PubMed Health⌕ Search

Biomedical subjects

David R Nelson

Publications and source records attributed to David R Nelson.

At least 19 recordsLinked to original sources
PubMed2003

Cytochrome p450 complement (CYPome) of the avermectin-producer Streptomyces avermitilis and comparison to that of Streptomyces coelicolor A3(2).

The genus Streptomyces produces about two-thirds of naturally occurring antibiotics and a wide array of other secondary metabolites, including antihelminthic agents, antitumor agents, antifungal agents, and herbicides. The newly completed genome sequence of the avermectin-producing bacterium Streptomyces avermitilis contains 33 cytochromes p450 (CYPs), many more than the 18 observed in Streptomyces coelicolor A3(2). Some of the likely metabolic functions are reported together with their genomic location and bioinformatic analysis. Seven entirely new CYP families were found together with close homologues of some forms observed in S. coelicolor A3(2). The presence of unusual CYP forms associated with conservons is revealed and of these, CYP157 forms in both S. avermitilis and S. coelicolor A3(2) deviate from the previously accepted rule for an EXXR motif within the K-helix of CYPs. Amongst this range of CYPs are forms associated with avermectin, filipin, geosmin, and pentalenolactone biosynthesis as well as unknown pathways of secondary metabolism.

Chromosomes, Fungal↗
PubMed2003

Systemic host responses in severe sepsis analyzed by causative microorganism and treatment effects of drotrecogin alfa (activated).

Clinical trials with novel therapeutic agents for severe sepsis have suggested that patients might respond differently depending on causative microorganism. Data from a large, placebo-controlled trial of recombinant human drotrecogin alfa (activated) (DrotAA) were analyzed by type of causative microorganism for treatment-associated differences in mortality, coagulopathy, and inflammatory response. Compared with placebo, mortality rates associated with DrotAA were consistently reduced for each microorganism group (gram-positive bacteria, gram-negative bacteria, mixed bacteria, fungi, other, and unknown microbial etiology), with a stratified relative risk (RR) of 0.80 (95% confidence interval [CI], 0.69-0.94). The greatest reduction in the mortality rate was for Streptococcus pneumoniae infection (RR, 0.56; 95% CI, 0.35-0.88). Levels of coagulation and inflammation biomarkers varied with different pathogens at study entry. Results demonstrate that DrotAA, administered as an adjunct to standard anti-infective therapy, can improve the rate of survival for patients who develop severe sepsis regardless of causative microorganism.

Anti-Bacterial Agents↗
PubMed2003

Hexatic undulations in curved geometries.

We discuss the influence of two-dimensional hexatic order on capillary waves and undulation modes in spherical and cylindrical geometries. In planar geometries, extended bond-orientational order has only a minor effect on the fluctuations of liquid surfaces or lipid bilayers. However, in curved geometries, the long-wavelength spectrum of these ripples is altered. We calculate this frequency shift and discuss applications to spherical vesicles, liquid metal droplets, bubbles and cylindrical jets coated with surface-active molecules, and to multielectron bubbles in liquid helium at low temperatures. Hexatic order also leads to a shift in the threshold for the fission instability of charged droplets and bubbles, and for the Plateau-Rayleigh instability of liquid jets.

Journal Article↗
PubMed2003

DNA unzipped under a constant force exhibits multiple metastable intermediates.

Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the unzipped length as a function of time is characterized by jumps during which the strands separate rapidly, followed by long pauses where the number of separated base pairs remains constant. Here, we report previously uncharacterized observations of this striking behavior carried out on a number of identical single molecules simultaneously. When several single lambda phage molecules are subject to the same applied force, the pause positions are reproducible in each. This reproducibility shows that the positions and durations of the pauses in unzipping provide a sequence-dependent molecular fingerprint. For small forces, the DNA remains in a partially unzipped state for at least several hours. For larger forces, the separation is still characterized by jumps and pauses, but the double-stranded DNA will completely unzip in less than 30 min.

Adsorption↗
PubMed2003

Comparison of P450s from human and fugu: 420 million years of vertebrate P450 evolution.

The fugu (pufferfish) genome has been sequenced, and a second genome assembly was released 17 May 2002. Exhaustive searches were made to identify all P450 genes and pseudogenes from the earlier release of 26 October 2001. P450 genes assembled as completely as possible from these data were used to do additional searches of the newer assembly and all P450 genes and pseudogenes in the available fugu sequence data have been identified, compared to human P450s, and assigned names. There are 54 P450 genes in fugu and 1 nearly intact pseudogene (CYP3A50P). CYP1A is missing much of its N-terminal half; however, 45 P450 genes are completely assembled. Eight others are lacking only one or two exons or less. CYP2X4 is known only from an EST. This may be a 55th P450 gene if it represents an accurate sequence. In addition to 2X4, there are 16 other pseudogene fragments or small pieces of P450 genes. At the P450 family level, 17 of 18 mammalian families are found in fugu. CYP39 is the only CYP family missing and it is not seen in any other fish sequence data either. The CYP2 family shows the largest degree of divergence. In the CYP2 family, only CYP2R1 and CYP2U1 are conserved as recognizable subfamilies across species. Intron-exon boundaries are largely preserved across 420 million years of evolution.

Algorithms↗
PubMed2003

Sexual dysfunction in men undergoing infertility evaluation: a cohort observational study.

OBJECTIVE: To study psychosexual problems in men undergoing infertility evaluation. DESIGN: A cohort observational study. SETTING: Male infertility diagnostic center. PATIENT(S): Four hundred twelve men undergoing infertility evaluation between 1999 and 2001. INTERVENTION(S): Baseline and follow-up data on sexual functions. Semen analysis for samples collected by masturbation. A second analysis was requested in 2 weeks upon finding an abnormality of semen parameters. Penile vibratory stimulation to help men who failed to collect semen on their second or subsequent appointments. MAIN OUTCOME MEASURE(S): Sexual functions (erection and orgasm) during the time of infertility evaluation. RESULT(S): Seven of 412 men were excluded from the analysis due to a past history of sexual dysfunction. Of the remaining 405 men, 46 (11%) failed to collect semen by masturbation for a second semen analysis after repeated (2-4 times) attempts at 2- to 3-day intervals. Nine of these men (20%) were able to collect semen using vibratory stimulation. All 46 men experienced problems with erection or orgasm and had severe anxiety during attempts to masturbate and during sexual contact with their partners. CONCLUSION(S): Our study indicates that some men may experience sexual dysfunction of a psychogenic nature in response to the diagnosis of infertility.

Adult↗
PubMed2003

Negative effects of increased sperm DNA damage in relation to seminal oxidative stress in men with idiopathic and male factor infertility.

OBJECTIVE: To examine the effects of increased sperm DNA damage in relation to seminal oxidative stress in men with idiopathic and male factor infertility. Prospective study. SETTINGS: Infertility clinic at a tertiary care academic institution. PATIENT(S): Ninety-two infertile men with normal female partners. Sixteen fertile donors served as the control group. INTERVENTION(S): Standard semen analysis and assessment of levels of seminal oxidative stress. Assisted reproductive techniques in 33 of the 92 patients (IUI [n = 19], IVF [n = 10], and intracytoplasmic sperm injection [n = 4]). MAIN OUTCOME MEASURE(S): Sperm DNA damage by sperm chromatin structure assay. Results were expressed as DNA fragmentation index. RESULT(S): Patients were classified as having either idiopathic (n = 23) or male factor infertility (n = 69). Patients with idiopathic and male factor infertility had significantly higher DNA fragmentation index and oxidative stress compared with the case of fertile donors. A clinical pregnancy was achieved in 9 (27%) of 33 patients with assisted reproductive techniques. Significantly higher DNA fragmentation index and oxidative stress were found in men who failed to initiate a pregnancy after assisted reproductive techniques (n = 24), compared with the cases of those who succeeded and of the fertile donors. DNA fragmentation index was correlated positively with oxidative stress (r = 0.27), and negatively with fertilization (r = -0.70) and embryo quality (r = -0.70). CONCLUSION(S): Sperm DNA damage is significantly increased in men with idiopathic and male factor infertility and in men who failed to initiate a pregnancy after assisted reproductive techniques. Such an increase may be related to high levels of seminal oxidative stress.

Adult↗
PubMed2003

Gene expression associated with interferon alfa antiviral activity in an HCV replicon cell line.

Interferon alfa (IFN-alpha)-based treatment is the only therapeutic option for chronic hepatitis C viral infection. However, the molecular mechanisms of IFN-alpha antiviral activity are not completely understood. The recent development of an HCV replicon cell culture system provides a feasible experimental model to investigate the molecular details of IFN-induced direct antiviral activity in hepatocytes. In this report, we show that IFN-alpha can effectively inhibit HCV subgenomic RNA replication and suppress viral nonstructural protein synthesis. Using cDNA microarray analysis, we also show that the replicon cells have different gene expression profile compared with the parental hepatoma cells (Huh7). IFN-alpha can induce a number of responsive genes in the replicon cells. One of the genes, 6-16 (G1P3), can enhance IFN-alpha antiviral efficacy. In addition, we demonstrate that IFN-alpha can significantly activate STAT3 in hepatoma cells, suggesting that this pathway plays a role in IFN-alpha signaling. In conclusion, our results indicate that IFN-alpha antiviral activity is associated with activation of STAT3-signaling pathway and intracellular gene activation. Our results also suggest that IFN-alpha-induced target genes may play an important role in IFN-alpha anti-HCV activity.

Antiviral Agents↗
PubMed2003

CD8+ T-cell interaction with HCV replicon cells: evidence for both cytokine- and cell-mediated antiviral activity.

The interaction between the host immune response and infected hepatocytes plays a central role in the pathogenesis of hepatitis C virus (HCV). The lack of a suitable animal or in vitro model has hindered our understanding of the host T-cell/HCV interaction. Our aim was to develop an in vitro model to study the mechanisms of HCV-specific T-cell-mediated antiviral and cytolytic function. The HCV replicon was HLA typed and lymphocytes were obtained from an HLA class I-matched subject. CD8(+) T cells were expanded with 2 HCV-specific/HLA-restricted peptides for NS3. Lymphocyte preparations were cocultured with HCV replicon (FCA1) and control (Huh7) cells labeled with (51)Cr. After a 48-hour incubation, the cells were harvested for RNA extraction. Standard blocking assays were performed in the presence of anti-interferon gamma (IFN-gamma), anti-tumor necrosis factor alpha (TNF-alpha), and anti-FasL. Cytolytic activity was measured by (51)Cr release. HCV replicon cells express homozygous HLA-A11 alleles and present HCV nonstructural proteins. HCV-specific expansion of CD8(+) cells led to a 10-fold decrease in HCV replication by Northern blot analysis and 21% specific lysis of FCA1 cells (compared with 2% of control Huh7 cells). Twenty percent of this antiviral activity was independent of T-cell binding, suggesting cytokine-mediated antiviral activity. The CD8(+) antiviral effect was markedly reduced by blocking either IFN-gamma or FasL but was unaffected by blocking TNF-alpha. In conclusion, HCV-specific CD8(+) cells inhibit viral RNA replication by cytokine-mediated and direct cytolytic effects. This T-cell/HCV subgenomic replicon system represents a model for the investigation of CD8 cell interaction with HCV-infected hepatocytes.

Antibodies↗
PubMed2003

Lack of antiviral effect of a short course of mycophenolate mofetil in patients with chronic hepatitis C virus infection.

Mycophenolate mofetil (MMF) is an immunosuppressive agent that is widely used in the management of liver transplant recipients. MMF inhibits the inosine monophosphate dehydrogenase that has been shown to have in vitro antiviral properties against flaviviruses, suggesting the possibility that it might also inhibit the hepatitis C virus (HCV). The goal of this short-term dose escalation study was to assess the antiviral effects of MMF on HCV replication. Patients with chronic hepatitis C who had not undergone liver transplantation were randomized to 8 weeks of treatment with one of four mycophenolate dose regimens (1000 mg orally twice daily, 500 mg orally twice daily, 250 mg orally twice daily, or a matched oral placebo twice daily). All groups were double-blinded. Quantitative HCV RNA levels and serum alanine aminotransferase were assessed at baseline, at weeks 2, 4, and 8 of dosing, and at weeks 4 and 8 of follow-up. Thirty patients met inclusion criteria, enrolled, and were randomized. HCV RNA levels did not change significantly during treatment. Specifically, no subject became virus negative or had a one-log decrease in virus level. Serum aminotransferase level did not normalize in any subject. The most common side effects were headache, nausea, and diarrhea. Mycophenolate alone does not appear to have a significant antiviral or biochemical effect in patients with chronic hepatitis C.

Adult↗
PubMed2003

Expression of spoT in Borrelia burgdorferi during serum starvation.

Borrelia burgdorferi, the causative agent of Lyme disease, is transmitted by the tick Ixodes scapularis. A 2.9-kb fragment containing a putative spoT gene was isolated from B. burgdorferi genomic DNA by PCR amplification and cloned into a pBAD24 vector. The cloned gene complemented Escherichia coli mutant strain CF1693, which contains deletions of both the relA and spoT genes. The spoT gene in E. coli encodes a bifunctional enzyme capable of synthesizing and degrading (p)ppGpp, which mediates the stringent response during carbon source starvation. B. burgdorferi has been reported to have a stress response to serum starvation. Thin-layer chromatography was used to detect (p)ppGpp extracted from H(3)(32)PO(4)-labeled B. burgdorferi cells starved for serum in RPMI. B. burgdorferi spoT gene expression was characterized during fatty acid starvation. Northern analysis of spoT revealed detectable message at 2.5 min of starvation in RPMI. Expression of spoT during serum starvation increased approximately 6-fold during the 30 min that starvation conditions were maintained. Further, expression of spoT decreased when serum was added to serum-starved cells. Reverse transcriptase PCR (RT-PCR) was used to detect spoT mRNA from approximately 10(6) cells starved for serum in RPMI for 2.5 to 30 min or incubated in tick saliva for 15 min. Northern blot analysis suggests that spoT transcript was approximately 900 nucleotides in length. RT-PCR amplification of the transcript using several sets of primers confirmed this finding. Additionally, a truncated clone containing only the first 950 bp of the 2,001-bp spoT open reading frame was able to complement E. coli CF1693. The data suggest that B. burgdorferi exhibits a stringent response to serum starvation and during incubation in tick saliva.

Animals↗
PubMed2002

C-reactive protein, arterial endothelial activation, and development of transplant coronary artery disease: a prospective study.

BACKGROUND: Arterial endothelial expression and raised serum concentrations of the soluble form of intercellular adhesion molecule-1 (ICAM-1) are implicated in development of transplant coronary artery disease. We investigated whether C-reactive protein, known to stimulate ICAM-1, was associated with increased ICAM-1 concentration and subsequent development of coronary artery disease. METHODS: With sandwich ELISAs, we measured C-reactive protein and soluble ICAM-1 in serial serum samples obtained during the first 3 months after transplantation in 109 heart-transplant patients. Matching endomyocardial biopsy samples were screened immunohistochemically for arterial endothelial ICAM-1. Serial coronary angiograms were assessed for development, severity, and progression of coronary artery disease. FINDINGS: We showed a significant correlation (p=0.001) between raised concentrations of C-reactive protein and arterial endothelial ICAM-1 expression in endomyocardial biopsy samples. We also noted a significant relation between C-reactive protein and soluble ICAM-1 concentrations soon after transplantation (p=0.003). Early raised C-reactive protein concentrations were associated with development (p=0.004), increased severity (p=0.02), and enhanced rate of progression (p=0.01) of coronary artery disease, and with heightened frequency of ischaemic events (p=0.049) and graft failure (p=0.04). INTERPRETATION: C-reactive protein concentration can be used to identify heart-transplant patients at increased risk of coronary artery disease and graft failure. Treatments directed at reduction of C-reactive protein concentration could improve patients' outcome.

Biopsy↗
PubMed2002

Single molecule statistics and the polynucleotide unzipping transition.

We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force value of order 10 pN, with different critical behavior for homopolymers and for random heteropolymers. We extend results on the disorder-averaged behavior of DNA's with random sequences [D. K. Lubensky and D. R. Nelson, Phys. Rev. Lett. 85, 1572 (2000)] to the more experimentally accessible problem of unzipping a single DNA molecule. As the applied force approaches the critical value, the double-stranded DNA unravels in a series of discrete, sequence-dependent steps that allow it to reach successively deeper energy minima. Plots of extension versus force thus take the striking form of a series of plateaus separated by sharp jumps. Similar qualitative features should reappear in micromanipulation experiments on proteins and on folded RNA molecules. Despite their unusual form, the extension versus force curves for single molecules still reveal remnants of the disorder-averaged critical behavior. Above the transition, the dynamics of the unzipping fork is related to that of a particle diffusing in a random force field; anomalous, disorder-dominated behavior is expected until the applied force exceeds the critical value for unzipping by roughly 5 pN.

Base Pairing↗
PubMed2002

Interleukin-10 inhibition of nitric oxide biosynthesis involves suppression of CAT-2 transcription.

Interleukin-10 (IL-10) has been shown to attenuate lipopolysaccharide (LPS) stimulation of inducible nitric oxide synthase (iNOS) in various cell types. Guanosine triphosphate cyclohydrolase I (GTPCH) and type-2 cationic amino acid transporter (CAT-2) are enzymes that regulate iNOS activity. We therefore sought to assess the effects of IL-10 on the expression of these regulatory enzymes in LPS-stimulated macrophages that are known to express iNOS. Five minutes after adding LPS to these macrophage cultures, various doses of recombinant human IL-10 were also added. The samples were harvested for analysis 18 h after exposure to both LPS and IL-10. In LPS-stimulated macrophages, IL-10 attenuated the upregulation of nitric oxide and iNOS protein but not iNOS mRNA. IL-10 also attenuated the LPS-induced upregulation of CAT-2 mRNA. However, IL-10 and LPS had no effect on GTPCH mRNA expression. We therefore conclude that IL-10 inhibits nitric oxide formation in LPS-stimulated macrophages partly by decreasing iNOS protein expression. Moreover, our data suggests that transcriptional control of CAT-2 plays a role in IL-10 mediated influences upon nitric oxide biosynthesis.

Animals↗
PubMed2002

Increased sperm nuclear DNA damage in normozoospermic infertile men: a prospective study.

OBJECTIVE: To evaluate levels of sperm nuclear DNA damage in infertile men with normal and abnormal standard semen parameters. DESIGN: Prospective study. SETTING: Male infertility clinic. PATIENT(S): Ninety-two men seeking infertility treatment and 16 fertile volunteers. INTERVENTION(S): Standard semen analysis was performed according to the World Health Organization guidelines. MAIN OUTCOME MEASURE(S): Sperm DNA damage was assessed by sperm chromatin structure assay and the results expressed as %DFI. RESULT(S): Of the 92 patients, 21 (23%) had normal standard sperm parameters (concentration, motility, and normal sperm forms), while 71 (77%) had an abnormality in one or more of these parameters. The %DFI [median (25th and 75th percentiles)] in infertile men with normal sperm parameters [23 (15, 32)] was significantly higher than fertile donors [15 (11, 20)] (P=.02), but not significantly different from infertile men with abnormal sperm parameters [28 (18, 41)] (P=.27). CONCLUSION(S): The results of this study indicate that a significant increase in SCSA-defined DNA damage can be found in sperm from infertile men with normal standard sperm parameters. Therefore, sperm DNA damage analysis may reveal a hidden abnormality of sperm DNA in infertile men classified as idiopathic based on apparently normal standard sperm parameters.

Cell Nucleus↗
PubMed2002

Effect of cigarette smoking on levels of seminal oxidative stress in infertile men: a prospective study.

OBJECTIVE: To investigate levels of seminal oxidative stress (OS) and sperm quality in a group of infertile men with a history of cigarette smoking. DESIGN: A prospective clinical study. SETTING: Male infertility clinic, Urological Institute, the Cleveland Clinic Foundation, Cleveland, Ohio. PATIENT(S): Infertile men who smoked cigarettes (n = 20), infertile men who were nonsmokers (n = 32), and healthy nonsmoking donors (n = 13). INTERVENTION(S): Genital examination, standard semen analysis, sperm DNA damage. MAIN OUTCOME MEASURE(S): Levels of seminal reactive oxygen species (ROS) and total antioxidant capacity (TAC) measured by a chemiluminescence assay and seminal OS assessed by calculating a ROS-TAC score. Sperm DNA damage was measured by sperm chromatin structure assay. RESULT(S): Smoking was associated with a 48% increase in seminal leukocyte concentrations (P<.0001), a 107% increase in ROS levels (P=.001), and a 10-point decrease in ROS-TAC scores (P=.003). Differences in standard sperm variables and DNA damage indices between the infertile smokers and infertile nonsmokers were not statistically significant. CONCLUSION(S): Infertile men who smoke cigarettes have higher levels of seminal OS than infertile nonsmokers. Given the potential adverse effects of seminal OS on fertility, physicians should advise infertile men who smoke cigarettes to quit.

Analysis of Variance↗