Hydroxymethylation of DNA

DNA methylation, an epigenetic mechanism is claimed to play essential roles in development, aging and disease over the past few decades. Cytosines (C) were known to exist in two functional states: unmethylated or methylated (5mC) in the mammalian genome for a very long time. However, the mechanisms controlling 5mC dynamics remain undefined. Recent studies of genomic DNA on human and mouse brain, neurons and from mouse embryonic stem cells have shown that 2-oxoglutarate and Fe(II)-dependent oxygenases of the ten-eleven translocation (Tet) proteins can catalyze the oxidation of 5mC at cpG dinucleotides to form 5-hydroxymethylcytosine (5-hmC). The exhilarating discovery of these novel 5-hmC has begun to focus on the dynamic nature of 5mC. The prevailing evidence has shown that Tet family proteins and 5-hmC are involved in the normal development as well as in many diseases. This review presents an overview of the role of Tet family proteins and 5-hmC. It also discusses their role as an epigenetic marker and the techniques used for their analysis

Apoptosis: molecular mechanisms and pathogenicity

Apoptosis triggered by exogenous and endogenous stimuli such as ultraviolet radiation, oxidative stress, and genotoxic chemicals is a crucial phenomenon within biological systems. DNA damage activates and stabilizes p53 in nucleus and cytoplasm and regulates other proteins that stimulate intrinsic and extrinsic apoptotic pathways. Apoptosis is morphologically distinct from that of necrosis and both the phenomena depend on the types, developmental stages, physiological environment of tissues and the nature of death signal. Malfunctioning of apoptotic pathway may cause human diseases like cancer, neurodegenerative and autoimmune disorders. Recently, potent apoptosis-inducing compounds associated with human health have been recorded that prevent tumor promotion, progression, and the occurrence of cellular inflammatory responses. Certain photosensitizing drugs are being employed in photodynamic therapy to induce apoptosis for the treatment of cancer and non-cancerous cells. This review emphasizes the molecular mechanisms of apoptosis, associated diseases and certain therapeutic agents implicated in the elimination of malignant cells

Genome mining of mycosporine-like amino acid (MAA) synthesizing and non-synthesizing cyanobacteria: A bioinformatics study

AbstractMycosporine-like amino acids (MAAs) are a family of more than 20 compounds having absorption maxima between 310 and 362 nm. These compounds are well known for their UV-absorbing/screening role in various organisms and seem to have evolutionary significance. In the present investigation we tested four cyanobacteria, e.g., Anabaena variabilis PCC 7937, Anabaena sp. PCC 7120, Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 6301, for their ability to synthesize MAA and conducted genomic and phylogenetic analysis to identify the possible set of genes that might be involved in the biosynthesis of these compounds. Out of the four investigated species, only A. variabilis PCC 7937 was able to synthesize MAA. Genome mining identified a combination of genes, YP_324358 (predicted DHQ synthase) and YP_324357 (O-methyltransferase), which were present only in A. variabilis PCC 7937 and missing in the other studied cyanobacteria. Phylogenetic analysis revealed that these two genes are transferred from a cyanobacterial donor to dinoflagellates and finally to metazoa by a lateral gene transfer event. All other cyanobacteria, which have these two genes, also had another copy of the DHQ synthase gene. The predicted protein structure for YP_324358 also suggested that this product is different from the chemically characterized DHQ synthase of Aspergillus nidulans contrary to the YP_324879, which was predicted to be similar to the DHQ synthase. The present study provides a first insight into the genes of cyanobacteria involved in MAA biosynthesis and thus widens the field of research for molecular, bioinformatics and phylogenetic analysis of these evolutionary and industrially important compounds. Based on the results we propose that YP_324358 and YP_324357 gene products are involved in the biosynthesis of the common core (deoxygadusol) of all MAAs

Molecular Mechanisms of Ultraviolet Radiation-Induced DNA Damage and Repair

DNA is one of the prime molecules, and its stability is of utmost importance for proper functioning and existence of all living systems. Genotoxic chemicals and radiations exert adverse effects on genome stability. Ultraviolet radiation (UVR) (mainly UV-B: 280–315 nm) is one of the powerful agents that can alter the normal state of life by inducing a variety of mutagenic and cytotoxic DNA lesions such as cyclobutane-pyrimidine dimers (CPDs), 6-4 photoproducts (6-4PPs), and their Dewar valence isomers as well as DNA strand breaks by interfering the genome integrity. To counteract these lesions, organisms have developed a number of highly conserved repair mechanisms such as photoreactivation, base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR). Additionally, double-strand break repair (by homologous recombination and nonhomologous end joining), SOS response, cell-cycle checkpoints, and programmed cell death (apoptosis) are also operative in various organisms with the expense of specific gene products. This review deals with UV-induced alterations in DNA and its maintenance by various repair mechanisms

DNA damage

Even under the best of circumstances, DNA is constantly subjected to chemical modifications. Several types of DNA damage such as SSB (single strand break), DSB (double strand break), CPDs (cyclobutane pyrimidine dimers), 6-4PPs (6-4 photoproducts) and their Dewar valence isomers have been identified that result from alkylating agents, hydrolytic deamination, free radicals and reactive oxygen species formed by various photochemical processes including UV radiation. There are a number of strategies such as PCR (polymerase chain reaction), comet, halo, TUNEL (Terminal deoxyribonucleotidyltransferase-mediated deoxyuridine triphosphate nick end labeling) assay, HPLC-Electrospray tandem mass spectrometry, FISH (Fluorescence in situ hybridization), FCM (Flow cytometry), annexin V labeling, immunological assays including immunofluorescent and chemiluminescence thymine dimer detection, immunohistochemical assay, Enzyme-linked immunosorbent assay (ELISA), Radio immunoassay (RIA), Gas chromatography-mass spectrometry and electrochemical methods, that are commonly used to detect DNA damage in various organisms. The main aim of this review is to present a brief account of the above mentioned DNA damage detection strategies for the convenience of interested readers

Hepatotoxicity of Microcystis aeruginosa Strains Growing as Blooms in Certain Eutrophic Ponds

Critical assessment of five eutrophicated ponds of Varanasi city (India) revealed the presence of heavy blooms of cyanobacteria consisting mainly of Microcystis aeruginosa. Crude aqueous extracts of blooms as well as laboratory grown M. aeruginosa isolated from three ponds, namely Lakshmikund, Durgakund and Adityanagar showed toxicity in mouse bioassay test. Crude aqueous extracts from these samples caused death of test mice within 1h of administration (i.p.) with a LD50 of 60 mg/kg body weight and the treated animals showed clinical signs of hepatotoxicity. However such an effect was not associated with the blooms from Laatbhairov and Surajkund ponds suggesting that not all strains of M. aeruginosa are toxic. Based on spectral properties (?max 230 nm), and comparison with standard microcystin-LR, the toxin is tentatively identified as microcystin-LR. The purified toxin caused death of test mice within 40 min of its administration with a LD50 of 100 µg/ kg body weight and induced gross morphological and functional changes in liver. A 1.55 fold increase in liver weight accompanied by deep red coloration most probably due to hemorrhage and blood pooling suggested the hepatotoxic properties of the toxin. Hepatotoxicity was also evident from the drastic increase (up to 2.5 fold) in activity of serum enzymes such as glutamate pyruvate transaminase/alanine aminotransferase (GPT/ALT), lactate dehydrogenase (LDH) and alkaline phosphatase (APase) following toxin treatment. ^14C-labelling experiments demonstrated maximum accumulation (~15%) of ^14C- toxin after 20 min. of toxin administration. Appreciable level of toxin was also detected in water of four ponds. In conclusion these results clearly demonstrate that microcystin-producing blooms of M. aeruginosa are common in eutrophicated ponds of Varanasi city but not all ponds harbour toxic blooms

Effects of UV radiation on aquatic ecosystems and interactions with other environmental factors

Interactions between climate change and UV radiation are having strong effects on aquatic ecosystems due to feedback between temperature, UV radiation, and greenhouse gas concentration. Higher air temperatures and incoming solar radiation are increasing the surface water temperatures of lakes and oceans, with many large lakes warming at twice the rate of regional air temperatures. Warmer oceans are changing habitats and the species composition of many marine ecosystems. For some, such as corals, the temperatures may become too high. Temperature differences between surface and deep waters are becoming greater. This increase in thermal stratification makes the surface layers shallower and leads to stronger barriers to upward mixing of nutrients necessary for photosynthesis. This also results in exposure to higher levels of UV radiation of surface-dwelling organisms. In polar and alpine regions decreases in the duration and amount of snow and ice cover on lakes and oceans are also increasing exposure to UV radiation. In contrast, in lakes and coastal oceans the concentration and colour of UV-absorbing dissolved organic matter (DOM) from terrestrial ecosystems is increasing with greater runoff from higher precipitation and more frequent extreme storms. DOM thus creates a refuge from UV radiation that can enable UV-sensitive species to become established. At the same time, decreased UV radiation in such surface waters reduces the capacity of solar UV radiation to inactivate viruses and other pathogens and parasites, and increases the difficulty and price of purifying drinking water for municipal supplies. Solar UV radiation breaks down the DOM, making it more available for microbial processing, resulting in the release of greenhouse gases into the atmosphere. In addition to screening solar irradiance, DOM, when sunlit in surface water, can lead to the formation of reactive oxygen species (ROS). Increases in carbon dioxide are in turn acidifying the oceans and inhibiting the ability of many marine organisms to form UV-absorbing exoskeletons. Many aquatic organisms use adaptive strategies to mitigate the effects of solar UV-B radiation (280–315 nm), including vertical migration, crust formation, synthesis of UV-absorbing substances, and enzymatic and non-enzymatic quenching of ROS. Whether or not genetic adaptation to changes in the abiotic factors plays a role in mitigating stress and damage has not been determined. This assessment addresses how our knowledge of the interactive effects of UV radiation and climate change factors on aquatic ecosystems has advanced in the past four years.Fil: Häder, Donat P.. Universitat Erlangen-Nuremberg; AlemaniaFil: Williamson, Craig E.. Miami University; Estados UnidosFil: Wängberg, Sten Åke. University of Gothenburg. Department of Biological and Environmental Science; SueciaFil: Rautio, Milla. Université du Québec à Chicoutimi. Département des Sciences Fondamentales and Centre for Northern Studies; CanadáFil: Rose, Kevin C.. University Of Wisconsin; Estados UnidosFil: Gao, Kunshan. Xiamen University. State Key Laboratory of Marine Environmental Science; ChinaFil: Helbling, Eduardo Walter. Fundación Playa Unión. Estación de Fotobiología Playa Unión; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Sinha, Rajeshwar P.. Banaras Hindu University. Centre of Advanced Study in Botany; IndiaFil: Worrest, Robert. Columbia University; Estados Unido

Phytoplankton assemblage and UV-protective compounds in the river Ganges

Interactions between physico-chemical parameters such as pH, temperature, nitrate, phosphate, alkalinity, acidity, biological oxygen demand (BOD), chemical oxygen demand (COD) and solar ultraviolet radiation (UVR) strongly affect aquatic ecosystems. Due to fluctuations in several environmental factors including river water pollution and UVR, organisms are under constant threat. However, phytoplankton protects themselves from environmental extremes by adopting several defense strategies including synthesis of photoprotective compounds such as scytonemin and mycosporine-like amino acids (MAAs).We investigated the presence of scytonemin and MAAs in phytoplankton of some polluted sites of one of the holy rivers of the world, the Ganges at Varanasi, India. We observed phytoplankton assemblages and studied certain environmental parameters which could possibly affect phytoplankton diversity in the river. Phytoplankton consisted mainly of 49 taxa of 34 genera belonging to Bacillariophyceae, Chlorophyceae, Cyanophyceae, and Chrysophyceae. The members belonging to Bacillariophyceae and Chlorophyceae were the two dominant classes, which comprised up to 75% of the total phytoplankton.Photoprotective compounds were isolated and characterized from phytoplankton. Electrospray ionization-mass spectrometry (ESI-MS) analysis of MAAs showed the presence of shinorine, palythinol, mycosporine-glycine and palythine. A high concentration of scytonemin was also observed with an absorption maximum at 386 nm in the studied phytoplankton

Screening and partial purification of photoprotective pigment scytonemin from cyanobacterial crusts dwelling on the historical monuments in and around Varanasi, India

In the present investigation, biological crusts from the surface of eight historical monuments of Varanasi, India, were examined for the presence of scytonemin (a cyanobacterial photoprotective pigment) containing cyanobacterial species. Lyngbya sp. and Scytonema sp. were the dominant cyanobacteria present in all crust samples. The absorption spectroscopic data of chlorophyll, carotenoids and scytonemin showed that scytonemin was more abundant than the carotene and chlorophyll in all the crusts. Identification of these compounds was done using UV-Vis spectroscopy and High Performance Liquid Chromatography (HPLC) analysis. HPLC analysis revealed the presence of scytonemin in seven out of eight samples and peaks of scytonemin with retention time ranging from 1.4-1.9 min with corresponding absorbance maxima at 386, 300 and 252±2 nm. As per our knowledge this is the first report of its kind from monuments of Varanasi. From this study, it can be concluded that synthesis of photoprotective compounds like scytonemin and its derivatives counteract the damaging effects of solar radiation which enable cyanobacteria to colonize and inhabit almost all kinds of habitats, including extreme lithic habitats, such as rocks and walls of monuments which face prolonged high intensity solar radiation

International Journal of Pharma and Bio Sciences REVIEW ARTICLE BIOTECH�OLOGY COLLOIDAL GOLD BASED DIPSTICK STRIP FOR DETECTIO � OF GE�ETICALLY MODIFIED CROPS A�D PRODUCE

The production of genetically modified (GM) crops is rapidly increasing every single year worldwide. The safety and quality evaluation of these crops is an important issue regarding to consumers ’ health. This led the regulatory authorities to implement a set of very strict procedures for the approval to grow and utilize GM produce. Therefore, for fulfilling regulatory compliance on GM labeling and identification of genetic traits, it generated a demand for analytical methods capable of detecting either transgenic DNA introduced or the protein expressed in GM crops. The detection methods include either DNA based PCR assay or protein based ELISA and dipstick assays. This article illustrates the advances in colloidal gold based dipstick procedure for visual discrimination of GM crops/produce from non-GM. This article can be downloaded from www.ijpbs.ne