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Biomedical subjects

J M Kelley

Publications and source records attributed to J M Kelley.

At least 19 recordsLinked to original sources
PubMed2001

The restricted expression of granzyme M in human lymphocytes.

We have analyzed the expression of human granzyme M (Gzm M) in various human leukocyte subsets using the specific mAb 4H10. Using FACS and Western blotting analysis we compared the expression of Gzm M with that of other granzymes (Gzm A and Gzm B) and the lytic protein perforin. Human Gzm M was constitutively highly expressed in NK cells as was perforin and Gzm A. Surprisingly, freshly isolated NK cells had very low (sometimes undetectable) levels of Gzm B. In contrast to Gzm B and perforin, Gzm M was not detected in highly purified CD4(+) and CD8(+) T cells either constitutively or after short term activation in vitro. However, low levels of Gzm M were observed in some T cell clones on prolonged passage in vitro. Gzm M was not detected in highly purified neutrophils, monocytes, or tumor cells of the myelomonocytic lineage. Examination of minor T cell subsets from human peripheral blood showed detectable Gzm M in CD3(+), CD56(+) T cells and gammadelta T cells. A histological staining procedure was developed that demonstrated a granular staining pattern for Gzm M and a cellular distribution similar to that observed by Western blotting. These data indicate that the expression of Gzm M does not always correlate with the lytic activity of cytotoxic cells. However, expression of Gzm M in NK cells, CD3(+), CD56(+) T cells, and gammadelta T cells suggests that this enzyme may play some role in innate immune responses.

Blotting, Western↗
PubMed2001

Size-fractionated plutonium isotopes in a coastal environment.

We have examined the distribution of individual Pu isotopes (239Pu, 240Pu, and 241Pu) in seawater from the Gulf of Maine (GOM). Samples were size-fractionated with a 1 kD cross-flow ultrafiltration (CFF) membrane. Subfractioned samples were radiochemically purified and Pu isotopes were analyzed using a three-stage thermal ionization mass spectrometer (TIMS). To our knowledge, this is the first time that both size class and Pu isotopic data have been obtained for seawater samples. Within measurement uncertainties a single 240Pu/239Pu atom ratio of 0.18 was found for all sample collection depths and sample size fractions. This signifies a current, single Pu source in GOM waters, namely global fallout, and suggests that no measurable isotopic fractionation occurred during CFF processing. The majority of Pu was found in the low molecular weight fraction (< 1 kD). Colloidal Pu varied from 8% of the total in surface waters to < 1% in the deepest (250 m) seawater sample. Evidence suggests that the vertical distribution of Pu in GOM is primarily controlled by conservative mixing processes. The high Pu fraction found in the low molecular size fraction implies that most of the Pu is in the non-particle-reactive oxidized fraction, and is consistent with the conservative Pu behavior. The activity levels are in agreement with other studies which show a slow decrease in Pu with time due to continued mixing and relatively slow particle removal.

Atlantic Ocean↗
PubMed2000

Assessing the risks of exposures to multiple chemicals with a common mechanism of toxicity: how to cumulate?

The Food Quality Protection Act (FQPA) of 1996 requires the U.S. EPA to consider the "cumulative effects" of pesticides and other substances that have a "common mechanism of toxicity." Several different methods for combining the exposures to estimate the risk of groups of common mechanism chemicals with different potencies and exposure characteristics are critically evaluated. These are the hazard index (HI), toxicity equivalence factor (TEF), and combined margin of exposure (MOE(T)) procedures as well as the point of departure index (PODI) and cumulative risk index (CRI) methods that are the reciprocals of the HI and MOE(T) approaches, respectively. Each of these methods ideally requires, at a minimum, the availability of in vivo toxicology data for the same toxicological endpoint in the same animal species. Furthermore, all assume that the effects of the individual components in the mixture are independent in nature (i.e., are additive rather than synergistic or antagonistic) and that the dose-response functions for all compounds have a similar slope. The point of departure (POD), preferably the dose corresponding to a given effect level (e.g., the ED(10)), can be used as a measure of the relative potency of the different chemicals in the group. If appropriate exposure and toxicology data are available, and the chemicals in the group have a common uncertainty factor (UF), all the procedures yield a numerically identical result. The fact that different chemicals in the group often have different UFs raises issues for all summation procedures and, in the case of the TEF approach, the UF of the index chemical selected dictates the final result of the assessment. A major distinction between the different methods for addition is the point in the process at which uncertainty is considered. The HI and CRI approaches are problematic because they require application of policy-driven UFs (in the form of RfDs) at that stage of the process where exposure should be expressed in terms of potency. In contrast, the PODI and MOE(T) approaches require application of a single group UF(G) at the end of the risk assessment process although they will also accommodate the application of data-based adjustments earlier in the analysis. Importantly, both the PODI and the MOE(T) approaches allow policy- and data-driven UFs to be separated and thus make the process more transparent; these should be considered the methods of choice for cumulative risk assessment. Assignment of a single group UF is somewhat different from developing an UF for a single chemical and the total weight of evidence available in the group database can be used to advantage to reduce the UFs that need to be applied to the group. This larger database can also be used to refine the PODs for individual members of the group. It is important to emphasize that there remains a great deal of scientific uncertainty about how to proceed with cumulative risk assessment as described in the FQPA. The serious difficulties associated with defining "common mechanism of toxicity" and "concurrent exposure" combined with the current paucity of data and methodology required to conduct cumulative risk assessment suggest that the procedure is not yet ready for use in pesticide regulation.

Algorithms↗
PubMed2000

Possible relationship between degenerative cardiac valvular pathology and lyme disease.

We report an unusual clinical presentation of Lyme carditis in a previously healthy 20-year-old black woman without any epidemiologic history of Lyme disease, fulminant in nature, involving a heart valve necessitating emergent mitral valve replacement, and requiring further surgical intervention because of the development of pericardial effusion and tamponade. A dilated right ventricle with normal contractility and severe tricuspid regurgitation with increase in the right atrial size diagnosed later remains under close surveillance.

Adult↗
PubMed1999

Global distribution of Pu isotopes and 237Np.

Inventories and compositions of Pu isotopes and 237Np in archived soil samples collected in the 1970s from 54 locations around the world were determined to provide regional baselines for recognizing possible future environmental inputs of non-fallout Pu and Np. As sample sizes used in this work were small (typically 1 g), inhomogeneities in Pu and Np concentrations were easily recognizable and, as a result, we were able to determine that atypical debris in South America, from French testing in the South Pacific, is more widely and uniformly distributed than previously supposed. From our results we conclude that fallout 237Np/239Pu atom ratios are generally lower in the Southern Hemisphere (approximately 0.35) than in the Northern Hemisphere (approximately 0.47.) Moreover, 237Np/239Pu atom ratios are more device-dependent, hence more variable, than counterpart 240Pu/239Pu atom ratios. Given predictable trends caused by sample inhomogeneities, with only two exceptions, the Pu results of this work are entirely consistent with (and in several instances improve on) results previously reported for these same samples. However, unlike earlier interpretations used to explain these results, we recommend that fallout isotopic signatures be represented by mixing lines, rather than averages, to better reflect regional variations of stratospheric fallout inventories relative to tropospheric fallout inventories, and provide the theoretical basis for doing so. Finally, the Np results of this work constitute one of the largest single compilations of such data reported to date.

Geography↗
PubMed1999

High throughput direct end sequencing of BAC clones.

Libraries constructed in bacterial artificial chromosome (BAC) vectors have become the choice for clone sets in high throughput genomic sequencing projects primarily because of their high stability. BAC libraries have been proposed as a source for minimally over-lapping clones for sequencing large genomic regions, and the use of BAC end sequences (i.e. sequences adjoining the insert sites) has been proposed as a primary means for selecting minimally overlapping clones for sequencing large genomic regions. For this strategy to be effective, high throughput methods for BAC end sequencing of all the clones in deep coverage BAC libraries needed to be developed. Here we describe a low cost, efficient, 96 well procedure for BAC end sequencing. These methods allow us to generate BAC end sequences from human and Arabidoposis libraries with an average read length of >450 bases and with a single pass sequencing average accuracy of >98%. Application of BAC end sequences in genomic sequen-cing is discussed.

Arabidopsis↗
PubMed1997

The complete genome sequence of the gastric pathogen Helicobacter pylori.

Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host-pathogen interaction. Based on the large number of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric tracts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal pathogens, probably uses recombination and slipped-strand mispairing within repeats as mechanisms for antigenic variation and adaptive evolution. Consistent with its restricted niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH.

Antigenic Variation↗
PubMed1995

The minimal gene complement of Mycoplasma genitalium.

The complete nucleotide sequence (580,070 base pairs) of the Mycoplasma genitalium genome, the smallest known genome of any free-living organism, has been determined by whole-genome random sequencing and assembly. A total of only 470 predicted coding regions were identified that include genes required for DNA replication, transcription and translation, DNA repair, cellular transport, and energy metabolism. Comparison of this genome to that of Haemophilus influenzae suggests that differences in genome content are reflected as profound differences in physiology and metabolic capacity between these two organisms.

Antigenic Variation↗
PubMed1995

Optimization of Applied Biosystems 373 sequencer stretch modification.

We have optimized the conditions for using the Stretch modification for the Applied Biosystems 373 Automated DNA Sequencers for sequencing double-stranded DNA using 34-cm well-to-read and 48-cm well-to-read configurations. With the manufacturer's recommended settings, uneven spacing within the first 100 bases was observed, which led to miscalls, insertions and deletions in the analyzed data. A significant decrease in accuracy for reads greater than 400 bases was also observed. Various gel concentrations were tested to improve the base spacing for the first 100 bases while maintaining accuracy and usable length of data. A longer average usable length and better resolution of smaller fragments were achieved by increased acrylamide concentration coupled with increased wattage. Using the Applied Biosystems CATALYST 800 Molecular Biology LabStation, Taq dye primer cycle sequencing reactions were optimized for -21 M13 and M13RP1 primers to produce a more even distribution of dye-labeled fragments that increased the overall signal strengths and decreased background signal. These reaction products, run on the Stretch sequencers using the new gel conditions, provided longer reads with increased reliability and accuracy of the data.

Acrylamides↗
PubMed1992

Sequence identification of 2,375 human brain genes.

We recently described a new approach for the rapid characterization of expressed genes by partial DNA sequencing to generate 'expressed sequence tags'. From a set of 600 human brain complementary DNA clones, 348 were informative nuclear-encoded messenger RNAs. We have now partially sequenced 2,672 new, independent cDNA clones isolated from four human brain cDNA libraries to generate 2,375 expressed sequence tags to nuclear-encoded genes. These sequences, together with 348 brain expressed sequence tags from our previous study, comprise more than 2,500 new human genes and 870,769 base pairs of DNA sequence. These data represent an approximate doubling of the number of human genes identified by DNA sequencing and may represent as many as 5% of the genes in the human genome.

Brain Chemistry↗
PubMed1992

Automated DNA sequencing and analysis of 106 kilobases from human chromosome 19q13.3.

A total of 116,118 basepairs (bp) derived from three cosmids spanning the ERCC1 locus of human chromosome 19q13.3 have been sequenced with automated fluorescence-based sequencers and analysed by polymerase chain reaction amplification and computer methods. The assembled sequence forms two contigs totalling 105,831 bp, which contain a human fosB proto-oncogene, a gene encoding a protein phosphatase, two genes of unknown function and the previously-characterized ERCC1 DNA repair gene. This light band region has a high average density of 1.4 Alu repeats per kilobase. Human chromosome light bands could therefore contain up to 75,000 genes and 1.5 million Alu repeats.

Amino Acid Sequence↗
PubMed1992

Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues.

A database containing mapped partial cDNA sequences from Caenorhabditis elegans will provide a ready starting point for identifying nematode homologues of important human genes and determining their functions in C. elegans. A total of 720 expressed sequence tags (ESTs) have been generated from 585 clones randomly selected from a mixed-stage C. elegans cDNA library. Comparison of these ESTs with sequence databases identified 422 new C. elegans genes, of which 317 are not similar to any sequences in the database. Twenty-six new genes have been mapped by YAC clone hybridization. Members of several gene families, including cuticle collagens, GTP-binding proteins, and RNA helicases were discovered. Many of the new genes are similar to known or potential human disease genes, including CFTR and the LDL receptor.

Amino Acid Sequence↗
PubMed1992

Expressed genes, Alu repeats and polymorphisms in cosmids sequenced from chromosome 4p16.3.

The sequences of three cosmids (90 kilobases) from the Huntington's disease region in chromosome 4p16.3 have been determined. A 30,837 base overlap of DNA sequenced from two individuals was found to contain 72 DNA sequence polymorphisms, an average of 2.3 polymorphisms per kilobase (kb). The assembled 58 kb contig contains 62 Alu repeats, and eleven predicted exons representing at least three expressed genes that encode previously unidentified proteins. Each of these genes is associated with a CpG island. The structure of one of the new genes, hda1-1, has been determined by characterizing cDNAs from a placental library. This gene is expressed in a variety of tissues and may encode a novel housekeeping gene.

Amino Acid Sequence↗
PubMed1992

Rapid and reliable fluorescent cycle sequencing of double-stranded templates.

Automated DNA sequencing is an extremely valuable technique which requires very high quality DNA templates to be carried out successfully. While it has been possible to readily produce large numbers of such templates from M13 or other single-stranded vectors for several years, the sequencing of double-stranded DNA templates using the ABI 373 DNA Sequencer has had a considerably lower success rate. We describe how the combination of a new fluorescent, dideoxy sequencing method, called cycle-sequencing, coupled with modifications to template isolation procedures based on Qiagen columns, makes fluorescent sequencing of double-stranded templates a reliable procedure. From a single five milliliter culture enough DNA can be isolated (up to 20 micrograms) to do 4-8 sequencing reactions, each of which yields 400-500 bases of high quality sequence data. These procedures make the routine use of double-stranded DNA templates a viable strategy in automated DNA sequencing projects.

Base Sequence↗
PubMed1991

Complementary DNA sequencing: expressed sequence tags and human genome project.

Automated partial DNA sequencing was conducted on more than 600 randomly selected human brain complementary DNA (cDNA) clones to generate expressed sequence tags (ESTs). ESTs have applications in the discovery of new human genes, mapping of the human genome, and identification of coding regions in genomic sequences. Of the sequences generated, 337 represent new genes, including 48 with significant similarity to genes from other organisms, such as a yeast RNA polymerase II subunit; Drosophila kinesin, Notch, and Enhancer of split; and a murine tyrosine kinase receptor. Forty-six ESTs were mapped to chromosomes after amplification by the polymerase chain reaction. This fast approach to cDNA characterization will facilitate the tagging of most human genes in a few years at a fraction of the cost of complete genomic sequencing, provide new genetic markers, and serve as a resource in diverse biological research fields.

Amino Acid Sequence↗
PubMed1990

Extracorporeal shock wave lithotripsy of urinary calculi. Theory, efficacy, and adverse effects.

Extracorporeal shock wave lithotripsy (ESWL) for the treatment of upper urinary tract stone disease is held in high regard by the public and the profession. Although the efficacy is good (77.4% to 100%) for the treatment of 1- to 2-cm stones in select patients, ESWL may require the assistance of adjuvant procedures in as many as 26% of patients and may need repeating in as many as 32% of patients. These represent more difficult situations in which larger, more numerous, or harder stones may be present and in which ureteral stones are manipulated before treatment. The predominant adverse effect of ESWL treatment is the microvascular disruption of the tissues through which the shock waves pass. In addition, the procedure is painful, with many patients requiring narcotic analgesia. Long-term complications such as the new onset of hypertension have occurred in as many as 8% of treated patients, but much speculation about the long-term effects remains.

Humans↗
PubMed1989

Evaluating the effectiveness of a school drug and alcohol prevention curriculum: a new look at "Here's Looking at You, Two".

The article reports on the results of an evaluation of a school drug and alcohol prevention curriculum marketed under the title, "Here's Looking at You, Two." Previous evaluations, unreported in the literature and having unresolved methodological problems, have found that while the program appears effective at transmitting information regarding drug and alcohol abuse, it has not been effective at changing the underlying attitudes and behaviors that, in part, explain substance abuse. Employing a more rigorous methodology, our examination of a relatively large sample across five school districts provides support for previous findings. Over the short-term of one year, the program was particularly effective at transmitting substance information to primary and middle school students. The program, however, produced very little of the expected effect on the underlying attitudes that are critical to changing substance abuse behaviors.

Adaptation, Psychological↗