Urea-water Dynamics In Proteins: An Ultrafast Spectroscopic Study

Water plays a vital role in many biological processes like enzyme activity, protein folding-refolding and denaturation. Interfacial water has a significant effect on the protein’s internal structure and dynamics. It is essential to know the time scales characteristic of both, the local protein rearrangements and water dynamics within the solvation shell to understand the protein-water interactions. Urea is a chaotropic agent and a well-known denaturant for proteins. The molecular picture of the interaction of urea with the water hydrogen bond network and thereby, the chemical denaturation of the proteins is still ambiguous. Time-resolved Optical Kerr effect (OKE) spectroscopy is a powerful spectroscopic technique to study the hydrogen-bonded structure and dynamics of complex aqueous systems, in the picosecond time scales. In this study, we have investigated the mechanism behind urea denaturation of three proteins of different hydrophobicities- lysozyme, BSA and trypsin. The OKE data reveals the effect that different concentrations of urea have on the aqueous protein solutions. The temporal profiles of the aqueous protein solutions are almost indistinguishable from that of pure water. Resolving the data in the frequency domain and subtracting the solvent contribution gives us a better picture of the water and water-urea interactions with the protein. The spectral density (SD) obtained contains the $\alpha$ relaxation at the lowest frequencies corresponding to the orientational diffusion of the molecules, linked by the stretched $\beta$ relaxation to the intermolecular librational modes at terahertz frequencies. The shape of the SDs resembles that of urea solutions; the addition of protein brings down the contribution from the $\alpha$ relaxation. At lower urea concentrations, this change is even more apparent. The OKE spectra of urea have a huge $\alpha$ contribution compared to that of water which masks the faster $\beta$ dynamics. Removing the diffusive contributions in the time domain itself leaves us with the Reduced Spectral Densities (RSD). Preliminary analysis of the RSDs shows the $\beta$ relaxation timescales of water changes on the addition of urea and the subtracted spectra for the urea denatured lysozyme shows two distinct $\beta$ processes characteristic of water and water-urea dynamics. A detailed analysis of the changes in the line shapes of the RSDs is required to elucidate the effect urea has on the water hydrogen bond network and to map out the structural changes occurring in three different proteins on the addition of urea

Structural Fluctuations In An Azeotrope: Understanding The Benzene-methanol Azeotrope

The structure and dynamics of molecular liquids and their binary mixtures have been of interest for a long time. Azeotropes is a particular class of liquid mixture that boils at a constant temperature at a specific composition. Understanding of azeotropic systems at the molecular level is limited. In this study, we try to investigate this azeotropic non-ideality, using ultrafast Optical Kerr Effect (OKE) spectroscopy, broadband (1-10 THz) THz-Time domain spectroscopy (THz-TDS) along with temperature-dependent Nuclear Magnetic Resonance spectroscopy (NMR) of the azeotropic as well as mixtures of different compositions of benzene and methanol. Vibrational and NMR spectroscopic studies show that the formation of the methanol-benzene azeotrope weakens the hydrogen bond network. Intermolecular forces between the benzene molecules are also reduced significantly. Methanol disrupts the stacking in benzene which is also evident from the depression in the boiling points. Ultrafast OKE spectroscopy is a powerful tool to probe both, the collective orientational diffusion and the intermolecular dynamics in liquids. The spectral density (SD) obtained by the Fourier deconvolution of the OKE time transients gives us information about the structural relaxation occurring in the liquid at the terahertz and sub terahertz frequencies. With the increase of methanol in the mixtures, the $\alpha$ relaxation timescales become faster. An azeotropic composition mixture was prepared at room temperature without further distillation. The spectral densities of this mixture and the azeotrope at frequencies pertaining to collective intermolecular dynamics were quite different from each other. All of benzene’s entire rotational dynamics show up as molecular reorientation having contributions throughout the OKE spectra. The centre-of-mass translational part is only visible when it affects the interaction induced (I-I) part of the polarizability\footnote{Ryu, S.; Stratt, R. M. J. Phys. Chem. B 2004, 108, 6782.}. The addition of methanol decreases this contribution of the translations to the I-I term for benzene. A detailed analysis of the similarity of the azeotrope spectral density to benzene and how they differ from the other composition mixtures can give us useful insights into the structural fluctuations happening in the picosecond timescales in the benzene-methanol mixtures

Detecting receiver attacks in VRTI-based device free localization

pre-printVariance-based Radio Tomographic Imaging (VRTI) is an emerging technology that locates moving objects in areas surrounded by simple and inexpensive wireless sensor nodes. VRTI uses human motion induced variation in RSS and spatial correlation between link variations to locate and track people. An artificially induced power variations in the deployed network by an adversary can introduce unprecedented errors in localization process of VRTI and, given the critical applications of VRTI, can potentially lead to serious consequences including loss of human lives. In this paper, we tackle the problem of detecting malicious receivers that report false RSS values to induce artificial power variations in a VRTI system. We use the term "Receiver Attack" to refer to such malicious power changes. We use a combination of statistical hypothesis testing and heuristics to develop real-time methods to detect receiver attack in a VRTI system. Our results show that we can detect receiver attacks of reasonable intensity and identify the source(s) of malicious activity with very high accuracy

Violating privacy through walls by passive monitoring of radio windows

pre-printWe investigate the ability of an attacker to passively use an otherwise secure wireless network to detect moving people through walls. We call this attack on privacy of people a "monitoring radio windows" (MRW) attack. We design and implement the MRW attack methodology to reliably detect when a person crosses the link lines between the legitimate transmitters and the attack receivers, by using physical layer measurements. We also develop a method to estimate the direction of movement of a person from the sequence of link lines crossed during a short time interval. Additionally, we describe how an attacker may estimate any artificial changes in transmit power (used as a countermeasure), compensate for these power changes using measurements from sufficient number of links, and still detect line crossings. We implement our methodology on WiFi and ZigBee nodes and experimentally evaluate the MRW attack by passively monitoring human movements through external walls in two real-world settings. We find that achieve close to 100% accuracy in detecting line crossings and determining direction of motion, even through reinforced concrete walls

Clinico-epidemiological profile of malaria: Analysis from a primary health centre in Karnataka, Southern India

Malaria continues to be a major public health problem in India and worldwide. The present study was based on records from a primary health centre in Karnataka. Morbidity patterns and important features of malaria transmission specific to Udupi district were investigated. The incidence of malaria and various morbidity patterns during 2010 and 2011 were compared and analyzed. Factors such as rapid urbanization, increased construction activities and influx of migratory workers were highlighted as the leading causes for the advent of malaria in the area. Recommendations have been provided for implementation in the near future

Comprehensive analysis of temporal alterations in cellular proteome of bacillus subtilis under curcumin treatment

Curcumin is a natural dietary compound with antimicrobial activity against various gram positive and negative bacteria. This study aims to investigate the proteome level alterations in Bacillus subtilis due to curcumin treatment and identification of its molecular/cellular targets to understand the mechanism of action. We have performed a comprehensive proteomic analysis of B. subtilis AH75 strain at different time intervals of curcumin treatment (20, 60 and 120 min after the drug exposure, three replicates) to compare the protein expression profiles using two complementary quantitative proteomic techniques, 2D-DIGE and iTRAQ. To the best of our knowledge, this is the first comprehensive longitudinal investigation describing the effect of curcumin treatment on B. subtilis proteome. The proteomics analysis revealed several interesting targets such UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1, putative septation protein SpoVG and ATP-dependent Clp protease proteolytic subunit. Further, in silico pathway analysis using DAVID and KOBAS has revealed modulation of pathways related to the fatty acid metabolism and cell wall synthesis, which are crucial for cell viability. Our findings revealed that curcumin treatment lead to inhibition of the cell wall and fatty acid synthesis in addition to differential expression of many crucial proteins involved in modulation of bacterial metabolism. Findings obtained from proteomics analysis were further validated using 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) assay for respiratory activity, resazurin assay for metabolic activity and membrane integrity assay by potassium and inorganic phosphate leakage measurement. The gene expression analysis of selected cell wall biosynthesis enzymes has strengthened the proteomics findings and indicated the major effect of curcumin on cell division

On the inadequacy of environment impact assessments for projects in Bhagwan Mahavir Wildlife Sanctuary and National Park of Goa, India : a peer review

The Environment Impact Assessment (EIA) is a regulatory framework adopted since 1994 in India to evaluate the impact and mitigation measures of projects, however, even after 25 years of adoption, EIAs continue to be of inferior quality with respect to biodiversity documentation and assessment of impacts and their mitigation measures. This questions the credibility of the exercise, as deficient EIAs are habitually used as a basis for project clearances in ecologically sensitive and irreplaceable regions. The authors reiterate this point by analysing impact assessment documents for three projects: the doubling of the National Highway-4A, doubling of the railway-line from Castlerock to Kulem, and laying of a 400-kV transmission line through the Bhagwan Mahavir Wildlife Sanctuary and National Park in the state of Goa. Two of these projects were recently granted ‘Wildlife Clearance’ during a virtual meeting of the Standing Committee of the National Board of Wildlife (NBWL) without a thorough assessment of the project impacts. Assessment reports for the road and railway expansion were found to be deficient on multiple fronts regarding biodiversity assessment and projected impacts, whereas no impact assessment report was available in the public domain for the 400-kV transmission line project. This paper highlights the biodiversity significance of this protected area complex in the Western Ghats, and highlights the lacunae in biodiversity documentation and inadequacy of mitigation measures in assessment documents for all three diversion projects. The EIA process needs to improve substantially if India is to protect its natural resources and adhere to environmental protection policies and regulations nationally and globally