PredictSuperFam-PSS-3D1D: A server for predicting superfamily for the annotation of twilight zone protein sequences.

Annotation of twilight zone protein sequences has been hitherto attempted by predicting the fold of the given sequence. We report here the PredictSuperFam-PSS-3D1D method, which predicts the superfamily for a given twilight zone (TZ) protein sequence. Earlier, we have reported that adding predicted secondary structure information into the threading methods could improve fold prediction especially for the TZ protein sequences. In this study, we have analysed the application of the same method to predict superfamilies. Here, in this method, the twilight zone protein sequence is threaded with the 3D1D profiles of the known protein superfamilies library. In addition, weightage for the predicted secondary structure (PSS) is also employed. The performance of the method is benchmarked with twilight zone sequences. In the benchmarks, 62 and 65 percentages of superfamily predictions are obtained with GOR IV and NPS@ predicted secondary structures, respectively. Receiver Operating Characteristic (ROC) curves indicate that the method is sensitive in predicting the superfamilies. A case study has been conducted with the hypothetical protein sequences of Schistosoma haematobium (Blood Fluke) using this method and the results are analyzed. Our method predicts the superfamily for TZ sequences for which, methods based on sequence similarity alone are inadequate. A web server has been developed for our method and it is available online at http://bioinfo.bdu.ac.in/psfpss.

Role of Annealing Temperatures on Mechanical, Optical, Electrical and Magnetic Properties of Nanohydroxyapatite Biomaterial.

Nanosized hydroxyapatite [Ca10(Po4)6(OH)2 or HAp] was prepared by applying wet-chemical precipitation technique. Thermogravimetric and Differential Scanning Calorimetry (TG/DSC) analyses, showed that the prepared sample was stable up to 919.2 °C. X-ray diffraction (XRD) pattern showed that as-prepared and annealed samples are in hexagonal structure. The average crystallite size is found to be 39, 46, 51 and 65 nm for the as-prepared, 700, 800 and 900 °C annealed HAp respectively. The dislocation density, strain and surface area were decreased with increase in annealing temperature. FT-IR and Raman spectra showed both as-prepared and annealed samples having characteristic bands of HAp. FE-SEM and TEM images which depicted and confirmed the hexagonal structure of HAp. The optical band gap calculated from the UV absorption behavior of as-prepared and annealed at 700, 800 and 900 °C HAp are 3.86, 3.84, 3.54, and 3.03 eV respectively. As the annealing temperature increases, the conductivity decreases whereas the impedance increases. The ac conductivity of as-prepared and annealed samples are in the order of 10-5 Sm-1. The VSM analysis confirmed that both as-prepared and annealed samples of HAp are in diamagnetic nature. The antibacterial activity of apatite samples depend on the types of bacterial strains and also their activity changed with the crystallite size.

Improved Tet-On and Tet-Off systems for tetracycline-regulated expression of genes in Candida.

Tetracycline-regulated expression of genes is often used for functional analysis of Candida albicans genes. However, the widely used Tet-On system has certain limitations such as prolonged lag time (up to 8 h) for induction and non-uniform expression among the cells. We speculated that poor expression of tetracycline-controlled transactivator (Tet-transactivator) from CaADH1 promoter could be responsible for this, and thus compared the effect of expressing this protein under the control of CaADH1, CaTDH3 and CaRP10 promoters on the expression of GFP from the TET promoter. Only CaRP10 promoter facilitated a more uniform and rapid induction of GFP. However, a high concentration of doxycycline was needed for induction, which is not desirable for assessing certain phenotypes. Tet-Off systems are known to require a low concentration of doxycycline, but a limitation of the widely used Tet-Off system for C. albicans is the use of CaENO1 promoter, which is known to be repressed in the presence of gluconeogenic carbon source, for expression of transactivator. Thus, we have converted the above-mentioned Tet-On systems to Tet-Off systems by site-directed mutagenesis of the Tet-transactivator. Compared to the Tet-On systems, the Tet-Off systems required about 200-fold less concentration of doxycycline for modulation of gene expression. Only the Tet-Off system with CaRP10 promoter driving the expression of transactivator allowed rapid and high level expression of GFP compared to those with CaADH1 or CaTDH3 promoters. The utility of CaRP10 based Tet-On and Tet-Off systems was further validated by the conditional expression of the CaTUP1 gene. We have also adapted these systems for use with Candida tropicalis and find that the Tet-Off system is functional in this species. The Tet systems reported here will be useful for conditional expression of genes in C. albicans as well as C. tropicalis.

A comparative study on defect estimation using XPS and Raman spectroscopy in few layer nanographitic structures.

Defects in planar and vertically oriented nanographitic structures (NGSs) synthesized by plasma enhanced chemical vapor deposition (PECVD) have been investigated using Raman and X-ray photoelectron spectroscopy. While Raman spectra reveal the dominance of vacancy and boundary type defects respectively in vertical and planar NGSs, XPS provides additional information on vacancy related defect peaks in the C 1s spectrum, which originate from non-conjugated carbon atoms in the hexagonal lattice. Although an excellent correlation prevails between these two techniques, our results show that estimation of surface defects by XPS is more accurate than Raman analysis. Nuances of these techniques are discussed in the context of assessing defects in nanographitic structures.

Prophylactic efficacy of S-2(2-aminoethylamino)ethyl phenyl sulfide (DRDE-07) against sulfur mustard induced lung toxicity in mice.

OBJECTIVE: The present study was planned to investigate the prophylactic efficacy of S-2(2-aminoethylamino)ethyl phenyl sulfide (DRDE-07), against topically applied SM induced pulmonary toxicity in mouse. MATERIALS AND METHODS: Animals were pretreated with S-2(2-aminoethylamino)ethyl phenyl sulfide (DRDE-07) (249.4 mg/kg by oral gavage) 30 minutes before SM exposure. The SM (6.48 mg/kg) was applied on hair clipped dorsocaudal region (percutaneous) of the animal. The animals were sacrificed on day 1, 3, 5 and 7. The biochemical changes those were observed in the bronchoalveolar lavage (BAL) fluid and lung tissue included protein, LDH, MPO, ß-glucuronidase, MMP-2, MMP-9, activated macrophages, reduced glutathione and lipid peroxidation level. RESULTS AND DISCUSSION: Pretreatment with DRDE-07 (0.2 LD50) attenuated SM-induced changes at all time point tested. BAL fluid biochemical endpoints indicated epithelial and endothelial cell damages as evidenced by increase in BAL protein, LDH level and increased number of activated macrophages. The increased myeloperoxidase activity and ß-glucuronidase level exhibited the degranulation of neutrophils due to SM toxicity in lung. The zymogrphy analysis of BAL fluid showed a significant increase in matrix metalloproteases (MMP) activity due to inflammatory cells accumulation. CONCLUSION: Thirty minutes pretreatment with DRDE-07 decreased vascular permeability reduced the inflammation and oxidative stress, hence may be recommended as a potential prophylactic agent for SM intoxication.

Ultrananocrystalline diamond-CMOS device integration route for high acuity retinal prostheses.

High density electrodes are a new frontier for biomedical implants. Increasing the density and the number of electrodes used for the stimulation of retinal ganglion cells is one possible strategy for enhancing the quality of vision experienced by patients using retinal prostheses. The present work presents an integration strategy for a diamond based, high density, stimulating electrode array with a purpose built application specific integrated circuit (ASIC). The strategy is centered on flip-chip bonding of indium bumps to create high count and density vertical interconnects between the stimulator ASIC and an array of diamond neural stimulating electrodes. The use of polydimethylsiloxane (PDMS) housing prevents cross-contamination of the biocompatible diamond electrode with non-biocompatible materials, such as indium, used in the microfabrication process. Micro-imprint lithography allowed edge-to-edge micro-scale pattering of the indium bumps on non-coplanar substrates that have a form factor that can conform to body organs and thus are ideally suited for biomedical applications. Furthermore, micro-imprint lithography ensures the compatibility of lithography with the silicon ASIC and aluminum contact pads. Although this work focuses on 256 stimulating diamond electrode arrays with a pitch of 150 µm, the use of indium bump bonding technology and vertical interconnects facilitates implants with tens of thousands electrodes with a pitch as low as 10 µm, thus ensuring validity of the strategy for future high acuity retinal prostheses, and bionic implants in general.

Control of Aedes aegypti and Ae. albopictus, the vectors of dengue and chikungunya, by using pheromone C21 with an insect growth regulator: Results of multicentric trials from 2007-12 in India.

BACKGROUND & OBJECTIVES: Aedes mosquito control has gained much importance nowadays in view of rise in number of reported cases of dengue and chikungunya in India and other countries. In the present study, C21 attracticide (containing a pheromone and an insect growth regulator­IGR, developed by Defence Research and Development Establishment (DRDE), Gwalior, India was tested for its feasibility for surveillance and control of Aedes mosquito in a multicentric mode from October 2007 to June 2012 in urban (Delhi, and Bengaluru district, Karnataka) and suburban (Alappuzha district, Kerala) settings of the country in three phases. METHODS: Across the randomly selected households in each study area, two to four containers treated with attracticide (experimental) and untreated (control) were placed and monitored by trained surveillance workers on weekly/ fortnightly basis for determining the presence of eggs, larvae and pupae. Container positivity, percent larvae, egg and pupae collected were determined during different phases and analyzed statistically using SPSS 18.0. RESULTS: Container positivity was found statistically significant at Bengaluru and Alappuzha, Kerala while in Delhi, it was found non-significant. Eggs collected from experimental containers were significantly higher in comparison to control at all the locations except Delhi. Also larvae collected from control containers were significantly higher at all the locations except Bengaluru. Pupae collected from control containers remained significantly higher at all the locations as no pupal formation was recorded from experimental containers. INTERPRETATION & CONCLUSION: The use of C21 attracticide hampered pupal formation, thus inhibiting adult population in the study areas. The study established that C21 attracticide was efficacious in the field conditions and has potential for use in surveillance and management of dengue and chikungunya mosquitoes.

Seasonal variation in nutritional composition of Kappaphycus alvarezii (Doty) Doty-an edible seaweed.

Seasonal variation in the proximate and mineral composition of Kappaphycus alvarezii were investigated in the present study, moreover, the relationship between the nutritive components of this seaweed and the environment were also established. Carbohydrates represented the major portion of the algae (i.e. average total carbohydrate content was 23.01 ± 1.64 g/100 g DW), while the lipid content was the lowest among the constituents investigated (0.39 ± 0.04 to 0.91 ± 0.51 g/100 g DW). The protein content of K. alvarezii varied from 12.69 ± 0.6 to 23.61 ± 0.02 g/100 g DW, and the fiber content varied between 9.68 ± 0.08 to 18.57 ± 0.15 g/100 g DW. Highest total mineral content (29939.61 ± 9340.38 mg/100 g DW) was observed in April 2005, while least values were recorded in January 2006 i.e. (10997.62 ± 1120.26 mg/100 g DW). The Na/K ratio during the study ranged from 0.34 to 0.87. All the samples showed remarkable semi-refined carrageenan (SRC) yield ranging from 42.70 ± 1.07 to 63.73 ± 1.73 % (average 53.90 ± 1.37 %), and, the samples collected during December 2004 and January 2006 demonstrated maximum gel strengths i.e. 743 ± 15.28 and 783.33 ± 15.28 g·cm(-2) respectively. Various environmental parameters influenced the chemical composition of K. alvarezii, and these parameters demonstrated seasonal fluctuations. Moreover, based on the nutritional composition obtained, it could be stated that this seaweed has great scope to be incorporated into several food products as an excellent nutritional supplement, or as a value additive in animal or pet food.

Sphingolipid biosynthetic pathway genes FEN1 and SUR4 modulate amphotericin B resistance.

Deletants of the sphingolipid biosynthetic pathway genes FEN1 and SUR4 of Saccharomyces cerevisiae, as well as deletants of their orthologs in Candida albicans, were found to be 2- to 5-fold-more sensitive to amphotericin B (AmB) than parent strains. The inhibition of sphingolipid biosynthesis in parent strains by myriocin sensitized them to AmB, which can be reversed by providing phytosphingosine, an intermediate in the sphingolipid pathway. These results indicate that sphingolipids modulate AmB resistance, with implications for mechanisms underlying AmB action and resistance.

Acute inhalation toxicity of smoke of fentanyl and its 1-substituted analogs in Swiss albino mice.

Fentanyl (N-(1-phenethyl-4-piperidinyl)propionanilide) is a synthetic, potent narcotic analgesic agent. However, it is known to have several side effects, which led to synthesis and evaluation of its new analogs for the management of pain. We have earlier reported the comparative bioassay of fentanyl and its eight 1-substituted analogs (1-8) in mice. Three compounds, viz., N-(1-(2-phenoxyethyl)-4-piperidinyl)propionanilide (2), N-isopropyl-3-(4-(N-phenylpropionamido)piperidin-1-yl)propanamide (5), and N-t-butyl-3-(4-(N-phenylpropionamido)piperidin-1-yl)propanamide (6) were found to be more effective and less toxic compared to fentanyl. The present study reports the comparative acute inhalation toxicity of smoke of fentanyl and its three analogs, viz., 2, 5, and 6 in mice. Animals were exposed to different concentrations of smoke generated by heating the compounds. Exposure was performed in a head only all glass static exposure assembly for 15 min to determine the median lethal concentration (LC50). The breathing pattern and various respiratory parameters of the animals were also monitored online using a polygraph. Out of three compounds tested, analog 5 was found to be most toxic (LC50 = 2820 mg/m3) while 2 was least toxic (LC50 = >8000 mg/m3). All the compounds caused long lasting respiratory depression in a dose-dependent manner, which did not completely resolve even after discontinuation of exposure. Aerodynamic median diameter and geometric standard deviation of smoke particles was determined employing eight-stage Andersen sampler. The particles were found to be within the respirable range. The study, however, concludes that due to possible decomposition of the compounds by heating or its poor absorption by the alveolar surface, the present inhalation technique cannot be employed to generate smoke of fentanyl and its analogs for any medical or surreptitious use.

Marker assisted selection of low phytic acid trait in maize (Zea mays L.).

Maize is the third important major food crop. Breeding for low phytate maize genotypes is an effective strategy for decreasing the content of kernel phytic acid (a chelator of cations such as Ca(2+) and Fe(3+) ) and thereby increasing the bioavailability of nutritive minerals in human diet and animal feed. Previous studies have established that a mutant plant with a lpa2-2 allele accumulates less phytic acid in seeds. Therefore, the marker assisted backcross breeding (MABB), which involves introgression of lpa2-2 recessive allele (which confer low phytate trait) from a lpa2-2 mutant line into a well-adapted line using backcrosses and selection of lines possessing lpa2-2 allele in each backcross population using molecular markers, is an effective strategy for developing low phytate maize. So far, no studies have developed any lpa2-2 allele specific molecular markers for this purpose. Here, using backcross and selfed progenies, obtained by crossing low phytate mutant line 'EC 659418' (i.e. donor of lpa2-2 allele) into agronomically superior line 'UMI395', we have validated that a SSR marker 'umc2230', located 0.4 cM downstream of lpa2-2, cosegregate, in a Mendelian fashion, with low phytic acid trait. Therefore umc2230 can be dependably used in MABB for the development of low phytate maize.

Aggregation responses of Cimex hemipterus F. to semiochemicals identified from their excreta.

BACKGROUND & OBJECTIVES: Bedbug Cimex hemipterus lives in cracks and crevices, and shows aggregation activity in the harbourage containing its fecal matter. Limited information is available on the chemicals influencing this aggregation behaviour in C. hemipterus. Possible components responsible for aggregation, if identified and evaluated can be helpful in designing bedbug management. METHODS: Study on the isolation and identification of chemicals from the excreta extract responsible for aggregation has been carried by GC-MS. The compounds identified were evaluated at different concentrations to C. hemipterus and their attraction index was determined. RESULTS: The GC-MS analysis of the excreta extract resulted in identification of 33 different types of semiochemicals such as esters, carboxylic acids, alcohols, aldehydes, ketones and other hydrocarbons. Among these 33 compounds of various groups, the carboxylic acid (E)-2-hexenoic acid and the aldehyde (E)-2-hexenal found to elicit highest positive aggregation behavioural response in all the stages followed by hexenal. INTERPRETATION & CONCLUSION: The fecal matter influence the aggregation behaviour in C. hemipterus. (E)-2-hexenoic acid, hexanoic acid, (E)-2-hexenal and hexanal found to exhibit aggregation in various stages of bedbug life cycle. These chemical components can be further exploited for designing and development tool for management of bedbugs.

Neurocognitive basis of model-based decision making and its metacontrol in childhood.

Human behavior is supported by both goal-directed (model-based) and habitual (model-free) decision-making, each differing in its flexibility, accuracy, and computational cost. The arbitration between habitual and goal-directed systems is thought to be regulated by a process known as metacontrol. However, how these systems emerge and develop remains poorly understood. Recently, we found that while children between 5 and 11 years displayed robust signatures of model-based decision-making, which increased during this developmental period, there were substantial individual differences in the display of metacontrol. Here, we inspect the neurocognitive basis of model-based decision-making and metacontrol in childhood and focus this investigation on executive functions, fluid reasoning, and brain structure. A total of 69 participants between the ages of 6-13 completed a two-step decision-making task and an extensive behavioral test battery. A subset of 44 participants also completed a structural magnetic resonance imaging scan. We find that individual differences in metacontrol are specifically associated with performance on an inhibition task and individual differences in thickness of dorsolateral prefrontal, temporal, and superior-parietal cortices. These brain regions likely reflect the involvement of cognitive processes crucial to metacontrol, such as cognitive control and contextual processing.

Dynamic stabilization of the optical resonances of single nitrogen-vacancy centers in diamond.

We report electrical tuning by the Stark effect of the excited-state structure of single nitrogen-vacancy (NV) centers located ≲100 nm from the diamond surface. The zero-phonon line (ZPL) emission frequency is controllably varied over a range of 300 GHz. Using high-resolution emission spectroscopy, we observe electrical tuning of the strengths of both cycling and spin-altering transitions. Under resonant excitation, we apply dynamic feedback to stabilize the ZPL frequency. The transition is locked over several minutes and drifts of the peak position on timescales ≳100 ms are reduced to a fraction of the single-scan linewidth, with standard deviation as low as 16 MHz (obtained for an NV in bulk, ultrapure diamond). These techniques should improve the entanglement success probability in quantum communications protocols.

PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences.

Annotation of any newly determined protein sequence depends on the pairwise sequence identity with known sequences. However, for the twilight zone sequences which have only 15-25% identity, the pair-wise comparison methods are inadequate and the annotation becomes a challenging task. Such sequences can be annotated by using methods that recognize their fold. Bowie et al. described a 3D1D profile method in which the amino acid sequences that fold into a known 3D structure are identified by their compatibility to that known 3D structure. We have improved the above method by using the predicted secondary structure information and employ it for fold recognition from the twilight zone sequences. In our Protein Secondary Structure 3D1D (PSS-3D1D) method, a score (w) for the predicted secondary structure of the query sequence is included in finding the compatibility of the query sequence to the known fold 3D structures. In the benchmarks, the PSS-3D1D method shows a maximum of 21% improvement in predicting correctly the α + ß class of folds from the sequences with twilight zone level of identity, when compared with the 3D1D profile method. Hence, the PSS-3D1D method could offer more clues than the 3D1D method for the annotation of twilight zone sequences. The web based PSS-3D1D method is freely available in the PredictFold server at http://bioinfo.bdu.ac.in/servers/ .

Acute toxicity studies of safer and more effective analogues of N,N-diethyl-2-phenylacetamide.

The present work was designed to evaluate the toxicity of various synthesized aromatic amides that are analogs of N,N-diethyl-2-phenylacetamide, a well known insect repellent. The toxicity profile of these compounds was compared with N,N-diethyl-2-phenylacetamide as well as other registered insect repellents namely N,N-diethyl-3-methyl benzamide and N,N-diethylbenzamide. The primary skin irritation index values of the compounds, dermal toxicity of the chemicals and acute oral toxicity data to assess the safety of the synthesized aromatic amides are reported in this paper. Results of hematological and biochemical studies of these analogues are reported and discussed.

Behavioral responses and bioefficacy of some aromatic amides against Aedes aegypti.

A series of substituted aromatic amides by varying the chain length, substitution of methyl, methoxy, chloro, and fluoro groups at ortho-, meta-, and para-positions of the phenyl ring of N,N-diethyl-2-phenylacetamide were synthesized. Laboratory studies were carried out to observe the behavioral responses and repellent activity of these newly synthesized aromatic amides against Aedes aegypti (L.) mosquitoes. The deterrent activity of these synthetic amides against any vectors has not been reported previously. These aromatic amides were tested for their behavioral responses and compared with the well known insect repellents, namely, N,N-diethyl toluamide; N,N-diethyl phenylacetamide; and N,N-diethylbenzamide. Out of the 14 compounds synthesized, seven compounds were selected on the basis of those showing >75% of repellent response for the bioefficacy test on human volunteers. The potential use of lead compounds in personal protection management is discussed.

Configuration spaces of hard spheres.

Hard sphere systems are often used to model simple fluids. The configuration spaces of hard spheres in a three-dimensional torus modulo various symmetry groups are comparatively simple and could provide valuable information about the nature of phase transitions. Specifically, the topological changes in the configuration space as a function of packing fraction have been conjectured to be related to the onset of first-order phase transitions. The critical configurations for 1 to 12 spheres are sampled using a Morse-theoretic approach, and they are available in an online, interactive database. Explicit triangulations are constructed for the configuration spaces of the two sphere system, and their topological and geometric properties are studied. The critical configurations are found to be associated with geometric changes to the configuration space that connect previously distant regions and reduce the configuration space diameter as measured by the commute time and diffusion distances. The number of such critical configurations around the packing fraction of the solid-liquid phase transition increases exponentially with the number of spheres, suggesting that the onset of the first-order phase transition in the thermodynamic limit is associated with a discontinuity in the configuration space diameter.

Use of the temporal extension of the buccal fat pad for closure of oro-antral communications.

Oro-antral communications/fistulae (OAC/OAF) can cause significant patient morbidity, with treatment for defects greater than 5mm in size requiring surgical reconstruction. This technical note evaluates the effectiveness, and proposes the use of, the temporal extension of the buccal fat pad (TEBFP) for the closure of large OAC. The TEBFP can be an effective means of large OAC closure due to its ease of harvesting, with minimal damage to surrounding structures or aesthetic changes. The use of the TEBFP provides stability, versatility, and tension-free closure, with minimal postoperative complications.

Electrophysiological, flight orientation and oviposition responses of three species of mosquito vectors to hexadecyl pentanoate: residual oviposition repellent activity.

Understanding on the chemical ecology of mosquito behavior is of paramount importance in developing control programs employing attractants and repellents. Several workers focused on topical repellents and oviposition attractants of mosquitoes, however, only limited work has been accomplished on mosquito oviposition repellents. The present systematic investigation provides evidence on the effectiveness of a C21 fatty acid ester- hexadecyl pentanoate, to stimulate antennal olfactory receptors of Aedes aegypti (L.), Ae. albopictus (Skuse), and Anopheles stephensi (Liston) that mediate their long-range olfaction guided flight orientation behavior by repelling the gravid females of these mosquito vectors in the olfactometer. The compound loaded onto an effervescent tablet retained its repellent property in the treated substrates for up to 1 wk at 10 mg/L. In places, where the mosquito breeding habitats are near to human habitations, could be treated with hexadecyl pentanoate to repel the ovipositing gravid females as a component of the integrated approach for mosquito management by disrupting the mosquito life cycle and population growth.