Comparison Of Transcriptomes Research Articles

Molecular fingerprints of cell size sensing and mating type differentiation in pennate diatoms.

A unique cell size-sensing mechanism is at the heart of the life cycle of diatoms. During population growth, cell size decreases until a sexual size threshold (SST) is reached, below which cells become sexually competent. In most pennate diatoms, the two mating types undergo biochemical and behavioral differentiation below the SST, although the molecular pathways underlying their size-dependent maturation remain unknown. Here, we developed a method to shorten the generation time of Cylindrotheca closterium through single-cell microsurgery, enabling the transcriptomic comparison of genetically identical large and undifferentiated cells with small, sexually competent cells for six different genotypes. We identified 21 genes upregulated in small cells regardless of their mating type, revealing how cells undergo specific transcriptional reprogramming when passing the SST. Furthermore, we revealed a size-regulated gene cluster with three mating type-specific genes susceptible to sex-inducing pheromones. In addition, comparative transcriptomics confirmed the shared mating type specificity of Mating-type Related Minus 2 homologs in three pennate diatoms, suggesting them to be part of a conserved partner recognition mechanism. This study sheds light on how diatoms acquire sexual competence in a strictly size-dependent manner, revealing a complex machinery underlying size-dependent maturation, mating behavior, and heterothally in pennate diatoms.

Bmlark is essential for embryonic development

BackgroundTranscription factor lark has been demonstrated to play multiple functions in Drosophila, but the function of this gene in embryonic development remains to be elucidated.ResultsIn this study, the CRISPR/Cas9 gene-editing method was used to construct a Bmlark mutant strain of Bombyx mori to investigate the roles of this gene. The results showed that the homozygous mutant Bmlark−/− was lethal. The Bmlark−/− embryos showed obvious developmental defects, such as defective sclerotization and melanization of the exoskeleton. A transcriptomic comparison of Bmlark−/− and wild-type embryos showed that the differentially expressed genes were mainly enriched in the structure and metabolic processes of chitin and cuticles. While the expression levels of chitin metabolism-related enzyme genes did not significantly change, in the mutant embryos compared to the wild-type embryos, the expression levels of 63 putative cuticle protein genes showed significant differences. Among which, 35 genes were downregulated and 28 genes were upregulated. The expression levels of the transcription factor BmPOUM2 and eight wing disc cuticle protein genes (WCP) also changed. BmPOUM2, WCP5, WCP9, WCP10, WCP11 were downregulated and WCP1, WCP2, WCP3, WCP6 were upregulated in Bmlark−/− embryos. While the expression level of TH in the tyrosine-mediated pigmentation pathway was upregulated in the mutant embryos, the expression levels of the four key pigment synthesis genes DDC, aaNAT, Laccase2A, and yellow-f2 were significantly downregulated.ConclusionsThe expression levels of 63 putative cuticle protein genes, eight WCP genes, and five pigment synthesis genes significantly changed in Bmlark mutant B. mori compared to those of the wildtype. These results suggest that Bmlark is essential for normal development of cuticle and tyrosine-mediated melanization in silkworm embryos.

Transcriptome Comparison between Resistant and Susceptible Soybean Cultivars in Response to Inoculation of Phytophthora sojae.

Phytophthora root and stem rot, caused by Phytophthora sojae, considerably reduces soybean yield worldwide. Our previous study identified two genomic regions on chromosome 18 (2.1-2.6 and 53.1-53.3 Mbp) that confer resistance to the P. sojae isolate 2457, through linkage analysis using progenies derived from the Daepung × Socheong2 population. These two regions contained 51 and 19 annotated genes, respectively. However, the specific gene responsible for resistance to P. sojae isolate 2457 has yet to be identified. In this study, we performed a comparative transcriptomic analysis of Socheong2 and Daepung, two Korean soybean varieties identified as resistant and susceptible to P. sojae isolate 2457, respectively. RNA sequencing was conducted on tissue samples collected at 0, 6, and 12 hours after inoculation (HAI), and significant differences in the expression of defense-related genes were observed across time points and between the two cultivars. Genes associated with the jasmonic acid, salicylic acid, ethylene, and systemic acquired resistance pathways were upregulated in both cultivars at 6 and 12 HAI compared to 0 HAI, with these biological processes were more strongly upregulated in Socheong2 compared to Daepung at 6 and 12 HAI. A comparison of differentially expressed genes (DEGs) and candidate genes within the previously identified QTL regions revealed an ortholog of the HS1 PRO-1 2 gene from Arabidopsis thaliana among the upregulated DEGs in Socheong2, particularly at 12 HAI compared to 0 HAI. This study will aid in targeted breeding efforts to develop soybean varieties with improved resistance to P. sojae.

Comparative transcriptomic insight into orchestrating mode of dielectric barrier discharge cold plasma and lactate in synergistic inactivation and biofilm-suppression of Pichia manshurica

Pichia manshurica is a representative species of biofilm-forming yeasts which usually induces the spoilage of fermented food. This study aims to investigate the synergistic inactivating and anti-biofilm effect of dielectric barrier discharge cold plasma (DBD) and lactate on Pichia manshurica (P. manshurica) and the underlying mechanism by comparison of survival rate, growth curve, biofilm-forming capacity and transcriptome of P. manshurica treated with control (CK), lactate (LA), DBD, and combination of DBD and lactate (DBD-LA). Results showed that CK and LA hardly influenced the growth and biofilm formation of P. manshurica. DBD and DBD-LA reduced survival rate to 35% and 10% immediately after treatment, respectively. Also, with growth curve remaining plateau, DBD-LA completely inhibited the growth and biofilm formation of P. manshurica, while DBD moderately reduced the growth density and biofilm. Comparative transcriptomic analysis revealed that single DBD treatment intervened in the functions and pathways associated with DNA replication and cell adhesion (down-regulated expression of flocculation protein-related genes and up-regulated expression of β-1,4-D-glucan cellobiohydrolase-related genes). Lactate reinforced the inactivating and anti-biofilm effect of DBD by stimulating redox reaction and suppressing functions and pathways involving synthesis and metabolism of lipid and membrane, cation binding and organelle assembly. This study demonstrated the potential of synergistic combination of DBD and lactate in efficient control of biofilm-related spoilage of food by yeast.

Identification of Key Genes Correlated with Economic Trait Superiorities and Their SNP Screening Through Transcriptome Comparisons, WGCNA and Pearson Correlation Coefficient in the Sea Cucumber Apostichopus Japonicus.

Variation in morphology-driven economic traits is a common issue hindering the development of the sea cucumber aquaculture industry. In this study, transcriptome comparisons, weighted gene correlation network analysis (WGCNA) and Pearson correlation coefficient (PCC) were first employed to identify key genes correlated with morphological variation in the sea cucumber Apostichopus japonicus, after which the relationship between identified key genes (relative expression and genotype) and economic trait phenotypes was investigated to screen potential biomarker targets for molecular-assisted breeding. The results showed that three genes (putative ficolin-2, fibrinogen c domain-containing protein 1, and angiopoietin-4) were closely associated with economic trait superiorities. Two single nucleotide polymorphisms (SNPs) were identified in the putative ficolin-2 gene as having a strong correlation with body weight and papilla number. The findings from this study will enrich breeding biomarker resources and benefit the development of molecular-assisted breeding techniques in sea cucumber aquaculture.

A transcriptomic comparison of in vitro models of the human placenta

IntroductionSelecting an in vitro culture model of the human placenta is challenging due to representation of different trophoblast cell types with distinct biological roles and limited comparative studies that define key characteristics of these models. The aim of this research was to compare the transcriptomes of common in vitro models of the human placenta compared to bulk human placental tissue. MethodsWe performed differential gene expression analysis on publicly available transcriptomic data from 7 in vitro models of the human placenta (HTR-8/SVneo, BeWo, JEG-3, JAR, Primary Trophoblasts, Villous Explants, and Trophoblast Stem Cells) and compared to bulk placental tissue from 2 cohort studies (CANDLE and GAPPS) or individual trophoblast cell types derived from bulk placental tissue. ResultsAll in vitro placental models had a substantial number of differentially expressed genes (DEGs, FDR<0.01) compared to the CANDLE and GAPPS placentas (Average DEGs = 10,624), and the individual trophoblast cell types (Average DEGs = 5413), indicating that there are vast differences in gene expression. Hierarchical clustering identified 54 gene clusters with distinct expression profiles across placental models, with 23 clusters enriched for specific KEGG pathways. Placental cell lines were classified by fetal sex based on expression of Y-chromosome genes that identified HTR-8/SVneo cells as female origin, while JEG-3, JAR, and BeWo cells are of male origin. DiscussionNone of the models were a close approximation of the human bulk placental transcriptome, highlighting the challenges with model selection. To enable appropriate model selection, we adapted our data into a web application: “Comparative Transcriptomic Placental Model Atlas (CTPMA)”.

Early autonomous patterning of the anteroposterior axis in gastruloids.

Minimal in vitro systems composed of embryonic stem cells (ESCs) have been shown to recapitulate the establishment of the anteroposterior (AP) axis. In contrast to the native embryo, ESC aggregates - such as gastruloids - can break symmetry, which is demarcated by polarization of the mesodermal marker T, autonomously without any localized external cues. However, associated earliest patterning events, such as the spatial restriction of cell fates and concomitant transcriptional changes, remain poorly understood. Here, we dissect the dynamics of AP axis establishment in mouse gastruloids, particularly before external Wnt stimulation. Through single-cell RNA sequencing, we identify key cell state transitions and the molecular signatures of T+ and T- populations underpinning AP polarization. We also show that this process is robust to modifications of aggregate size. Finally, transcriptomic comparison with the mouse embryo indicates that gastruloids develop similar mesendodermal cell types, despite initial differences in their primed pluripotent populations, which adopt a more mesenchymal state in lieu of an epiblast-like transcriptome. Hence, our findings suggest the possibility of alternate ESC states in vivo and in vitro that can converge onto similar cell fates.

Genomic and Transcriptomic Comparison Between Invasive Non-Typhoidal Salmonella and Non-Invasive Isolates.

Invasive non-typhoidal Salmonella (iNTS) poses a significant threat to global public health. Salmonella enterica Enteritidis and Typhimurium are the primary serovars responsible for both invasive diseases and gastroenteritis. This study aims to investigate the genomic and transcriptomic differences between isolates associated with these contrasting clinical presentations. We retrieved genomes of Salmonella Enteritidis and Salmonella Typhimurium from Enterobase, utilizing blood and stool isolates as representatives for iNTS and non-iNTS, respectively. An indistinguishable phylogenetic relationship was revealed between the blood and stool isolates for both serovars. Few genes were specifically identified in iNTS. Random forest and principal coordinates analysis permitted moderate discrimination between the two sources of isolates based on overall genome content. Notably, the blood isolates of Salmonella Typhimurium displayed an elevated level of antimicrobial resistance and genome degradation compared to stool isolates. Meanwhile, transcriptome sequencing identified few genes that were differentially expressed between blood and stool isolates. Hierarchical clustering and principal component analysis did not effectively differentiate the expression profile of iNTS from non-iNTS. In summary, few genes could serve as reliable biomarkers to distinguish iNTS and non-iNTS at either the genomic or transcriptomic level. Nevertheless, iNTS has indeed accumulated subtle genomic differences from non-iNTS, which might contribute to invasiveness.

The SA-WRKY70-PR-Callose Axis Mediates Plant Defense Against Whitefly Eggs.

The molecular mechanisms of plant responses to phytophagous insect eggs are poorly understood, despite their importance in insect-plant interactions. This study investigates the plant defense mechanisms triggered by the eggs of whitefly Bemisia tabaci, a globally significant agricultural pest. A transcriptome comparison of tobacco plants with and without eggs revealed that whitefly eggs may activate the response of defense-related genes, including those involved in the salicylic acid (SA) signaling pathway. SA levels are induced by eggs, resulting in a reduction in egg hatching, which suggests that SA plays a key role in plant resistance to whitefly eggs. Employing Agrobacterium-mediated transient expression, virus-induced gene silencing assays, DNA-protein interaction studies, and bioassays, we elucidate the regulatory mechanisms involved. Pathogenesis-related proteins NtPR1-L1 and NtPR5-L2, downstream of the SA pathway, also affect whitefly egg hatching. The SA-regulated transcription factor NtWRKY70a directly binds to the NtPR1-L1 promoter, enhancing its expression. Moreover, NtPR1-L1 promotes callose deposition, which may impede the eggs' access to water and nutrients. This study establishes the SA-WRKY70-PR-callose axis as a key mechanism linking plant responses and defenses against whitefly eggs, providing new insights into the molecular interactions between plants and insect eggs.

Single-cell transcriptomic and cross-species comparison analyses reveal distinct molecular changes of porcine testes during puberty

The pig is an important model for studying human diseases and is also a significant livestock species, yet its testicular development remains underexplored. Here, we employ single-cell RNA sequencing to characterize the transcriptomic landscapes across multiple developmental stages of Bama pig testes from fetal stage through infancy, puberty to adulthood, and made comparisons with those of humans and mice. We reveal an exceptionally early onset of porcine meiosis shortly after birth, and identify a distinct subtype of porcine spermatogonia resembling transcriptome state 0 spermatogonial stem cells identified in humans, which were previously thought to be primate specific. We also discover the persistent presence of proliferating progenitors for myoid cells in postnatal testes. The regulatory roles of Leydig cell steroidogenesis and estrogen synthesis in supporting cell lineages are also explored, including the potential impact of estrogen on Sertoli cell maturation and spermatogenesis. Overall, this study offers valuable insights into porcine testicular development, paving the way for future research in reproductive biology, advancements in agricultural breeding, and potential applications in translational medicine.

Characterization of A Bronchoscopically Induced Transgenic Lung Cancer Pig Model for Human Translatability.

There remains a need for animal models with human translatability in lung cancer (LC) research. Findings in pigs have high impact on humans due to similar anatomy and physiology. We present the characterization of a bronchoscopically-induced LC model in Oncopigs carrying inducible KRAS G12D and TP53 R167H mutations. Twelve Oncopigs underwent 29 injections via flexible bronchoscopy. Eighteen Adenovirus-Cre recombinase gene (AdCre) inductions were performed endobronchially (n=6) and transbronchially with a needle (n=12). Eleven control injections were performed without AdCre. Oncopigs underwent serial contrast-enhanced chest CT with clinical follow-up for 29 weeks. Following autopsy, lung and organ tissues underwent histopathology, immunohistochemistry, and RNA-sequencing with comparative analysis with The Cancer Genome Atlas (TCGA) human LC data. All 18 sites of AdCre injections had lung consolidations on CT imaging. Transbronchial injections led to histopathologic invasive cancer and/or carcinoma in situ (CIS) in 11/12 (91.7%), and invasive cancer (excluding CIS) in 8/12 (66.6%). Endobronchial inductions led to invasive cancer in 3/6 (50%). A soft tissue metastasis was observed in one Oncopig. Immunohistochemistry confirmed expression of Pan-CK+/epithelial cancer cells, with macrophages and T cells infiltration in the tumor microenvironment. Transcriptome comparison showed 54.3% overlap with human LC (TCGA), in contrast to 29.88% overlap of KRAS-mutant mouse LC with human LC. The transgenic and immunocompetent Oncopig model has a high rate of LC following bronchoscopic transbronchial induction. Overlap of the Oncopig LC transcriptome with human LC transcriptome was noted. This pig model is expected to have high clinical translatability to the human LC patient.

High level of aneuploidy and recurrent loss of chromosome 11 as relevant features of somatotroph pituitary tumors

BackgroundSomatotroph neuroendocrine pituitary tumors (sPitNET) are a subtype of pituitary tumors that commonly cause acromegaly. Our study aimed to determine the spectrum of DNA copy number abnormalities (CNAs) in sPitNETs and their relevance.MethodsA landscape of CNAs in sPitNETs was determined using combined whole-genome approaches involving low-pass whole genome sequencing and SNP microarrays. Fluorescent in situ hybridization (FISH) was used for microscopic validation of CNAs. The tumors were also subjected to transcriptome and DNA methylation analyses with RNAseq and microarrays, respectively.ResultsWe observed a wide spectrum of cytogenetic changes ranging from multiple deletions, recurrent chromosome 11 loss, stable genomes, to duplication of the majority of the chromosomes. The identified CNAs were confirmed with FISH. sPitNETs with multiple duplications were characterized by intratumoral heterogeneity in chromosome number variation in individual tumor cells, as determined with FISH. These tumors were separate CNA-related sPitNET subtype in clustering analyses with CNA signature specific for whole genome doubling-related etiology. This subtype encompassed GNAS-wild type, mostly densely granulated tumors with favorable expression level of known prognosis-related genes, notably enriched with POUF1/NR5A1-double positive PitNETs. Chromosomal deletions in sPitNETs are functionally relevant. They occurred in gene-dense DNA regions and were related to genes downregulation and increased DNA methylation in the CpG island and promoter regions in the affected regions. Recurrent loss of chromosome 11 was reflected by lowered MEN1 and AIP. No such unequivocal relevance was found for chromosomal gains. Comparisons of transcriptomes of selected most cytogenetically stable sPitNETs with tumors with recurrent loss of chromosome 11 showed upregulation of processes related to gene dosage compensation mechanism in tumors with deletion. Comparison of stable tumors with those with multiple duplications showed upregulation of processes related to mitotic spindle, DNA repair, and chromatin organization. Both comparisons showed upregulation of the processes related to immune infiltration in cytogenetically stable tumors and deconvolution of DNA methylation data indicated a higher content of specified immune cells and lower tumor purity in these tumors.ConclusionssPitNETs fall into three relevant cytogenetic groups: highly aneuploid tumors characterized by known prognostically favorable features and low aneuploidy tumors including specific subtype with chromosome 11 loss.

Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection

Low-abundance members of microbial communities are difficult to study in their native habitats, including Escherichia coli, a minor but common inhabitant of the gastrointestinal tract, and key opportunistic pathogen of the urinary tract. While multi-omic analyses have detailed interactions between uropathogenic Escherichia coli (UPEC) and the bladder mediating urinary tract infection (UTI), little is known about UPEC in its pre-infection reservoir, the gastrointestinal tract, partly due to its low relative abundance (<1%). To sensitively explore the genomes and transcriptomes of diverse gut E. coli, we develop E. coli PanSelect, which uses probes designed to specifically capture E. coli’s broad pangenome. We demonstrate its ability to enrich diverse E. coli by orders of magnitude, in a mock community and in human stool from a study investigating recurrent UTI (rUTI). Comparisons of transcriptomes between gut E. coli of women with and without history of rUTI suggest rUTI gut E. coli are responding to increased oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease. E. coli PanSelect is well suited for investigations of in vivo E. coli biology in other low-abundance environments, and the framework described here has broad applicability to other diverse, low-abundance organisms.

Genomic and Transcriptomic Analyses Revealed DdSTE2 Play a Role in Constricting Ring Formation in the Nematode-Trapping Fungi Drechslerella dactyloides.

The carnivorous fungus Drechslerella dactyloides can form constricting rings through hyphal specialization to capture nematodes. The formation of constricting rings is a prerequisite for capturing nematodes and a characteristic of entering the carnivorous stage. Currently, there is limited research on the molecular mechanism of constricting ring formation. In this study, two D. dactyloides mutants unable to form constricting rings were obtained through UV irradiation mutagenesis, and their growth and development phenotypes were compared with the wild-type strain. Transcriptome comparisons revealed differences between the mutants and the wild-type strain in metabolic pathways related to cell wall structure, peroxisomes, lipid metabolism, and MAPK signal transduction, which we validated through qPCR. We further deleted one differentially expressed gene, DdSTE2, of the MAPK pathway and confirmed its role in conidiogenesis and trap formation in D. dactyloides. Together, our results indicate that the remodeling of cell wall structure, peroxisomes, lipid metabolism, and MAPK signal transduction pathways are involved in the formation and maturation of D. dactyloides constricting rings. We discuss the implications of these results for utilizing these fungi to control animal and plant parasitic nematodes.

Impact of gonadotropin on certain testis-related genes identified through testicular transcriptome analysis in the Asian and the African catfish

Induction of spawning in catfish is well demonstrated in females while stimulation of spermiation in males seems difficult. This has led to least understanding of gene profile changes during testicular maturation. Expression of the factors after hormonal induction that control reproductive processes has become an intense research area in fish endocrinology. In view of this, de novo assemblies of testicular transcriptomes of the Asian catfish, Clarias batrachus and the African catfish, C. gariepinus, were performed to identify genes/factors involved in testicular maturation. For testicular induction, human chorionic gonadotropin (hCG) was administered in vivo to both the catfish species during active phase of reproduction. 1,68,071 and 1,26,232 assembled transcripts were obtained from C. batrachus and C. gariepinus testicular transcriptomes and were annotated using different databases. Further, in silico analysis suggested the presence of several transcripts that were involved in steroidogenesis and male reproduction. Comparison of transcriptomes of both species revealed the presence of certain unique genes related to reproduction differentially. Expression profiles after hCG induction in testis showed higher expression of certain steroidogenesis related genes such as star, cyp11b1, cyp17a and cyp21a in both the species. Further, expression levels of crucial factors related to testis, such as dmrt1/2/3, were also found to be significantly higher after gonadotropin induction. However, amh, tgfα and dmrt4/5 expression levels were significantly low. Factors related to male reproduction i.e., tekt1, tekt2, sox9, spag1, spata2 and spata7 were found to be differentially upregulated in hCG treated testicular tissues of both the species. Histology analysis indicated that the gonadotropin induction either short or long term is a better strategy to highlight expression profile changes during testicular maturation in teleost.

Oligotrophic state reduces the time dependence of the observed survival fraction for heavy ion beam-irradiated Saccharomyces cerevisiae and provides new insights into DNA repair.

Heavy ion beam (HIB) irradiation is widely utilized in studies of cosmic rays-induced cellular effects and microbial breeding. Establishing an accurate dose-survival relationship is crucial for selecting the optimal irradiation dose. Typically, after irradiating logarithmic-phase cell suspensions with HIB, the survival fraction (SF) is determined by the ratio of clonal-forming units in irradiated versus control groups. However, our findings indicated that SF measurements were time sensitive. For the Saccharomyces cerevisiae model, the observed SF initially declined and subsequently increased in a eutrophic state; conversely, in an oligotrophic state, it remained relatively stable within 120 minutes. This time effect of SF observations in the eutrophic state can be ascribed to HIB-exposed cells experiencing cell cycle arrest, whereas the control proliferated rapidly, resulting in an over-time disproportionate change in viable cell count. Therefore, an alternative involves irradiating oligotrophic cells, determining SF thereafter, and transferring cells to the eutrophic state to facilitate DNA repair-mutation. Transcriptomic comparisons under these two trophic states yield valuable insights into the DNA damage response. Although DNA repair was postponed in an oligotrophic state, cells proactively mobilized specific repair pathways to advance this process. Effective nutritional supplementation should occur within 120 minutes, beyond this window, a decline in SF indicates an irreversible loss of repair capability. Upon transition to the eutrophic state, S. cerevisiae swiftly adapted and completed the repair. This study helps to minimize time-dependent variability in SF observations and to ensure effective damage repair and mutation in microbial breeding using HIB or other mutagens. It also promotes the understanding of microbial responses to complex environments.IMPORTANCEMutation breeding is a vital means of developing excellent microbial resources. Consequently, understanding the mechanisms through which microorganisms respond to complex environments characterized by mutagens and specific physiological-biochemical states holds significant theoretical and practical values. This study utilized Saccharomyces cerevisiae as a microbial model and highly efficient heavy ion beam (HIB) radiation as a mutagen, it revealed the time dependence of observations of survival fractions (SF) in response to HIB radiation and proposed an alternative to avoid the indeterminacy that this variable brings. Meanwhile, by incorporating an oligotrophic state into the alternative, this study constructed a dynamic map of gene expression during the fast-repair and slow-repair stages. It also highlighted the influence of trophic states on DNA repair. The findings apply to the survival-damage repair-mutation effects of single-celled microorganisms in response to various mutagens and contribute to elucidating the biological mechanisms underlying microbial survival in complex environments.

Intraspecific venom variation in the medically important puff adder (Bitis arietans): Comparative venom gland transcriptomics, in vitro venom activity and immunological recognition by antivenom.

Variation in snake venoms is well documented, both between and within species, with intraspecific venom variation often correlated with geographically distinct populations. The puff adder, Bitis arietans, is widely distributed across sub-Saharan Africa and into the Arabian Peninsula where it is considered a leading cause of the ~310,000 annual snakebites across the region, with its venom capable of causing substantial morbidity and mortality. Despite its medical importance and wide geographic distribution, there is little known about venom variation between different B. arietans populations and the potential implications of this variation on antivenom efficacy. We applied a range of analyses, including venom gland transcriptomics, in vitro enzymatic assays and reverse phase chromatography to comparatively analyse B. arietans venoms originating from Nigeria, Tanzania, and South Africa. Immunological assays and in vitro enzymatic neutralisation assays were then applied to investigate the impact of venom variation on the potential efficacy of three antivenom products; SAIMR Polyvalent, EchiTAb-Plus and Fav-Afrique. Through the first comparison of venom gland transcriptomes of B. arietans from three geographically distinct regions (Nigeria, Tanzania, and South Africa), we identified substantial variation in toxin expression. Findings of venom variation were further supported by chromatographic venom profiling, and the application of enzymatic assays to quantify the activity of three pathologically relevant toxin families. However, the use of western blotting, ELISA, and in vitro enzymatic inhibition assays revealed that variation within B. arietans venom does not appear to substantially impact upon the efficacy of three African polyvalent antivenoms. The large distribution and medical importance of B. arietans makes this species ideal for understanding venom variation and the impact this has on therapeutic efficacy. The findings in this study highlight the likelihood for considerable venom toxin variation across the range of B. arietans, but that this may not dramatically impact upon the utility of treatment available in the region.

Rapidly Evolved Genes in Three Reaumuria Transcriptomes and Potential Roles of Pentatricopeptide Repeat Superfamily Proteins in Endangerment of R. trigyna.

Reaumuria genus (Tamaricaceae) is widely distributed across the desert and semi-desert regions of Northern China, playing a crucial role in the restoration and protection of desert ecosystems. Previous studies mainly focused on the physiological responses to environmental stresses; however, due to the limited availability of genomic information, the underlying mechanism of morphological and ecological differences among the Reaumuria species remains poorly understood. In this study, we presented the first catalog of expressed transcripts for R. kaschgarica, a sympatric species of xerophyte R. soongorica. We further performed the pair-wise transcriptome comparison to determine the conserved and divergent genes among R. soongorica, R. kaschgarica, and the relict recretohalophyte R. trigyna. Annotation of the 600 relatively conserved genes revealed that some common genetic modules are employed by the Reaumuria species to confront with salt and drought stresses in arid environment. Among the 250 genes showing strong signs of positive selection, eight pentatricopeptide repeat (PPR) superfamily protein genes were specifically identified, including seven PPR genes in the R. soongorica vs. R. trigyna comparison and one PPR gene in the R. kaschgarica vs. R. trigyna comparison, while the cyclin D3 gene was found in the R. soongorica vs. R. trigyna comparison. These findings suggest that genetic variations in PPR genes may affect the fertility system or compromise the extent of organelle RNA editing in R. trigyna. The present study provides valuable genomic information for R. kaschgarica and preliminarily reveals the conserved genetic bases for the abiotic stress adaptation and interspecific divergent selection in the Reaumuria species. The rapidly evolved PPR and cyclin D3 genes provide new insights on the endangerment of R. trigyna and the leaf length difference among the Reaumuria species.

Mobilome impacts on physiology in the widely used non-toxic mutant Microcystis aeruginosa PCC 7806 ΔmcyB and toxic wildtype

The Microcystis mobilome is a well-known but understudied component of this bloom-forming cyanobacterium. Through genomic and transcriptomic comparisons, we found five families of transposases that altered the expression of genes in the well-studied toxigenic type-strain, Microcystis aeruginosa PCC 7086, and a non-toxigenic genetic mutant, Microcystis aeruginosa PCC 7806 ΔmcyB. Since its creation in 1997, the ΔmcyB strain has been used in comparative physiology studies against the wildtype strain by research labs throughout the world. Some differences in gene expression between what were thought to be otherwise genetically identical strains have appeared due to insertion events in both intra- and intergenic regions. In our ΔmcyB isolate, a sulfate transporter gene cluster (sbp-cysTWA) showed differential expression from the wildtype, which may have been caused by the insertion of a miniature inverted repeat transposable element (MITE) in the sulfate-binding protein gene (sbp). Differences in growth in sulfate-limited media also were also observed between the two isolates. This paper highlights how Microcystis strains continue to “evolve” in lab conditions and illustrates the importance of insertion sequences / transposable elements in shaping genomic and physiological differences between Microcystis strains thought otherwise identical. This study forces the necessity of knowing the complete genetic background of isolates in comparative physiological experiments, to facilitate the correct conclusions (and caveats) from experiments.

Cholic acid-based inhibition of SVCV replication by modulating polyunsaturated fatty acid content

Spring Viremia of Carp Virus (SVCV) is a highly pathogenic pathogen that infects carp fish, and SVCV infection frequently causes a severe inflammatory response in the affected fish. The viral infection is extremely lethal in carp larvae, often leading to heavy economic losses. Cholic acid (CA) is a primary bile acid synthesized directly from cholesterol in the liver and has been found to have an inhibitory effect on viral infections. To substantiate this antiviral potential, 500 μM CA was tested against SVCV replication in vitro and showed a significant inhibitory effect on viral replication. Further experimental tests demonstrated that CA exerted antiviral effects during its replication phase but not at viral adsorption and entry stages. In vivo experiments demonstrated that CA increased the survival rate of SVCV-infected zebrafish by 40 %, reduced viral load in tissues and reduced histopathological lesions. Comparison of the liver transcriptome of zebrafish between CA treatment and control (NC) groups revealed that CA treatment was able to promote the synthesis of polyunsaturated fatty acids, with the most significant changes in docosahexaenoic acid (DHA). Inhibition assay on fatty acid desaturase 2 (Fads2), the first rate-limiting enzyme for the synthesis of polyunsaturated fatty acid, showed that the antiviral effect of CA on SVCV disappeared. These new findings suggest that CA may exert its antiviral effects by regulating the synthesis of polyunsaturated fatty acid. In addition, this study also verified that DHA has antiviral activity against SVCV. In conclusion, CA shows promise as a potential anti-SVCV drug or feed additive that could help mitigate SVCV outbreaks in aquaculture.