielded 395 upregulated and 234 downregulated genes, which were shared by B1 and B3 events. The metabolic pathways and gene ontology categories identified are known to be involved in plant responses to drought. Hormonal, photosynthetic, carbohydrate and amino acid metabolism, reactive oxygen species, and post-translational modifications pathways were significantly modulated in transgenic plants. Altogether, the results suggest that osmotin promotes tolerance through an increment in the plant responses elicited by drought. [ABSTRACT FROM AUTHOR]

The global prevalence of iron deficiency-induced "hidden hunger" highlights a critical health concern, underscoring the pressing need to improve iron nutrition through safe and efficient means, such as increasing iron intake from plant-based foods. Yellow Stripe-Like (YSL) genes play a crucial role in long-distance iron transport between source and sink tissues in plants. Here, we report on the analysis of YSL family genes in the common bean (Phaseolus vulgaris L.), an iron-rich legume crop. We identified 9 YSL genes in the common bean genome using BLAST and HMM methods. Gene duplication analysis revealed that PvYSL7a and PvYSL7b originated through tandem duplication events. Structural analysis noted an absence of conservative motifs in PvYSL3b and PvYSL7a, which led to distinct predicted 3D protein structures. Leveraging publicly available RNA-seq data from developing bean pods, the expression patterns of PvYSL genes alongside pod and seed development were analyzed. Notably, PvYSL7a and PvYSL7b, as well as PvYSL1a and PvYSL1b, exhibited diverged expression patterns in seeds, signifying their functional divergence in this tissue. Moreover, PvYSL3a and PvYSL3b exhibited divergent expression patterns in both pod walls and seeds during pod development, underscoring their distinct roles in facilitating iron transportation between pods and seeds. This study provides valuable insights into the gene regulatory basis of iron accumulation in bean pods and seeds. [ABSTRACT FROM AUTHOR]

Multicollinearity, characterized by significant co-expression patterns among genes, often occurs in high-throughput expression data, potentially impacting the predictive model's reliability. This study examined multicollinearity among closely related genes, particularly in RNA-Seq data obtained from embryoid bodies (EB) exposed to 5-fluorouracil perturbation to identify genes associated with embryotoxicity. Six genes—Dppa5a, Gdf3, Zfp42, Meis1, Hoxa2, and Hoxb1—emerged as candidates based on domain knowledge and were validated using qPCR in EBs perturbed by 39 test substances. We conducted correlation studies and utilized the variance inflation factor (VIF) to examine the existence of multicollinearity among the genes. Recursive feature elimination with cross-validation (RFECV) ranked Zfp42 and Hoxb1 as the top two among the seven features considered, identifying them as potential early embryotoxicity assessment biomarkers. As a result, a t test assessing the statistical significance of this two-feature prediction model yielded a p value of 0.0044, confirming the successful reduction of redundancies and multicollinearity through RFECV. Our study presents a systematic methodology for using machine learning techniques in transcriptomics data analysis, enhancing the discovery of potential reporter gene candidates for embryotoxicity screening research, and improving the predictive model's predictive accuracy and feasibility while reducing financial and time constraints. [ABSTRACT FROM AUTHOR]

Schimke immuno-osseous dysplasia is a rare multisystemic disorder caused by biallelic loss of function of the SMARCAL1 gene that plays a pivotal role in replication fork stabilization and thus DNA repair. Individuals affected from this disease suffer from disproportionate growth failure, steroid resistant nephrotic syndrome leading to renal failure and primary immunodeficiency mediated by T cell lymphopenia. With infectious complications being the leading cause of death in this disease, researching the nature of the immunodeficiency is crucial, particularly as the state is exacerbated by loss of antibodies due to nephrotic syndrome or immunosuppressive treatment. Building on previous findings that identified the loss of IL-7 receptor expression as a possible cause of the immunodeficiency and increased sensitivity to radiation-induced damage, we have employed spectral cytometry and multiplex RNA-sequencing to assess the phenotype and function of T cells ex-vivo and to study changes induced by in-vitro UV irradiation and reaction of cells to the presence of IL-7. Our findings highlight the mature phenotype of T cells with proinflammatory Th1 skew and signs of exhaustion and lack of response to IL-7. UV light irradiation caused a severe increase in the apoptosis of T cells, however the expression of the genes related to immune response and regulation remained surprisingly similar to healthy cells. Due to the disease’s rarity, more studies will be necessary for complete understanding of this unique immunodeficiency. [ABSTRACT FROM AUTHOR]

UDP-glucose pyrophosphorylase is ubiquitously present in animals, plants and bacteria and plays essential role in biosynthesis of UDP-glucose which is a fundamentally important molecule in biology. In this paper, we cloned an E. ulmoides UGP1 gene and alignment of the EuUGP1 protein showed it belonged to A-type UGPase (UGPase-A) with characteristics of cytoplasm-localization. Further study showed the EuUGP1 introduction improved UGPase activity and UDP-Glc content in transgenic tobaccos, which subsequently acted as the donor for synthesis of glucose, sucrose, and cellulose, etc. Actually, the EuUGP1-overexpression increased the contents of glucose, cellulose, sucrose and soluble sugar in transgenic tobaccos. Transcriptome data showed that the differentially expressed genes (DEGs) were mainly enriched in metabolic pathway and secondary metabolic pathway, especially the genes related to glycosyltransferase activity (e.g. UGT) being significantly up-regulated. Further, metabolomic data showed that the differentially accumulated metabolites (DAMs) were also mainly enriched in metabolic pathway, secondary metabolic pathway and flavonoid metabolic pathway, and the content of secondary metabolites in transgenic tobaccos was significantly higher than that in wild-type plants. Among these metabolites, the flavonoids and their derivatives including glycosides metabolites accounted for 34% compared with other secondary metabolites, which suggesting EuUGP1 could significantly regulate the UDP-Glc accumulation and the latter provided free glucoside for flavonoid glycosides synthesis. These findings provide a theoretical basis for further study of the function of E. ulmoides EuUGP1 gene.Key message: The overexpression of EuUGP1 augmented the activity of UGPase and the level of UDP-Glc, concurrently elevating the levels of sucrose, glucose, and soluble sugars. At the same time, the content of flavonoids was increased. [ABSTRACT FROM AUTHOR]

The spotted sea bass (Lateolabrax maculatus), a eurythermal species, exhibits strong adaptability to temperature variations and presents an ideal model for studying heat stress-responsive mechanisms in fish. This study examined the liver transcriptome of spotted sea bass over a 24-h period following exposure to elevated temperatures, rising from 25 to 32 °C. The results revealed significant alterations in gene expression in response to this thermal stress. Specifically, we identified 1702, 1199, 3128, and 2636 differentially expressed genes at 3, 6, 12, and 24 h post-stress, respectively. Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify specific gene modules responsive to heat stress, containing hub genes such as aco2, eci2, h6pd, suclg1, fgg, fga, fgb, f2, and apoba, which play central roles in the heat stress response. Enrichment analyses via KEGG and GSEA indicated that upregulated differentially expressed genes (DEGs) are predominantly involved in protein processing in the endoplasmic reticulum, while downregulated genes are primarily associated with the AGE-RAGE signaling pathways. Additionally, 272 genes exhibited differential alternative splicing, primarily through exon skipping, underscoring the complexity of transcriptomic adaptations. These findings provide deeper insights into the molecular responses to thermal stress and are crucial for advancing the breeding of heat-resistant strains of spotted sea bass. [ABSTRACT FROM AUTHOR]

As a prerequisite for the success of embryo development, embryonic genome activation (EGA) is an important biological event in which zygotic gene products in the embryo are activated to replace maternal-derived transcripts. Although EGA has been extensively studied in a large number of vertebrates and invertebrates, there is a lack of information regarding this event in crustacean crab. In this study, the timing of EGA was confirmed by examining a transcriptomic dataset of early embryonic development, including mature oocytes and embryos through six early developmental stages, and signaling pathways associated with EGA were identified in the mud crab, S. paramamosain. The comprehensive transcriptomic data identified a total of 53,915 transcripts from these sequencing samples. Notable transcriptomic change was evident at the 1-cell stage, indicated by a 36% transcript number shift and a reduction in transcript fragment length, compared to those present in the mature oocytes. Concurrently, a substantial increase in the expression of newly transcribed transcripts was observed, with gene counts reaching 3485 at the 1-cell stage, indicative of the onset of EGA. GO functional enrichment revealed key biological processes initiated at the 1-cell stage, such as protein complex formation, protein metabolism, and various biosynthetic processes. KEGG analysis identified several critical signaling pathways activated during EGA, including the "cell cycle," "spliceosome," "RNA degradation", and "RNA polymerase", pathways. Furthermore, transcription factor families, including zinc finger, T-box, Nrf1, and Tub were predominantly enriched at the 1-cell stage, suggesting their pivotal roles in regulating embryonic development through the targeting of specific DNA sequences during the EGA process. This groundbreaking study not only addresses a significant knowledge gap regarding the developmental biology of S. paramamosain, especially for the understanding of the mechanism underlying EGA, but also provides scientific data crucial for the research on the individual synchronization of seed breeding within S. paramamosain aquaculture. Additionally, it serves as a reference basis for the study of early embryonic development in other crustacean species. [ABSTRACT FROM AUTHOR]

Hyalomma anatolicum is a tick of significant one-health importance due to its role as a vector for various pathogens affecting humans, animals and the environment, such as Theileria annulata, which causes tropical theileriosis in cattle, leading to severe economic losses. When infected with pathogens like T. annulata, the salivary glands of H. anatolicum undergo gene expression changes, secrete modified proteins and activate immune responses, all of which facilitate pathogen survival and transmission by modulating the host immune response and optimizing conditions for pathogen development. Understanding these responses is crucial for developing control strategies for tick-borne diseases. To understand the interaction between H. anatolicum and T. annulata, we performed a differential gene expression analysis of H. anatolicum salivary glands. An average of approximately 25 million raw sequencing reads were generated in each replicate using Illumina Sequencing. The sequenced reads were de novo assembled and the assembled transcriptome yielded approximately 50,231 non-redundant transcripts after clustering with CD-HIT using a sequence identity of 95% and alignment coverage of 90%. The assembly quality was evaluated with BUSCO analysis and found to be 86% complete using the Arachnida dataset and then blasted against non-redundant protein sequence database from NCBI followed by counting of reads and differential expression analysis. Overall, around 2400 and 400 genes were found differentially expressed with logFC > 1 and logFC > 2 respectively at FDR < 0.05. Top up-regulated genes included Calpain, Papilin, Neprilysin, and Ankyrin repeat-containing protein. Top down-regulated genes included Scoloptoxin, and Selenoprotein S and other uncharacterized proteins. Many other up-regulated proteins with high significance were uncharacterized suggesting room for further H. anatolicum functional and structural characterization studies. To our best knowledge, this is the first study of H. anatolicum sialotranscriptome which greatly contributes to sialotranscriptome information not only as sequence database but also indicates the potential targets for development of vaccine against ticks and transmission-blocking vaccines against T. annulata. [ABSTRACT FROM AUTHOR]

The postmenopausal decrease in circulating estradiol (E2) levels has been shown to contribute to several adverse physiological and psychiatric effects. To elucidate the molecular effects of E2 on the brain, we examined differential gene expression and DNA methylation (DNAm) patterns in the nonhuman primate brain following ovariectomy (Ov) and subsequent subcutaneous bioidentical E2 chronic treatment. We identified several dysregulated molecular networks, including MAPK signaling and dopaminergic synapse response, that are associated with ovariectomy and shared across two different brain areas, the occipital cortex (OC) and prefrontal cortex (PFC). The finding that hypomethylation (p = 1.6 × 10−51) and upregulation (p = 3.8 × 10−3) of UBE2M across both brain regions provide strong evidence for molecular differences in the brain induced by E2 depletion. Additionally, differential expression (p = 1.9 × 10−4; interaction p = 3.5 × 10−2) of LTBR in the PFC provides further support for the role E2 plays in the brain, by demonstrating that the regulation of some genes that are altered by ovariectomy may also be modulated by Ov followed by hormone replacement therapy (HRT). These results present real opportunities to understand the specific biological mechanisms that are altered with depleted E2. Given E2's potential role in cognitive decline and neuroinflammation, our findings could lead to the discovery of novel therapeutics to slow cognitive decline. Together, this work represents a major step toward understanding molecular changes in the brain that are caused by ovariectomy and how E2 treatment may revert or protect against the negative neuro-related consequences caused by a depletion in estrogen as women approach menopause. [ABSTRACT FROM AUTHOR]

Illuminate the genome-wide dynamic response to salt stress in Periploca sepium Bunge and the mining of the key salt-tolerant genes. After 30 days of growth and treatment with 1% NaCl, transcriptome sequencing was performed and select genes were tested for RT-qPCR to ensure transcriptome accuracy. The results showed that there were 2225, 2579, 3852 and 3811 differentially expressed genes (DEGs) under salt stress for 4 h, 12 h, 24 h and 48 h, respectively. In the early stage, the redox balance in P. sepium was broken, and with the increase of ROS, the expression of antioxidant enzymes was also increased, and plant growth was inhibited, which was manifested in the significantly down-regulated expression of GA synthesis genes. With the increase of salt stress time, the process of energy metabolism and resource recombination in P. sepium was strengthened, and protein degradation and synthesis occurred accordingly. After 2 days of response adjustment, the differential genes in plants gradually stabilized, and the expression of genes related to reducing substances such as flavonoids was significantly up-regulated, and the plants re-established a stable state to adapt to the new environment. [ABSTRACT FROM AUTHOR]

Yaghooti grape, as the earliest grape variety in Iran, is considered as more resistant to heat, drought, and salinity than other cultivars. Cluster compactness is regarded as an inappropriate feature for the productivity of Yaghooti grape as a critical commercial and nutritional product. In plants, lncRNAs play a critical role in regulating biological processes related to growth and development. However, the potential role of lncRNAs was not assessed in cluster compactness. Totally, 1549 lncRNAs were identified by RNA-Seq data analysis in three steps of cluster formation, berry formation, and final cluster size after a thorough screening process. In addition, 229 lncRNAs were differentially expressed in the cluster development steps. Based on the functional analysis, lncRNAs are related to AG and MYB, bHLH, LBD, NAC, and WRKY TFs. Further, the target genes enrichment analysis revealed a relationship between lncRNAs with grape growth and development, as well as resistance to abiotic stresses such as heat and drought, plant defense against pathogens, and early grapes ripening. The study identified four lncRNAs as precursors of miRNAs, predicting that 112 other lncRNAs could potentially be targeted by 166 miRNAs. The results provide new insights into the regulatory functions of lncRNAs in Yaghooti grape to improve overall understanding of the molecular mechanisms related to grape compactness. [ABSTRACT FROM AUTHOR]

The pathogenesis of pulmonary arterial hypertension (PAH) is closely linked to the abnormal proliferation of pulmonary artery smooth muscle cells. Studies have demonstrated that microRNAs play pivotal roles in the progression of pulmonary hypertension. We found that microRNA-637 (miR-637) and microRNA-661 (miR-661) are expressed at low levels in the serum of PAH patients. Moreover, the overexpression of miR-637 or miR-661 inhibited human pulmonary artery smooth muscle cell (HPASMC) proliferation and migration in hypoxic culture. Mechanistically, we overexpressed these two microRNAs in HPASMCs, and the RNA-sequencing (RNA-seq) results demonstrated that TRIM29 mRNA was suppressed, indicating that TRIM29 is a substrate. TRIM29 accumulates in the serum of patients with PAH and promotes cell proliferation and migration by activating AKT/mTOR signalling. In addition, overexpression of miR-637 or miR-661 reversed TRIM29-mediated HPASMC proliferation and migration. This study revealed that miR-637 and miR-661 are able to inhibit the proliferation ability of HPASMCs under hypoxic conditions through targeting TRIM29, suggesting that the microRNA-637/661/TRIM29 axis may act as a target for PAH treatment. [ABSTRACT FROM AUTHOR]

We investigated the long-term effects of prenatal nutrition on pre-slaughter Nelore bulls using integrative transcriptome and metabolome analyses of liver tissue. Three prenatal nutritional treatments were administered to 126 cows: NP (control, mineral supplementation only), PP (protein-energy supplementation in the third trimester), and FP (protein-energy supplementation throughout pregnancy). Liver samples from 22.5 ± 1-month-old bulls underwent RNA-Seq and targeted metabolomics. Weighted correlation network analysis (WGCNA) identified treatment-associated gene and metabolite co-expression modules, further analyzed using MetaboAnalyst 6.0 (metabolite over-representation analysis and transcriptome-metabolome integrative analysis) and Enrichr (gene over-representation analysis). We identified several significant gene and metabolite modules, as well as hub components associated with energy, protein and oxidative metabolism, regulatory mechanisms, epigenetics, and immune function. The NP transcriptome-metabolome analysis identified key pathways (aminoacyl t-RNA biosynthesis, gluconeogenesis, and PPAR signaling) and hub components (glutamic acid, SLC6A14). PP highlighted pathways (arginine and proline metabolism, TGF-beta signaling, glyoxylate and dicarboxylate metabolism) with arginine and ODC1 as hub components. This study highlights the significant impact of prenatal nutrition on the liver tissue of Nelore bulls, shedding light on critical metabolic pathways and hub components related to energy and protein metabolism, as well as immune system and epigenetics. [ABSTRACT FROM AUTHOR]

Mongolian horses are characterized by strong endurance in sports and their meat is a special food resource in Inner Mongolia, China. To assess the characteristics of the Mongolian horses in terms of exercise and meat quality, in this study, we selected healthy and untrained adult stallions and collected a total of 24 skeletal muscles from representative parts of the whole body (head and neck, forelimb, trunk, abdominal wall side, and hindlimb) for transcriptome sequencing. After grouping by site, using RNA-Sequencing (RNA-Seq) data, differential expression analysis between two sites was performed to obtain the differentially expressed genes (DEGs) between different skeletal muscle sites, and the up-regulated DEGs at each site were pooled and enriched to obtain the relevant genes and pathways specific to each skeletal muscle site. The semimembranosus and gastrocnemius were selected from the hindlimb for phenotypic studies of fast and slow muscle fibers as well as RNA-Seq analysis. We found that the semimembranosus had 71.69% of slow muscle fibers and 124 up-regulated DEGs. The gastrocnemius had 78.93% of fast muscle fibers and 31 up-regulated DEGs. The results showed that the biochemical properties of horse skeletal muscle were altered by site and the percentage of fast and slow muscle fibers in the skeletal muscle. [ABSTRACT FROM AUTHOR]

Ultraviolet A (UVA) radiation is the major fraction of UV radiation reaching the Earth's surface. Its harmful effects on microorganisms, due mainly to oxidative damage, have been exploited for development of natural solar and commercial UVA-based disinfection methods. In this work, the global transcriptional response of Pseudomonas aeruginosa exposed to ultraviolet A (UVA) radiation was analyzed. To conduct this study, we analyzed the whole transcriptome of the PAO1 strain grown to logarithmic phase under sublethal doses of UVA or in the dark. We found that a total of 298 genes responded to UVA with a change of at least two-fold (5.36% of the total P. aeruginosa genome), and showed equal amount of induced and repressed genes. An important fraction of the induced genes were involved in the response to DNA damage and included induction of SOS, prophage and pyocins genes. The results presented in this study suggest that one of the main UVA targets are proteins carrying [Fe–S] clusters since several genes involved in the processes of synthesis, trafficking and assembly of these structures were upregulated. The management of intracellular iron levels also seems to be a robust response to this stress factor. The strong induction of genes involved in denitrification suggest that this pathway and/or reactive nitrogen species such as nitric oxide could have a role in the response to this radiation. Regarding the down-regulated genes, we found many involved in the biosynthesis of PQS, a quorum-sensing signal molecule with a possible role as endogenous photosensitizer. [ABSTRACT FROM AUTHOR]

The olfactory organ of tetrapods, with few exceptions, comprises the main and accessory organs: olfactory epithelium (OE) and vomeronasal organ (VNO). Unlike tetrapods, teleost fish lack a VNO. However, lungfish, a type of sarcopterygian fish closely related to tetrapods, possesses a lamellar OE similar to the OE of teleosts and a recess epithelium (RecE) resembling the amphibian VNO. The RecE has been hypothesized as a primordial VNO. Olfactory receptors in tetrapods are distinctively expressed in the OE and VNO. For instance, type 2 vomeronasal receptors (V2Rs) in Xenopus are categorized into those exclusively expressed in the OE and those solely expressed in the VNO. It remains unclear whether V2Rs are differentially expressed between the lamellar OE and RecE in lungfish. This study investigated V2R expression in the lamellar OE and RecE of the African lungfish, Protopterus annectens. P. annectens V2Rs were categorized into three groups: those exclusively expressed in the lamellar OE, those exclusively expressed in the RecE, and those expressed in both the lamellar OE and RecE. V2Rs exclusively expressed in the RecE and those expressed in both the lamellar OE and RecE formed a distinct clade in the phylogenetic tree, whereas others were solely expressed in the lamellar OE. These findings suggest that lungfish V2R expression represents an intermediate stage toward complete segregation between V2Rs expressed in the OE and those expressed in the VNO. [ABSTRACT FROM AUTHOR]

The green alga Pediastrum duplex forms colonies through asexual reproduction and has a unique life cycle. To elucidate the mechanisms that regulate the asexual reproductive cycle in P. duplex, we analyzed the effects of light on the processes and gene expression involved in each step of the asexual reproductive cycle, revealing light irradiation to be essential for increasing the number of colonies. Among the processes in the asexual reproductive cycle, the transition from cell hypertrophy to zoospore formation could proceed even in the dark if glucose was added to the medium. Transcriptome analysis revealed that the expression of different groups of genes was significantly promoted or suppressed before and after the number of colonies increased. Our findings indicate that the asexual reproductive cycle of P. duplex includes a process promoted by photosynthesis. This study enhances our understanding of the growth characteristics of P. duplex and other microalgae. [ABSTRACT FROM AUTHOR]

Aortic aneurysm is characterized by a pathological dilation at specific predilection sites of the vessel and potentially results in life-threatening vascular rupture. Herein, we established a modified "Häutchen method" for the local isolation of endothelial cells (ECs) from mouse aorta to analyze their spatial heterogeneity and potential role in site-specific disease development. When we compared ECs from aneurysm predilection sites of healthy mice with adjacent control segments we found regulation of genes related to extracellular matrix remodeling, angiogenesis and inflammation, all pathways playing a critical role in aneurysm development. We also detected enhanced cortical stiffness of the endothelium at these sites. Gene expression of ECs from aneurysms of the AngII ApoE−/− model when compared to sham animals mimicked expression patterns from predilection sites of healthy animals. Thus, this work highlights a striking genetic and functional regional heterogeneity in aortic ECs of healthy mice, which defines the location of aortic aneurysm formation in disease. [ABSTRACT FROM AUTHOR]

Main conclusion: A novel genomic map of the apogamous gametophyte of the fern Dryopteris affinis unlocks oldest hindrance with this complex plant group, to gain insight into evo-devo approaches. The gametophyte of the fern Dryopteris affinis ssp. affinis represents a good model to explore the molecular basis of vegetative and reproductive development, as well as stress responses. Specifically, this fern reproduces asexually by apogamy, a peculiar case of apomixis whereby a sporophyte forms directly from a gametophytic cell without fertilization. Using RNA-sequencing approach, we have previously annotated more than 6000 transcripts. Here, we selected 100 of the inferred proteins homolog to those of Arabidopsis thaliana, which were particularly interesting for a detailed study of their potential functions, protein–protein interactions, and distance trees. As expected, a plethora of proteins associated with gametogenesis and embryogenesis in angiosperms, such as FERONIA (FER) and CHROMATING REMODELING 11 (CHR11) were identified, and more than a dozen candidates potentially involved in apomixis, such as ARGONAUTE family (AGO4, AGO9, and AGO 10), BABY BOOM (BBM), FASCIATED STEM4 (FAS4), FERTILIZATION-INDEPENDENT ENDOSPERM (FIE), and MATERNAL EFFECT EMBRYO ARREST29 (MEE29). In addition, proteins involved in the response to biotic and abiotic stresses were widely represented, as shown by the enrichment of heat-shock proteins. Using the String platform, the interactome revealed that most of the protein–protein interactions were predicted based on experimental, database, and text mining datasets, with MULTICOPY SUPPRESSOR OF IRA4 (MSI4) showing the highest number of interactions: 16. Lastly, some proteins were studied through distance trees by comparing alignments with respect to more distantly or closely related plant groups. This analysis identified DCL4 as the most distant protein to the predicted common ancestor. New genomic information in relation to gametophyte development, including apomictic reproduction, could expand our current vision of evo-devo approaches. [ABSTRACT FROM AUTHOR]

Wireworms, the larva of click beetle (Agriotes species), are one of the most destructive pests of horticultural crops in North America, responsible for considerable economic losses in Canada. Agriotes sputator (A. sputator) species is a predominant wireworm pest attacking potato fields in Eastern Canada. However, no information about its genome-wide gene expression profile, specifically for the genes involved with development is available to date. Therefore, we generated the transcriptome profile of A. sputator during five developmental stages, including the three larval stages and adult male and female click beetle. Out of 714.7 million raw reads, de novo assembly generated 564,561 transcripts. The data were subjected to differential expression analysis using DESeq2, gene ontology, annotation, and pathway analyses. A total of 34,709 differentially expressed genes (DEGs) were significant (log2 fold change > 2, padj < 0.05) across the developmental stages. Functional analysis of DEGs identified development signaling, metabolism, transport, cellular mechanisms, and drug metabolism (cytochrome p450) pathways. This study provides comprehensive sequence resources and potential gene differences at different developmental stages of A. sputator. These findings will represent a major step towards developing sustainable methods to control this widely distributed pest in agricultural fields. [ABSTRACT FROM AUTHOR]

Both the quality of chicken meat and the quality of chicks are influenced by the level of breast muscle glycogen reserves. In order to study the role of digestive metabolism in establishing this muscular phenotype, we compared two divergent chicken lines for the ultimate pH (pHu) of the breast meat, a proxy for glycogen reserves. Males aged 4 weeks had twice the breast muscle glycogen content in the pHu- line (low pHu) than in the pHu + line (high pHu). The increase in glycogen reserves (pHu-) was associated with a higher relative weight of the proventriculus and gizzard, as well as better apparent ileal digestibility of nitrogen and calcium. The diversity of the cecal microbiota was comparable, but three bacterial genera (Lachnospira, Lachnospiraceae UCG-010, Caproiciproducens) varied between the lines. The differences observed could lead to down-regulation of carbon fixation in prokaryotes and of the citrate cycle in the pHu + line. RNA-seq analysis of the jejunum, the major site of nutrient absorption, revealed 149 genes differentially expressed (DE) between the lines, including several genes linked to immunity, hormonal response and circadian rhythms that are less expressed in pHu + animals. Others involved in cell migration and proliferation, and more generally tissue morphogenesis, also differed between the lines. Among the DE genes, several co-localized with Quantitative Trait Loci (QTL) controlling pHu and selection signatures identified in the divergent lines, such as the gene coding for ghrelin, a hormone regulating appetite. [ABSTRACT FROM AUTHOR]

Climate change is a major global concern that has increased the frequency and intensity of extreme drought. Severe drought stress negatively affected tree survival and growth. Poplars are fast-growing trees that can effectively sequester atmospheric carbon dioxide, the most important greenhouse gas. Recently, poplar has attracted attention as a bioenergy fuel source, owing to its fast-growing traits and abiotic stress tolerance. However, the molecular mechanisms underlying drought tolerance in poplars remain uncertain. Therefore, we compared the transcriptomes of P. davidiana and its hybrid with Populus alba grown under drought stress. Before drought stress, genes related to root development processes were up-regulated, and aboveground tissue development genes were down-regulated in P. davidiana compared to P. alba × P. davidiana. After 6 days of drought treatment, P. alba × P. davidiana showed susceptibility to drought stress, whereas P. davidiana exhibited a resistant phenotype. At the transcriptional level, cell wall and lignin biosynthesis genes were up-regulated on day 6 of drought treatment. We concluded that P. davidiana showed more resistance to drought stress than its hybrid and that cell wall biosynthetic processes contributed to drought tolerance by preventing xylem damage. These results could provide valuable information for poplar breeding to improve drought stress tolerance. [ABSTRACT FROM AUTHOR]

Climatic changes pose a continuing danger to food production, impacting people's livelihoods worldwide. Salt and drought stresses have significantly impeded global maize output. RNA editing (RE) is a post-transcriptional process and has a unique function in regulating responses to environmental stimuli. The function of RNA editing sites (RES) in maize plants exposed to salt and water stresses has not been well investigated. In this study, two maize genotypes, sensitive to salt (SS) and resistant to salt (ST) were used. We investigated how salt and water stressors impact RNA editing sites in the whole mRNA derived from the maize nuclear genome. The average alignment rate was 90% for SS and 80% for ST genotypes when compared to the reference genome. Most of the editing events were non-synonymous codon alterations, and the trend in amino acid modifications was mostly hydrophobic. When we compared the root and shoot samples from the treated and control groups, we found that both groups had twelve different types of REs including A/C, A/G (A/I), A/T, C/A, C/G, C/T (C/U), G/A, G/C, G/T, T/A, T/C, and T/G. The treated samples showed an overall improvement in RE efficiency. Gene Ontology analysis showed that the mapped genes participated in several biological processes and molecular activities. The analysis of the whole genome's encoded RNA-edited genes showed that 26 sites were altered from C to T (C to U) in the genes ZemaCp023, ZemaCp001, and Zm00001eb437010. Three A/G (A/I) REs were exclusively linked to ZemaCp001. These results will serve as a foundation for identifying RES in other crops and will also be helpful in the development of salt and water tolerance in maize. [ABSTRACT FROM AUTHOR]

Rice production is significantly affected by drought at various developmental stages. The identification and shortlisting of candidate genes for developing drought-tolerant rice varieties are ongoing. To identify core drought-responsive genes, we compared the transcriptomic changes between ten drought-tolerant rice varieties. Through our meta-analysis of publicly available RNA-Seq datasets, we identified 3080 core differentially expressed genes (DEGs) in response to drought stress. K-means clustering analysis showed that the expression of core DEGs can be grouped into two clusters with distinct expression dynamics under drought stress. Gene ontology enrichment analysis revealed that the functional distribution of 1282 genes in cluster 1 showing upregulation in all the tolerant lines was mainly related to the abiotic stress response. A weighted gene co-expression network analysis of all the genes in cluster 1 revealed that among the 11 co-expressed modules, the blue module showed significant positive correlation (195 genes; R2 = 0.73, P = 3.0 × 10–19) with drought stress, which assisted us to narrow down the genes to identify candidates for drought stress tolerance. Through a literature search to identify functionally characterized genes, six drought tolerance-related candidate genes were detected, including LEA4-5 (LOC_Os08g23870), LEA14 (LOC_Os01g12580), OsRab16A (LOC_Os11g26790), OsADF3 (LOC_Os03g60580), OsPP108 (LOC_Os09g15670) and GBF3 (LOC_Os01g46970). Finally, we constructed a protein–protein interaction network and selected the hub genes in the blue module, two of which overlapped with candidates and may play a critical role in drought tolerance. Our results provide promising candidate genes that may be useful in transgenic studies or molecular marker-assisted selection for improving drought tolerance and increasing rice yields. [ABSTRACT FROM AUTHOR]

Hollowness is a physiological disorder that frequently occurs during the growth and postharvest storage phases of fleshy radish roots, significantly diminishing quality, yield, and marketability. However, the molecular mechanism for hollowness remains elusive. To identify the QTLs and potential candidate genes for hollowness tolerance in radish, F2 and BC1 populations were constructed from hollowness-tolerant radish (C16) and hollowness-sensitive radish (C17) in the present study. Genetic analysis indicated that hollowness tolerance may be governed by two independent recessive genes. By employing bulked segregant analysis sequencing (BSA-seq), two significant candidate genomic intervals were pinpointed on chromosomes R04 (960 kb, 6.48–7.44 Mb) and R05 (600 kb, 31.44–32.04 Mb), which together harbor 107 annotated genes. Transcriptomic sequencing revealed that the downregulated differentially expressed genes (DEGs) were significantly enriched in biological processes related to cell death and the response to water stress, whereas the upregulated DEGs were significantly associated with the chitin catabolic process and the cell wall macromolecule metabolic process. A total of 46 intersecting genes were identified among these DEGs within the genomic intervals of interest. One gene with high expression (Rsa10025345) and two with low expression (Rsa10025320 and Rsa10018106) were detected in the tolerant variety C16. Furthermore, a SNP within Rsa10025320 resulting in an amino acid change (A188E) was characterized through sequence variation observed in both BSA-seq and RNA-seq data and further developed as a derived cleaved amplified polymorphic sequence (dCAPS) marker. Our study reveals potential target genes for tolerance to hollowness and paves the way for marker-assisted breeding of hollowness tolerance in red-skinned radishes. [ABSTRACT FROM AUTHOR]

Purpose: Over 550 loci have been associated with human pulmonary function in genome-wide association studies (GWAS); however, the causal role of most remains uncertain. Single nucleotide polymorphisms in a disintegrin and metalloprotease domain 19 (ADAM19) are consistently related to pulmonary function in GWAS. Thus, we used a mouse model to investigate the causal link between Adam19 and pulmonary function. Methods: We created an Adam19 knockout (KO) mouse model and validated the gene targeting using RNA-Seq and RT-qPCR. Mouse body composition was assessed using dual-energy X-ray absorptiometry. Mouse lung function was measured using flexiVent. Results: Contrary to prior publications, the KO was not neonatal lethal. KO mice had lower body weight and shorter tibial length than wild-type (WT) mice. Their body composition revealed lower soft weight, fat weight, and bone mineral content. Adam19 KO had decreased baseline respiratory system elastance, minute work of breathing, tissue damping, tissue elastance, and forced expiratory flow at 50% forced vital capacity but higher FEV0.1 and FVC. Adam19 KO had attenuated tissue damping and tissue elastance in response to methacholine following LPS exposure. Adam19 KO also exhibited attenuated neutrophil extravasation into the airway after LPS administration compared to WT. RNA-Seq analysis of KO and WT lungs identified several differentially expressed genes (Cd300lg, Kpna2, and Pttg1) implicated in lung biology and pathogenesis. Gene set enrichment analysis identified negative enrichment for TNF pathways. Conclusion: Our murine findings support a causal role of ADAM19, implicated in human GWAS, in regulating pulmonary function. [ABSTRACT FROM AUTHOR]

Rahnella aquatilis causes seafoods to spoil by metabolizing sulfur-containing amino acids and/or proteins, producing H2S in products. The type II secretion system (T2SS) regulates the transport of proteases from the cytoplasm to the surrounding environment and promotes bacterial growth at low temperatures. To prevent premature fish spoilage, new solutions for inhibiting the T2SS of bacteria should be researched. In this study, global transcriptome sequencing was used to analyze the spoilage properties of R. aquatilis KM05. Two of the mapped genes/coding sequences (CDSs) were matched to the T2SS, namely, qspF and gspE, and four of the genes/CDSs, namely, ftsH, rseP, ptrA and pepN, were matched to metalloproteases or peptidases in R. aquatilis KM05. Subinhibitory concentrations of citric (18 µM) and acetic (41 µM) acids caused downregulation of T2SS-related genes (range from − 1.0 to -4.5) and genes involved in the proteolytic activities of bacteria (range from − 0.5 to -4.0). The proteolytic activities of R. aquatilis KM05 in vitro were reduced by an average of 40%. The in situ experiments showed the antimicrobial properties of citric and acetic acids against R. aquatilis KM05; the addition of an acidulant to salmon fillets limited microbial growth. Citric and acetic acids extend the shelf life of fish-based products and prevent food waste. [ABSTRACT FROM AUTHOR]

It remains to be elucidated whether Ca2+ antagonists induce pharmacological preconditioning to protect the heart against ischemia/reperfusion injury. The aim of this study was to determine whether and how pretreatment with a Ca2+ antagonist, azelnidipine, could protect cardiomyocytes against hypoxia/reoxygenation (H/R) injury in vitro. Using HL-1 cardiomyocytes, we studied effects of azelnidipine on NO synthase (NOS) expression, NO production, cell death and apoptosis during H/R. Action potential durations (APDs) were determined by the whole-cell patch-clamp technique. Azelnidipine enhanced endothelial NOS phosphorylation and NO production in HL-1 cells under normoxia, which was abolished by a heat shock protein 90 inhibitor, geldanamycin, and an antioxidant, N-acetylcysteine. Pretreatment with azelnidipine reduced cell death and shortened APDs during H/R. These effects of azelnidipine were diminished by a NOS inhibitor, L-NAME, but were influenced by neither a T-type Ca2+ channel inhibitor, NiCl2, nor a N-type Ca2+ channel inhibitor, ω-conotoxin. The azelnidipine-induced reduction in cell death was not significantly enhanced by either additional azelnidipine treatment during H/R or increasing extracellular Ca2+ concentrations. RNA sequence (RNA-seq) data indicated that azelnidipine-induced attenuation of cell death, which depended on enhanced NO production, did not involve any significant modifications of gene expression responsible for the NO/cGMP/PKG pathway. We conclude that pretreatment with azelnidipine protects HL-1 cardiomyocytes against H/R injury via NO-dependent APD shortening and L-type Ca2+ channel blockade independently of effects on gene expression. [ABSTRACT FROM AUTHOR]

Generalized pustular psoriasis (GPP) is a rare but severe form of psoriasis. However, the pathogenesis of GPP has not been fully elucidated. Although RNA-binding proteins (RBPs) and the alternative splicing (AS) process are essential for regulating post-transcriptional gene expression, their roles in GPP are still unclear. We aimed to elucidate the regulatory mechanisms to identify potential new therapeutic targets. Here, We analyzed an RNA sequencing (RNA-seq) dataset (GSE200977) of peripheral blood mononuclear cells (PBMCs) of 24 patients with GPP, psoriasis vulgaris (PV), and healthy controls (HCs) from the Gene Expression Omnibus (GEO) database. We found that the abnormal alternative splicing (AS) events associated with GPP were mainly “alt3p/alt5p”, and 15 AS genes were differentially expressed. Notably, the proportions of different immune cell types were correlated with the expression levels of regulatory alternatively spliced genes (RASGs): significant differences were observed in expression levels of DTD2, NDUFAF3, NBPF15, and FBLN7 in B cells and ARFIP1, IPO11, and RP11-326L24.9 in neutrophils in the GPP samples. Furthermore, We identified 32 differentially expressed RNA-binding proteins (RBPs) (18 up-regulated and 14 down-regulated). Co-expression networks between 14 pairs of differentially expressed RBPs and RASGs were subsequently constructed, demonstrating that these differentially expressed RBPs may affect the progression of GPP by regulating the AS of downstream immune/inflammatory-related genes such as LINC00989, ENC1 and MMP25-AS1. Our results were innovative in revealing the involvement of inflammation-related RBPs and RASGs in the development of GPP from the perspective of RBP-regulated AS. [ABSTRACT FROM AUTHOR]

Polyethylene microplastics (PE-MPs) were widespread in the marine environment; thus, their influences on marine hermaphroditic fish cannot be ignored. This study intends to evaluate the adverse biological effects of two different sources of PE, identified by Raman spectroscopy, on protandrous yellowfin seabream (Acanthopagrus latus) larvae. Growth retardation, brain lesions, head/body length ratio increase, and neuroendocrine system disorders were found, and growth and neuroendocrine regulation-related genes such as sstr2, ghrb, irs1, UGT2B15, UGT2C1, drd4a, esr2b, hsd3b7, and hsd17b2 were identified. PE microbeads (100 μm) showed more severe tissue damage on fish, while environmental PE fibers (500–2500 μm) showed more imperceptible adverse effects. There were 218 DEGs up-regulated and 147 DEGs down-regulated in the environmental PE group, while 1284 (up) and 1267 (down) DEGs were identified in the virgin PE group. PE-MP stress influenced physiological processes like growth and neuroendocrine regulation and cholesterol-steroid metabolism, and caused tissue damage in the fish larvae. The study highlights the effects of environmental PE exposure on hermaphroditic protandrous fish. [ABSTRACT FROM AUTHOR]

Maize is a valuable raw material for feed and food production. Healthy seed germination is important for improving the yield and quality of maize. Seed aging occurs relatively fast in crops and it is a process that delays germination as well as reduces its rate and even causes total loss of seed viability. However, the physiological and transcriptional mechanisms that regulate maize seeds, especially aging seed germination remain unclear. Coronatine (COR) which is a phytotoxin produced by Pseudomonas syringae and a new type of plant growth regulator can effectively regulate plant growth and development, and regulate seed germination. In this study, the physiological and transcriptomic mechanisms of COR-induced maize seed germination under different aging degrees were analyzed. The results showed that 0.001–0.01 μmol/L COR could promote the germination of aging maize seed and the growth of primary roots and shoots. COR treatment increased the content of gibberellins (GA3) and decreased the content of abscisic acid (ABA) in B73 seeds before germination. The result of RNA-seq analysis showed 497 differentially expressed genes in COR treatment compared with the control. Three genes associated with GA biosynthesis (ZmCPPS2, ZmD3, and ZmGA2ox2), and two genes associated with GA signaling transduction (ZmGID1 and ZmBHLH158) were up-regulated. Three genes negatively regulating GA signaling transduction (ZmGRAS48, ZmGRAS54, and Zm00001d033369) and two genes involved in ABA biosynthesis (ZmVP14 and ZmPCO14472) were down-regulated. The physiological test results also showed that the effects of GA and ABA on seed germination were similar to those of high and low-concentration COR, respectively, which indicated that the effect of COR on seed germination may be carried out through GA and ABA pathways. In addition, GO and KEGG analysis suggested that COR is also highly involved in antioxidant enzyme systems and secondary metabolite synthesis to regulate maize seed germination processes. These findings provide a valuable reference for further research on the mechanisms of maize seed germination. [ABSTRACT FROM AUTHOR]

Edwardsiella anguillarum and Aeromonas hydrophila are two common bacterial pathogens affecting cultivated eels, and the differences in their virulence remain unclear. In this study, after two groups of American eels (Anguilla rostrata) were administered the LD50 dose of E. anguillarum and A. hydrophila, respectively, the histopathology of the liver, trunk kidney, and spleen, as well as transcriptomic RNA sequencing (RNA-seq) analysis of the spleen, was examined at three time points: pre-infection (Con group) and post-infection at 36 h (Ea_36 group, Ah_36 group) and 60 h (Ea_60 group, Ah_60 group). The results showed that the differences in pathological changes were characterized by severe hepatocyte edema at 36 h post-infection (hpi) and hepatocyte atrophy at 60 hpi in the livers of eels infected by A. hydrophila, in contrast to the severe atrophy of glomeruli in the trunk kidneys and numerous bacterial nodules in the spleens of eels infected by E. anguillarum. The RNA-seq results revealed 906 and 77 typical differentially expressed genes (DEGs) in eels infected with E. anguillarum and A. hydrophila, respectively, compared to the control eels. The DEGs between the infected and control groups were predominantly annotated in GO terms related to binding, catalytic activity, membrane part, cell part, and cellular process, as well as in KEGG pathways associated with human diseases and organismal systems. The GO enrichment analysis showed 83 and 146 differential GO terms, along with 32 and 78 differential KEGG pathways in two comparisons of Ea_36 vs Con versus Ah_36 vs Con and Ea_60 vs Con versus Ah_60 vs Con, respectively. Furthermore, the analysis of differential alternative splicing genes (DASs) showed 1244 and 1341 DASs out of 12,907 and 12,833 AS genes, respectively, in the comparisons of Ea_36 vs Ah_36 and Ea_60 vs Ah_60. These DASs were enriched in two common KEGG pathways: "NOD-like receptor signaling pathway" and "necroptosis" which shared 11 hub DASs. Finally, analysis of protein–protein interactions revealed that 91 of 412 cross DASs between Ea_36 vs Ah_36 and Ea_60 vs Ah_60 potentially play an essential role in the difference in virulence of E. anguillarum and A. hydrophila in American eels, with 12 encoded proteins being particularly notable. Together, this study is the first to report a comparative pathogenicity and RNA-seq analysis of E. anguillarum and A. hydrophila in American eels, shedding new light on our understanding of the differences in virulence as revealed by pathological changes, DEGs, and DASs, contributing to more effective control strategies to prevent outbreaks of bacterial infections. [ABSTRACT FROM AUTHOR]

Escherichia coli (E. coli) is commonly found in dairy farms and can invade mammary gland tissue, often causing acute clinical mastitis. Mammary infections with E. coli have shown a wide range of clinical signs, causing abnormal appearance of the milk, udder inflammation and systemic signs of illness. Circular RNA is a class of endogenous non-coding RNA that plays an important role in the occurrence and development of various inflammatory diseases. However, there is little information on the circRNA associated with bovine mastitis. In this study investigated the involvement of circRNAs in bovine mastitis through the construction of an E. coli-infected bovine mastitis model by injecting of E. coli into the mammary gland of dairy cows, using healthy gland mammary tissue as a control (M_C). High-throughput RNA-seq was performed on the E. coli-infected mammary gland tissue (M_E) and differentially expressed circRNAs between theM_C and M_E groups, followed by an analysis of their potential functions using bioinformatics methods. A total of 164 differentially expressed circRNAs were identified, including 92 downregulated circRNAs and 72 upregulated circRNAs. As shown by Gene Ontology enrichment analysis these DE circRNAs were mostly enriched in ras protein signal transduction, cytoplasmic vesicle parts, and enzyme binding, and Kyoto Encyclopedia of Genes and genome singal pathway enrichment analysis indicated significant associations with phagosome signal pathway. Additionally, the expression of bovine mastitis-related circRNAs, including novel_circRNA_0000128, novel_circRNA_0011103, novel_circRNA_0012656, novel_circRNA_0015099, novel_circRNA_005648, novel_circRNA_000074, and novel_circRNA_0011796 were verified via quantitative reverse-transcription polymerase chain reaction (RT-qPCR). These results provide a new direction for further investigation of the molecular mechanisms underlying bovine mastitis. [ABSTRACT FROM AUTHOR]

Single cell RNA-seq (scRNAseq) workflows typically start with a count matrix and end with the clustering of sampled cells. While a range of methods have been developed to cluster scRNAseq datasets, no theoretical tools exist to explain why a particular cluster exists or why a hypothesized cluster is missing. Recently, several authors have shown that eigenvalues of scRNAseq count matrices can be approximated using random matrix models. In this work, we extend these previous works to the study of a scRNAseq workflow. We model scaled count matrices using random matrices with normally distributed entries. Using these random matrix models, we quantify the differential expression of a cluster and develop predictions for the workflow, and in particular clustering, as a function of the differential expression. We also use results from random matrix theory (RMT) to develop predictive formulas for portions of the scRNAseq workflow. Using simulated and real datasets, we show that our predictions are accurate if certain conditions hold on differential expression, with our RMT based predictions requiring particularly stringent condition. We find that real datasets violate these conditions, leading to bias in our predictions, but our predictions are better than a naive estimator and we point out future work that can improve the predictions. To our knowledge, our formulas represents the first predictive results for scRNAseq workflows. [ABSTRACT FROM AUTHOR]

Accurate measurement of gene expression levels is vital for advancing plant biology research. This study explores the identification and validation of stable reference genes (RGs) for gene expression analysis in Spinacia oleracea. Leveraging transcriptome data from various developmental stages, we employed rigorous statistical analyses to identify potential RGs. A total of 1196 candidate genes were initially screened based on expression variability, with subsequent refinement using criteria such as low variance and stability. Among 12 commonly used candidate RGs, EF1α and H3 emerged as the most stable across diverse experimental conditions, while GRP and PPR exhibited lower stability. These findings were further validated through qRT-PCR assays and comprehensive statistical analyses, including geNorm, NormFinder, BestKeeper, and RefFinder. Our study underscores the importance of systematic RG selection to ensure accurate normalization in gene expression studies, particularly in the context of S. oleracea developmental stages and physiological processes like flowering. These validated RGs provide a robust foundation for future gene expression analysis in S. oleracea and contribute to the advancement of molecular research in plant biology. [ABSTRACT FROM AUTHOR]

The drastic change in global climate has led to in-depth studies of the geneticresources of native cattle adapted to challenging environments. Native cattle breeds may harbor unique genetic mechanisms that have enabled them adapt to their given environmental conditions. Adipose tissues are key factors in the regulation of metabolism and energy balance and are crucial for the molecular switches needed to adapt to rapid environmental and nutritional changes. The transcriptome landscape of four adipose tissues was used in this study to investigate the differential gene expression profiles in three local breeds, Yakutian cattle (Sakha Republic), Northern Finncattle (Finland), Mirandesa cattle (Portugal) and commercial Holstein cattle. A total of 26 animals (12 cows, 14 bulls) yielded 81 samples of perirenal adipose tissue (n = 26), metacarpal adipose tissue (n = 26), tailhead adipose tissue (n = 26) and prescapular adipose tissue (n = 3). More than 17,000 genes were expressed in our dataset. Principal component analysis of the normalized expression profiles revealed a differential expression profile of the metacarpal adipose tissue. We found that the genes upregulated in the metacarpal adipose tissue of Yakutian cattle, such as NR4A3, TEKT3, and FGGY, were associated with energy metabolism and response to cold temperatures. In Mirandesa cattle, the upregulated genes in perirenal adipose tissue were related to immune response and inflammation (AVPR2, CCN1, and IL6), while in Northern Finncattle, the upregulated genes appeared to be involved in various physiological processes, including energy metabolism (IGFBP2). According to the sex-based comparisons, the most interesting result was the upregulation of the TPRG1 gene in three tissues of Yakutian cattle females, suggesting that adaptation is related to feed efficiency. The highest number of differentially expressed genes was found between Yakutian cattle and Holstein, several of which were associated with immunity in Yakutian cattle, indicating potential differences in disease resistance and immunity between the two breeds. This study highlights the vast difference in gene expression profiles in adipose tissues among breeds from different climatic environments, most likely highlighting selective pressure and the potential significance of the uniquely important regulatory functions of metacarpal adipose tissue. [ABSTRACT FROM AUTHOR]

Background: The tumor microenvironment (TME) provides a region for intricate interactions within or between immune and non-immune cells. We aimed to reveal the tissue architecture and comprehensive landscape of cells within the TME of colorectal cancer (CRC). Methods: Fresh frozen invasive adenocarcinoma of the large intestine tissue from 10× Genomics Datasets was obtained from BioIVT Asterand. The integration of microarray-based spatial transcriptomics (ST) and RNA sequencing (RNA-seq) was applied to characterize gene expression and cell landscape within the TME of CRC tissue architecture. Multiple R packages and deconvolution algorithms including MCPcounter, XCELL, EPIC, and ESTIMATE methods were performed for further immune distribution analysis. Results: The subpopulations of immune and non-immune cells within the TME of the CRC tissue architecture were appropriately annotated. According to ST and RNA-seq analyses, a heterogeneous spatial atlas of gene distribution and cell landscape was comprehensively characterized. We distinguished between the cancer and stromal regions of CRC tissues. As expected, epithelial cells were located in the cancerous region, whereas fibroblasts were mainly located in the stroma. In addition, the fibroblasts were further subdivided into two subgroups (F1 and F2) according to the differentially expressed genes (DEGs), which were mainly enriched in pathways including hallmark-oxidative-phosphorylation, hallmark-e2f-targets and hallmark-unfolded-protein-response. Furthermore, the top 5 DEGs, SPP1, CXCL10, APOE, APOC1, and LYZ, were found to be closely related to immunoregulation of the TME, methylation, and survival of CRC patients. Conclusions: This study characterized the heterogeneous spatial landscape of various cell subtypes within the TME of the tissue architecture. The TME-related roles of fibroblast subsets addressed the potential crosstalk among diverse cells. [ABSTRACT FROM AUTHOR]

Gravity has profoundly influenced life on Earth, yet how organisms adapt to changes in gravity remains largely unknown. This study examines vestibular plasticity, specifically how the vestibular system responds to altered gravity. We subjected male C57BL/6J mice to hypergravity (2 G) followed by normal gravity (1 G) to analyze changes in vestibular function and gene expression. Mice showed significant vestibular dysfunction, assessed by righting reflex tests, which persisted for days but reversed at 1 G after exposure to 2 G. Gene expression analysis in the vestibular ganglion identified significant changes in 212 genes out of 49,585 due to gravitational changes. Specifically, 25 genes were upregulated under 2 G and recovered at 1 G after 2 G exposure, while one gene showed the opposite trend. Key neural function genes like Shisa3, Slc25a37, Ntn4, and Snca were involved. Our results reveal that hypergravity-induced vestibular dysfunction is reversible and highlight genes critical for adaptation. [ABSTRACT FROM AUTHOR]

The gut microbiome of worms from composting facilities potentially harbors organisms that are beneficial to plant growth and development. In this experiment, we sought to examine the potential impacts of rhizosphere microbiomes derived from Eisenia fetida worm castings (i.e. vermicompost) on tomato (Solanum lycopersicum, L.) plant growth and physiology. Our experiment consisted of a greenhouse trial lasting 17 weeks total in which tomato plants were grown with one of three inoculant treatments: a microbial inoculant created from vermicompost (V), a microbial inoculant created from sterilized vermicompost (SV), and a no-compost control inoculant (C). We hypothesized that living microbiomes from the vermicompost inoculant treatment would enhance host plant growth and gene expression profiles compared to plants grown in sterile and control treatments. Our data showed that bacterial community composition was significantly altered in tomato rhizospheres, but fungal community composition was highly variable in each treatment. Plant phenotypes that were significantly enhanced in the vermicompost and sterile vermicompost treatments, compared to the control, included aboveground biomass and foliar δ15N nitrogen. RNA sequencing revealed distinct gene expression changes in the vermicompost treatment, including upregulation of nutrient transporter genes such as Solyc06g074995 (high affinity nitrate transporter), which exhibited a 250.2-fold increase in expression in the vermicompost treatment compared to both the sterile vermicompost and control treatments. The plant transcriptome data suggest that rhizosphere microbiomes derived from vermicompost can influence tomato gene expression and growth-related regulatory pathways, which highlights the value of RNA sequencing in uncovering molecular responses in plant microbiome studies. [ABSTRACT FROM AUTHOR]

Oligodendroglioma, IDH-mutant and 1p/19q-codeleted has highly variable outcomes that are strongly influenced by patient age. The distribution of oligodendroglioma age is non-Gaussian and reportedly bimodal, which motivated our investigation of age-associated molecular alterations that may drive poorer outcomes. We found that elevated HOXD12 expression was associated with both older patient age and shorter survival in the TCGA (FDR < 0.01, FDR = 1e−5) and the CGGA (p = 0.03, p < 1e−3). HOXD12 gene body hypermethylation was associated with older age, higher WHO grade, and shorter survival in the TCGA (p < 1e−6, p < 0.001, p < 1e−3) and with older age and higher WHO grade in Capper et al. (p < 0.002, p = 0.014). In the TCGA, HOXD12 gene body hypermethylation and elevated expression were independently prognostic of NOTCH1 and PIK3CA mutations, loss of 15q, MYC activation, and standard histopathological features. Single-nucleus RNA and ATAC sequencing data showed that HOXD12 activity was elevated in neoplastic tissue, particularly within cycling and OPC-like cells, and was associated with a stem-like phenotype. A pan-HOX DNA methylation analysis revealed an age and survival-associated HOX-high signature that was tightly associated with HOXD12 gene body methylation. Overall, HOXD12 expression and gene body hypermethylation were associated with an older, atypically aggressive subtype of oligodendroglioma. [ABSTRACT FROM AUTHOR]

Synthetic peptides have a wide range of clinical effects. Of particular interest are peptides based on adrenocorticotropic hormone (ACTH) both as already used and as potential drugs for preventing consequences of cerebral ischemia. However, it is necessary to study influence of the peptide on the brain cells under normal physiological conditions, including understanding the risks of their use. Here, we used high-throughput RNA sequencing (RNA-Seq) to identify differentially expressed genes (DEGs) in the brain frontal cortex of rat receiving intraperitoneal administration of ACTH-like peptides ACTH(4-7)PGP (Semax) and ACTH(6-9)PGP, or saline. We identified 258 and 228 DEGs, respectively, with the fold change > 1.5 and Padj < 0.05 at 22.5 h after the first administration of Semax and ACTH(6-9)PGP. Metabolic pathways, characterizing both common and specific effects of the peptides on the transcriptome were identified. Both peptides predominantly caused decrease in expression of the genes associated with the immune system. At the same time, when comparing the effects of ACTH(6-9)PGP relative to Semax, DEGs were identified that characterized the main differences in the effects of the peptides. These genes were mostly downregulated and associated with neurosignaling systems and regulation of ion channels, thus characterizing differences in the effects of the peptides. Our data show how differences in the structure of ACTH derivatives are associated with the changes in the brain cell transcriptome following exposure to these related peptides. Furthermore, our results demonstrate that when studying influence of regulatory peptides on transcriptome under pathological conditions, it is necessary to take into account their actions under normal physiological conditions. [ABSTRACT FROM AUTHOR]

Aflatoxin B1 (AFB1) is a pro-carcinogenic compound bioactivated in the liver by cytochromes P450 (CYPs). In mammals, CYP1A and CYP3A are responsible for AFB1 metabolism, with the formation of the genotoxic carcinogens AFB1-8,9-epoxide and AFM1, and the detoxified metabolite AFQ1. Due to climate change, AFB1 cereals contamination arose in Europe. Thus, cattle, as other farm animals fed with grains (pig, sheep and broiler), are more likely exposed to AFB1 via feed with consequent release of AFM1 in milk, posing a great concern to human health. However, knowledge about bovine CYPs involved in AFB1 metabolism is still scanty. Therefore, CYP1A1- and CYP3A74-mediated molecular mechanisms of AFB1 hepatotoxicity were here dissected. Molecular docking of AFB1 into CYP1A1 model suggested AFB1 8,9-endo- and 8,9-exo-epoxide, and AFM1 formation, while docking of AFB1 into CYP3A74 pointed to AFB1 8,9-exo-epoxide and AFQ1 synthesis. To biologically confirm these predictions, CYP1A1 and CYP3A74 knockout (KO) BFH12 cell lines were exposed to AFB1. LC–MS/MS investigations showed the abolished production of AFM1 in CYP1A1 KO cells and the strong increase of parent AFB1 in CYP3A74 KO cells; the latter result, coupled to a decreased cytotoxicity, suggested the major role of CYP3A74 in AFB1 8,9-exo-epoxide formation. Finally, RNA-sequencing analysis indirectly proved lower AFB1-induced cytotoxic effects in engineered cells versus naïve ones. Overall, this study broadens the knowledge on AFB1 metabolism and hepatotoxicity in cattle, and it provides the weight of evidence that CYP1A1 and CYP3A74 inhibition might be exploited to reduce AFM1 and AFBO synthesis, AFB1 toxicity, and AFM1 milk excretion. [ABSTRACT FROM AUTHOR]

Per- and polyfluoroalkyl substances (PFAS) such as perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS) and perfluoro-2-methyl-3-oxahexanoic acid (GenX), the new replacement PFAS, are major environmental contaminants. In rodents, these PFAS induce several adverse effects on the liver, including increased proliferation, hepatomegaly, steatosis, hypercholesterolemia, nonalcoholic fatty liver disease and liver cancers. Activation of peroxisome proliferator receptor alpha by PFAS is considered the primary mechanism of action in rodent hepatocyte-induced proliferation. However, the human relevance of this mechanism is uncertain. We investigated human-relevant mechanisms of PFAS-induced adverse hepatic effects using FRG liver-chimeric humanized mice with livers repopulated with functional human hepatocytes. Male FRG humanized mice were treated with 0.067 mg/L of PFOA, 0.145 mg/L of PFOS, or 1 mg/L of GenX in drinking water for 28 days. PFOS caused a significant decrease in total serum cholesterol and LDL/VLDL, whereas GenX caused a significant elevation in LDL/VLDL with no change in total cholesterol and HDL. All three PFAS induced significant hepatocyte proliferation. RNA-sequencing with alignment to the human genome showed a total of 240, 162, and 619 differentially expressed genes after PFOA, PFOS, and GenX exposure, respectively. Upstream regulator analysis revealed that all three PFAS induced activation of p53 and inhibition of androgen receptor and NR1D1, a transcriptional repressor important in circadian rhythm. Further biochemical studies confirmed NR1D1 inhibition and in silico modeling indicated potential interaction of all three PFAS with the DNA-binding domain of NR1D1. In conclusion, our studies using FRG humanized mice have revealed new human-relevant molecular mechanisms of PFAS including their previously unknown effect on circadian rhythm. [ABSTRACT FROM AUTHOR]

Age-related macular degeneration (AMD) is one of the most common causes of irreversible vision loss in the elderly. Its pathogenesis is likely multifactorial, involving a complex interaction of metabolic and environmental factors, and remains poorly understood. Previous studies have shown that mitochondrial dysfunction and oxidative stress play a crucial role in the development of AMD. Oxidative damage to the retinal pigment epithelium (RPE) has been identified as one of the major mediators in the pathogenesis of age-related macular degeneration (AMD). Therefore, this article combines transcriptome sequencing (RNA-seq) and single-cell sequencing (scRNA-seq) data to explore the role of mitochondria-related genes (MRGs) in AMD. Firstly, differential expression analysis was performed on the raw RNA-seq data. The intersection of differentially expressed genes (DEGs) and MRGs was performed. This paper proposes a deep subspace nonnegative matrix factorization (DS-NMF) algorithm to perform a multi-layer nonlinear transformation on the intersection of gene expression profiles corresponding to AMD samples. The age of AMD patients is used as prior information at the network’s top level to change the data distribution. The classification is based on reconstructed data with altered distribution. The types obtained significantly differ in scores of multiple immune-related pathways and immune cell infiltration abundance. Secondly, an optimal AMD diagnosis model was constructed using multiple machine learning algorithms for external and qRT-PCR verification. Finally, ten potential therapeutic drugs for AMD were identified based on cMAP analysis. The AMD subtypes identified in this article and the diagnostic model constructed can provide a reference for treating AMD and discovering new drug targets. [ABSTRACT FROM AUTHOR]

Background: Schizophrenia is a mental disorder that causes considerable morbidity, whose risk largely results from genetic factors. Setd1a is a gene implicated in schizophrenia. Objective: To study the gene expression changes found in heterozygous Setd1a± knockout mice in order to gain useful insight into schizophrenia pathogenesis. Methods: We mined a single-cell RNA sequencing (scRNAseq) dataset from the prefrontal cortex (PFC) and striatum of Setd1a± mice and identified cell type-specific differentially expressed genes (DEGs) and differential transcript usage (DTU). DEGs and genes containing DTU found in each cell type were used to identify affected biological pathways using Ingenuity Pathway Analysis (IPA). Results: We identified 273 unique DEGs across all cell types in PFC and 675 unique gene peaks containing DTU. In striatum, we identified 327 unique DEGs across all cell types and 8 unique gene peaks containing DTU. Key IPA findings from the analysis of DEGs found in PFC and striatum implicate processes involved in protein synthesis, mitochondrial function, cell metabolism, and inflammation. IPA analysis of genes containing DTU in PFC points to protein synthesis, as well as cellular activities involving intracellular signaling and neurotransmission. One canonical pathway, 'EIF2 Signaling', which is involved in the regulation of protein synthesis, was detected in PFC DEGs, striatum DEGs, and PFC genes containing DTU, drawing attention to its importance in schizophrenia pathophysiology. Conclusion: Processes involving protein synthesis in general and the 'EIF2 Signaling' pathway in particular could be targets for the development of new research strategies and biomarkers in schizophrenia. [ABSTRACT FROM AUTHOR]

Salmonella Typhimurium (ST) infection in pigs poses a significant threat to animal health and food safety; the intricate mechanisms underlying host–immune responses and pathogen persistence remain poorly understood. To address this knowledge gap, we comprehensively analyzed the peripheral blood transcriptome in piglets infected with ST. We performed histopathological evaluation, blood parameter analysis, advanced RNA-sequencing techniques, and quantitative reverse transcription PCR (RT-qPCR)-based validation. The increasement in the monocyte counts at 2 days post-infection suggested its potential to serve as a hematological marker for ST infection in piglets. Functional and pathway enrichment analyses of the differentially expressed genes highlighted the pivotal roles of innate and adaptive immune responses, notably in pathways associated with Toll-like receptors, NIK/NF-κB signaling, cytokine signaling, and T cell proliferation. RT-qPCR-based validation using peripheral blood mononuclear cells provided additional insights into the immune system dynamics in response to ST infection, revealing the marked elevation of the interleukin (IL)-15, IL-27, and CXCL10 levels being significantly elevated in ST-infected piglets. Our comprehensive analysis underscores the multifaceted impact of ST infection on piglets and offers valuable insights into the host–pathogen interactions and the role of host immune system during ST infection. [ABSTRACT FROM AUTHOR]

Maize is highly sensitive to waterlogging stress, and seeds fail to germinate under hypoxic conditions induced by submergence, leading to severe yield losses. We conducted a comparative transcriptome analysis during the initial stages of seed germination, exploring aerobic and hypoxic conditions in two inbred lines, B73 and Okcheon Chal-1. Notably, significant differences emerged between aerobic and hypoxic conditions on the first day of germination, particularly in genes associated with fermentation and phytohormone regulation. However, consistent transcriptomic changes were observed in primary metabolic pathways such as glycolysis, the TCA cycle, and the pentose phosphate pathway. These differences strongly correlate with each other, illustrating the efficacy of the hypoxic response for survival in water. Furthermore, this suggests that germinating seeds serve as a promising model for studying plant hypoxia responses with controlled environmental conditions. Insights from this study contribute to understanding the fundamental mechanisms of hypoxia response and hold promise for developing strategies to cultivate waterlogging-tolerant maize cultivars. [ABSTRACT FROM AUTHOR]

The Murray cod (Maccullochella peelii), an economically and recologically valuable fish species, is extensively cultured in the aquaculture industry. However, the severe skeletal deformities that occur during the rearing process pose a significant challenge, profoundly impacting growth performance and economic sustainability. Despite recognition of these deformities, comprehensive studies investigating the underlying mechanisms of skeletal deformities in Murray cod remain scarce. To solve this problem, our study combines histological and molecular studies to understand the characteristics and mechanisms of these deformities. The results are as follows: (i) At the histological level, we observed notable abnormalities in the brain and muscle tissues of deformed Murray cod, including an enlarged ventricle and irregular muscle fiber structure. These observed abnormalities could potentially impact the skeletal development of Murray cod. (ii) At the molecular level, we performed a comprehensive transcriptome analysis of the brain and muscle tissues of normal and deformed Murray cod. Our analysis identified 8834 differentially expressed genes (DEGs), of which 3788 up-regulated genes and 4555 down-regulated genes. Enrichment analysis of GO and KEGG pathways showed that Cell Adhesion, Notch Signaling, Wnt Signaling, Cell Adhesion Molecules, The ECM-Receptor Interaction Pathway, and PI3K-Akt Signaling pathways may be involved in vertebral deformities. Notably, in deformed Murray cod, we observed significant changes in the expression of certain genes closely associated with skeletal development. For example, down-regulated expression of Fibronectin 1 (FN1) and Bone Morphogenetic Protein 2 (BMP2) was found in brain tissue. These genes may play a crucial role in the process of skeletal formation and development. At the same time, we verified through qRT-PCR to ensure the reliability of our data. In conclusion, our study provides a comprehensive understanding of Murray cod's skeletal deformities through histological and transcriptomic analyses and reveals the molecular mechanism of Murray cod's skeletal development. And provide insights to address these economically important anomalies. [ABSTRACT FROM AUTHOR]

Transcription factors (TFs) play a crucial role in gene expression, and studying them can lay the foundation for future research on the functional characterization of TFs involved in various biological processes. In this study, we conducted a genome-wide identification and analysis of TFs in the thermotolerant basidiomycete fungus, Coriolopsis trogii. The TF repertoire of C. trogii consisted of 350 TFs, with C2H2 and Zn2C6 being the largest TF families. When the mycelia of C. trogii were cultured on PDA and transferred from 25 to 35 °C, 14 TFs were up-regulated and 14 TFs were down-regulated. By analyzing RNA-seq data from mycelia cultured at different temperatures and under different carbon sources, we identified 22 TFs that were differentially expressed in more than three comparisons. Co-expression analysis revealed that seven differentially expressed TFs, including four Zn2C6s, one Hap4_Hap_bind, one HMG_box, and one Zinc_knuckle, showed significant correlation with 729 targeted genes. Overall, this study provides a comprehensive characterization of the TF family and systematically screens TFs involved in the high-temperature adaptation of C. trogii, laying the groundwork for further research into the specific roles of TFs in the heat tolerance mechanisms of filamentous fungi. [ABSTRACT FROM AUTHOR]