Implementation of biomolecular logic gate using DNA and electrically doped GaAs nano-pore: a first principle paradigm.

One of the emerging areas of today's research arena is molecular modeling and molecular computing. The molecular logic gate can be theoretically implemented from single-strand DNA which consists of four basic nucleobases. In this study, the electronic transmission characteristics of DNA chain are investigated to form the logic gate. This biomolecular single-strand DNA chain is passed through an electrically doped gallium-arsenide nano-pore to achieve reasonably improved transmission along <1 1 1> direction. Current-voltage characteristic and device density of states with HOMO-LUMO plot of the device are explained along with the conductivity of the device to confirm the characteristics of some important logic gates like a universal gate. Ultimately the property of resistivity proves the law of Boolean logic of AND gate and universal logic gate, viz., NAND and NOR gate. All the electronic properties of the Boolean logic gate are explored based on the first principle approach by non-equilibrium Green's function coupled with density functional theory in room temperature.

Electrically Doped Nanoscale Devices Using First-Principle Approach: A Comprehensive Survey.

Doping is the key feature in semiconductor device fabrication. Many strategies have been discovered for controlling doping in the area of semiconductor physics during the past few decades. Electrical doping is a promising strategy that is used for effective tuning of the charge populations, electronic properties, and transmission properties. This doping process reduces the risk of high temperature, contamination of foreign particles. Significant experimental and theoretical efforts are demonstrated to study the characteristics of electrical doping during the past few decades. In this article, we first briefly review the historical roadmap of electrical doping. Secondly, we will discuss electrical doping at the molecular level. Thus, we will review some experimental works at the molecular level along with we review a variety of research works that are performed based on electrical doping. Then we figure out importance of electrical doping and its importance. Furthermore, we describe the methods of electrical doping. Finally, we conclude with a brief comparative study between electrical and conventional doping methods.

Allergenicity assessment of fungal species using immunoclinical and proteomic techniques: a study on Fusarium lateritium.

Airborne fungal spores are extensively reported as the elicitors of respiratory allergies in human. Fusarium lateritium is one such fungal species reported for eliciting significant skin prick results from India. The present study aims to analyze the allergenic potential of F. lateritium followed by the identification of allergens. The total protein of F. lateritium was subjected to 1dimensional (1D) and 2D gel electrophoresis followed by corresponding IgE-specific immunoblots. We found 8 immunoreactive bands/zones in (1D) immunoblot using 11 F. lateritium-sensitised patient sera. In 1D immunoblot, a 34 kDa band was detected in >80% of the patients and hence considered as a potential allergen of F. lateritium. Corresponding 34 kDa spot in 2D-immunoblot was analyzed by mass spectrometric analysis and identified as Glyceraldehyde 3-phosphate dehydrogenase. The identified F. lateritium allergen holds the potential to instigate vaccine development for immunotherapy of F. lateritium sensitized patients.

Assessment of Hymenoptera and Non-Hymenoptera Insect Bite and Sting Allergy Among Patients of Tropical Region of West Bengal, India.

West Bengal, India, is inhabited by abundance and variety of insects that triggers sensitization in some humans to inhalant allergens and/or insect stings/venoms. Lack of research on this topic prevented accurate diagnosis and proper follow-up treatments to patients suffering from insect-induced allergies. The aim of our study was to identify the allergy-causing insects and evaluate resulting sensitization among a study population in West Bengal, India. The skin prick test (SPT) evaluated sensitivity of 450 patients who sought treatment at the Allergy and Asthma Research Center from July 2017 to June 2018. Eight insect allergens were tested: Common Black Ant (Lasius niger, Linnaeus 1758), Fire Ant (Solenopsis invicta, Buren 1972), Honey Bee (Apis cerana indica, Fabricius 1798), Common Wasp (Vespula vulgaris, Linnaeus 1758), Mosquito (Aedes aegypti, Linnaeus in Hasselquist 1762), American Cockroach (Periplaneta americana, Linnaeus 1758), House Fly (Musca domestica, Linnaeus 1758), and Grasshopper (Gesonula punctifrons, Stal 1861). From a total of 450 patients evaluated, 370 patients had positive SPT reaction from at least one of the 8 insect allergens tested. Sensitivity to some Hymenoptera insects (common black ant, 87.62%; fire ant, 84.59%; and honey bee, 67.02%) was found in higher proportion than non-Hymenoptera group (mosquito, 66.67%; American cockroach, 33.33%; house fly, 10.41%; and grasshopper, 5.14%). There was significant difference in sensitivity among child, adolescent, and adult (P < 0.001). While female patients showed more sensitivity than males to SPT, the difference was statistically insignificant. In regards to occupation, farmers and bee keepers were most sensitive of field workers sensitive to Hymenoptera-derived allergens.

Investigation of house dust mite induced allergy using logistic regression in West Bengal, India.

BACKGROUND: The diagnosis of house dust mite (HDM) allergy based on Skin prick test (SPT) is not accurate, especially in lower risk cases. Our aim is to develop and validate a predictive model to diagnose the HDM allergic symptoms (urticaria, allergic rhinitis, asthma). METHODS: A forward-step logistic regression model was developed using a data set of 537 patients of West Bengal, India consisting of clinical variables (SPT based on 6 allergens of house dust and house dust mites, total IgE) and demographic characteristics (age, sex, house conditions). The output probability was estimated from the allergic symptoms shown by the patients. We finally prospectively validated a data set of 600 patients. RESULTS: The gradual inclusion of the variables increased the correlation between observed and predicted probabilities (correlation coefficient (r2) = 0.97). The model development using group-1 showed an accuracy rate of 99%, sensitivity and specificity of 99.7% and 88.6% respectively and the area under the receiver operating characteristics (ROC) curve (AUC) of 99%. The corresponding numbers for the validation of our model with group-2 were 87%, 95.6% and 66% and 86% respectively. The model predicted the probability of symptoms better than SPTs in combination (accuracy rate 0.76-0.80), especially in lower risk cases (probability< 0.8) that are highly difficult to diagnose. CONCLUSION: This is perhaps the first attempt to model the outcome of HDM allergy in terms of symptoms, which could open up an alternative but highly efficient way for accurate diagnosis of HDM allergy enhancing the efficiency of immunotherapy.

First principle study of the self-switching characteristics of the guanine based single optical molecular switch using carbon nanotube electrodes.

The switching property of an optical single molecular switch based on a single DNA molecule guanine with a single walled carbon nanotube electrode has been investigated using density functional theory along with non-equilibrium Green's function based first principle approach. The semi-empirical model of this single bio-molecular switch has been operated at an ultra-high 25 THz frequency in mid-UV range. This single bio-molecule comprises switching activity upon UV photo-excitation. The influence of the highest occupied molecular orbital and lowest unoccupied molecular orbital gap and the quantum ballistic transmission into the switching activity are discussed in detail in this study. It has been observed that the maximum ON-OFF ratio, i.e. 327 is obtained at +0.8 V bias voltage. Theoretical results show that current through the twisted form is sufficiently larger than the straightened form, which recommends that this structure has smart prospective application in the future generation switching nanotechnology.

A review of house dust mite allergy in India.

House dust mites (HDMs) are extensively reported as potent allergens worldwide with India being in the top row. HDM sensitization is hugely reported from India and has led to the concern of implementing proper guidelines for treatment of the sufferers. Climatic conditions and a rapid shift of life style toward a more indoor and urbanised pattern are denoted as the probable causes of increased HDM exposure and sensitization. On the contrary, the varying rate of HDM allergy from similar climate and urbanised areas throughout the world suggest the influence of genetic predisposition. At present, in India, avoidance of HDM exposure is recommended as the baseline defence. Allergen immunotherapy (AIT) guidelines are proposed in India to maintain uniformity in the diagnosis techniques and management strategies throughout the country. Considering the genetic susceptibility toward allergic diseases, the concept of 'personalised medicine' is preferred over the 'mass targeted treatment'. From the Indian perspective, the present problem is Dermatophagoides pteronyssinus and D. farinae allergens are not well characterised at the molecular level. As a consequence, India is still reliant on less standardised allergen extracts. The proper identification, purification, and molecular characterization of HDM allergens can combat this problem. In this review, we aimed to portray a complete account of HDM allergy in India with respect to prevalence, probable triggers, diagnosis and therapy. We have attempted to present the current ambiguities along with the likely deciphering that would pave the way to solve HDM allergy-related queries in India.

First principle approach towards logic design using hydrogen-doped single-strand DNA.

Molecular logic gate has been proposed using single-strand DNA (ssDNA) consisting of basic four nucleobases. In this study, density functional theory and non-equilibrium Green's function based first principle approach is applied to investigate the electronic transmission characteristics of ssDNA chain. The heavily hydrogen-doped-ssDNA (H-ssDNA) chain is connected with gold electrode to achieve enhanced quantum-ballistic transmission along 〈1 1 1〉 direction. Logic gates OR, Ex-OR, NXOR have been implemented using this analytical model of H-ssDNA device. Enhanced logic properties have been observed for ssDNA after H adsorption due to improved electronic transmission. Dense electron cloud is considered as logic 'high' (1) output in presence of hydrogen molecule and on the contrary sparse cloud indicate logic 'low' (0) in the absence of hydrogen molecule. Device current is significantly increased from 0.2 nA to 2.4 µA (approx.) when ssDNA chain is heavily doped with hydrogen molecule. The current-voltage characteristics confirm the formation of various Boolean logic gate operations.

Sensitization to Common Aeroallergens in the Atopic Population of West Bengal, India: An Investigation by Skin Prick Test.

BACKGROUND: Aeroallergen sensitization is increasing worldwide. The optimal management of allergic disease requires the identification of the allergic sensitivities of the patient. Complete data of offending aeroallergens are scant from West Bengal, India. Hence, we employed a retrospective analysis of an atopic population of West Bengal to investigate the rate of sensitivity toward common aeroallergens including pollens, molds and house dust mites. OBJECTIVES: The aim of the present study was to evaluate the profile of skin prick test (SPT) reactivity of an atopic population of eastern India. METHODS: The prevalence aeroallergen sensitization was investigated by SPT along with a questionnaire survey of patients who visited the Allergy and Asthma Research Center of West Bengal, India, from June 2016 to May 2018. Patients were categorized according to the demographic (age, gender) and clinical aspects. Statistical tests were applied to differentiate between age and gender of the sufferers. RESULTS: 524 out of 605 patients exhibited a positive SPT response toward one or more aeroallergens tested. One-way ANOVA following Tukey's post hoc test reveals the age group of 15-40 years was more sensitized than that of < 15 years and no male-female discrimination was found using the paired t test. House dust mites, namely Dermatophagoides pteronyssinus and Dermatophagoides farinae, elicited most significant SPT results (80.34 and 84.92%, respectively) followed by Cocos (73.28%) and Azaridacta (57.25%) pollen. The most sensitive mold was Alternaria alternata (26.9%). Allergic rhinitis, bronchial asthma and atopic dermatitis were recorded as the common symptoms. Other influencing factors were family history, nature and season/time of onset and house conditions. CONCLUSION: Following the increasing trend, house dust mite sensitization still held the dominance like in any other Indian population reported earlier. This study would pave the way to construct a standard and minimal SPT panel for the atopic patients of eastern India.

Evaluation of Sensitivity Toward Storage Mites and House Dust Mites Among Nasobronchial Allergic Patients of Kolkata, India.

House dust mites (HDMs) are the major constituents of house dust (HD). HD and HDM sensitization is well documented worldwide. Storage mite (SM) sensitization is presently lacking from India. The present study evaluated the sensitization of both HDM and SM among 372 allergic rhinitis patients reported to the Allergy and Asthma Research Center of Kolkata metropolitan, India. HD samples were collected from the patients' home and analyzed for the major constituent mites. HD and six constituent mites Dermatophagoides pteronyssinus (DP), Dermatophagoides farina Hughes (Acari: Pyroglyphidae) (DF), Blomia tropicalis (BT), Acarus siro Linnaeus (Acari: Acaridae) (AS), Lepidoglyphus destructor (LD), and Tyrophagus putrescentiae (Schrank) (Acari: Acaridae) (TP) are tested for the allergenic potential through Skin Prick Test (SPT). Three SMs, namely AS, LD, and TP, were newly included in the mite SPT extract for the first time in Kolkata. In total, 330 patients showed significant positive SPT toward any one allergen tested. HD was the major elicitor exhibiting 92.42% response. Individuals of age group 15-40 were the worst sufferers. DF showed the highest sensitization (87.87%) among the dust mites. The SMs also contributed significantly to prove their sensitizing potential. SPT rates for AS, LD, and TP were 33, 25, and 18%, respectively. SPT grades and total Immunoglobulin E (IgE) were positively correlated for each of the allergens. Most of the patients were multi-sensitized (95%) and represented markedly high total IgE levels (>500 IU/ml). Three SMs proved to be significant allergens for the studied population. The sensitization toward these SMs is first time reported from India and can be recommended for inclusion of routine SPT for better outcome in the future.

Atomic scale modeling of electrically doped p-i-n FET from adenine based single wall nanotube.

The Field Effect Transistor (FET) characteristics has been observed from a single-walled Adenine nanotube device using Density Functional Theory associated with Non Equilibrium Green's Function based First Principle approach. This device is electrically doped which shows both n and p channel characteristics of a p-i-n FET. This device is designed and originated from a single-walled biomolecular nanotube structure. The p and n regions have been induced at the two ends of the device using electrical doping process. Thus both n and p channel current-voltage response can be obtained within a single nano-scale device at room temperature operation. The device is 3.35nm long and 1.4nm wide. The quasi-ballistic quantum transmission property reveals impressive and almost ideal current-voltage characteristics of the FET. Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) gap reveals the possibility of quasi-ballistic coherent transmission of the device. The electronic properties based on Molecular Projected Self-consistent Hamiltonian are analyzed using Hilbert space spanned basis functions. The maximum tunneling current observed for the bio-molecular FET is 15.9µA for n-channel and 13.8µA for p-channel. The device is operated in atomic scale regime with 1000THz frequency. The present results reveal the role of quantum-ballistic tunneling phenomenon in the current-voltage characteristics and channel conductance properties of the bio nanotube structure, which is useful in future generation nano-electronics.

Mass spectrometry-based identification of allergens from Curvularia pallescens, a prevalent aerospore in India.

The worldwide prevalence of fungal allergy in recent years has augmented mining allergens from yet unexplored ones. Curvularia pallescens (CP) being a dominant aerospore in India and a major sensitiser on a wide range of allergic population, pose a serious threat to human health. Therefore, we aimed to identify novel allergens from CP in our present study. A cohort of 22 CP-sensitised patients was selected by positive Skin prick grade. Individual sera exhibited elevated specific IgE level and significant histamine release on a challenge with antigenic extract of CP. First gel-based profiling of CP proteome was done by 1- and 2-dimensional gel. Parallel 1- and 2-dimensional immunoblot were performed applying individual as well as pooled patient sera. Identification of the sero-reactive spots from the 2-dimensional gel was found to be challenging as CP was not previously sequenced. Hence, mass spectrometry-based proteomic workflow consisting of conventional database search was not alone sufficient. Therefore, de novo sequencing preceded homology search was implemented for further identification. Altogether 11 allergenic proteins including Brn-1, vacuolar protease, and fructose-bis-phosphate aldolase were identified with high statistical confidence (p<0.05). This is the first study to report on any allergens from CP. This kind of proteome-based analysis provided a catalogue of CP allergens that would lead an improved way of diagnosis and therapy of CP-related allergy.

A hospital-based survey on food allergy in the population of Kolkata, India.

BACKGROUND: Food allergy is increasing worldwide, and Asian countries are not the exception. Still, ample data are lacking in India. We conducted a cross-sectional study in a metropolis of Eastern India to record the presence of food allergy among the local population. METHODS: The prevalence of food allergy was investigated among patients reporting to The Institute of Child Health and Mediland Diagnostics in Kolkata, India. A total of 5,161 patients were subdivided into 3 age groups and surveyed accordingly. The evaluation was conducted via a questionnaire and a skin prick test. RESULTS: Among the 5,161 patients tested, 4,160 showed a positive response to one or more food items. Banana (32%), brinjal (29%), wheat (22%), and egg (23%) were found to be dominant allergens. Sixty-three percent of patients with a family history of allergy showed either a sudden or an insidious mode of onset, whereas the remaining 37% suffered insidious allergic symptoms with no record of a family history of allergy. Skin rashes, cough, and sneezing were the major symptoms observed. Patients in the age group of 15-40 years were the most susceptible. CONCLUSION: It has been observed that certain specific foods consumed in specific regions cause allergies that are unique to their respective populations. In the present study, the most commonly consumed foods in the studied area, e.g. banana, brinjal, wheat, and egg, had severe effects on the local population. Complementary studies in other countries as well as in other parts of India will allow us to gain further insight into this fact. Some other influencing factors were found to be genetics, cultural habits, and occupation. Avoidance of the allergy-causing food is the best way to deal with food allergy.

Aromatic amino acids in high selectivity bismuth(III) recognition.

The three aromatic amino acids, tyrosine, tryptophan and phenylalanine, play different physiological roles in life processes. Metal ions capable of binding these amino acids may aid in the reduction of effective concentration of these amino acids in any physiological system. Here we have studied the efficacy of some heavy metals for their complexation with these three amino acids. Bismuth has been found to bind selectively with these aromatic amino acids and this was confirmed using spectrofluorimetric, spectrophotometric and cyclic voltammetric studies. The series of heavy metals has been chosen because each of these metals remains associated with the others at very low concentration levels and Bi(III) is the least toxic amongst the other elements. So, selective recognition for Bi(III) would also mean no response for the other heavy elements if contaminants are present even at low concentration levels. The affinity towards these amino acids has been found to be in the order tryptophan < phenylalanine < tyrosine. The association constants of these amino acids have been calculated using Benesi-Hildebrand equations and the corresponding free energy change has also been calculated. The values of the association constants obtained from BH equations using absorbance values corroborate with the Stern-Volmer constants obtained from fluorimetric studies. The evidence for complexation is also supported by the results of cyclic voltammetry.

Poly(ethylene glycol) vesicles: self-assembled site for luminescence generation.

Fluorescence in poly(ethylene glycol) (PEGs 400-12000) solutions is reported here for the first time. PEG solutions form a vesicular organization with the hydrophilic groups attached at both ends which arrange themselves beyond a particular concentration and offer electron-dense regions at the center of the vesicle. These vesicles provide an inherent site for fluorescence generation in PEG solutions. Fluorescence emission was observed at ~380 nm with an excitation wavelength of 300 nm. PEG of molecular weight 6000 was found to show maximum emission intensity at a particular concentration. The formation of PEG vesicles (~1 nm size) was confirmed by dynamic light scattering (DLS) and confocal laser microscopy. On addition of metal ions the polymeric vesicle breaks up to monomeric PEG, and hence, the fluorescence intensity decreases with a red shift. Fluorescence lifetime measurements indicate the nature of complexation of the metals with PEG. Since PEGs are used as one of the phases in aqueous biphasic systems (ABS) of liquid-liquid extractions, the nature of the fluorescence emission spectrum of the PEG phase after extraction was studied. Metal extraction in the PEG-rich phase of an ABS leads to quenching of fluorescence in PEG.

Influence of heterogeneity of confined water on photophysical behavior of acridine with amines: a time-resolved fluorescence and laser flash photolysis study.

The photophysical behavior of acridine (Acr) shows facilitated water-assisted protonation equilibrium between its deprotonted (Acr* ∼ 10 ns) and protonated forms (AcrH(+*) ∼ 28 ns) within confined region of ordered water molecules inside AOT/H(2)O/n-heptane reverse micelles (RMs). The time-resolved-area-normalized-emission spectra confirm both Acr* and AcrH(+*), while time-resolved-emission spectra depict time evolution between them. Quenching of AcrH(+*) with N,N-dimethylaniline (DMA) is a purely diffusion-controlled bimolecular quenching with linear Stern-Volmer (S-V) plot, while nonlinearity arises with triethylamine (TEA) that forms ground state complex with AcrH(+) (AcrH(+)··H(2)O··TEA) indicating both static and dynamic quenching. Transient intermediates, DMA(•+) and AcrH(•) infer photoinduced electron transfer from DMA to Acr, while those from AcrH(+)··H(2)O··TEA complex suggest water mediated excited-state proton transfer (ESPT) between AcrH(+) and TEA. The ESPT becomes faster in larger RMs due to enhanced mobility of hydronium ions in AcrH(+)··H(2)O··TEA, which reduces in smaller RMs as water becomes much more constrained owing to stronger complexation by excess confinement.

Exploring the mechanism of electron transfer between DNA and a ternary copper complex.

Photoinduced intramolecular electron transfer occurs in the triplet state within the complex [Htyr-Cu-phen](+) (Htyr = l-tyrosinato; phen = 1,10-phenanthroline) from tyrosine to phenanthroline. For this linked donor-acceptor system, a prominent magnetic field effect (MFE) is observed for the triplet-born radicals. The competitive binding study in the presence of ethidium bromide suggests that the complex interacts with calf thymus DNA (CT DNA) through partial intercalation. The photoexcited copper complex can oxidize DNA in a deoxygenated environment. Though the oxidation of tyrosine is thermodynamically more favorable than the oxidation of guanine, the primary electron transfer occurs from the DNA base to the phen ligand. A prominent MFE is observed for this noncovalently bound triplet-born guanine radical and phen radical anion. The process of partial intercalation of the copper complex within DNA is responsible for this rare observation.

Interactions of guanine and guanosine hydrates with quinones: a laser flash photolysis and magnetic field effect study.

Laser flash photolysis and an external magnetic field have been used to study the interaction of two quinone molecules, namely, 9,10-anthraquinone (AQ) and 2-methyl 1,4-naphthoquinone, commonly known as menadione (MQ), with one of the DNA bases, guanine (G) and its nucleoside guanosine hydrate (dG). In organic homogeneous medium, it has been observed that G undergoes a predominant hydrogen (H) abstraction reaction with both the quinones while dG supports photoinduced electron transfer (PET) along with H abstraction. On the other hand, in SDS medium, G supports PET with AQ but not with MQ. However, behavior of dG remains unperturbed toward AQ and MQ with the change in medium. All of these observations have been explained on the basis of stabilization of radical ion pair and difference in size of the quinones, which can affect the distance of approach among the interacting molecules.

Magnetic field effect on photoinduced electron transfer between [Cu(phen)2]2+ and DNA.

The magnetic field effect (MFE) on the photoinduced electron transfer (PET) reaction between the [Cu(phen)2]2+ complex and DNA has been studied in homogeneous buffer medium and in reverse micelles. The copper complex on photoexcitation can oxidize DNA in a deoxygenated environment. A prominent MFE is found even in a homogeneous aqueous medium for the triplet born radicals. The process of partial intercalation of [Cu(phen)2]2+ complex within DNA is responsible for such a rare observation. In reverse micelles, the MFE is not very much prominent because of the large separation distance between the component radicals of the geminate radical ion pairs generated through PET.

Laser flash photolysis and magnetic-field-effect studies on interaction of thymine and thymidine with menadione: role of sugar in controlling reaction pattern.

The magnetic field effect (MFE) in conjunction with laser flash photolysis has been used for the study of the interaction of one of the small drug like quinone molecules, 2-methyl, 1,4-naphthoquinone, commonly known as menadione (MQ), with one of the DNA bases, thymine (THN), and its corresponding nucleoside, thymidine (THDN), in acetonitrile (ACN) and sodium dodecylsulfate (SDS) micelles. It has been observed that THN undergoes electron transfer (ET) and hydrogen (H) abstraction with MQ, while THDN undergoes only H abstraction in both the media. However, our earlier studies showed that a purine base, adenine (ADN), and its nucleoside, 2'-deoxyadenosine (ADS), undergo ET in ACN and H abstraction in SDS. Here we have attempted to explain the differences in the reactions of these DNA bases with MQ. We also reveal the crucial role of a sugar unit in altering the behavior of purine and pyrimidine bases with respect to ET and H abstraction.