Protein sequence landscapes are not so simple: on reference-free versus reference-based inference

In a recent preprint, Park, Metzger, and Thornton reanalyze 20 empirical protein sequence-function landscapes using a "reference-free analysis" (RFA) method they recently developed. They argue that these empirical landscapes are simpler and less epistatic than earlier work suggested, and attribute the difference to limitations of the methods used in the original analyses of these landscapes, which they claim are more sensitive to measurement noise, missing data, and other artifacts. Here, we show that these claims are incorrect. Instead, we find that the RFA method introduced by Park et al. is exactly equivalent to the reference-based least-squares methods used in the original analysis of many of these empirical landscapes (and also equivalent to a Hadamard-based approach they implement). Because the reanalyzed and original landscapes are in fact identical, the different conclusions drawn by Park et al. instead reflect different interpretations of the parameters describing the inferred landscapes; we argue that these do not support the conclusion that epistasis plays only a small role in protein sequence-function landscapes.

Genotype-phenotype landscapes for immune-pathogen coevolution

Our immune systems constantly coevolve with the pathogens that challenge them, as pathogens adapt to evade our defense responses, with our immune repertoires shifting in turn. These coevolutionary dynamics take place across a vast and high-dimensional landscape of potential pathogen and immune receptor sequence variants. Mapping the relationship between these genotypes and the phenotypes that determine immune-pathogen interactions is crucial for understanding, predicting, and controlling disease. Here, we review recent developments applying high-throughput methods to create large libraries of immune receptor and pathogen protein sequence variants and measure relevant phenotypes. We describe several approaches that probe different regions of the high-dimensional sequence space and comment on how combinations of these methods may offer novel insight into immune-pathogen coevolution.

The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution

The Omicron BA.1 variant of SARS-CoV-2 escapes convalescent sera and monoclonal antibodies that are effective against earlier strains of the virus. This immune evasion is largely a consequence of mutations in the BA.1 receptor binding domain (RBD), the major antigenic target of SARS-CoV-2. Previous studies have identified several key RBD mutations leading to escape from most antibodies. However, little is known about how these escape mutations interact with each other and with other mutations in the RBD. Here, we systematically map these interactions by measuring the binding affinity of all possible combinations of these 15 RBD mutations (215=32,768 genotypes) to 4 monoclonal antibodies (LY-CoV016, LY-CoV555, REGN10987, and S309) with distinct epitopes. We find that BA.1 can lose affinity to diverse antibodies by acquiring a few large-effect mutations and can reduce affinity to others through several small-effect mutations. However, our results also reveal alternative pathways to antibody escape that does not include every large-effect mutation. Moreover, epistatic interactions are shown to constrain affinity decline in S309 but only modestly shape the affinity landscapes of other antibodies. Together with previous work on the ACE2 affinity landscape, our results suggest that the escape of each antibody is mediated by distinct groups of mutations, whose deleterious effects on ACE2 affinity are compensated by another distinct group of mutations (most notably Q498R and N501Y).

Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody

Broadly neutralizing antibodies (bnAbs) that neutralize diverse variants of a particular virus are of considerable therapeutic interest. Recent advances have enabled us to isolate and engineer these antibodies as therapeutics, but eliciting them through vaccination remains challenging, in part due to our limited understanding of how antibodies evolve breadth. Here, we analyze the landscape by which an anti-influenza receptor binding site (RBS) bnAb, CH65, evolved broad affinity to diverse H1 influenza strains. We do this by generating an antibody library of all possible evolutionary intermediates between the unmutated common ancestor (UCA) and the affinity-matured CH65 antibody and measure the affinity of each intermediate to three distinct H1 antigens. We find that affinity to each antigen requires a specific set of mutations - distributed across the variable light and heavy chains - that interact non-additively (i.e., epistatically). These sets of mutations form a hierarchical pattern across the antigens, with increasingly divergent antigens requiring additional epistatic mutations beyond those required to bind less divergent antigens. We investigate the underlying biochemical and structural basis for these hierarchical sets of epistatic mutations and find that epistasis between heavy chain mutations and a mutation in the light chain at the V_H-V_L interface is essential for binding a divergent H1. Collectively, this is the first work to comprehensively characterize epistasis between heavy and light chain mutations and shows that such interactions are both strong and widespread. Together with our previous study analyzing a different class of anti-influenza antibodies, our results implicate epistasis as a general feature of antibody sequence-affinity landscapes that can potentiate and constrain the evolution of breadth.

Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations

Evolutionary adaptation to a constant environment is driven by the accumulation of mutations which can have a range of unrealized pleiotropic effects in other environments. These pleiotropic consequences of adaptation can influence the emergence of specialists or generalists, and are critical for evolution in temporally or spatially fluctuating environments. While many experiments have examined the pleiotropic effects of adaptation at a snapshot in time, very few have observed the dynamics by which these effects emerge and evolve. Here, we propagated hundreds of diploid and haploid laboratory budding yeast populations in each of three environments, and then assayed their fitness in multiple environments over 1000 generations of evolution. We find that replicate populations evolved in the same condition share common patterns of pleiotropic effects across other environments, which emerge within the first several hundred generations of evolution. However, we also find dynamic and environment-specific variability within these trends: variability in pleiotropic effects tends to increase over time, with the extent of variability depending on the evolution environment. These results suggest shifting and overlapping contributions of chance and contingency to the pleiotropic effects of adaptation, which could influence evolutionary trajectories in complex environments that fluctuate across space and time.

Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies

Over the past two decades, several broadly neutralizing antibodies (bnAbs) that confer protection against diverse influenza strains have been isolated. Structural and biochemical characterization of these bnAbs has provided molecular insight into how they bind distinct antigens. However, our understanding of the evolutionary pathways leading to bnAbs, and thus how best to elicit them, remains limited. Here, we measure equilibrium dissociation constants of combinatorially complete mutational libraries for two naturally isolated influenza bnAbs (CR9114, 16 heavy-chain mutations; CR6261, 11 heavy-chain mutations), reconstructing all possible evolutionary intermediates back to the unmutated germline sequences. We find that these two libraries exhibit strikingly different patterns of breadth: while many variants of CR6261 display moderate affinity to diverse antigens, those of CR9114 display appreciable affinity only in specific, nested combinations. By examining the extensive pairwise and higher order epistasis between mutations, we find key sites with strong synergistic interactions that are highly similar across antigens for CR6261 and different for CR9114. Together, these features of the binding affinity landscapes strongly favor sequential acquisition of affinity to diverse antigens for CR9114, while the acquisition of breadth to more similar antigens for CR6261 is less constrained. These results, if generalizable to other bnAbs, may explain the molecular basis for the widespread observation that sequential exposure favors greater breadth, and such mechanistic insight will be essential for predicting and eliciting broadly protective immune responses.

The genetic basis of differential autodiploidization in evolving yeast populations

Spontaneous whole-genome duplication, or autodiploidization, is a common route to adaptation in experimental evolution of haploid budding yeast populations. The rate at which autodiploids fix in these populations appears to vary across strain backgrounds, but the genetic basis of these differences remains poorly characterized. Here, we show that the frequency of autodiploidization differs dramatically between two closely related laboratory strains of Saccharomyces cerevisiae, BY4741 and W303. To investigate the genetic basis of this difference, we crossed these strains to generate hundreds of unique F1 segregants and tested the tendency of each segregant to autodiplodize across hundreds of generations of laboratory evolution. We find that variants in the SSD1 gene are the primary genetic determinant of differences in autodiploidization. We then used multiple laboratory and wild strains of S. cerevisiae to show that clonal populations of strains with a functional copy of SSD1 autodiploidize more frequently in evolution experiments, while knocking out this gene or replacing it with the W303 allele reduces autodiploidization propensity across all genetic backgrounds tested. These results suggest a potential strategy for modifying rates of spontaneous whole-genome duplications in laboratory evolution experiments in haploid budding yeast. They may also have relevance to other settings in which eukaryotic genome stability plays an important role, such as biomanufacturing and the treatment of pathogenic fungal diseases and cancers.

Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations

Laboratory experimental evolution provides a window into the details of the evolutionary process. To investigate the consequences of long-term adaptation, we evolved 205 Saccharomyces cerevisiae populations (124 haploid and 81 diploid) for ~10,000,000 generations in three environments. We measured the dynamics of fitness changes over time, finding repeatable patterns of declining adaptability. Sequencing revealed that this phenotypic adaptation is coupled with a steady accumulation of mutations, widespread genetic parallelism, and historical contingency. In contrast to long-term evolution in E. coli, we do not observe long-term coexistence or populations with highly elevated mutation rates. We find that evolution in diploid populations involves both fixation of heterozygous mutations and frequent loss-of-heterozygosity events. Together, these results help distinguish aspects of evolutionary dynamics that are likely to be general features of adaptation across many systems from those that are specific to individual organisms and environmental conditions.

Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin

We systematically and quantitatively evaluate whether endoplasmic reticulum (ER) proteostasis factors impact the mutational tolerance of secretory pathway proteins. We focus on influenza hemaggluttinin (HA), a viral membrane protein that folds in the host’s ER via a complex pathway. By integrating chemical methods to modulate ER proteostasis with deep mutational scanning to assess mutational tolerance, we discover that upregulation of ER proteostasis factors broadly enhances HA mutational tolerance across diverse structural elements. Remarkably, this proteostasis network-enhanced mutational tolerance occurs at the same sites where mutational tolerance is most reduced by propagation at fever-like temperature. These findings have important implications for influenza evolution, because influenza immune escape is contingent on HA possessing sufficient mutational tolerance to evade antibodies while maintaining the capacity to fold and function. More broadly, this work provides the first experimental evidence that ER proteostasis mechanisms define the mutational tolerance and, therefore, the evolution of secretory pathway proteins.

Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones

The threat of viral pandemics demands a comprehensive understanding of evolution at the host-pathogen interface. Here, we show that the accessibility of adaptive mutations in influenza nucleoprotein at fever-like temperatures is mediated by host chaperones. Particularly noteworthy, we observe that the Pro283 nucleoprotein variant, which (1) is conserved across human influenza strains, (2) confers resistance to the Myxovirus resistance protein A (MxA) restriction factor, and (3) critically contributed to adaptation to humans in the 1918 pandemic influenza strain, is rendered unfit by heat shock factor 1 inhibition-mediated host chaperone depletion at febrile temperatures. This fitness loss is due to biophysical defects that chaperones are unavailable to address when heat shock factor 1 is inhibited. Thus, influenza subverts host chaperones to uncouple the biophysically deleterious consequences of viral protein variants from the benefits of immune escape. In summary, host proteostasis plays a central role in shaping influenza adaptation, with implications for the evolution of other viruses, for viral host switching, and for antiviral drug development.

Host proteostasis modulates influenza evolution

Predicting and constraining RNA virus evolution require understanding the molecular factors that define the mutational landscape accessible to these pathogens. RNA viruses typically have high mutation rates, resulting in frequent production of protein variants with compromised biophysical properties. Their evolution is necessarily constrained by the consequent challenge to protein folding and function. We hypothesized that host proteostasis mechanisms may be significant determinants of the fitness of viral protein variants, serving as a critical force shaping viral evolution. Here, we test that hypothesis by propagating influenza in host cells displaying chemically-controlled, divergent proteostasis environments. We find that both the nature of selection on the influenza genome and the accessibility of specific mutational trajectories are significantly impacted by host proteostasis. These findings provide new insights into features of host–pathogen interactions that shape viral evolution, and into the potential design of host proteostasis-targeted antiviral therapeutics that are refractory to resistance.

Influenza viruses, commonly called flu, can evade our immune system and develop resistance to treatments by changing frequently. Specifically, mutations in their genome cause influenza proteins to change in ways that can help the virus evade our defences. However, these mutations come at a cost and can prevent the viral proteins from forming functional and stable three-dimensional shapes – a process known as protein folding – thereby hampering the virus’ ability to replicate.

In human cells, proteins called chaperones can help our other proteins fold properly. Influenza viruses do not have their own chaperones and, instead, hijack those of their host. Host chaperones are therefore crucial to the virus’ ability to replicate. However, until now, it was not known if host chaperones can influence how these viruses evolve.

Here, Phillips et al. used mammalian cells to study how host chaperones affect an evolving influenza population. First, cells were engineered to either have normal chaperone levels, elevated chaperone levels, or inactive chaperones. Next, the H3N2 influenza strain was grown in these different conditions for nearly 200 generations and sequenced to determine how the virus evolved in each distinctive host chaperone environment.

Phillips et al. discovered that host chaperones affect the rate at which mutations accumulate in the influenza population, and also the types of mutations in the influenza genome. For instance, when a chaperone called Hsp90 was inactivated, mutations became prevalent in the viral population more slowly than in cells with normal or elevated chaperone levels. Moreover, some specific mutations fared better in cells with high chaperone levels, whilst others worked better in cells with inactivated chaperones.

These results suggest that influenza evolution is affected by host chaperone levels in complex and important ways. Moreover, whether chaperones will promote or hinder the effects of any single mutation is difficult to predict ahead of time. This discovery is significant, as the chaperones available to influenza can vary in different tissues, organisms and infectious conditions, and may therefore influence the virus' ability to change and evolve in a context-specific manner.

The findings are likely to extend to other viruses such as HIV and Ebola, which also hijack host chaperones for the same purpose. More work is now needed to systematically quantify these effects so that we can better predict how specific chaperones will affect the ability of viruses to adapt, especially in pathologically relevant conditions like fever or viral host-switching. In the future, such insights could help shape the design of treatments to which viruses do not evolve resistance.

Urbanization impact on sulfur content of groundwater revealed by the study of urban speleothem-like deposits: Case study in Paris, France

Speleothem-like deposits that develop underground in urban areas are an archive of the environmental impact of anthropic activities that has been little studied so far. In this paper, the sulfate content in shallow groundwater from northern Paris (France) is compared with the sulfur content in two 300-year-old urban carbonate deposits that grew in a historical underground aqueduct. The present-day waters of the aqueduct have very high sulfur and calcium contents, suggesting pollution from gypsum dissolution. However, geological gypsum levels are located below the water table. Sulfur content was measured by micro-X-ray fluorescence in these very S-rich carbonate deposits (0.5 to 1% of S). A twofold S increase during the second half of the 1800s was found in both samples. These dates correspond to two major periods of urbanization above the site. We discus three possible S sources: anthropic sources (industries, fertilizers…), volcanic eruptions and input within the water through gypsum brought for urbanization above the studied site (backfill with quarry waste) since the middle of the 19th century. For the younger second half of the studied section, S input from gypsum brought during urbanization was confirmed by the study of isotopic sulfur composition (δ³⁴S=+15.2‰ at the top). For the oldest part, several sulfur peaks could be related to early industrial activity in Paris, that caused high local air pollution, as reported in historical archives but also to historical gypsum extraction. This study provides information on the origin and timing of the very high SO₄^2- levels measured nowadays within the shallow groundwater, thus demonstrating the interest in using carbonate deposits in urban areas as a proxy for the history of urbanization or human activities and their impact on water bodies.

Potency enhancement of the κ-opioid receptor antagonist probe ML140 through sulfonamide constraint utilizing a tetrahydroisoquinoline motif

Optimization of the sulfonamide-based kappa opioid receptor (KOR) antagonist probe molecule ML140 through constraint of the sulfonamide nitrogen within a tetrahydroisoquinoline moiety afforded a marked increase in potency. This strategy, when combined with additional structure-activity relationship exploration, has led to a compound only six-fold less potent than norBNI, a widely utilized KOR antagonist tool compound, but significantly more synthetically accessible. The new optimized probe is suitably potent for use as an in vivo tool to investigate the therapeutic potential of KOR antagonists.

Quantifying Drosophila food intake: comparative analysis of current methodology

Food intake is a fundamental parameter in animal studies. Despite the prevalent use of Drosophila in laboratory research, precise measurements of food intake remain challenging in this model organism. Here, we compare several common Drosophila feeding assays: the Capillary Feeder (CAFE), food-labeling with a radioactive tracer or a colorimetric dye, and observations of proboscis extension (PE). We show that the CAFE and radioisotope-labeling provide the most consistent results, have the highest sensitivity, and can resolve differences in feeding that dye-labeling and PE fail to distinguish. We conclude that performing the radiolabeling and CAFE assays in parallel is currently the best approach for quantifying Drosophila food intake. Understanding the strengths and limitations of food intake methodology will greatly advance Drosophila studies of nutrition, behavior, and disease.

Development of functionally selective, small molecule agonists at kappa opioid receptors

The kappa opioid receptor (KOR) is widely expressed in the CNS and can serve as a means to modulate pain perception, stress responses, and affective reward states. Therefore, the KOR has become a prominent drug discovery target toward treating pain, depression, and drug addiction. Agonists at KOR can promote G protein coupling and βarrestin2 recruitment as well as multiple downstream signaling pathways, including ERK1/2 MAPK activation. It has been suggested that the physiological effects of KOR activation result from different signaling cascades, with analgesia being G protein-mediated and dysphoria being mediated through βarrestin2 recruitment. Dysphoria associated with KOR activation limits the therapeutic potential in the use of KOR agonists as analgesics; therefore, it may be beneficial to develop KOR agonists that are biased toward G protein coupling and away from βarrestin2 recruitment. Here, we describe two classes of biased KOR agonists that potently activate G protein coupling but weakly recruit βarrestin2. These potent and functionally selective small molecule compounds may prove to be useful tools for refining the therapeutic potential of KOR-directed signaling in vivo.

Oxidative folding and preparation of α-conotoxins for use in high-throughput structure-activity relationship studies

α-Conotoxins are peptide neurotoxins that selectively inhibit various subtypes of nicotinic acetylcholine receptors. They are important research tools for studying numerous pharmacological disorders, with profound potential for developing drug leads for treating pain, tobacco addiction, and other conditions. They are characterized by the presence of two disulfide bonds connected in a globular arrangement, which stabilizes a bioactive helical conformation. Despite extensive structure-activity relationship studies that have produced α-conotoxin analogs with increased potency and selectivity towards specific nicotinic acetylcholine receptor subtypes, the efficient production of diversity-oriented α-conotoxin combinatorial libraries has been limited by inefficient folding and purification procedures. We have investigated the optimized conditions for the reliable folding of α-conotoxins using simplified oxidation procedures for use in the accelerated production of synthetic combinatorial libraries of α-conotoxins. To this end, the effect of co-solvent, redox reagents, pH, and temperature on the proportion of disulfide bond isomers was determined for α-conotoxins exhibiting commonly known Cys loop spacing frameworks. In addition, we have developed high-throughput 'semi-purification' methods for the quick and efficient parallel preparation of α-conotoxin libraries for use in accelerated structure-activity relationship studies. Our simplified procedures represent an effective strategy for the preparation of large arrays of correctly folded α-conotoxin analogs and permit the rapid identification of active hits directly from high-throughput pharmacological screening assays.

Retrievable inferior vena cava filter use in major trauma

Venous thromboembolism (VTE) remains a devastating complication among trauma patients. However, conventional VTE prophylaxis is often contraindicated in major trauma patients due to concurrent injuries. This article discusses the use of retrievable inferior vena cava filters as a method for VTE prophylaxis in major trauma patients.

Vitamin D-Dependent Non-Type 1, Non-Type 2 Rickets in a 3-Month-Old Cornish Rex Kitten

Case presentation and assessment A 3-month-old female Cornish Rex kitten was found to have non-painful swelling of the carpal and tarsal regions when presented for routine neutering. The kitten was smaller in stature and less active than its siblings and, according to the owner, had a bunny-hopping gait, was reluctant to climb stairs and strained during defecation. Radiography of the affected limbs and a subsequent radiographic survey of the entire skeleton demonstrated features consistent with rickets. The three littermates were clinically and radiographically normal. As a nutritionally complete diet was being fed, it seemed most likely that the kitten had an inborn error related to vitamin D metabolism. Serum biochemistry demonstrated reduced total alkaline phosphatase activity and increased concentrations of parathyroid hormone. Concentrations of 1,25- and 25-hydroxycholecalciferol were markedly reduced, confirming the diagnosis of rickets.

Treatment The kitten was treated with calcitriol, administered orally once daily, and improved rapidly both clinically and radiologically. Serial laboratory studies suggested that the error in vitamin D metabolism was transient, and, at the time of writing, as an adult, the cat appears to require no ongoing replacement calcitriol therapy.

Clinical relevance This case emphasises the value of examining a full ‘calcium profile’ via a human or veterinary reference laboratory, and a favourable prognosis in some kittens with rickets makes such investigations worthwhile. Even when finances preclude detailed investigation, trial therapy using a nutritionally complete diet and physiological doses of calcitriol or cholecalciferol is inexpensive and can produce a good response.

Measuring flux of soil fumigants using the aerodynamic and dynamic flux chamber methods

Methods for measuring and estimating flux density of soil fumigants under field conditions are important for the purpose of providing inputs to air dispersion models and for comparing the effects of management practices on emission reduction. The objective of this study was to measure the flux of 1,3-dichloropropene (1,3-D) and chloropicrin at a site in Georgia (GA) using the aerodynamic method and the dynamic flux chamber (FC) method. A secondary objective was to compare the effects of high density polyethylene (HDPE), and virtually impermeable film (VIF) tarps on fumigant flux at a site in Florida (FL). Chloropicrin and 1,3-D were applied by surface drip application of In-Line soil fumigant on vegetable beds covered by low density polyethylene (LDPE), HDPE, or VIF. The surface drip fumigation using In-Line and LDPE tarp employed in this study resulted in volatilization of 26.5% of applied 1,3-D and 11.2% of the applied chloropicrin at the GA site, as determined using the aerodynamic method. Estimates of mass loss obtained from dynamic FCs were 23.6% for 1,3-D and 18.0% for chloropicrin at the GA site. Flux chamber trials at the FL site indicate significant additional reduction in flux density, and cumulative mass loss when VIF tarp is used. This study supports the use of dynamic FCs as a valuable tool for estimating gas flux density from agricultural soils, and evaluating best management practices for reducing fumigant emissions to the atmosphere.

Cannabidiol displays unexpectedly high potency as an antagonist of CB1 and CB2 receptor agonists in vitro

BACKGROUND AND PURPOSE

A nonpsychoactive constituent of the cannabis plant, cannabidiol has been demonstrated to have low affinity for both cannabinoid CB1 and CB2 receptors. We have shown previously that cannabidiol can enhance electrically evoked contractions of the mouse vas deferens, suggestive of inverse agonism. We have also shown that cannabidiol can antagonize cannabinoid receptor agonists in this tissue with a greater potency than we would expect from its poor affinity for cannabinoid receptors. This study aimed to investigate whether these properties of cannabidiol extend to CB1 receptors expressed in mouse brain and to human CB2 receptors that have been transfected into CHO cells.

EXPERIMENTAL APPROACH

The [35S]GTPS binding assay was used to determine both the efficacy of cannabidiol and the ability of cannabidiol to antagonize cannabinoid receptor agonists (CP55940 and R-(+)-WIN55212) at the mouse CB1 and the human CB2 receptor.

KEY RESULTS

This paper reports firstly that cannabidiol displays inverse agonism at the human CB2 receptor. Secondly, we demonstrate that cannabidiol is a high potency antagonist of cannabinoid receptor agonists in mouse brain and in membranes from CHO cells transfected with human CB2 receptors.

CONCLUSIONS AND IMPLICATIONS

This study has provided the first evidence that cannabidiol can display CB2 receptor inverse agonism, an action that appears to be responsible for its antagonism of CP55940 at the human CB2 receptor. The ability of cannabidiol to behave as a CB2 receptor inverse agonist may contribute to its documented anti-inflammatory properties.

A randomized, placebo-controlled study of rofecoxib with paracetamol in early post-tonsillectomy pain in adults

BACKGROUND AND OBJECTIVE

Effective and early treatment of postoperative pain and nausea have become pivotal for the early discharge of patients after tonsillectomy. Opioid-based analgesia is standard practice but the use of non-steroidal anti-inflammatory drugs is discouraged due to their platelet inhibiting properties. The cyclo-oxygenase-2 selective non-steroidal anti-inflammatory drugs are effective analgesics and do not affect platelet function. We hypothesized that premedication with cyclo-oxygenase-2 selective non-steroidal anti-inflammatory drug in addition to paracetamol would provide effective analgesia and decrease opioid consumption during early recovery from tonsillectomy.

METHODS

In a randomized, placebo-controlled study of adult tonsillectomy patients (n=40) one group (R-group; n=20) was premedicated with paracetamol 1.5 g and rofecoxib 50 mg and a control group (P-group; n=20) was premedicated with paracetamol 1.5 g and placebo. Morphine was used as rescue medication. Postoperative (24 h) pain scores (0--10), morphine consumption as well as intraoperative blood loss were recorded.

RESULTS

We found no overall difference in pain scores between the groups but significantly more patients in the placebo group had pain scores >5 within the first 8 h. The rofecoxib group consumed less morphine during the first 12 h. A lower intraoperative blood loss was observed in the rofecoxib group.

CONCLUSION

Our results suggest an early although clinically minor analgesic benefit of the addition of a cyclo-oxygenase-2 selective non-steroidal anti-inflammatory drug to paracetamol as premedication for adult tonsillectomy.

Overview of the fracture healing cascade

Fracture healing is a dynamic process being governed by a variety of cellular elements and stimulating agents. Our knowledge in understanding the molecular and cellular processes occurring in healing fractures has vastly expanded as a result of the advances made in all aspects of medicine. The ability to manipulate mesenchymal stem cells and to deliver locally growth factors in order to create new bone has led to a proliferation of research papers. The purpose of this article is to provide a brief overview of the current level of understanding of the physiological processes regulating the healing of fractures.

On-line high-precision stable hydrogen isotopic analyses on nanoliter water samples

We describe a new on-line chromium reduction technique for the measurement of stable hydrogen (deltaD) isotopes in waters using continuous-flow isotope ratio mass spectrometry. The on-line Cr reduction method has low intersample memory effects (< 1%) and excellent precision and accuracy for deltaD (+/-0.5% and was used to analyze waters samples as small as 50 nL. The on-line Cr method has a number of significant advantages over conventional offline Zn and U reduction and on-line carbon-based pyrolysis techniques. A single Cr reactor can be used to analyze approximately 1,000 water samples using an injection volume of 0.5 microL, with an individual sample analysis time of 4 min. Intersample memory effects are negligible. The Cr reactor temperature of 1050 degree C is easily attainable on standard elemental analyzers and so does not require the specialized and costly high-temperature furnaces of carbon-based pyrolysis reactors. Furthermore, hydrogen isotopes in extremely small water samples in the 100-nL range or less can be easily measured; hence, this new method opens up a number of exciting application areas in earth and environmental sciences, for example, natural abundance deltaD measurements of individual fluid inclusions in geologic materials using a laser source and measurements of body fluids in physiological and metabolic research.

Assessment of dermal exposure--empirical models and indicative distributions

The Health and Safety Executive embarked upon a program of work to address the issue of exposure to nonagricultural pesticides in the United Kingdom. Early on it became clear that the primary route of exposure was via the skin. Empirical dermal exposure models have been developed which allow estimates of potential dermal exposure to be derived from distributions of rate of contamination with in-use formulations during typical use conditions in the workplace. Estimates of actual dermal exposure (what gets onto the skin) may also be anticipated and used in quantitative risk assessment to inform product registration. The key interpreted data from the empirical models are presented. Data are presented for six models. Separate summary data are presented for exposure to the body, hands, and feet. In the case of hand exposure, data are presented, in some cases, for contamination arising from wearing used (previously worn, of unknown history) and clean protective gloves. This article proposes a mechanism for addressing exposure assessment where little or no direct dermal exposure data are available--the indicative distribution approach. The empirical distributions of rate of contamination have been studied to seek commonalities which may allow the construction of a universal tool for use in screening level risk assessment. A simple 12-box matrix is proposed.

Potential exposure of hands inside protective gloves-a summary of data from non-agricultural pesticide surveys

The results of individual surveys are compared and general observations are made about the protective nature of protective gloves. A total of 190 measurements of contamination by involatile components of pesticide products were made inside the gloves. Protective gloves were nearly always found to be contaminated inside, except for public hygiene insecticide uses. Disposable gloves were sometimes used when applying public hygiene insecticides, while gloves worn for other applications were normally re-used. The data suggest that when expressing inner glove exposure as 'amount of product per unit time', the data distributions of the non-zero results appeared similar for all activities except for the application of antifoulings. A median value for all non-zero data was indicated at 1.36mg product per minute; a 75th percentile at 4.21mg min(-1) and a 95th percentile at 71.9mg min(-1), assuming product densities of 1.0g ml(-1). In default of better information, these indicators can be used in health-based risk assessment. A further 47 data related to exposure inside new gloves, and 21 data to deposition on outer gloves. These indicate that in general, gloves provide a reasonable degree of protection to non-agricultural pesticides. Due regard should be paid to 'human factors' when considering contamination inside gloves. When people take off dirty gloves, it is difficult to avoid touching the glove exterior. With gloves off, the subject can touch contaminated surfaces. Donning dirty gloves furnishes an inevitable contact with contamination on the outside of the gloves, and can introduce that contamination inside. A common mode of contamination could contribute to the similar distributions for hand contamination inside gloves, from very different uses.

The products of the Drosophila stoned locus interact with synaptic vesicles via synaptotagmin

The stoned locus of Drosophila melanogaster encodes two novel proteins, stonedA (STNA) and stonedB (STNB), both of which are expressed in the nervous system. Flies with defects at the stoned locus have abnormal behavior and altered synaptic transmission. Genetic interactions, in particular with the shibire (dynamin) mutation, indicated a presynaptic function for stoned and suggested an involvement in vesicle cycling. Immunological studies revealed colocalization of the stoned proteins at the neuromuscular junction with the integral synaptic vesicle protein synaptotagmin (SYT). We show here that stoned interacts genetically with synaptotagmin to produce a lethal phenotype. The STNB protein is found by co-immunoprecipitation to be associated with synaptic vesicles, and glutathione S-transferase pull-downs demonstrate an in vitro interaction between the micro2-homology domain of STNB and the C2B domain of the SYTI isoform. The STNA protein is also found in association with vesicles, and it too exhibits an in vitro association with SYTI. However, we find that the bulk of STNA is in a nonmembranous fraction. By using the shibire mutant to block endocytosis, STNB is shown to be present on some synaptic vesicles before exocytosis. However, STNB is not associated with all synaptic vesicles. We hypothesize that STNB specifies a subset of synaptic vesicles with a role in the synaptic vesicle cycle that is yet to be determined.

Determination of spinosad and its metabolites in food and environmental matrices. 3. Immunoassay methods

Spinosad is an insect control agent that is derived from a naturally occurring soil bacterium and is effective on several classes of insects, especially Lepidopteran larvae. Spinosad is registered in many countries for use on a variety of crops, including cotton, corn, soybeans, fruits, and vegetables. Residue methods utilizing a magnetic particle-based immunoassay (IA) test kit have been developed and validated for determining spinosad in environmental and food matrices. These methods involve an extraction of the residues from the matrices with appropriate solvents. For some matrices, the sample extracts can be diluted and measured directly by IA without any cleanup. For other matrices, sample extracts are purified using liquid-liquid partitioning and/or solid phase extraction prior to measurement by IA. The methods determine the total residue of spinosad, which includes the active ingredients (spinosyns A and D) and several minor metabolites, including spinosyn B, spinosyn K, and N-demethylspinosyn D. The methods have validated limits of quantitation of 0.0001 microgram/mL in water, 0.05 microgram/g in sediment, and 0.010 microgram/g in crops, crop processed commodities, and animal tissues. This paper briefly summarizes the residue methodology and method validation data for spinosad in 34 food, feed, and environmental matrices.

The pathologic features and mechanism of traumatic dislocation of the hip

The term traumatic dislocation of the hip encompasses a heterogenous group of dislocations, and more commonly, fracture-dislocations which have been subclassified. The current study describes the pathologic features in terms of an anatomic description of the displaced parts of the joint and what is known of the associated injured structures in each of the subtypes. The events that lead to traumatic dislocation of the hip are well documented, but understanding of the mechanics of the injury can only be presumptive.

Brain stem stroke causing baroreflex failure and paroxysmal hypertension

BACKGROUND

Paroxysmal neurogenic hypertension has been associated with a variety of diseases affecting the brain stem but has only rarely been reported after brain stem stroke. The mechanism is thought to involve increased sympathetic activity and baroreflex dysfunction. We undertook microneurographic recordings of muscle sympathetic nerve activity (MNSA) during beat-to-beat blood pressure (BP) monitoring to investigate this hypothesis.

CASE DESCRIPTION

We investigated a 75-year-old woman who developed paroxysmal hypertension (BP 220/110 mm Hg) after a large left-sided medullary infarct. The paroxysms were triggered by changes in posture and were accompanied by tachycardia, diaphoresis, and headache. Serum catecholamines were substantially increased (norepinephrine level, 23.9 nmol/L 9 days after stroke; normal level, <3.8 nmol/L), and heart rate variability, measured by spectral analysis, was decreased in both low- and high-frequency domains (0.04 and 0.06 ms(2), respectively; normal level, 0.14+/-0.02 ms(2)). MNSA was increased in frequency (61 bursts per minute; normal level, 34+/-18 bursts per minute), and the burst amplitude was not inversely related to diastolic BP. BP and MNSA responses to cold pressor and isometric handgrip stimuli were intact.

CONCLUSIONS

Extensive unilateral infarction of the brain stem in the region of the nucleus tractus solitarius may result in partial baroreflex dysfunction, increased sympathetic activity, and neurogenic paroxysmal hypertension.

Presynaptic glutamic acid decarboxylase is required for induction of the postsynaptic receptor field at a glutamatergic synapse

We have systematically screened EMS-mutagenized Drosophila for embryonic lethal strains with defects in glutamatergic synaptic transmission. Surprisingly, this screen led to the identification of several alleles with missense mutations in highly conserved regions of Dgad1. Analysis of these gad mutants reveals that they are paralyzed owing to defects in glutamatergic transmission at the neuromuscular junction. Further electrophysiological and immunohistochemical examination reveals that these mutants have greatly reduced numbers of postsynaptic glutamate receptors in an otherwise morphologically normal synapse. By overexpressing wild-type Dgad1 in selected neurons, we show that GAD is specifically required in the presynaptic neuron to induce a postsynaptic glutamate receptor field, and that the level of postsynaptic receptors is closely dependent on presynaptic GAD function. These data demonstrate that GAD plays an unexpected role in glutamatergic synaptogenesis.

Acromioclavicular dislocation. Conservative or surgical therapy

A literature review was performed to clarify available information which influences decisions whether to advise a young adult patient to undergo surgery for a severely displaced acromioclavicular dislocation. Twenty-four papers were retrieved yielding 1172 patients of whom the mean followup for the 833 surgically treated patients was 43.7 months and not surgically treated was 60.4 months. Of the 24 papers, only five reported surgical and conservative outcomes; two of these papers used prospective randomized methodology and three used nonrandomized methodology. Fourteen papers reported surgical outcome only and five papers reported conservative outcome only. Overall, 88% of surgically treated patients and 87% of nonsurgically treated patients had a satisfactory outcome. Complications most commonly listed were (surgically treated versus nonsurgically treated): need for further surgery (59% versus 6%), infection (6% versus 1%), and deformity (3% versus 37%). Return to activity was no quicker with surgery. Pain was not any more common without surgery. Range of movement was more frequently normal or near normal without surgery (95% versus 86% if surgically treated) and so was strength (92% versus 87%). Meta-analysis of the four studies including data from surgical and conservative therapy showed on significant benefit from surgery. Power studies suggest that to show a statistically significant benefit from surgery, large studies would be required, which, given the relative incidence of these injuries, would probably be multicenter and therefore vulnerable to methodologic difficulties. There does not seem to be any reason to recommend an operative procedure to a patient with a Rockwood et al Type III injury based on the evidence currently available.

Orthopaedic surgery in hemophilic patients with human immunodeficiency virus

Patients registered at the author's hemophilia center between 1982 and 1994 were studied to establish whether major orthopaedic surgical procedures accelerate the fall of CD4 lymphocyte counts of patients with hemophilia who are infected with the human immunodeficiency virus, and whether patients who had surgery had different rates of development of acquired immune deficiency syndrome or death when compared with patients who did not have surgery. The patients were divided into four groups: Group 1, 22 patients who were human immunodeficiency virus positive undergoing orthopaedic surgery; Group 2, 89 patients who were human immunodeficiency virus positive not undergoing orthopaedic surgery; Group 3, 18 patients who were human immunodeficiency virus negative undergoing orthopaedic surgery; and Group 4, 135 patients who were human immunodeficiency virus negative not undergoing orthopaedic surgery. There was no significant difference between the rates of decline of CD4 lymphocyte counts for patients who were human immunodeficiency virus positive who underwent surgery when compared with human immunodeficiency virus positive patients who did not undergo surgery, nor was there any significant difference between the two human immunodeficiency virus negative groups. There were no significant differences in the rate of development of acquired immune deficiency syndrome or mortality rates between patients who had surgery and those who did not.

Identification of a gene family from Drosophila melanogaster encoding proteins with homology to invertebrate sarcoplasmic calcium-binding proteins (SCPS)

Using antibodies raised against the Drosophila Ca(2+)-binding protein DCABP-23, we have isolated two distinct cDNA clones that encode Ca(2+)-binding proteins of the invertebrate sarcoplasmic calcium-binding protein (SCP) family. Southern blot analysis of whole genomic DNA has shown that one of the clones, Dcabp-A.1, is present in more than one copy in the genome of the fly, and is located in the beta-heterochromatic region at cytological division 80 on chromosome III. The expression pattern of this transcript shows that it is present in the tubular but not the fibrillar muscles of the adult thorax. This expression pattern is consistent with this being a true SCP. In contrast, the expression pattern of the transcript corresponding to the second cDNA clone is exclusive to neural tissue. This transcript derives from a single copy gene, and is located at cytological position 89 D on chromosome III. Comparative analysis of the amino acid sequences from the proteins encoded by the two cDNAs with that of the original DCABP-23 protein indicates that the purified DCABP-23 contained mainly the DCABP-A.1 protein. The identification of members of the SCP family of proteins in Drosophila, will allow for a future genetic investigation of the function of these ubiquitous proteins.

Protective gloves for use in high-risk patients: how much do they affect the dexterity of the surgeon?

Twenty-five orthopaedic surgeons underwent eight motor and sensory tests while using four different glove combinations and without gloves. As well as single and double latex, surgeons wore a simple Kevlar glove with latex inside and outside and then wore a Kevlar and Medak glove with latex inside and outside, as recommended by the manufacturers. The effect of learning with each sequence was neutralised by randomising the glove order. The time taken to complete each test was recorded and, where appropriate, error rates were noted. Simple sensory tests took progressively longer to perform so that using the thickest glove combination led to the completion times being doubled. Error rates increased significantly. Tests of stereognosis also took longer and use of the thickest glove combination caused these tests to take three times as long on average. Error rates again increased significantly. However, prolongation of motor tasks was less marked. We conclude that, armed with this quantitative analysis of sensitivity and dexterity impairment, surgeons can judge the relative difficulties that may be incurred as a result of wearing the gloves against the benefits that they offer in protection.

Current techniques in total knee replacement: results of a national survey

A postal questionnaire was sent to all Fellows of the British Orthopaedic Association to obtain a census of total knee replacement (TKR) preferences in the United Kingdom; 1162 questionnaires were sent and 721 replies received. There were 92 Fellows who had retired or filled in the forms incorrectly, and 32 no longer perform TKR. Thus, 597 responded correctly, giving a 62% response rate. This gives an extrapolated total of 34,677 TKRs being implanted per year in the UK, with an average of 34.3 being performed by each surgeon per year. Only 9% perform more than 90 per year. There were 41 different prostheses in current use among the respondents to our questionnaire, of which five prostheses constituted 61% of the total. Cemented prostheses were used by 95.2%. Resurfacing of the patella was always carried out by 32%, while 19% never resurface it; the most common reason for doing so being patellofemoral arthropathy at operation. Intramedullary alignment was used for the femoral component in 86%, 76% preferred extramedullary alignment for the tibial component. Regarding cementing technique, 43% use pulsatile lavage, 9% used a cement gun, 88% dry the bone and 56% seal the hole made by the femoral alignment device in the femur before cementing. All components were cemented simultaneously by 65% and one at a time by 31%. Metal-backed tibial prostheses are now used by 98% of surgeons, modular tibial components being preferred by 80%. Metal-backed patellar components were used by 13%. An onlay type of patella was preferred by 51%. This survey highlights the great diversity of surgical practice in the UK, which may reflect uncertainty regarding best practice in total knee replacement.

Drosophila melanogaster contains both X-linked and autosomal homologues of the gene encoding calcineurin B

A transcription unit was identified in the 43E polytene band region of the second chromosome of Drosophila melanogaster (Dm) whose putative translation product has 85% amino acid (aa) identity with the B subunit of the calcineurin protein (CnB) from humans. Unlike the previously described intronless Dm CnB gene homologue, which is located within the 4F band region of the X chromosome, the coding region of this second CnB is found to be interrupted by three introns. Conceptual translation of both Dm CnB genes predict proteins of identical size that are 98% identical in aa sequence. Northern blot analyses indicate that Dm pupae and adults express two different CnB-encoding transcripts that are differentially regulated.

Hemophilic ankle arthropathy

Ankle arthropathy remains a frequent source of disability in the hemophilic patient. Bleeding into the ankle most commonly commences in the second decade, and, once established as a target joint, progressive damage leads to significant pain, stiffness, and deformity affecting general mobility and leisure and occupational pursuits. Review of cohorts of hemophilic patients at the Royal Free Hospital has monitored this deterioration and there is no evidence that, despite improvements in medical treatment, the pattern of insidious decline in hindfoot function has changed during the past 4 decades. Based on these observations, a combined clinical and radiologic scoring system has been developed, incorporating ankle specific features, such as talar tilt, tibial osteophytes, and talar dome flattening, which give a better correlation than traditional systems with objective measures, such as treadmill walking. There is no substitution for prophylactic treatment in arresting ankle function decline, and surgical interventions are rare. However, the types of potential procedures are numerous and choices must be made according to the degree of disability and state of overall damage to the joint and adjacent soft tissues.

Ipsilateral total shoulder and elbow prosthetic replacement in a patient with severe haemophilia B

Since factor replacement concentrates became widely available in the 1970s, total prosthetic replacement of joints in haemophilic patients has become increasingly common, with success particularly in the knee and hip. However, there has been no published series of elbow or shoulder replacements large enough to draw conclusions about the advisability of these procedures in this group of patients. We report a case of prosthetic replacement of the shoulder in a 58-year-old man with haemophilia B, and replacement of the elbow joint of the same limb 21 months later. The results are initially very encouraging, with no pain in either joint since the early post-operative period. There have been no bleeds into either joint since surgery. Ranges of movement are satisfactory. Follow-up is now 37 months for the shoulder and 16 months for the elbow.

Evaluation of three methods for the rapid identification of Staphylococcus aureus in blood cultures

A total of 445 blood cultures containing Gram-positive cocci in clusters were tested for the presence of Staphylococcus aureus with the Accuprobe, heat-stable thermonuclease, and latex agglutination using Staphaurex. The results show that the Accuprobe, thermonuclease, and Staphaurex correctly identified 95, 96, and 62 of the 100 specimens containing S. aureus. The corresponding specificity for the methods was 99.1%, 100%, and 98.5%, respectively.

A neural gene from Drosophila melanogaster with homology to vertebrate and invertebrate glutamate decarboxylases

Cross-species hybridization has been used to isolate a second Drosophila gene, with homology to a feline glutamate decarboxylase (Gad) cDNA. The gene differs in sequence, chromosomal location, and spatial expression from the previously reported Drosophila Gad gene, but both encode proteins of 58 kDa. The derived amino acid sequence reveals a typical pyridoxal phosphate binding site and sequence homology consistent with a glutamate decarboxylase function. The protein includes an amino-terminal polyasparagine sequence, and a beta-pleated sheet region, with regularly spaced glutamine and arginine residues, not found in other decarboxylases. Expression in the adult is limited to the neuropil of the first optic ganglion and to regions of the thoracic musculature that may correspond to the location of motor neuron axons. This is consistent with a glial localization for the transcript. There is no overlap with the reported expression of Drosophila Gad. Although the molecular evidence suggests that this gene encodes a pyridoxal phosphate-dependent decarboxylase, glutamate decarboxylase activity associated with this gene could not be demonstrated, and the in vivo substrate is unknown. It is possible that the protein encoded by this gene is novel, not only in sequence and spatial expression, but also in substrate specificity.

Laser-induced protein-DNA cross-links via psoralen furanside monoadducts

We have developed a technique for cross-linking DNA binding proteins to DNA using psoralen furanside monoadducts as photoaffinity probes and a continuous-wave argon ion laser (366 nm) as a light source. Several DNA binding proteins (T7 RNA polymerase, UvrB, single-stranded DNA binding protein of Escherichia coli, T4 gp32, and RecA of E. coli) are shown to cross-link to single-stranded psoralen monoadducted DNA oligos differing in length and sequence. Increasing fluences of laser light on a fixed ratio of DNA/protein resulted in an increase in the yield of cross-links. Titration experiments were carried out to measure the apparent cross-linking constant (KappXL) for T7 RNA polymerase or UvrB to a monoadducted 24 mer DNA. The estimated values for the apparent cross-linking constant were in the range of (2-3) x 10(-7) M for both T7 RNA polymerase and UvrB. The efficiency of cross-linking was investigated as a function of the length of adducted DNA and also as a fraction of the total noncovalent binding of proteins of psoralenated DNAs. The results showed that in the cases of T7 RNA polymerase and UvrB cross-linking was more efficient with short oligos (8 and 19 mers) as compared to longer oligos (50 mer). A tryptic peptide of T7 RNA polymerase that was conjugated to a psoralen furanside monoadducted 12 mer DNA was isolated by high-performance liquid chromatography. Mass spectrometry and amino acid composition of this peptide revealed that it originated from a region between residues 558 and 608 of the primary structure of T7 RNA polymerase. Two other peptides cross-linked to oligos were also purified. Repeated attempts to perform Edman sequencing of the peptide-DNA conjugates failed. Overall evidence indicates that photo-cross-linking of furanside monoadducts occurred at multiple sites on the proteins. We have shown that T7 RNA polymerase molecules in a ternary complex arrested at the furanside monoadduct can be cross-linked to the DNA templates with laser light. Evidence suggests that the arrested polymerase molecules existed in multiple conformations on the DNA template. This method of transcriptional cross-linking offers a new method for preparing highly stable elongation complexes for further studies.

Active site of (A)BC excinuclease. II. Binding, bending, and catalysis mutants of UvrB reveal a direct role in 3' and an indirect role in 5' incision

UvrB plays a central role in (A)BC excinuclease. To study its role in the incision reactions, conserved His and Asp residues in this subunit were mutagenized. All His and the majority of Asp mutants behaved like wild-type protein in vivo and in vitro. However, three mutants, D337A, D478A, and D510A, either completely or partially abolished UvrB activity. All three mutant proteins associate with UvrA normally but D337A and D510A were unable to bind to DNA specifically. The UvrB-D478A mutant bound to DNA specifically but failed to denature and kink the DNA. However, UvrB-D478A was efficiently loaded onto DNA preincised at the 3' site and promoted near-normal incision by UvrC at the 5' site. We propose that D478 is involved in bending DNA and catalysis of the 3' incision and that the 3' incision precedes the 5' incision. UvrB which is missing the carboxyl-terminal 43 amino acids binds to, and kinks DNA but is unable to make the 3' incision suggesting that it is missing a residue involved in catalysis. This residue was identified to be E639 by site-specific mutagenesis.

Identification of a Drosophila gene encoding a calmodulin-binding protein with homology to the trp phototransduction gene

We have isolated a number of Drosophila cDNAs on the basis of their encoding calmodulin-binding proteins. A full-length cDNA clone corresponding to one of these genes has been cloned and sequenced. Conservation of amino acid sequence and tissue-specific expression are observed between this gene and the transient receptor potential (trp) gene. We propose the name transient receptor potential-like (trpl) to describe this newly isolated gene. The trpl protein contains two possible calmodulin-binding sites, six transmembrane regions, and a sequence homologous to an ankyrin-like repeat. Structurally, the trpl and trp proteins resemble cation channel proteins, particularly the brain isoform of the voltage-sensitive Ca2+ channel. The identification of a protein similar to the trp gene product, yet also able to bind Ca2+/calmodulin, allows for a reinterpretation of the phenotype of the trp mutations and suggests that both genes may encode light-sensitive ion channels.