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PubMed2003

Time-resolved Fourier transform infrared spectroscopic imaging.

Fourier transform infrared (FT-IR) imaging allows simultaneous spectral characterization of large spatial areas due to its multichannel detection advantage. The acquisition of large amounts of data in the multichannel configuration results, however, in a poor temporal resolution of sequentially acquired data sets, which limits the examination of dynamic processes to processes that have characteristic time scales of the order of minutes. Here, we introduce the concept and instrumental details of a time-resolved infrared spectroscopic imaging modality that permits the examination of repetitive dynamic processes whose half-lives are of the order of milli-seconds. As an illustration of this implementation of step-scan FT-IR imaging, we examine the molecular responses to external electric-field perturbations of a microscopically heterogeneous polymer-liquid crystal composite. Analysis of the spectroscopic data using conventional univariate and generalized two-dimensional (2D) correlation methods emphasizes an additional capability for accessing of simultaneous spatial and temporal chemical measurements of molecular dynamic processes.

Crystallization↗
PubMed1997

Cytochrome cd1 structure: unusual haem environments in a nitrite reductase and analysis of factors contributing to beta-propeller folds.

The central tunnel of the eight-bladed beta-propeller domain of cytochrome cd1 (nitrite reductase) is seen, from a 1.28 A resolution structure, to contain hydrogen donors and acceptors that are satisfied by interaction either with water or the d1 haem. The d1 haem, although bound by an extensive network of hydrogen bonds, is not distorted in its binding pocket and is confirmed to have exactly the dioxoisobacteriochlorin structure proposed from chemical studies. A biological rationale is advanced for the undistorted structure of the d1 haem and the large number of hydrogen bonds it makes. The beta-propeller domain can be closely superimposed on that of methanol dehydrogenase despite the enzymes sharing no common sequence motifs and using a different set of interactions to "Velcro" close the propeller. The sequence and likely structural relationships between cytochrome cd1 or methanol dehydrogenase and other predicted eight-bladed beta-propeller domains in proteins, such as the pyrolloquinoline quinone-dependent alcohol dehydrogenase, are discussed and compared with other propeller proteins. From sequencing the nirS gene of Thiosphaera pantotropha, it is established that the amino acid sequence deduced previously in part from X-ray diffraction data at lower resolution was largely correct, as was the proposal that eight N-terminal amino acid residues were not seen in the structure. The unusual haem iron environments in both the c-type cytochrome domain, with His/His coordination, and the d1-type cytochrome domain with Tyr/His coordination are related to the functions of the redox centres.

Amino Acid Sequence↗
PubMed2006

Avian GIS models signal human risk for West Nile virus in Mississippi.

BACKGROUND: West Nile virus (WNV) poses a significant health risk for residents of Mississippi. Physicians and state health officials are interested in new and efficient methods for monitoring disease spread and predicting future outbreaks. Geographic Information Systems (GIS) models have the potential to support these efforts. Environmental conditions favorable for mosquito habitat were modeled using GIS to derive WNV risk maps for Mississippi. Variables important to WNV dissemination were selected and classified as static and dynamic. The static variables included road density, stream density, slope, and vegetation. The dynamic variable represented seasonal water budget and was calculated using precipitation and evaporation estimates. Significance tests provided deterministic evidence of variable importance to the models. RESULTS: Several models were developed to estimate WNV risk including a landscape-base model and seasonal climatic sub-models. P-values from t-tests guided variable importance ranking. Variables were ranked and weights assigned as follows: road density (0.4), stream density (0.3), slope (0.2) and vegetation (0.1). This landscape-base model was modified by climatic conditions to assess the importance of climate to WNV risk. Human case data at the zip code level were used to validate modeling results. All models were summarized by zip codes for interpretation and model validation. For all models, estimated risk was higher for zip codes with at least one human case than for zip codes where no human cases were recorded. Overall median measure of risk by zip code indicated that 67% of human cases occurred in the high-risk category. CONCLUSION: Modeling results indicated that dead bird occurrences are correlated with human WNV risk and can facilitate the assessment of environmental variables that contribute to that risk. Each variable's importance in GIS-based risk predictions was assigned deterministically. Our models indicated non-uniform distribution of risk across the state and showed elevated risk in urban and as well as rural areas. Model limitations include resolution of human data, zip code aggregation issues, and quality/availability of vegetation and stream density layers. Our approach verified that WNV risk can be modeled at the state level and can be modified for risk predictions of other vector-borne diseases in varied ecological regions.

Animals↗
PubMed1998

Disequilibrium likelihoods for fine-scale mapping of a rare allele.

Genetic linkage studies based on pedigree data have limited resolution, because of the relatively small number of segregations. Disequilibrium mapping, which uses population associations to infer the location of a disease mutation, provides one possible strategy for narrowing the candidate region. The coalescent process provides a model for the ancestry of a sample of disease alleles, and recombination events between disease locus and marker may be placed on this ancestral phylogeny. These events define the recombinant classes, the sets of sampled disease copies descending from the meiosis at which a given recombination occurred. We show how Monte Carlo generation of the recombinant classes leads to a linkage likelihood for fine-scale mapping from disease haplotypes. We compare single-marker disequilibrium mapping with interval-disequilibrium mapping and discuss how the approach may be extended to multipoint-disequilibrium mapping. The method and its properties are illustrated with an example of simulated data, constructed to be typical of fine-scale mapping of a rare disease in the Japanese population. The method can take into account known features of population history, such as changing patterns of population growth.

Algorithms↗
PubMed2005

An adaptive multirate algorithm for acquisition of fluorescence microscopy data sets.

We propose an algorithm for adaptive efficient acquisition of fluorescence microscopy data sets using a multirate (MR) approach. We simulate acquisition as part of a larger system for protein classification based on their subcellular location patterns and, thus, strive to maintain the achieved level of classification accuracy as much as possible. This problem is similar to image compression but unique due to additional restrictions, namely causality; we have access only to the information scanned up to that point. While we do want to acquire fewer samples with as low distortion as possible to achieve compression, our goal is to do so while affecting the overall classification accuracy as little as possible. We achieve this by using an adaptive MR scanning scheme which samples the regions of the image area that hold the most pertinent information. Our results show that we can achieve significant compression which we can then use to aquire faster or to increase space resolution of our data set, all while minimally affecting the classification accuracy of the entire system.

Algorithms↗
PubMed2002

The crystal structure of the H48Q active site mutant of human group IIA secreted phospholipase A2 at 1.5 A resolution provides an insight into the catalytic mechanism.

The human group IIA secreted PLA(2) is a 14 kDa calcium-dependent extracellular enzyme that has been characterized as an acute phase protein with important antimicrobial activity and has been implicated in signal transduction. The selective binding of this enzyme to the phospholipid substrate interface plays a crucial role in its physiological function. To study interfacial binding in the absence of catalysis, one strategy is to produce structurally intact but catalytically inactive mutants. The active site mutants H48Q, H48N, and H48A had been prepared for the secreted PLA(2)s from bovine pancreas and bee venom and retained minimal catalytic activity while the H48Q mutant showed the maximum structural integrity. Preparation of the mutant H48Q of the human group IIA enzyme unexpectedly produced an enzyme that retained significant (2-4%) catalytic activity that was contrary to expectations in view of the accepted catalytic mechanism. In this paper it is established that the high residual activity of the H48Q mutant is genuine, not due to contamination, and can be seen under a variety of assay conditions including assays in the presence of Co(2+) and Ni(2+) in place of Ca(2+). The crystallization of the H48Q mutant, yielding diffraction data to a resolution of 1.5 A, allowed a comparison with the corresponding recombinant wild-type enzyme (N1A) that was also crystallized. This comparison revealed that all of the important features of the catalytic machinery were in place and the two structures were virtually superimposable. In particular, the catalytic calcium ion occupied an identical position in the active site of the two proteins, and the catalytic water molecule (w6) was clearly resolved in the H48Q mutant. We propose that a variation of the calcium-coordinated oxyanion ("two water") mechanism involving hydrogen bonding rather than the anticipated full proton transfer to the histidine will best explain the ability of an active site glutamine to allow significant catalytic activity.

Anions↗
PubMed1996

Anti-tumor effects of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) in seborrheic keratosis.

1,25-dihydroxyvitamin D3 (1,25(OH)2D3) is a drug with potent antiproliferative action on keratinocytes that have nuclear receptors for 1,25(OH)2D3. We investigated the effects of 1,25(OH)2D3 on widespread seborrheic keratoses in 51 patients with these tumors. The data indicated that resolution of these tumors was dependent on both tumor size and dose of 1,25(OH)2D3. Among 15 patients treated with a high dose (0.5 microgram/d) of oral 1,25(OH)2D3, the lesions of widespread seborrheic keratoses changed from brown-black papules to brownish papules with erythema and/or crust as early as 2 wk after the start of treatment. The tumors finally developed into an atrophic scar or brownish pigmented macule. Histologically, vacuolation of the spinous cells, vesicle formation, and liquefaction degeneration of the basaloid cells were observed. Numerous lymphocytes had infiltrated in the papillary dermis. Among 36 patients treated with a low dose (0.25 microgram/d) of 1,25(OH)2D3, brownish papules became pale to normal in color and reduced in size, without erythematous change. Histologically, acanthosis of the epidermis was reduced, but degenerative change of the tumor cells was not observed. These data suggest that oral therapy of 1,25(OH)2D3 is an acceptable method well suited to the removal of seborrheic keratoses, especially those that are predominantly small tumors.

Adult↗
PubMed2000

Three-dimensional multiplanar ultrasound for fetal gender assignment: value of the mid-sagittal plane.

OBJECTIVE: To evaluate the feasibility and accuracy of fetal gender assignment from three-dimensional ultrasound (3D US) data at 10-24 weeks' gestation. METHODS: Three-dimensional ultrasound volume data on 47 fetuses were reviewed and divided into groups: 10-14, 15-18, and 19-24 weeks. Fetal genitalia were studied in axial and sagittal planes for gender assignment, using published criteria. The most valuable plane for assignment was noted. Gender assignment was compared with gender at birth. RESULTS: Gender assignment was possible in 44 of 47 fetuses; 25 assigned male and 19 female. Between 10 and 14 weeks the mid-sagittal plane alone was diagnostic for all fetuses. Accuracy of assignment between 11 and 14 weeks was 100%. Between 15 and 18 and 19 to 24 weeks, male assignment was 100% accurate. Female assignment was 100% accurate between 15 and 18 weeks. Accuracy decreased to 60% in the 19 to 24 week group, however, in two of the five cases in which gender was wrongly assigned to be male, the assignment was prospectively considered doubtful due to poor resolution of volume data. Excluding these two cases, accuracy for female assignment in the 19-24 week group was 100%. CONCLUSION: Using 3D US, gender assignment was possible in 44 of 47 of fetuses, as early as 11 weeks' gestation. In early gestation, 11-14 weeks, accuracy of male and female gender assignment was 100%.

Feasibility Studies↗
PubMed1988

Three-dimensional structure of proteinase K at 0.15-nm resolution.

The crystal and molecular structure of proteinase K was determined by X-ray diffraction data to 0.15-nm resolution. The enzyme belongs to the subtilisin family with an active-site catalytic triad Asp39--His69--Ser224 but is a representative of a subgroup with a free Cys73 close to and 'below' the active His69. Besides this Cys72, proteinase K has two disulfide bonds, Cys34--Cys123 and Cys178--Cys249, which contribute to the stability of the tertiary structure consisting of an extended central parallel beta-sheet decorated by six alpha-helices, three short antiparallel beta-sheets, 18 beta-turns and involving several internal, structurally important water molecules. Proteinase K exhibits two Ca2+-binding sites, one very strong and the other weak, which were the sites of the heavy atoms (Pb2+, Sm3+) used to solve the crystal structure. The weak binding site is liganded to the N and C termini, Thr16 and Asp260, and is only incompletely coordinated by oxygen ligands. The strong binding site is coordinated in the form of a pentagonal bipyramid with the side chain carboxylate of Asp200 and the C = O of Pro175 as apex, and C = O of Val177 and four water molecules in the equatorial plane. Upon removal of this Ca2+, proteinase K loses activity which is interpreted in terms of a local structural deformation involving the substrate-recognition site (Ser132--Gly136), probably associated with a cis----trans isomerization of cis Pro171. Several water molecules are located in the active site. One, W335, is positioned in the 'oxyanion hole' and is displaced by the C = O of the scissile peptide bond of the substrate, as indicated by crystallographic studies with peptide chloromethane inhibitors. Based on these experiments, a reaction mechanism is proposed where the peptide substrate forms a three-stranded antiparallel pleated sheet with the recognition site of proteinase K consisting of Ser132--Leu133--Gly134 on one side and Gly100--Ser101 on the other, followed by expulsion of the oxyanion hole water W335 and hydrolytic cleavage by the Asp39--His69--Serr224 triad. These latter residues display low thermal motion corresponding to well-defined geometry and are hardly accessible to solvent molecules, whereas the recognition-site amino acids are more flexible and partially exposed to solvent.

Amino Acid Sequence↗
PubMed1993

The sequence and X-ray structure of the trypsin from Fusarium oxysporum.

The trypsin from Fusarium oxysporum is equally homologous to trypsins from Streptomyces griseus, Streptomyces erythraeus and to bovine trypsin. A DFP (diisopropylfluorophosphate) inhibited form of the enzyme has been crystallized from 1.4 M Na2SO4, buffered with citrate at pH 5.0-5.5. The crystals belong to space group P2(1) with cell parameters a = 33.43 A, b = 67.65 A, c = 39.85 A and beta = 107.6 degrees. There is one protein molecule in the asymmetric unit. X-ray diffraction data to a resolution of 1.8 A were collected on film using synchrotron radiation. The structure was solved by molecular replacement using models of bovine and S. griseus trypsins and refined to an R-factor of 0.141. The overall fold is similar to other trypsins, with some insertions and deletions. There is no evidence of the divalent cation binding sites seen in other trypsins. The covalently bound inhibitor molecule is clearly visible.

Amino Acid Sequence↗
PubMed1977

[Improvement of resolution of positron annihilation radiation energy spectrum measurement by data analysis (author's transl)].

Recently much attention is being paid to positron annihilation radiation energy spectrum measurement as a simple method that gives information about the momentum distribution of an annihilating pair. However, this method has a disadvantage that it is sensitive to drifts of the measuring system and the resolution is still insufficient. We have succeeded to reduce the influence of the drifts to a negligibly small degree by using, in addition to the necessary procedure for a temperature control and stabilizing of AC power lines, a compensation technique in data analysis. We have further attempted to improve the resolution by deconvolution processing. By these procedures, we have been able to separate a narrow component which has not otherwise been resolved directly from the spectrum. The resolution attained by this way is 0.43 keV (FWHM), and is two- or three-fold superior to those ever reported.

Models, Theoretical↗
PubMed1994

DNA sequencing by hybridization to oligonucleotide matrix. Calculation of continuous stacking hybridization efficiency.

In this paper we consider the efficiency of additional rounds of "continuous stacking" hybridization in DNA sequence reconstruction by hybridization with oligonucleotide matrix (SHOM). After the initial hybridization of target DNA with the matrix of oligonucleotides of fixed length L some additional hybridizations should be carried out in the presence of fluorescently labeled oligonucleotides of another length l. These additional oligonucleotides can hybridize in tandem with matrix tuples (continuous stacking hybridization) thus forming an extended duplex with the target DNA strand. The additional data obtained allows resolutions of branching points arising in the reconstruction procedure. Multiple rounds of continuous stacking hybridization considerably increase the efficiency of the sequencing method, eventually approaching the power of (L+l)-matrix. We develop here an algorithm that allows us to minimize the number of additional hybridization steps, by assembling sets of l-tuples to be added together in each round of continuous stacking hybridization. For SHOM using a matrix of octanucleotides, continuous stacking hybridization with pentanucleotides increases the length of unambiguously sequenced DNA from 200 to several thousands of base pairs.

Algorithms↗
PubMed1988

Structure of native porcine pancreatic elastase at 1.65 A resolutions.

The structure of native porcine pancreatic elastase in 70% methanol has been refined using film data to 1.65 A resolution, R = 0.169. A total of 134 molecules of water (but no methanol) has been refined. This structure, because of its native state and modestly high resolution, serves as the basis for comparison with other elastase structures complexed with natural or synthetic ligands. Internal structured water occupies distinct regions. Two regions (IW1 and IW7) suggest a mechanism for equalizing 'hydrostatic pressure' related to ligand binding and release. A third region (IW4) forms part of a hydrogen-bonding network linking the catalytic Ser 195 O gamma with a remote (13.4 A) surface of the enzyme. A comparison with the structures of all known serine proteases reveals that a linkage of Ser O gamma to remote surface is conserved in all cases, suggesting that the accepted catalytic mechanism of serine proteases needs to be re-evaluated. One possible mechanism for base catalysis of Ser O gamma H proton extraction is presented.

Animals↗
PubMed2006

Application of a new leaf area index algorithm to China's landmass using MODIS data for carbon cycle research.

An operational system was developed for mapping the leaf area index (LAI) for carbon cycle models from the moderate resolution imaging spectroradiometer (MODIS) data. The LAI retrieval algorithm is based on Deng et al. [2006. Algorithm for global leaf area index retrieval using satellite imagery. IEEE Transactions on Geoscience and Remote Sensing, 44, 2219-2229], which uses the 4-scale radiative transfer model [Chen, J.M., Leblancs, 1997. A 4-scale bidirectional reflection model based on canopy architecture. IEEE Transactions on Geoscience and Remote Sensing, 35, 1316-1337] to simulate the relationship of LAI with vegetated surface reflectance measured from space for various spectral bands and solar and view angles. This algorithm has been integrated to the MODISoft platform, a software system designed for processing MODIS data, to generate 250 m, 500 m and 1 km resolution LAI products covering all of China from MODIS MOD02 or MOD09 products. The multi-temporal interpolation method was implemented to remove the residual cloud and other noise in the final LAI product so that it can be directly used in carbon models without further processing. The retrieval uncertainties from land cover data were evaluated using five different data sets available in China. The results showed that mean LAI discrepancies can reach 27%. The current product was also compared with the NASA MODIS MOD15 LAI product to determine the agreement and disagreement of two different product series. LAI values in the MODIS product were found to be 21% larger than those in the new product. These LAI products were compared against ground TRAC measurements in forests in Qilian Mountain and Changbaishan. On average, the new LAI product agrees with the field measurement in Changbaishan within 2%, but the MODIS product is positively biased by about 20%. In Qilian Mountain, where forests are sparse, the new product is lower than field measurements by about 38%, while the MODIS product is larger by about 65%.

Algorithms↗
PubMed2002

A quantitative evaluation of IMRT dose distributions: refinement and clinical assessment of the gamma evaluation.

BACKGROUND AND PURPOSE: Although intensity modulated radiotherapy (IMRT) is a step forward in comparison to conventional, static beam delivery, quality assurance is more complex and labour intensive, demanding detailed two-dimensional dosimetric verification. Regardless of the technique used for measuring the dose distribution, what is essential to the implementation of routine verification of IMRT fields is the efficient and accurate comparison of the measured versus desired dose distribution. In order to achieve a fast, yet accurate quantitative measure of the correspondence between measured and calculated dose, the theoretical concept of the gamma evaluation method presented by Low et al. (Med. Phys., 25 (1998) 656) was converted into a calculation algorithm, taking into account practical considerations related to the discrete nature of the data. MATERIALS AND METHODS: A filter cascade of multiple levels was designed to obtain fast and accurate comparison of the two dose distributions under evaluation. The actual comparison consists of classification into accepted or rejected datapoints with respect to user-defined acceptance criteria (dose difference and distance to agreement). The presented algorithm was tested on dosimetric images calculated and/or acquired by means of a liquid filled portal imaging device during the course of intensity modulated treatments of prostate cancer, including pre-treatment verification as well as verification during treatment. To assess its ability to intercept possible errors in dose delivery, clinically relevant errors were deliberately introduced into the dose distributions. RESULTS: The developed gamma filter method proves successful in the efficient comparison of calculated versus measured IMRT dose distribution. Secondly, intercomparison of dosimetric images acquired during different treatment sessions illustrate its potential to highlight variations in the dosimetric images. The simulated errors were unmistakably intercepted. CONCLUSIONS: The readily obtained gamma evaluation images are an easy tool for quality control of IMRT fields. To reduce the artefacts related to the discrete nature and limited resolution of the data, a fast and accurate filter cascade was developed, offering the possibility to use the gamma method for day to day evaluation of patient dosimetric portal images with or without comparison to a predicted portal dose distribution.

Algorithms↗
PubMed1990

Structural and thermodynamic studies on the adenine.guanine mismatch in B-DNA.

The structure of the synthetic dodecamer d(CGCAAATTGGCG) has been shown by single crystal X-ray diffraction methods to be that of a B-DNA helix containing two A(anti).G(syn) base pairs. The refinement, based on data to a resolution of 2.25 A shows that the mismatch base pairs are held together by two hydrogen bonds. The syn-conformation of the guanine base of the mismatch is stabilised by hydrogen bonding to a network of solvent molecules in both the major and minor grooves. A pH-dependent ultraviolet melting study indicates that the duplex is stabilised by protonation, suggesting that the bases of the A.G mispair are present in their most common tautomeric forms and that the N(1)-atom of adenine is protonated. The structure refinement shows that there is some disorder in the sugar-phosphate backbone.

Adenine↗
PubMed2000

Resolution measurement in structures derived from single particles.

Analytical expressions are derived and computer simulations are presented to assess the accuracy of procedures commonly used to estimate the resolution of three-dimensional (3D) structures derived from images of single protein molecules or complexes. It is shown that in the case of a low signal-to-noise ratio in the images, the Fourier ring correlation between two structures, each calculated using one half of the data, significantly overestimates the resolution when the two half data sets were aligned against the same reference structure. The overestimate arises because of a correlation between the noise components present in the images. The correlation is introduced by the alignment and becomes more serious as the signal-to-noise ratio is reduced. A reliable resolution measure is only obtained when the two half data sets are aligned against two independent reference structures. It is further shown that the noise correlation also significantly affects the spectral signal-to-noise ratio and the Q factor, making them unreliable measures of signal present in a 3D structure and in the original images, respectively. It is concluded that the alignment of images is always accompanied by a correlation of the noise and that this correlation is indistinguishable from a correlation arising from a signal.

Crystallography, X-Ray↗
PubMed2004

Structure of potato calmodulin PCM6: the first report of the three-dimensional structure of a plant calmodulin.

The crystal structure of a potato calmodulin (PCM6) was solved by molecular replacement and refined to a crystallographic R factor of 22.8% (R(free) = 25.0%) using X-ray diffraction data in the resolution range 8.0-2.0 A. This is the first report of the three-dimensional structure of a plant Ca(2+)-calmodulin. PCM6 crystallizes in a crystal form that belongs to space group P2(1)2(1)2(1), which is different to that of most other calmodulin crystals. The main structural difference between PCM6 and the other calmodulins is in the central helix region and appears to be caused by crystal packing. The surface properties of PCM6 molecules were compared with those of animal calmodulins, which provided an explanation for the unique crystal-packing state of PCM6.

Amino Acid Sequence↗