Biomedical subjects

S T Rao

Publications and source records attributed to S T Rao.

At least 19 recordsLinked to original sources

PubMed2003

Spatial and temporal variations in the trace elemental data over the northeastern United States.

Time series of trace elemental concentrations (14 species) of atmospheric fine particles measured in the northeastern United States between 1988 and 1998 are analyzed for spatial and temporal variations. The influence of synoptic-scale systems to the transport and accumulation of pollutants can be investigated successfully if the short-term fluctuations (i.e. weather-induced variations) embedded in the time series of pollutant concentrations are separated from the original time series. The spatial short-term correlation coefficients for Al, Br, Fe, Se, and Zn permit good predictions of pollutant concentrations up to distances of about 350 km from a given monitor. The species correlation matrices for individual sites reveal that As, Br, Se, and Zn are highly correlated in New York State, while Fe, Mn, and V show also strong correlations, suggesting the commonality of source regions for these industrial and urban pollutants impacting New York.

Air Pollutants↗

PubMed2003

Assessing the effects of transboundary ozone pollution between Ontario, Canada and New York, USA.

We investigated the effects of transboundary pollution between Ontario and New York using both observations and modeling results. Analysis of the spatial scales associated with ozone pollution revealed the regional and international character of this pollutant. A back-trajectory-clustering methodology was used to evaluate the potential for transboundary pollution trading and to identify potential pollution source regions for two sites: CN tower in Toronto and the World Trade Center in New York City. Transboundary pollution transport was evident at both locations. The major pollution source areas for the period examined were the Ohio River Valley and Midwest. Finally, we examined the transboundary impact of emission reductions through photochemical models. We found that emissions from both New York and Ontario were transported across the border and that reductions in predicted O3 levels can be substantial when emissions on both sides of the border are reduced.

Air Pollutants↗

PubMed2002

An evaluation of the UAM-V predicted concentrations of carbon monoxide and reactive nitrogen compounds over the eastern United States during summer 1995.

While there is a clear need to evaluate a photochemical model's ability in predicting not only the concentrations of O3, but also precursors and other trace species, many previous studies have focused only on the assessment of During the 1995 summer season, in addition to the routine monitoring of criteria pollutants, several research-oriented monitoring campaigns were conducted over the eastern United States, providing an extensive database of reactive nitrogen compounds, CO, and speciated hydrocarbon data. In this study, we examine the ability of a photochemical modeling system, RAMS/ UAM-V, to reproduce the measured concentrations of CO, NO2, and NOy over the region during the summer of 1995. The results demonstrate that there is agreement between modeled and measured seasonal average concentrations of NO2, both at the routine and research monitors. The same is true for NOy, but to a lesser degree. However, the model is found to significantly underpredict CO for the routine monitors in comparison to the research monitors.

Air Pollutants↗

PubMed2001

Ozone air quality over north america: part II--an analysis of trend detection and attribution techniques.

Assessment of regulatory programs aimed at improving ambient O3 air quality is of considerable interest to the scientific community and to policymakers. Trend detection, the identification of statistically significant long-term changes, and attribution, linking change to specific climatological and anthropogenic forcings, are instrumental to this assessment. Detection and attribution are difficult because changes in pollutant concentrations of interest to policymakers may be much smaller than natural variations due to weather and climate. In addition, there are considerable differences in reported trends seemingly based on similar statistical methods and databases. Differences arise from the variety of techniques used to reduce nontrend variation in time series, including mitigating the effects of meteorology and the variety of metrics used to track changes. In this paper, we review the trend assessment techniques being used in the air pollution field and discuss their strengths and limitations in discerning and attributing changes in O3 to emission control policies.

Air Pollutants↗

PubMed2001

Ozone air quality over North America: part I--a review of reported trends.

Ozone and precursor trends can be used to measure the effectiveness of regulatory programs that have been implemented. In this paper, we review trends in the concentrations of O3 NOx, and HCs over North America that have been reported in the literature. Although most existing trend studies are confounded by meteorological variability, both the raw data trends and the trends adjusted for meteorology collectively indicate a general decreasing trend in O3 concentrations in most areas of the United States during 1985-1996. In Canada, mean daily maximum 1-hr O3 concentrations at urban sites show mixed trends with a majority of sites showing an increase from 1980 to 1993. Mean daily maximum 1-hr O3 at most regionally representative Canadian sites appears to decrease from 1985 to 1993 or shows no significant change. There are far fewer data and analyses of NOx and HC trends. Available studies covering various ranges of years indicate decreases in ambient NO and HC concentrations in Los Angeles, CA, decreases in HC concentrations in northeastern U.S. cities, and decreases in NOx concentrations in Canadian cities. Two key needs are long-term HC and NOx measurements, particularly at rural sites, and a systematic comparison of trend detection techniques on a reference data set.

Air Pollution↗

PubMed2001

A comparison of measured and simulated ozone concentrations in the rural areas of the eastern United States during summer 1995.

The recent regulatory actions toward a longer-term (i.e., 8-hr) average ozone standard have brought forth the potential for many rural areas in the eastern United States to be in noncompliance. However, since a majority of these rural areas have generally few sources of anthropogenic emissions, the measured ozone levels primarily reflect the effects of the transport of ozone and its precursor pollutants and natural emissions. While photochemical grid models have been applied to urban areas to develop ozone mitigation measures, these efforts have been limited to high ozone episode events only and do not adequately cover rural regions. In this study, we applied a photochemical modeling system, RAMS/UAM-V, to the eastern United States from June 1-August 31, 1995. The purpose of the study is to examine the predictive ability of the modeling system at rural monitoring stations that are part of the Clean Air Status Trends Network (CASTNet) and the Gaseous Pollutant Monitoring Program (GPMP). The results show that the measured daily 1-hr ozone maxima and the seasonal average of the daily 1-hr ozone maxima are in better agreement with the predictions of the modeling system than those for the daily 8-hr ozone maxima. Also, the response of the modeling system in reproducing the measured range of ozone levels over the diurnal cycle is poor, suggesting the need for improvement in the treatment of the physical and chemical processes of the modeling system during the nighttime and morning hours if it is to be used to address the 8-hr ozone standard.

Air Pollutants↗

PubMed2001

Demonstrating attainment of the air quality standards: integration of observations and model predictions into the probabilistic framework.

This paper introduces an integrated observational-modeling approach to transform the deterministic nature of attainment demonstrations of the National Ambient Air Quality Standard (NAAQS) into the probabilistic framework. While the methods presented here can be used to address any air quality standard that is based on extreme values, this paper focuses on the application to the 1-hr and 8-hr NAAQS for ozone. Extreme value statistics and resampling techniques are applied to estimate the probability of exceeding the NAAQS for both 1-hr and 8-hr ozone concentrations. Within the integrated observation-modeling analysis approach, we show that the model-to-model differences in the predicted responses to emission reductions are smaller than the model-to-model differences in predicted absolute ozone concentrations. We illustrate that the emission reductions stemming from a real-world emission control strategy would substantially reduce the probability of exceeding the NAAQS over a large portion of the eastern United States, especially for the 8-hr average ozone concentrations.

Air Pollution↗

PubMed2001

Do we understand trends in atmospheric sulfur species?

Anomalies appear to exist in our understanding of atmospheric sulfur compounds, specifically as evidenced in the time trends of the different chemical forms of these compounds. Trends determined at a number of locations by several different groups seem to indicate that, responding to emission reductions across North America, the concentration of SO2 in the atmosphere is declining more rapidly than that of aerosol SO4(2-). A number of possible reasons for this discrepancy are examined, but it is not possible to provide a definitive answer at this stage. The intent is to stimulate debate, because shortcomings in our understanding of the processes involved could have profound implications for the credibility of abatement strategies and policies for both acid deposition and fine particulate matter (PM).

Acid Rain↗

PubMed1998

A novel end-to-end binding of two netropsins to the DNA decamers d(CCCCCIIIII)2, d(CCCBr5CCIIIII)2and d(CBr5CCCCIIIII)2.

Netropsin is bound to the DNA decamer d(CCCCCIIIII)2, the C-4 bromo derivative d(CCCBr5CCIIIII)2and the C-2 bromo derivative d(CBr5CCCCIIIII)2in a novel 2:1 mode. Complexes of the native decamer and the C-4 bromo derivative are isomorphous, space group P1, unit cell dimensions a = 32.56 A (32.66), b = 32.59 A (32.77), c = 37.64 A (37.71), alpha = 86.30 degrees (86.01 degrees), beta = 84.50 degrees (84.37 degrees), gamma = 68.58 degrees (68.90 degrees) with two independent molecules (A and B) in the asymmetric unit (values in parentheses are for the derivative). The C-2 bromo derivative is hexagonal P61, unit cell dimensions a = b = 32.13 A, c = 143.92, gamma = 120 degrees with one molecule in the asymmetric unit. The structures were solved by the molecular replacement method. The novelty of the structures is that there are two netropsins bound end-to-end in the minor groove of each B-DNA decamer which has nearly a complete turn. The netropsins are held by hydrogen bonding interactions to the base atoms and by sandwiching van der Waal's interactions from the sugar-phosphate backbones of the double helix similar to every other drug.DNA complex. Each netropsin molecule spans approximately 5 bp. The netropsins refined with their guanidinium heads facing each other at the center, although an orientational disorder for the netropsins cannot be excluded. The amidinium ends stretch out toward the junctions and bind to the adjacent duplexes in the columns of stacked symmetry-related complexes. Both cationic ends of netropsin are bridged by water molecules in one of the independent molecules (molecule A) of the triclinic structures and also the hexagonal structure to form pseudo-continuous drug.decamer helices.

Bromine↗

PubMed1996

X-ray structures of Mn, Cd and Tb metal complexes of troponin C.

The crystal structures of three metal complexes of troponin C (TnC) have been determined and refined where the two occupied structural Ca(2+) sites in the C domain have been substituted by Mn(2+), Cd(2+) and Tb(3+). The X-ray intensity data were collected to 2.1, 1.8 and 1.8 A resolution, respectively, on the three metal complexes, which are isomorphous with Ca-TnC. The three complexes have r.m.s. deviations of 0.27, 0.25 and 0.35 A, respectively, for all protein atoms, from Ca-TnC. Irrespective of the charge on the metal (+2 or +3), the occupied sites 3 and 4 exhibit a distorted pentagonal bipyramidal coordination, like Ca-TnC, with seven ligands, six from the 12-residue binding loop and the seventh from a water molecule. Mn(2+) at site 4 seems to display a longer distance to one of the carboxyl bidentate ligands representing an intermediate coordination simulating the six-coordinate Mg(2+). The carboxyl O atoms of the bidentate Glu12 are displaced on the side of the equatorial plane passing through the remaining three ligands with one O atom closer to the plane (Delta of 0.11 to 0.76 A) than the other (Delta of 0.93 to 1.38 A). The two axial ligands are an aspartic carboxyl O atom and a water molecule. The metal is displaced (0.18 to 0.56 A) towards the water facing the water channel.

Journal Article↗

PubMed1996

Studies of monoclinic hen egg-white lysozyme. IV. X-ray refinement at 1.8 A resolution and a comparison of the variable regions in the polymorphic forms.

Monoclinic crystals of hen egg-white lysozyme (E.C. 3.2.1.17, HEL) grown at low pH in the presence of NaNO(3) belong to space group P2(1) with unit-cell dimensions, a = 28.0, b = 62.5, c = 60.9 A and beta= 90.8 degrees with two molecules in the asymmetric unit. 1.8 A resolution intensity data, collected on a CAD-4 diffractometer, contained 17 524 reflections with F > 3sigma (93% complete). Our earlier preliminary 1.8 A model was refitted and refined using X-PLOR to an R value of 0.189. The deviations in the model from ideal geometry are 0.013 A in bond lengths and 2.8 degrees in bond angles. The r.m.s. deviation in the backbone atoms between the two molecules is 0.42 A. A comparison of HEL in different polymorphic crystal forms reveals that the prominent structural variability among them resides in two exposed regions 45-50 and 65-73 which are also regions of lattice contacts.

Journal Article↗

PubMed1996

Crystal structure of the B-DNA hexamer d(CTCGAG): model for an A-to-B transition.

The crystal structure of the B-DNA hexamer d(CTCGAG) has been solved at 1.9 A resolution by iterative single isomorphous replacement, using the brominated derivative d(CG5BrCGAG), and refined to an R-factor of 18.6% for 120 nonhydrogen nucleic acid atoms and 32 water molecules. Although the central four base pairs form a typical B-form helix, several parameters suggest a transition to an A-like conformation at the termini. Based on this observation, a B-to-A transition was modeled, maintaining efficient base stacking across the junction. The wide minor groove (approximately 6.9 A) is reminiscent of that in the side-by-side double drug-DNA complexes and hosts a double spine of hydration. The global helix axes of the pseudo-continuous helices are at an acute angle of 60 degrees. The pseudocontinuous stacking is reinforced by the minor groove water structure extending between the two duplexes. The crossover point of two pairs of stacked duplexes is at the stacking junction, unlike that observed in the B-DNA decamers and dodecamers. This arrangement may have implications for the structure of a four-way DNA junction. The duplexes are arranged around a large (approximately 20 A diameter) channel centered on a 6(2) screw axis.

Base Sequence↗

PubMed1996

The structure of r(UUCGCG) has a 5'-UU-overhang exhibiting Hoogsteen-like trans U.U base pairs.

The crystal structure of the RNA fragment, 5'-r(UUCGCG)-3', has been determined at 1.4 A resolution by a combination of single isomorphous replacement and molecular search methods. The 3'-terminal CGCG portion of the hexamer engages in Watson-Crick hydrogen bonding while the 5'-terminal UU-overhang forms novel Hoogsteen-like U.U self-base pairs with the overhang of an adjacent duplex. The U.U pairs display a single conventional hydrogen bond between O4 (U1) and N3 (U8) and a CH-O hydrogen bond between C5-H (U1) and O4 (U8), through the Hoogsteen face of the pyrimidine base U1. This unusual arrangement of one of the bases results in a trans U.U pair on antiparallel strands in contrast to the usual cis base pairs. The structure emphasizes the pronounced polymorphism of U.U pairs and has implications for folding of RNA molecules.

Animals↗

PubMed1995

X-ray structures of the B-DNA dodecamer d(CGCGTTAACGCG) with an inverted central tetranucleotide and its netropsin complex.

The crystal structures of the B-DNA dodecamer d(CGCGTTAACGCG) duplex (T2A2), with the inverted tetranucleotide core from the duplex d(CGCGAATTCGCG) [A2T2, Dickerson & Drew (1981). J. Mol. Biol. 149, 761-768], and its netropsin complex (T2A2-N) have been determined at 2.3 A resolution. The crystals are orthorhombic, space group P2(1)2(1)2(1), unit-cell dimensions of a = 25.7, b = 40.5 and c = 67.0 A, for T2A2 and a = 25.49, b = 40.87, c = 67.02 A for T2A2-N and are isomorphous with A2T2. The native T2A2 structure, with 70 water molecules had a final R value of 0.15 for 1522 reflections (F > 2sigma), while for the netropsin complex, with 87 water molecules, the R value was 0.16 for 2420 reflections. In T2A2, a discontinuous string of zig-zagging water molecules hydrate the narrow A.T minor groove. In T2A2-N, netropsin binds in one orientation in the minor groove, covering the TTAA central region, by displacing the string of waters, forming the majority of hydrogen bonds with DNA atoms in one strand, and causing very little perturbation of the native structure. The helical twist angle in T2A2 is largest at the duplex center, corresponding to the cleavage site by the restriction enzymes HpaI and HincII. The sequence inversion AATT-->TTAA of the tetranucleotide at the center of the molecule results in a different path for the local helix axis in T2A2 and A2T2 but the overall bending is similar in both cases.

Journal Article↗

PubMed1995

Determining temporal and spatial variations in ozone air quality.

Unless the change in emissions is substantial, the resulting improvement in ozone air quality can be easily masked by the meteorological variability. Therefore, the meteorological and chemical signals must be separated in examining ozone trends. In this paper, we discuss the use of the Kolmogorov-Zurbenko filter in evaluating the temporal and spatial variations in ozone air quality utilizing ozone concentration data from several monitoring locations in the northeastern United States. The results indicate a downward trend in the ozone concentrations during the period 1983-1992 at most locations in the northeastern United States. The results also reveal that ozone is a regional-scale problem in the Northeast.

Air Pollutants↗

PubMed1994

Structure of chicken skeletal muscle troponin C at 1.78 A resolution.

The structure of chicken skeletal muscle troponin C (TnC) has been refined to an R value of 0.168, using 14 788 reflections, in the resolution range 8.0-1.78 A. Our earlier 2 A resolution structure [Satyshur, Rao, Pyzalska, Drendel, Greaser & Sundaralingam (1988). J. Biol. Chem. 263, 1628-1647] served as the starting model. The refined model includes atoms for all protein residues (1-162), 2 Ca(2+) ions, 169 water molecules and one sulfate ion. The high-resolution refinement shows more clearly the details of the protein and water structure. The side chains Glu63, Cysl01, Arg123, Aspl40 and Asp152 adopt two discretely ordered conformations. The long central helix is only slightly curved/bent (7.9 degrees ) and all the central helix NH.O=C hydrogen bonds are intact. Seven of the nine carbonyl O atoms of the mid segment of this helix, including the D/E linker region, are hydrogen bonded to water molecules which weakens the helix hydrogen bonds. In contrast, in each of the protected upper and lower thirds of the long central helix, only two carbonyl O atoms are hydrogen bonded to water molecules. The hydrogen-bonding patterns displayed by some of the carbonyl O atoms of NT and A helices of the N-terminal domain and the F and H helices of the C-terminal domain, which are on the exposed surface of the protein, are similar. The B helix of the calcium-free site I is kinked, with the local helix axes at either end making an angle of 39 degrees, by two inserted water molecules between N-H and O=C groups, breaking the adjacent helix hydrogen bonds. A sulfate ion from the crystallization buffer is also trapped in the B helix between the guanidinium group of Arg47 and these two inserted water molecules. The C helix of site II is devoid of similar hydration and is probably responsible for the different interhelical angles A/B at site I (134 degrees ) and C/D at site II (149 degrees ). Extensive interhelix hydrogen bonds occur between the side chains of the C and D helices of the 'apo' site II: Gln51-Asp89, Asn52-Asp89, Glu57-Gln85, Glu57-Glu88 and Glu64-Arg84, which apparently are disrupted upon Ca uptake and the resulting rearrangement of the helices expose the side chains, lining the palm of the N-(and C-) terminal domains, for interaction with specific peptide fragment of troponin I (Tnl) during muscle contraction. The dominant crystal packing motif involves a head-to-tail interaction between the N-terminal domain A helix of one molecule and the palm of the C-terminal domain of the 3(2)-related molecule, in a manner similar to that which can be expected for the TnC-TnI complex. Similar interactions may also be responsible for the dimerization of TnC at low pH.

Journal Article↗

PubMed1994

Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex.

Here we report the 1.8A X-ray structure of a 2:1 drug-DNA complex between distamycin A and an alternating B-DNA octamer duplex d(ICICICIC)2. The two distamycin A molecules are bound side by side with dyad symmetry in an antiparallel orientation in the expanded minor groove. The amides of each drug molecule are hydrogen bonded to the minor groove base atoms of only one DNA strand. The complex not only shows binding of two drug molecules, but the DNA duplex also exhibits striking low-high alternations in the helical twist angles, the sugar puckering and the phosphate conformations, providing the basis for a new model for an alternating B-DNA with a dinucleotide repeat.

Base Sequence↗

PubMed1994

Detecting and tracking changes in ozone air quality.

This paper presents a statistical method for filtering out or moderating the influence of meteorological fluctuations on ozone concentrations. Use of this technique in examining trends in ambient ozone air quality is demonstrated with ozone data from a monitoring location in New Jersey. The results indicate that this method can detect changes in ozone air quality due to changes in emissions in the presence of meteorological fluctuations. This method can be useful in examining the effectiveness of regulatory initiatives in improving ozone air quality.

Air Pollutants, Occupational↗