Extension of molecular similarity analysis approach to classification of DNA sequences using DNA descriptors

Several alignment-free sequence comparison methods are available which use similarity, based on a particular numerical descriptor of biological sequences. Any loss of information incurred in the transformation of a sequence into a numerical descriptor affects the results. A pool of descriptors that use different algorithms in their computation is expected to suffer minimum loss of information and an attempt is made in this direction to study the similarity of DNA sequences. A number of descriptors based on information theory and connectivity were computed for DNA sequences. Principal component analysis (PCA) was used to extract minimum number (N) of orthogonal descriptors, principal components (PCs). Similarity/dissimilarity clustering of DNA sequences were carried out in the N-dimensional similarity space constructed using the PCs extracted from the DNA descriptors. The paper explains the extension of quantitative molecular similarity analysis (QMSA) from the prediction of physicochemical properties and toxicity of chemicals to bioinformatics for the classification of DNA sequences.

New topological indices with very high discriminatory power

Several molecular descriptors are used in developing quantitative structure-activity relationships (QSARs). A large number of them are already in use and new descriptors are added every year. Two new topological indices with very high discriminatory power are reported in this paper. The two indices ranked all planar graphs of alkanes C(4) to C(6) uniquely and were found to have non-degenerate values for all the 7668 constitutional isomers (alkane trees) from C(4) to C(15). Low intercorrelation with several of the commonly used topological indices was studied using a diverse data set of 820 chemicals and the new indices proposed in the study were found to cluster in different nodes. This further confirmed their low intercorrelation with other molecular descriptors used in the study. The new descriptors were found to be useful in QSAR modelling.

Systematic list of the species added to the mosquito museum at the Vector Control Research Centre, Pondicherry, India

Mosquito species housed in the mosquito museum at the Vector Control Research Centre, Pondicherry, India, were increased from 181 to 266 species belonging to 22 genera. The systematic list of the 85 species added to the collection is provided. The collection consists of a total of 31,874 adult specimens, of which 23,696 are individually mounted on minuten pins, while the rest are held in stock vials. It also includes 2,456 male genitalia and 470 female genitalia preparations, 3,523 larvae, 4,745 larval exuviae, and 3,057 pupal exuviae on microscope slides. Representative specimens of different species are available from 16 states and 3 union territories of India.

First record of genus Ayurakitia in India: occurrence of Ayurakitia peytoni in Meghalaya state

Larvae of Ayurakitia peytoni were collected in July 2008 from Pandanus axils during a survey of mosquito fauna in Meghalaya. This is the 1st record of the genus Ayurakitia in India, extending the known distribution of this genus farther west.

Hypoxia inducible factor-1α in human emphysema lung tissue

The pathobiology of chronic obstructive pulmonary disease (COPD) is not completely understood. The aim of this study was to assess the expression of hypoxia inducible factor (HIF)-1α in lung tissue from patients with COPD/emphysema. Lung tissue samples from 26 patients were included in this study. Seven samples were obtained from patients with normal lung function, the remainder of the samples were taken from patients with moderate COPD (n = 6; stage I and II Global Initiative for Chronic Obstructive Lung Disease classification) and severe COPD (n = 13; stage III and IV). We analysed mRNA and protein expression in the lung tissue samples and found that: 1) HIF-1α and histone deacetylase 2 proteins were significantly decreased and were correlated; 2) HIF-1α and vascular endothelial growth factor (VEGF) proteins, and forced expiratory volume in 1 s % predicted were correlated in all patients; 3) the changes in VEGF and HIF-1α protein levels in all patients were not age-related and not related to the pack-yr smoking history; and 4) the reduced HIF-1α protein expression was seen in lung endothelial cells and alveolar septal cells by immunohistochemistry. In conclusion, reduced expression of HIF-1α protein in severe COPD is consistent with the concept of a lung structure maintenance programme which is impaired on a molecular level.

Description of a new species of Culex (Lophoceraomyia) from Orissa, India

Female and male adults, male genitalia, pupae, and larvae of Culex (Lophoceraomyia) singhbhumensis, a new mosquito species, are described from Orissa, India.

Studies on the extraction of uranium by N-octanoyl-N-phenylhydroxamic acid

N-octanoyl-N-phenylhydroxamic acid (OHA) has been prepared by partial reduction of nitrobenzene with Zn dust/NH4Cl, followed by acylation with n-octanoyl chloride. Structure of OHA was confirmed by 1H NMR, IR spectra and CHNS microanalysis. The extraction of uranium by OHA has been studied as a function of pH, temperature and concentration of OHA. The extraction of uranium was found to increase with increase in pH. Uranium forms a 1:2 complex with OHA. IR Spectra & NMR Spectra of the uranium-OHA complex and slope analysis obtained from extraction studies indicated that the extraction of uranium was due to the formation of a chelate. The enthalpy change accompanied by the extraction of uranium by OHA has been obtained by temperature variation method. The extraction process was found to be endothermic at pH 2 and exothermic at pH 6.

Vitamin B6 status in patients with cancer of the uterine cervix

The activities of aspartate aminotransferase and alanine aminotransferase in erythrocytes with and without the addition of pyridoxal phosphate were determined in healthy controls and in Indian women with cancer of the uterine cervix. The percent stimulation of the erythrocyte transferases as a result of the addition of pyridoxal phosphate was negligible in the case of normal subjects (less than 5% stimulation). In the patients with cervical cancer, a 23-35% stimulation was observed, indicating a deficiency of vitamin B6. It is not yet known whether the deficiency is the cause of the disease or due to the tumor.

White-out from a Wii: traumatic haemothorax sustained playing Nintendo Wii

A case is reported of a patient who sustained a significant haemothorax while playing with a Nintendo Wii console.

Mosquitoes of the mangrove forests of India: part 7--an overview

Parts 1 to 6 of this series on the mosquitoes of the mangrove forests of India dealt with the mosquito species recorded in the mangroves of Bhitarkanika, Sundarbans, Andaman and Nicobar islands, Coringa, Chorao and Vikhroli, and Kundapur and Kannur. This concluding part provides an overview of the distribution of the mosquito species in different mangrove forests, including the mangroves of Muthupet in Tamilnadu and the mangroves of Gulf of Kutch and Gulf of Kambhat in Gujarat, species collected as larvae, species in relation to the salinity of the larval habitats, species landing on humans for feeding in the mangroves, and the impact of habitat degradation on species diversity.

Thermal decomposition of expanded polystyrene in a pebble bed reactor to get higher liquid fraction yield at low temperatures

Expanded polystyrene is one of the polymers produced in large quantities due to its versatile application in different fields. This polymer is one of the most intractable components in municipal solid waste. Disposal of polymeric material by pyrolysis or catalytic cracking yields valuable hydrocarbon fuels or monomers. Literature reports different types of reactors and arrangements that have uniform temperatures during pyrolysis and catalytic cracking. The present study focuses on reducing the temperature to maximize the quantity of styrene monomer in the liquid product. A bench scale reactor has been developed to recover the styrene monomer and other valuable chemicals. Experiments were carried under partial oxidation and vacuum conditions in the temperature range of 300-500 degrees C. In the pyrolysis optimization studies, the best atmospheric condition was determined to be vacuum, the pyrolysis temperature should be 500 degrees C, yield of liquid product obtained was 91.7% and yield of styrene obtained was 85.5%. In the characterization studies, distillation and IR spectroscopy experiments were carried out. The remaining of the liquid product comprises of benzene, ethyl benzene, and styrene dimers and trimers.

LR-90 prevents dyslipidaemia and diabetic nephropathy in the Zucker diabetic fatty rat

AIMS/HYPOTHESIS

Previous studies have shown that LR-90, a new inhibitor of AGE formation, prevented the development of experimental type 1 diabetic nephropathy. In this study, we examined the effects of LR-90 in the Zucker diabetic fatty (ZDF) rat, a model of type 2 diabetes and metabolic syndrome, and investigated the mechanisms by which it may protect against renal injury.

METHODS

Male ZDF rats were treated without or with LR-90 from age 13 to 40 weeks. Metabolic and kidney functions and renal histology were evaluated. AGE accumulation and the production of the receptor for AGE (AGER) were measured. Profibrotic growth factors, extracellular matrix proteins and intracellular signalling pathways associated with glomerular and tubular damage were also analysed.

RESULTS

LR-90 dramatically reduced plasma lipids in ZDF rats, with only modest effects on hyperglycaemia. Renal AGE, AGER and lipid peroxidation were all attenuated by LR-90. LR-90 significantly retarded the increase in albuminuria and proteinuria. This was associated with reduction in glomerulosclerosis and tubulointerstitial fibrosis, concomitant with marked inhibition of renal overproduction of TGF-beta1, connective tissue growth factor, fibronectin and collagen IV. Additionally, LR-90 downregulated the activation of key mitogen-activated protein kinases (MAPKs) and nuclear factor kappa B (NF-kappaB) in the renal cortex.

CONCLUSIONS/INTERPRETATION

These results support our earlier studies on the renoprotective effects of LR-90 on type 1 diabetic nephropathy and provide further evidence that LR-90, an AGE inhibitor with pleiotrophic effects, may also be beneficial for the prevention of type 2 diabetic nephropathy, where multiple risk factors, such as hyperglycaemia, dyslipidaemia, obesity, insulin resistance and hypertension, contribute to renal injury.

Mosquitoes of the mangrove forests of India: part 5--Chorao, Goa, and Vikhroli, Maharashtra

Mosquitoes of 14 species belonging to 9 subgenera and 9 genera were recorded in Chorao mangroves of Goa, and 12 species belonging to 9 subgenera and 7 genera in the mangroves of Vikhroli, Maharashtra, in India. Genera recorded were Aedes, Anopheles, Armigeres, Culex, Mansonia, Ochlerotatus, Orthopodomyia, Toxorhynchites, Uranotaenia, and Verrallina. Species common to both the mangroves were Ae. albopictus, Ae. novalbopictus, An. subpictus, Cx. sitiens, Oc. wardi, Ur. atra, and Ve. lugubris. Tree holes, crab holes, and swamp pools were the common larval habitats in Chorao, but tree holes were absent in Vikhroli. Adults of Ae. albopictus, Ae. novalbopictus, Ar. subalbatus, Cx. gelidus Cx. sitiens, Ma. indiana, Ur. atra, and Ve. lugubris were found landing on humans. Aedes novalbopictus, Oc. wardi, and Or. anopheloides are new records for the state of Goa.

Three dimensional structure-activity relationships (3D-QSAR) for insect repellency of diastereoisomeric compounds: a hierarchical molecular overlay approach

2-(2-Hydroxyethyl)-1-piperidinecarboxylic acid 1-methylpropyl ester (Picaridin), and 1-(cyclohex-3-ene-1-ylcarbonyl)-2-methylpiperidine (AI3-37220; 220) are alternatives to DEET (N,N-diethyl-3-methylbenzamide), the most popular mosquito repellent. Picaridin and AI3-37220 exhibit polychiral diastereoisomerism and each has four diastereoisomers due to the presence of two asymmetric centers in their molecules. The diastereoisomers of these compounds have differing degrees of mosquito-repellent activity according to quantitative behavioral assays conducted at the United States Department of Agriculture. An insight into the stereochemical requirements for repellency is of great importance in the development of better repellents. Molecular overlay of the optimized geometries of the diastereoisomers was considered as a novel tool for Stereochemical Structure-Activity Relationship (SSAR) modeling. An earlier study using molecular mechanics (MM2) optimized geometries showed good promise. In continuation of this effort and to overcome certain defects in using MM2 geometries, a hierarchical overlay approach was developed. In this method geometry of the low energy conformer of each diastereoisomer was optimized using: the following quantum chemical methods in a graduated manner: (a) semiempirical AM1, (b) Hartree Fock (STO3G, 3-21G, 6-31G, and 6-311G), and (c) Density Functional Theory (B3LYP/6-31G, B3LYP/6-311G). The optimized geometries of different diastereoisomers were overlaid in various user defined combinations to calculate the root mean square distances (RMSD) of the overlaid structures. The RMSD with respect to the most active diastereoisomer (220SS) were found to have a strong relationship with biological potency. Common motifs in shapes and molecular surfaces that are probably critical for effective repellent activity were identified. The hierarchical approach gave valuable information on the quantum chemical level (basis set) at which optimization must be carried out to get the correct order of repellency of the diastereoisomers of Picaridin and 220.

DNA barcodes can distinguish species of Indian mosquitoes (Diptera: Culicidae)

Species identification of mosquitoes (Diptera: Culicidae) based on morphological characteristics remains often difficult in field-collected mosquito specimens in vector-borne disease surveillance programs. The use of DNA barcodes has been proposed recently as a tool for identification of the species in many diverse groups of animals. However, the efficacy of this tool for mosquitoes remains unexplored. Hence, a study was undertaken to construct DNA barcodes for several species of mosquitoes prevalent in India, which included major vector species. In total, 111 specimens of mosquitoes belonging to 15 genera, morphologically identified to be 63 species, were used. This number also included multiple specimens for 22 species. DNA barcode approach based on DNA sequences of mitochondrial cytochrome oxidase gene sequences could identify 62 species among these, in confirmation with the conventional taxonomy. However, two closely related species, Ochlerotatus portonovoensis (Tiwari & Hiriyan) and Ochlerotatus wardi (Reinert) could not be identified as separate species based on DNA barcode approach, their lineages indicating negligible genetic divergence (Kimura two-parameter genetic distance = 0.0043).

DNA barcodes can distinguish species of Indian mosquitoes (Diptera: Culicidae)

Species identification of mosquitoes (Diptera: Culicidae) based on morphological characteristics remains often difficult in field-collected mosquito specimens in vector-borne disease surveillance programs. The use of DNA barcodes has been proposed recently as a tool for identification of the species in many diverse groups of animals. However, the efficacy of this tool for mosquitoes remains unexplored. Hence, a study was undertaken to construct DNA barcodes for several species of mosquitoes prevalent in India, which included major vector species. In total, 111 specimens of mosquitoes belonging to 15 genera, morphologically identified to be 63 species, were used. This number also included multiple specimens for 22 species. DNA barcode approach based on DNA sequences of mitochondrial cytochrome oxidase gene sequences could identify 62 species among these, in confirmation with the conventional taxonomy. However, two closely related species, Ochlerotatus portonovoensis (Tiwari & Hiriyan) and Ochlerotatus wardi (Reinert) could not be identified as separate species based on DNA barcode approach, their lineages indicating negligible genetic divergence (Kimura two-parameter genetic distance = 0.0043).

Mosquitoes of the mangrove forests of India: part four--Coringa, Andhra Pradesh

Mosquitoes of 12 species belonging to 5 subgenera and 9 genera--Aedes, Anopheles, Culex, Diceromyia, Lorrainea, Rhinoskusea, Stegomyia, Toxorhynchites, and Verrallina--were recorded in the Coringa mangrove forest in Andhra Pradesh, India. Tree holes, crab holes, and swamp pools constituted the larval habitats with Lo. fumida being predominant in tree holes. Adults were found resting in tree holes, tree trunks, root bases, and in crab holes. Species involved in daytime feeding on humans were Ae. cancricomes, Cx. sitiens, Lo. fumida, Rh. wardi, and Ve. lugubris.

Mosquitoes of the mangrove forests of India: part six--Kundapur, Karnataka and Kannur, Kerala

Mosquitoes of 26 species belonging to 16 subgenera and 11 genera were recorded in the Kundapur mangroves of Karnataka, and 17 species belonging to 11 subgenera and 7 genera were recorded in the mangroves of Kannur, Kerala along the west coast of India. Genera recorded were Aedes, Anopheles, Armigeres, Culex, Heizmannia, Lutzia, Mansonia, Ochlerotatus, Tripteroides, Uranotaenia, and Verrallina. Species common to both mangrove forests were Ae. albopictus, Ae. vittatus, An. jamesi, Ar. subalbatus, Cx. gelidus, Cx. infantulus, Cx. pseudovishnui, Cx. sitiens, Cx. tritaeniorhynchus, Oc. wardi, Ur. atra, and Ve. luguhris. Tree holes and swamp pools were the common larval habitats, with more species occurring in tree holes in Kundapur than in Kannur. Adults of Ae. albopictus, Ae. vittatus, Ar. aureolineatus, Ar. subalbatus, Cx. bitaeniorhynchus, Cx. sitiens, Ma. uniformis, and Ve. lugubris bloodfed on humans.

Mosquitoes of the mangrove forests of India: Part 3--Andaman and Nicobar Islands, including an update on the mosquito fauna of the islands

ABSTRACT. Fifty-three mosquito species belonging to 20 subgenera and 18 genera--Aedes, Anopheles, Armigeres, Culex, Downsiomyia, Finlaya, Heizmannia, Kenknightia, Lorrainea, Lutzia, Ochlerotatus, Orthopodomyia, Rhinoskusea, Stegomyia, Toxorhynchites, Tripteroides, Uranotaenia, and Verrallina--were recorded in the mangroves of Andaman and Nicobar Islands, India, in collections made during May and June 2001. Larvae of 43 species were collected from different mangrove habitats. Together with collections made in nonmangrove areas, 83 species in 22 subgenera and 20 genera in total were recorded of which 33 species are new records for the Andaman and Nicobar Islands. Rhinoskusea wardi, Fl. flavipennis, and Ve. consonensis are 3 new country records for India. Collections included topotype specimens of St. seampi. Together with species known from earlier records, the mosquito fauna of Andaman and Nicobar Islands is updated to 107 species in 23 subgenera and 24 genera.