Venom gland transcriptomes of two elapid snakes (Bungarus multicinctus and Naja atra) and evolution of toxin genes

A comparative analysis of toxin gene families across diverse sea anemone species

All species from order Actiniaria (sea anemones) are venomous, even though most are of no threat to humans. Currently, we know very little about the toxin gene complement of highly venomous members of this order. To address this gap in knowledge, we sequenced the transcriptome of the highly venomous and medically significant Hell's Fire sea anemone, Actinodendron plumosum, as well as five distantly related species, Cryptodendrum adhaesivum, Epiactis australiensis, Heteractis aurora, Isactinia olivacea and Stichodactyla mertensii. We used bioinformatic approaches to identify their toxin gene complements and performed a comparative evolutionary analysis of seven understudied toxin families. Of the 16 toxin families identified, 12-40 candidate toxins were found in the six new sea anemone transcriptomes, with only 12 candidates in eight toxin families identified in A. plumosum. Across 26 sea anemone species, six neurotoxin families showed evidence of taxonomic restriction, whereas the phospholipase A2 toxin family was ubiquitously distributed. Additionally, we identified two alternative forms for the phospholipase A2 toxin family, a 10- and 14-cysteine framework, which warrant further structural and functional characterisation. Overall, we have identified a comprehensive list of toxins from a wide diversity of sea anemone species that provides the basis for future research to structurally and functionally characterise novel candidates for potential use as therapeutics or for agricultural applications.

WGCNA and integrative network analysis identify CHRNA5 and CTLA4 as potential therapeutic targets against angiosarcoma

Angiosarcomas are a type of soft-tissue sarcoma characterized by aggressive malignant tumors originating from endothelial cells of blood vessels or lymphatic vessels. Limited studies have been done to explore the molecular pathophysiology of the disease, with rather limited studies involving transcriptomic analyzes. This study was undertaken to identify the shared molecular signatures and gene modules associated with angiosarcomas of various origin. Transcriptomic data analysis of publicly available data was done followed by WGCNA to identify shared signature gene modules. The Maximal Clique Centrality algorithm was applied to gene modules, and unclustered network analysis was conducted on differentially expressed genes to identify true hub genes. The expression of candidate genes in various cancer types was analyzed using GEPIA. WGCNA analysis identified five significant modules, with the most enriched module being associated with angiogenesis and cell junction regulators. The intersection of true hub genes from MCC analysis of WGCNA modules and high-degree nodes from an unclustered network revealed eight consistently overexpressed genes in all angiosarcoma samples.Among the eight enriched genes, CHRNA5 and CTLA4, are exclusively overexpressed in angiosarcoma and not in other cancers of the same tissue origin, with significant drug-protein interactions suggesting their potential as therapeutic targets.

Deciphering sperm functions using biological networks

The global human population is exponentially increasing, which requires the production of quality food through efficient reproduction as well as sustainable production of livestock. Lack of knowledge and technology for assessing semen quality and predicting bull fertility is hindering advances in animal science and food animal production and causing millions of dollars of economic losses annually. The intent of this systemic review is to summarize methods from computational biology for analysis of gene, metabolite, and protein networks to identify potential markers that can be applied to improve livestock reproduction, with a focus on bull fertility. We provide examples of available gene, metabolic, and protein networks and computational biology methods to show how the interactions between genes, proteins, and metabolites together drive the complex process of spermatogenesis and regulate fertility in animals. We demonstrate the use of the National Center for Biotechnology Information (NCBI) and Ensembl for finding gene sequences, and then use them to create and understand gene, protein and metabolite networks for sperm associated factors to elucidate global cellular processes in sperm. This study highlights the value of mapping complex biological pathways among livestock and potential for conducting studies on promoting livestock improvement for global food security.

Enhancing snakebite management: The role of small molecule therapeutics in complementing antivenom strategies

The variability in snake composition presents a significant challenge in accessing an effective broad-spectrum antivenom. These highly complex mixtures can result in numerous deleterious effects affecting thousands of individuals worldwide, particularly in Asia, sub-Saharan Africa, and Latin America. While the administration of antivenom remains a recommended treatment for snakebite envenomation and is the primary means to prevent systemic damage, there are limitations concerning specificity, reversal of local effects, and economic factors that hinder the availability of these antibodies. In this review, we have compiled information on the use of small molecule therapeutics in initial first-aid treatments before antivenom administration. These enzyme inhibitors have shown promise as viable candidates to broaden our treatment approaches, simplify procedures, reduce costs, and improve the clinical outcomes of affected patients.

Characterizing Excretory-Secretory Products Proteome Across Larval Development Stages in Ascaris suum

Introduction

Ascaris lumbricoides and Ascaris suum are parasitic nematodes that primarily infest the small intestines of humans and pigs, respectively. Ascariasis poses a significant threat to human health and swine health. Understanding Ascaris larval development is crucial for developing novel therapeutic interventions that will prevent ascariasis in both humans and pigs. This study aimed to characterize the excretory-secretory (ES) proteome of different Ascaris suum larval stages (L3-egg, L3-lung, L3-trachea) to identify potential targets for intervention to prevent Ascaris -induced global morbidity.

Methods

Stage-specific larvae were isolated, cultured in vitro and ES-product was collected. Third-stage Ascaris larvae (L3) were isolated from embryonated eggs (L3-egg), isolated from the lungs of Balb/c mice infected with Ascaris suum eggs at day 8 post infection (L3-lungs) and isolated from the trachea of Balb/c mice infected with Ascaris suum eggs at day 12 post infection (L3-trachea). ES products were obtained by culturing larvae. Proteomic analysis was conducted using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and bioinformatic tools including MaxQuant, Perseus, and Andromeda, following a detailed protocol available on GitHub. The analysis encompassed peptide identification, scoring, and quantification against an organism-specific database, with subsequent quality control, correlation assessment, and differential abundance determination using the Amica algorithm.

Results

A total of 58 unique proteins were identified in the ES products. Fourteen proteins were common across all stages, while others were stage-specific. Principal component analysis revealed distinct protein profiles for each stage, suggesting qualitatively different proteomes. Gene ontology analysis indicated stage-specific GO enrichment of specific protein classes, such as nuclear proteins in L3-egg ES products and metabolic enzymes in L3-lung and L3-trachea ES products.

Discussion

This study revealed stage-specific differences in the composition of Ascaris ES products. Further investigation into the functional roles of these proteins and their interactions with host cells is crucial for developing novel therapeutic and diagnostic strategies against ascariasis.

Assessment of Genomic and Metabolic Characteristics of Cholesterol-Reducing and GABA Producer Limosilactobacillus fermentum AGA52 Isolated from Lactic Acid Fermented Shalgam Based on "In Silico" and "In Vitro" Approaches

This study aimed to characterize the genomic and metabolic properties of a novel Lb. fermentum strain AGA52 which was isolated from a lactic acid fermented beverage called "shalgam." The genome size of AGA52 was 2,001,184 bp, which is predicted to carry 2024 genes, including 50 tRNAs, 3 rRNAs, 3 ncRNAs, 15 CRISPR repeats, 14 CRISPR spacers, and 1 CRISPR array. The genome has a GC content of 51.82% including 95 predicted pseudogenes, 56 complete or partial transposases, and 2 intact prophages. The similarity of the clusters of orthologous groups (COG) was analyzed by comparison with the other Lb. fermentum strains. The detected resistome on the genome of AGA52 was found to be intrinsic originated. Besides, it has been determined that AGA52 has an obligate heterofermentative carbohydrate metabolism due to the absence of the 1-phosphofructokinase (pfK) enzyme. Furthermore, the strain is found to have a better antioxidant capacity and to be tolerant to gastrointestinal simulated conditions. It was also observed that the AGA52 has antimicrobial activity against Yersinia enterocolitica ATCC9610, Bacillus cereus ATCC33019, Salmonella enterica sv. Typhimurium, Escherichia coli O157:h7 ATCC43897, Listeria monocytogenes ATCC7644, Klebsiella pneumoniae ATCC13883, and Proteus vulgaris ATCC8427. Additionally, AGA52 exhibited 42.74 ± 4.82% adherence to HT29 cells. Cholesterol assimilation (33.9 ± 0.005%) and GABA production capacities were also confirmed by "in silico" and "in vitro." Overall, the investigation of genomic and metabolic features of the AGA52 revealed that is a potential psychobiotic and probiotic dietary supplement candidate and can bring functional benefits to the host.

Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

BACKGROUND

The genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on Sanicula provided us with a good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China. Moreover, the evolutionary history of this genus also remains inadequately understood. The plastid genomes possessing highly conserved structure and limited evolutionary rate have proved to be an effective tool for studying plant phylogeny and evolution.

RESULTS

In the current study, we newly sequenced and assembled fifteen Sanicula complete plastomes. Combined with two previously reported plastomes, we performed comprehensively plastid phylogenomics analyses to gain novel insights into the evolutionary history of this genus. The comparative results indicated that the seventeen plastomes exhibited a high degree of conservation and similarity in terms of their structure, size, GC content, gene order, IR borders, codon bias patterns and SSRs profiles. Such as all of them displayed a typical quadripartite structure, including a large single copy region (LSC: 85,074-86,197 bp), a small single copy region (SSC: 17,047-17,132 bp) separated by a pair of inverted repeat regions (IRs: 26,176-26,334 bp). And the seventeen plastomes had similar IR boundaries and the adjacent genes were identical. The rps19 gene was located at the junction of the LSC/IRa, the IRa/SSC junction region was located between the trnN gene and ndhF gene, the ycf1 gene appeared in the SSC/IRb junction and the IRb/LSC boundary was located between rpl12 gene and trnH gene. Twelve specific mutation hotspots (atpF, cemA, accD, rpl22, rbcL, matK, ycf1, trnH-psbA, ycf4-cemA, rbcL-accD, trnE-trnT and trnG-trnR) were identified that can serve as potential DNA barcodes for species identification within the genus Sanicula. Furthermore, the plastomes data and Internal Transcribed Spacer (ITS) sequences were performed to reconstruct the phylogeny of Sanicula. Although the tree topologies of them were incongruent, both provided strong evidence supporting the monophyly of Saniculoideae and Apioideae. In addition, the sister groups between Saniculoideae and Apioideae were strongly suggested. The Sanicula species involved in this study were clustered into a clade, and the Eryngium species were also clustered together. However, it was clearly observed that the sections of Sanicula involved in the current study were not respectively recovered as monophyletic group. Molecular dating analysis explored that the origin of this genus was occurred during the late Eocene period, approximately 37.84 Ma (95% HPD: 20.33-52.21 Ma) years ago and the diversification of the genus was occurred in early Miocene 18.38 Ma (95% HPD: 10.68-25.28 Ma).

CONCLUSION

The plastome-based tree and ITS-based tree generated incongruences, which may be attributed to the event of hybridization/introgression, incomplete lineage sorting (ILS) and chloroplast capture. Our study highlighted the power of plastome data to significantly improve the phylogenetic supports and resolutions, and to efficiently explore the evolutionary history of this genus. Molecular dating analysis explored that the diversification of the genus occurred in the early Miocene, which was largely influenced by the prevalence of the East Asian monsoon and the uplift of the Hengduan Mountains (HDM). In summary, our study provides novel insights into the plastome evolution, phylogenetic relationships, taxonomic framework and evolution of genus Sanicula.

Single nucleotide polymorphisms cumulating to genetic variation for fertility in crossbred (Bos taurus × Bos indicus) bull spermatozoa

Spermatozoa from high-fertile (HF) and low-fertile (LF) breeding bulls were subjected to high-throughput next-generation sequencing to identify important Single nucleotide polymorphisms (SNPs) and novel variants associated with fertility. A total of 77,038 genome-wide SNPs were identified, among which, 10,788 were novel variants. A total of 42,290 and 34,748 variants were recorded with 6115 and 4673 novel variants in in HF and LF bulls, respectively. Higher number of SNPs were identified in HF compared to LF bulls. GO analysis of filtered genes with significant variations in HF bulls indicated their involvement in oxidative phosphorylation and metabolic pathways. GO analysis of filtered genes with significant variation in LF bulls revealed their involvement in Ca2++ ion binding, structural constituent of ribosome, and biological processes like translation and ribosomal small subunit assembly. The study identified SNPs in candidate genes including TPT1, BOLA-DRA, CD74, RPS17, RPS28, RPS29, RPL14, RPL13, and RPS27A, which are linked to sperm functionality, survival, oxidative stress, and bull fertility. The identified SNPs could be used in selection of bulls for high fertility and the variation in these genes could be established as an explanation for the fertility differences in bulls upon validation in large number of bulls.

Analysis of global DNA methylation and epigenetic modifiers (DNMTs and HDACs) in human foetal endothelium exposed to gestational and type 2 diabetes

Foetuses exposed to maternal gestational diabetes (GDM) and type 2 diabetes (T2D) have an increased risk of adverse perinatal outcomes. Epigenetic mechanisms, including DNA methylation and histone modifications, may act as mediators of persistent metabolic memory in endothelial cells (ECs) exposed to hyperglycaemia, even after glucose normalization. Therefore, we investigated alterations in global DNA methylation and epigenetic modifier expression (DNMT1, DNMT3a, DNMT3b, HDAC1, and HDAC2) in human umbilical vein ECs (HUVECs) from the umbilical cords of mothers with GDM (n = 8) and T2D (n = 3) compared to that of healthy mothers (n = 6). Global DNA alteration was measured using a 5-methylation cytosine colorimetric assay, followed by quantitative real-time polymerase chain reaction to measure DNA methyltransferase and histone acetylase transcript expression. We revealed that DNA hypermethylation occurs in both GDM- and T2D-HUVECs compared to that in Control-HUVECs. Furthermore, there was a significant increase in HDAC2 mRNA levels in GDM-HUVECs and increase in DNMT3b mRNA levels in T2D-HUVECs. Overall, our results suggest that GDM and T2D are associated with global DNA hypermethylation in foetal endothelial cells under normoglycemic conditions and the aberrant mRNA expression of HDAC2 and DNMT3b could play a role in this dysregulation.

Genome-wide transcriptional profiling and physiological investigation elucidating the molecular mechanism of multiple abiotic stress response in Stevia rebaudiana Bertoni

Considering the major source of plant-derived low/non-calorie steviol glycosides (SGs), comprehensive physiological, biochemical, and deep transcriptional investigations were conducted to explicit deeper insight into multiple abiotic stress responses in Stevia rebaudiana. The physiological indicators including photosynthesis, chlorophyll, relative water content, shoot growth, electrolyte leakage, and SG biosynthesis were negatively impacted under drought (DS), followed by salinity (SS) and waterlogging (WS). Global transcriptional analysis revealed significant upregulated expression of the genes encoding for ROS detoxification (GST, SOD, APX, glutathione peroxidase), osmotic adjustment (alpha-trehalose-phosphate and S-adenosylmethionine decarboxylase), ion transporters (CAX, NHX, CNGS, VPPase, VATPase), water channel (PIP1, TIP) and abiotic stress-responsive candidate genes (LEA, HSPs, and Dehydrins) regulating abiotic stress response in S. rebaudiana. These inferences were complemented with predicted interactome network that revealed regulation of energy metabolism by key stress-responsive genes (GST, HKT1, MAPKs, P5CSs, PIP), transcription factors (HSFA2, DREB1A, DREB2A), and abiotic stress responsive pathways (ABA, ethylene, ion stress). This is the first detailed study to comprehend the molecular regulation of stress response and their interplay under DS, SS, and WS. The key genes and regulators can be functionally validated, and will facilitate targeted gene editing for genetic improvement of crop sustainability under changing environmental conditions in S. rebaudiana.

Birth prevalence and risk factors of neural tube defects in Ethiopia: a systematic review and meta-analysis

OBJECTIVE

This study aims to estimate the prevalence of neural tube defects (NTDs) and to identify potential risk factors in the Ethiopian context.

STUDY DESIGN

Systematic review and meta-analysis.

STUDY PARTICIPANTS

A total of 611 064 participants were included in the review obtained from 42 studies.

METHODS

PubMed (Medline), Embase and Cochrane Library databases in combination with other potential sources of literature were systematically searched, whereby studies conducted between January 2010 and December 2022 were targeted in the review process. All observational studies were included and heterogeneity between studies was verified using Cochrane Q test statistics and I2 test statistics. Small study effects were checked using Egger's statistical test at a 5% significance level.

RESULT

The pooled prevalence of all NTDs per 10 000 births in Ethiopia was 71.48 (95% CI 57.80 to 86.58). The between-study heterogeneity was high (I2= 97.49%, p<0.0001). Birth prevalence of spina bifida (33.99 per 10 000) was higher than anencephaly (23.70 per 10 000), and encephalocele (4.22 per 10 000). Unbooked antenatal care (AOR 2.26, 95% CI (1.30 to 3.94)), preconception intake of folic acid (AOR 0.41, 95% CI (0.26 to 0.66)), having chronic medical illness (AOR 2.06, 95% CI (1.42 to 2.99)), drinking alcohol (AOR 2.70, 95% CI (1.89 to 3.85)), smoking cigarette (AOR 2.49, 95% CI (1.51 to 4.11)), chewing khat (AOR 3.30, 95% CI (1.88 to 5.80)), exposure to pesticides (AOR 3.87, 95% CI (2.63 to 5.71)), maternal age ≥35 (AOR 1.90, 95% CI (1.13 to 3.25)), maternal low educational status (AOR 1.60, 95% CI (1.13 to 2.24)), residing in urban areas (AOR 0.75, 95% CI (0.58 to 0.97))and family history of NTDs (AOR 2.51, 95% CI (1.36 to 4.62)) were associated with NTD cases.

CONCLUSION

The prevalence of NTDs in Ethiopia is seven times as high as in other Western countries where prevention measures are put in place. Heredity, maternal and environmental factors are associated with a high prevalence of NTDs. Mandatory fortification of staple food with folic acid should be taken as a priority intervention to curb the burden of NTDs. To smoothen and overlook the pace of implementation of mass fortification, screening, and monitoring surveillance systems should be in place along with awareness-raising measures.

PROSPERO REGISTRATION NUMBER

CRD42023413490.

Proteomic characteristics of six snake venoms from the Viperidae and Elapidae families in China and their relation to local tissue necrosis

Patients envenomed by snakes from the Viperidae and Elapidae families in China often have varying degrees of local tissue necrosis. Due to the relative clinical characteristics of local tissue necrosis and ulceration following envenoming, this study has analyzed the proteome of six snake venoms from the Viperidae and Elapidae family, and the toxin profiles of each snake were compared and correlated with the clinical manifestations that follow cytotoxic envenoming. Deinagkistrodon acutus and Naja atra envenomation induce severe ulceration, which is absent in Bungarus multicinctus envenomation and mild in the other three vipers. It is interesting to note that the proportion of c-type lectins (CTL) (20.63%) in Deinagkistrodon acutus venom was relatively high, which differs from the venom of other vipers. In addition, three-fingered toxin (3FTx) (2.15%) is present in the venom of Deinagkistrodon acutus, but has not been detected in the remaining three vipers. Snake venom metalloprotease (SVMP) (34.4%-44.7%), phospholipase A2 (PLA2) (9.81%-40.83%), and snake venom serine protease (SVSP) (9.44%-16.2%) represent the most abundant families of toxin in Viperidae venom. The Elapidae venom proteome was mainly composed of neurotoxins and cytotoxins, including 3FTx (39.28%-60.08%) and PLA2 (8.24%-58.95%) toxins, however, the proportion of CRISPS (26.36%) in Naja atra venom was relatively higher compared to Bungarus multicinctus venom. Significant differences in SVMP, SVSP, and 3FTx expression levels exist between the Viperidae and the Elapidae family. The main toxins responsible for the development of tissue necrosis and ulcerations following Viperidae envenoming are hematotoxins (SVSMP, SVSP) and myotoxins (PLA2). Deinagkistrodon acutus venom contains high levels of CTL and traces of 3FTx, leading to more severe local necrosis. However, Naja atra venom can also cause severe local necrosis through the effects of myotoxin (3FTx, CRISP, PLA2). Bungarus multicinctus venom does not contain myotoxins, resulting in pure systemic neurological manifestations no obvious necrosis of local tissue in patients.

Panicle transcriptome of high-yield mutant indica rice reveals physiological mechanisms and novel candidate regulatory genes for yield under reproductive stage drought stress

BACKGROUND

Reproductive stage drought stress (RDS) is a major global threat to rice production. Due to climate change, water scarcity is becoming an increasingly common phenomenon in major rice-growing areas worldwide. Understanding RDS mechanisms will allow candidate gene identification to generate novel rice genotypes tolerant to RDS.

RESULTS

To generate novel rice genotypes that can sustain yield under RDS, we performed gamma-irradiation mediated mutation breeding in the drought stress susceptible mega rice variety, MTU1010. One of the mutant MM11 (MTU1010 derived mutant11) shows consistently increased performance in yield-related traits under field conditions consecutively for four generations. In addition, compared to MTU1010, the yield of MM11 is sustained in prolonged drought imposed during the reproductive stage under field and in pot culture conditions. A comparative emerged panicle transcriptome analysis of the MTU1010 and MM11 suggested metabolic adjustment, enhanced photosynthetic ability, and hormone interplay in regulating yield under drought responses during emerged panicle development. Regulatory network analysis revealed few putative significant transcription factor (TF)-target interactions involved in integrated signalling between panicle development, yield and drought stress.

CONCLUSIONS

A gamma-irradiate rice mutant MM11 was identified by mutation breeding, and it showed higher potential to sustain yield under reproductive stage drought stress in field and pot culture conditions. Further, a comparative panicle transcriptome revealed significant biological processes and molecular regulators involved in emerged panicle development, yield and drought stress integration. The study extends our understanding of the physiological mechanisms and candidate genes involved in sustaining yield under drought stress.

Comparing morphological and secretory aspects of cephalic glands among the New World coral snakes brings novel insights on their biological roles

Oral and other cephalic glands have been surveyed by several studies with distinct purposes. Despite the wide diversity and medical relevance of the New World coral snakes, studies focusing on understanding the biological roles of the glands within this group are still scarce. Specifically, the venom glands of some coral snakes were previously investigated but all other cephalic glands remain uncharacterized. In this sense, performing morphological and molecular analysis of these glands may help better understand their biological role. Here, we studied the morphology of the venom, infralabial, rictal, and harderian glands of thirteen species of Micrurus and Micruroides euryxanthus. We also performed a molecular characterization of these glands from selected species of Micrurus using transcriptomic and proteomic approaches. We described substantial morphological variation in the cephalic glands of New World coral snakes and structural evidence for protein-secreting cells in the inferior rictal glands. Our molecular analysis revealed that the venom glands, as expected, are majorly devoted to toxin production, however, the infralabial and inferior rictal glands also expressed some toxin genes at low to medium levels, despite the marked morphological differences. On the other hand, the harderian glands were dominated by the expression of lipocalins, but do not produce toxins. Our integrative analysis, including the prediction of biological processes and pathways, helped decipher some important traits of cephalic glands and better understand their biology.

Analytical Size Exclusion Chromatography Coupled with Mass Spectrometry in Parallel with High-Throughput Venomics and Bioassaying for Venom Profiling

Modern analytical size exclusion chromatography (SEC) is a suitable technique to separate venom toxin families according to their size characteristics. In this study, a method was developed to separate intact venom toxins from Bungarus multicinctus and Daboia russelii venoms via analytical SEC using volatile, non-salt-containing eluents for post-column mass spectrometry, coagulation bioassaying and high-throughput venomics. Two venoms were used to demonstrate the method developed. While the venom of Bungaurs multicinctus is known to exert anticoagulant effects on plasma, in this study, we showed the existence of both procoagulant toxins and anticoagulant toxins. For Daboia russelii venom, the method revealed characteristic procoagulant effects, with a 90 kDa mass toxin detected and matched with the Factor X-activating procoagulant heterotrimeric glycoprotein named RVV-X. The strong procoagulant effects for this toxin show that it was most likely eluted from size exclusion chromatography non-denatured. In conclusion, the separation of snake venom by size gave the opportunity to separate some specific toxin families from each other non-denatured, test these for functional bioactivities, detect the eluting mass on-line via mass spectrometry and identify the eluted toxins using high-throughput venomics.

Serotonin neurons in mating female mice are activated by male ejaculation

Sexual stimulation triggers changes in female physiology and behavior, including sexual satiety and preparing the uterus for pregnancy. Serotonin is an important regulator of reproductive physiology and sexual receptivity, but the relationship between sexual stimulation and serotonin neural activity in females is poorly understood. Here, we investigated dorsal raphe serotonin neural activity in females during sexual behavior. We found that serotonin neural activity in mating females peaked specifically upon male ejaculation, and remained elevated above baseline until disengagement. Artificial intravaginal mechanical stimulation was sufficient to elicit increased 5-HT neural activity but the delivery of ejaculatory fluids was not. Distal penis erectile enlargement ("penile cupping") at ejaculation and forceful expulsion of ejaculatory fluid each provided sufficient mechanical stimulation to elicit serotonin neuron activation. Our study identifies a female ejaculation-specific signal in a major neuromodulatory system and shows that intravaginal mechanosensory stimulation is necessary and sufficient to drive this signal.

HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data

Multi-region DNA sequencing of primary tumors and metastases from individual patients helps identify somatic aberrations driving cancer development. However, most methods to infer copy-number aberrations (CNAs) analyze individual samples. We introduce HATCHet2 to identify haplotype- and clone-specific CNAs simultaneously from multiple bulk samples. HATCHet2 introduces a novel statistic, the mirrored haplotype B-allele frequency (mhBAF), to identify mirrored-subclonal CNAs having different numbers of copies of parental haplotypes in different tumor clones. HATCHet2 also has high accuracy in identifying focal CNAs and extends the earlier HATCHet method in several directions. We demonstrate HATCHet2's improved accuracy using simulations and a single-cell sequencing dataset. HATCHet2 analysis of 50 prostate cancer samples from 10 patients reveals previously-unreported mirrored-subclonal CNAs affecting cancer genes.

Discovery of long non-coding RNAs in Aspergillus flavus response to water activity, CO2 concentration, and temperature changes

Although the role of long non-coding RNAs (lncRNAs) in key biological processes in animals and plants has been confirmed for decades, their identification in fungi remains limited. In this study, we discovered and characterized lncRNAs in Aspergillus flavus in response to changes in water activity, CO₂ concentration, and temperature, and predicted their regulatory roles in cellular functions. A total of 472 lncRNAs were identified in the genome of A. flavus, consisting of 470 novel lncRNAs and 2 putative lncRNAs (EFT00053849670 and EFT00053849665). Our analysis of lncRNA expression revealed significant differential expression under stress conditions in A. flavus. Our findings indicate that lncRNAs in A. flavus, particularly down-regulated lncRNAs, may play pivotal regulatory roles in aflatoxin biosynthesis, respiratory activities, cellular survival, and metabolic maintenance under stress conditions. Additionally, we predicted that sense lncRNAs down-regulated by a temperature of 30 °C, osmotic stress, and CO₂ concentration might indirectly regulate proline metabolism. Furthermore, subcellular localization analysis revealed that up-and down-regulated lncRNAs are frequently localized in the nucleus under stress conditions, particularly at a water activity of 0.91, while most up-regulated lncRNAs may be located in the cytoplasm under high CO₂ concentration.

Genome-wide identification and expression analysis of BZR gene family and associated responses to abiotic stresses in cucumber (Cucumis sativus L.)

BACKGROUND

BRASSINAZOLE-RESISTANT (BZR) is a class of specific transcription factor (TFs) involved in brassinosteroid (BR) signal transduction. The regulatory mechanism of target genes mediated by BZR has become one of the key research areas in plant BR signaling networks. However, the functions of the BZR gene family in cucumber have not been well characterized.

RESULTS

In this study, six CsBZR gene family members were identified by analyzing the conserved domain of BES1 N in the cucumber genome. The size of CsBZR proteins ranges from 311 to 698 amino acids and are mostly located in the nucleus. Phylogenetic analysis divided CsBZR genes into three subgroups. The gene structure and conserved domain showed that the BZR genes domain in the same group was conserved. Cis-acting element analysis showed that cucumber BZR genes were mainly involved in hormone response, stress response and growth regulation. The qRT-PCR results also confirmed CsBZR response to hormones and abiotic stress.

CONCLUSION

Collectively, the CsBZR gene is involved in regulating cucumber growth and development, particularly in hormone response and response to abiotic stress. These findings provide valuable information for understanding the structure and expression patterns of BZR genes.

A gene regulatory network inference model based on pseudo-siamese network

MOTIVATION

Gene regulatory networks (GRNs) arise from the intricate interactions between transcription factors (TFs) and their target genes during the growth and development of organisms. The inference of GRNs can unveil the underlying gene interactions in living systems and facilitate the investigation of the relationship between gene expression patterns and phenotypic traits. Although several machine-learning models have been proposed for inferring GRNs from single-cell RNA sequencing (scRNA-seq) data, some of these models, such as Boolean and tree-based networks, suffer from sensitivity to noise and may encounter difficulties in handling the high noise and dimensionality of actual scRNA-seq data, as well as the sparse nature of gene regulation relationships. Thus, inferring large-scale information from GRNs remains a formidable challenge.

RESULTS

This study proposes a multilevel, multi-structure framework called a pseudo-Siamese GRN (PSGRN) for inferring large-scale GRNs from time-series expression datasets. Based on the pseudo-Siamese network, we applied a gated recurrent unit to capture the time features of each TF and target matrix and learn the spatial features of the matrices after merging by applying the DenseNet framework. Finally, we applied a sigmoid function to evaluate interactions. We constructed two maize sub-datasets, including gene expression levels and GRNs, using existing open-source maize multi-omics data and compared them to other GRN inference methods, including GENIE3, GRNBoost2, nonlinear ordinary differential equations, CNNC, and DGRNS. Our results show that PSGRN outperforms state-of-the-art methods. This study proposed a new framework: a PSGRN that allows GRNs to be inferred from scRNA-seq data, elucidating the temporal and spatial features of TFs and their target genes. The results show the model's robustness and generalization, laying a theoretical foundation for maize genotype-phenotype associations with implications for breeding work.

Antisense transcription and its roles in adaption to environmental stress in E. coli

It has been reported that a highly varying proportion (1% ∼ 93%) of genes in various prokaryotes have antisense RNA (asRNA) transcription. However, the extent of the pervasiveness of asRNA transcription in the well-studied E. coli K12 strain has thus far been an issue of debate. Furthermore, very little is known about the expression patterns and functions of asRNAs under various conditions. To fill these gaps, we determined the transcriptomes and proteomes of E. coli K12 at multiple time points in five culture conditions using strand-specific RNA-seq, differential RNA-seq, and quantitative mass spectrometry methods. To reduce artifacts of possible transcriptional noise, we identified asRNA using stringent criteria with biological replicate verification and transcription start sites (TSSs) information included. We identified a total of 660 asRNAs, which were generally short and largely condition-dependently transcribed. We found that the proportions of the genes which had asRNA transcription highly depended on the culture conditions and time points. We classified the transcriptional activities of the genes in six transcriptional modes according to their relative levels of asRNA to mRNA. Many genes changed their transcriptional modes at different time points of the culture conditions, and such transitions can be described in a well-defined manner. Intriguingly, the protein levels and mRNA levels of genes in the sense-only/sense-dominant mode were moderately correlated, but the same was not true for genes in the balanced/antisense-dominant mode, in which asRNAs were at a comparable or higher level to mRNAs. These observations were further validated by western blot on candidate genes, where an increase in asRNA transcription diminished gene expression in one case and enhanced it in another. These results suggest that asRNAs may directly or indirectly regulate translation by forming duplexes with cognate mRNAs. Thus, asRNAs may play an important role in the bacterium's responses to environmental changes during growth and adaption to different environments.

IMPORTANCE

The cis -antisense RNA (asRNA) is a type of understudied RNA molecules in prokaryotes, which is believed to be important in regulating gene expression. Our current understanding of asRNA is constrained by inconsistent reports about its identification and properties. These discrepancies are partially caused by a lack of sufficient samples, biological replicates, and culture conditions. This study aimed to overcome these disadvantages and identified 660 putative asRNAs using integrated information from strand-specific RNA-seq, differential RNA-seq, and mass spectrometry methods. In addition, we explored the relative expression between asRNAs and sense RNAs and investigated asRNA regulated transcriptional activity changes over different culture conditions and time points. Our work strongly suggests that asRNAs may play a crucial role in bacterium's responses to environmental changes during growth and adaption to different environments.

Identification evidence unraveled by strict proteomics rules toward forensic samples

Snake venom is a complex mixture of proteins and peptides secreted by venomous snakes from their poison glands. Although proteomics for snake venom composition, interspecific differences, and developmental evolution has been developed for a decade, current diagnosis or identification techniques of snake venom in clinical intoxication and forensic science applications are mainly dependent on morphological and immunoassay. It could be expected that the proteomics techniques directly offer great help. This work applied a bottom-up proteomics method to identify proteins' types and species attribution in suspected snake venom samples using ultrahigh-performance liquid chromatography-quadrupole-electrostatic field Orbitrap tandem mass spectrometric technique, and cytotoxicity assay was amended to provide a direct evidence of toxicity. Toward the suspicious samples seized in the security control, sample pretreatment (in-sol and in-gel digestion) and data acquisition (nontargeted and targeted screening) modes complemented and validated each other. We have implemented two consequent approaches in identifying the species source of proteins in the samples via the points of venom proteomics and strict forensic identification. First, we completed a workflow consisting of a proteomics database match toward an entire SWISS-PROT (date 2018-11-22) database and a result-directed specific taxonomy database. The latter was a helpful hint to compare master protein kinds and reveal the insufficiency of specific venom proteomics characterization rules. Second, we suggested strict rules for protein identification to meet the requirements of forensic science on improved identification correctness, that is, (1) peptide spectrum matches confidence, peptide confidence, and protein confidence were both high (with the false-discovery ratio less than 1%); (2) the number of unique peptides was more than or equal to two in one protein, and (3) within unique peptides, which at least 75% of the ∆m/z of the matched y and b ions were less than 5 ppm. We identified these samples as cobra venom containing 10 highly abundant proteins (P00597, P82463, P60770, Q9YGI4, P62375, P49123, P80245, P60302, P01442, and P60304) from two snake venom protein families (acid phospholipase A2 and three-finger toxins), and the most abundant proteins were cytotoxins.

Identification, classification, and expression profile analysis of heat shock transcription factor gene family in Salvia miltiorrhiza

In response to abiotic stresses, transcription factors are essential. Heat shock transcription factors (HSFs), which control gene expression, serve as essential regulators of plant growth, development, and stress response. As a model medicinal plant, Salvia miltiorrhiza is a crucial component in the treatment of cardiovascular illnesses. But throughout its growth cycle, S.miltiorrhiza is exposed to a series of abiotic challenges, including heat and drought. In this study, 35 HSF genes were identified based on genome sequencing of Salvia miltiorrhiza utilizing bioinformatics techniques. Additionally, 35 genes were classified into three groups by phylogeny and gene structural analysis, comprising 22 HSFA, 11 HSFB, and two HSFC. The distribution and sequence analysis of motif showed that SmHSFs were relatively conservative. In SmHSF genes, analysis of the promoter region revealed the presence of many cis-acting elements linked to stress, hormones, and growth and development, suggesting that these factors have regulatory roles. The majority of SmHSFs were expressed in response to heat and drought stress, according to combined transcriptome and real-time quantitative PCR (qRT-PCR) analyses. In conclusion, this study looked at the SmHSF gene family using genome-wide identification, evolutionary analysis, sequence characterization, and expression analysis. This research serves as a foundation for further investigations into the role of HSF genes and their molecular mechanisms in plant stress responses.

Candidate genes for marker-assisted selection for growth, carcass and meat quality traits in rabbits

Growth and meat production are the most relevant targets for animal breeders, there are strong relationships between animal growth regulation, body composition and meat quality. Therefore, it is essential to identify the genetic factors that are controlling growth, carcass, and meat quality traits and to explore the correlations between identified genes of those traits. Identification of candidate genes may shift rabbit breeding from classical to modern approaches, which offer great potential to accelerate genetic improvement plans, especially in developing countries. The current work reviews several genes and mutations affecting growth, carcass and meat quality traits. These candidate genes and mutations can be incorporated into MAS programs to improve rabbit breeds especially local breeds, provided that a reasonable proportion of trait additive genetic variance is explained by the significant marker. Furthermore, we highlighted the indispensable need for more researches investigating candidate genes for different traits.

Venom Variation of Neonate and Adult Chinese Cobras in Captivity Concerning Their Foraging Strategies

The venom and transcriptome profile of the captive Chinese cobra (Naja atra) is not characterized until now. Here, LC-MS/MS and illumine technology were used to unveil the venom and trascriptome of neonates and adults N. atra specimens. In captive Chinese cobra, 98 co-existing transcripts for venom-related proteins was contained. A total of 127 proteins belong to 21 protein families were found in the profile of venom. The main components of snake venom were three finger toxins (3-FTx), snake venom metalloproteinase (SVMP), cysteine-rich secretory protein (CRISP), cobra venom factor (CVF), and phosphodiesterase (PDE). During the ontogenesis of captive Chinese cobra, the rearrangement of snake venom composition occurred and with obscure gender difference. CVF, 3-FTx, PDE, phospholipase A2 (PLA2) in adults were more abundant than neonates, while SVMP and CRISP in the neonates was richer than the adults. Ontogenetic changes in the proteome of Chinese cobra venom reveals different strategies for handling prey. The levels of different types of toxin families were dramatically altered in the wild and captive specimens. Therefore, we speculate that the captive process could reshape the snake venom composition vigorously. The clear comprehension of the composition of Chinese cobra venom facilitates the understanding of the mechanism of snakebite intoxication and guides the preparation and administration of traditional antivenom and next-generation drugs for snakebite.

Bibliometric Analysis of Literature in Snake Venom-Related Research Worldwide (1933-2022)

Snake envenomation is a severe economic and health concern affecting countries worldwide. Snake venom carries a wide variety of small peptides and proteins with various immunological and pharmacological properties. A few key research areas related to snake venom, including its applications in treating cancer and eradicating antibiotic-resistant bacteria, have been gaining significant attention in recent years. The goal of the current study was to analyze the global profile of literature in snake venom research. This study presents a bibliometric review of snake venom-related research documents indexed in the Scopus database between 1933 and 2022. The overall number of documents published on a global scale was 2999, with an average annual production of 34 documents. Brazil produced the highest number of documents (n = 729), followed by the United States (n = 548), Australia (n = 240), and Costa Rica (n = 235). Since 1963, the number of publications has been steadily increasing globally. At a worldwide level, antivenom, proteomics, and transcriptomics are growing hot issues for research in this field. The current research provides a unique overview of snake venom research at global level from 1933 through 2022, and it may be beneficial in guiding future research.

Genome-wide identification and expression analysis of the cucumber PP2C gene family

Background

Type 2C protein phosphatase (PP2C) is a negative regulator of ABA signaling pathway, which plays important roles in stress signal transduction in plants. However, little research on the PP2C genes family of cucumber (Cucumis sativus L.), as an important economic vegetable, has been conducted.

Results

This study conducted a genome-wide investigation of the CsPP2C gene family. Through bioinformatics analysis, 56 CsPP2C genes were identified in cucumber. Based on phylogenetic analysis, the PP2C genes of cucumber and Arabidopsis were divided into 13 groups. Gene structure and conserved motif analysis showed that CsPP2C genes in the same group had similar gene structure and conserved domains. Collinearity analysis showed that segmental duplication events played a key role in the expansion of the cucumber PP2C genes family. In addition, the expression of CsPP2Cs under different abiotic treatments was analyzed by qRT-PCR. The results reveal that CsPP2C family genes showed different expression patterns under ABA, drought, salt, and cold treatment, and that CsPP2C3, 11–17, 23, 45, 54 and 55 responded significantly to the four stresses. By predicting the cis-elements in the promoter, we found that all CsPP2C members contained ABA response elements and drought response elements. Additionally, the expression patterns of CsPP2C genes were specific in different tissues.

Conclusions

The results of this study provide a reference for the genome-wide identification of the PP2C gene family in other species and provide a basis for future studies on the function of PP2C genes in cucumber.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08734-y.

The structural and functional divergence of a neglected three-finger toxin subfamily in lethal elapids

Bungarus multicinctus is a widely distributed and medically important elapid snake that produces lethal neurotoxic venom. To study and enhance existing antivenom, we explore the complete repertoire of its toxin genes based on de novo chromosome-level assembly and multi-tissue transcriptome data. Comparative genomic analyses suggest that the three-finger toxin family (3FTX) may evolve through the neofunctionalization of flanking LY6E. A long-neglected 3FTX subfamily (i.e., MKA-3FTX) is also investigated. Only one MKA-3FTX gene, which evolves a different protein conformation, is under positive selection and actively transcribed in the venom gland, functioning as a major toxin effector together with MKT-3FTX subfamily homologs. Furthermore, this lethal snake may acquire self-resistance to its β-bungarotoxin via amino acid replacements on fast-evolving KCNA2. This study provides valuable resources for further evolutionary and structure-function studies of snake toxins, which are fundamental for the development of effective antivenoms and drug candidates.

Whole-genome sequence analysis of Clostridium chauvoei isolated from clinical case of black quarter (BQ) from India

Black quarter (BQ) is an infectious disease affecting cattle and small ruminants worldwide caused by Gram-positive anaerobic bacterium Clostridium chauvoei. In this study, a draft genome sequence of C. chauvoei NIVEDIBQ1 strain isolated from clinical case of black quarter was analyzed. Sequence analysis indicated that genome had 2653 predicted coding DNA sequences, harbored numerous genes, mobile genetic elements for pathogenesis, and virulence factors. Computational analysis revealed that strain contained 30 virulence-associated genes. An intact genomic region highly similar to the Clostridium phage was present in the genome. Presence of CRISPR systems and the transposon components likely contribute to the genome plasticity. Strain encode diverse spectrum of degradative carbohydrate-active enzymes (CAZymes). Comparative SNP analysis revealed that the genomes of the C. chauvoei strains analyzed were highly conserved. Phylogenetic analysis of strains and available genome (n = 21) based on whole-genome multi-locus sequence typing (wgMLST) and core orthologous genes showed the clustering of strains into two different clusters suggesting geographical links.

Multilayered control of splicing regulatory networks by DAP3 leads to widespread alternative splicing changes in cancer

The dynamic regulation of alternative splicing requires coordinated participation of multiple RNA binding proteins (RBPs). Aberrant splicing caused by dysregulation of splicing regulatory RBPs is implicated in numerous cancers. Here, we reveal a frequently overexpressed cancer-associated protein, DAP3, as a splicing regulatory RBP in cancer. Mechanistically, DAP3 coordinates splicing regulatory networks, not only via mediating the formation of ribonucleoprotein complexes to induce substrate-specific splicing changes, but also via modulating splicing of numerous splicing factors to cause indirect effect on splicing. A pan-cancer analysis of alternative splicing across 33 TCGA cancer types identified DAP3-modulated mis-splicing events in multiple cancers, and some of which predict poor prognosis. Functional investigation of non-productive splicing of WSB1 provides evidence for establishing a causal relationship between DAP3-modulated mis-splicing and tumorigenesis. Together, our work provides critical mechanistic insights into the splicing regulatory roles of DAP3 in cancer development.

RNA binding proteins (RBPs) can participate in regulatory networks to control alternative splicing. Here the authors show that DAP3 functions as an RBP splicing modulator via two mechanisms, and that its overexpression leads to mis-splicing events in cancers.

Elucidating the functional role of heat stress transcription factor A6b (TaHsfA6b) in linking heat stress response and the unfolded protein response in wheat

TaHsfA6b-4D relocalizes intracellularly upon heat stress and play a significant role in linking the heat stress response to unfolded-protein response so as to maintain cellular homeostasis. Heat stress transcription factors (Hsfs) play a crucial role in protecting the plants against heat stress (HS). In case of wheat, TaHsfA6b-4D (earlier known as TaHsfA2d) has been identified as a seed preferential transcription factor and its role has been shown in various abiotic stresses such as heat, salt and drought stress. In the present study, a homeologue of TaHsfA6b gene (TaHsfA6b-4A) was identified and was found to be transcriptionally inactive but it localized to the nucleus. Interestingly, TaHsfA6b-4D localized to the endoplasmic reticulum-Golgi complex and peroxisomes under non-stress conditions, but was observed to accumulate in the nucleus upon HS. The expression of TaHsfA6b-4D was upregulated by dithiothreitol (DTT), which is a known ER stress inducer. Consistent with this, Arabidopsis transgenic plants overexpressing TaHsfA6b-4D performed better on DTT containing media, which further corroborated with the increased expression of ER stress marker genes in these transgenic plants in comparison to the wild type plants. Thus, these studies together suggest that TaHsfA6b-4D may relocalize intracellularly upon heat stress and may play a significant role in linking the unfolded-protein response with heat stress response so as to maintain protein homeostasis inside the cell under heat stress.

Genetic characterization of flowering and phytochrome genes in peanut (Arachis hypogaea L.) for early maturity

BACKGROUND

Peanut (Arachis hypogaea L.) production and cropping pattern is highly influenced by the climatic factors including temperature and rain pattern fluctuations. It is one of the most important cash crop in the rain fed areas of Pakistan and its production, under changing climatic conditions, that can be improved by developing short duration varieties. The present study was based on the molecular characterization of the maturity associated gene families in the peanut under two light conditions.

METHODS AND RESULTS

Genomic analysis based on the in silico study of important gene families for early maturity associated attributes like flowering time, their pattern, duration and photoperiodism was done for a comprehensive mapping of maturity related genes. Phytochromes genes Phy A, Phy B and Phy E and flowering genes FT2a, Ft5a and COL2 were selected for in silico characterization for protein based analysis including Multiple Sequence Alignment (MSA), and Neighbor Joining (NJ) tree. MSA and NJ trees of the peanut with Arabidopsis thaliana and Glycine max showed a clear picture of the phylogenetic relationship on the basis of selected gene proteins. Expression profile of phytochrome and flowering genes revealed that photoperiod conditions i.e. short and long days, have great influence on the Phy A, Phy B and Phy E, Ft2a, FT5a and COL2 gene expression pattern. In current study, the relative expression of all studied genes was found higher in short day light condition at flower initiation stage of the plants than in the long light day condition with exception of COL2 gene protein.

CONCLUSIONS

The molecular characterization based on the in silico study of the particular genes and qPCR based gene expression profiling of the selected genes provided an evidence of the role of these genes and their comparative analysis under two photoperiodic conditions.

Unfolding molecular switches in plant heat stress resistance: A comprehensive review

Plant heat stress response is a multi-factorial trait that is precisely regulated by the complex web of transcription factors from various families that modulate heat stress responsive gene expression. Global warming due to climate change affects plant growth and development throughout its life cycle. Adds to this, the frequent occurrence of heat waves is drastically reducing the global crop yield. Molecular plant scientists can help crop breeders by providing genetic markers associated with stress resistance. Plant heat stress response (HSR), however, is a multi-factorial trait and using a single stress resistance trait might not be ideal to develop thermotolerant crops. Transcription factors participate in regulation of plant biological processes and environmental stress responses. Recent studies have revealed that plant HSR is precisely regulated by the complex web of transcription factors from various families. These transcription factors enhance plant heat stress tolerance by regulating the expression level of several stress-responsive genes independently or in cross talk with different other transcription factors. This review explores how signaling pathways triggered by heat stress are regulated by multiple transcription factor families. To our knowledge, we for the first time analyze the role of major transcription factor families in plant HSR along with their regulatory mechanisms. In the end, we will also discuss the potential of emerging technologies to improve thermotolerance in plants.

Genome-wide identification of Tomato Golden 2-Like transcription factors and abiotic stress related members screening

BACKGROUND

Golden 2-Like (G2-like) transcription factors play an important role in plant development. However, the roles of these G2-like regulatory genes in response to abiotic stresses in tomato are not well understood.

RESULTS

In this study, we identified 66 putative G2-like genes in tomato (Solanum lycopersicum) and classified them into 5 groups (I to V) according to gene structure, motif composition and phylogenetic analysis. The G2-like genes were unevenly distributed across all 12 chromosomes. There were nine pairs of duplicated gene segments and four tandem duplicated SlGlk genes. Analysis of the cis-regulatory elements (CREs) showed that the promoter regions of SlGlks contain many kinds of stress- and hormone-related CREs. Based on RNA-seq, SlGlks were expressed in response to three abiotic stresses. Thirty-six differentially expressed SlGlks were identified; these genes have multiple functions according to Gene Ontology (GO) analysis and are enriched mainly in the zeatin biosynthesis pathway. Further studies exhibited that silencing SlGlk16 in tomato would reduce drought stress tolerance by earlier wilted, lower superoxide dismutase (SOD), peroxidase (POD) activities, less Pro contents and more MDA contents.

CONCLUSIONS

Overall, the results of this study provide comprehensive information on G2-like transcription factors and G2-like genes that may be expressed in response to abiotic stresses.

Genome-wide identification and expression analysis of the cucumber PYL gene family

Abscisic acid (ABA) is a very important hormone in plants. It regulates growth and development of plants and plays an important role in biotic and abiotic stresses. The Pyrabactin resistance 1-like (PYR/PYL) proteins play a central role in ABA signal transduction pathways. The working system of PYL genes in cucumber, an important economical vegetable (Cucumis sativus L.), has not been fully studied yet. Through bioinformatics, a total of 14 individual PYL genes were identified in Chinese long '9930' cucumber. Fourteen PYL genes were distributed on six chromosomes of cucumber, and their encoded proteins predicted to be distributed in cytoplasm and nucleus. Based on the phylogenetic analysis, the PYL genes of cucumber, Arabidopsis, rice, apple, Brachypodium distachyon and soybeancould be classified into three groups. Genetic structures and conserved domains analysis revealed that CsPYL genes in the same group have similar exons and conserved domains. By predicting cis-elements in the promoters, we found that all CsPYL members contained hormone and stress-related elements. Additionally, the expression patterns of CsPYL genes were specific in tissues. Finally, we further examined the expression of 14 CsPYL genes under ABA, PEG, salt stress. The qRT-PCR results showed that most PYL gene expression levels were up-regulated. Furthermore, with different treatments about 3h, the relative expression of PYL8 was up-regulated and more than 20 times higher than 0h. It indicated that this gene may play an important role in abiotic stress.

Compositional and toxicological investigation of pooled venom from farm-raised Naja atra

Background:

Naja atra is a venomous snake species medically relevant in China. In the current study, we evaluated the composition and toxicological profile of venom collected from farm-raised N. atra.

Methods:

Venom was collected from third-generation captive bred N. atra on a snake farm in Hunan Province, China. The venom was analyzed using sodium dodecyl sulfate polyacrylamide gel electrophoresis and nano-liquid chromatography with electrospray ionization tandem mass spectrometry. In addition, hemolytic activity, median lethal dose, serum biochemical and histopathological parameters were accessed.

Results:

N. atra venom proteome was dominated by phospholipase A₂ (46.5%) and three-finger toxins (41.4 %), and a set of common low relative abundance proteins, including cysteine-rich secretory proteins (4.7%), NGF-beta (2.4%), snake venom metalloproteinase (1.5%), glutathione peroxidase (0.6%), vespryn (0.3%), and 5ʹ-nucleotidases (0.2%) were also found. Furthermore, the venom exhibited direct hemolytic activity, neurotoxicity, myotoxicity, and high lethal potency in mice, with a subcutaneous median lethal dose of 1.02 mg/kg. Histopathological analysis and serum biochemical tests revealed that venom caused acute hepatic, pulmonary and renal injury in mice.

Conclusion:

This study revealed the composition and toxicity of venom collected from farm-raised N. atra, thereby providing a reference for the analysis of venom samples collected from captive-born venomous snakes in the future.

New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean

BACKGROUND

SPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes.

RESULTS

We analyzed SPX gene family evolution in legumes and in a number of key species from algae to angiosperms. We found that SPX harboring proteins showed fluctuations in domain fusions from algae to the angiosperms with, finally, four classes appearing and being retained in the land plants. Despite these fluctuations, Lysine Surface Cluster (KSC), and the third residue of Phosphate Binding Sites (PBS) showed complete conservation in almost all of SPXs except few proteins in Selaginella moellendorffii and Papaver sumniferum, suggesting they might have different ligand preferences. In addition, we found that the WGD/segmentally or dispersed duplication types were the most frequent contributors to the SPX expansion, and that there is a positive correlation between the amount of WGD contribution to the SPX expansion in individual species and its number of EXS genes. We could also reveal that except SPX class genes, other classes lost the collinearity relationships among Arabidopsis and legume genomes. The sub- or neo-functionalization of the duplicated genes in the legumes makes it difficult to find the functional orthologous genes. Therefore, we used two different methods to identify functional orthologs in soybean and Medicago. High variance in the dynamic and spatial expression pattern of GmSPXs proved the new or sub-functionalization in the paralogs.

CONCLUSION

This comprehensive analysis revealed how SPX gene family evolved from algae to legumes and also discovered several new domains fused to SPX domain in algae. In addition, we hypothesized that there different phosphate sensing mechanisms might occur in S. moellendorffii and P. sumniferum. Finally, we predicted putative functional orthologs of AtSPXs in the legumes, especially, orthologs of AtPHO1, involved in long-distance Pi transportation. These findings help to understand evolution of phosphate signaling and might underpin development of new legume varieties with improved phosphate use efficiency.

Transcriptome and metabolome analysis to reveal major genes of saikosaponin biosynthesis in Bupleurum chinense

BACKGROUND

Bupleurum chinense DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of B. chinense, but relatively little is known about saikosaponin biosynthesis. In the present study, we performed an integrated analysis of metabolic composition and the expressed genes involved in saikosaponin biosynthetic pathways among four organs (the root, flower, stem, and leaf) of B. chinense to discover the genes related to the saikosaponin biosynthetic pathway.

RESULTS

Transcript and metabolite profiles were generated through high-throughput RNA-sequencing (RNA-seq) data analysis and liquid chromatography tandem mass spectrometry, respectively. Evaluation of saikosaponin contents and transcriptional changes showed 152 strong correlations (P < 0.05) over 3 compounds and 77 unigenes. These unigenes belonged to eight gene families: the acetoacetyl CoA transferase (AACT) (6), HMG-CoA synthase (HMGS) (2), HMG-CoA reductase (HMGR) (2), mevalonate diphosphate decarboxylase (MVD) (1), 1-deoxy-D-xylulose-5-phosphate synthase (DXS) (3), farnesyl diphosphate synthase (FPPS) (11), β-amyrin synthase (β-AS) (13) and cytochrome P450 enzymes (P450s) (39) families.

CONCLUSIONS

Our results investigated the diversity of the saikosaponin triterpene biosynthetic pathway in the roots, stems, leaves and flowers of B. chinese by integrated transcriptomic and metabolomic analysis, implying that manipulation of P450s genes such as Bc95697 and Bc35434 might improve saikosaponin biosynthesis. This is a good candidate for the genetic improvement of this important medicinal plant.

Viper venoms drive the macrophages and hepatocytes to sequester and clear platelets: novel mechanism and therapeutic strategy for venom-induced thrombocytopenia

Venomous snakebites cause clinical manifestations that range from local to systemic and are considered a significant global health challenge. Persistent or refractory thrombocytopenia has been frequently reported in snakebite patients, especially in cases caused by viperidae snakes. Viper envenomation-induced thrombocytopenia may persist in the absence of significant consumption coagulopathy even after the antivenom treatment, yet the mechanism remains largely unknown. Our study aims to investigate the mechanism and discover novel therapeutic targets for coagulopathy-independent thrombocytopenia caused by viper envenomation. Here we found that patients bitten by Protobothrops mucrosquamatus and Trimeresurus stejnegeri, rather than Naja. atra may develop antivenom-resistant and coagulopathy-independent thrombocytopenia. Crude venoms and the derived C-type lectin-like proteins from these vipers significantly increased platelet surface expression of neuraminidase and platelet desialylation, therefore led to platelet ingestion by both macrophages and hepatocytes in vitro, and drastically decreased peripheral platelet counts in vivo. Our study is the first to demonstrate that desialylation-mediated platelet clearance is a novel mechanism of viper envenomation-induced refractory thrombocytopenia and C-type lectin-like proteins derived from the viper venoms contribute to snake venom-induced thrombocytopenia. The results of this study suggest the inhibition of platelet desialylation as a novel therapeutic strategy against viper venom-induced refractory thrombocytopenia.

Identification of suitable reference genes for expression profiling studies using qRT-PCR in an important insect pest, Maruca vitrata

BACKGROUND

Maruca vitrata is one of the potential insect pests that cause devastating losses to legume cultivation worldwide. Gene functional studies facilitate dissecting the molecular mechanisms underlying the infection process and enable devising appropriate molecular strategies to control this insect pest. Expression profiling using quantitative real-time PCR (qRT-PCR) provides insights into the functional characterization of target genes; however, ideal reference genes should be deployed in such studies to nullify the background variation and improve the accuracy of target gene expression. An ideal reference gene should have a stable expression across developmental stages, biological conditions, tissues, or experimental conditions.

METHODS AND RESULTS

Given this, the stability of eight candidate reference genes was evaluated in M. vitrata at different developmental stages, diets, and sexes by qRT-PCR method, and the data was analyzed using four independent algorithms, namely GeNorm, NormFinder, BestKeeper, and ΔCt, and one comprehensive algorithm, RefFinder.

CONCLUSION

The analysis showed that RP49 and RPL13 were the best suitable reference genes for studying target gene expression at different developmental stages. Further, the study identified RP49 and RPL24, and GAPDH and RPL24 as the ideal reference genes in M. vitrata fed with different diets and sexes, respectively. The reference genes reported in the present study will ensure the accuracy of target gene expression, and thus, will serve as an important resource for gene functional studies in M. vitrata.

Elucidating the Venom Diversity in Sri Lankan Spectacled Cobra (Naja naja) through De Novo Venom Gland Transcriptomics, Venom Proteomics and Toxicity Neutralization

Inadequate effectiveness of Indian antivenoms in treating envenomation caused by the Spectacled Cobra/Indian Cobra (Naja naja) in Sri Lanka has been attributed to geographical variations in the venom composition. This study investigated the de novo venom-gland transcriptomics and venom proteomics of the Sri Lankan N. naja (NN-SL) to elucidate its toxin gene diversity and venom variability. The neutralization efficacy of a commonly used Indian antivenom product in Sri Lanka was examined against the lethality induced by NN-SL venom in mice. The transcriptomic study revealed high expression of 22 toxin genes families in NN-SL, constituting 46.55% of total transcript abundance. Three-finger toxins (3FTX) were the most diversely and abundantly expressed (87.54% of toxin gene expression), consistent with the dominance of 3FTX in the venom proteome (72.19% of total venom proteins). The 3FTX were predominantly S-type cytotoxins/cardiotoxins (CTX) and α-neurotoxins of long-chain or short-chain subtypes (α-NTX). CTX and α-NTX are implicated in local tissue necrosis and fatal neuromuscular paralysis, respectively, in envenomation caused by NN-SL. Intra-species variations in the toxin gene sequences and expression levels were apparent between NN-SL and other geographical specimens of N. naja, suggesting potential antigenic diversity that impacts antivenom effectiveness. This was demonstrated by limited potency (0.74 mg venom/ml antivenom) of the Indian polyvalent antivenom (VPAV) in neutralizing the NN-SL venom. A pan-regional antivenom with improved efficacy to treat N. naja envenomation is needed.

Venom-gland transcriptomic, venomic, and antivenomic profiles of the spine-bellied sea snake (Hydrophis curtus) from the South China Sea

Background

A comprehensive evaluation of the -omic profiles of venom is important for understanding the potential function and evolution of snake venom. Here, we conducted an integrated multi-omics-analysis to unveil the venom-transcriptomic and venomic profiles in a same group of spine-bellied sea snakes (Hydrophis curtus) from the South China Sea, where the snake is a widespread species and might generate regionally-specific venom potentially harmful to human activities. The capacity of two heterologous antivenoms to immunocapture the H. curtus venom was determined for an in-depth evaluation of their rationality in treatment of H. curtus envenomation. In addition, a phylogenetic analysis by maximum likelihood was used to detect the adaptive molecular evolution of full-length toxin-coding unigenes.

Results

A total of 90,909,384 pairs of clean reads were generated via Illumina sequencing from a pooled cDNA library of six specimens, and yielding 148,121 unigenes through de novo assembly. Sequence similarity searching harvested 63,845 valid annotations, including 63,789 non-toxin-coding and 56 toxin-coding unigenes belonging to 22 protein families. Three protein families, three-finger toxins (3-FTx), phospholipase A₂ (PLA₂), and cysteine-rich secretory protein, were detected in the venom proteome. 3-FTx (27.15% in the transcriptome/41.94% in the proteome) and PLA₂ (59.71%/49.36%) were identified as the most abundant families in the venom-gland transcriptome and venom proteome. In addition, 24 unigenes from 11 protein families were shown to have experienced positive selection in their evolutionary history, whereas four were relatively conserved throughout evolution. Commercial Naja atra antivenom exhibited a stronger capacity than Bungarus multicinctus antivenom to immunocapture H. curtus venom components, especially short neurotoxins, with the capacity of both antivenoms to immunocapture short neurotoxins being weaker than that for PLA₂s.

Conclusions

Our study clarified the venom-gland transcriptomic and venomic profiles along with the within-group divergence of a H. curtus population from the South China Sea. Adaptive evolution of most venom components driven by natural selection appeared to occur rapidly during evolutionary history. Notably, the utility of commercial N. atra and B. multicinctus antivenoms against H. curtus toxins was not comprehensive; thus, the development of species-specific antivenom is urgently needed.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07824-7.

Transposon sequencing analysis of Bradyrhizobium diazoefficiens 110spc4

Bradyrhizobium diazoefficiens USDA110 is one of the most effective nitrogen-fixing symbionts of soybeans. Here we carried out a large-scale transposon insertion sequencing (Tn-seq) analysis of strain Bd110spc4, which is derived from USDA110, with the goal of increasing available resources for identifying genes crucial for the survival of this plant symbiont under diverse conditions. We prepared two transposon (Tn) insertion libraries of Bd110spc4 with 155,042 unique Tn insertions when the libraries were combined, which is an average of one insertion every 58.7 bp of the reference USDA110 genome. Application of bioinformatic filtering steps to remove genes too small to be expected to have Tn insertions, resulted in a list of genes that were classified as putatively essential. Comparison of this gene set with genes putatively essential for the growth of the closely related alpha-proteobacterium, Rhodopseudomonas palustris, revealed a small set of five genes that may be collectively essential for closely related members of the family Bradyrhizobiaceae. This group includes bacteria with diverse lifestyles ranging from plant symbionts to animal-associated species to free-living species.

Genome wide analysis of kinesin gene family in Citrullus lanatus reveals an essential role in early fruit development

BACKGROUND

Kinesin (KIN) as a motor protein is a versatile nano-machine and involved in diverse essential processes in plant growth and development. However, the kinesin gene family has not been identified in watermelon, a valued and nutritious fruit, and yet their functions have not been characterized. Especially, their involvement in early fruit development, which directly determines the size, shape, yield and quality of the watermelon fruit, remains unclear.

RESULTS

In this study, we performed a whole-genome investigation and comprehensive analysis of kinesin genes in C. lanatus. In total, 48 kinesins were identified and categorized into 10 kinesin subfamilies groups based on phylogenetic analysis. Their uneven distribution on 11 chromosomes was revealed by distribution analysis. Conserved motif analysis showed that the ATP-binding motif of kinesins was conserved within all subfamilies, but not the microtubule-binding motif. 10 segmental duplication pairs genes were detected by the syntenic and phylogenetic approaches, which showed the expansion of the kinesin gene family in C. lanatus genome during evolution. Moreover, 5 ClKINs genes are specifically and abundantly expressed in early fruit developmental stages according to comprehensive expression profile analysis, implying their critical regulatory roles during early fruit development. Our data also demonstrated that the majority of kinesin genes were responsive to plant hormones, revealing their potential involvement in the signaling pathways of plant hormones.

CONCLUSIONS

Kinesin gene family in watermelon was comprehensively analyzed in this study, which establishes a foundation for further functional investigation of C. lanatus kinesin genes and provides novel insights into their biological functions. In addition, these results also provide useful information for understanding the relationship between plant hormone and kinesin genes in C. lanatus.

Character changes and Transcriptomic analysis of a cassava sexual Tetraploid

BACKGROUND

Cassava (Manihot esculenta Crantz) is an important food crop known for its high starch content. Polyploid breeding is effective in its genetic improvement, and use of 2n gametes in sexual polyploid breeding is one of the potential methods for cassava breeding and improvement. In our study, the cassava sexual tetraploid (ST), which carries numerous valuable traits, was successfully generated by hybridizing 2n female gametes SC5 (♀) and 2n male gametes SC10 (♂). However, the molecular mechanisms remain unclear. To understand these underlying molecular mechanisms behind the phenotypic alterations and heterosis in ST plants, we investigated the differences in gene expression between polyploids and diploids by determining the transcriptomes of the ST plant and its parents during the tuber root enlargement period. We also compared the characters and transcriptomes of the ST plant with its parents.

RESULTS

The ST plant was superior in plant height, stem diameter, leaf area, petiole length, plant weight, and root weight than the parent plants, except the leaf number, which was lower. The number of starch granules was higher in the roots of ST plants than those in the parent plants after five months (tuber root enlargement period), which could be due to a higher leaf net photosynthetic rate leading to early filling of starch granules. Based on transcriptome analysis, we identified 2934 and 3171 differentially expressed genes (DEGs) in the ST plant as compared to its female and male parents, respectively. Pathway enrichment analyses revealed that flavonoid biosynthesis and glycolysis/gluconeogenesis were significantly enriched in the ST plants, which might contribute to the colors of petiole (purple-red), root epidermis (dark brown), and tuber starch accumulation, respectively.

CONCLUSIONS

After sexual polyploidization, the phenotype of ST has changed significantly in comparison to their diploid parents, mainly manifest as enlarged biomass, yield, early starch filling, deep colored petiole and root epidermis. The tetraploid plants were also mature early due to early starch grain filling. Owing to enriched flavonoid biosynthesis and glycolysis/gluconeogenesis, they are possibly resistant to adversity stresses and provide better yield, respectively.

Genome-wide analysis and functional characterization of the Dof transcription factor family in rice (Oryza sativa L.)

Exhaustive searches of the rice genome have revealed 30 different potential OsDof (Oryza sativa DNA binding with One Finger) genes. Their subcellular localization, phylogenetic relationship, conserved motifs identification, chromosomal allocation, expression patterns, and interaction networks were analyzed. The Dof (DNA binding with One Finger) family of transcription factors represents a particular class of plant-specific transcriptional regulators, contain a highly conserved region of 50-52 amino acids (Dof domain) and involved in various plant developmental processes and response to various environmental stresses. Few (Oryza sativa) OsDof genes have been demonstrated previously for their biological functions but there is no comprehensive study on most of the Dof genes of rice. In the current study, exhaustive searches of the rice genome revealed 30 different potential OsDof genes, and then their subcellular localization, phylogenetic relationship, conserved motifs identification, chromosomal allocation, expression patterns, and interaction networks were analyzed. Phylogenetic analysis of Dof proteins in rice showed that they are distributed in 4 groups. By genome-wide observation of gene expression profiles, we found that OsDof genes showed significant variances in expression levels in different tissues across multiple developmental stages. Protein-protein correlation network analysis, shows a statically significant overlap of some OsDofs, suggesting their similar functions and a high degree of co-expression. The Dof family transcription factors have been reported for their involvement in the regulation of various gene expression processes in rice but still, most of the Dof genes are not characterized for their specific physiological functions. This study revealed useful information and clues about predicting the potential roles of OsDofs in rice by combining their genome-wide characterization, expression profiling, protein-protein interactions, and for further studies to develop high-quality rice varieties.

Genome survey and high-resolution genetic map provide valuable genetic resources for Fenneropenaeus chinensis

Fenneropenaeus chinensis is one of the most important aquaculture species in China. Research on its genomic and genetic structure not only helps us comprehend the genetic basis of complex economic traits, but also offers theoretical guidance in selective breeding. In the present study, a genome survey sequencing was performed to generate a rough reference genome utilized for groping preliminary genome characteristics and facilitate linkage and quantitative trait locus (QTL) mapping. Linkage mapping was conducted using a reduced-representation sequencing method 2b-RAD. In total, 36,762 SNPs were genotyped from 273 progenies in a mapping family, and a high-resolution linkage map was constructed. The consensus map contained 12,884 markers and spanned 5257.81 cM with an average marker interval of 0.41 cM, which was the first high-resolution genetic map in F. chinensis to our knowledge. QTL mapping and association analysis were carried out in 29 characters including body size, sex and disease resistance. 87 significant QTLs were detected in several traits and they were also evaluated by association analysis. Results of this study provide us valuable suggestions in genetic improvement and breeding of new varieties and also lay a basic foundation for further application of cloning of economic genes in selective breeding program and marker-assisted selection.

Multiple lines of evidence reveal a new species of Krait (Squamata, Elapidae, Bungarus) from Southwestern China and Northern Myanmar

Kraits of the genus Bungarus Daudin 1803 are widely known venomous snakes distributed from Iran to China and Indonesia. Here, we use a combination of mitochondrial DNA sequence data and morphological data to describe a new species from Yingjiang County, Yunnan Province, China: Bungarussuzhenaesp. nov. Phylogenetically, this species forms a monophyletic lineage sister to the Bungaruscandidus/multicinctus/wanghaotingi complex based on cyt b and ND4 genes but forms a sister species pair with the species B.magnimaculatus Wall & Evans, 1901 based on COI gene fragments. Morphologically, B.suzhenaesp. nov. is similar to the B.candidus/multicinctus/wanghaotingi complex but differs from these taxa by a combination of dental morphology, squamation, coloration pattern, as well as hemipenial morphology. A detailed description of the cranial osteology of the new species is given based on micro-CT tomography images. We revised the morphological characters of B.candidus/multicinctus/wanghaotingi complex and verified the validity of three species in this complex. The distribution of these species was revised; the records of B.candidus in China should be attributed to B.wanghaotingi. We also provide an updated key to species of Bungarus.