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Deepak Bhatnagar

Publications and source records attributed to Deepak Bhatnagar.

At least 19 recordsLinked to original sources
PubMed2006

Promising nucleic acid analogs and mimics: characteristic features and applications of PNA, LNA, and morpholino.

Nucleic acid analogs and mimics are commonly the modifications of native nucleic acids at the nucleobase, the sugar ring, or the phosphodiester backbone. Many forms of promising nucleic acid analogs and mimics are available, such as locked nucleic acids (LNAs), peptide nucleic acids (PNAs), and morpholinos. LNAs, PNAs, and morpholinos can form both duplexes and triplexes and have improved biostability. They have become a general and versatile tool for DNA and RNA recognition. LNA is a general and versatile tool for specific, high-affinity recognition of single-stranded DNA (ssDNA) and single-stranded RNA (ssRNA). LNA can be used for designing LNA oligoes for hybridization studies or as real time polymerase chain reaction probes in the form of Taqman probes. LNA also has therapeutic and diagnostic applications. PNA is another type of DNA analog with neutral charge. The extreme stability of PNA makes it an ideal candidate for the antisense and antigene application. PNA is used as probe for gene cloning, mutation detection, and in homologous recombination studies. It was also used to design transcription factor decoy molecules for target gene induction. Morpholino, another structural type, was devised to circumvent cost problems associated with DNA analogs. It has become the premier knockdown tool in developmental biology due to its cytosolic delivery in the embryos by microinjection. Thus, the nucleic acid analogs provide an advantage to design and implementation, therapies, and research assays, which were not implemented due to limitations associated with standard nucleic acids chemistry.

Biotechnology↗
PubMed2006

Understanding the genetics of regulation of aflatoxin production and Aspergillus flavus development.

Aflatoxins are polyketide-derived, toxic, and carcinogenic secondary metabolites produced primarily by two fungal species, Aspergillus flavus and A. parasiticus, on crops such as corn, peanuts, cottonseed, and treenuts. Regulatory guidelines issued by the U.S. Food and Drug Administration (FDA) prevent sale of commodities if contamination by these toxins exceeds certain levels. The biosynthesis of these toxins has been extensively studied. About 15 stable precursors have been identified. The genes involved in encoding the proteins required for the oxidative and regulatory steps in the biosynthesis are clustered in a 70 kb portion of chromosome 3 in the A. flavus genome. With the characterization of the gene cluster, new insights into the cellular processes that govern the genes involved in aflatoxin biosynthesis have been revealed, but the signaling processes that turn on aflatoxin biosynthesis during fungal contamination of crops are still not well understood. New molecular technologies, such as gene microarray analyses, quantitative polymerase chain reaction (PCR), and chromatin immunoprecipitation are being used to understand how physiological stress, environmental and soil conditions, receptivity of the plant, and fungal virulence lead to episodic outbreaks of aflatoxin contamination in certain commercially important crops. With this fundamental understanding, we will be better able to design improved non-aflatoxigenic biocompetitive Aspergillus strains and develop inhibitors of aflatoxin production (native to affected crops or otherwise) amenable to agricultural application for enhancing host-resistance against fungal invasion or toxin production. Comparisons of aflatoxin-producing species with other fungal species that retain some of the genes required for aflatoxin formation is expected to provide insight into the evolution of the aflatoxin gene cluster, and its role in fungal physiology. Therefore, information on how and why the fungus makes the toxin will be valuable for developing an effective and lasting strategy for control of aflatoxin contamination.

Aflatoxins↗
PubMed2006

The aflatoxin pathway regulator AflR induces gene transcription inside and outside of the aflatoxin biosynthetic cluster.

Aflatoxin contamination of food and feed is a major concern due to the carcinogenic properties of this mycotoxin. Previous studies using classical approaches have identified a cluster of genes responsible for aflatoxin production under the control of the pathway-specific transcriptional regulator aflR, but it is unknown whether aflR controls expression of other genes within the genome. Transcription profiling comparing wild type and DeltaaflR strains of Aspergillus parasiticus grown under conditions conducive for aflatoxin production identified only 23 upregulated genes in the wild type. These included 20 genes in the aflatoxin biosynthetic cluster, and three additional genes outside the aflatoxin biosynthetic cluster (nadA, hlyC, and niiA), all with AflR binding sites. This report is the first to demonstrate genes outside the biosynthetic cluster as being associated with aflR expression.

Aflatoxins↗
PubMed2006

Diagnosis and screening for familial hypercholesterolaemia: finding the patients, finding the genes.

Familial hypercholesterolaemia (FH) is a genetic disorder in which the concentration of serum cholesterol is elevated from birth and leads to premature coronary heart disease. FH is commonly caused by a mutation in the LDL receptor, but mutations in other genes can lead to a phenotype similar to FH. FH exhibits marked phenotypic variability due to genetic, metabolic and environmental factors. The presence of tendon xanthomata is the characteristic clinical sign seen in many patients with FH, but they may also have other non-specific signs of lipid disorders such as corneal arcus and xanthelasmata. Premature vascular disease is apparent in many patients. The wide variety of mutations and phenotypic variability have made it difficult to establish definite diagnostic criteria, but three sets of clinical criteria commonly used are the Simon Broome criteria, the Dutch Lipid Clinic criteria and the American criteria. FH screening fits the Wilson and Jungner recommendations for validity of a screening programme. Screening could be carried out on a population basis, in a clinical setting or by application to relatives of probands. This latter approach, termed cascade testing, appears to be the more cost-effective compared with population screening and can be carried out using clinical criteria or genetic testing, or by a combination of both methods. Clinicians need to be made more aware of the clinical features of FH and how to diagnose it in order to increase the index of suspicion and instigate appropriate treatment early, with the aim of preventing premature coronary heart disease.

Adolescent↗
PubMed2005

Genome sequencing and analysis of Aspergillus oryzae.

The genome of Aspergillus oryzae, a fungus important for the production of traditional fermented foods and beverages in Japan, has been sequenced. The ability to secrete large amounts of proteins and the development of a transformation system have facilitated the use of A. oryzae in modern biotechnology. Although both A. oryzae and Aspergillus flavus belong to the section Flavi of the subgenus Circumdati of Aspergillus, A. oryzae, unlike A. flavus, does not produce aflatoxin, and its long history of use in the food industry has proved its safety. Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans and Aspergillus fumigatus. Comparison of the three aspergilli species revealed the presence of syntenic blocks and A. oryzae-specific blocks (lacking synteny with A. nidulans and A. fumigatus) in a mosaic manner throughout the genome of A. oryzae. The blocks of A. oryzae-specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.

Aspartic Acid Endopeptidases↗
PubMed2005

Protective role of Vitamin E pre-treatment on N-nitrosodiethylamine induced oxidative stress in rat liver.

Nitrosamine compounds are known hepatic carcinogens. In the metabolism of nitrosamines, such as N-nitrosodiethylamine (NDEA), there is evidence of the formation of reactive oxygen species (ROS) resulting in oxidative stress, which may be one of the factors in the etiology of cancer. The formation of ROS may alter the antioxidant system, while the presence of Vitamin E may counteract NDEA induced oxidative stress. This study was planned to determine whether pre-treatment with Vitamin E (40 mg/kg body weight, i.p., twice a week for 4 weeks) to NDEA induced rats provides protection against oxidative stress in liver caused by the carcinogen. A single necrogenic dose of NDEA (200mg/kg body weight) was administered i.p. to the male albino rats with or without Vitamin E pre-treatment and the animals were sacrificed on Days 7, 14 or 21 after the administration of NDEA. The result showed enhanced levels of hepatic lipid peroxidation (LPO) and conjugated dienes of NDEA treated rats as the indices of oxidative stress, however, Vitamin E pre-treated rats administered NDEA showed decreased LPO and conjugated dienes (Day 21). Superoxide dismutase (SOD) activity in liver was not altered significantly in NDEA treated rats with or without Vitamin E pre-treatment. Catalase (CAT) activity was inhibited with NDEA treatment, however, Vitamin E pre-treatment showed recovery in hepatic CAT activity (Days 14 and 21). Total and Se-glutathione peroxidase (GSH-Px) activities and glutathione-S-transferase (GST) activity in liver increased in NDEA treated rats irrespective of Vitamin E pre-treatment. Glutathione reductase (GSH-R) activity as well as total glutathione (GSH) content in liver decreased in NDEA treated animals, both of which were recovered in Vitamin E pre-treated rats administered NDEA. Activities of serum aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP) and lactate dehydrogenase (LDH) were increased significantly following NDEA treatment to rats with or without Vitamin E pre-treatment. The activities of AST and ALT enzymes were significantly reduced on Days 14 and 21 and ALP activity was reduced on Day 21 in NDEA+Vitamin E treated animals when compared to NDEA treated alone. LDH enzyme activity was normalized on Day 14 in Vitamin E pre-treated animals administered NDEA. However, the AST, ALT and ALP enzyme activities remained high in all treatment groups as compared to control group. Normal control and Vitamin E treated alone rats revealed normal histology of liver. On the other hand, NDEA treated animals showed alterations in normal hepatic histoarchitecture, which comprised of necrosis and vacuolization of the cells. However, the rats treated with Vitamin E+NDEA showed that the liver cells were normal, with very little necrosis (Day 21). This study concludes that the pre-treatment with Vitamin E prior to the administration of NDEA, reduced the degree of oxidative stress, although this vitamin produced only slight changes in the hepatic injury, in a time-dependent manner.

Animals↗
PubMed2004

Examination of fungal stress response genes using Saccharomyces cerevisiae as a model system: targeting genes affecting aflatoxin biosynthesis by Aspergillus flavus Link.

Saccharomyces cerevisiae served as a model fungal system to examine functional genomics of oxidative stress responses and reactions to test antioxidant compounds. Twenty-two strains of S. cerevisiae, including a broad spectrum of singular gene deletion mutants, were exposed to hydrogen peroxide (H2O2) to examine phenotypic response to oxidative stress. Responses of particular mutants treated with gallic, tannic or caffeic acids, or methyl gallate, during H2O2 exposure, indicated that these compounds alleviated oxidative stress. These compounds are also potent inhibitors of aflatoxin biosynthesis in Aspergillus flavus. To gain further insights into a potential link between oxidative stress and aflatoxin biosynthesis, 43 orthologs of S. cerevisiae genes involved in gene regulation, signal transduction (e.g., SHO1, HOG1, etc.) and antioxidation (e.g., CTT1, CTA1, etc.) were identified in an A. flavus expressed sequence tag library. A successful exemplary functional complementation of an antioxidative stress gene from A. flavus, mitochondrial superoxide dismutase (sodA), in a sod2Delta yeast mutant further supported the potential of S. cerevisiae deletion mutants to serve as a model system to study A. flavus. Use of this system to further examine functional genomics of oxidative stress in aflatoxigenesis and reduction of aflatoxin biosynthesis by antioxidants is discussed.

Aflatoxins↗
PubMed2004

A novel approach to treatment of hypertension in diabetic patients - a multicenter, double-blind, randomized study comparing the efficacy of combination therapy of Eprosartan versus Ramipril with low-dose Hydrochlorothiazide and Moxonidine on blood pressure levels in patients with hypertension and associated diabetes mellitus type 2 - rationale and design [ISRCTN55725285].

Hypertension and diabetes mellitus are closely interrelated and coexist in as many as two-thirds of patients with type 2 diabetes. The consequent risk of such an association is an accelerated development of atherosclerotic cardiovascular disease and nephropathy complications.In choosing an antihypertensive agent, effectiveness needs to be accompanied by favourable metabolic, cardioprotective, and nephroprotective properties. Given the multifactorial nature of hypertension, the approach that has gained widespread agreement is treatment with more than one agent. Agents with different mechanisms of action increase antihypertensive efficacy because of synergistic impacts on the cardiovascular system. Combination therapy allows the use of lower doses of each antihypertensive agent which accounts for the excellent tolerability of combination products.The aim of the present study is to quantify the efficacy of combination therapy of Eprosartan 600 mg respectively Ramipril 5 mg with low-dose Hydrochlorothiazide and Moxonidine on blood pressure levels in patients with essential hypertension and associated diabetes mellitus type 2.The use of monotherapy (Eprosartan or Ramipril) followed by addition of low-dose Hydrochlorothiazide as second agent and of Moxonidine as a third agent will be individualized to the severity of hypertension in the particular patient and to his/her degree of response to current treatment.

Journal Article↗
PubMed2004

Aspergillus flavus expressed sequence tags for identification of genes with putative roles in aflatoxin contamination of crops.

Aflatoxins, produced primarily by Aspergillus flavus and A. parasiticus, are among the most toxic and carcinogenic naturally occurring compounds. In an attempt to identify genes potentially involved in aflatoxin contamination of crops, and to better understand the biology of A. flavus, a large scale sequencing of A. flavus expressed sequence tags (EST) was conducted. The 5' ends of 26,110 cDNA clones from a normalized cDNA expression library were sequenced. After annotation, a total of 7218 unique ESTs in A. flavus were assembled into 3749 tentative concensus sequences and 3469 singleton sequences. The functional classifications of the genes or Gene Ontology (GO) terms were assigned to these ESTs. Genes potentially involved in the aflatoxin contamination process were identified in the ESTs sequenced. These include the aflatoxin biosynthetic pathway, signal transduction, global regulation, pathogenicity of the fungus, and stress response.

Aflatoxins↗
PubMed2004

Completed sequence of aflatoxin pathway gene cluster in Aspergillus parasiticus.

An 82-kb Aspergillus parasiticus genomic DNA region representing the completed sequence of the well-organized aflatoxin pathway gene cluster has been sequenced and annotated. In addition to the 19 reported and characterized aflatoxin pathway genes and the four sugar utilization genes in this cluster, we report here the identification of six newly identified genes which are putatively involved in aflatoxin formation. The function of these genes, the cluster organization and its significance in gene expression are discussed.

Aflatoxins↗
PubMed2004

RNA interference silencing the transcriptional message: aspects and applications.

RNA interference (RNAi) is silencing of gene expression by double-stranded RNA (dsRNA) having complementary sequence to the target gene to be silenced. This phenomenon has transformed into a complete technology for functional genomic studies. Small interfering RNAs (siRNAs) are 21- to 23-nucleotide dsRNAs, in which the sense strand is the same as the target mRNA and the antisense strand is the complement of the target mRNA sequence. These are the effector molecules for inducing RNAi, leading to posttranscriptional gene silencing with RNA-induced silencing complex. Besides siRNA, which can be chemically synthesized, various other systems in the form of potential effector molecules for posttranscriptional gene silencing are available, such as short hairpin RNAs (shRNAs), long dsRNAs, short temporal RNAs, and micro RNAs (miRNAs). These effector molecules either are processed into siRNA such as in the case of shRNA or directly aid gene silencing as in the case of miRNA. RNAi for various unknown genes may facilitate to elucidate inherited genetic diseases and provide drug candidates for viral and oncogenic diseases. This can be achieved by targeting mRNA from oncogenic genes or mRNA for viral cellular receptor and viral structural proteins for RNAi. In this article, we evaluate various aspects and applications of RNAi technology and provide comprehensive information for the system currently available for inducing RNAi.

Agriculture↗
PubMed2003

Genetic analysis of morphological variants of Aspergillus parasiticus deficient in secondary metabolite production.

Aflatoxins (AFs) are secondary metabolites produced mainly by Aspergillus parasiticus and A. flavus. To study AF regulation, previously isolated non-toxigenic A. parasiticus sec- (for secondary metabolism minus) variants were genetically analysed. In parasexual crossing, the sec- strains failed to form heterokaryons and diploids with other sec- strains. Heterokaryon test results suggested that involvement of cytoplasmic elements in the formation of sec- phenotype was unlikely. At the molecular level, the coding sequence of the sec- aflR (the only known positive regulator of AF pathway) was identical to that of their toxigenic sec+ (for secondary metabolism plus) parents. However, the sec- aflR expression was 5- to 10-fold lower compared to that in the sec+ forms. RT-PCR analysis demonstrated that the AF pathway genes were expressed in the sec- forms but in trace amounts and in their unprocessed forms. Combined, these results suggest that aflR is necessary but not sufficient for AF production and that elements involved in fungal development directly or indirectly influence its proper function.

Aflatoxins↗