Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes

© 2017 Wong et al.; Published by Cold Spring Harbor Laboratory Press. Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted noncoding RNAs to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes

Lepra Reactions: Mimickers and Mirror to Unmask Complex Cases of Leprosy

Leprosy is a silent disease with protean manifestations, especially during lepra reactions (LRs). Cases with atypical leprosy or LR simulate a number of conditions misdiagnosed frequently. Here, three classical cases of leprosy are reported for their complex presentation. Leprosy was hidden in Case 1 due to co-existing diabetes. COVID vaccination induced LR unmasked all leprosy lesions, which were extensive, large, bizarre and spreading to various immune zones. Case 2 presented with high-grade fever, tachycardia, generalized erythema and body aches. A detailed workup unveiled his leprosy with a rare presentation of Type 1 lepra reaction (T1LR) with erythroderma and severe systemic symptoms. Case 3 mimicked sarcoidosis and lupus erythematosus (LE) on routine workup. She had facial lesions in the malar area, photosensitivity, joint pains, raised angiotensin-converting enzyme (ACE) levels and positive anti-nuclear antibodies. Peri-appendageal granulomas on histopathology and therapeutic response to multidrug therapy helped in the early diagnosis of leprosy

The changing trend of syphilis: Is it a sign of impending epidemic?

Background: Syphilis is a treatable bacterial infection caused by Treponema pallidum. There has been a change in incidence of syphilis in various nations over the years. Aim: To study the epidemiological trends, demographic profile, high-risk behaviour, clinical pattern, and stage of syphilis over the last ten years in patients presenting to an STD clinic in a tertiary care hospital. Material and Methods: This was a retrospective observational study over ten years. Records of all confirmed syphilis cases were analysed in relation to demography and clinical profile. Results: There were a total of 3,110 STD patients among whom 31 cases (accounting for 0.99%) of confirmed syphilis were seen. There was a significant increase in cases in the last five years of study, especially in the last year. An increase in primary (PS) and secondary syphilis (SS) was observed. Males outnumbered females (3:1). Mean age of patients was 35.0 ± 11.53 years. Professionals were most common (22.6%) having syphilis followed by farmers (19.35%). A significant proportion (45.1%) of our patients were at least graduates. Unprotected sex was seen in all the patients followed by extramarital/premarital sex (71.35%). There were 16.12% of cases who had a history of paid sex and 9.7% were homosexuals. SS and latent syphilis were more common (38.7% each) than PS (19.35%). In PS single chancre and in SS truncal asymptomatic rash was the commonest clinical presentation. Limitation: Single-centre study, including only self-reported patients leading to a small sample size, is the major limitation of the study. Conclusion: The increased trend of primary and secondary syphilis in recent years highlights that there is a risk of an impending epidemic

Chitosan–iron oxide nano-composite platform for mismatch-discriminating DNA hybridization for Neisseria gonorrhoeae detection causing sexually transmitted disease

Electrochemically fabricated nano-composite film of chitosan (CH)–iron oxide (Fe3O4) has been used to detect gonorrhoea, a sexually transmitted disease (STD) via immobilization of biotinylated probe DNA (BDNA) using avidin–biotin coupling for rapid and specific (mismatch-discriminating) DNA hybridization. The presence of Fe3O4 nanoparticles (∼18 nm) increases the electro-active surface area of the nano-biocomposite that provides desirable environment for loading of DNA with better conformation leading to increased electron transfer kinetics between the medium and electrode. The differential pulse voltammetric (DPV) studies have been conducted using BDNA/avidin/CH–Fe3O4/ITO electrode owing to the reduction of the methylene blue (MB) indicator and investigate electron transfer between MB moieties and electrode for one and two-bases mismatch. This STD biosensor is found to have a detection limit (1 × 10−15 M) and a wide dynamic range (from 1 × 10−16 M to 1 × 10−6 M) using the complementary target DNA. In addition, the sensing system can be utilized to accurately discriminate complementary sequence from mismatch sequences

Cannabidiol Inhibits Tumorigenesis in Cisplatin-Resistant Non-Small Cell Lung Cancer via TRPV2

Chemotherapy forms the backbone of current treatments for many patients with advanced non-small-cell lung cancer (NSCLC). However, the survival rate is low in these patients due to the development of drug resistance, including cisplatin resistance. In this study, we developed a novel strategy to combat the growth of cisplatin-resistant (CR) NSCLC cells. We have shown that treatment with the plant-derived, non-psychotropic small molecular weight molecule, cannabidiol (CBD), significantly induced apoptosis of CR NSCLC cells. In addition, CBD treatment significantly reduced tumor progression and metastasis in a mouse xenograft model and suppressed cancer stem cell properties. Further mechanistic studies demonstrated the ability of CBD to inhibit the growth of CR cell lines by reducing NRF-2 and enhancing the generation of reactive oxygen species (ROS). Moreover, we show that CBD acts through Transient Receptor Potential Vanilloid-2 (TRPV2) to induce apoptosis, where TRPV2 is expressed on human lung adenocarcinoma tumors. High expression of TRPV2 correlates with better overall survival of lung cancer patients. Our findings identify CBD as a novel therapeutic agent targeting TRPV2 to inhibit the growth and metastasis of this aggressive cisplatin-resistant phenotype in NSCLC