A cell-free antigen processing system informs HIV-1 epitope selection and vaccine design

Distinct CD4+ T cell epitopes have been associated with spontaneous control of HIV-1 replication, but analysis of antigen-dependent factors that influence epitope selection is lacking. To examine these factors, we used a cell-free antigen processing system that incorporates soluble HLA-DR (DR1), HLA-DM (DM), cathepsins, and full-length protein antigens for epitope identification by LC-MS/MS. HIV-1 Gag, Pol, Env, Vif, Tat, Rev, and Nef were examined using this system. We identified 35 novel epitopes, including glycopeptides. Epitopes from smaller HIV-1 proteins mapped to regions of low protein stability and higher solvent accessibility. HIV-1 antigens associated with limited CD4+ T cell responses were processed efficiently, while some protective epitopes were inefficiently processed. 55% of epitopes obtained from cell-free processing induced memory CD4+ T cell responses in HIV-1+ donors, including eight of 19 novel epitopes tested. Thus, an in vitro processing system utilizing the components of Class II processing reveals factors influencing epitope selection of HIV-1 and represents an approach to understanding epitope selection from non-HIV-1 antigens.

TCR-mimic bispecific antibodies to target the HIV-1 reservoir

HIV-1 infection is incurable due to the persistence of the virus in a latent reservoir of resting memory CD4+ T cells. “Shock-and-kill” approaches that seek to induce HIV-1 gene expression, protein production, and subsequent targeting by the host immune system have been unsuccessful due to a lack of effective latency-reversing agents (LRAs) and kill strategies. In an effort to develop reagents that could be used to promote killing of infected cells, we constructed T cell receptor (TCR)-mimic antibodies to HIV-1 peptide-major histocompatibility complexes (pMHC). Using phage display, we panned for phages expressing antibody-like variable sequences that bound HIV-1 pMHC generated using the common HLA-A*02:01 allele. We targeted three epitopes in Gag and reverse transcriptase identified and quantified via Poisson detection mass spectrometry from cells infected in vitro with a pseudotyped HIV-1 reporter virus (NL4.3 dEnv). Sequences isolated from phages that bound these pMHC were cloned into a single-chain diabody backbone (scDb) sequence, such that one fragment is specific for an HIV-1 pMHC and the other fragment binds to CD3ε, an essential signal transduction subunit of the TCR. Thus, these antibodies utilize the sensitivity of T cell signaling as readouts for antigen processing and as agents to promote killing of infected cells. Notably, these scDbs are exquisitely sensitive and specific for the peptide portion of the pMHC. Most importantly, one scDb caused killing of infected cells presenting a naturally processed target pMHC. This work lays the foundation for a novel therapeutic killing strategy toward elimination of the HIV-1 reservoir.

The role of skeletal muscle in liver glutathione metabolism during acetaminophen overdose

Marked alterations in systemic glutamate-glutamine metabolism characterize the catabolic state, in which there is an increased breakdown and decreased synthesis of skeletal muscle protein. Among these alterations are a greatly increased net release of glutamine (Gln) from skeletal muscle into blood plasma and a dramatic depletion of intramuscular Gln. Understanding the catabolic state is important because a number of pathological conditions with very different etiologies are characterized by its presence; these include major surgery, sepsis, trauma, and some cancers. Acetaminophen (APAP) overdose is also accompanied by dramatic changes in systemic glutamate-glutamine metabolism including large drops in liver glutathione (for which glutamate is a precursor) and plasma Gln. We have constructed a mathematical model of glutamate and glutamine metabolism in rat which includes liver, blood plasma and skeletal muscle. We show that for the normal rat, the model solutions fit experimental data including the diurnal variation in liver glutathione (GSH). We show that for the rat chronically dosed with dexamethasone (an artificial glucocorticoid which induces a catabolic state) the model can be used to explain empirically observed facts such as the linear decline in intramuscular Gln and the drop in plasma glutamine. We show that for the Wistar rat undergoing APAP overdose the model reproduces the experimentally observed rebound of liver GSH to normal levels by the 24-h mark. We show that this rebound is achieved in part by the action of the cystine-glutamate antiporter, an amino acid transporter not normally expressed in liver but induced under conditions of oxidative stress. Finally, we explain why supplementation with Gln, a Glu precursor, assists in the preservation of liver GSH during APAP overdose despite the fact that under normal conditions only Cys is rate-limiting for GSH formation.

Robustness of a neural network model for differencing

A neural network, originally proposed as a model for nuclei in the auditory brainstem, uses gradients of cell thresholds to reliably compute the difference of inputs over wide input ranges. The encoding of difference is linear even though the individual components of the network are finite, saturating, nonlinear devices highly dependent on input level. Theorems are proven that explain the linear dependence of network output on difference and that show the robustness of the network to perturbations of the threshold gradients. There is some evidence that the network exists in the neural tissue of the auditory brainstem.

Physicians pulling back from charity care

Physicians have long provided care to the medically indigent for free or at reduced rates. However, recent findings from the Center for Studying Health System Change (HSC) indicate that the proportion of physicians providing charity care dropped from 76 percent to 72 percent between 1997 and 1999. In the short term, most medically indigent people are still getting care. But policy makers should take note that reduced physician participation in charity care will hurt the poor if-as projected-growth in physician supply slows and the number of uninsured rises along with escalating health care costs. This Issue Brief discusses the extent of the decline in physician provision of charity care, the reasons for the decline and implications for the future of the safety net.

Model calculations of time dependent responses to binaural stimuli in the dorsal nucleus of the lateral lemniscus

In a previous paper (Reed and Blum, 1999), we examined the connectional hypotheses put forward by Markovitz and Pollak (1994) to explain the steady-state behavior of cells in the dorsal nucleus of the lateral lemniscus (DNLL). We found that the steady-state outputs of the four major binaural types of cells found in the DNLL (EI, EI/F, EE/I, and EE/FI) could be accounted for by known connectional patterns using only one or two cells per nucleus and quite simple hypotheses on cell behavior. In this study, we examine the time course of DNLL outputs in response to constant, ongoing, monaural or binaural sounds of various intensities. The model auditory nerve fibers ramp up linearly (usually in 2 ms) to full firing and the anteroventral cochlear nucleus cells have primary-like discharge patterns. Fixed time delays of 1 ms at each synapse are included; other time delays are employed when necessary to understand and reproduce specific features of the experimental data. We find that the connectional patterns utilized in our previous study can account for the rich variety of temporal response patterns found experimentally in the DNLL. Our main findings are: (1) all of the four major binaural types of cells can arise from modifications of the basic connectional pattern that produces EI cells; (2) both excitation and inhibition from the ipsilateral lateral superior olive (LSO) are required to understand DNLL responses; (3) pauser behavior can arise either from time delayed inhibition from a DNLL interneuron or by projection from the LSO; (4) two different mechanisms can account for the ipsilaterally evoked onset response; (5) to explain completely the temporal discharge pattern and binaural interactions of EE/FI cells, a projection from the contralateral DNLL via the commissure of Probst is necessary.

Why people change their health care providers

This Data Bulletin presents findings from the Household Survey, a nationally representative telephone survey of the civilian, non-institutionalized population conducted as part of the Community Tracking Study. The 1996-1997 survey includes nearly 33,000 families and 60,000 individuals, while the 1998-1999 survey includes approximately 32,000 families and 59,000 individuals.

A mathematical model quantifying GnRH-induced LH secretion from gonadotropes

A mathematical model is developed to investigate the rate of release of luteinizing hormone (LH) from pituitary gonadotropes in response to short pulses of gonadotropin-releasing hormone (GnRH). The model includes binding of the hormone to its receptor, dimerization, interaction with a G protein, production of inositol 1,4, 5-trisphosphate, release of Ca(2+) from the endoplasmic reticulum, entrance of Ca(2+) into the cytosol via voltage-gated membrane channels, pumping of Ca(2+) out of the cytosol via membrane and endoplasmic reticulum pumps, and release of LH. Cytosolic Ca(2+) dynamics are simplified (i.e., oscillations are not included in the model), and it is assumed that there is only one pool of releasable LH. Despite these and other simplifications, the model explains the qualitative features of LH release in response to GnRH pulses of various durations and different concentrations in the presence and absence of external Ca(2+).

Changes in the scope of care provided by primary care physicians

BACKGROUND

Strategies to control medical costs and improve the quality of care often translate into decisions affecting the range of services primary care physicians provide to patients, which patients are referred for specialty care, and the points in disease processes at which referrals are made. This study focused on physicians' assessments of changes in the scope of care provided by primary care physicians and their assessments of the appropriateness of the scope of the care that primary care physicians are expected to provide.

METHODS

We analyzed data from the 1996-1997 Community Tracking Study Physician Survey. Telephone interviews were conducted with 12,385 physicians (reflecting a response rate of 65 percent) who were drawn from a representative random sample of physicians providing direct patient care in the continental United States and not employed by the federal government. The analysis was based on responses from the 7015 primary care physicians and 5092 specialists who had been in practice for at least two years.

RESULTS

Thirty percent of the primary care physicians and 50 percent of the specialists reported that the scope of care provided by primary care physicians had increased during the previous two years. Twenty-four percent of the primary care physicians and 38 percent of the specialists reported that the scope of care expected to be provided by primary care physicians was greater than it should be. According to multivariate analysis, primary care physicians other than general or family practitioners (i.e., pediatricians and general internists), those who were in one- or two-physician practices, those who received revenues from capitation, and those who served as gatekeepers for their patients' care were significantly more likely to report that the scope of care they were expected to provide was greater than it should be.

CONCLUSIONS

The finding that nearly one in four primary care physicians reported that the scope of care they were expected to provide was greater than it should be arouses concern about the potential impact of changes in the delivery of health care. The associations we found between financial and administrative aspects of managed care and physicians' concern about the scope of care they provide to their patients deserve careful consideration.

The scope of care expected of primary care physicians: is it greater than it should be?

The United States has long relied on specialist physicians more heavily than other countries, and some policy experts have repeatedly recommended that the share and role of primary care physicians (PCPs) be increased as a way of providing cost-effective care. The growth of managed care, changing practice arrangements and new medical technology are forces that may be increasing the role of PCPs. This Issue Brief reports findings published in the New England Journal of Medicine showing that many physicians believe the scope of care provided by PCPs without referral to specialists is increasing. Moreover, almost a quarter of PCPs report that the scope of care they are expected to provide is greater than it should be. The likelihood of PCPs' concern is related to specific managed care techniques, practice size and specialty, among other factors.

Model calculations of steady state responses to binaural stimuli in the dorsal nucleus of the lateral lemniscus

Several studies have been performed in which both the time-dependent and steady state output of cells in the dorsal nucleus of the lateral lemniscus (DNLL) have been measured in response to binaural sound stimulation. In this paper, a mathematical and computational model for the steady state output of DNLL cells is formulated. The model includes ascending connections from both lateral and medial superior olives (LSO and MSO) as well connections from interneurons in the DNLL and connections from the contralateral DNLL through the commissure of Probst. Our intent is to understand how the steady state behavior arises from the cell properties in and connectional patterns from lower brainstem nuclei. In particular, we examine the connectional hypotheses put forward by Markovitz and Pollak (1994) to explain the observed behavior of EI, EI/F, EE/I and EE/FI cells. Using these connections (with minor modifications) and cells with simple input-output relations, we are able to account for the steady state behavior of these cell types. We are able to explain interesting features of the data not commented on before, for example, the initial dip in spike output for EE cells at low ipsilateral sound levels. The presence of an inhibitory interneuron in the DNLL is essential for facilitation. In addition, we examine the effects of the MSO and the commissure of Probst on DNLL output. Furthermore, we propose a simple mechanism by which the cells of the DNLL and LSO could create a topographic place map in the inferior colliculus.

Effects of wide band inhibitors in the dorsal cochlear nucleus. II. Model calculations of the responses to complex sounds

In a previous modeling study of signal processing in the dorsal cochlear nucleus [Reed and Blum, J. Acoust. Soc. Am 96, 1442-1453 (1997)] it was shown that inclusion of a wideband inhibitor (WBI) greatly improved the fit between model response maps and the experimental response maps of type IV units to pure tones. In this study we examine the effect of the WBI on the responses to complex sound stimuli such as broadband noise (BBN), notch noise, noise bands, and band/notch combinations. A new and more realistic model for auditory nerve (AN) response in the presence of different levels of noise is used. It is shown that one can explain and understand the qualitative features of virtually all the published data on type II and type IV unit responses to BBN, notch noise and noise bands. The monotone decreasing response of the maximum firing rate of type II units to noise bands of increasing width that is observed experimentally occurs in the model due to the increasing inhibition of type II cells by the WBI. Similarly, the various nonmonotone patterns of maximum firing rate of type IV units to noise bands of increasing width is shown to arise from the complex and highly nonlinear effects of inhibition from the type II to type IV and the WBI to type IV cells and the nonlinear direct excitation from the AN to the type IV cells. A number of experiments using double notches, double noise bands, or notch-noise band pairs are suggested which, by comparison with model results, would allow one to infer probable connectional patterns between type II and type IV units and between the WBI units and the type IV units.

Model calculations of the effects of wide-band inhibitors in the dorsal cochlear nucleus

In two previous papers [Reed and Blum, J. Acoust. Soc. Am. 97, 425-438 (1995), Blum et al., J. Acoust. Soc. Am. 98, 181-191 (1995)] a computational model for signal processing in the dorsal cochlear nucleus (DCN) was developed. In those modelling studies, stellate cells inhibited only type II cells. In this study, the effect of including wide-band inhibitory (WBI) connections from stellate cells to type IV cells, as proposed by Nelken and Young [J. Neurophysiol. 71, 2446-2462 (1994)], is examined. Inclusion of the WBI connections improves the fit to the experimental pure tone response maps for both the "standard" and "non-standard" cells examined by Spirou and Young [J. Neurophysiol. 66, 1750-1768 (1991)]. Thus, these modelling studies support the hypothesis of Nelken and Young [J. Neurophysiol. 71, 2446-2462 (1994)]. The degree of improvement is greatest for cells with prominent upper inhibitory sidebands. The qualitative features of the pure tone response map and the theoretical model allow one to deduce the probable frequency bias of the type II to type IV and stellate to type IV connections.

A computational model for signal processing by the dorsal cochlear nucleus. II. Responses to broadband and notch noise

In a previous paper a computational model was developed which was shown to account for most of the essential features of the variety of experimentally observed response maps of type-IV cells in the dorsal cochlear nucleus to pure tones. In the present study, the responses of the same model DCN to broadband noise and notch noise are investigated. It is shown that the previous model qualitatively accounts for the observed responses to these more complex sounds. Predictions of the model for inverted notches and for the behavior of type-IV cell output as notch center is varied for different amplitudes are presented. It is shown that the model is suitable for feature detection of auditory signals and an expansion is given as to how this ability arises from the properties of the stellate, type-II, and type-IV cells and the variations in the connectional patterns that were previously shown to account for the response patterns of type-IV cells to pure tones.

A computational model for signal processing by the dorsal cochlear nucleus. I. Responses to pure tones

Much information is available on the anatomical organization and neurophysiological properties of the major cell types in the dorsal cochlear nucleus (DCN). The complicated response properties of individual cells and units in the DCN indicate that substantial information processing already occurs at the level of the DCN. A large number of connectional hypotheses have been put forward to explain various aspects of the response characteristics of DCN cells, but many of the consequences of these hypotheses have not been investigated quantitatively. In this paper, we investigate these hypotheses by constructing and testing mathematical and computational models and compare our results to those of previous modeling studies. The simplest versions of our models include auditory nerve (AN) fibers, type II cells (inhibitory interneurons) and type IV cells (fusiform and giant cells). The model response maps, i.e., the pattern of output of model type IV cells, generated by the simplest model have some but not all the features of the experimental response maps of type IV neurons. In particular, the excitatory region which occurs at best frequency is not isolated and the excitatory region at low frequencies and high amplitude is narrower than observed. Since experimental evidence exists that some of the connections between these cell types are divergent or convergent across adjacent isofrequency sheets, the effect of such convergence and divergence was then investigated. Response maps so obtained reproduce many of the qualitative features of the experimental maps. Enlargement of the model by including inhibitory interneurons (e.g., stellate cells) that receive convergent input from AN fibers and which inhibit type II cells results in the generation of response maps that, with some variations in connectional patterns and physiological properties of neurons, match most of the essential features seen in the large variety of experimental maps obtained from the cat DCN.

Theoretical analysis of lipid transport in sciatic nerve

We modify our previous mathematical model of axonal transport to analyze data on the fast transport of lipids in rat sciatic nerve given in Toews et al. (J. Neurochem. 40, 555-562 (1983)). The theoretical model accounts well for the shapes of the profiles of phosphatidylcholine, phosphatidylethanolamine, cholesterol and diphosphatidylglycerol. The parameters obtained support the qualitative conclusions of Toews et al. and provide quantitative estimates of the underlying processes, e.g., rates of vesicle and mitochondria translocation, rate constants for association and dissociation between vesicles, kinesin and microtubules, rates of deposition and rates of loss of each class of lipid from the nerve by leakage or via removal by the retrograde transport system. The analysis suggests that two classes of vesicles moving at different speeds may be involved in the transport of phosphatidylcholine and phosphatidylethanolamine.

A model for slow axonal transport and its application to neurofilamentous neuropathies

A model for slow axonal transport is developed in which the essential features are reversible binding of cytoskeletal elements and of soluble cytosolic proteins to each other and to motile elements such as actin microfilaments. Computer simulation of the equations of the model demonstrate that the model can account for many of the features of the SCa and SCb waves observed in pulse experiments. The model also provides a unified explanation for the increase and decrease of neurofilament transport rates observed in various toxicant-induced neuropathies.

Theoretical analysis of radioactivity profiles during fast axonal transport: effects of deposition and turnover

In a preceding study [Blum, J.J., and Reed, M.C. (1985): Cell Motil. 5:507-527], factors responsible for the shape and velocity of the leading edge of the radiolabeled organelle profile were analyzed, but processes that might influence the shape of the plateau-like region behind the advancing wave were ignored. It is now shown that deposition of material from the fast transport system into membrane-associated structures, degradation of such deposited material and its return to the soma by the retrograde transport system, or leakage of radiolabeled material from the axon can account for the shape of the plateau. Furthermore, these processes are compatible with the maintenance of such structural inhomogeneities as the nodes of Ranvier.

A model for fast axonal transport

A model for fast axonal transport is developed in which the essential features are that organelles may interact with mechanochemical cross-bridges that in turn interact with microtubules, forming an organelle-engine-microtubule complex which is transported along the microtubules. Computer analysis of the equations derived to describe such a system show that most of the experimental observations on fast axonal transport can be simulated by the model, indicating that the model is useful for the interpretation and design of experiments aimed at clarifying the mechanism of fast axonal transport.