Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants

The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs1-3, but also revealed how quickly viral escape can curtail effective options4,5. With the emergence of the SARS-CoV-2 Omicron variant in late 2021, many clinically used antibody drug products lost potency, including Evusheld™ and its constituent, cilgavimab4,6. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4 and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies with a known clinical profile to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign COV2-2130 to rescue in vivo efficacy against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the contemporaneously dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and many variants of concern that subsequently emerged, and provides protection in vivo against the strains tested, WA1/2020, BA.1.1, and BA.5. Deep mutational scanning of tens of thousands pseudovirus variants reveals 2130-1-0114-112 improves broad potency without incurring additional escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Because our approach is computationally driven, not requiring experimental iterations or pre-existing binding data, it could enable rapid response strategies to address escape variants or pre-emptively mitigate escape vulnerabilities.

Temperature-related chest pain presentations and future projections with climate change

Background

Climate change has led to increased interest in studying adverse health effects relating to ambient temperatures. It is unclear whether incident chest pain is associated with non-optimal temperatures and how chest pain presentation rates might be affected by climate change.

Methods

The study included ambulance data of chest pain presentations in Melbourne, Australia from 1/1/2015 to 30/6/2019 with linkage to hospital and emergency discharge diagnosis data. A time series quasi-Poisson regression with a distributed lag nonlinear model was fitted to assess the temperature-chest pain presentation associations, after adjusting for season, day of the week and long-term trend. Future excess chest pain presentations associated with cold and heat were projected under six general circulation models under medium and high emission scenarios.

Results

In 206,789 chest pain presentations, mean (SD) age was 61.2 (18.9) years and 50.3% were female. Significant heat- and cold-related increased risk of chest pain presentations were observed for mean air temperatures above and below 20.8°C, respectively (Figure 1). Excess chest pain presentations related to heat were observed in all subgroups, but appeared to be attenuated for older patients (≥70 years) and patients of higher socioeconomic status (SES). We projected no significant change in net temperature-related chest pain presentations with climate change under medium- and high-emission scenarios, with increases in heat-related chest pain presentations offset by decreases in chest pain presentations related to cold temperatures.

Conclusions

Heat- and cold-exposure appear to increase risk of chest pain presentations, especially among younger patients and patients of lower SES. In Melbourne, Australia, chest pain presentations overall were not projected to increase with climate change, but increases in heat-related chest pain presentations highlight the importance of risk mitigation strategies to minimise adverse health impacts on hotter days.

Funding Acknowledgement

Type of funding sources: Public hospital(s). Main funding source(s): Alfred Health.

Impact of ambulance off-load delays on mortality in patients with chest pain

Background

Ambulance off-load delays in transferring patient care to emergency departments (EDs) are increasingly common, but it is unclear whether clinical outcomes are impacted.

Methods

Population-based cohort study of ambulance attendances for non-traumatic chest pain transported to ED in Victoria, Australia (1/1/2015–30/6/2019) excluding patients transported to hospital with “lights and sirens” or triaged as ED category 1. Multivariable models were used to assess the relationship between ambulance off-load times and 30-day mortality and ambulance re-attendance for chest pain.

Results

The study included 213,544 ambulance attendances for chest pain (mean age 62 [SD 18] years; 51% female). Median ambulance off-load times increased across the study period from 21 minutes (interquartile range [IQR] 15–30) in 2015 to 24 minutes (IQR 17–37) in 2019. Patients were divided into tertiles according to off-load times with 69,247 patients included in tertile 1 (0–17 minutes), 73,109 patients in tertile 2 (18–28 minutes), and 71,188 patients in tertile 3 (>28 minutes). In multivariable models, ambulance off-load delays were associated with higher unadjusted and adjusted rates of 30-day mortality (1.57% tertile 3 vs. 1.29% tertile 1, adjusted risk difference 0.28% [95% CI 0.16% - 0.42%], p<0.001) and ambulance re-attendance for chest pain (9.89% tertile 3 vs. 8.59% tertile 1, adjusted risk difference 1.30% [95% CI 1.00% - 1.61%], p<0.001). Similarly, in analysis using off-load times as a continuous variable with restricted cubic splines, a non-linear increase in adjusted odds ratio for mortality was observed (Figure 1).

Conclusions

Delays in ambulance off-load times appear to be associated with increased mortality and ambulance re-attendance risk among chest pain cohorts. This study has important policy implications given the increasing frequency of off-load delays in many healthcare settings.

Funding Acknowledgement

Type of funding sources: Public hospital(s). Main funding source(s): Alfred health

Variation in health-care quality and outcomes according to time of chest pain presentation: a state-wide prospective cohort study

Background

Previous studies examining temporal variation in cardiovascular care have largely been limited to assessing weekend and after-hours effects whereby those presenting on the weekend or after-hours have a poorer outcome. However, emerging evidence suggests more complex patterns in patterns and outcomes may exist.

Purpose

We aimed to determine patterns of temporal variation in chest pain presentations and subsequent health-care quality and outcomes.

Methods

This was an observational, prospective-cohort study of adult patients aged 18 and over who were attended by emergency medical services for non-traumatic chest pain between 1 January 2015 and 30 June 2019 in Victoria, Australia. Major exclusion criteria included pre-hospital diagnosis of ST elevation myocardial infarction or an out of hospital cardiac arrest. The exposure variable was time of day and day of week stratified into 168 hourly time periods. The primary outcome measure was 30-day mortality.

Results

The study cohort comprised 196,365 ambulance attendances for acute non-traumatic chest pain; mean age 62.4 years (SD 18.3) and 99,497 (50.7%) females. Three temporal patterns were observed for chest pain presentations (Figure 1): (1) a diurnal pattern with a sharp increase in presentations from 8 am, peaking around midday, before decreasing into late evening with a nadir between 3–4 am, (2) a weekend effect where Saturday and Sunday had a relatively lower rate of presentations compared to during the week, and (3) a Monday – Sunday gradient where more presentations were likely earlier in the week, than later. Six patterns were identified across pre-hospital and hospital key performance indicators (KPI) (diurnal, in/after-hours, weekend effect, Monday – Sunday gradient, a peak period and morning vs afternoon/evening effect. Risk of 30-day mortality was associated with weekend presentation (OR 1.15, 95% CI 1.06–1.24, p=0.001) and morning presentation between midnight and midday (OR 1.17, 95% CI 1.09–1.25, p<0.001) (Figure 2).

Conclusion

Chest pain presentations, care quality and outcomes demonstrate complex temporal variation beyond the already established weekend and after-hours effect. Such relationships should be considered during resource allocation and quality improvement programs in order to improve treatment quality across all days and times of the week.

Funding Acknowledgement

Type of funding sources: None.

LB9. Longitudinal antibody dynamics in children infected with SARS-CoV-2 through 6 months post-infection

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection elicits antibodies (Abs) that bind several viral proteins such as the spike entry protein and the abundant nucleocapsid (N) protein. We examined convalescent sera collected through 6 months (~24wks) post-SARS-CoV-2 infection in children to evaluate changes in neutralization potency and N-binding.

Methods

Outpatient, hospitalized, and community recruited volunteers < 18 years with COVID-19 were enrolled in a longitudinal study at Seattle Children’s Hospital. Analysis includes symptomatic and asymptomatic children with laboratory-confirmed SARS-CoV-2 infection who provided blood samples at approximately 4wks (range: 2-18wks, IQR:4-8wks) and 24 wks (range: 23-35wks, IQR:25-27wks) after diagnosis. We measured neutralizing Ab using an in-house pseudoneutralization assay and anti-N binding Ab using the Abbott Architect assay.

Results

Of 32 children enrolled between April 2020 and January 2021, 27 had no underlying immunocompromised state and 25 of these 27 children had symptomatic disease. Ten of 27 had a > 2-fold decrease neutralization titers between 4 and 24wks (most were < 10-fold); 12 had < 2-fold change; and 5 had neutralization titers that increased > 2-fold over time (Fig. 1A). All but one of these 27 children had detectable neutralizing activity at 24wks. Anti-N Abs were assessed for 25 children at 4wks and 17 children at 24wks (data pending for 14 samples); all children with paired samples had a > 1.75-fold Abbott index reduction at 24wks, and 5 children had no detectable anti-N Abs by 24wks (Fig. 2A). An additional 5 children with symptomatic disease had complicating immunosuppression or multiple blood transfusions; 2 had decreasing neutralizing titers, 2 increased, and 1 had no change (Fig. 1B). Anti-N Abs were undetectable for one child by 24wks (data pending for 4 samples) (Fig. 2B). No participants received COVID-19 vaccine.

Figure 1. Pseusoneutralization titers in children over time.

Figure 2. Nucleocapsid-binding antibody titers in children over time.

Conclusion

We show neutralizing Abs wane to a small degree over 24wks post-SARS-CoV-2 infection and remain detectable in most children. In contrast, anti-N Abs decreased, becoming undetectable in some children by 24wks. These findings add to understanding of the natural history of SARS-CoV-2 immunity in children.

* This study was supported by CDC BAA75D301-20-R-67897

Disclosures

Jesse Bloom, PhD, Flagship Labs 77 (Consultant)Moderna (Consultant) Janet A. Englund, MD, AstraZeneca (Consultant, Grant/Research Support)GlaxoSmithKline (Research Grant or Support)Meissa Vaccines (Consultant)Pfizer (Research Grant or Support)Sanofi Pasteur (Consultant)Teva Pharmaceuticals (Consultant)

Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines

Understanding vaccine-elicited protection against SARS-CoV-2 variants and other sarbecoviruses is key for guiding public health policies. We show that a clinical stage multivalent SARS-CoV-2 spike receptor-binding domain nanoparticle (RBD-NP) vaccine protects mice from SARS-CoV-2 challenge after a single immunization, indicating a potential dose-sparing strategy. We benchmarked serum neutralizing activity elicited by RBD-NPs in non-human primates against a lead prefusion-stabilized SARS-CoV-2 spike (HexaPro) using a panel of circulating mutants. Polyclonal antibodies elicited by both vaccines are similarly resilient to many RBD residue substitutions tested, although mutations at and surrounding position 484 have negative consequences for neutralization. Mosaic and cocktail nanoparticle immunogens displaying multiple sarbecovirus RBDs elicit broad neutralizing activity in mice and protect mice against SARS-CoV challenge even in the absence of SARS-CoV RBD in the vaccine. This study provides proof of principle that multivalent sarbecovirus RBD-NPs induce heterotypic protection and motivates advancing such broadly protective sarbecovirus vaccines to the clinic.

A(H1N1)pdm09 influenza viruses replicating in ferret upper or lower respiratory tract differed in onward transmission potential by air

BACKGROUND

A(H1N1)pdm09 influenza viruses replicate efficiently in respiratory epithelia and are transmitted via respiratory droplets and aerosols expelled by infected hosts. The relative onward transmission potential of influenza viruses replicating in the upper and lower respiratory epithelial cells has not been fully defined.

METHODS

Wild-type and barcoded A(H1N1)pdm09 viruses that differed by 2 synonymous mutations per gene segment were inoculated into ferrets via intra-nasal and intra-tracheal routes. Naïve recipients were exposed to the exhaled breath of inoculated donors for 8 hours on day 2 post-inoculation. Onward transmission potential of wild-type and barcoded genotypes were monitored by next generation sequencing.

RESULTS

Transmissible airborne particles were respired from the upper but not the lower respiratory epithelial cells of donor ferrets. There was limited mixing of viral populations replicating in the upper and lower respiratory tissues.

CONCLUSIONS

The ferret upper respiratory epithelium was mapped as the anatomic site that generated influenza virus-laden particles mediating onward transmission by air. Our results suggest that vaccines and antivirals should aim to reduce viral loads in the upper respiratory tract for prevention of influenza transmission.

Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines

Understanding the ability of SARS-CoV-2 vaccine-elicited antibodies to neutralize and protect against emerging variants of concern and other sarbecoviruses is key for guiding vaccine development decisions and public health policies. We show that a clinical stage multivalent SARS-CoV-2 receptor-binding domain nanoparticle vaccine (SARS-CoV-2 RBD-NP) protects mice from SARS-CoV-2-induced disease after a single shot, indicating that the vaccine could allow dose-sparing. SARS-CoV-2 RBD-NP elicits high antibody titers in two non-human primate (NHP) models against multiple distinct RBD antigenic sites known to be recognized by neutralizing antibodies. We benchmarked NHP serum neutralizing activity elicited by RBD-NP against a lead prefusion-stabilized SARS-CoV-2 spike immunogen using a panel of single-residue spike mutants detected in clinical isolates as well as the B.1.1.7 and B.1.351 variants of concern. Polyclonal antibodies elicited by both vaccines are resilient to most RBD mutations tested, but the E484K substitution has similar negative consequences for neutralization, and exhibit modest but comparable neutralization breadth against distantly related sarbecoviruses. We demonstrate that mosaic and cocktail sarbecovirus RBD-NPs elicit broad sarbecovirus neutralizing activity, including against the SARS-CoV-2 B.1.351 variant, and protect mice against severe SARS-CoV challenge even in the absence of the SARS-CoV RBD in the vaccine. This study provides proof of principle that sarbecovirus RBD-NPs induce heterotypic protection and enables advancement of broadly protective sarbecovirus vaccines to the clinic.

Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail

The SARS-CoV-2 pandemic has led to an urgent need to understand the molecular basis for immune recognition of SARS-CoV-2 spike (S) glycoprotein antigenic sites. To define the genetic and structural basis for SARS-CoV-2 neutralization, we determined the structures of two human monoclonal antibodies COV2-2196 and COV2-21301, which form the basis of the investigational antibody cocktail AZD7442, in complex with the receptor binding domain (RBD) of SARS-CoV-2. COV2-2196 forms an 'aromatic cage' at the heavy/light chain interface using germline-encoded residues in complementarity determining regions (CDRs) 2 and 3 of the heavy chain and CDRs 1 and 3 of the light chain. These structural features explain why highly similar antibodies (public clonotypes) have been isolated from multiple individuals1-4. The structure of COV2-2130 reveals that an unusually long LCDR1 and HCDR3 make interactions with the opposite face of the RBD from that of COV2-2196. Using deep mutational scanning and neutralization escape selection experiments, we comprehensively mapped the critical residues of both antibodies and identified positions of concern for possible viral escape. Nonetheless, both COV2-2196 and COV2130 showed strong neutralizing activity against SARS-CoV-2 strain with recent variations of concern including E484K, N501Y, and D614G substitutions. These studies reveal germline-encoded antibody features enabling recognition of the RBD and demonstrate the activity of a cocktail like AZD7442 in preventing escape from emerging variant viruses.

P960Association of peri-procedural intravenous morphine use on clinical outcomes in ST-elevation myocardial infarction treated by percutaneous coronary intervention: systematic review and meta-analysis

Background

Morphine analgesia may affect absorption of co-prescribed P2Y12 antagonists attenuating platelet inhibition. The impact of peri-procedural intravenous (IV) morphine administration on clinical outcomes in patients undergoing primary percutaneous coronary intervention (PPCI) for ST-elevation myocardial infarction (STEMI) is not well defined.

Purpose

To conduct a systematic review and meta-analysis exploring clinical outcomes with peri-procedural IV morphine in patients undergoing PPCI for STEMI.

Methods

Analysis of the electronic databases MEDLINE, EMBASE, CENTRAL, Scopus, Web of Science and ClinicalTrials.gov for association of peri-PCI IV morphine use with myocardial infarction (MI) and mortality. Primary and secondary outcomes were in-hospital or 30-day MI and all-cause mortality respectively.

Results

Eleven studies (1 randomised controlled trial; 10 cohort studies) were included for systematic review. Five studies, including 3,748 patients were included in meta-analysis of the primary outcome. Of 3,748 patients, 2,239 were treated concurrently with ticagrelor, 1,256 treated with clopidogrel and 253 with prasugrel. As shown in the Figure, there was a trend towards increased risk of myocardial infarction with IV morphine (odds ratio 1.88; 95% CI 0.87–4.09, I2 0%). Across seven studies and 6585 patients, no increased risk of mortality at the same composite time endpoint was evident (odds ratio 0.70, 95% CI 0.40–1.23, I2 19%).

Figure 1. MI in hospital or at 30 days

Conclusion

Based on current literature, evidence of an association between IV morphine and myocardial infarction in patients undergoing PPCI for STEMI is limited by observational methodology and conflicting results. There is no evidence of an association between intravenous peri-procedural morphine and mortality. Clinical trial evidence with strong documentation of adverse events data is required to demonstrate association or causality.

Acknowledgement/Funding

None

Influenza Immunizations in the Elderly: A Continuous Quality Improvement Project

As part of the continuous quality improvement program at The Toronto Hospital’s Department of Family & Community Medicine (TTH-DFCM), it was considered necessary to examine the structures, processes and outcomes of influenza immunization for the elderly. Objective: The study sought to (a) document the current influenza immunization process; (b) quantify influenza immunization rates for elderly patients during two consecutive immunization seasons (1996 and 1997), and compare these rates across physician teams, attending staff vs. residents, patient gender, and patient age groups; (c) compare influenza immunization rates with other centers; and (d) identify barriers and propose solutions to improve influenza immunization rates in the elderly. Design: Evaluation Formative Research. Setting: A computerized roster of 15,000 patients at The Toronto Hospital, Department of Family and Community Medicine, a University of Toronto academic teaching center. Participants: Active patients age 65 years and over. Dependent variable: Influenza immunization. Independent variables: Physician Teams, Physician status, Patient gender, and Patient age group. Results: Immunization rates of attendees increased from 75.4% to 78.7%; over 3% increase from 1996 to 1997. Major subgroups which benefited from increased immunization rates were patients in the Blue team, patients age 70-74 years, and female patients. Conclusion: This study presents a rigorous examination of the components of the influenza immunization program, and demonstrates improved immunization rates over a two-year period. Suggestions for future action have been identified. The study design can also serve as a model for future clinical quality improvement projects.

Premenopausal Breast Cancer: Exercise and Leukocyte Telomere Length

Leukocyte telomere length (LTL) may function as a marker of health, the immune system and cancer survival. We evaluated whether premenopausal breast cancer survivors (PBCS) that successfully increased exercise levels also increased LTL. This study is the first to describe LTLs in a population-based sample of PBCS before and after an exercise intervention. We analyzed LTL before and after the Exercise for Bone Health Intervention, a randomized, controlled trial of 273 premenopausal women 55 years of age or younger at diagnosis that started the intervention within 2 years of receipt of initial chemotherapy. This pilot analysis included 60 women with the greatest increase in exercise from pre to post intervention. Those with longer LTLs at pre-intervention (PRE) had LTLs that grew shorter during the study, however, they still had longer LTLs at post-intervention (POST) than those who started with shorter LTLs. The group whose LTLs shortened the most during the study were those with longer LTLs and more exercise at PRE, ANOVA across four levels P = 0.030. In multivariable regression models of LTL change adjusted for age and LTL at PRE, factors that were independently associated with LTLs that became shorter were older age (P = 0.017), longer telomeres at PRE (P = 0.0004), higher levels of exercise (P = 0.013), higher income (P = 0.011), feeling down-hearted and blue (P = 0.003), higher levels of sociability (P = 0.015), more chronic medical conditions (P = 0.018), and higher levels of insulin-like grown factor-1 at POST (P = 0.003). While this is a pilot sub-study and requires additional confirmation, we postulate that women accustomed to exercising and being highly sociable pre-diagnosis may have experienced a greater impact on their lifestyles post-diagnosis resulting in a more rapid rate of LTL shortening. We hypothesize that time to return to LTL homeostasis for YBCS may be dependent upon a combination of physical health and psychosocial networks pre and post diagnosis and the immune system may be an important modifier. Further studies combining new technology to improve the capture of exercise and psychosocial well-being, and monitor levels of inflammation are needed to determine whether lifestyle interventions can be used to impact biomarkers of health in YBCS.

Exercise with compression stockings improves reflux in patients with mild chronic venous insufficiency

Purpose: This study evaluates the effectiveness of calf muscle strengthening with compression stockings on the haemodynamics in patients with venous disease.

Method: Patients were assigned to a protocol of aggressive management of their chronic venous insufficiency (CVI) including compression stockings (Jobst knee high, 30–40 mmHg ankle), intermittent leg elevation, and a supervised calf muscle strengthening programme. Patients underwent baseline air plethysmography (APG) with and without stockings (T1) and SF-12, Aberdeen varicose vein questionnaire and venous severity score. Exercise sessions included a total of 18, 1 h supervised sessions, 2–3 times per week, consisting of 15 min on treadmill, 10 min on a Stairmaster, 10 min on a Nustep, and 5 min on an airdyne bicycle and lower body strength training. The sessions were supervised by an exercise physiologist. At completion, patients underwent a second APG (T2) and a third (T3) one month later, as well as answering questionnaires. A final venous severity score was assigned.

Results: Eleven patients (7M, 4F), 22 limbs, 14 with CVI and eight without CVI, mean age 60, made up this study. Only two patients suffered from postphlebitic syndrome. In all, 10/11 subjects completed the entire protocol. Although no significant differences were noted in any of the APG parameters between T1 and T2 or T2 and T3, there were significant differences when segregating into C2 ( n = 6 patients with eight involved limbs) and C4, 5 ( n = 5 patients with six involved limbs). Concerning the affected extremities, statistically significant decreases in venous volume (VV) with stockings on between T1 and T2, which reverted back to baseline at T3, and in venous filling index (VFI) between T2 and T3 without stockings were noted ( P<0.05) in C2 limbs. Similar findings were not observed in the C4, C5 limbs, with actual increases in these parameters. Greater increases in ejection fraction were noted in C2 limbs than in C4, C5 limbs. Despite the decrease in reflux in C2 limbs, residual volume fraction (RVF) increased in C2 limbs at T2 both with ( P<0.05) and without stockings, while it decreased in C4, C5 limbs with stockings in place. Finally, outflow fraction (OF) increased only in C2 limbs without stockings in place. Regarding the other parameters, all patients noted improvement in swelling by Aberdeen questionnaire, physical health was improved by SF-12 and patients lost a mean of 3.8 lb of weight.

Conclusions: An exercise programme along with compression stockings resulted in a decrease in reflux, especially during the supervised exercise programme, in patients with mild (C2) chronic venous disease. For more extensive disease (C4, C5), the programme tended to decrease RVF.

Growth trajectory of children and adolescents with isolated cleft lip and/or palate through the first two decades of life

A wide body of evidence shows that patients with clefts exhibit decreased growth in their early years. Less evidence regarding their growth trajectory, specifically their body mass indices (BMIs), in later years is available. This study analyzes BMIs of patients with isolated clefts and/or palate over time using age-adjusted BMI z-scores based on the CDC 2000 references for height and weight for age. At least two height and weight measurements were obtained during 2-10 years and at least two height and weight measurements were obtained during 10-20 years. Mean BMI z-score for all patients was 0.117. Males had a mean z-score of 0.087 and females a mean of 0.160 (p=0.407). Patients under 10 years of age had a mean z-score of 0.208, while patients older than 10 years had a mean z-score of -0.028 (p=0.223). While significance was not achieved in the statistical analysis, the results suggest that overall, the cleft population maintains a mean BMI that is similar to that of the general population during childhood and adolescence. A larger analysis is warranted to investigate this phenomenon further and to investigate specifically the rate of obesity within this group.

The interface of protein structure, protein biophysics, and molecular evolution

Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction.

Mucin biopolymers as broad-spectrum antiviral agents

Mucus is a porous biopolymer matrix that coats all wet epithelia in the human body and serves as the first line of defense against many pathogenic bacteria and viruses. However, under certain conditions viruses are able to penetrate this infection barrier, which compromises the protective function of native mucus. Here, we find that isolated porcine gastric mucin polymers, key structural components of native mucus, can protect an underlying cell layer from infection by small viruses such as human papillomavirus (HPV), Merkel cell polyomavirus (MCV), or a strain of influenza A virus. Single particle analysis of virus mobility inside the mucin barrier reveals that this shielding effect is in part based on a retardation of virus diffusion inside the biopolymer matrix. Our findings suggest that purified mucins may be used as a broad-range antiviral supplement to personal hygiene products, baby formula or lubricants to support our immune system.

Survival of patients with glioblastoma multiforme is not influenced by altered expression of p16, p53, EGFR, MDM2 or Bcl-2 genes

Deregulated expression of one or more growth control genes including p16, p53, EGF receptor (EGFR), MDM2 or Bcl-2 may contribute to the treatment resistance phenotype of GBM and generally poor patient survival. Clinically, GBM have been divided into two major groups defined by (1) histologic progression from a low grade tumor ("progressive" or "secondary" GBM) contrasted with (2) those which show initial clinical presentation without a prior history ("de novo" or "primary" GBM). Using molecular genetic analysis for p53 gene mutations together with immunophenotyping for overexpression of EGFR, up to four GBM variants can be distinguished, including the p53+/EGFR- progressive or the p53-/EGFR+ de novo variant. We examined the survival of 80 adult patients diagnosed with astrocytic GBM stratified by age category (>40, 41-60 or 61-80) to determine whether alterations in any one given growth control gene or whether different genetic variants of GBM (progressive versus de novo) were associated with different survival outcomes. Survival testing using Kaplan-Meier plots for GBM patients with or without altered expression of p16, p53, EGFR, MDM2 or Bcl-2 showed no significant differences by age group or by gene expression indicating a lack of prognostic value for GBM. Also the clinical outcome among patients with GBM showed no significant differences within each age category for any GBM variant including the progressive and de novo GBM variants indicating similar biologic behavior despite different genotypes. Using a pairwise comparison, one-third of the GBM with normal p16 expression showed accumulation of MDM2 protein and this association approached statistical significance (0.01 < P < 0.05) using the Bonferroni procedure. These GBM may represent a variant in which the p19ARF/MDM2/p53 pathway may be deregulated rather than the p16/cyclin D-CDK4/Rb pathway.

The elongation of yeast prion fibers involves separable steps of association and conversion

A self-perpetuating change in the conformation of the translation termination factor Sup35p is the basis for the prion [PSI+], a protein-based genetic element of Saccharomyces cerevisiae. In a process closely allied to in vivo conversion, the purified soluble, prion-determining region of Sup35p (NM) converts to amyloid fibers by means of nucleated conformational conversion. First, oligomeric species convert to nuclei, and these nuclei then promote polymerization of soluble protein into amyloid fibers. To elucidate the nature of the polymerization step, we created single-cysteine substitution mutants at different positions in NM to provide unique attachment sites for various probes. In vivo, the mutants behaved like wild-type protein in both the [psi-] and [PSI+] states. In vitro, they assembled with wild-type kinetics and formed fibers with the same morphologies. When labeled with fluorescent probes, two mutants, NMT158C and NME167C, exhibited a change in fluorescence coincident with amyloid assembly. These mutants provided a sensitive measure for the kinetics of fiber elongation, and the lag phase in conversion. The cysteine in the mutant NMK184C remained exposed after assembly. When labeled with biotin and bound to streptavidin beads, it was used to capture radiolabeled soluble NM in the process of conversion. This process established the existence of a detergent-susceptible intermediate in fiber elongation. Thus, the second stage of nucleated conformational conversion, fiber elongation, itself contains at least two steps: the association of soluble protein with preformed fibers to form an assembly intermediate, followed by conformational conversion into amyloid.

Community-based cancer screening for underserved women: design and baseline findings from the Breast and Cervical Cancer Intervention Study

BACKGROUND

Underutilization of breast and cervical cancer screening has been observed in many ethnic groups and underserved populations. Effective community-based interventions are needed to eliminate disparities in screening rates and thus to improve prospects for survival.

METHODS

The Breast and Cervical Cancer Intervention Study was a controlled trial of three interventions in the San Francisco Bay Area from 1993 to 1996: (1) community-based lay health worker outreach; (2) clinic-based provider training and reminder system; and (3) patient navigator for follow-up of abnormal screening results. Study design and a description of the interventions are reported along with baseline results of a household survey conducted in four languages among 1599 women, aged 40-75.

RESULTS

Seventy-six percent of women ages 40 and over had had at least one mammogram, and most had had a clinical breast examination (88%) and Pap smear (89%). Rates were significantly lower for non-English-speaking Latinas and Chinese women (56 and 32%, respectively, for mammography), and maintenance screening (three mammograms in the past 5 years) varied from 7% (non-English-speaking Chinese) to 53% (Blacks). Pap smear screening in the past 3 years was low among non-English-speaking Latinas (72%) and markedly lower among non-English-speaking Chinese women (24%). The strongest predictors of screening behavior were having private health insurance and frequent use of medical services. Having a regular clinic and speaking English were also important. Race/ethnicity, education, household income, and employment status were, overall, not significant predictors of screening behavior.

CONCLUSIONS

These baseline results support the importance of cancer screening interventions targeted to persons of foreign origin, particularly those less acculturated.

Influenza immunizations in the elderly: a continuous quality improvement project

As part of the continuous quality improvement program at The Toronto Hospital's Department of Family & Community Medicine (TTH-DFCM), it was considered necessary to examine the structures, processes and outcomes of influenza immunization for the elderly.

OBJECTIVE

The study sought to (a) document the current influenza immunization process; (b) quantify influenza immunization rates for elderly patients during two consecutive immunization seasons (1996 and 1997), and compare these rates across physician teams, attending staff vs. residents, patient gender, and patient age groups; (c) compare influenza immunization rates with other centers; and (d) identify barriers and propose solutions to improve influenza immunization rates in the elderly.

DESIGN

Evaluation Formative Research.

SETTING

A computerized roster of 15,000 patients at The Toronto Hospital, Department of Family and Community Medicine, a University of Toronto academic teaching center.

PARTICIPANTS

Active patients age 65 years and over.

DEPENDENT VARIABLE

Influenza immunization.

INDEPENDENT VARIABLES

Physician Teams, Physician status, Patient gender, and Patient age group.

RESULTS

Immunization rates of attendees increased from 75.4% to 78.7%; over 3% increase from 1996 to 1997. Major subgroups which benefited from increased immunization rates were patients in the Blue team, patients age 70-74 years, and female patients.

CONCLUSION

This study presents a rigorous examination of the components of the influenza immunization program, and demonstrates improved immunization rates over a two-year period. Suggestions for future action have been identified. The study design can also serve as a model for future clinical quality improvement projects.