Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome

Productive infections by RNA viruses require faithful replication of the entire genome. Yet many RNA viruses also produce deletion-containing viral genomes (DelVGs), aberrant replication products with large internal deletions. DelVGs interfere with the replication of wild-type virus and their presence in patients is associated with better clinical outcomes. The DelVG RNA itself is hypothesized to confer this interfering activity. DelVGs antagonize replication by out-competing the full-length genome and triggering innate immune responses. Here, we identify an additionally inhibitory mechanism mediated by a new class of viral proteins encoded by DelVGs. We identified hundreds of cryptic viral proteins translated from DelVGs. These DelVG-encoded proteins (DPRs) include canonical viral proteins with large internal deletions, as well as proteins with novel C-termini translated from alternative reading frames. Many DPRs retain functional domains shared with their full-length counterparts, suggesting they may have activity during infection. Mechanistic studies of DPRs derived from the influenza virus protein PB2 showed that they poison replication of wild-type virus by acting as dominant-negative inhibitors of the viral polymerase. These findings reveal that DelVGs have a dual inhibitory mechanism, acting at both the RNA and protein level. They further show that DPRs have the potential to dramatically expand the functional proteomes of diverse RNA viruses.

An easy to use tool for the analysis of subcellular mRNA transcript colocalisation in smFISH data

Single molecule fluorescence in situ hybridisation (smFISH) has become a valuable tool to investigate the mRNA expression of single cells. However, it requires a considerable amount of programming expertise to use currently available open-source analytical software packages to extract and analyse quantitative data about transcript expression. Here, we present FISHtoFigure, a new software tool developed specifically for the analysis of mRNA abundance and co-expression in QuPath-quantified, multi-labelled smFISH data. FISHtoFigure facilitates the automated spatial analysis of transcripts of interest, allowing users to analyse populations of cells positive for specific combinations of mRNA targets without the need for computational image analysis expertise. As a proof of concept and to demonstrate the capabilities of this new research tool, we have validated FISHtoFigure in multiple biological systems. We used FISHtoFigure to identify an upregulation in the expression of Cd4 by T-cells in the spleens of mice infected with influenza A virus, before analysing more complex data showing crosstalk between microglia and regulatory B-cells in the brains of mice infected with Trypanosoma brucei brucei. These analyses demonstrate the ease of analysing cell expression profiles using FISHtoFigure and the value of this new tool in the field of smFISH data analysis.

Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome

Productive infections by RNA viruses require faithful replication of the entire genome. Yet many RNA viruses also produce deletion-containing viral genomes (DelVGs), aberrant replication products with large internal deletions. DelVGs interfere with the replication of wild-type virus and their presence in patients is associated with better clinical outcomes as they. The DelVG RNA itself is hypothesized to confer this interfering activity. DelVGs antagonize replication by out-competing the full-length genome and triggering innate immune responses. Here, we identify an additionally inhibitory mechanism mediated by a new class of viral proteins encoded by DelVGs. We identified hundreds of cryptic viral proteins translated from DelVGs. These DelVG-encoded proteins (DPRs) include canonical viral proteins with large internal deletions, as well as proteins with novel C-termini translated from alternative reading frames. Many DPRs retain functional domains shared with their full-length counterparts, suggesting they may have activity during infection. Mechanistic studies of DPRs derived from the influenza virus protein PB2 showed that they poison replication of wild-type virus by acting as dominant-negative inhibitors of the viral polymerase. These findings reveal that DelVGs have a dual inhibitory mechanism, acting at both the RNA and protein level. They further show that DPRs have the potential to dramatically expand the functional proteomes of diverse RNA viruses.

Multiplexed Biosensing of Proteins and Virions with Disposable Plasmonic Assays

Our growing ability to tailor healthcare to the needs of individuals has the potential to transform clinical treatment. However, the measurement of multiple biomarkers to inform clinical decisions requires rapid, effective, and affordable diagnostics. Chronic diseases and rapidly evolving pathogens in a larger population have also escalated the need for improved diagnostic capabilities. Current chemical diagnostics are often performed in centralized facilities and are still dependent on multiple steps, molecular labeling, and detailed analysis, causing the result turnaround time to be over hours and days. Rapid diagnostic kits based on lateral flow devices can return results quickly but are only capable of detecting a handful of pathogens or markers. Herein, we present the use of disposable plasmonics with chiroptical nanostructures as a platform for low-cost, label-free optical biosensing with multiplexing and without the need for flow systems often required in current optical biosensors. We showcase the detection of SARS-CoV-2 in complex media as well as an assay for the Norovirus and Zika virus as an early developmental milestone toward high-throughput, single-step diagnostic kits for differential diagnosis of multiple respiratory viruses and any other emerging diagnostic needs. Diagnostics based on this platform, which we term "disposable plasmonics assays," would be suitable for low-cost screening of multiple pathogens or biomarkers in a near-point-of-care setting.

BTN3A3 evasion promotes the zoonotic potential of influenza A viruses

Spillover events of avian influenza A viruses (IAVs) to humans could represent the first step in a future pandemic1. Several factors that limit the transmission and replication of avian IAVs in mammals have been identified. There are several gaps in our understanding to predict which virus lineages are more likely to cross the species barrier and cause disease in humans1. Here, we identified human BTN3A3 (butyrophilin subfamily 3 member A3)2 as a potent inhibitor of avian IAVs but not human IAVs. We determined that BTN3A3 is expressed in human airways and its antiviral activity evolved in primates. We show that BTN3A3 restriction acts primarily at the early stages of the virus life cycle by inhibiting avian IAV RNA replication. We identified residue 313 in the viral nucleoprotein (NP) as the genetic determinant of BTN3A3 sensitivity (313F or, rarely, 313L in avian viruses) or evasion (313Y or 313V in human viruses). However, avian IAV serotypes, such as H7 and H9, that spilled over into humans also evade BTN3A3 restriction. In these cases, BTN3A3 evasion is due to substitutions (N, H or Q) in NP residue 52 that is adjacent to residue 313 in the NP structure3. Thus, sensitivity or resistance to BTN3A3 is another factor to consider in the risk assessment of the zoonotic potential of avian influenza viruses.

The SARS-CoV-2 Spike Protein Mutation Explorer: using an interactive application to improve the public understanding of SARS-CoV-2 variants of concern

Due to the COVID-19 pandemic the virus responsible, SARS-CoV-2, became a source of intense interest for non-expert audiences. The viral spike protein gained particular public interest as the main target for protective immune responses, including those elicited by vaccines. The rapid evolution of SARS-CoV-2 resulted in variations in the spike that enhanced transmissibility or weakened vaccine protection. This created new variants of concern (VOCs). The emergence of VOCs was studied using viral sequence data which was shared through portals such as the online Mutation Explorer of the COVID-19 Genomics UK consortium (COG-UK/ME). This was designed for an expert audience, but the information it contained could be of general interest if suitably communicated. Visualisations, interactivity and animation can improve engagement and understanding of molecular biology topics, and so we developed a graphical educational resource, the SARS-CoV-2 Spike Protein Mutation Explorer (SSPME), which used interactive 3D molecular models and animations to explain the molecular biology underpinning VOCs. User testing showed that the SSPME had better usability and improved participant knowledge confidence and knowledge acquisition compared to COG-UK/ME. This demonstrates how interactive visualisations can be used for effective molecular biology communication, as well as improving the public understanding of SARS-CoV-2 VOCs.

Virology under the Microscope-a Call for Rational Discourse

Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.

Respiratory viruses: New frontiers-a Keystone Symposia report

Respiratory viruses are a common cause of morbidity and mortality around the world. Viruses like influenza, RSV, and most recently SARS-CoV-2 can rapidly spread through a population, causing acute infection and, in vulnerable populations, severe or chronic disease. Developing effective treatment and prevention strategies often becomes a race against ever-evolving viruses that develop resistance, leaving therapy efficacy either short-lived or relevant for specific viral strains. On June 29 to July 2, 2022, researchers met for the Keystone symposium "Respiratory Viruses: New Frontiers." Researchers presented new insights into viral biology and virus-host interactions to understand the mechanisms of disease and identify novel treatment and prevention approaches that are effective, durable, and broad.

Virology under the Microscope-a Call for Rational Discourse

Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.

Virology under the Microscope-a Call for Rational Discourse

Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.

Superinfection exclusion creates spatially distinct influenza virus populations

Interactions between viruses during coinfections can influence viral fitness and population diversity, as seen in the generation of reassortant pandemic influenza A virus (IAV) strains. However, opportunities for interactions between closely related viruses are limited by a process known as superinfection exclusion (SIE), which blocks coinfection shortly after primary infection. Using IAVs, we asked whether SIE, an effect which occurs at the level of individual cells, could limit interactions between populations of viruses as they spread across multiple cells within a host. To address this, we first measured the kinetics of SIE in individual cells by infecting them sequentially with 2 isogenic IAVs, each encoding a different fluorophore. By varying the interval between addition of the 2 IAVs, we showed that early in infection SIE does not prevent coinfection, but that after this initial lag phase the potential for coinfection decreases exponentially. We then asked how the kinetics of SIE onset controlled coinfections as IAVs spread asynchronously across monolayers of cells. We observed that viruses at individual coinfected foci continued to coinfect cells as they spread, because all new infections were of cells that had not yet established SIE. In contrast, viruses spreading towards each other from separately infected foci could only establish minimal regions of coinfection before reaching cells where coinfection was blocked. This created a pattern of separate foci of infection, which was recapitulated in the lungs of infected mice, and which is likely to be applicable to many other viruses that induce SIE. We conclude that the kinetics of SIE onset segregate spreading viral infections into discrete regions, within which interactions between virus populations can occur freely, and between which they are blocked.

The mutational variety of the live-attenuated influenza vaccine proteome

Influenza viruses evolve rapidly, and for this reason the influenza vaccine needs to be updated every year. It is therefore important to identify where new mutations could be tolerated. To assess this, we asked which mutations could be identified in the proteins that had passed quality checks by being correctly folded, transported and assembled into influenza virus particles. We re-analysed mass spectrometry proteomics data obtained from the virus particles of genetically well-defined vaccine strains and identified point mutations within viral proteins. Point mutations were tolerated in virus particles at appreciable frequencies in proteins of both influenza A and B viruses, including HA, NA, M1, NP, NS1, PA and PB2. Structural analyses were used to assess the likely impact of this protein diversity on the molecular biology of the virus. As would be expected, mutations that were tolerated the virus particle generally occurred at sites that would not be expected to perturb protein function. We suggest that using proteomics to identify sites in viral proteins that either can or cannot tolerate mutations could inform influenza vaccine development by highlighting areas that have the potential for antigenic drift.

Using Molecular Visualisation Techniques to Explain the Molecular Biology of SARS-CoV-2 Spike Protein Mutations to a General Audience

Since the COVID-19 pandemic started in 2019, the virus responsible for the outbreak-SARS-CoV-2-has continued to evolve. Mutations of the virus' spike protein, the main protein driving infectivity and transmissibility, are especially concerning as they may allow the virus to improve its infectivity, transmissibility, and ability to evade the immune system. Understanding how specific molecular changes can alter the behaviour of a virus is challenging for non-experts, but this information helps us to understand the pandemic we are living through and the public health measures and interventions needed to bring it under control. In response to communication challenges arising from the COVID-19 pandemic, we recently developed an online educational application to explain the molecular biology of SARS-CoV-2 spike protein mutations to the general public. We used visualisation techniques such as 3D modelling and animation, which have been shown to be highly effective teaching tools in molecular biology, allowing the viewer to better understand protein structure, function, and dynamics. We also included interactive elements for users to learn actively by engaging with the digital content, and consequently improve information retention.This chapter presents the methodological and technological framework which we used to create this resource, the 'SARS-CoV-2 Spike Protein Mutation Explorer' (SSPME). It explains how molecular visualisation and 3D modelling software were used to develop accurate models of relevant proteins; how 3D animation software was used to accurately visualise the dynamic molecular processes of SARS-CoV-2 infection, transmission, and antibody evasion; and how game development software was used to compile the 3D models and animations into a comprehensive, informative interactive application on SARS-CoV-2 spike protein mutations. This chapter indicates how cutting-edge visualisation techniques and technologies can be used to improve science communication about complex topics in molecular biology and infection biology to the general public, something that is critical to gaining control of the continuing COVID-19 pandemic.

Visualising Viruses

Viruses pose a challenge to our imaginations. They exert a highly visible influence on the world in which we live, but operate at scales we cannot directly perceive and without a clear separation between their own biology and that of their hosts. Communication about viruses is therefore typically grounded in mental images of virus particles. Virus particles, as the infectious stage of the viral replication cycle, can be used to explain many directly observable properties of transmission, infection and immunity. In addition, their often striking beauty can stimulate further interest in virology. The structures of some virus particles have been determined experimentally in great detail, but for many important viruses a detailed description of the virus particle is lacking. This can be because they are challenging to describe with a single experimental method, or simply because of a lack of data. In these cases, methods from medical illustration can be applied to produce detailed visualisations of virus particles which integrate information from multiple sources. Here, we demonstrate how this approach was used to visualise the highly variable virus particles of influenza A viruses and, in the early months of the COVID-19 pandemic, the virus particles of the then newly characterised and poorly described SARS-CoV-2. We show how constructing integrative illustrations of virus particles can challenge our thinking about the biology of viruses, as well as providing tools for science communication, and we provide a set of science communication resources to help visualise two viruses whose effects are extremely apparent to all of us.

Can machine learning augment clinician adjudication of events in cardiovascular trials? A case study of major adverse cardiovascular events (MACE) across CVRM trials

Background and introduction

Accurate identification of clinical outcome events is critical to obtaining reliable results in cardiovascular outcomes trials (CVOTs). Current processes for event adjudication are expensive and hampered by delays. As part of a larger project to more reliably identify outcomes, we evaluated the use of machine learning to automate event adjudication using data from the SOCRATES trial (NCT01994720), a large randomized trial comparing ticagrelor and aspirin in reducing risk of major cardiovascular events after acute ischemic stroke or transient ischemic attack (TIA).

Purpose

We studied whether machine learning algorithms could replicate the outcome of the expert adjudication process for clinical events of ischemic stroke and TIA. Could classification models be trained on historical CVOT data and demonstrate performance comparable to human adjudicators?

Methods

Using data from the SOCRATES trial, multiple machine learning algorithms were tested using grid search and cross validation. Models tested included Support Vector Machines, Random Forest and XGBoost. Performance was assessed on a validation subset of the adjudication data not used for training or testing in model development. Metrics used to evaluate model performance were Receiver Operating Characteristic (ROC), Matthews Correlation Coefficient, Precision and Recall. The contribution of features, attributes of data used by the algorithm as it is trained to classify an event, that contributed to a classification were examined using both Mutual Information and Recursive Feature Elimination.

Results

Classification models were trained on historical CVOT data using adjudicator consensus decision as the ground truth. Best performance was observed on models trained to classify ischemic stroke (ROC 0.95) and TIA (ROC 0.97). Top ranked features that contributed to classification of Ischemic Stroke or TIA corresponded to site investigator decision or variables used to define the event in the trial charter, such as duration of symptoms. Model performance was comparable across the different machine learning algorithms tested with XGBoost demonstrating the best ROC on the validation set for correctly classifying both stroke and TIA.

Conclusions

Our results indicate that machine learning may augment or even replace clinician adjudication in clinical trials, with potential to gain efficiencies, speed up clinical development, and retain reliability. Our current models demonstrate good performance at binary classification of ischemic stroke and TIA within a single CVOT with high consistency and accuracy between automated and clinician adjudication. Further work will focus on harmonizing features between multiple historical clinical trials and training models to classify several different endpoint events across trials. Our aim is to utilize these clinical trial datasets to optimize the delivery of CVOTs in further cardiovascular drug development.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): AstraZenca Plc

Constitutive TRIM22 Expression in the Respiratory Tract Confers a Pre-Existing Defence Against Influenza A Virus Infection

The induction of antiviral effector proteins as part of a homeostatically controlled innate immune response to infection plays a critical role in limiting the propagation and transmission of respiratory pathogens. However, the prolonged induction of this immune response can lead to lung hyperinflammation, tissue damage, and respiratory failure. We hypothesized that tissues exposed to the constant threat of infection may constitutively express higher levels of antiviral effector proteins to reduce the need to activate potentially harmful innate immune defences. By analysing transcriptomic data derived from a range of human tissues, we identify lung tissue to express constitutively higher levels of antiviral effector genes relative to that of other mucosal and non-mucosal tissues. By using primary cell lines and the airways of rhesus macaques, we show the interferon-stimulated antiviral effector protein TRIM22 (TRIpartite Motif 22) to be constitutively expressed in the lung independently of viral infection or innate immune stimulation. These findings contrast with previous reports that have shown TRIM22 expression in laboratory-adapted cell lines to require interferon stimulation. We demonstrate that constitutive levels of TRIM22 are sufficient to inhibit the onset of human and avian influenza A virus (IAV) infection by restricting the onset of viral transcription independently of interferon-mediated innate immune defences. Thus, we identify TRIM22 to confer a pre-existing (intrinsic) intracellular defence against IAV infection in cells derived from the respiratory tract. Our data highlight the importance of tissue-specific and cell-type dependent patterns of pre-existing immune gene expression in the intracellular restriction of IAV from the outset of infection.

Targeted anti-corruption in LMICs: developmental governance and health systems research

Traditional approaches to anti-corruption have relied upon broad-based legal change and the introduction transparency and accountability measures. The evidence to date shows that these have been unsuccessful in reducing corruption in health and other sectors in low and middle income countries. Traditional approaches often assume that corruption is driven by individual greed, immorality or opportunism caused by a lack of accountability measures and that once corruption is rendered visible that there will be a channel through which it can be acted upon. In many LMICs, however, corruption and rule breaking is widespread and much better understood as a systemic problem. In these settings, health workers often break rules to solve the problems of working in overstretched, underfunded health systems. In these settings, policy often does not match the realities of an underfunded health system, and so sticking to the rules can have harm career progression or the ability to care for ones family. New approaches to anti-corruption based on Mushtaq Khan's idea of developmental governance take these context specific factors into account and look for targeted, feasible and high impact action that can create improvements of rule abiding behaviour that benefit the health system and the delivery of care. This presentation examines how it can be applied to the health system and the adaptations that it makes in the ways that we work on anti-corruption in health. It examines the ways in which policy can be changed so that groups of actors in the system are be incentivised to engage in abiding behaviour as they recognize that it is in their interests to do so.

Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection

RNA viruses are a major human health threat. The life cycles of many highly pathogenic RNA viruses like influenza A virus (IAV) and Lassa virus depends on host mRNA, because viral polymerases cleave 5'-m7G-capped host transcripts to prime viral mRNA synthesis ("cap-snatching"). We hypothesized that start codons within cap-snatched host transcripts could generate chimeric human-viral mRNAs with coding potential. We report the existence of this mechanism of gene origination, which we named "start-snatching." Depending on the reading frame, start-snatching allows the translation of host and viral "untranslated regions" (UTRs) to create N-terminally extended viral proteins or entirely novel polypeptides by genetic overprinting. We show that both types of chimeric proteins are made in IAV-infected cells, generate T cell responses, and contribute to virulence. Our results indicate that during infection with IAV, and likely a multitude of other human, animal and plant viruses, a host-dependent mechanism allows the genesis of hybrid genes.

Educational Material about Influenza Viruses

To supplement a special edition of the journal Viruses, entitled "What's New with Flu?", influenza virus researchers have worked together to generate simple educational material to communicate their science to school students. Educational materials suitable for a range of ages are included, from coloring exercises for younger students through to explanations of cutting-edge science in straightforward language for older students. This article contains a handout with influenza facts, a coloring page, a glossary and word find and a connect-the-dots exercise explaining the ideas behind recently published scientific papers. Together, these materials are intended to make research on influenza viruses more accessible to students and teachers.

Cancer Therapeutic Resistance: Progress and Perspectives (April 7-8, 2016 - Barcelona, Spain)

At the Cancer Therapeutic Resistance: Progress and Perspectives conference, in Barcelona, Spain, April 7-8, 2016, researchers, clinicians and students gathered to discuss our current understanding of intrinsic and acquired resistance of tumors to cancer therapies and to explore how to translate strategies to predict risk or overcome resistance to the clinic. The sessions covered a wide range of topics, including cancer omics, molecular classification, clinically relevant tumor models, biomarkers and novel therapeutic targets, and personalized medicine, with talks from many international experts in the field. This report highlights the main presentations that demonstrate the progress being made in predicting and identifying drug resistance in patients with cancer, personalized approaches to direct treatment and understanding the mechanisms involved. With better models of human cancer and powerful high-throughput screening techniques, translation to the clinic leading to tangible benefits for patients is attainable.

Age-dependent long-term structural and functional effects of early-life seizures: evidence for a hippocampal critical period influencing plasticity in adulthood

Neural activity promotes circuit formation in developing systems and during critical periods permanently modifies circuit organization and functional properties. These observations suggest that excessive neural activity, as occurs during seizures, might influence developing neural circuitry with long-term outcomes that depend on age at the time of seizures. We systematically examined long-term structural and functional consequences of seizures induced in rats by kainic acid, pentylenetetrazol, and hyperthermia across postnatal ages from birth through postnatal day 90 in adulthood (P90). Magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), and electrophysiological methods at ⩾P95 following seizures induced from P1 to P90 demonstrated consistent patterns of gross atrophy, microstructural abnormalities in the corpus callosum (CC) and hippocampus, and functional alterations in hippocampal circuitry at ⩾P95 that were independent of the method of seizure induction and varied systematically as a function of age at the time of seizures. Three distinct epochs were observed in which seizures resulted in distinct long-term structural and functional outcomes at ⩾P95. Seizures prior to P20 resulted in DTI abnormalities in CC and hippocampus in the absence of gross cerebral atrophy, and increased paired-pulse inhibition (PPI) in the dentate gyrus (DG) at ⩾P95. Seizures after P30 induced a different pattern of DTI abnormalities in the fimbria and hippocampus accompanied by gross cerebral atrophy with increases in lateral ventricular volume, as well as increased PPI in the DG at ⩾P95. In contrast, seizures between P20 and P30 did not result in cerebral atrophy or significant imaging abnormalities in the hippocampus or white matter, but irreversibly decreased PPI in the DG compared to normal adult controls. These age-specific long-term structural and functional outcomes identify P20-30 as a potential critical period in hippocampal development defined by distinctive long-term structural and functional properties in adult hippocampal circuitry, including loss of capacity for seizure-induced plasticity in adulthood that could influence epileptogenesis and other hippocampal-dependent behaviors and functional properties.

Sport-related differences in biomarkers of bone resorption and cartilage degradation in endurance athletes

OBJECTIVE

By measuring urinary cross-linked N-telopeptide (NTx) as a bone resorption marker and urinary C-telopeptide of type II collagen (CTx-II) as a cartilage degradation marker, we asked whether differences in skeletal stresses in college athletes undergoing high-intensity training for diverse types of aerobic sports affect their skeletal metabolism and, if so, differentially or in unison.

METHODS

The study was cross-sectional at a Division 1 college campus with 60 student athletes representing crew, cross-country running and swimming. Controls were 16 non-athlete undergraduates. Urine samples were collected for NTx and CTx-II analysis by enzyme-linked immunosorbent assay, normalizing results to creatinine. Two-way analysis of variance models and pair-wise comparisons were used to test whether biomarker levels differed by sport and the significance when adjusted for body mass index (BMI).

RESULTS

NTx and CTx-II showed significant differences between groups before and after adjusting for BMI. NTx was highest in the rowers, and higher in rowers and runners than in swimmers or controls. CTx-II was significantly higher in runners than in crew, swimmers or controls, when unadjusted for BMI. After adjusting for BMI, these group differences remained significant except for runners over crew.

CONCLUSION

Athletes in-training in the three sports show significant differences in these markers of bone resorption and cartilage collagen degradation. The results suggest that crew undergo the highest bone remodeling and runners the highest cartilage degradation. The results also show how these markers can vary physiologically between individuals, at extremes of skeletal exercise.

The effects of a double blind, placebo controlled, artificial food colourings and benzoate preservative challenge on hyperactivity in a general population sample of preschool children

AIMS

To determine whether artificial food colourings and a preservative in the diet of 3 year old children in the general population influence hyperactive behaviour.

METHODS

A sample of 1873 children were screened in their fourth year for the presence of hyperactivity at baseline (HA), of whom 1246 had skin prick tests to identify atopy (AT). Children were selected to form the following groups: HA/AT, not-HA/AT, HA/not-AT, and not-HA/not-AT (n = 277). After baseline assessment, children were subjected to a diet eliminating artificial colourings and benzoate preservatives for one week; in the subsequent three week within subject double blind crossover study they received, in random order, periods of dietary challenge with a drink containing artificial colourings (20 mg daily) and sodium benzoate (45 mg daily) (active period), or a placebo mixture, supplementary to their diet. Behaviour was assessed by a tester blind to dietary status and by parents' ratings.

RESULTS

There were significant reductions in hyperactive behaviour during the withdrawal phase. Furthermore, there were significantly greater increases in hyperactive behaviour during the active than the placebo period based on parental reports. These effects were not influenced by the presence or absence of hyperactivity, nor by the presence or absence of atopy. There were no significant differences detected based on objective testing in the clinic.

CONCLUSIONS

There is a general adverse effect of artificial food colouring and benzoate preservatives on the behaviour of 3 year old children which is detectable by parents but not by a simple clinic assessment. Subgroups are not made more vulnerable to this effect by their prior levels of hyperactivity or by atopy.

Oxygen in nitrogen versus nitrous oxide during pediatric general anesthesia

BACKGROUND

Induction of anesthesia decreases lung volumes, giving areas of non-ventilated lung. Nitrogen is a slowly-absorbed gas that could prevent resorption of gases from these closed spaces, preventing atelectasis and improving oxygen saturations during recovery.

METHODS

We evaluated oxygen saturations during emergence after intra-operative administration of 33% oxygen in nitrogen versus 33% oxygen in nitrous oxide in 62 children having elective urologic surgery. Patients were randomly assigned to either group A (2.5 L/min air with 0.5 L/min oxygen) or group N (2 L/min nitrous oxide and 1 L/min oxygen). Flowmeters were covered to maintain blinding. Anesthetic technique was standardized (laryngeal mask airway, caudal, halothane, and deep extubation). Patients breathed room air during emergence, while a blinded observer recorded duration of desaturations by stopwatch for 15 min.

RESULTS

We found similar desaturations in both groups. The difference in desaturations < 94% at an interim 2-min total probably reflects diffusion hypoxia and was not significant at 15 min. The frequency of desaturations < 87% during emergence was significantly greater in children who were crying during induction.

CONCLUSIONS

The intra-operative use of air versus nitrous oxide has no substantial effect on oxygen saturations during emergence from anesthesia in children. These results are consistent with a recently published mathematical model.

Can parents accurately perceive hyperactivity in their child?

In all, 1872 children were recruited as part of a larger study concerning food additives and behaviours in preschool children. This figure represented 70% of the whole population of 3 1/4 -year-old children resident on the Isle of Wight, UK. Parents completed an assessment concerning their perceptions of their child's behaviour. The results of this assessment were compared with scores on two validated parental questionnaires, the Weiss Werry Peters (WWP) hyperactivity scale and the Emotionality, Activity and Sociability Temperament Questionnaire (EAS), which were used to assess hyperactivity. The accuracy of parents in perceiving hyperactivity in their children was found to be around 50% if the child was hyperactive, and 89% if the child was not hyperactive. The implications of these findings for services are discussed. Frequencies of potential risk groups for future Attention Deficit Hyperactivity Disorder (ADHD) and Conduct Disorder were also suggested.

Assessing outcome in lumbar disc surgery using patient completed measures

Measuring outcome after spinal surgery is difficult. The objective of this study was to assess the use of four measures in establishing outcome in patients undergoing lumbar discectomy. Forty-six consecutive patients who had undergone two operations for lumbar disc prolapse and 54 patients who had undergone one operation for the same condition over the same period were identified. The SF-36 questionnaire was used to assess general health. The Roland-Morris questionnaire and a simple modification of the Roland-Morris questionnaire were used to assess back and leg related disability, respectively. Analogue pain scales were used to measure back pain and sciatica. The SF-36 scores revealed significantly worse health status in the two operation compared with the one operation patients and in all patients compared with the normal population. Using the Roland-Morris and the leg disability questionnaires, patients who had undergone two operations reported significantly worse disability (Roland-Morris, 53%, poor outcome) than those who had undergone one operation (Roland-Morris, 19%, poor outcome). There was significantly greater back disability than leg disability in both groups of patients and this was confirmed by the analogue pain scales. In patients who had undergone two operations, 25% classified their back pain as very bad or unbearable, and 22.5% described very bad or unbearable leg pain. For the one operation patients these figures were 9.5 and 2.4%, respectively. The results demonstrate that both generic and condition specific patient completed measures have the potential to detect differences in outcome between patients who have undergone either one or two lumbar disc operations. The study provides support for the use of these patient completed measures in assessing outcome in lumbar disc surgery.

A novel human GnRH receptor homolog gene: abundant and wide tissue distribution of the antisense transcript

Gonadotropin releasing hormone (GnRH) regulates the reproductive system through a specific G-protein-coupled receptor (GPCR) in pituitary gonadotropes. The existence of two (or more) forms of GnRH in most vertebrates suggested the existence of GnRH receptor subtypes (I and II). Using sequence information for extracellular loop 3 of a putative Type II GnRH receptor from a reptile species, we have looked for a Type II GnRH receptor gene in the human genome EST (expressed sequence tag) database. A homolog was identified which has 45% and 41% amino acid identity with exons 2 and 3 of the known human GnRH pituitary receptor (designated Type I) and much lower homology with all other GPCRs. A total of 27 contiguous ESTs was found and comprised a continuous sequence of 1642 nucleotides. The EST sequences were confirmed in the cloned human gene and in PCR products of cDNA from several tissues. All EST transcripts detected were in the antisense orientation with respect to the novel GnRH receptor sequence and were highly expressed in a wide range of human brain and peripheral tissues. PCR of cDNA from a wide range of tissues revealed that intronic sequence equivalent to intron 2 of the Type I GnRH receptor was retained. The failure to splice out putative intron sequences in transcripts which spanned exon-intron boundaries is expected in antisense transcripts, as candidate donor and acceptor sites were only present in the gene when transcribed in the orientation encoding the GnRH receptor homolog. No transcripts extended 5' to the sequence corresponding to intron 2 of the Type I GnRH as the antisense transcripts terminated in poly A due to the presence of a polyadenylation signal sequence in the putative intron 2 when transcribed in the antisense orientation. These findings suggest that a Type II GnRH receptor gene has arisen during vertebrate evolution and is also present in the human. However, the receptor may have become vestigial in the human, possibly due to the abundant and universal tissue transcription of the opposite DNA strand to produce antisense RNA.

American Society of Gene Therapy--First Annual Meeting. Education session: the ABCs of non-viral vectors for gene therapy. 28-31 May 1998, Seattle, Washington, USA

In July 1996, the American Society of Gene Therapy (ASGT) was established in San Francisco by George Stamatoyannopoulos (President of ASGT, Professor of Genetics and Medical Genetics at the University of Washington, USA), James M Wilson (President Elect of ASGT, Director of the Institute for Human Gene Therapy, University of Pennsylvania, USA) and other gene therapy experts. In May 1998, this society held its first annual meeting, in Seattle, WA. The aim of the annual meeting is to provide a forum for all investigators, including students, young scientists, academic researchers and those working in industry. To avoid the risk of bias through election of one program committee, symposia, workshops and poster sessions are organized by different committees. There are nine committees in total, so each discipline within the diverse field of gene therapy is properly represented. An education program was organized by Savio LC Woo (Mount Sinai of Medicine, New York, USA) and there was a high school student symposium to encourage interest from the younger generation. Professor Stamatoyannopoulos said that he would like to see the NIH establishing centers of excellence of gene therapy, as they did for cancer 25 years ago. James Wilson then thanked George for all his work founding the society, as he took over as president. There are already 14,000 members of the ASGT and more than 1500 scientists attended this conference. There were 18 sessions of oral presentations and 750 abstracts.

The feasibility of MRI feedback control for intracavitary phased array hyperthermia treatments

Temperature feedback control has the potential to enhance hyperthermia treatments by providing more uniform heating of the target volume and improving the transient temperature response. A multivariable least squares batch algorithm was used to estimate system parameters for simulated prostate hyperthermia treatments. A multi-input, multi-output (MIMO) linear quadratic regulator (LQR) controller was designed for prostate hyperthermia treatments with an intracavitary phased array. A parametric study was performed for the one-dimensional control case, investigating factors relevant to magnetic resonance imaging (MRI) feedback control such as spatial resolution of temperature measurements (size of the averaging volume), sampling rate (image acquisition time), thermometry noise, control width, control depth, physiological parameter changes and reference input structure. Simulations utilizing the two dimensional (2-D) thermometry of MRI and the 2-D focusing capabilities of phased arrays demonstrated that near field heating can be controlled such that the size and shape of the heated volume can be tailored in 2-D. The control algorithms developed in this study show promising potential for incorporation into a non-invasive prostate hyperthermia system utilizing MRI feedback.

Survey of human immunodeficiency virus infection among pregnant women in England and Wales: 1990-93

We report on the first four years (1990-93) of a survey within the national HIV prevalence monitoring programme. The survey's objective is to monitor the prevalence of infection with the human immunodeficiency virus (HIV) in pregnant women in London and elsewhere in England. The survey--based in forty centres that offer antenatal care in London, Greater Manchester, West Yorkshire, and adjacent non-metropolitan areas--uses repeated cross sectional serosurveillance for anti-HIV-1 and 2 and the unlinked anonymous test method on blood left over from specimens collected for antenatal screening for immunity to rubella. The seroprevalence of HIV-1 ranged from 0.007% (1 in 14,530) in non-metropolitan areas, to 0.011% (1 in 8790) in metropolitan areas outside London, and 0.23% (1 in 440) in London. Evidence of HIV-2 infection was found in only four specimens, in London (1 in 50,300). The seroprevalence of HIV-1 in London varied more than tenfold between centres, from 0.03% (1 in 3190) to 0.51% (1 in 200). The highest prevalence of infection was in London in women aged between 20 and 30 (0.30%; 1 in 335). The seroprevalence in London centres rose from 0.18% in 1990 (1 in 560) to 0.26% in 1993 (1 in 390) and the rise was significant in all age groups. If voluntary confidential HIV testing (with counselling) among pregnant women in England were to be promoted, its cost effectiveness would be greater if focused on particular centres that provide antenatal care in London.

Lamellar ichthyosis with episodic psoriasiform reaction pattern

The skin of a girl born with the typical appearance of "collodion baby," evolved into an exfoliative erythroderma that clinically was lamellar ichthyosis. However, biopsy specimens done in early infancy showed psoriasis. Over the ensuing sixteen years she has continued to have clinical lamellar ichthyosis with rare occasions of febrile episodes and superficial pustules. Some biopsy specimens have been diagnosed as showing lamellar ichthyosis, while others have again shown psoriasis.

Methicillin-resistant Staphylococcus aureus (MRSA): risk and outcome of colonized vs. infected patients

A retrospective study of 204 patients culture positive for methicillin-resistant Staphylococcus aureus compared infected and colonized patients. Seventy-eight patients were colonized and never developed infection (C), 24 were colonized and subsequently infected (C----I), and 102 patients had 1 or more nosocomial infections with MRSA at time of first culture (I). The most prevalent sites of infection were wound (26.5%) and blood-stream (20.7%), whereas the respiratory tract and surgical wounds were both frequent sites of colonization. Stepwise discriminant analysis found the most important factors in differentiating likelihood of colonization vs. infection were recent prior hospitalization, history of wound debridement, and number of invasive procedures. Ten percent of (C) died and 25.5% of (I) died. MRSA contributed to death in 57.6% of the (I) deaths (p less than .05). These results underscore the importance of differentiating (C) vs. (I) in hospitals where MRSA is endemic so that early specific treatment may be initiated. Risk factors for infection should be discriminated from those for acquisition of the organism.