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D R Walker

Publications and source records attributed to D R Walker.

At least 19 recordsLinked to original sources
PubMed2005

Measurement of Fourier-synthesized optical waveforms.

Following the experiments of Shverdin and colleagues [Phys. Rev. Lett. 94, 033904 (2005)], we describe a technique for determining the temporal envelope of an optical beam whose spectrum consists of n discrete, equally spaced frequency components. Four-wave mixing is employed to generate n-1 higher-frequency sidebands. The relative intensities of these sidebands, together with the intensities of the incident side-bands, determine the unknown relative phases of the incident beam.

Journal Article↗
PubMed2005

Generation of a single-cycle optical pulse.

We make use of coherent control of four-wave mixing to the ultraviolet as a diagnostic and describe the generation of a periodic optical waveform where the spectrum is sufficiently broad that the envelope is approximately a single-cycle in length, and where the temporal shape of this envelope may be synthesized by varying the coefficients of a Fourier series. Specifically, using seven sidebands, we report the generation of a train of single-cycle optical pulses with a pulse width of 1.6 fs, a pulse separation of 11 fs, and a peak power of 1 MW.

Journal Article↗
PubMed2004

Comparison of four flow cytometric SNP detection assays and their use in plant improvement.

Single nucleotide polymorphisms (SNPs) are attractive DNA markers due to their abundance and potential for use in automated high-throughput genotyping. Numerous SNP genotyping assays have been developed, but it is unclear which assays are best suited and most efficient for various types of plant improvement research. The objective of this study was to compare the accuracy, efficiency, and cost of four SNP genotyping assays: single-base extension (SBE), allele-specific primer extension (ASPE), oligonucleotide ligation (OL), and direct hybridization (DH). All four assay methods used the same Luminex 100 flow cytometer platform. Fifty-eight F(2)-derived soybean [Glycine max (L.) Merr.] lines from a cross between inbred lines G99-G725 and N00-3350 were genotyped at four SNPs. SBE and ASPE clearly differentiated between the two homozygotes and the heterozygote at each SNP. Results were in agreement with those identified using the SNaPshot minisequencing assay as a control. In contrast, the OL and DH assays were unable to differentiate between genotypes at some of the SNPs. However, when the cost per data point for the four different assays was compared, the cost of OL and DH was only about 70% of that for SBE, with DH requiring the least time of the four assays. On the basis of cost and labor, ASPE is more cost-effective and simpler than SBE, and would therefore be a good method for genetic mapping and diversity studies which require a large number of markers and a high level of multiplexing. DH appears to be the most economical assay for marker-assisted selection, though optimization for DH would be required for some SNP markers.

Base Sequence↗
PubMed2003

Quasiperiodic Raman technique for ultrashort pulse generation.

We report the experimental demonstration of a new Raman technique that produces 200 sidebands, ranging in wavelength from 3 microm to 195 nm. By studying multiphoton ionization of nitric oxide (NO) molecules, we show mutual phase coherence among 15 visible sidebands covering 0.63 octaves of bandwidth.

Journal Article↗
PubMed2001

Femtosecond light source for phase-controlled multiphoton ionization.

We describe a femtosecond Raman light source with more than an octave of optical bandwidth. We use this source to demonstrate phase control of multiphoton ionization under conditions where ionization requires eleven photons of the lowest frequency of the spectrum or five photons of the highest frequency. The nonlinearity of the photoionization process allows us to characterize the light source. Experiment-to-theory comparison implies generation of a near single-cycle waveform.

Journal Article↗
PubMed2000

Raman generation by phased and antiphased molecular states.

We use molecular deuterium and two driving lasers to demonstrate collinear generation of mutually coherent equidistant sidebands, covering 50 000 cm(-1) of spectral bandwidth and ranging from 2.94 microm to 195 nm in wavelength. The essential idea is the adiabatic preparation of a single, highly coherent (|rho(ab)| = 0.33) molecular eigenstate.

Journal Article↗
PubMed2000

Field evaluation of soybean engineered with a synthetic cry1Ac transgene for resistance to corn earworm, soybean looper, velvetbean caterpillar (Lepidoptera: Noctuidae), and lesser cornstalk borer (Lepidoptera: Pyralidae).

A transgenic line of the soybean 'Jack', Glycine max (L.) Merrill, expressing a synthetic cry1Ac gene from Bacillus thuringiensis variety kurstaki (Jack-Bt), was evaluated for resistance to four lepidopteran pests in the field. Jack-Bt and genotypes serving as susceptible and resistant controls were planted in field cages and artificially infested with larvae of corn earworm, Helicoverpa zea (Boddie), and velvetbean caterpillar, Anticarsia gemmatalis (Hübner), in 1996, 1997, and 1998, and also with soybean looper, Pseudoplusia includens (Walker), in 1996. Susceptible controls included Jack (1996-1998), 'Cobb' (1996), and Jack-HPH (1996). GatIR 81-296 was used as the resistant control in all 3 yr. Compared with untransformed Jack, Jack-Bt showed three to five times less defoliation from corn earworm and eight to nine times less damage from velvetbean caterpillar. Defoliation of GatIR 81-296 was intermediate between that of Jack and Jack-Bt for corn earworm, and similar to that of Jack for velveltbean caterpillar. Jack-Bt exhibited significant, but lower resistance to soybean looper. Jack-Bt also showed four times greater resistance than Jack to natural infestations of lesser cornstalk borer, Elasmopalpus lignosellus (Zeller), in conventional field plots at two locations in 1998. Data from these experiments suggest that expression of this cry1Ac construct in soybean should provide adequate levels of resistance to several lepidopteran pests under field conditions.

Animals↗
PubMed1999

Conserved domains in DNA repair proteins and evolution of repair systems.

A detailed analysis of protein domains involved in DNA repair was performed by comparing the sequences of the repair proteins from two well-studied model organisms, the bacterium Escherichia coli and yeast Saccharomyces cerevisiae, to the entire sets of protein sequences encoded in completely sequenced genomes of bacteria, archaea and eukaryotes. Previously uncharacterized conserved domains involved in repair were identified, namely four families of nucleases and a family of eukaryotic repair proteins related to the proliferating cell nuclear antigen. In addition, a number of previously undetected occurrences of known conserved domains were detected; for example, a modified helix-hairpin-helix nucleic acid-binding domain in archaeal and eukaryotic RecA homologs. There is a limited repertoire of conserved domains, primarily ATPases and nucleases, nucleic acid-binding domains and adaptor (protein-protein interaction) domains that comprise the repair machinery in all cells, but very few of the repair proteins are represented by orthologs with conserved domain architecture across the three superkingdoms of life. Both the external environment of an organism and the internal environment of the cell, such as the chromatin superstructure in eukaryotes, seem to have a profound effect on the layout of the repair systems. Another factor that apparently has made a major contribution to the composition of the repair machinery is horizontal gene transfer, particularly the invasion of eukaryotic genomes by organellar genes, but also a number of likely transfer events between bacteria and archaea. Several additional general trends in the evolution of repair proteins were noticed; in particular, multiple, independent fusions of helicase and nuclease domains, and independent inactivation of enzymatic domains that apparently retain adaptor or regulatory functions.

Amino Acid Sequence↗
PubMed1999

Evolutionary conservation and somatic mutation hotspot maps of p53: correlation with p53 protein structural and functional features.

Missense mutations in p53 frequently occur at 'hotspot' amino acids which are highly conserved and represent regions of structural or functional importance. Using the p53 mutation database and the p53 DNA sequences for 11 species, we more precisely defined the relationships among conservation, mutation frequency and protein structure. We aligned the p53 sequences codon-by-codon and determined the degree of substitution among them. As a whole, p53 is evolving at an average rate for a mammalian protein-coding gene. As expected, the DNA binding domain is evolving more slowly than the carboxy and amino termini. A detailed map of evolutionary conservation shows that within the DNA binding domain there are repeating peaks and valleys of higher and lower evolutionary constraint. Mutation hotspots were identified by comparing the observed distribution of mutations to the pattern expected from a random multinomial distribution. Seventy-three hotspots were identified; these 19% of codons account for 88% of all reported p53 mutations. Both high evolutionary constraint and mutation hotspots are noted at amino acids close to the protein-DNA interface and at others more distant from DNA, often buried within the core of the folded protein but sometimes on its surface. The results indicate that targeting highly conserved regions for mutational and functional analysis may be efficient strategies for the study of cancer-related genes.

Chromosome Mapping↗
PubMed1999

A deviation bar chart for detecting dengue outbreaks in Puerto Rico.

OBJECTIVES: A Centers for Disease Control and Prevention deviation bar chart (Statistical Software for Public Health Surveillance) and laboratory-based surveillance data were evaluated for their utility in detecting dengue outbreaks in Puerto Rico. METHODS: A significant increase in dengue incidence was defined as an excess of suspected cases of more than 2 SDs beyond the mean for all 4-week periods from April through June (the period of lowest seasonal incidence), 1989 through 1993. An outbreak was defined as a cumulative annual rate of reported dengue greater than 3 per 1000 population. RESULTS: Retrospective application of the system to 1994 data showed agreement with previous analyses. In 1995 and 1996, 36.4% and 27.3%, respectively, of municipalities with a significant increase in reports for 2 or more consecutive weeks before the first week of September had an outbreak, compared with 9.0% (in 1995, P = .042) and 6.0% (in 1996, P = .054) of towns without a significant increase. The system showed sensitivity near 40%, specificity near 89%, and accuracy in classifying municipalities near 84%. CONCLUSIONS: This method provides a statistically based, visually striking, specific, and timely signal for dengue control efforts.

Data Interpretation, Statistical↗
PubMed1998

Analogous enzymes: independent inventions in enzyme evolution.

It is known that the same reaction may be catalyzed by structurally unrelated enzymes. We performed a systematic search for such analogous (as opposed to homologous) enzymes by evaluating sequence conservation among enzymes with the same enzyme classification (EC) number using sensitive, iterative sequence database search methods. Enzymes without detectable sequence similarity to each other were found for 105 EC numbers (a total of 243 distinct proteins). In 34 cases, independent evolutionary origin of the suspected analogous enzymes was corroborated by showing that they possess different structural folds. Analogous enzymes were found in each class of enzymes, but their overall distribution on the map of biochemical pathways is patchy, suggesting multiple events of gene transfer and selective loss in evolution, rather than acquisition of entire pathways catalyzed by a set of unrelated enzymes. Recruitment of enzymes that catalyze a similar but distinct reaction seems to be a major scenario for the evolution of analogous enzymes, which should be taken into account for functional annotation of genomes. For many analogous enzymes, the bacterial form of the enzyme is different from the eukaryotic one; such enzymes may be promising targets for the development of new antibacterial drugs.

Amino Acid Sequence↗
PubMed1998

Comparison of digital angiographic images with conventional radiographs for detection of pneumothorax after needle biopsy of lung.

OBJECTIVE: To compare the rate of detection of pneumothoraces from images obtained from a digital angiographic system (1024 x 1024 matrix) and from conventional film-screen chest radiographs, following fine-needle biopsy of the lung. PATIENTS AND METHOD: For 102 patients who underwent fine-needle biopsy, 2 digital fluoroscopic chest images and 1 film-screen chest radiograph were obtained during expiration after the biopsy. The images were interpreted by 4 blinded readers. RESULTS: There were 30 pneumothoraces, of which 96.6% were detected from standard chest radiographs and 54.2% were detected from digital images. CONCLUSIONS: The detection of pneumothorax from digital images was far inferior to that from standard film-screen chest radiographs. Therefore, standard chest radiographs are recommended after fine-needle biopsy of the lung.

Adult↗
PubMed1997

Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea.

Protein sequences encoded in three complete bacterial genomes, those of Haemophilus influenzae, Mycoplasma genitalium and Synechocystis sp., and the first available archaeal genome sequence, that of Methanococcus jannaschii, were analysed using the BLAST2 algorithm and methods for amino acid motif detection. Between 75% and 90% of the predicted proteins encoded in each of the bacterial genomes and 73% of the M. jannaschii proteins showed significant sequence similarity to proteins from other species. The fraction of bacterial and archaeal proteins containing regions conserved over long phylogenetic distances is nearly the same and close to 70%. Functions of 70-85% of the bacterial proteins and about 70% of the archaeal proteins were predicted with varying precision. This contrasts with the previous report that more than half of the archaeal proteins have no homologues and shows that, with more sensitive methods and detailed analysis of conserved motifs, archaeal genomes become as amenable to meaningful interpretation by computer as bacterial genomes. The analysis of conserved motifs resulted in the prediction of a number of previously undetected functions of bacterial and archaeal proteins and in the identification of novel protein families. In spite of the generally high conservation of protein sequences, orthologues of 25% or less of the M. jannaschii genes were detected in each individual completely sequenced genome, supporting the uniqueness of archaea as a distinct domain of life. About 53% of the M. jannaschii proteins belong to families of paralogues, a fraction similar to that in bacteria with larger genomes, such as Synechocystis sp. and Escherichia coli, but higher than that in H. influenzae, which has approximately the same number of genes as M. jannaschii. Certain groups of proteins, e.g. molecular chaperones and DNA repair enzymes, thought to be ubiquitous and represented in the minimal gene set derived by bacterial genome comparison, are missing in M. jannaschii, indicating massive non-orthologous displacement of genes responsible for essential functions. An unexpectedly large fraction of the M. jannaschii gene products, 44%, shows significantly higher similarity to bacterial than to eukaryotic proteins, compared with 13% that have eukaryotic proteins as their closest homologues (the rest of the proteins show approximately the same level of similarity to bacterial and eukaryotic homologues or have no homologues). Proteins involved in translation, transcription, replication and protein secretion are most closely related to eukaryotic proteins, whereas metabolic enzymes, metabolite uptake systems, enzymes for cell wall biosynthesis and many uncharacterized proteins appear to be 'bacterial'. A similar prevalence of proteins of apparent bacterial origin was observed among the currently available sequences from the distantly related archaeal genus, Sulfolobus. It is likely that the evolution of archaea included at least one major merger between ancestral cells from the bacterial lineage and the lineage leading to the eukaryotic nucleocytoplasm.

Algorithms↗
PubMed1997

SEALS: a system for easy analysis of lots of sequences.

We present a system of programs designed to facilitate sequence analysis projects involving large amounts of data. SEALS (System for Easy Analysis of Lots of Sequences) is a logically organized set of flexible, easily modifiable research tools, designed to run on open systems. Functionality is divided into approximately 50 commands which follow consistent syntax and semantics; wrappers are also provided for commonly used sequence analysis software to effect similar syntax for these programs. SEALS includes software for retrieving sequence information, scripting database search tools such as BLAST and MoST, viewing and analyzing search outputs, searching in and processing nucleotide and protein sequences using regular expressions, and constructing rational predictions of protein features. The system is designed to provide modular elements which can be combined, modified, and integrated with other methods in order to quickly design and execute computer experiments for sequence analysis projects at the scale of whole genomes.

Artificial Intelligence↗
PubMed1995

Magnesium flux during and after open heart operations in children.

Hypomagnesemia and depletion of the body's magnesium stores is known to be associated with an increased incidence of both cardiac arrhythmias and neurological irritability. In a two-part prospective study we have evaluated whether magnesium deficiency is a significant occurrence in children treated in the intensive care unit after open heart operations, and subsequently have sought to identify how intraoperative metabolic changes were related to the resultant findings. In 41 children studied after operation the plasma magnesium concentration showed a significant decrease from 0.92 mmol/L (10th to 90th centile, 0.71 to 1.15 mmol/L) immediately after operation to 0.77 mmol/L (0.65 to 0.91 mmol/L) on the following morning. The subsequent change in grouped values was not significant but 14 (34.2%) and 7 (17.1%) possessed values of less than 0.7 mmol/L and 0.6 mmol/L, respectively. The occurrence of cardiac arrhythmias was not statistically related to the occurrence of hypomagnesemia. In 21 children perioperative changes in extracellular and tissue magnesium, potassium, and calcium content were measured. It was found that hemodilution with a prime low in magnesium caused a reduction from a median of 0.81 mmol/L to 0.61 mmol/L (p < 0.01). Plasma potassium level, however, was elevated from 3.7 mmol/L to 4.15 mmol/L (p < 0.05) and the ionized calcium content from 1.17 mmol/L (1.07 to 1.25 mmol/L) to 1.49 mmol/L (1.25 to 2.56 mmol/L) (p = 0.0009). The myocardial content of magnesium did not change significantly but skeletal muscle content was depleted from 6.75 mumol/g (2.85 to 8.35 mumol/g) to 5.65 mumol/g (2.45 to 7.2 mumol/g) (p < 0.01).(ABSTRACT TRUNCATED AT 250 WORDS)

Arrhythmias, Cardiac↗