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Biomedical subjects

R W Hammond

Publications and source records attributed to R W Hammond.

At least 19 recordsLinked to original sources
PubMed2000

Differential transport of DNA by a rectified Brownian motion device.

An interdigitated electrode array (IDEA) device has been designed and used to transport DNA based on a Brownian ratchet mechanism. This migration is produced by the periodic formation of an asymmetric sawtooth electric field in the device. Oligonucleotides of 25, 50, and 100 bases in length were tested using two different array geometries. DNA transport as a function of DNA size, electric field frequency, and array geometry is shown to be in qualitative agreement with theory. Such a device could provide for DNA separations over a broad size range, and can be readily scaled as a component in a microfabricated DNA analysis system.

Animals↗
PubMed2000

Both point mutation and RNA recombination contribute to the sequence diversity of citrus viroid III.

Field-grown citrus trees often harbor complex mixtures of 4-5 different viroid species, and the presence of citrus viroid III (CVd-III) has been shown to reduce the rate of tree growth without inducing disease. To more fully define the structure of its quasi-species, we have examined nine citrus viroid complexes for the presence of previously undescribed sequence variants of CVd-III. Analysis of 86 full-length cDNAs generated from these nine viroid complexes by RT-PCR revealed the presence of 20 new CVd-III variants. Chain lengths ranged from 293-297 nucleotides, and sequence changes were confined largely to the lower portions of the central conserved region and variable domain. The previously described variants CVd-IIIa (297 nt) and CVd-IIIb (294 nt) were clearly predominant, but phylogenetic analysis indicated that certain isolates may contain representatives of two additional fitness peaks. At least one group of CVd-III variants appears to have arisen as a result of RNA recombination. Populations recovered from diseased/declining trees were the most diverse, but even dwarfing isolates originating from old line Shamouti trees showed considerable variability.

Base Sequence↗
PubMed2000

Characterization of a tomato protein kinase gene induced by infection by Potato spindle tuber viroid.

Viroids--covalently closed, circular RNA molecules in the size range of 250 to 450 nucleotides-are the smallest known infectious agents and cause a number of diseases of crop plants. Viroids do not encode proteins and replicate within the nucleus without a helper virus. In many cases, viroid infection results in symptoms of stunting, epinasty, and vein clearing. In our study of the molecular basis of the response of tomato cv. Rutgers to infection by Potato spindle tuber viroid (PSTVd), we have identified a specific protein kinase gene, pkv, that is transcriptionally activated in plants infected with either the intermediate or severe strain of PSTVd, at a lower level in plants inoculated with a mild strain, and not detectable in mock-inoculated plants. A full-length copy of the gene encoding the 55-kDa PKV (protein kinase viroid)-induced protein has been isolated and sequence analysis revealed significant homologies to cyclic nucleotide-dependent protein kinases. Although the sequence motifs in the catalytic domain suggest that it is a serine/threonine protein kinase, the recombinant PKV protein autophosphorylates in vitro on serine and tyrosine residues, suggesting that it is a putative member of the class of dual-specificity protein kinases.

Amino Acid Sequence↗
PubMed1999

DNA transport by a micromachined Brownian ratchet device.

We have micromachined a silicon-chip device that transports DNA with a Brownian ratchet that rectifies the Brownian motion of microscopic particles. Transport properties for a DNA 50-mer agree with theoretical predictions, and the DNA diffusion constant agrees with previous experiments. This type of micromachine could provide a generic pump or separation component for DNA or other charged species as part of a microscale lab-on-a-chip. A device with reduced feature size could produce a size-based separation of DNA molecules, with applications including the detection of single-nucleotide polymorphisms.

DNA↗
PubMed1999

Differentiation of closely related but biologically distinct cherry isolates of Prunus necrotic ringspot virus by polymerase chain reaction.

Prunus necrotic ringspot ilarvirus (PNRSV) exists as a number of biologically distinct variants which differ in host specificity, serology, and pathology. Previous nucleotide sequence alignment and phylogenetic analysis of cloned reverse transcription-polymerase chain reaction (RT-PCR) products of several biologically distinct sweet cherry isolates revealed correlations between symptom type and the nucleotide and amino acid sequences of the 3a (putative movement protein) and 3b (coat protein) open reading frames. Based upon this analysis, RT-PCR assays have been developed that can identify isolates displaying different symptoms and serotypes. The incorporation of primers in a multiplex PCR protocol permits rapid detection and discrimination among the strains. The results of PCR amplification using type-specific primers that amplify a portion of the coat protein gene demonstrate that the primer-selection procedure developed for PNRSV constitutes a reliable method of viral strain discrimination in cherry for disease control and will also be useful for examining biological diversity within the PNRSV virus group.

DNA Restriction Enzymes↗
PubMed1998

Effect of a pharmacist-education initiative on ketorolac use and costs in a Medicaid program.

The effects of a pharmacist-education initiative on the use and costs of ketorolac in a state Medicaid program are reviewed. An intervention letter describing changes in the manufacturer's prescribing guidelines for ketorolac and providing suggestions for interacting with physicians regarding the use of ketorolac was sent to 150 of the 301 pharmacies that participate in New Mexico's Medicaid program. The remaining 151 pharmacies served as a control group. Ketorolac claims records for three months before and after the intervention were reviewed. The mean quantity of ketorolac tablets, total days' supply, and number of prescriptions filled per pharmacy per month were calculated for both periods. The number of prescriptions not filled as a result of the intervention as well as the number that could have been avoided, the number of cases of peptic ulceration (ketorolac's major adverse effect) that would be avoided, and the associated cost savings if all the state's Medicaid pharmacies had been included in the intervention were estimated. A total of 167 pharmacies (90 intervention and 77 control) dispensed ketorolac for Medicaid patients during the study period. Ketorolac dispensing rates declined during the postintervention period in both the intervention group and the control group, but the reduction was greater in the intervention group. It was predicted that if all pharmacies were included in an intervention, 135.6 fewer prescriptions for ketorolac would be filled each year; as a result, 1.14 cases of peptic ulceration would be avoided and net Medicaid costs would be reduced by $1638. Sending educational letters to pharmacists was associated with a modest reduction in ketorolac use in a state Medicaid program; a net reduction in Medicaid costs if the intervention were extended to all pharmacies that participate in the state's Medicaid program was projected.

Analysis of Variance↗
PubMed1998

High-speed separation of linear and supercoiled DNA by capillary electrophoresis. Buffer, entangling polymer, and electric field effects.

Capillary electrophoresis in dilute and semidilute (slightly entangled) hydroxyethyl cellulose (HEC) is shown to separate linear double-stranded DNA (ds-DNA) and supercoiled plasmid DNA in the size range 1-16 thousand base pairs in 3 min. The mobilities of linear ds-DNA fragments are stronger functions of electric field strength and buffer concentration than the mobilities of supercoiled plasmids. The effects of HEC concentration and molecular weight are similar for both forms of DNA. The behavioral differences, which are attributed to the greater stiffness of the plasmids, can be used to define conditions that maximize resolution of supercoiled and linear ds-DNA of the same or similar number of base pairs.

Buffers↗
PubMed1998

Virulence and molecular polymorphism of Prunus necrotic ringspot virus isolates.

Prunus necrotic ringspot virus (PNRSV) occurs as numerous strains or isolates that vary widely in their pathogenic, biophysical and serological properties. Prior attempts to distinguish pathotypes based upon physical properties have not been successful; our approach was to examine the molecular properties that may distinguish these isolates. The nucleic acid sequence was determined from 1.65 kbp RT-PCR products derived from RNA 3 of seven distinct isolates of PNRSV that differ serologically and in pathology on sweet cherry. Sequence comparisons of ORF 3a (putative movement protein) and ORF 3b (coat protein) revealed single nucleotide and amino acid differences with strong correlations to serology and symptom types (pathotypes). Sequence differences between serotypes and pathotypes were also reflected in the overall phylogenetic relationships between the isolates.

Amino Acid Sequence↗
PubMed1997

Capillary electrophoresis of supercoiled and linear DNA in dilute hydroxyethyl cellulose solution.

Capillary electrophoresis in dilute hydroxyethyl cellulose is shown to separate supercoiled DNA in the size range 2000-16,000 base pairs. The plasmids migrate more slowly than linear ds-DNA of the same sizes. Plasmid bandwidths are larger than observed for ds-DNA, allowing identification of the type of DNA by bandwidth. The differing dependence of mobility on chain length can be explained by assuming that a plasmid migrates as an elastic rod, while ds-DNA migrates as a wormlike chain.

Cellulose↗
PubMed1997

Variability of geographically distinct isolates of maize rayado fino virus in Latin America.

We have examined the molecular epidemiology of the leafhopper-borne maize rayado fino virus (MRFV) in Latin America. The coat protein gene and 3' non-translated region of 14 isolates of MRFV collected from Latin America and the United States were sequenced and phylogenetic relationships examined. The nucleotide sequence revealed remarkable conservation, with a sequence similarity of 88-99%. Phylogenetic analysis of sequence data obtained from a 633 bp fragment showed that MRFV has diverged into three main clusters, i.e. the geographically distinct northern and southern isolates and the Colombian isolates. Significant differences between the isolates collected from Colombia, previously named maize rayado colombiana virus, based upon differences in symptomatology and serological relationships to MRFV, and the other MRFV isolates, provides additional evidence supporting its designation as a unique strain of MRFV.

Amino Acid Sequence↗
PubMed1997

Destabilization of potato spindle tuber viroid by mutations in the left terminal loop.

Infectivity studies with highly infectious RNA inocula generated by ribozyme cleavage were used to compare the biological properties of three apparently nonviable mutants of potato spindle tuber viroid (PSTVd). One of these mutants (PSTVd-P) contains three nucleotide substitutions in the left terminal loop, and mechanical inoculation of tomato seedlings with RNA transcripts at levels equivalent to 10(3)-10(5) times the ID50 for PSTVd-Intermediate failed to result in systemic infection. Viable progeny containing a spontaneous C-->G change at position 4 could, however, be recovered from transgenic Nicotiana benthamiana plants that constitutively expressed PSTVd-P RNA. The initial mutations in PSTVd-P led to an overall weakening of its native structure in vitro, and the precisely-full-length molecule released by ribozyme cleavage in vivo was also unstable. Even RT-PCR analysis failed to reveal detectable amounts of circularized PSTVd-P among the RNAs isolated from uninfected plants. Predicted stabilizing effects of a spontaneous mutation at position 4 suggest that the appearance of viable progeny was dependent on a combination of events: errors by host RNA polymerase II during transcription of the mutant transgene coupled with a strong selective pressure against alterations in the native structure of PSTVd.

Mutation↗
PubMed1997

Treatment of ocular bacterial infections: an update.

BACKGROUND: Because of increased bacterial resistance and the addition of new antimicrobial medications, the current and appropriate treatment of ocular bacterial infections is an important issue for eye care practitioners. METHODS: The literature on the antimicrobial treatment of ocular bacterial infections is reviewed to provide the practicing optometrist with an overview of the issues and medications involved in therapy. RESULTS: New topical, oral, and parenteral antibiotic medications continuously become available to eye care practitioners. Clinicians must routinely reassess the conventional antimicrobial therapy in light of the drugs available for the treatment of bacterial eye infections. The clinician must be familiar with distinct protocols and medications for the management of different ocular bacterial infections. CONCLUSIONS: Knowledge of the results of controlled antimicrobial studies and a review of standard practices in managing bacterial eye disease can provide the necessary background to help the eye care clinician make appropriate antimicrobial therapeutic decisions in patient care.

Anti-Bacterial Agents↗
PubMed1997

Occurrence of citrus viroids in Costa Rica.

A survey for citrus viroids was conducted in the major citrus commercial growing areas in Costa Rica. Screening of 36 sweet orange and 12 lemon trees resulted in the detection of members of four of the five citrus viroid groups as determined by nucleic acid hybridization using specific RNA probes and polymerase chain reaction (PCR) using specific oligonucleotide primers. CEVd, CVd-IIa, CVD-IIb and CVd-III viroids were found to be widespread in the three main regions of commercial citrus production. CVd-Ib was only found in lemon in Nicoya.

Citrus↗
PubMed1996

RNA structural features responsible for potato spindle tuber viroid pathogenicity.

The native structure of potato spindle tuber viroid (PSTVd) contains a series of short double helices and small internal loops that are organized into five structural domains. Nucleotides within the pathogenicity domain are known to play a critical role in modulating PSTVd symptom expression, and it has been suggested that disruption of a comparatively unstable "premelting region" within the pathogenicity domain may be required for disease induction. We have used a combination of quantitative bioassays, temperature gradient gel electrophoresis of circularized RNA transcripts, and thermodynamic calculations to compare the biological and structural properties of 12 representative PSTVd sequence variants. Certain mutations appeared to act indirectly, downregulating pathogenicity by suppressing the rate of PSTVd replication/accumulation. The effects of other mutations appeared to be more direct, but there was no consistent correlation between symptom severity and melting temperature. Taking into account the three-dimensional shape of RNA helices, comparison of the optimal secondary structures for these variants point to major differences in the geometry of their pathogenicity domains; i.e., variants producing intermediate symptoms possess a linear arrangement of three consecutive helices, whereas for variants producing mild or severe symptoms this domain is bent in opposing directions. Such alterations in RNA structure together with concomitant alterations in RNA-protein interaction(s) may be the primary cause of viroid pathogenicity.

Base Sequence↗
PubMed1996

Fluorescence resonance energy transfer visualization of DNA aggregates formed during electrophoretic separations in ultradilute hydroxyethylcellulose.

Fluorescence resonance energy transfer (FRET) microscopy is used to observe structures of DNA aggregates formed during electrophoresis in ultradilute hydroxyethylcellulose (HEC). FRET gives evidence of aggregates with a tightly packed core and random entanglement of DNA in the outer portions. HEC concentrations also appear to play a role in aggregate formation. DNA aggregates take longer to assemble in higher HEC concentration solutions and assume a less compact form than those formed at lower HEC concentrations.

Cellulose↗
PubMed1996

Extemporaneous preparation of antibiotic ophthalmic solutions.

Until the introduction of ocular ciprofloxacin, the standard of practice in treating bacterial corneal ulcers required topical antibiotic ophthalmic solutions that were either not commercially available or not available in the higher concentrations needed. A survey was mailed to 125 hospital pharmacies and 125 community pharmacies in Oklahoma to determine the availability of extemporaneously prepared antibiotic ophthalmic solutions. Of 72 hospital pharmacies and 60 community pharmacies that responded, 17 hospital and 2 community pharmacies reported that they do compound these solutions. The main reasons given by the other pharmacies for not offering this service were the lack of a laminar flow hood or other equipment and lack of an aseptic environment. If extemporaneously prepared antibiotic ophthalmic solutions are needed to treat corneal ulcers, then pharmacists have a responsibility to prepare them. The recent publication of a handbook providing formulations for those products and the "ASHP Technical Assistance Bulletin on Pharmacy-Prepared Ophthalmic Products" may encourage more pharmacies to provide this needed service.

Administration, Topical↗
PubMed1995

Dynamics of DNA during pulsed field electrophoresis in entangled and dilute polymer solutions.

Using fluorescence video microscopy, DNA electrophoretic behavior under field inversion conditions has been investigated in hydroxyethyl cellulose (HEC) solutions both above and below its entanglement limit. DNA conformational fluctuation periods are found to be strongly influenced by the frequency of the applied electric field. DNA maximum extension is found to be dependent on both the frequency and the strength of the applied field. It is proposed that both above and below the HEC entanglement limit, field inversion serves to keep the average DNA conformation in a size-dependent regime intermediate between full extension and random coil. In this time-averaged geometry, efficient long-chain DNA electrophoretic separation is enabled.

DNA, Fungal↗