scholarly journals Conotoxin Diversity in the Venom Gland Transcriptome of the Magician’s Cone, Pionoconus magus

Marine Drugs ◽  
2019 ◽  
Vol 17 (10) ◽  
pp. 553 ◽  
Author(s):  
Pardos-Blas ◽  
Irisarri ◽  
Abalde ◽  
Tenorio ◽  
Zardoya
Keyword(s):  
Atlantic Ocean ◽  
Differential Expression ◽  
Venom Gland ◽  
The Philippines ◽  
Rna Seq ◽  
Additional Specimen ◽  
Signal Region ◽  
Venom Glands ◽  
Total Diversity

The transcriptomes of the venom glands of two individuals of the magician’s cone, Pionoconus magus, from Okinawa (Japan) were sequenced, assembled, and annotated. In addition, RNA-seq raw reads available at the SRA database from one additional specimen of P. magus from the Philippines were also assembled and annotated. The total numbers of identified conotoxin precursors and hormones per specimen were 118, 112, and 93. The three individuals shared only five identical sequences whereas the two specimens from Okinawa had 30 sequences in common. The total number of distinct conotoxin precursors and hormones for P. magus was 275, and were assigned to 53 conotoxin precursor and hormone superfamilies, two of which were new based on their divergent signal region. The superfamilies that had the highest number of precursors were M (42), O1 (34), T (27), A (18), O2 (17), and F (13), accounting for 55% of the total diversity. The D superfamily, previously thought to be exclusive of vermivorous cones was found in P. magus and contained a highly divergent mature region. Similarly, the A superfamily alpha 4/3 was found in P. magus despite the fact that it was previously postulated to be almost exclusive of the genus Rhombiconus. Differential expression analyses of P. magus compared to Chelyconus ermineus, the only fish-hunting cone from the Atlantic Ocean revealed that M and A2 superfamilies appeared to be more expressed in the former whereas the O2 superfamily was more expressed in the latter.

scholarly journals Dissecting Toxicity: The Venom Gland Transcriptome and the Venom Proteome of the Highly Venomous Scorpion Centruroides limpidus (Karsch, 1879)

Toxins ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 247 ◽  
Author(s):  
Jimena I. Cid-Uribe ◽  
Erika P. Meneses ◽  
Cesar V. F. Batista ◽  
Ernesto Ortiz ◽  
Lourival D. Possani
Keyword(s):  
Ion Channel ◽  
High Throughput Sequencing ◽  
Venom Gland ◽  
K Channel ◽  
Rna Seq ◽  
Illumina Platform ◽  
Host Defense Peptides ◽  
Venom Glands ◽  
Mass Spectometry ◽  
First Time

Venom glands and soluble venom from the Mexican scorpion Centruroides limpidus (Karsch, 1879) were used for transcriptomic and proteomic analyses, respectively. An RNA-seq was performed by high-throughput sequencing with the Illumina platform. Approximately 80 million reads were obtained and assembled into 198,662 putative transcripts, of which 11,058 were annotated by similarity to sequences from available databases. A total of 192 venom-related sequences were identified, including Na+ and K+ channel-acting toxins, enzymes, host defense peptides, and other venom components. The most diverse transcripts were those potentially coding for ion channel-acting toxins, mainly those active on Na+ channels (NaScTx). Sequences corresponding to β- scorpion toxins active of K+ channels (KScTx) and λ-KScTx are here reported for the first time for a scorpion of the genus Centruroides. Mass fingerprint corroborated that NaScTx are the most abundant components in this venom. Liquid chromatography coupled to mass spectometry (LC-MS/MS) allowed the identification of 46 peptides matching sequences encoded in the transcriptome, confirming their expression in the venom. This study corroborates that, in the venom of toxic buthid scorpions, the more abundant and diverse components are ion channel-acting toxins, mainly NaScTx, while they lack the HDP diversity previously demonstrated for the non-buthid scorpions. The highly abundant and diverse antareases explain the pancreatitis observed after envenomation by this species.

scholarly journals Proteomics and Deep Sequencing Comparison of Seasonally Active Venom Glands in the Platypus Reveals Novel Venom Peptides and Distinct Expression Profiles

2012 ◽  
Vol 11 (11) ◽  
pp. 1354-1364 ◽  
Author(s):  
Emily S. W. Wong ◽  
David Morgenstern ◽  
Ehtesham Mofiz ◽  
Sara Gombert ◽  
Katrina M. Morris ◽  
...  
Keyword(s):  
Breeding Season ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Venom Gland ◽  
Rna Seq ◽  
Growth Differentiation Factor 15 ◽  
Stress Response Pathway ◽  
Venom Glands ◽  
Venom Evolution ◽  
Venom Proteins

The platypus is a venomous monotreme. Male platypuses possess a spur on their hind legs that is connected to glands in the pelvic region. They produce venom only during the breeding season, presumably to fight off conspecifics. We have taken advantage of this unique seasonal production of venom to compare the transcriptomes of in- and out-of-season venom glands, in conjunction with proteomic analysis, to identify previously undiscovered venom genes. Comparison of the venom glands revealed distinct gene expression profiles that are consistent with changes in venom gland morphology and venom volumes in and out of the breeding season. Venom proteins were identified through shot-gun sequenced venom proteomes of three animals using RNA-seq-derived transcripts for peptide-spectral matching. 5,157 genes were expressed in the venom glands, 1,821 genes were up-regulated in the in-season gland, and 10 proteins were identified in the venom. New classes of platypus-venom proteins identified included antimicrobials, amide oxidase, serpin protease inhibitor, proteins associated with the mammalian stress response pathway, cytokines, and other immune molecules. Five putative toxins have only been identified in platypus venom: growth differentiation factor 15, nucleobindin-2, CD55, a CXC-chemokine, and corticotropin-releasing factor-binding protein. These novel venom proteins have potential biomedical and therapeutic applications and provide insights into venom evolution.

scholarly journals Best practices on the differential expression analysis of multi-species RNA-seq

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Matthew Chung ◽  
Vincent M. Bruno ◽  
David A. Rasko ◽  
Christina A. Cuomo ◽  
José F. Muñoz ◽  
...  
Keyword(s):  
Best Practices ◽  
Differential Expression ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Single Species ◽  
Rna Seq ◽  
Species Analysis ◽  
Differential Gene ◽  
Multiple Species ◽  
Downstream Analysis

AbstractAdvances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.

scholarly journals High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Weitong Cui ◽  
Huaru Xue ◽  
Lei Wei ◽  
Jinghua Jin ◽  
Xuewen Tian ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Small Sample ◽  
Differentially Expressed ◽  
Cancer Type ◽  
Rna Seq ◽  
Sample Sizes ◽  
Large Sample ◽  
Expression Levels ◽  
Gene Expression Levels

Abstract Background RNA sequencing (RNA-Seq) has been widely applied in oncology for monitoring transcriptome changes. However, the emerging problem that high variation of gene expression levels caused by tumor heterogeneity may affect the reproducibility of differential expression (DE) results has rarely been studied. Here, we investigated the reproducibility of DE results for any given number of biological replicates between 3 and 24 and explored why a great many differentially expressed genes (DEGs) were not reproducible. Results Our findings demonstrate that poor reproducibility of DE results exists not only for small sample sizes, but also for relatively large sample sizes. Quite a few of the DEGs detected are specific to the samples in use, rather than genuinely differentially expressed under different conditions. Poor reproducibility of DE results is mainly caused by high variation of gene expression levels for the same gene in different samples. Even though biological variation may account for much of the high variation of gene expression levels, the effect of outlier count data also needs to be treated seriously, as outlier data severely interfere with DE analysis. Conclusions High heterogeneity exists not only in tumor tissue samples of each cancer type studied, but also in normal samples. High heterogeneity leads to poor reproducibility of DEGs, undermining generalization of differential expression results. Therefore, it is necessary to use large sample sizes (at least 10 if possible) in RNA-Seq experimental designs to reduce the impact of biological variability and DE results should be interpreted cautiously unless soundly validated.

scholarly journals How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

RNA ◽  
2016 ◽  
Vol 22 (6) ◽  
pp. 839-851 ◽  
Author(s):  
Nicholas J. Schurch ◽  
Pietá Schofield ◽  
Marek Gierliński ◽  
Christian Cole ◽  
Alexander Sherstnev ◽  
...  
Keyword(s):  
Differential Expression ◽  
Rna Seq

Venom gland morphology in Pepsis pallidolimbata pallidolimbata and biological use and activity of Pepsis venom

1997 ◽  
Vol 75 (7) ◽  
pp. 1014-1019 ◽  
Author(s):  
E. Schoeters ◽  
J. Billen ◽  
J. O. Schmidt
Keyword(s):  
Venom Gland ◽  
Social Wasps ◽  
Morphological Organization ◽  
The Social ◽  
The Family ◽  
Venom Glands ◽  
Glandular Structures ◽  
Sibling Family

Spider wasps, i.e., the family Pompilidae, in general, and those belonging to the genus Pepsis in particular, are acknowledged to possess venoms that are algogenic to humans and thus have the parsimonious functions of causing paralysis and providing defense against predators. The morphological organization of the venom system and its complex convoluted gland closely resembles that in social members of the Vespidae. These features distinguish the venom glands of the Pompilidae from those of the sibling family Mutillidae as well as those of the family Sphecidae, which lack convoluted glands. Although the venom glands in Pepsis species are very similar in morphology to those of social vespids, the lethality of Pepsis venom to mammals is several times less than that of the social common wasps. These findings suggest that in terms of the evolution of venom activity and the associated glandular structures, there was apparently no need for social wasps to develop extra parts of the venom system for producing toxic, lethal, or powerful algogenic components. All of the glandular parts of the venom gland of social wasps were already present in pompilids (and eumenids) and, presumably, in their ancestors.

scholarly journals The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Xueyi Dong ◽  
Luyi Tian ◽  
Quentin Gouil ◽  
Hasaru Kariyawasam ◽  
Shian Su ◽  
...  
Keyword(s):  
Differential Expression ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Transcriptomic Analysis ◽  
Statistical Testing ◽  
Rna Seq ◽  
Sequencing Data ◽  
Short Read ◽  
Sequencing Platform ◽  
Long Read

Abstract Application of Oxford Nanopore Technologies’ long-read sequencing platform to transcriptomic analysis is increasing in popularity. However, such analysis can be challenging due to the high sequence error and small library sizes, which decreases quantification accuracy and reduces power for statistical testing. Here, we report the analysis of two nanopore RNA-seq datasets with the goal of obtaining gene- and isoform-level differential expression information. A dataset of synthetic, spliced, spike-in RNAs (‘sequins’) as well as a mouse neural stem cell dataset from samples with a null mutation of the epigenetic regulator Smchd1 was analysed using a mix of long-read specific tools for preprocessing together with established short-read RNA-seq methods for downstream analysis. We used limma-voom to perform differential gene expression analysis, and the novel FLAMES pipeline to perform isoform identification and quantification, followed by DRIMSeq and limma-diffSplice (with stageR) to perform differential transcript usage analysis. We compared results from the sequins dataset to the ground truth, and results of the mouse dataset to a previous short-read study on equivalent samples. Overall, our work shows that transcriptomic analysis of long-read nanopore data using long-read specific preprocessing methods together with short-read differential expression methods and software that are already in wide use can yield meaningful results.

Histochemical Distribution of 5-Nucleotidase in Snake Tissues: Presence of 5-Nucleotidase and Absence of Alkaline Phosphomonoesterase in Venom Glands of the Rattlesnake

1952 ◽  
Vol s3-93 (24) ◽  
pp. 391-394
Author(s):  
D. E. BRAGDON ◽  
J.F. A. MCMANUS
Keyword(s):  
Alkaline Phosphatase ◽  
Smooth Muscle ◽  
Phosphatase Activity ◽  
Alkaline Phosphatase Activity ◽  
Venom Gland ◽  
Specific Alkaline Phosphatase ◽  
Rattlesnake Venom ◽  
Great Vessels ◽  
Venom Glands ◽  
Thyroid Epithelium

1. Activity of the specific alkaline phosphatase, 5-nucleotidase, is intense in the epithelium and secretion of the rattlesnake venom gland. Non-specific alkaline phosphatase activity is lacking. 2. Thyroid epithelium, the smooth muscle of great vessels, and (inconstantly) smooth muscle of abdominal hollow viscera show greater 5-nucleotidase than nonspecific activity. 3. These findings confirm the specificity of 5-nucleotidase.

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