Hari Prasanna Deka Boruah

Complete genome sequence analysis of Pseudomonas aeruginosa N002 reveals its genetic adaptation for crude oil degradation.

The present research work reports the whole genome sequence analysis of Pseudomonas aeruginosa strain N002 isolated from crude oil contaminated soil of Assam, India having high crude oil degradation ability. The whole genome of the strain N002 was sequenced by shotgun sequencing using Ion Torrent method and complete genome sequence analysis was done. It was found that the strain N002 revealed versatility for degradation, emulsification and metabolizing of crude oil. Analysis of cluster of orthologous group (COG) revealed that N002 has significantly higher gene abundance for cell motility, lipid transport and metabolism, intracellular trafficking, secretion and vesicular transport, secondary metabolite biosynthesis, transport and catabolism, signal transduction mechanism and transcription than average levels found in other genome sequences of the same bacterial species. However, lower gene abundance for carbohydrate transport and metabolism, replication, recombination and repair, translation, ribosomal structure, biogenesis was observed in N002 than average levels of other bacterial species.

Diagnostic and Prognostic Biomarkers in ovarian cancer and the potential roles of cancer stem cells – An updated review

Abstract Ovarian carcinomas relate to highest death rate in gynecologic malignancies as absence of symptoms shield the disease in the early stage. Current evidences have been devoted to discovering early effective screening mechanism prior to the onset of clinical symptoms. Therefore, biomarkers are the crucial tools that are capable of predicting progression, risk stratification and overall therapeutic benefit to fight against this deadly disease. Although recent studies have revealed serum protein markers, CA‐125, HE4, mesothelin etc. have higher sensitivity and specificity at the early stages of the cancer; the critical questions arise regarding the applicability and reproducibility of genomic profiling across different patient groups. Hence, our hypothesis is that the panels of signature biomarkers will be much more effective to improve the diagnosis and prediction of patient survival outcome with high sensitivity and specificity. Ovarian cancer is heterogeneous in nature and contain a sub‐population of stem cell‐like characteristics that has the ability to grow as anchorage‐independent manner and subsequently is able to metastasize. Highly tumorigenic and chemotherapy‐resistant cancer stem cells (CSCs)‐specific biomarkers therefore reflects the interesting possibilities to be targeted to minimize the high frequency of relapse and resistance to drugs. Several putative ovarian CSC markers such as CD24, CD44, CD133, SSEA have already been proposed in recent studies, yet, a large panel of updated biomarkers have high clinical relevance to define the prospective isolation of viable circulating CSCs. Therefore, this review highlights current evidence based updated ovarian cancer specific prognostic and diagnostic biomarkers and potential importance of CSCs in context of tumorigenicity and metastatic activity for fundamental biological and clinical implications. HighlightsCurrent updated potential prognostic and diagnostic biomarkers in ovarian cancer.Potential importance of cancer stem cells in tumorigenesis and metastasis.Signature biomarkers improve the prediction of survival in cancer patients.

PPL catalyzed four-component PASE synthesis of 5-monosubstituted barbiturates: Structure and pharmacological properties.

Enzymatic four-component reactions are very rare although three-component enzymatic promiscuous reactions are widely reported. Herein, we report an efficient PASE protocol for the synthesis of potentially lipophilic zwitterionic 5-monosubstituted barbiturates by four component reaction of mixture of ethyl acetoacetate, hydrazine hydrate, aldehyde and barbituric acid in ethanol at room temperature. Seven different lipases were screened for their promiscuous activity towards the synthesis of 5-monosubstituted barbiturates and the lipase from porcine pancreas (PPL) found to give optimum efficiency. The zwitterionic 5-monosubstituted barbiturates with pyrazolyl ring showed promising pharmacological activity upon screening for antibacterial and apoptotic properties.

Synthesis of steroidal and nonsteroidal vicinal heterocyclic alcohols, N-(1-cycloalkenyl)heterocycles and their antibacterial studies.

A solvent free steroidal and nonsteroidal epoxide ring opening reaction by nitrogen containing heterocycles under microwave irradiation is described. Some of the epoxide ring opening compounds were converted to their corresponding N-(1-cycloalkenyl)heterocycles via an acid catalyzed dehydration reaction. The antimicrobial activities of the epoxide ring opening compounds and N-(1-cycloalkenyl)heterocyclic compounds were tested by agar diffusion assay. Compounds 6, 9-12, 24 and 27 showed moderate inhibition against the growth of pathogenic bacteria Escherichia coli, Pseudomonas syringae, Bacillus subtilis, Proteus vulgaris and Staphylococcus aureus.

Complete genome sequencing and comparative analyses of broad-spectrum antimicrobial-producing Micromonospora sp. HK10.

Micromonospora genus produces >700 bioactive compounds of medical relevance. In spite of its ability to produce high number of bioactive compounds, no genome sequence is available with comprehensive secondary metabolite gene clusters analysis for anti-microbial producing Micromonospora strains. Thus, here we contribute the full genome sequence of Micromonospora sp. HK10 strain, which has high antibacterial activity against several important human pathogens like, Mycobacterium abscessus, Mycobacterium smegmatis, Bacillus subtillis, Staphylococcus aureus, Proteus vulgaris, Pseudomonas aeruginosa, Salmonella and Escherichia coli. We have generated whole genome sequence data of Micromonospora sp. HK10 strain using Illumina NexSeq 500 sequencing platform (2×150bp paired end library) and assembled it de novo. The sequencing of HK10 genome enables identification of various genetic clusters associated with known- and probably unknown- antimicrobial compounds, which can pave the way for new antimicrobial scaffolds.

Molecular genetics and functional genomics of abiotic stress-responsive genes in oilseed rape (Brassica napus L.): a review of recent advances and future

Abiotic stresses are the key factors which negatively influence plant development and productivity and are the main cause of extensive agricultural production losses worldwide. Brassica napus is an oilseed crop of global economic significance and major contributor to the total oilseed production, quite often encounters abiotic stresses, resulting in reduced agricultural productivity. Hence, there is an immediate need being felt to raise B. napus cultivars which would be more suitable for various abiotic stress conditions presently and in the years to come. Biotechnology and molecular plant breeding has emerged as an important tool for molecular understanding of plant response to various abiotic stresses. Currently, various stress-responsive genes and mechanisms have been identified and functionally characterized in model plant Arabidopsis and other major crop plants such as Oryza sativa and Zea mays. However, very inadequate success has been achieved in this direction in a major oilseed crop such as B. napus. In this review, we present the latest methods and approaches of studying abiotic stress in B. napus. In this review, we describe the genes functioning as markers for crop breeding and discuss the recent progress and advances in genome editing by break through CRISPR/Cas9 multigene–multiplex approaches for developing multiple abiotic stress tolerance with our on-going research as a scheme. We also throw some light on molecular genetics, plant breeding and abiotic stress biotechnology of B. napus which offer a new prospective on the research directions for the practical plant breeding and functional genomics of B. napus in response to different abiotic stress conditions.

Origins based clinical and molecular complexities of epithelial ovarian cancer

Ovarian cancer is the most lethal of all common gynaecological malignancies in women worldwide. Ovarian cancer comprises of >15 distinct tumor types and subtypes characterized by histopathological features, environmental and genetic risk factors, precursor lesions and molecular events during oncogenesis. Recent studies on gene signature profiling of different subtypes of ovarian cancer have revealed significant genetic heterogeneity between and within each ovarian cancer histological subtype. Thus, an immense interest have shown towards a more personalized medicine for understanding the clinical and molecular complexities of four major types of epithelial ovarian cancer (serous, endometrioid, clear cell, and mucinous). As such, further in depth studies are needed for identification of molecular signalling network complexities associated with effective prognostication and targeted therapies to prevent or treat metastasis. Therefore, understanding the metastatic potential of primary ovarian cancer and therapeutic interventions against lethal ovarian cancer for the development of personalized therapies is very much indispensable. Consequently, in this review we have updated the key dysregulated genes of four major subtypes of epithelial carcinomas. We have also highlighted the recent advances and current challenges in unravelling the complexities of the origin of tumor as well as genetic heterogeneity of ovarian cancer.

Efflux pump inhibition by 11H-pyrido[2,1-b]quinazolin-11-one analogues in mycobacteria

Mycobacterium tuberculosis infection causes 1.8 million deaths worldwide, of which half a million has been diagnosed with resistant tuberculosis (TB). Emergence of multi drug resistant and extensive drug resistant strains has made all the existing anti-TB therapy futile. The major involvement of efflux pump in drug resistance has made it a direct approach for therapeutic exploration against resistant M. tuberculosis. This study demarcates the role of 11H-pyrido[2,1-b]quinazolin-11-one (quinazolinone) analogues as efflux pump inhibitor in Mycobacterium smegmatis. Sixteen quinazolinone analogues were synthesized by treating 2-aminopyridine and 2-fluorobenzonitrile with KtOBu. Analogues were tested, and 3a, 3b, 3c, 3g, 3j, 3l, 3m, and 3p were found to modulate EtBr MIC by >4 whereas 3a, 3g, 3i and 3o showed >4 modulation on norfloxacin MIC. 3l and 3o in addition to their very low toxicity they showed high EtBr and norfloxacin accumulation respectively. Time kill curve showed effective log reduction in colony forming unit in presence of these analogues, thus confirming their role as efflux pump inhibitor. Through docking and alignment studies, we have also shown that the LfrA amino acid residues that the analogues are interacting with are present in Rv2333c and Rv2846c of M. tuberculosis. This study have shown for the first time the possibility of developing the 11H-pyrido[2,1-b]quinazolin-11-one analogues as efflux pump inhibitors for M. smegmatis and hence unbolts the scope to advance this study against resistant M. tuberculosis as well.

Anti-Proliferative Activities of Vasicinone on Lung Carcinoma Cells Mediated via Activation of Both Mitochondria-Dependent and Independent Pathways

Vasicinone, a quinazoline alkaloid from Adhatoda vasica Nees. is well known for its bronchodilator activity. However its antiproliferative activities is yet to be elucidated. Here-in we investigated the anti-proliferative effect of vasicinone and its underlying mechanism against A549 lung carcinoma cells. The A549 cells upon treatment with various doses of vasicinone (10, 30, 50, 70 µM) for 72 h showed significant decrease in cell viability. Vasicinone treatment also showed DNA fragmentation, LDH leakage, and disruption of mitochondrial potential, and lower wound healing ability in A549 cells. The Annexin V/PI staining showed disrupted plasma membrane integrity and permeability of PI in treated cells. Moreover vasicinone treatment also lead to down regulation of Bcl-2, Fas death receptor and up regulation of PARP, BAD and cytochrome c, suggesting the anti-proliferative nature of vasicinone which mediated apoptosis through both Fas death receptors as well as Bcl-2 regulated signaling. Furthermore, our preliminary studies with vasicinone treatment also showed to lower the ROS levels in A549 cells and have potential free radical scavenging (DPPH, Hydroxyl) activity and ferric reducing power in cell free systems. Thus combining all, vasicinone may be used to develop a new therapeutic agent against oxidative stress induced lung cancer.

Isolation, purification, and characterization of staphylocoagulase, a blood coagulating protein from Staphylococcus sp. MBBJP S43

Staphylocoagulase, a protein produced by S. aureus, play major role in blood coagulation and investigations are in advance to discover more staphylocoagulase producing species. The present study demonstrates the identification of a coagulase producing bacteria and isolation, purification and characterization of the protein. The bacteria was identified using 16S rDNA sequencing and phylogenetic investigation, classified the bacteria as Staphylococcus sp. MBBJP S43 with Genbank accession number KX907247. Tube test and Chromozym TH assay were used to study enzyme activity and comparison was made with five standard coagulase positive strains. The SEM images of the fibrin threads provide evidence of coagulation. The optimum temperature for enzyme activity was 37°C and pH of 6.5-7.5. Glucose and lactose as a carbon source and ammonium chloride as nitrogen source greatly influenced the bacterial growth. Staphylocoagulase has been purified to homogeneity (766 fold) by 80% (NH4)2SO4 precipitation, Sephadex G-75 gel filtration, DEAE anion exchange chromatography, and HPLC using C18 column. SDS PAGE revealed the molecular weight of the protein to be approximately 66kD and FTIR spectra of the purified protein demonstrated the presence of α helical structure. Present study revealed that the Staphylococcus sp. MBBJP S43 strain is a potential staphylocoagulase producing bacteria.