Central Retinal Artery Occlusion With Triple Cilioretinal Artery Sparing.

We report a rare case of central retinal artery occlusion (CRAO) with triple cilioretinal artery sparing in a 76-year-old male with hypertension who presented with sudden diminution of vision in the left eye (OS) for one day. Optical coherence tomography angiography (OCTA) demonstrated the presence of three cilioretinal arteries and the absence of flow signals in the rest of the macula. Primary ophthalmic treatment was instituted immediately in the form of ocular massage, and acetazolamide 500 mg per oral (PO) stat was given. Systemic investigations revealed a significant blockage in coronary circulation on coronary angiography and an atheromatous plaque at the origin of the left internal carotid artery with 50% stenosis on digital subtraction angiography. Systemic anticoagulants and lipid-lowering agents (statins) were initiated by the cardiologist. Percutaneous transluminal coronary angioplasty was subsequently performed. At the eight-week follow-up visit, best-corrected visual acuity had improved to 2/60 OS. Fundus examination of the OS revealed optic disc pallor with normal retinal background. Spectral-domain optical coherence tomography showed diffuse retinal thinning except in the area supplied by the three patent cilioretinal arteries. En face OCTA OS showed restoration of retinal flow signal in the macula. Non-invasive imaging (OCTA) is critical in establishing early diagnosis and initiating prompt treatment in this ocular emergency with underlying potentially life-threatening systemic associations.

In silico and in vitro evaluation of newly synthesized pyrazolo-pyridine fused tetrazolo-pyrimidines derivatives as potential anticancer and antimicrobial agents.

Diversely functionalized pyrazolo-pyridine fused tetrazolo-pyrimidines 10aa-am and 10ba-bn were successfully synthesized via a catalyst-free synthetic protocol with moderate to very good yields. The compounds were evaluated for cytotoxicity against MCF-7 and HEK-293 cells using MTT assay. Among the tested compounds, 10ab (IC50- 23.83 µM) and 10ah (IC50- 23.30 µM) demonstrated the highest potency against MCF-7 cells, while 10bc (IC50- 14.46 µM) and 10bh (IC50- 2.53 µM) exhibited excellent cytotoxicity against HEK-293 cells. Additionally, antibacterial screening was performed against three Gram-negative bacteria (E. coli, P. aeruginosa, and S. enterica) and three Gram-positive bacteria (S. aureus, B. megaterium, and B. subtilis) using broth dilution method, while antifungal activity was assessed against three fungal strains (A. niger, Penicillium, and S. cerevisiae) using agar well diffusion method. In antimicrobial screening, the majority of the compounds demonstrated significant antibacterial efficacy compared to antifungal activity. We also conducted comprehensive computational studies, including DFT calculations, molecular docking and dynamics, and drug-likeness assessments. In the DFT study, compounds 10ac and 10bc displayed stable conformations, indicating their potential for higher therapeutic activity. Molecular docking analyses revealed compelling interactions, with compound 10ah demonstrating docking score -7.42 kcal/mol against catalytical domain PARP1 (PDB ID: 7KK4) and 10bh exhibiting a best docking score -10.77 kcal/mol against human corticotropin-releasing factor receptor 1 (PDB ID: 4Z9G). A 100 ns molecular dynamics (MD) simulation study of compounds 10ah and 10bh revealed the stable conformation and binding energy in a stimulating environment. In drug-likeness assessments, both the compounds 10ah and 10bh adhere all the established guidelines.Communicated by Ramaswamy H. Sarma.

Pediatric Lupus Retinopathy: A Rare Manifestation of a Grave Systemic Disorder.

We describe a rare case of pediatric systemic lupus erythematosus (pSLE) and its successful management. A nine-year-old female presented with bilateral diminution of vision, fever, and rash in the malar region, chest, abdomen, back, and arms for three months. Clinical examination and multimodal imaging revealed bilateral extensive retinal vasculitis with macular edema. Laboratory investigations revealed anemia, leucopenia, positive serum antinuclear antibody (ANA), and anti-extractable nuclear antigen (ENA) antibodies. A diagnosis of pediatric lupus retinopathy was made. Ocular and systemic manifestations responded well to intense systemic immunosuppression (pulse intravenous {IV} methylprednisolone, oral prednisolone and hydroxychloroquine {HCQ}, six cycles of IV cyclophosphamide, and oral azathioprine) along with topical steroids and laser photocoagulation, over the next 10 months. Though ocular manifestations are not a part of the diagnostic criteria for SLE, they may be markers of active systemic disease. Ophthalmologists and rheumatologists must treat this complex disease in tandem in order to provide optimum patient care.

Multimodal Imaging in a Case of Chronic Sympathetic Ophthalmia.

We report a case of chronic sympathetic ophthalmia (SO) in a one-eyed patient who was successfully managed with systemic immunosuppression therapy. A 77-year-old one-eyed female presented with progressive diminution of vision in the left eye (OS) for one month. She had previously undergone a right eye (OD) pars plana vitrectomy elsewhere for exogenous post-operative endophthalmitis (after manual small incision cataract surgery five months ago), following which she developed phthisis. Granulomatous panuveitis and advanced cataract were noted in the OS. Findings on multimodal imaging, including spectral domain optical coherence tomography (SD-OCT), fundus fluorescein angiography (FFA), indocyanine green angiography (ICGA), and B-scan ultrasonography, were consistent with those of chronic SO. Promptly, oral steroids and systemic immunosuppressants were initiated under the supervision of a rheumatologist. At the three-week follow-up, complete resolution of clinical signs was observed on multimodal imaging. Chronic SO may present with ambiguous clinical signs, leading to a diagnostic dilemma. This may cause a delay in initiating treatment, which can prove to be highly detrimental, especially in one-eyed patients. Multimodal imaging is critical in excluding differential diagnoses and proves to be indispensable in the timely management of this sight-threatening condition.

Synthetic approach toward spiro quinoxaline-ß-lactam based heterocyclic compounds: Spectral characterization, SAR, pharmacokinetic and biomolecular interaction studies.

Series of spiro quinoxaline-ß-lactam based heterocyclic compounds (QL 1 - QL 21) were synthesized and characterized by spectroscopic techniques like 1H-NMR, LC-MS, FT-IR spectroscopy and elemental analysis. The binding mode and binding strength between compounds and calf thymus-DNA were estimated by UV-visible spectroscopy, viscosity measurement and molecular docking studies. The compounds bind with the DNA through partial intercalation mode. In the absorption titration experiment, the Kb values for all the synthesized compounds were found in the range of 0.24-0.64 × 105 M-1. The protein binding studies of all the synthesized compounds were evaluated by absorption titration experiment, and the Kb value for all the compounds was obtained in the range of 0.030-1.571 × 104 M-1. The compounds were screened against two Gram (+ve) and three Gram (-ve) bacteria for antimicrobial activity. The MIC values for all the synthesized compounds were found in 95-255 µM. The LC50 values (cytotoxicity) of the synthesized compounds (QL 1-QL 21) were found in the range of 4.00-12.89 µg/mL. The ADME study was carried out using the online platform SwissADME and admetSAR to evaluate the pharmacokinetic profile of all the synthesized compounds. All the compounds were screened for anticancer activity against the human osteosarcoma (MG-63) cell line. The result shows that all the compounds exhibit effective anticancer activity.Communicated by Ramaswamy H. Sarma.

Meglumine-Promoted Eco-Compatible Pseudo-Three-Component Reaction for the Synthesis of 1,1-Dihomoarylmethane Scaffolds and Their Green Credentials.

A simple, straightforward, and energy-efficient greener route for the synthesis of a series of biologically interesting functionalized 1,1-dihomoarylmethane scaffolds has been developed in the presence of meglumine as an efficient and eco-friendly organo-catalyst via one-pot pseudo-three-component reaction at room temperature. Following this protocol, it is possible to synthesize 1,1-dihomoarylmethane scaffolds of an assortment of C-H activated acids such as dimedone, 1,3-cyclohexadione, 4-hydroxy-6-methyl-2-pyrone, 4-hydroxycoumarin, and 1-phenyl-3-methyl-pyrazolone. The salient features of the present green protocol are mild reaction conditions, good to excellent yields, operational simplicity, easy isolation of products, no cumbersome post treatment, high atom economy, and low E-factor. In addition, this chemistry portrays several green advantages including the reusability of reaction media and product scalability, which makes protocol sustainably efficient. Additionally, several control experiments such as protection of catalyst reactive site, D2O exchange, and 1H NMR studies revealed possible pathways for meglumine-promoted reactions. Inspired by the natural physiological environment of 1,1-dihomoarylmethane scaffolds, we reconnoitered the biological profile of our compounds and synthesized compounds that were promising for their antiproliferative and antibacterial activities.

A review on touch DNA collection, extraction, amplification, analysis and determination of phenotype.

DNA is used as confirmatory evidence in criminal investigations for a long time. With advancements in DNA collection and analysis, investigators can analyse samples collected at nanogram levels. For decades now, touch DNA has been used for comparison and individualization as it has a greater probability of being present at a crime scene. With the advancements in sciences, today there are methods available for the determination of phenotype for DNA sequences through analysis of Single Nucleotide Polymorphisms (SNPs). A freely available and forensically validated web software is HIrisPlex-S developed by the Erasmus Medical Centre, Netherlands in collaboration with the Walsh Laboratory of Indiana-University-Purdue-University-Indianapolis (IUPUI), USA. It can expand the horizons in forensic science enabling investigators to get an idea of the phenotype of a suspected perpetrator and thereby reduce the suspect list to a great extent. There are numerous methods enlisted for the collection and processing of touch DNA. The review paper attempts to compile the various methods adopted in touch DNA collection and analysis as well as the related literature on phenotyping using the HIrisPlex-S Software.

Lung cancer targeting efficiency of Silibinin loaded Poly Caprolactone /Pluronic F68 Inhalable nanoparticles: In vitro and In vivo study.

Silibinin (SB) is shown to have an anticancer properties. However, its clinical therapeutic effects have been restricted due to its low water solubility and poor absorption after oral administration. The aim of this study was to develop SB-loaded PCL/Pluronic F68 nanoparticles for pulmonary delivery in the treatment of lung cancer. A modified solvent displacement process was used to make nanoparticles, which were then lyophilized to make inhalation powder, Nanoparticles were characterized with DSC, FTIR,SEM and In vitro release study. Further, a validated HPLC method was developed to investigate the Biodistribution study, pharmacokinetic parameters. Poly Caprolactone PCL / Pluronic F68 NPs showed the sustained release effect up to 48 h with an emitted (Mass median Aerodynamic diameter)MMAD and (Geometric size distribution)GSD were found to be 4.235 ±0.124 and 1.958±1.23 respectively. More specifically, the SB Loaded PCL/Pluronic F 68 NPs demonstrated long circulation and successful lung tumor-targeting potential due to their cancer-targeting capabilities. SB Loaded PCL/Pluronic F68 NPs significantly inhibited tumour growth in lung cancer-induced rats after inhalable administration. In a pharmacokinetics study, PCL/ Pluronic F68 NPs substantially improved SB bioavailability, with a more than 4-fold rise in AUC when compared to IV administration. These findings indicate that SB-loaded PCL/PluronicF68 nanoparticles may be a successful lung cancer therapy delivery system.

Silibinin loaded inhalable solid lipid nanoparticles for lung targeting.

AIM: In the current study, efforts are being made to prepare Inhalable Silibinin loaded solid lipid nanoparticles (SLNs) with narrow size distribution with improved bioavailability. METHODS: SLNs were formulated by high shear homogenisation method SLNs were characterised, including Differential Scanning Calorimetry (DSC), Fourier transform infra-red spectroscopy (FTIR), particle size analysis, entrapment efficiency with Aerodynamic behaviour. The MTT assay was performed against A549 cell line, to measure their anticancer cell activity with In vivo study. RESULTS: Optimized formulation exhibited spherical surface with a mean particle size of 221 ± 1.251 nm, PI of 0.121 ± 0.081, zeta potential of -4.12 ± 0.744. Aerodynamic behaviour such as Mass median aerodynamic diameter (MMAD) and Geometric size distribution (GSD) were found to be 5.487 ± 0.072 and 2.321 ± 0.141 respectively proved formulation is suitable for inhalation. In vitro cellular efficacy against A549 cells, revealed that the optimised formulations were more effective and potent. CONCLUSION: The Inhalable SLNs approach was successfully engineered and administered to the lungs safely without causing any problems.

Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India.

Humankind has suffered many pandemics in history including measles, SARS, MERS, Ebola, and recently the novel Coronavirus disease caused by SARS-CoV-2. As of September 2021, it has affected over 200 million people and caused over 4 million deaths. India is the second most affected country in the world. Up to this date, more than 38 Lakh viral genomes have been submitted to public repositories like GISAID and NCBI to analyze the virus phylogeny and mutations. Here, we analyzed 2349 genome sequences of SARS-CoV-2 submitted in GISAID by a single institute pertaining to infections from the Gujarat state to know their variants and phylogenetic distributions with a major focus on the spike protein. More than 93% of the genomes had one or more mutations in the spike glycoprotein. The D614G variant in spike protein is reported to have a very high frequency of >95% globally followed by the L452R and P681R, thus getting significant attention. The antigenic propensity of a small peptide of 29 residues from 597 to 625 of the spike protein variants having D614 and G614 showed that G614 has a little higher antigenic propensity. Thus, the D614G is the cause for higher viral antigenicity, however, it has not been reported to be effective to be causing more deaths.

In Vitro Antibacterial Evaluation of Terminalia chebula as an Alternative of Antibiotics against Bovine Subclinical Mastitis.

The extent of subclinical mastitis in three breeds of cattle, Kankrej, Gir, and Crossbred, was performed at cattle farms in Anand town of Gujarat State, India. The prevalence of subclinical mastitis in crossbred cattle was higher compared to local breed of cattle. Causative agents identified using 16S rDNA polymerase chain reaction (PCR)-based molecular method were Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Bacillus megaterium. In vitro antibacterial activity of ethyl acetate extract of plant Terminalia chebula (Combretaceae) was checked by agar well diffusion method against four isolated and molecularly identified microorganisms. Ethyl acetate extract shows antimicrobial activity with varying magnitudes against all identified isolates. Among the three different concentrations, 500 µg/mL conc. of extract is as effective as that of standard amoxicillin. In vitro results support the use of plant extract from T. chebula as an alternative to antibiotics therapy against bovine subclinical mastitis.

Metagenomic data of DNA viruses of poultry affected with respiratory tract infection.

The incidence and severity of respiratory diseases in commercial broiler chicken flocks have increased recently in India because of intensification of the broiler industry. Viral population are predominant in respiratory tract infections and they pose continuous economic burden to poultry industry by causing severe economic losses through decreased productivity [1], [2]. To understand viral metagenome of poultry associated with respiratory infections, we performed DNA virome sequencing and data analysis of broilers from 8 districts of Gujarat State in India. We report high quality sequencing reads and highly abundant DNA viral population present in the infected broiler birds. The raw sequencing data used to perform metagenomic analysis is available in the Sequence Read Archive (SRA) under the BioProject No. PRJNA322592 and Accession No. MAUZ00000000, MAVA00000000, MAVB00000000, MAVC00000000, MAVD00000000, MAVE00000000, MAVF00000000, MAVG00000000 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA322592).

RNA-Seq reveals the molecular mechanism of trapping and killing of root-knot nematodes by nematode-trapping fungi.

Nematode-trapping fungi are well known for their inherent potential to trap and kill nematodes using specialized trapping devices. However, the molecular mechanisms underlying the trapping and subsequent processes are still unclear. Therefore, in this study, we examined differential genes expression in two nematode-trapping fungi after baiting with nematode extracts. In Arthrobotrys conoides, 809 transcripts associated with diverse functions such as signal transduction, morphogenesis, stress response and peroxisomal proteins, proteases, chitinases and genes involved in the host-pathogen interaction showed differential expression with fold change (>±1.5 fold) in the presence of nematode extract with FDR (p-value < 0.001). G-proteins and mitogen activated protein kinases are considered crucial for signal transduction mechanism. Results of qRT-PCR of 20 genes further validated the sequencing data. Further, variations in gene expression among Duddingtonia flagrans and A. conoides showed septicity of nematode-trapping fungi for its host. The findings illustrate the molecular mechanism of fungal parasitism in A. conoides which may be helpful in developing a potential biocontrol agent against parasitic nematodes.

Transcriptome analysis of the adult rumen fluke Paramphistomum cervi following next generation sequencing.

Rumen flukes are parasitic trematodes (Platyhelminthes: Digenea) of major socioeconomic importance in many countries. Key representatives, such as Paramphistomum cervi, can cause "Rumen fluke disease" or paramphistomosis and undermine economic animal productivity and welfare. P. cervi is primarily a problem in sheep, goat and buffalo production as a consequence of reduced weight gain and milk production, clinical disease or death. Recent technological advances in genomics and bioinformatics now provide unique opportunities for the identification and pre-validation of drug targets and vaccines through improved understanding of the biology of pathogens such as P. cervi and their relationship with their hosts at the molecular level. Here, we report next generation transcriptome sequencing analysis for P. cervi. RNAseq libraries were generated from RNA extracted from 15 adult P. cervi parasites sampled from each of three different host species (sheep, goat and buffalo) and a reference transcriptome was generated by assembly of all Ion Torrent PGM sequencing data. Raw reads (7,433,721 in total) were initially filtered for host nucleotide contamination and ribosomal RNAs and the remaining reads were assembled into 43,753 high confidence transcript contigs. In excess of 50% of the assembled transcripts were annotated with domain- or protein sequence similarity derived functional information. The reference adult P. cervi transcriptome will serve as a basis for future work on the biology of this important parasite. Using the widely investigated trematode virulence factor and vaccine candidate Cathepsin L as an example, the epitope GPISIAINA was found to be conserved in P. cervi isolated from three different host species supporting its candidacy for vaccine development and illustrating the utility of the adult P. cervi transcriptome.

De Novo Assembly and Transcriptome Characterization of Canine Retina Using High-Throughput Sequencing.

We performed transcriptome sequencing of canine retinal tissue by 454 GS-FLX and Ion Torrent PGM platforms. RNA-Seq analysis by CLC Genomics Workbench mapped expression of 10,360 genes. Gene ontology analysis of retinal transcriptome revealed abundance of transcripts known to be involved in vision associated processes. The de novo assembly of the sequences using CAP3 generated 29,683 contigs with mean length of 560.9 and N50 of 619 bases. Further analysis of contigs predicted 3,827 full-length cDNAs and 29,481 (99%) open reading frames (ORFs). In addition, 3,782 contigs were assigned to 316 KEGG pathways which included melanogenesis, phototransduction, and retinol metabolism with 33, 15, and 11 contigs, respectively. Among the identified microsatellites, dinucleotide repeats were 68.84%, followed by trinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides in proportions of 25.76, 9.40, 2.52, and 0.96%, respectively. This study will serve as a valuable resource for understanding the biology and function of canine retina.

Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak.

The present study reports isolation and characterization of H9N2 virus responsible for disease characterized by symptoms including difficulty in respiration, head swelling, nasal discharge, reduced feed intake, cyanotic comb, reduced egg production and mortality. Virus isolation from allantoic fluid inoculated with tracheal aspirates and whole genome sequencing of two isolates were performed on an Ion-Torrent sequencer. Phylogenetic analysis revealed that the two H9N2 isolates are reassortant viruses showing a G1-like lineage for HA, NA and NP, a Hok/49/98-like lineage for PB1 and PA, PK/UDL-01/05-like lineage for PB2, IL/90658/00-like lineage for NS and an unknown lineage for M gene. Analyses of the HA cleavage site showed a sequence of (333PARSSR↓GL340) indicating that these isolates are of low pathogenicity. Isolate 2 has leucine at amino acid position 226, a substitution which is associated with mammalian adaptation of avian influenza virus. Isolate 1 has the S31N substitution in the M2 gene that has been associated with drug resistance as well as R57Q and C241Y mutations in the NP gene which are associated with human adaptation. The result reported here gives deep insight in to H9N2 viruses circulating in domestic poultry of India and supports the policy of active efforts to control and manage H9N2 infections in Indian poultry.

Transcriptomic dissection of myogenic differentiation signature in caprine by RNA-Seq.

Muscle growth and development from the embryonic to the adult stage of an organism consists of a series of exquisitely regulated and orchestrated changes in expression of genes leading to muscle maturation. In this study, we performed whole transcriptome profiling of adult caprine skeletal muscle derived myoblast and fused myotubes. Using Ion Torrent PGM sequencing platform, a total of 948,776 and 799,976 reads were generated in myoblasts and fused myotubes, respectively. The sequence reads were analyzed on CLC Genomics Workbench using Bos taurus RNA database to study the gene expression in both stages to study different genes responsible for muscle development and regeneration. The up and down-regulated genes were analyzed for gene ontology (GO) and KEGG pathways by Database for Annotation, Visualization and Integrated Discovery (DAVID) database. We found many genes exclusive to multinuclear fused myotubes and contractile nature of skeletal muscle, whereas up-regulated genes in myoblast stage were related to cell division and transcriptional regulation. Out of 27 genes selected for expression validation by RT-qPCR (reverse transcriptase-quantitative polymerase chain reaction), 19 genes showed the expression pattern comparable with CLC Genomics Workbench findings. Further, mRNA originated muscle specific microRNAs (miRNA-1 and miRNA-133b) were also observed in the fused myotubes along with other miRNAs with possible importance in muscle development. This study highlights important genes responsible for muscle development and differentiation in adult skeletal muscle system.

Evaluation of a topical herbal drug for its in-vivo immunomodulatory effect on cytokines production and antibacterial activity in bovine subclinical mastitis.

BACKGROUND: Antibiotics have been in use in the treatment of bovine mastitis since decades; however, their use is associated with cost issues and human health concern. Use of herbal drugs does not generally carry these disadvantages. Many plants/herbs have been evaluated in the treatment of bovine mastitis with additional property of immunomodulation in affected mammary gland. AIM: To evaluate a topical herbal drug in two breeds of cattle for its in-vivo immunomodulatory effect on cytokines production and antibacterial activity in bovine subclinical mastitis. MATERIALS AND METHODS: The response to treatment was evaluated by enumerating somatic cell count (SCC), determining total bacterial load, and studying the expression of different cytokines (interleukin [IL]-6, IL-8, IL-12, granulocyte macrophage-colony stimulating factor, interferon (IFN)-γ and tumor necrosis factor [TNF]-α). RESULTS: The pre- and post-treatment SCC in mastitic quarters statistically did not differ significantly, however, total bacterial load declined significantly from day 0 onwards in both the breeds. Highly significant differences (P < 0.01) were observed in all the cytokines on day 0, 5, and 21 postlast treatment in both the breeds. The expression level of all the cytokines showed a significant increase on day 5, while a decrease was noticed on day 21 in both the breeds of cattle. The comparison of cytokine expression profiles between crossbred and Gir cattle revealed a significant difference in expression of IL-6 and TNF-α. However, other cytokines exhibited a similar pattern of expression in both breeds, which was non-significant. CONCLUSION: The topical herbal drug exhibited antibacterial and immunomodulatory activities in subclinical mastitis and thus the work supports its use as alternative herbal therapy against subclinical udder infection in bovines.

Transcriptome analysis and SNP identification in SCC of horn in (Bos indicus) Indian cattle.

Single Nucleotide Polymorphisms (SNPs) have become the marker of choice for genome wide association studies. In order to provide the best genome coverage for the analysis of disease, production and performance traits, a large number of relatively evenly distributed SNPs are needed. The main objective of present work was to identify large numbers of gene-associated SNPs using high-throughput sequencing in squamous cell carcinoma of horn. RNA-seq analysis was conducted on 2 tissues viz. Horn Cancer (HC) and Horn Normal (HN) in Kankrej breed of cattle. A total of 909,362 reads with average read length of 405 bp for HC and 583,491 reads with average read length of 411 bp for HN were obtained. We found 9532 and 7065 SNPs as well as 1771 and 1172 Indels in HC and HN, respectively, from which, 7889 SNPs and 1736 Indels were uniquely present in HC, 5886 SNPs and 1146 Indels were uniquely present in HN and reported first time in Bos indicus, whereas the rest are already reported in Bos taurus dbSNP database. The gene-associated SNPs and Indels were high in upregulated genes of HC as compared to HN. Analysis of differentially expressed genes was identified, these genes are involved in regulation of cell proliferation, apoptosis, gene transcription, cell survival and metabolism through various metabolic pathways. The result of transcriptome expression profiling was validated using Real Time quantitative PCR in nine randomly selected genes. We identified numbers aberrant signaling pathways responsible for carcinogenesis in HC which are also commonly altered in squamous cell carcinoma (SCC) of lung in human being. We conclude that a large number of altered genes and dysfunction of multiple pathways are involved in the development of Horn Cancer. The present findings contribute to theoretical information for further screening of genes and identification of markers for early diagnosis of HC as well as SNPs identified in this report provide a much needed resource for genetic studies in B. indicus and shall contribute to the development of a high density SNP array. Validation and testing of these SNPs using SNP arrays will form the material basis for gene associated SNPs in HC.

The landscape of alternative splicing in buccal mucosa squamous cell carcinoma.

OBJECTIVES: Alternative splicing (AS) is a key regulatory mechanism in the process of protein synthesis generating transcriptome and proteome diversity. In this study, we attempted to identify alternative splicing in a pair of BMSCC cancer and adjacent normal tissue using RNAseq datasets and also assessed the potential of these datasets to provide quantitative measurements for alternative splicing levels. MATERIALS AND METHODS: We performed high-throughput sequencing of buccal mucosal cancer and healthy tissue cDNA library which resulted in a transcriptome map of BMSCC cancer. RNAseq analysis was performed to assess alternative splicing complexity in cancer tissue and to search splice junction sequences that represent candidate 'new' splicing events. The splice junctions were predicted by SpliceMap software and putative assembled transcripts validated using the RT-PCR. We also analyzed the coding potential of alternative spliced candidate by HMMER. RESULTS: We detected a total of 11 novel splice junctions derived mostly from alternate 5' splice site; including two of them which contained new translation initiation sites (TISs). We have identified novel IgG pseudogene and a fusion transcript of MEMO1 and RPS9, which were further confirmed by PCR from genomic DNA. We also found novel putative long non-coding RNA (lncRNA), which is antisense to SPINK5 gene. The coding potential of these AS variants revealed that alternative splicing caused premature termination, insertion/deletion of amino acid (s) or formation of novel N-terminus. CONCLUSIONS: Differential splicing of these novel AS variants between cancer and adjacent normal tissue suggests their involvement in BMSCC cancer development and progression.