Biology subjects

S, A.

Publications and source records attributed to S, A..

22 records · Page 2Linked to original sources

bioRxiv2022

Detection of Fortunate Molecules Induce PArticle Resolution Shift (PAR-shift) towards Single-molecule Limit in SMLM: A Technique for Resolving Molecular Clusters in Cellular System

Molecules capable of emitting a large number of photons (also known as fortunate molecules) are crucial for achieving resolution close to a single molecule limit (the actual size of a single molecule). We propose a long-exposure single molecule localization microscopy (leSMLM) technique that enables detection of fortunate molecules, which is based on the fact that detecting a relatively small subset of molecules with large photon emission increases its localization [Formula]. Fortunate molecules have the ability to emit a large burst of photons over a prolonged time (> average triplet-state lifetime). So, a long exposure time allows the time window necessary to detect these elite molecules. The technique involves the detection of fortunate molecules to generate enough statistics for a quality reconstruction of the target protein distribution in a cellular system. Studies show a significant PArticle Resolution Shift (PAR-shift) of about 6 nm and 11 nm towards Single-molecule-limit (away from diffraction-limit) for an exposure time window of 60 ms and 90 ms, respectively. In addition, a significant decrease in the fraction of fortunate molecules (single molecules with small localization precision) is observed. Specifically, 8.33% and 3.43% molecules are found to emit in 30 - 60 ms and 60 - 90 ms, respectively, when compared to SMLM. The long exposure has enabled better visualization of Dendra2HA molecular cluster, with sub-clusters within a large cluster. Thus, the proposed technique (leSMLM) facilitates a better study of cluster formation in fixed samples. Overall, the method enables better spatial resolution at the cost of relatively poor temporal resolution.

biophysics↗

bioRxiv2021

Skin specimen as an alternative to brain tissue for post mortem rabies diagnosis in animals to scale up animal rabies surveillance

BackgroundDetection of the virus or some of its specific components using WHO and OIE recommended standard laboratory tests is the only way to get a reliable diagnosis of rabies. Brain tissue is the preferred specimen for post-mortem diagnosis of rabies in both humans and animals. Higher biosecurity requirements, skill and transportation facilities required for collection and transport of brain or whole carcass to the laboratory is one of the reasons for the poor rabies surveillance in animals. Point of care testing with simple, reliable and easy to operate devices would be an ideal approach for providing rapid results. MethodsThe study evaluated diagnostic performance of two reference tests, DFAT and RTPCR on skin specimen, to assess its suitability as an alternative of brain tissue for post mortem rabies diagnosis in animals. Brain tissue and skin sample belonging to different species of animals (n=90) collected at necropsy were compared using Fluorescent Antibody Test and RT PCR, internationally approved methods for rabies diagnosis. ResultsValidation of RT-PCR on skin and DFAT on skin in comparison with DFAT on brain as gold standard gave a sensitivity of 98% (95% CI:94.1-100) and 80% (95% CI:71.8-88.2) respectively. Specificity was 100% in both tests. ConclusionThe findings highlight the potential of skin specimen for improving rabies surveillance in animals especially in resource poor countries. Author SummaryThe present study was undertaken to define a reliable protocol for diagnosing animal rabies using skin specimen, a superficial tissue sample which is collected in a non-invasive manner for post-mortem diagnosis. Our aim was to design a protocol to replace the classical post-mortem diagnostic method that uses brain biopsy with an ultimate target of stepping up rabies surveillance in animals. Brain tissue and skin sample belonging to different species of animals collected at necropsy were compared using Fluorescent Antibody Test and RT PCR, internationally approved methods for rabies diagnosis. The study established that RT PCR on skin specimen is rapid, sensitive and specific, opening its potential as an ideal rabies surveillance tool overcoming the logistical challenges of carcass transportation to reference laboratories and alleviating biosafety concerns associated with brain collection. The study highlights the potential of skin specimen for improving rabies surveillance in animals especially in resource poor countries.

microbiology↗

bioRxiv2020

STIL a novel link in Shh and Wnt signaling, endowing oncogenic and stem like attributes to colorectal cancer

Discovery of potent gene regulating tumorigenesis and drug resistance is of high clinical importance. STIL is an oncogene, however its molecular insights and role in colorectal oncogenesis are unknown. In this study we have explored role of STIL in tumorigenesis and studied its molecular targets in colorectal cancer (CRC). STIL silencing reduced proliferation and tumor growth in CRC. Further, STIL was found to regulate stemness markers CD133 & CD44 and drug resistant markers Thymidylate synthase, ABCB1 & ABCG2 both in in-vitro and in-vivo CRC models. In addition, over expression of STIL mRNA was found to be associated with reduced disease free survival in CRC cases. To our surprise we observed an Shh independent regulation of stemness and drug resistant genes mediated by STIL. Interestingly, we found an Shh independent regulation of {beta}-catenin mediated by STIL via p-AKT, which partially answers Shh independent regulatory mechanism of CSC markers by STIL. Our study suggest an instrumental role of STIL in molecular manifestation of CRC and progression.

cancer biology↗

bioRxiv2019

Molecular Docking of Glycyrrhiza glabra against the Conserved Target M1, NA andNS1 Proteins of Influenza A Viral Strains Identified through Pangenome Analysis

Influenza viruses that infect humans are known to swiftly evolve over time. Influenza A virus has a negative single-stranded RNA genome in eight segments. Pangenome analysis of twelve strains of Influenza A viruses H1N1, H1N2, H2N2, H3N2, H5N1, H5N6, H7N2, H7N3, H7N7, H7N9, H9N2, and H10N8 gave insight on the core genes that are conserved and accessory genes that are specific for the strains. The proteins Neuraminidase, Matrix M1 and Nonstructural protein 1 were encoded by the core genes of segments 6, 7, and 8 respectively which proves that they are conserved in almost all the strains of influenza. The 3Dimensional structures of the core genes were interpreted by homology modeling and compared with corresponding Protein Data Bank structures (4MWQ, IEA3, 2GX9). Among several anti-viral phytocompounds that were virtually screened against the modeled and PDB target proteins, three molecules of Indian plant Glycyrrhiza glabra had high scores and interactions. Compounds 2,4,4 Trihydrochalcone, Davidigenin and Licoflavone B docked well with the Neuraminidase, Matrix protein M1 and Nonstructural Protein NS1 respectively with good scores, minimized energy and interacted with the active sites. The compounds obeyed Lipinskis Rule of five and exhibited drugability as well. Thus the present study focused on the drugable lead compounds from glabra that has inhibitory activities against the viral attachment, replication and matrix structure.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC=\"FIGDIR/small/831461v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (24K):\norg.highwire.dtl.DTLVardef@de27deorg.highwire.dtl.DTLVardef@10b9cc9org.highwire.dtl.DTLVardef@1628b20org.highwire.dtl.DTLVardef@9c2336_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗