PPS: A computing engine to find Palindromes in all Protein sequences

The primary structure of a protein molecule comprises a linear chain of amino acid residues. Certain parts of this linear chain are unique in nature and function. They can be classified under different categories and their roles studied in detail. Two such unique categories are the palindromic sequences and the Single Amino Acid Repeats (SAARs), which plays a major role in the structure, function and evolution of the protein molecule. In spite of their presence in various protein sequences, palindromes have not yet been investigated in detail. Thus, to enable a comprehensive understanding of these sequences, a computing engine, PPS, has been developed. The users can search the occurrences of palindromes and SAARs in all the protein sequences available in various databases and can view the three-dimensional structures (in case it is available in the known three-dimensional protein structures deposited to the Protein Data Bank) using the graphics plug-in Jmol. The proposed server is the first of its kind and can be freely accessed through the World Wide Web.

Availability

URL http://pranag.physics.iisc.ernet.in/pps/     

Chemical composition and antioxidant activity of Strobilanthes crispus leaf extract

This study investigated the components present in and the total antioxidant activity of leaves of Strobilanthes crispus (L.) Bremek or Saricocalyx crispus (L.) Bremek (Acanthacea). Proximate analyses and total antioxidant activity using ferric thiocyanate and thiobarbituric acid methods were employed. Minerals content was determined using the atomic absorption spectrophotometer, whereas the water-soluble vitamins were determined by means of the UV-VIS spectrophotometer (vitamin C) and fluorimeter (vitamins B₁ and B₂). Catechin, tannin, caffeine, and alkaloid contents were also studied. All data were compared to the previously reported results of Yerbamate, green tea, black tea, and Indian tea. The dried leaves contained a high amount of total ash (21.6%) as a result of a high amount of minerals including potassium (51%), calcium (24%), sodium (13%), iron (1%), and phosphorus (1%). High content of water-soluble vitamins (C, B₁, and B₂) contributed to the high antioxidant activity of the leaves. The leaves also contained a moderate amount of other proximate composition as well as other compounds such as catechins, alkaloids, caffeine, and tannin, contributing further to the total antioxidant activity. Catechins of Strobilanthes crispus leaves showed highest antioxidant activity when compared to Yerbamate and vitamin E. Consumption of the leafy extract daily (5 g/day) as an herbal tea could contribute to the additional nutrients and antioxidants needed in the body to enhance the defense system, especially toward the incidence of degenerative diseases.     

Isolation of hexachlorocyclohexane-degrading Sphingomonas sp. by dehalogenase assay and characterization of genes involved in gamma-HCH degradation

Aim: To screen and identify bacteria from contaminated soil samples which can degrade hexachlorocyclohexane (HCH)‐isomers based on dechlorinase enzyme activity and characterize genes and metabolites. Methods and Results: Dechlorinase activity assays were used to screen bacteria from contaminated soil samples for HCH‐degrading activity. A bacterium able to grow on α‐, β‐, γ‐ and δ‐HCH as the sole carbon and energy source was identified. This bacterium was a novel species belonging to the Sphingomonas and harbour linABCDE genes similar to those found in other HCH degraders. γ‐Pentachlorocyclohexene 1,2,4‐trichlorobenzene and chlorohydroquinone were identified as metabolites. Conclusions: The study demonstrates that HCH‐degrading bacteria can be identified from large environmental sample‐based dehalogenase enzyme assay. This kind of screening is more advantageous compared to selective enrichment as it is specific and rapid and can be performed in a high‐throughput manner to screen bacteria for chlorinated compounds. Significance and Impact of the Study: The chlorinated pesticide HCH is a persistent and toxic environmental pollutant which needs to be remediated. Isolation of diverse bacterial species capable of degrading all the isomers of HCH will help in large‐scale bioremediation in various parts of the world.     

The crosslinking and antimicrobial properties of tunichrome

Tunichromes are small peptides containing one or more dehydrodopa derived units that have been identified in the blood cells of at least eleven species of tunicates. Incubation of tunichromes isolated from Ascidia nigra hemocytes (or model dopa-containing compounds) under oxidative conditions with either lysozyme, cytochrome c or ovalbumin resulted in a time-dependent polymerization of these test proteins to dimers, trimers, tetramers and potentially to other oligomers. These results indicate that the oxidation products of tunichromes possess inherent crosslinking properties. Hence it is possible that tunichromes participate in tunic production by forming adducts and crosslinks with structural proteins and/or carbohydrate polymers, similar to the well-understood process of insect cuticle hardening. Since such crosslinking potentials could also be beneficial for defense reactions against invading microorganisms, antibacterial activity of tunichromes was tested using both a radial diffusion assay and the Microtox(R) test. Tunichromes exhibited antimicrobial activity against gram-negative bacteria Escherichia coli and Photobacterium phosphorium. However, they did not show any antimicrobial activity against the gram-positive bacteria Staphylococcus aureus at the concentrations tested. We propose that the crosslinking and antimicrobial functions are both based on the reactivity of dehydrodopa units present in the tunichromes, and their subsequent ability to form highly reactive quinone methides.     

Simultaneous Biodegradation of Polyaromatic Hydrocarbons by a <Emphasis Type="Italic">Stenotrophomonas</Emphasis> sp: Characterization of <Emphasis Type="Italic">nid</Emphasis> Genes and Effect of Surfactants on Degradation

A polyaromatic hydrocarbon degrading bacterium was isolated from a petroleum contaminated site and designated as Stenotrophomonas sp. strain IITR87. It was found to utilize pyrene, phenanthrene and benzo(a)pyrene as sole carbon source, but not anthracene, chrysene and fluoranthene. Gas chromatography and mass spectroscopy analysis resulted in identification of pyrene metabolites namely monohydroxypyrene, 4-oxa-pyrene-5-one, dimethoxypyrene and monohydroxyphenanthrene. Southern hybridization using naphthalene dioxygenase gene (nidA) as probe against the DNA of strain IITR87 revealed the presence of nidA gene. PCR analysis suggests dispersed occurrence of nid genes in the genome instead of a cluster as reported in a PAH-degrading Mycobacterium vanbaalenii PYR-1. The nid genes in strain IITR87, dioxygenase large subunit (nidA), naphthalene dioxygenase small subunit (nidB) and aldehyde dehydrogenase gene (nidD) showed more than 97 % identity to the reported nid genes from Mycobacterium vanbaalenii PYR-1. Most significantly, the biodegradation of PAHs was enhanced 25–60 % in the presence of surfactants rhamnolipid and Triton X-100 due to increased solubilization and bioavailability. These results could be useful for the improved biodegradation of high-molecular-weight PAHs in contaminated habitats.     

A new species of Beilschmiedia (Lauraceae) from the Western Ghats,India

Beilschmiedia tirunelvelica is described and illustrated as a new species from the Western Ghats of Agasthiyamalai Biosphere Reserve, India. The differences to similar taxa are provided with dichotomous key and table.     

Leptospermum flavescens Constituent-LF1 Causes Cell Death through the Induction of Cell Cycle Arrest and Apoptosis in Human Lung Carcinoma Cells

Leptospermum flavescens Sm. (Myrtaceae), locally known as ‘Senna makki’ is a smallish tree that is widespread and recorded to naturally occur in the montane regions above 900 m a.s.l from Burma to Australia. Although the species is recorded to be used traditionally to treat various ailments, there is limited data on biological and chemical investigations of L. flavescens. The aim of the present study was to investigate and understand the ability of L. flavescens in inducing cell death in lung cancer cells. The cytotoxic potentials of the extraction yields (methanol, hexane, ethyl acetate and water extracts as wells as a semi pure fraction, LF1) were evaluated against two human non-small cell lung carcinoma cell lines (A549 and NCI-H1299) using the MTT assay. LF1 showed the greatest cytotoxic effect against both cell lines with IC₅₀ values of 7.12 ± 0.07 and 9.62 ± 0.50 μg/ml respectively. LF1 treated cells showed a sub-G₁ region in the cell cycle analysis and also caused the presence of apoptotic morphologies in cells stained with acridine orange and ethidium bromide. Treatment with LF1 manifested an apoptotic population in cells that were evaluated using the Annexin V/ propidium iodide assay. Increasing dosage of LF1 caused a rise in the presence of activated caspase-3 enzymes in treated cells. Blockage of cell cycle progression was also observed in LF1-treated cells. These findings suggest that LF1 induces apoptosis and cell cycle arrest in treated lung cancer cells. Further studies are being conducted to isolate and identify the active compound as well to better understand the mechanism involved in inducing cell death.     

Biological treatment of waste with high ash content using a hydrolytically assisted extended aeration process

In previous reports from this laboratory it has been shown that the extended aeration process for biological treatment of organically laden municipal and/or industrial waste could be successfully employed for concurrent purification and sludge disposal. Also results using a modified process in which autodigestion was aided and controlled by periodic partial hydrolysis of small portions of the recycle sludge showed that operational control was feasible. There was some question regarding the success of such a process if the original waste contained a large portion of inorganic solids. Accordingly, a 1½ year pilot plant study was made using a waste (hydrolyzed trickling filter sludge) of exceptionally high ash content (50–60%). It was found that the ash content of activated sludge grown on this substrate did not continually increase nor did the high ash content of the waste interfere in any way with the efficiency of removal of organic matter. In general it exceeded 90 percent. Also a highly nitrified effluent was produced. A variety of analyses were performed: COD, BOD, TOC, suspended solids, NH₃-N, organic-N, NO₃-N, etc. Interrelationships between these important monitoring parameters for assessing plant performance offered useful insight into operational control for hydrolytically assisted extended aeration processes.     

Insect cuticular melanins are distinctly different from those of mammalian epidermal melanins

Melanin from several insect samples was isolated and subjected to chemical degradation and HPLC analysis for melanin markers. Quantification of different melanin markers reveals that insect melanins are significantly different from that of the mammalian epidermal melanins. The eumelanin produced in mammals is derived from the oxidative polymerization of both 5,6‐dihydroxyindole and 5,6‐dihydroxyindole‐2‐carboxylic acids. The pheomelanin is formed by the oxidative polymerization of cysteinyldopa. Thus, dopa is the major precursor for both eumelanin and pheomelanin in mammals. But insect eumelanin appears to be mostly made from 5,6‐dihydroxyindole and originates from dopamine. More importantly, our study points out the wide spread occurrence of pheomelanin in many insect species. In addition, cysteinyldopamine and not cysteinyldopa is the major precursor for insect pheomelanin. Thus, both eumelanin and pheomelanin in insects differ from higher animals using dopamine and not dopa as the major precursor.