Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation

Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced H3K27ac. Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data supports clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.

Routine versus clinically driven laboratory monitoring of HIV antiretroviral therapy in Africa (DART): a randomised non-inferiority trial

BACKGROUND

HIV antiretroviral therapy (ART) is often managed without routine laboratory monitoring in Africa; however, the effect of this approach is unknown. This trial investigated whether routine toxicity and efficacy monitoring of HIV-infected patients receiving ART had an important long-term effect on clinical outcomes in Africa.

METHODS

In this open, non-inferiority trial in three centres in Uganda and one in Zimbabwe, 3321 symptomatic, ART-naive, HIV-infected adults with CD4 counts less than 200 cells per microL starting ART were randomly assigned to laboratory and clinical monitoring (LCM; n=1659) or clinically driven monitoring (CDM; n=1662) by a computer-generated list. Haematology, biochemistry, and CD4-cell counts were done every 12 weeks. In the LCM group, results were available to clinicians; in the CDM group, results (apart from CD4-cell count) could be requested if clinically indicated and grade 4 toxicities were available. Participants switched to second-line ART after new or recurrent WHO stage 4 events in both groups, or CD4 count less than 100 cells per microL (LCM only). Co-primary endpoints were new WHO stage 4 HIV events or death, and serious adverse events. Non-inferiority was defined as the upper 95% confidence limit for the hazard ratio (HR) for new WHO stage 4 events or death being no greater than 1.18. Analyses were by intention to treat. This study is registered, number ISRCTN13968779.

FINDINGS

Two participants assigned to CDM and three to LCM were excluded from analyses. 5-year survival was 87% (95% CI 85-88) in the CDM group and 90% (88-91) in the LCM group, and 122 (7%) and 112 (7%) participants, respectively, were lost to follow-up over median 4.9 years' follow-up. 459 (28%) participants receiving CDM versus 356 (21%) LCM had a new WHO stage 4 event or died (6.94 [95% CI 6.33-7.60] vs 5.24 [4.72-5.81] per 100 person-years; absolute difference 1.70 per 100 person-years [0.87-2.54]; HR 1.31 [1.14-1.51]; p=0.0001). Differences in disease progression occurred from the third year on ART, whereas higher rates of switch to second-line treatment occurred in LCM from the second year. 283 (17%) participants receiving CDM versus 260 (16%) LCM had a new serious adverse event (HR 1.12 [0.94-1.32]; p=0.19), with anaemia the most common (76 vs 61 cases).

INTERPRETATION

ART can be delivered safely without routine laboratory monitoring for toxic effects, but differences in disease progression suggest a role for monitoring of CD4-cell count from the second year of ART to guide the switch to second-line treatment.

FUNDING

UK Medical Research Council, the UK Department for International Development, the Rockefeller Foundation, GlaxoSmithKline, Gilead Sciences, Boehringer-Ingelheim, and Abbott Laboratories.

Expression of CC chemokine receptor 7 in tonsillar cancer predicts cervical nodal metastasis, systemic relapse and survival

The aim of this study was to evaluate the expression of CC chemokine receptor 7 (CCR7) in squamous cell cancer of the tonsil with respect to patterns of spread, relapse-free, overall and disease-specific survival. Eighty-four patients with squamous cell cancer of the tonsil were identified. There was a male predominance of 3 : 1 and the median age at diagnosis was 53 (range 35–86) years. The median duration of follow-up was 33 (range 2–124) months. There was a significant association between CCR7 immunopositivity and synchronous cervical nodal metastasis in patients with tonsillar cancer (Spearman's correlation coefficient 0.564; P<0.001). Relapse-free (P=0.0175), overall (P=0.0136) and disease-specific (P=0.0062) survival rates were significantly lower in patients whose tumours expressed high levels of CCR7. On multivariate analysis, high-level CCR7 staining predicted relapse-free (hazard ratio 3.0, 95% confidence intervals 1.1–8.0, P=0.026) and disease-specific (hazard ratio 10.2, 95% confidence intervals 2.1–48.6, P=0.004) survival. Fifteen percent of patients with the highest level of tumour CCR7 immunopositivity relapsed with systemic metastases. These data demonstrated that CCR7 expression was associated with cervical nodal and systemic metastases from tonsillar cancers. High levels of CCR7 expression predicted a poor prognosis.

Not just music but medicine. Podcasting surgical procedures in otolaryngology

Audiovisual teaching material can now be watched using a personal computer or portable media device. The cost of delivering video across the Internet has fallen considerably in recent years. Podcasting technology automates the distribution of audio and video across the Internet. Podcasting technology, with the Internet, has the potential to improve learning. To access podcasts all you need is a computer, free software and an Internet connection.

Ameloblastoma: a rare nasal polyp

Ameloblastoma is an odontogenic neoplasm of enamel organ type tissue which does not undergo transformation to the point of enamel formation. We present the second case in the English literature of maxillary ameloblastoma that presented with nasal obstruction and rhinorrhoea, and the first to be excised using a combined maxillotomy and endoscopic ethmoidectomy. The patient had no previous dental history. The unusual presenting symptoms, as well as the highly destructive nature of these lesions when arising in the maxilla, make them worthy of consideration in the differential diagnosis of nasal and maxillary masses. We discuss the clinical features, pathology and management of these lesions and review the literature.

B cell ligand discrimination through a spreading and contraction response

B cells recognize foreign antigens by virtue of cell surface immunoglobulin receptors and are most effectively activated by membrane-bound ligands. Here, we show that in the early stages of this process, B cells exhibit a two-phase response in which they first spread over the antigen-bearing membrane and then contract, thereby collecting bound antigen into a central aggregate. The extent of this response, which is both signaling- and actin-dependent, determines the quantity of antigen accumulated and hence the degree of B cell activation. Brownian dynamic simulations reproduce essential features of the antigen collection process and suggest a possible basis for affinity discrimination. We propose that dynamic spreading is an important step of the immune response.

Aneurysmal bone cyst of the spine

The authors present the case of an 11-year-old boy with a painful, rapidly expanding lesion in the posterior triangle of the neck. There was no history of cervical trauma. Computerized tomography of the neck revealed a unicameral (single-chambered) aneurysmal bone cyst involving the C3 vertebra. Treatment was by open resection and curettage; no recurrence was seen at six months. We discuss the natural history, differential diagnosis, radiographic appearance and treatment modalities for this unusual, benign, expanding, osteolytic lesion containing blood-filled cystic cavities.

The midfacial degloving approach to sinonasal tumours in children

The midfacial degloving approach was originally described by Denker and Kahler in 1926 but has been little used in the paediatric population. The procedure allows access to benign and malignant lesions of the sinonasal region with the avoidance of an external scar. The advantages and application of this technique are presented in 9 paediatric patients, ranging from 3 months to 15 years of age with a mean follow-up of 7 months. Eight children had benign pathology. There were two juvenile angiofibromas, two nasal gliomas, one ossifying fibroma, one fibroma, one fibrous dysplasia and one benign myofibroblastic proliferation. One child had malignant disease in the form of recurrent embryonal rhabdomyosarcoma. All had excellent cosmetic results and no complications were encountered during follow-up.

How we do it: the Owa (Addenbrookes) grommet

. Grommet insertion is one of the most common procedures performed under general anaesthesia. . The authors describe an innovative grommet that, through an anatomically contoured and user friendly design has been designed to minimize anaesthetic time by facilitating and expediting its placement and/or removal.

Epistaxis: are temperature and seasonal variations true factors in incidence?

OBJECTIVE

To investigate the previously documented inverse association between ambient temperature and presentation rates for patients with epistaxis and seasonal variation of emergency presentation rates for patients with epistaxis.

STUDY DESIGN

A retrospective analysis of all consecutive emergency patients with epistaxis presenting to hospital from the community over a five-year period, 1997-2002 (1830 days), including those who required admission to hospital with epistaxis over the same period. Patients in whom there was a clear aetiology for the epistaxis (traumatic, recurrent, iatrogenic, coagulopathic and hypertensive) were excluded.

SETTING

A tertiary referral centre in south-west London serving a population in excess of 2.8 million.

METHOD

A retrospective analysis of all patients presenting or admitted to St George's Hospital with epistaxis over a five-year period. Daily ambient temperature readings from London Heathrow airport were recorded for the same period. Presentations were correlated with monthly temperature variations and the month itself. Statistical analysis with Pearson's correlation coefficient was performed.

RESULTS

1373 patients with epistaxis presented to our department, of whom 386 (28.1 per cent) were admitted to hospital. No correlation is seen between ambient temperature and presentation rate for patients with epistaxis. No seasonal preponderance is noted for presentation rate (Pearson r = 0.160, p = 0.221) in this series.

CONCLUSION

To our knowledge, this is the largest study to date examining ambient temperature association and epistaxis, and the first to investigate presentation rate in place of admission rate. We feel that the exclusion of all patients with epistaxis not admitted to hospital introduces a bias. In this series, there is no correlation between ambient temperature, seasonal preponderance, presentation rate or admission rate for patients with epistaxis. This is contrary to previously reported findings. We do not support the view that there is a relationship between epistaxis and temperature or seasonal variation. This contradicts the current belief that incidence of epistaxis displays seasonality, and has implications for the allocation of resources for healthcare provision within ENT departments.

The use of camera mobile phone to assess emergency ENT radiological investigations

OBJECTIVES

To determine the accuracy of assessment of common ENT emergency radiological investigations using mobile phone digital images.

DESIGN

Prospective case controlled series.

SETTING

Tertiary referral otolaryngology centre.

PARTICIPANTS

Fourteen randomly selected patients who underwent emergency ENT radiological investigations over a 1-month period.

MAIN OUTCOME MEASURES

The accuracy and confidence of six ENT consultants and five specialist registrars in making diagnoses based on a brief history and assessment of CT scans and X-ray images taken from and transmitted via a mobile phone, compared with examination of the same films on a conventional X-ray box.

RESULTS

With 14 films, a total of 154 cases were assessed by the 11 subjects. All doctors made the correct diagnosis for every case examined. Overall, the relative confidence of diagnosis was ranked highly for both image media, although the overall confidence of diagnosis using the X-ray box was significantly greater than the mobile phone (95% CI upper bound = 1.6 lower bound = 0.9; paired t-test P < 0.0001). The seniority of the clinician did not predict a difference in the confidence of diagnosis (P = 0.3). There is no statistical relationship between confidence of diagnosis of the original films and degradation of film quality on the mobile phone (P = 0.7).

CONCLUSIONS

The accuracy and confidence of diagnosis of common ENT emergency radiological investigations using mobile phone digital images seem compatible with X-ray box. Financially it is a much cheaper than conventional telemedicine technology. It may be used to augment information sent to non-resident specialists in the management of emergency ENT cases.

Pleomorphic adenoma and severe obstructive sleep apnoea

Two cases of deep lobe parotid tumours extending into the parapharyngeal space and causing obstructive sleep apnoea are described. Post-operatively, marked improvements in nocturnal hypoxic episodes and the symptoms of obstructive sleep apnoea were seen. Although minor salivary gland pleomorphic adenomas have been described as a cause of airway compromise, pleomorphic adenomata arising from the deep lobe of the parotid, causing proven obstructive sleep apnoea, have not previously been documented. The anatomy and common pathologies of the parapharyngeal space are discussed.

Airborne environmental pollutant concentration and hospital epistaxis presentation: a 5-year review

To investigate the hypothesized relationship between various daily atmospheric pollutant concentrations and hospital epistaxis presentation. A retrospective analysis of all presentations of non-traumatic epistaxis to our institution was performed, and the results were cross-referenced with London air quality data supplied by the National Air Quality Data Archive at the National Environmental Technology Centre (NETCEN) at the multi-centre tertiary referral ENT Department. An analysis of epistaxis presentation to St George's Hospital during the 5-year period January 1997-2002 was made from the patient administration system and accident and emergency records. The study includes 1373 emergency patients after traumatic and iatrogenic epistaxis were excluded. Factors measured were atmospheric ozone (O(3)), carbon monoxide (CO), sulphur dioxide (SO(2)), nitrogen dioxide (NO(2)) and particulate matter less than 10 mum in diameter (PM(10)). Hospital epistaxis presentation and atmospheric pollutant concentration were documented for each day of the 5-year period, weekly change in both parameters was recorded and statistical analysis was performed. The statistical methods used are linear correlation using Pearson's coefficient. Increased hospital epistaxis presentation was strongly associated with increased concentration of airborne particulate matter (r = 0.289, P < 0.001; significant if P < 0.05) and less strongly associated with increased concentrations of atmospheric O(3) (r = 0.150, P = 0.019; significant if P < 0.05). There was no association between epistaxis attendance and atmospheric concentrations of CO, NO(2) and SO(2) in this study. The concentrations of local airborne particulate matter and atmospheric O(3) in the days preceding hospital attendance for epistaxis are relevant when considering the associations of the episode. This further increases understanding of the pathophysiology of spontaneous epistaxis.

An innovative approach to anterior rhinoscopy

Anterior rhinoscopy with a Thudicum's or Killian's speculum is essential in the assessment and treatment of anterior epistaxis. A simple technique for visualization of the nasal septum is described which enables a two-handed approach to treatment and is achieved with materials readily available in the emergency department.

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

MOTIVATION

Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively.

RESULTS

We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others.

AVAILABILITY

The specification of SBML Level 1 is freely available from http://www.sbml.org/

Local variation in endoparasite intensities of bank voles (Clethrionomys glareolus) from ecologically similar sites: morphometric and endocrine correlates

Much interest has centred recently on the role of adaptive trade-offs between the immune system and other components of life history in determining resistance and parasite intensities among hosts. Steroid hormones, particularly glucocorticoids and sex steroids, provide a plausible mechanism for mediating such trade-offs. A basic assumption behind the hypothesis, however, is that steroid activity will generally correlate with reduced resistance and thus greater parasite intensities. Here, we present some findings from a field study of bank voles (Clethrionomys glareolus) in which we have looked at associations between parasite intensities, anatomical and morphometric measures relating to endocrine function and life history variation in three local populations inhabiting similar but mutually isolated woodland habitats. In general, sites with greater parasite intensities were those in which male C. glareolus had significantly larger adrenal glands, testes and seminal vesicles for their age and body size. Females also showed a site difference in adrenal gland weight. Some aspects of site-related parasite intensity were associated with asymmetry in adrenal gland weight and hind foot length, which may have reflected developmental effects on glucocorticoid activity.

Variation in the helminth community structure in bank voles (Clethrionomys glareolus) from three comparable localities in the Mazury Lake District region of Poland

We tested the null hypothesis that populations of hosts trapped in isolated neighbouring locations showing comparable habitat quality, should support similar helminth parasite communities. The study was undertaken in a 2-week period in late summer in NE Poland in a single year, thereby eliminating seasonal and between-year variation in parasite burdens. A total of 139 Clethrionomys glareolus (bank vole) were sampled from 3 forest sites of similar habitat quality. Total species richness was 11 (6 nematodes and 5 cestodes) with 85.6% of the voles carrying at least 1 species and an overall mean species richness of 1.4. At the component community level, the fewest species of helminths were recorded from site 2 (n = 6, compared with 9 at each of the other sites), but site 3 had the lowest Berger-Parker Dominance Index and the highest Simpson's Index of Diversity. At the infracommunity level, site 3 had the highest mean no. of helminth species/vole, the highest mean Brillouin's Index of Diversity but the lowest mean no. of helminths/vole. Voles from sites 1 and 3 differed in the nematodes that were most common (site 1, Heligmosum mixtum-95%; site 3, Heligmosomoides glareoli -79.3%). At site 2 no species exceeded 50% but prevalence of Syphacia petrusewiczi was higher than at the other sites. The prevalence of cestodes was too low to test reliably (12.%), but the highest prevalence of adult cestodes was recorded at site 1 (22.5% compared with 4.9 and 1.7% for sites 2 and 3 respectively). Host sex did not influence infection, but mean species richness increased with age. The different sites were responsible for most of the variation in our data, and the intrinsic factors (sex and age) were less important in shaping the component community structure of helminths. We conclude that even locations in relative close proximity to one another (13-25 km), selected on the basis of similar habitat quality, have rodent populations that differ in their helminth parasite communities, although for reasons other than the factors quantified in the present study.

Conformational spread in a ring of proteins: a stochastic approach to allostery

We recently suggested that the sensitivity and range of a cluster of membrane receptors in bacteria would be enhanced by cooperative interactions between neighbouring proteins. Here, we examine the consequences of this "conformational spread" mechanism for an idealised one-dimensional system comprising a closed ring of identical allosteric protomers (protein molecules, or a group of protein domains operating as a unit). We show analytically and by means of Monte Carlo simulations that a ring of allosteric protomers can exhibit a switch-like response to changes in ligand concentration. We derive expressions for the sensitivity and cooperativity of switching and show that the maximum sensitivity is proportional to the number of protomers in the ring. A ring of this kind can reproduce the sensitivity and kinetics of the switch complex of a bacterial flagellar motor, for example, which is based on a ring of 34 FliM proteins. We also compare smaller rings of conformationally coupled protomers to classical allosteric proteins such as haemoglobin and show that the canonical MWC and KNF models arise naturally as limiting cases. Conformational spread appears to be a natural extension of the familiar mechanism of allostery: a physically realistic mechanism that should apply widely to many structures built from protein molecules.

In vitro immunomodulatory properties of tucaresol in HIV infection

The immunomodulatory properties of tucaresol (compound 589C80) were tested on in vitro antigen- and mitogen-stimulated proliferation and cytokine production by peripheral blood mononuclear cells (PBMC) of HIV-infected individuals and healthy controls (HC). Results showed that tucaresol: (1) increases influenza A virus-, gp 160 peptide-, and HLA alloantigen-stimulated proliferation as well as interleukin (IL)-2 and interferon gamma (IFN gamma) production by PBMC of HIV-infected individuals with higher CD4 counts (>500/microl) but had only a marginal immunomodulatory effect on PBMC of patients with lower CD4 counts (<500/microl); (2) did not modify IL-10 production; (3) augmented CD25 expression on mitogen-stimulated T cells of HC but not of HIV-infected individuals; and (4) marginally increased CTL activity. The immunomodulatory properties of tucaresol were confirmed by PCR analyses; additional data showed that tucaresol costimulated CD3-dependent triggering of T cells and that this stimulation was independent of CD28 costimulation. The immunomodulatory effects of tucaresol on T cell functions are characterized by a bell-shaped dose response curve; the action of the compound is optimal in the 100 to 300 microM range. Analyses of mitogen-stimulated apoptosis demonstrated that the lack of effect of tucaresol at higher doses is not the result of increased cell death, suggesting a role of functional impairment. These data confirm that tucaresol can stimulate T helper cell function and enhance the production of type 1 cytokines, thus eliciting cell-mediated immunity, and warrant its potential utility in the therapy of HIV infection.

Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis

Coliform bacteria detect chemical attractants by means of a membrane-associated cluster of receptors and signalling molecules. We have used recently determined molecular structures, in conjunction with plastic models generated by three-dimensional printer technology, to predict how the proteins of the complex are arranged in relation to the plasma membrane. The proposed structure is a regular two-dimensional lattice in which the cytoplasmic ends of chemotactic-receptor dimers are inserted into a hexagonal array of CheA and CheW molecules. This structure creates separate compartments for adaptation and downstream signalling, and indicates a possible basis for the spread of activity within the cluster.

Effect of two different combinations of antiretrovirals (AZT+ddI and AZT+3TC) on cytokine production and apoptosis in asymptomatic HIV infection

Nineteen HIV-seropositive antiretroviral therapy-naive and asymptomatic individuals (200-500 CD4/microl) were enrolled in a prospective study aimed at analyzing the immunologic and virologic effects of two different combinations of nucleoside reverse transcriptase inhibitors (AZT+ddI and AZT+3TC), and randomly assigned to one of the treatment group. Immunologic (CD4 and CD8 counts, mitogen-stimulated cytokine production, unstimulated and mitogen-stimulated apoptosis) and virologic (HIV viral load) determinations were performed pre-therapy and 15, 30, 90, 200 and 360 days after initiation of therapy. Results showed that the two combinations had comparable effects on increasing CD4 counts and the CD4/CD8 ratio and in reducing HIV viral load. In contrast, AZT+3TC was more efficient in improving interleukin-2 (IL-2) and interferon gamma (IFNgamma) production as well as the type 1/type 2 cytokine ratio and in down modulating the susceptibility of peripheral blood mononuclear cells to in vitro mitogen-stimulated apoptotic cell death. These data suggest that the combination of AZT+3TC has a stronger effect on potentially beneficial immune parameters (IL-2 production; reduction of apoptosis) than the one between AZT+ddI. The combination of AZT+3TC could be more advantageous in the therapy of HIV infection even when used in association with a protease inhibitor.

Intrapartum and neonatal single-dose nevirapine compared with zidovudine for prevention of mother-to-child transmission of HIV-1 in Kampala, Uganda: HIVNET 012 randomised trial

BACKGROUND

The AIDS Clinical Trials Group protocol 076 zidovudine prophylaxis regimen for HIV-1-infected pregnant women and their babies has been associated with a significant decrease in vertical HIV-1 transmission in non-breastfeeding women in developed countries. We compared the safety and efficacy of short-course nevirapine or zidovudine during labour and the first week of life.

METHODS

From November, 1997, to April, 1999, we enrolled 626 HIV-1-infected pregnant women at Mulago Hospital in Kampala, Uganda. We randomly assigned mothers nevirapine 200 mg orally at onset of labour and 2 mg/kg to babies within 72 h of birth, or zidovudine 600 mg orally to the mother at onset of labour and 300 mg every 3 h until delivery, and 4 mg/kg orally twice daily to babies for 7 days after birth. We tested babies for HIV-1 infection at birth, 6-8 weeks, and 14-16 weeks by HIV-1 RNA PCR. We assessed HIV-1 transmission and HIV-1-free survival with Kaplan-Meier analysis.

FINDINGS

Nearly all babies (98.8%) were breastfed, and 95.6% were still breastfeeding at age 14-16 weeks. The estimated risks of HIV-1 transmission in the zidovudine and nevirapine groups were: 10.4% and 8.2% at birth (p=0.354); 21.3% and 11.9% by age 6-8 weeks (p=0.0027); and 25.1% and 13.1% by age 14-16 weeks (p=0.0006). The efficacy of nevirapine compared with zidovudine was 47% (95% CI 20-64) up to age 14-16 weeks. The two regimens were well tolerated and adverse events were similar in the two groups.

INTERPRETATION

Nevirapine lowered the risk of HIV-1 transmission during the first 14-16 weeks of life by nearly 50% in a breastfeeding population. This simple and inexpensive regimen could decrease mother-to-child HIV-1 transmission in less-developed countries.

Heightened sensitivity of a lattice of membrane receptors

Receptor proteins in both eukaryotic and prokaryotic cells have been found to form two-dimensional clusters in the plasma membrane. In this study, we examine the proposition that such clusters might show coordinated responses because of the spread of conformational states from one receptor to its neighbors. A Monte Carlo simulation was developed in which receptors flipped in probabilistic fashion between an active and an inactive state. Conformational energies depended on (i) ligand binding, (ii) a chemical modification of the receptor conferring adaptation, and (iii) the activity of neighboring receptors. Rate constants were based on data from known biological receptors, especially the bacterial Tar receptor, and on theoretical constraints derived from an analogous Ising model. The simulated system showed a greatly enhanced sensitivity to external signals compared with a corresponding set of uncoupled receptors and was operational over a much wider range of ambient concentrations. These and other properties should make a lattice of conformationally coupled receptors ideally suited to act as a "nose" by which a cell can detect and respond to extracellular stimuli.

A free-energy-based stochastic simulation of the Tar receptor complex

We recently developed a stochastic-based program that allows individual molecules in a cell signalling pathway to be simulated. This program has now been used to model the Tar complex, a multimeric signalling complex employed by coliform bacteria. This complex acts as a solid-state computational cassette, integrating and disseminating information on the presence of attractants and repellents in the environment of the bacterium. In our model, the Tar complex exists in one of two conformations which differ in the rate at which they generate labile phosphate groups and hence signal to the flagellar motor. Individual inputs to the complex (aspartate binding, methylation at different sites, binding of CheB, CheR and CheY) are represented as binary flags, and each combination of flags confers a different free energy to the two conformations. Binding and catalysis by the complex are performed stochastically according to the complete set of known reactions allowing the swimming performance of the bacterium to be predicted. The assumption of two conformational states together with the use of free energy values allows us to bring together seemingly unrelated experimental parameters. Because of thermodynamic constraints, we find that the binding affinity for aspartate is linked to changes in phosphorylation activity. We estimate the pattern of Tar methylation and effective affinity constant of receptors over a range of aspartate levels. We also obtain evidence that both the methylating and demethylating enzymes must operate exclusively on one or other of the two conformations, and that sites of methylation of the complex are occupied in sequential order rather than independently. Detailed analysis of the response to aspartate reveals several quantitative discrepancies between simulated and experimental data which indicate areas for future research.

Computer-aided resolution of an experimental paradox in bacterial chemotaxis

Escherichia coli responds to its environment by means of a network of intracellular reactions which process signals from membrane-bound receptors and relay them to the flagellar motors. Although characterization of the reactions in the chemotaxis signaling pathway is sufficiently complete to construct computer simulations that predict the phenotypes of mutant strains with a high degree of accuracy, two previous experimental investigations of the activity remaining upon genetic deletion of multiple signaling components yielded several contradictory results (M. P. Conley, A. J. Wolfe, D. F. Blair, and H. C. Berg, J. Bacteriol. 171:5190-5193, 1989; J. D. Liu and J. S. Parkinson, Proc. Natl. Acad. Sci. USA 86:8703-8707, 1989). For example, "building up" the pathway by adding back CheA and CheY to a gutted strain lacking chemotaxis genes resulted in counterclockwise flagellar rotation whereas "breaking down" the pathway by deleting chemotaxis genes except cheA and cheY resulted in alternating episodes of clockwise and counterclockwise flagellar rotation. Our computer simulation predicts that trace amounts of CheZ expressed in the gutted strain could account for this difference. We tested this explanation experimentally by constructing a mutant containing a new deletion of the che genes that cannot express CheZ and verified that the behavior of strains built up from the new deletion does in fact conform to both the phenotypes observed for breakdown strains and computer-generated predictions. Our findings consolidate the present view of the chemotaxis signaling pathway and highlight the utility of molecularly based computer models in the analysis of complex biochemical networks.

Signaling complexes: biophysical constraints on intracellular communication

This review surveys the kinds of protein complex that participate in cell communication and identifies, where possible, general principles by which they form and act. It also advances the notion that biophysical constraints imposed by macromolecular crowding and diffusion have had a controlling influence on the evolution of cell signaling pathways. Complexes associated with the bacterial aspartate receptor, with eucaryotic tyrosine kinase receptors, with T-cell receptors, and with focal contacts are examined together with proteins that serve as adaptors, anchors, and scaffolds for signaling complexes. The importance of diffusion in controlling the numbers and locations of signaling complexes is discussed, as is the special role played by membranes in signaling pathways.

Predicting temporal fluctuations in an intracellular signalling pathway

We used a newly developed stochastic-based program to predict the fluctuations in numbers of molecules in a chemotactic signalling pathway of coliform bacteria. Specifically, we examined temporal changes in molecules of CheYp, a cytoplasmic protein known to influence the direction of rotation of the flagellar motor. Signalling molecules in the vicinity of a flagellar motor were represented as individual software objects interacting according to probabilities derived from experimentally-observed concentrations rate constants. The simulated CheYp molecules were found to undergo random fluctuations in number about an average corresponding to the deterministically calculated concentration. Both the relative amplitude of the fluctuations, as a proportion of the total number of molecules, and their average duration, increased as the simulated volume was reduced. In a simulation corresponding to 10% of the volume of a bacterium, the average duration of fluctuations was found to be 80.7 ms, which is much shorter than the observed alternations between clockwise and counter clockwise rotations of tethered bacteria (typically 2.6 s). Our results are therefore not in agreement with a simple threshold-crossing model for motor switching. However, it is possible to filter the CheYp fluctuations to produce temporal distributions closer to the observed swimming behaviour and we discuss the possible implications for the control of motor rotation.

Receptor clustering as a cellular mechanism to control sensitivity

Chemotactic bacteria such as Escherichia coli can detect and respond to extremely low concentrations of attractants, concentrations of less than 5 nM in the case of aspartate. They also sense gradients of attractants extending over five orders of magnitude in concentration (up to 1 mM aspartate). Here we consider the possibility that this combination of sensitivity and range of response depends on the clustering of chemotactic receptors on the surface of the bacterium. We examine what will happen if ligand binding changes the activity of a receptor, propagating this change in activity to neighbouring receptors in a cluster. Calculations based on these assumptions show that sensitivity to extracellular ligands increases with the extent of spread of activity through an array of receptors, but that the range of concentrations over which the array works is severely diminished. However, a combination of low threshold of response and wide dynamic range can be attained if the cell has both clusters and single receptors on its surface, particularly if the extent of activity spread can adapt to external conditions. A mechanism of this kind can account quantitatively for the sensitivity and response range of E. coli to aspartate.

Origins of individual swimming behavior in bacteria

Cells in a cloned population of coliform bacteria exhibit a wide range of swimming behaviors--a form of non-genetic individuality. We used computer models to examine the proposition that these variations are due to differences in the number of chemotaxis signaling molecules from one cell to the next. Simulations were run in which the concentrations of seven gene products in the chemotaxis pathway were changed either deterministically or stochastically, with the changes derived from independent normal distributions. Computer models with two adaptation mechanisms were compared with experimental results from observations on individuals drawn from genetically identical populations. The range of swimming behavior predicted for cells with a standard deviation of protein copy number per cell of 10% of the mean was found to match closely the experimental range of the wild-type population. We also make predictions for the swimming behaviors of mutant strains lacking the adaptational mechanism that can be tested experimentally.

Computer-based analysis of the binding steps in protein complex formation

Computer models were used to examine whether and under what conditions the multimeric protein complex is inhibited by high concentrations of one of its components-an effect analogous to the prozone phenomenon in precipitin tests. A series of idealized simple "ball-and-stick" structures representing small oligomeric complexes of protein molecules formed by reversible binding reactions were analyzed to determine the binding steps leading to each structure. The equilibrium state of each system was then determined over a range of starting concentrations and Kds and the steady-state concentration of structurally complete oligomer calculated for each situation. A strong inhibitory effect at high concentrations was shown by any protein molecule forming a bridge between two or more separable parts of the complex. By contrast, proteins linked to the outside of the complex by a single bond showed no inhibition whatsoever at any concentration. Nonbridging, multivalent proteins in the body of the complex could show an inhibitory effect or not depending on the structure of the complex and the strength of its bonds. On the basis of this study, we suggest that the prozone phenomenon will occur widely in living cells and that it could be a crucial factor in the regulation of protein complex formation.

The riddle of slow transport — an introduction

The three articles in this debate section are intended to be read as a unit. Dennis Bray's introduction sets the scene, then Baas and Brown (pages 380-384) and Hirokawa et al. (pages 384-388) argue in favour of two different models for the mechanism by which the microtubules, microfilaments and neurofilaments that make up the neuronal cytoskeleton are transported along axons. These discussions frequently involve very different interpretations of the same experiments, and finding the real answer is a complicated task. As Dennis Bray says, it's a fascinating riddle, and we hope that you will enjoy thinking about possible solutions.

A computer program for the analysis of protein complex formation

MOTIVATION

We needed an efficient way to explore the binding reactions leading to protein complexes of known composition and structure.

RESULTS

A new program is described that allows the user to define a set of protein elements and to link these elements into an oligomeric 'ball-and-stick' assembly in a graphical interface. Once the structure of the oligomer has been defined, the program then employs a novel algorithm to deduce the binding reactions and intermediate complexes needed to make the oligomer from its starting protein components. The program also finds the equilibrium state of the system, using either default starting concentrations and Kd values or data supplied by the user.

Implementing a directly observed therapy program in an urban community hospital

St. Clare's Health and Hospital Center has implemented a directly observed therapy (DOT) program for a challenging urban population of largely HIV+ patients in response to a need for the prevention of the spread of multidrug-resistant tuberculosis in the population. Identified treatment barriers are needs of patient subgroups within the population. Issues in the implementation include: patient compliance, effectiveness of patient identification and follow-up, and continuity of care. Challenges to continuity of care include patients signing out of the hospital against medical advice and missed clinic appointments. Patient identification and follow-up is enhanced by coordinating DOT treatment with the methadone maintenance treatment program.

The dynamics of growing axons. Membrane biophysics

Experiments with laser optical tweezers throw light on the old question of where membrane is added in a growing nerve axon.

Computer analysis of the binding reactions leading to a transmembrane receptor-linked multiprotein complex involved in bacterial chemotaxis

The chemotactic response of bacteria is mediated by complexes containing two molecules each of a transmembrane receptor and the intracellular signaling proteins CheA and CheW. Mutants in which one or the other of the proteins of this complex are absent, inactive, or expressed at elevated amounts show altered chemotactic behavior and the phenotypes are difficult to interpret for some overexpression mutants. We have examined the possibility that these unexpected phenotypes might arise from the binding steps that lead to active complex formation. A limited genetic algorithm was used to search for sets of binding reactions and associated binding constants expected to give mutant phenotypes in accord with experimental data. Different sets of binding equilibria and different assumptions about the activity of particular receptor complexes were tried. Computer analysis demonstrated that it is possible to obtain sets of binding equilibria consistent with the observed phenotypes and provided a simple explanation for these phenotypes in terms of the distribution of active and inactive complexes formed under various conditions. Optimization methods of this kind offer a unique way to analyze reactions taking place inside living cells based on behavioral data.

Protein molecules as computational elements in living cells

Many proteins in living cells appear to have as their primary function the transfer and processing of information, rather than the chemical transformation of metabolic intermediates or the building of cellular structures. Such proteins are functionally linked through allosteric or other mechanisms into biochemical 'circuits' that perform a variety of simple computational tasks including amplification, integration and information storage.

Rapid numerical integration algorithm for finding the equilibrium state of a system of coupled binding reactions

We have adapted a simple method of numerical integration to predict the equilibrium state of a population of components undergoing reversible association according to the Law of Mass Action. Its particular application is to populations of protein molecules in aqueous solution. The method is based on Euler integration but employs an adaptive step size: the time increment being reduced if it would make the concentration of any component negative and increased while the concentration of any component changes at greater than a specified rate. Parameters of the algorithm have been optimized empirically using a model set of binding equilibria with dissociation constants ranging from 10(-5) M to 10(-9) M. The method obtains the solution to a set of binding equilibria more rapidly than the conventional initial value methods (simple Euler, 4th order Runge-Kutta and variable-step Runge-Kutta methods were tested) for the same accuracy. A computer code in standard C is presented.

Computer simulated evolution of a network of cell-signaling molecules

We have trained a computer model of a simple cell-signaling pathway to give specified responses to a pulse of an extracellular ligand. The pathway consists of two initially identical membrane receptors, each of which relays the concentration of the ligand to the level of phosphorylation of an intracellular molecule. Application of random "mutational" changes to the rate constants of the pathway, followed by selection in favor of certain outputs, generates a variety of wave forms and dose-response curves. The phenotypic effect of mutations and the frequency of selection both affect the efficiency with which the pathway achieves its target. When the pathway is trained to give a maximal response at a specific concentration of the stimulating ligand, it gives a consistent pattern of changes in which the two receptors diverge, producing a high-affinity form with excitatory output and a low-affinity form with inhibitory output. We suggest that some high- and low-affinity forms of receptors found in present-day cells might have originated by a similar process.