Search PubMed⌕ Search

Biomedical subjects

David R Nelson

Publications and source records attributed to David R Nelson.

At least 37 records · Page 2Linked to original sources
PubMed2005

Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel.

We characterize the voltage-driven motion and the free motion of single-stranded DNA (ssDNA) molecules captured inside the approximately 1.5-nm alpha-hemolysin pore, and show that the DNA-channel interactions depend strongly on the orientation of the ssDNA molecules with respect to the pore. Remarkably, the voltage-free diffusion of the 3'-threaded DNA (in the trans to cis direction) is two times slower than the corresponding 5'-threaded DNA having the same poly(dA) sequence. Moreover, the ion currents flowing through the blocked pore with either a 3'-threaded DNA or 5' DNA differ by approximately 30%. All-atom molecular dynamics simulations of our system reveal a microscopic mechanism for the asymmetric behavior. In a confining pore, the ssDNA straightens and its bases tilt toward the 5' end, assuming an asymmetric conformation. As a result, the bases of a 5'-threaded DNA experience larger effective friction and forced reorientation that favors co-passing of ions. Our results imply that the translocation process through a narrow pore is more complicated than previously believed and involves base tilting and stretching of ssDNA molecules inside the confining pore.

Bacterial Toxins↗
PubMed2005

Direct visualization of dislocation dynamics in grain-boundary scars.

Mesoscale objects with unusual structural features may serve as the analogues of atoms in the design of larger-scale materials with novel optical, electronic or mechanical behaviour. In this paper we investigate the structural features and the equilibrium dynamics of micrometre-scale spherical crystals formed by polystyrene particles adsorbed on the surface of a spherical water droplet. The ground state of sufficiently large crystals possesses finite-length grain boundaries (scars). We determine the elastic response of the crystal by measuring single-particle diffusion, and quantify the fluctuations of individual dislocations about their equilibrium positions within a scar by determining the dislocation spring constants. We observe rapid dislocation glide with fluctuations over the barriers separating one local Peierls minimum from the next and rather weak binding of dislocations to their associated scars. The long-distance (renormalized) dislocation diffusion glide constant is extracted directly from the experimental data and is found to be moderately faster than single-particle diffusion. We are also able to determine the parameters of the Peierls potential induced by the underlying crystalline lattice.

Journal Article↗
PubMed2005

Dynamics of molecular motors with finite processivity on heterogeneous tracks.

The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered. Motivated by recent single-molecule experiments, we study a simple model for a motor moving along a disordered track using chemical energy while an external force opposes its motion. The motors also have finite processivity, i.e., they can leave the track with a position-dependent rate. We show that the response of the system to disorder in the hopping-off rate depends on the value of the external force. For most values of the external force, strong disorder causes the motors which survive for long times on the track to be localized at preferred positions. However, near the stall force, localization occurs for any amount of disorder. To obtain these results, we study the complex eigenvalue spectrum of the time evolution operator. Existence of localized states near the top of the band implies a stretched exponential contribution to the decay of the survival probability. A similar spectral analysis also provides a very efficient method for studying the dynamics of motors with infinite processivity.

Algorithms↗
PubMed2005

Reconstitution of hepatitis C virus-specific T-cellmediated immunity after liver transplantation.

Hepatitis C virus (HCV)-related liver failure is the leading indication for liver transplantation worldwide. After transplantation, virological recurrence is the rule, but the spectrum of histological injury is wide, ranging from the development of allograft cirrhosis within a few years to minimal hepatitis despite long-term follow-up. The immunological correlates of this variable natural history are poorly understood. Here, we studied the kinetics of the cellular immune responses, viral replication, and allograft histology in 24 patients who had undergone liver transplantation for HCV-related liver failure. Using direct ex vivo methodologies (i.e., interferon-gamma ELISPOT and major histocompatibility complex class I-peptide tetrameric complexes), we found that patients who experienced viral eradication after antiviral therapy showed restoration of HCV-specific T-cell responses, whereas patients with progressive HCV recurrence that failed to respond to therapy showed declining frequencies of these viral-specific effector cells. The cytotoxic T lymphocytes that peripherally reconstituted after transplantation were clonotypically identical to those present within the recipient explant liver, defined at the level of the T-cell receptor beta chain (one epitope/one clone). Moreover, the subset of patients who spontaneously demonstrated minimal histologic recurrence had more vigorous CD4+ T-cell responses in the first 3 months, particularly targeting nonstructural proteins. We provide evidence that T-cell responses emerge after liver transplantation, and their presence correlates with improved histological and clinical outcomes. In conclusion, these results may help identify patients more likely to develop severe HCV recurrence and therefore benefit from current antiviral therapy, as well as provide a rationale for the future use of novel immunotherapeutic approaches. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience. wiley.com/jpages/0270-9139/suppmat/index.html).

Adult↗
PubMed2005

A randomized, open-label study to evaluate the safety and pharmacokinetics of human hepatitis C immune globulin (Civacir) in liver transplant recipients.

Chronic hepatitis C is the most common indication for liver transplantation, but viral recurrence is universal and progressive graft injury occurs in most recipients. Our aim was to assess the safety, pharmacokinetics (PK), and antiviral effects of high doses of a human hepatitis C antibody enriched immune globulin product (HCIG) in patients undergoing liver transplantation for chronic hepatitis C. This was a multicenter, randomized, open-label, controlled trial conducted at 4 transplant centers in the United States. A total of 18 patients with chronic hepatitis C, who underwent liver transplantation, were randomized to receive low-dose HCIG (75 mg/kg) or high-dose HCIG (200 mg/kg), or no treatment. A total of 17 infusions of HCIG were administered in each treated patient over 14 weeks using a time-dependent dosing strategy based on the PK of anti-hepatitis B immune globulin in liver transplant recipients. Hepatitis C virus levels, liver enzymes, and liver biopsies were obtained serially throughout the study period. PK profiles of HCV antibodies were determined on days 4, 10, and 98. HCIG infusions were safe and tolerated. The infusion rate could not be maximized because of symptoms for 18% to 30% of the doses. The half-life of HCIG was extremely short immediately after transplantation but was gradually prolonged. In the high-dose group, serum alanine aminotransferase (ALT) levels normalized in most subjects and no patient developed hepatic fibrosis. However, serum HCV RNA levels were not suppressed at either dose. In conclusion, HCIG, an anti-HCV enriched immune globulin product, appears to be safe in patients with chronic hepatitis C undergoing liver transplantation. Further studies are required to determine whether the drug has beneficial effects in this group of patients.

Adult↗
PubMed2005

Early hepatic stellate cell activation is associated with advanced fibrosis after liver transplantation in recipients with hepatitis C.

Recurrent hepatitis C after liver transplantation is a serious problem faced by liver transplant recipients. Activation of hepatic stellate cells is an early step in hepatic fibrogenesis. The aim of this study was to evaluate hepatic stellate cell activation, early after liver transplantation, as a predictor for the subsequent development of advanced fibrosis. Forty-six patients who underwent liver transplantation for hepatitis C and protocol liver biopsies were divided into rapid fibrosers (n = 21), defined as recipients who developed bridging fibrosis or cirrhosis within 2 years of liver transplantation, and slow fibrosers (n = 25). The protocol liver biopsy obtained 4 months after transplantation was stained and quantitated for hepatic stellate cell activation with antibody to alpha smooth muscle actin. Hepatic stellate cell activity was independently associated with rapid fibrosis (odds ratio: 1.6 [95% CI: 1.1,2.2], P = 0.013). The c-statistics for the receiver operating characteristic curve for stellate cell activity and fibrosis were 0.78 and 0.67, respectively, P = 0.36. The receiver operating characteristic curve for a model including stellate cell activity, histology activity index, and alanine aminotransferase. obtained at month 4 had the best c-statistic (0.88). In recipients with stage 0 or 1 fibrosis on the month 4 liver biopsy who subsequently developed advanced fibrosis, the c-statistic for the receiver operating characteristic curves was significantly better for stellate cell activity than for stage of fibrosis (0.77 and 0.51, respectively; P = 0.004). In conclusion, hepatic stellate cell activation early after liver transplantation complements traditional testing for identifying liver transplant recipients with hepatitis C at greatest risk for developing advanced fibrosis.

Adult↗
PubMed2005

Relationship between cytokines and the embryotoxicity of hydrosalpingeal fluid.

OBJECTIVE: The exact chemical composition of hydrosalpingeal fluid is unknown. The objective of this study was to characterize cytokines in hydrosalpingeal fluid (HSF) and examine their possible role in the embryo development. STUDY DESIGN: HSF was aspirated at laparoscopic salpingectomy in eight infertile women. Levels of IL-1beta, IL-13, IL-8, IL-6 and TNF-alpha in the HSF were determined by quantitative immunoassay kits. Two-cell mouse embryos were incubated with 0, 25, 50 and 75% concentrations of HSF. The blastocyst development rate (BDR) of mouse embryos was measured at each HSF concentration. RESULT(S): The embryotoxicity of HSF was concentration dependent. An increase in the HSF concentration resulted in significant decrease in % BDR (p < 0.01). IL-1beta was present in six of the eight HSF samples with a mean (+/-SD) concentration of 0.9 +/- 0.8 pg/mL. IL-13 was not detected in any of the HSF samples. IL-8, IL-6 and TNF-alpha were detected in all samples with a mean (+/-SD) concentration of 4741.2 +/- 6554.4 pg/mL, 204.8+/-132.8 pg/ml and 12 +/- 12.8 pg/mL respectively. IL-6 was positively correlated with BDR (r = 0.53; p < 0.04). CONCLUSION(S): We demonstrated for the first time the presence of IL-1beta, IL-8, IL-6 and TNF-alpha and the absence of IL-13 in human hydrosalpingeal fluid. IL-6 was positively related to the BDR.

Adult↗
PubMed2005

A quasispecies on a moving oasis.

A population evolving in an inhomogeneous environment will adapt differently to different areas. We study the conditions under which such a population can maintain adaptations to a particular region when that region is not stationary, but can move. In particular, we consider a haploid population living near a moving favorable patch ("oasis") in the middle of a large "desert." At one genetic locus, individuals may have one of a few gene sequences that convey an advantage while in the oasis at the cost of a disadvantage in the desert. The distribution of genetic states in the population, possibly localized in genome space around the oasis-adapted genotypes, is known as a quasispecies. We find that the ratio of oasis-adapted individuals to desert-adapted ones exhibits sharp transitions at particular oasis velocities. We calculate an extinction velocity, and a switching velocity above which the dominance switches from the oasis-adapted genotype to the desert-adapted one. This switching velocity is analogous to the quasispecies mutational error threshold. Above this velocity, the population cannot maintain adaptations to the properties of the oasis.

Genetics, Population↗
PubMed2005

Short recovery time after percutaneous liver biopsy: should we change our current practices?

BACKGROUND & AIMS: Percutaneous liver biopsy is the gold standard in the diagnosis and staging of a wide variety of hepatic disorders. Complications, post-procedure monitoring, and recovery time have limited the ability for liver biopsies to be performed in a busy gastroenterology community practice. The aim of this study was to determine whether ambulatory patients requiring percutaneous liver biopsy can be safely discharged after a short recovery time period. METHODS: All ambulatory patients undergoing a percutaneous liver biopsy at the University of Florida between February 1995 and June 2004 were evaluated in this study. A 15-gauge Jamshidi needle was used after percussion (before February 2002) or ultrasound guidance (starting February 2002). Major complications were defined as those events that required either immediate or delayed hospitalization or resulted in death within 2 weeks after the liver biopsy. RESULTS: Three thousand two hundred fourteen outpatient liver biopsies were performed at our institution from March 1995 to June 2004. During this time, our recovery time was gradually decreased from 6 hours before 1997 to 1 hour in 2002. The majority of the complications occurred within 1 hour of the observation period or within 24 hours after discharge. The major complication rate was < or =1.7%, regardless of the observation period. CONCLUSIONS: A shorter observation time after ambulatory percutaneous liver biopsy is safe and might facilitate the physician's ability to optimally utilize procedural space and ancillary staff in a busy ambulatory care unit.

Biopsy, Needle↗
PubMed2005

Defective Jak-Stat activation in hepatoma cells is associated with hepatitis C viral IFN-alpha resistance.

Interferon-alpha (IFN-alpha) has been widely used to treat viral infections and certain types of cancers. Large numbers of patients with chronic hepatitis C viral (HCV) infection do not respond to IFN and ribavirin combination therapy, and the majority of patients do not respond to IFN monotherapy. The underlying mechanisms of HCV nonresponse to IFN are unknown. In this report, using a HCV subgenomic replicon cell culture system, we show that (1) long-term IFN stimulation can select cells defective for Stat3 activation, and the defect appears to be responsible for HCV IFN resistance in cell culture, (2) HCV subgenomic sequence mutations associated with long-term culture do not appear to be responsible for IFN resistance, (3) expression of the activated Stat3 reverses IFN resistance while a dominant negative form of Stat3 renders an IFN-sensitive cell line resistant to IFN, and (4) the IFN-resistant cell line exhibits enhanced suppressor of cytokine signaling 3 (SOCS3) expression in response to IFN stimulation, and blocking SOCS3 in the IFN-resistant cell line partially restores IFN sensitivity. These findings strongly suggest that the IFN-resistant phenotype in vitro is associated with defective Stat3 activation and an enhanced SOCS3 response but is not associated with viral sequence mutations. Our study implies that long-term IFN stimulation in vitro selects cells that exhibit alterations in the host Jak-Stat signaling pathway, thereby representing a potential mechanism by which HCV resists IFN therapy.

Antiviral Agents↗
PubMed2005

Protein supplementation and the incidence of apoptosis and oxidative stress in mouse embryos.

OBJECTIVE: To estimate the effect of protein supplementation of culture media on reactive oxygen species production and incidence of apoptosis in preimplantation mouse embryos. METHODS: A total of 72 two-cell mouse embryos were cultured in human tubal fluid (HTF) alone (HTF-alone, control) and 71 embryos in HTF with protein supplementation (10% serum substitute supplement; HTF-SSS) for 72 hours. Total cell number per embryo was determined by staining with Hoechst 33258. Allocation of inner cell mass and trophectoderm in blastocysts and incidence of apoptosis were determined by confocal microscopy. Levels of reactive oxygen species in culture media were measured by chemiluminescence assay using luminol as probe. RESULTS: Blastocyst development, total cell number, and the inner cell mass/trophectoderm ratio were similar between the 2 groups. The blastocyst hatching rate was significantly higher in the HTF-SSS group than in the HTF-alone group (20% compared with 4%, P = .007). Level of reactive oxygen species was significantly higher in HTF-alone compared with HTF-SSS at 24 hours (median and interquartile range 28 [13, 43] compared with 0 [0, 1], P = .02), 48 hours (24 [21, 26] compared with 2 [1, 2], P = .02), and 72 hours (26 [9, 32] compared with 2 [2, 3], P = .03). The incidence of apoptosis in blastocysts cultured in HTF-SSS was significantly lower than those in HTF-alone group (mean +/- standard deviation 2.38 +/- 0.68 and 5.81 +/- 1.11, respectively, P = .001). CONCLUSION: Protein supplementation of culture media improves the hatching rate and reduces reactive oxygen species levels and the incidence of apoptosis in mouse preimplantation embryos.

Animals↗
PubMed2005

Dynamic evolution of coagulopathy in the first day of severe sepsis: relationship with mortality and organ failure.

OBJECTIVE: To determine whether changes in coagulation biomarkers during the first day of severe sepsis correlate with progression from single to multiple organ failure and subsequent death. DESIGN: Analysis of secondary endpoints in a prospective, randomized, placebo-controlled, multinational clinical trial (PROWESS). SETTING: The study involved 164 medical centers. PATIENTS: A total of 840 patients who met criteria for severe sepsis and were randomized to receive placebo plus supportive care. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Coagulation biomarkers, prothrombin time, antithrombin activity, and D-dimer and protein C levels were measured, and Sequential Organ Failure Assessment was performed daily. Multiple logistic regression analysis identified baseline antithrombin activity <54% and changes in prothrombin time, D-dimer, and antithrombin activity during the first calendar day after the onset of the first sepsis-induced organ dysfunction (i.e., the first day of severe sepsis, day 1) as predictive of 28-day mortality (p < or = .01). A composite coagulopathy score was determined using points for predetermined levels of change from baseline to day 1. The composite coagulopathy score correlated with progression from single to multiple organ failure (p = .0007), time to resolution of organ failure (p = .0004), and 28-day mortality (p < .0001). Combining the composite coagulopathy score with the Acute Physiology and Chronic Health Evaluation (APACHE) II score improved ability to identify patients who would progress to multiple organ failure (area under receiver operating characteristic curve 0.61 APACHE II vs. 0.65 APACHE II + composite coagulopathy score) and who would die (area under receiver operating characteristic curve 0.69 APACHE II vs. 0.74 APACHE II + composite coagulopathy score). CONCLUSIONS: Continuation or worsening of coagulopathy during the first day of severe sepsis was associated with increased development of new organ failure and 28-day mortality. These results further suggest that coagulation abnormalities contribute to organ failure and death.

APACHE↗
PubMed2005

Regulation of the Vibrio anguillarum metalloprotease EmpA by posttranslational modification.

The zinc metalloprotease EmpA is a virulence factor in the fish pathogen Vibrio anguillarum. Previous studies have shown that two strains of V. anguillarum regulate empA differently. Strain M93Sm exhibits protease activity only in the presence of fish gastrointestinal mucus, while protease activity is detected in NB10 culture supernatant under all stationary-phase conditions. In this study, we use real-time reverse transcription-PCR to show that even in conditions where no protease activity is detected, empA transcription occurs. Western blot analysis revealed that EmpA is secreted as a approximately 48-kDa proenzyme and that activation occurs extracellularly by the removal of a approximately 10-kDa peptide. The presence of stable extracellular pro-EmpA in M93Sm culture supernatants suggests that activation of EmpA is not autolytic.

Gene Expression Regulation, Bacterial↗
PubMed2005

'A variant of uncertain significance' and the proliferation of human disease gene databases.

The rapid accumulation of mutation data has led to the creation of nearly 300 locus-specific mutation databases. These sites may contain a few dozen to almost 20,000 mutations for a given gene. Many of the mutations are uncharacterised and have no known effects on the gene product, the 'variant of uncertain significance'. Here, the statistics of mutation distribution are examined for six different gene databases: BRCA1 and BRCA2, haemoglobin-beta (HBB), HPRT1, CFTR and TP53. The percentage of all possible point mutations for a protein (the mutation space) is calculated for each gene and the question 'How much mutation data is enough?' is raised.

Databases, Genetic↗
PubMed2005

Gene nomenclature by default, or BLASTing to Babel.

The current proliferation of mammalian genomes is creating a nomenclature issue caused by naming genes based on their best BLAST hit to a gene in another annotated genome. The rat genome is relying heavily on the mouse genome for nomenclature, but not all rat genes have direct orthologues in the mouse; often, there are paralogous groups of genes--due to expansions of that gene subfamily in one or the other genome. Many of these genes have already been assigned names in the rat, so that renaming them based on BLAST scores leads to duplicate sets of names. The supposed orthology created by name sharing across genomes is not always found. These inaccurate names are appearing in frequently used sites, such as the University of California Santa Cruz Genome Browser. The example of rat cytochrome P450 (Cyp) genes is presented here, but other gene families are also likely to be affected.

Animals↗
PubMed2005

A brief psychological intervention to improve adherence following transplantation.

Poor adherence is recognized as a major contributor to morbidity, mortality, decreased quality of life, higher medical costs, and over-utilization of health care services among transplant recipients. While there is universal recognition that poor adherence negatively impacts transplant outcomes, interventions designed to improve adherence have not been the focus of much attention in the transplant literature. The purpose of this article is to describe a brief, theory-based and individually tailored intervention to promote adherence. This intervention is currently used with all liver transplant recipients at our institution. The main goal of the intervention is to reduce the effects of known barriers to adherence by providing recipients with the education, skills, and resources needed to optimize adherence. Adherence is measured at 1, 3, 6, and 12 months post-transplant and additional adherence booster sessions are provided as needed. This intervention has been very favorably received by patients, caregivers, transplant physicians, and nurse coordinators.

Adaptation, Psychological↗
PubMed2004

Defect generation and deconfinement on corrugated topographies.

We investigate topography-driven generation of defects in liquid crystal films coating frozen surfaces of spatially varying Gaussian curvature whose topology does not automatically require defects in the ground state. We study in particular disclination-unbinding transitions with increasing aspect ratio for a surface shaped as a Gaussian bump with a hexatic phase draped over it. The instability of a smooth ground state texture to the generation of a single defect is also discussed. Free boundary conditions for a single bump are considered as well as periodic arrays of bumps. Finally, we argue that defects on a bump encircled by an aligning wall undergo sharp deconfinement transitions as the aspect ratio of the surface is lowered.

Journal Article↗