US National Institutes of Health Prioritization of SARS-CoV-2 Variants

Since late 2020, SARS-CoV-2 variants have regularly emerged with competitive and phenotypic differences from previously circulating strains, sometimes with the potential to escape from immunity produced by prior exposure and infection. The Early Detection group is one of the constituent groups of the US National Institutes of Health National Institute of Allergy and Infectious Diseases SARS-CoV-2 Assessment of Viral Evolution program. The group uses bioinformatic methods to monitor the emergence, spread, and potential phenotypic properties of emerging and circulating strains to identify the most relevant variants for experimental groups within the program to phenotypically characterize. Since April 2021, the group has prioritized variants monthly. Prioritization successes include rapidly identifying most major variants of SARS-CoV-2 and providing experimental groups within the National Institutes of Health program easy access to regularly updated information on the recent evolution and epidemiology of SARS-CoV-2 that can be used to guide phenotypic investigations.

1409. Genomic Variation Among Respiratory Syncytial Viruses

Background

Respiratory Syncytial Virus (RSV) can be easily classified into two subtypes (A and B) based on the nucleic acid sequence of their genome. Phylogenic approaches have shown that within both subtypes separate lineages of viruses exist and new lineages continue to emerge. The role these genomic variations play in disease severity during RSV infection is largely unknown.

Methods

Next-generation viral RNA sequencing was performed on archived frozen nasal swabs of children infected with RSV in Rochester, NY between 1977-1998. Genomic variation was compared across year-of-isolation, age of host, and inpatient/outpatient status of host. Local RSV genomic variation was compared to variation of publicly available sequences isolated from hosts residing in other parts of the world.

Results

A and B subtypes demonstrated significant differences in the genetic sequence and primary-protein structure over time. G-protein was the most variable in both subtypes, but they differed in the number of unique genotypes detected. We found a significant association with disease severity (inpatient/outpatient status) and RSV phylogenetic topology, although the magnitude of the association differed by subtype. Variation in the primary protein structure of RSV viral proteins was also significantly associated with disease severity, but depended on which viral protein, and which subtype, was investigated. Lastly, local RSV genomic and protein-structure variation was similar to what was seen globally during this time period.

Conclusion

Overall, both subtypes demonstrated significant genetic change over time and these changes were associated with disease severity. These results suggest that the genetic variability of RSV may affect RSV disease in humans.

Disclosures

All Authors: No reported disclosures

Integrated Single-Cell Atlases Reveal an Oral SARS-CoV-2 Infection and Transmission Axis

Despite signs of infection, the involvement of the oral cavity in COVID-19 is poorly understood. To address this, single-cell RNA sequencing data-sets were integrated from human minor salivary glands and gingiva to identify 11 epithelial, 7 mesenchymal, and 15 immune cell clusters. Analysis of SARS-CoV-2 viral entry factor expression showed enrichment in epithelia including the ducts and acini of the salivary glands and the suprabasal cells of the mucosae. COVID-19 autopsy tissues confirmed in vivo SARS-CoV-2 infection in the salivary glands and mucosa. Saliva from SARS-CoV-2-infected individuals harbored epithelial cells exhibiting ACE2 expression and SARS-CoV-2 RNA. Matched nasopharyngeal and saliva samples found distinct viral shedding dynamics and viral burden in saliva correlated with COVID-19 symptoms including taste loss. Upon recovery, this cohort exhibited salivary antibodies against SARS-CoV-2 proteins. Collectively, the oral cavity represents a robust site for COVID-19 infection and implicates saliva in viral transmission.

The new versatile general purpose surface-muon instrument (GPS) based on silicon photomultipliers for μSR measurements on a continuous-wave beam

We report on the design and commissioning of a new spectrometer for muon-spin relaxation/rotation studies installed at the Swiss Muon Source (SμS) of the Paul Scherrer Institute (PSI, Switzerland). This new instrument is essentially a new design and replaces the old general-purpose surface-muon (GPS) instrument that has been for long the workhorse of the μSR user facility at PSI. By making use of muon and positron detectors made of plastic scintillators read out by silicon photomultipliers, a time resolution of the complete instrument of about 160 ps (standard deviation) could be achieved. In addition, the absence of light guides, which are needed in traditionally built μSR instrument to deliver the scintillation light to photomultiplier tubes located outside magnetic fields applied, allowed us to design a compact instrument with a detector set covering an increased solid angle compared with the old GPS.

A mathematical framework for virtual IMRT QA using machine learning

PURPOSE

It is common practice to perform patient-specific pretreatment verifications to the clinical delivery of IMRT. This process can be time-consuming and not altogether instructive due to the myriad sources that may produce a failing result. The purpose of this study was to develop an algorithm capable of predicting IMRT QA passing rates a priori.

METHODS

From all treatment, 498 IMRT plans sites were planned in eclipse version 11 and delivered using a dynamic sliding window technique on Clinac iX or TrueBeam Linacs. 3%/3 mm local dose/distance-to-agreement (DTA) was recorded using a commercial 2D diode array. Each plan was characterized by 78 metrics that describe different aspects of their complexity that could lead to disagreements between the calculated and measured dose. A Poisson regression with Lasso regularization was trained to learn the relation between the plan characteristics and each passing rate.

RESULTS

Passing rates 3%/3 mm local dose/DTA can be predicted with an error smaller than 3% for all plans analyzed. The most important metrics to describe the passing rates were determined to be the MU factor (MU per Gy), small aperture score, irregularity factor, and fraction of the plan delivered at the corners of a 40 × 40 cm field. The higher the value of these metrics, the worse the passing rates.

CONCLUSIONS

The Virtual QA process predicts IMRT passing rates with a high likelihood, allows the detection of failures due to setup errors, and it is sensitive enough to detect small differences between matched Linacs.

VDJServer: a web-accessible analysis portal for immune repertoire sequence data (HUM1P.317)

Despite the importance and widespread application of detailed antigen receptor repertoire profiling via high-throughput sequencing, there is currently no suite of software tools for seamless, reproducible analysis of repertoire sequence data. Tools exist for only a subset of analysis tasks. They do not function together and are difficult to reuse without modification that requires bioinformatics expertise. This leaves researchers to perform repetitive and error-prone tasks by hand, to develop internal, idiosyncratic algorithms not easily generalizable or systematically applied, and to expend significant manual labor reformatting primary and derived data for passing between tools. This approach is not only error-prone and time- and labor-intensive, but it comes at the expense of reproducibility, both within and between research groups. We have addressed this problem by developing VDJServer, a suite of repertoire analysis tools accessible via a web interface that allows users to upload a set of antigen receptor repertoire sequences and pass them through a seamless, customizable workflow that executes all steps in the analysis and generates analysis reports complete with data summary tables, statistical analyses, figures, and workflow logs. VDJServer runs on the high-performance computing resources at the Texas Advanced Computing Center, thus enabling users to process extremely large data sets. VDJServer is funded by the NIAID and is freely available.

Direct spectroscopic observation of a shallow hydrogenlike donor state in insulating SrTiO3

We present a direct spectroscopic observation of a shallow hydrogenlike muonium state in SrTiO(3) which confirms the theoretical prediction that interstitial hydrogen may act as a shallow donor in this material. The formation of this muonium state is temperature dependent and appears below ∼ 70K. From the temperature dependence we estimate an activation energy of ∼ 50 meV in the bulk and ∼ 23 meV near the free surface. The field and directional dependence of the muonium precession frequencies further supports the shallow impurity state with a rare example of a fully anisotropic hyperfine tensor. From these measurements we determine the strength of the hyperfine interaction and propose that the muon occupies an interstitial site near the face of the oxygen octahedron in SrTiO(3). The observed shallow donor state provides new insight for tailoring the electronic and optical properties of SrTiO(3)-based oxide interface systems.

FlowCAP: comparison of automated and manual gating of standardized lyoplate flow cytometry data (P3374)

Standardization of immunological assays, including flow cytometry, in terms of reagents, sample handling, instrument setup, and data analysis, is essential for successful cross-study and cross-center analysis in order to mitigate the effects of technical variability in assay results. The Human Immunology Project and the Federation of Clinical Immunology Societies (FOCIS) have partnered to develop five standardized, lyophilized, eight-color staining reagent panels (termed lyoplates) for this purpose. In collaboration with the FlowCAP consortium, standardized samples (Cytotrol control cells) were distributed to nine participating centers and analyzed by flow cytometry using the lyoplate reagents and SOP's to minimize experimental variability. Data from two of these panels (T-cell and B-cell) were entered into the FlowCAP-III challenge, where participants analyzed the data using automated gating methods for comparison against cell population statistics for major T and B-cell subsets as defined by a consensus manual gating scheme. This evaluation showed that several automated gating algorithms could successfully recapitulate centralized manual gating statistics for T-cell and B-cell subsets with little statistical bias, and with within-center and between-center variability as low or lower than centralized manual gating. These results demonstrate that automated gating algorithms are ready for use in performing reproducible analyses and comparisons of immunological data.

New Vesicle Gels in Household Applications

Stable dispersions of either gas bubbles or solid particles like abrasives become increasingly attractive for the home care market. The property to yield a stable dispersion is not necessarily linked to a high viscosity in general but requires a highly viscous, solid-like behaviour under rest as well as a liquid-like flow behaviour under shear. A gel comprising such a yield zone can be obtained by creating multi-lamellar vesicles with a rather stiff shell. Due to the repulsion forces of opposite electric charges the combination of suitable anionic and cationic surfactants yields vesicles that are inflexible enough to comprise a yield zone. Surfactants which are appropriate to yield suitable vesicle gels can be chosen according to their spatial dimensions since the geometry of the molecules determines their aggregation behaviour. With this, new formulation possibilities for bathroom cleaners or scouring liquids are available.

Photo-induced persistent inversion of germanium in a 200-nm-deep surface region

The controlled manipulation of the charge carrier concentration in nanometer thin layers is the basis of current semiconductor technology and of fundamental importance for device applications. Here we show that it is possible to induce a persistent inversion from n- to p-type in a 200-nm-thick surface layer of a germanium wafer by illumination with white and blue light. We induce the inversion with a half-life of ~12 hours at a temperature of 220 K which disappears above 280 K. The photo-induced inversion is absent for a sample with a 20-nm-thick gold capping layer providing a Schottky barrier at the interface. This indicates that charge accumulation at the surface is essential to explain the observed inversion. The contactless change of carrier concentration is potentially interesting for device applications in opto-electronics where the gate electrode and gate oxide could be replaced by the semiconductor surface.

Significant association of specific DRB1 & DQB1 sequence feature variant types with systemic sclerosis autoantibodies types and racial groups (159.20)

The sequence feature variant type (SFVT) approach to genetic association analysis has previously identified parts of HLA proteins that are associated with development of a variety of autoimmune diseases. Using the SFVT approach, we analyzed DRB1 and DQB1 typing data in a cohort of patients with Systemic Sclerosis (SSc). While no traditional class II alleles were significant across three racial groups (African American, Caucasian and Hispanic), 23 related DRB1 SFVTs were found in common. We also found that while more than 80% of the same sequence features (SFs) were significantly associated with the presence of either anti-centromere or anti-topoisomerase antibodies for each of the loci, only 2 (3%) and 5 (8%) of the risk-associated variant types (VTs) for DRB1 and DQB1, respectively, were shared, indicating that the same SFs but different VTs are associated with the presence of the different autoantibodies. Intriguingly, several protective anti-topoisomerase VTs corresponded to the risky anti-centromere VTs. We found that SFVTs that differ by only a few amino acids can give rise to different autoantibodies in SSc patients (e.g. association of the antigen binding motif 67L_70Q_71R with anti-centromere, versus association of 67F_70D_71R with anti-topoisomerase). Tools in ImmPort (www.immport.org) for the conversion of four-digit HLA typing data into an SFVT data matrix and the calculation of chi-squared association statistics were used for the analysis.

Design and commissioning of a high magnetic field muon spin relaxation spectrometer at the ISIS pulsed neutron and muon source

The high magnetic field (HiFi) muon instrument at the ISIS pulsed neutron and muon source is a state-of-the-art spectrometer designed to provide applied magnetic fields up to 5 T for muon studies of condensed matter and molecular systems. The spectrometer is optimised for time-differential muon spin relaxation studies at a pulsed muon source. We describe the challenges involved in its design and construction, detailing, in particular, the magnet and detector performance. Commissioning experiments have been conducted and the results are presented to demonstrate the scientific capabilities of the new instrument.

Comparison of antibody gene mutation patterns in first attack optic neuritis and transverse myelitis leading to Multiple Sclerosis (47.18)

Multiple Sclerosis (MS) is the leading disease of the central nervous system and a significant, costly cause of disability in young adults. Patients at risk for MS often present with a single demyelinating event, typically called a “clinically isolated syndrome” (CIS). A CIS can occur in the brain, spinal cord (Acute Partial Transverse Myelitis, APTM), or optic nerve (Optic Neuritis, ON) at similar rates and present a challenging diagnostic and therapeutic dilemma. Stratifying CIS patients most likely to develop MS is a complicated process, but desirable since treatment with the appropriate immunomodulatory agents early in the disease course can delay long-term disability. Thus, a primary focus of our laboratory has been to develop a completely novel type of biomarker that can identify CIS patients that will develop MS. This unique biomarker is based on a pattern of antibody gene mutations (i.e. antibody gene signature or “AGS”) that is exclusive to B cells from the cerebrospinal fluid and brain lesions of MS patients that initially presented with either TM or ON. In fact, the AGS is consistently elevated in patients with one attack of ON that go on to develop definite MS, and can predict conversion to MS with 91% accuracy. More recently, we are testing the hypothesis that the AGS serves as a predictor for conversion to MS in CIS patients that present with TM. Preliminary data demonstrate that the AGS is also prevalent in CIS patients presenting with TM.

Automated analysis of multi-dimensional B-cell flow cytometry data (44.23)

Understanding B cell diversity and its functional correlates requires the combined study of large numbers of surface and intracellular molecules. Advances in multi-parameter flow cytometry (FCM) allow for the independent detection of many fluorochromes on individual cells. However, traditional gating strategies based on single or two-color displays are inadequate for separating cell populations defined in multi-dimensional space. We have developed a novel program, FLOCK, which uses density-based clustering to algorithmically identify cell subsets in multi-dimensional space in an unbiased fashion, reducing operator variability. FLOCK has been used to accurately identify and quantify 17 distinct B cell subsets in human peripheral blood, including novel plasmablast subsets after tetanus vaccination. It is being used to monitor B cell subsets in different autoimmune conditions including systemic lupus erythematosus patients treated with BAFF inhibitors. FLOCK has been assessed by the FlowCAP consortium (Critical Assessment of Population Identification Methods), and achieved encouraging results in a recent FlowCAP competition compared with other automated methods. FLOCK has been implemented in the publically available Immunology Database and Analysis Portal - ImmPort (www.immport.org) for open use by the immunology research community. Core modules of FLOCK will also be integrated into GenePattern of the Broad Institute as a component of the FCM analysis suite.

FlowCAP: critical assessment of flow cytometry population identification methods (65.2)

Traditional methods for flow cytometry (FCM) data processing have relied on manual gating of cell events to define cell populations for statistical analysis. However, this approach has become increasingly problematic with the advances in instrumentation and reagents that allow for evaluation of larger numbers of cell properties. Recently several groups have developed computational methods for automatically identifying cell populations in multidimensional FCM data obviating the need for manual gating. In order to compare the performance of these methods, the Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP) competition was established to make available a common set of FCM data together with manual gating results for comparative analysis. The first FlowCAP competition included 5 different data sets with data from 12-30 samples containing 5000-100,000 cell events stained with 3-10 fluorochrome markers. We received 36 analysis result submissions from 14 research groups. Both model fitting and density-based clustering methods were found to perform well in comparison with manual gating by domain experts as the gold standard, using statistical tests to measure and rank algorithm performance. In addition, combining results using a computational “ensemble” method was found to outperform all individual methods. These results suggest that, in the near future, automated computational methods may become an integral part of routine FCM data analysis.

Analysis of DRB1 sequence feature variant type associations with systemic sclerosis autoantibodies types and racial groups (47.28)

A novel sequence feature variant type (SFVT) approach to genetic association analysis has been previously shown to identify parts of HLA proteins that are associated with the development of a variety of autoimmune diseases. Using the SFVT approach, we analyzed DRB1 typing data in a cohort of patients with Systemic Sclerosis (SSc) and demographically matched controls. We found no allele that was significant at p-value of 0.05 across all the three racial groups (African American, Caucasian and Hispanic) in the dataset. But, we found 23 SFVTs that were significant across the all three racial groups. In the analysis of SFVT association with the presence or absence of different auto-antibodies, we found a large overlap among the top significant sequence features (SFs). In spite of such overlap of SFs the top 100 SFVTs were exclusively associated with the presence of either anti-centromere or anti-topoisomerase but not both, indicating that different DRB1 sequences predispose to the development of different auto-antibody types. In addition, we found that SFVTs that differ by only a few amino acids can give rise to different autoantibodies in SSc patients (e.g. association of the antigen binding motif 67L_70Q_71R with anti-centromere, versus association of 67F_70D_71R with anti-topoisomerase). Tools for the conversion of four-digit HLA typing data into an SFVT data matrix and the calculation of chi-squared association statistics have been implemented in ImmPort (www.immport.org).

An HLA allele frequency-based approach to resolving allelic and genotypic ambiguity in HLA typing data and its implementation in ImmPort (65.22)

The classical human leukocyte antigen (HLA) loci are the most polymorphic loci in the human genome, with hundreds of new alleles reported yearly. HLA polymorphisms in exons 2 and 3 of class I loci and in exon 2 of class II loci distinguish the peptide binding regions of HLA proteins. Current HLA typing methodologies focus on identifying variant positions in these exons, and most do not detect allelic variation in other exons or non-coding regions of HLA genes. Because of the limitations in detecting polymorphic variants and the pace of new allele discovery, commonly used HLA typing methodologies cannot unambiguously identify all known HLA alleles or genotypes. Consequently, many HLA genotyping results are ambiguous in that both alleles of each HLA locus for a given subject may have multiple possible identities, and each subject may have multiple possible genotypes. Here, we describe an approach to allelic and genotypic ambiguity resolution that uses published HLA allele frequencies in 10 world regions to determine the most likely diploid alleles and genotype for each subject in an HLA typing study. This method has been implemented in an online tool at www.ImmPort.org, and is freely available for use by the immunology community. This ambiguity reduction tool will allow investigators studying autoimmune disease, adverse drug reactions, transplantation outcome and other HLA associated conditions to more accurately determine the contribution of specific HLA alleles to disease.

Automated determination of optimal microarray data processing (144.11)

Gene expression microarrays are widely used to study genome-wide gene expression profiles. Many microarray analysis methods are available, making it challenging to decide which method to use. While the effectiveness of some of these methods has been assessed using artificial spike-in data sets, analytical approaches that work well with spike-in data may not work as well with data from real biological samples. To evaluate these methods we applied Gene Ontology (GO) term co-clustering as a comparative tool to evaluate 300 different data processing pipelines composed of various background correction, normalization and summarization methods using real biological data, based on the premise that an improvement in any step of microarray data analysis should be reflected in improved co-clustering of related genes. Our results suggest that background correction has little affect on GO term co-clustering characteristics, normalization has a big impact, some summarization methods constantly outperform others, some interdependencies exist among these methods, e.g., a good normalization method may work well with one summarization method but not another. An automated method for running and assessing these 300 pipelines has been made available through the Immunology Database and Analysis Portal (ImmPort; www.immport.org) - a public database resource funded by NIAID to support the management and analysis of clinical and mechanistic data generated by their funded investigators.

Minimum Information About a Genotyping Experiment (MIGen) (88.8)

Genotyping experiments are widely used in clinical and basic research laboratories to identify associations between genes and normal/abnormal phenotypes. Genotyping assay techniques vary from PCR reactions in a test tube with gel electrophoresis detection to high throughput chip or bead array assay employing various technologies for automatic genotype calls. Depending on the study purpose and design, the resulting genotype data could involve millions of markers for thousands of individuals, requiring substantial data analysis using various statistical, modeling or other methodologies. To date, there is no standard for reporting genotyping experiments. Here we present the Minimum Information About a Genotyping Experiment (MIGen) standard. MIGen recommends the standard information required to report a genotyping experiment, covering: study and experiment design, subject information, sample collection and processing, genotyping procedure, and data analysis methods, if applicable. The goal of MIGen is to set a reporting standard for adoption by the research community to facilitate consistent data interpretation and independent validation/reproduction, and to serve as guidance for database design for storing genotyping experiment data. MIGen is being developed as a collaborative project involving international domain experts and is a registered project under MIBBI: Minimum Information for Biological and Biomedical Investigations. Supported by NIH N01AI40076.

HLA motifs associated with autoantibody production and cross-racial similarities in systemic sclerosis using the SFVT approach (93.37)

Significant associations have been found between specific HLA alleles and a variety of autoimmune diseases. Current studies treat each HLA allele as a single complete unit, which does not distinguish the parts of the molecule associated with disease or the production of particular autoantibodies. This approach also cannot uncover similarities in different predisposing alleles across races. We previously developed a novel approach for genetic association analysis in which HLA proteins are broken down into smaller sequence features (SF) with polymorphisms in these features categorized as variant types (VT). Using the SFVT approach, we analyzed DRB1, DQA1 and DQB1 typing data in a cohort of patients with Systemic Sclerosis (SSc) and demographically matched controls. We found similar predisposing and protective SFVTs in African Americans, Caucasians and Hispanics (e.g. the predisposing 67F_70D_71R peptide binding/TCR recognition motif) despite differences in the frequencies of predisposing and protective alleles that carry these SFVTs in these populations. In addition, we found that SFVTs that differ by only a few amino acids are significantly associated with the presence or absence of different autoantibodies in SSc patients (e.g. the antigen binding motif 9W_57D_60Y_67L was associated with anti-centromere, while 9E_57D_60Y_67F was associated with anti-topoisomerase). These results highlight the ability of the SFVT approach to shed light on the role of HLA in autoimmune disease.

Automated analysis of flow cytometry data for the identification of cellular markers of allergy therapeutic responses (91.2)

Mechanistic studies of biological specimens obtained during the conduct of clinical trials are frequently used to identify markers of therapeutic responses and to understand the underlying physiological processes associated with therapeutic efficacy. The Immunology Database and Analysis Portal (ImmPort; www.immport.org) is a public database resource funded by NIAID to support the management and analysis of clinical and mechanistic data generated by their funded investigators. We demonstrate the use of the ImmPort clinical data management platform and novel data analysis methods in the analysis of the allergen immunotherapy experiments conducted by the Casale group of Immune Tolerance Network. In the Casale study, immune response assays were conducted on samples taken before, during and after a 12-week course of allergen-specific immunotherapy to investigate whether anti-IgE antibody (omalizumab) can enhance the safety and efficacy of rush immunotherapy. Flow cytometry data was re-analyzed with FLOCK, a novel automated flow cytometry analysis pipeline in ImmPort, to determine if the level of any blood cell population correlated with treatment conditions. The analysis has identified a unique cell population expressing CD14, CXCR3 and high levels of the Fc-epsilon receptor (CD23), which is significantly increased in patients undergoing rush immunotherapy. Such data-driven analysis using ImmPort can generate hypotheses for further experimental design and verification.

Direct measurement of the electronic spin diffusion length in a fully functional organic spin valve by low-energy muon spin rotation

Electronic devices that use the spin degree of freedom hold unique prospects for future technology. The performance of these 'spintronic' devices relies heavily on the efficient transfer of spin polarization across different layers and interfaces. This complex transfer process depends on individual material properties and also, most importantly, on the structural and electronic properties of the interfaces between the different materials and defects that are common to real devices. Knowledge of these factors is especially important for the relatively new field of organic spintronics, where there is a severe lack of suitable experimental techniques that can yield depth-resolved information about the spin polarization of charge carriers within buried layers of real devices. Here, we present a new depth-resolved technique for measuring the spin polarization of current-injected electrons in an organic spin valve and find the temperature dependence of the measured spin diffusion length is correlated with the device magnetoresistance.

Intrinsic mobility limit for anisotropic electron transport in Alq3

Muon spin relaxation has been used to probe the charge carrier motion in the molecular conductor Alq3 (tris[8-hydroxy-quinoline] aluminum). At 290 K, the magnetic field dependence of the muon spin relaxation corresponds to that expected for highly anisotropic intermolecular electron hopping. Intermolecular mobility in the fast hopping direction has been found to be 0.23+/-0.03 cm2 V-1 s(-1) in the absence of an electric- field gradient, increasing to 0.32+/-0.06 cm2 V-1 s(-1) in an electric field gradient of 1 MV m(-1). These intrinsic mobility values provide an estimate of the upper limit for mobility achievable in bulk material.

Using spin polarised positive muons for studying guest molecule partitioning in soft matter structures

Fully polarised positive muons substituted for protons in organic free radicals can be used as spin labels which reveal information about the structure, dynamics and environment of these radicals. In applications via the technique of avoided-level-crossing muon spin resonance (ALC-microSR), the positive muon has been used to study the partitioning of phenyl alcohols in lamellar phase colloidal dispersions of a cationic dichain surfactant. Here we describe the experimental technique which permits highly sensitive spectroscopy as previously demonstrated for surfactant mixtures. We also demonstrate its capability in the study of partitioning of cosurfactant molecules in surfactant bilayers in order to elucidate the main factors which contribute to cosurfactant ordering at interfaces. The technique takes advantage of the positive muon combining with an electron to a hydrogen-like atom that is called muonium. This atom attaches to a phenyl group, forming a cyclohexadienyl-type radical that contains the muon as a polarised spin label, providing an excellent probe even for very low phenyl alcohol concentrations. The position of one type of resonance, which on the basis of spectroscopic selection rules is denoted as Delta(0), is related to the solvent polarity of the radicals' environment. The results derived from Delta(0) measurements reveal a systematic trend where the increasing chain length of the phenyl alcohol results in a deeper immersion of the phenyl ring of the alcohol into the surfactant bilayer with the OH group anchored at the interface. In addition, the data suggest partial penetration of water molecules into the bilayer. Furthermore, data ensuing from a second resonance (called Delta(1), which is dependent upon the degree of confinement of the radical within the surfactant aggregate structure) indicates not only that the phenyl alcohol resides in an anisotropic environment, (i.e. that the host molecule is unable to undergo full 3-D reorientation on a timescale of 50 ns), but the resonance line widths indicate that the radicals are undergoing fast rotation about a particular axis, in this instance about the first C-C substituent bond at the phenyl ring. Detailed analysis of these Delta(1) line shapes suggests that other types of motion involving reorientation of the above rotation axis are also present. At room temperature, the hydrocarbon chains of the double layers form an aggregate state commonly referred to as the L(beta) phase, where the motions of surfactant alkyl chains are effectively frozen out. These chains melt on heating over a temperature range which is solution composition dependent (ca. 51 to 67 degrees C), but in all cases leading to a liquid-like disordered hydrocarbon regime whilst retaining the overall lamellar structure (and in this state is termed L(alpha)). Above the L(alpha)/L(beta) chain ordering phase transition the tracer molecules reside within the bilayer, but below this transition (and depending on their water-oil solubility) they are completely or partly expelled. This interpretation is further supported by Heisenberg spin exchange experiments. The water-bilayer partitioning reflects both typical classical and nonclassical hydrophobic solvation depending on temperature and chain length of phenyl alcohols.

Cancer dormancy: from mice to man

In this review, we focused on our studies of cancer dormancy in a murine B cell lymphoma and human breast cancer. Lifelong dormancy was induced in syngeneic mice by prior immunization to the idiotype of the tumor cell (TC) Ig before TC challenge. The mice maintained approximately 10(6) lymphoma cells in their spleen throughout their lifetime despite replication of the TCs at a reduced rate. Recurrences occurred randomly. Because of the balance between replication and cell death, we hypothesized that a similar balance might occur in long-term survivors of breast cancer when the risk of recurrences is very low. We developed a sensitive assay for circulating tumor cells (CTCs) which none were found in normal age-matched women. One third of patients, 7-22 years after mastectomy and without any evidence of disease, had CTCs. The half-life of these CTCs could be deduced from other studies as probably 2-3 hours. Hence, there was a precise balance between replication of TCs (presumably from micrometastases) and cell death. Therefore, a major population of clinically cured breast cancer patients have a chronic disease controlled by their own physiological mechanisms. We speculate on underlying mechanisms based both on studies in experimental models and clinical trials.

The immunoglobulin heavy-chain matrix-associating regions are bound by Bright: a B cell-specific trans-activator that describes a new DNA-binding protein family

B lymphocyte-restricted transcription of immunoglobulin heavy-chain (IgH) genes is specified by elements within the variable region (VH) promoter and the intronic enhancer (E mu). The gene encoding a protein that binds a VH promoter proximal site necessary for induced mu-heavy-chain transcription has been cloned. This B-cell specific protein, termed Bright (B cell regulator of IgH transcription), is found in both soluble and matrix insoluble nuclear fractions. Bright binds the minor groove of a restricted ATC sequence that is sufficient for nuclear matrix association. This sequence motif is present in previously described matrix-associating regions (MARs) proximal to the promoter and flanking E mu. Bright can activate E mu-driven transcription by binding these sites, but only when they occur in their natural context and in cell lines permissive for E mu activity. To bind DNA, Bright requires a novel tetramerization domain and a previously undescribed domain that shares identity with several proteins, including SWI1, a component of the SWI/SNF complex.

[Early functional treatment of the injured shoulder supported by an active shoulder bandage]

The following study shows the results of treatment of 29 patients suffering from rotatory cuff lesion and of 20 patients with tendinosis. The results of functional physiotherapy of the patients with rotatory cuff lesion correspond to the results of post-operative treatment described in other studies. As a result of early functional physiotherapy backed up by an active shoulder support, the treatment was both improved and shortened considerably. The accompanying pain relief achieved an earlier usability of the shoulder joint in both groups of patients. Four patients with rotatory cuff lesions were resistant to physiotherapy and finally had to undergo surgery.

Simultaneous gas exchange and fluorescence measurements indicate differences in the response of sunflower, bean and maize to water stress

Gas exchange and fluorescence measurements of attached leaves of water stressed bean, sunflower and maize plants were carried out at two light intensities (250 μmol quanta m(-2)s(-1) and 850 μmol quanta m(-2)s(-1)). Besides the restriction of transpiration and CO2 uptake, the dissipation of excess light energy was clearly reflected in the light and dark reactions of photosynthesis under stress conditions. Bean and maize plants preferentially use non-photochemical quenching for light energy dissipation. In sunflower plants, excess light energy gave rise to photochemical quenching. Autoradiography of leaves after photosynthesis in (14)CO2 demonstrated the occurrence of leaf patchiness in sunflower and maize but not in bean. The contribution of CO2 recycling within the leaves to energy dissipation was investigated by studies in 2.5% oxygen to suppress photorespiration. The participation of different energy dissipating mechanisms to quanta comsumption on agriculturally relevant species is discussed.

Light Energy Dissipation under Water Stress Conditions: Contribution of Reassimilation and Evidence for Additional Processes

Using (14)CO(2) gas exchange and metabolite analyses, stomatal as well as total internal CO(2) uptake and evolution were estimated. Pulse modulated fluorescence was measured during induction and steady state of photosynthesis. Leaf water potential of Digitalis lanata EHRH. plants decreased to -2.5 megapascals after withholding irrigation. By osmotic adjustment, leaves remained turgid and fully exposed to irradiance even at severe water stress. Due to the stress-induced reduction of stomatal conductance, the stomatal CO(2) exchange was drastically reduced, whereas the total CO(2) uptake and evolution were less affected. Stomatal closure induced an increase in the reassimilation of internally evolved CO(2). This ;CO(2) recycling' consumes a significant amount of light energy in the form of ATP and reducing equivalents. As a consequence, the metabolic demand for light energy is only reduced by about 40%, whereas net photosynthesis is diminished by about 70% under severe stress conditions. By CO(2) recycling, carbon flux, enzymatic substrate turnover and consumption of light energy were maintained at high levels, which enabled the plant to recover rapidly after rewatering. In stressed D. lanata plants a variable fluorescence quenching mechanism, termed ;coefficient of actinic light quenching,' was observed. Besides water conservation, light energy dissipation is essential and involves regulated metabolic variations.

Identification of the epsilon-subunit of Escherichia coli DNA polymerase III holoenzyme as the dnaQ gene product: a fidelity subunit for DNA replication

Based on extensive genetic and biochemical studies, the multisubunit DNA polymerase III holoenzyme is considered responsible for the chain-elongation stage in replication of the genome of Escherichia coli and is thus expected to be the major determinant of fidelity as well. Previous experiments have shown that two mutations conferring a very high mutation rate on E. coli, mutD5 and dnaQ49, decrease severely the 3' leads to 5' exonucleolytic editing activity of the polymerase III holoenzyme. To identify more precisely the nature of these mutations, we have carried out genetic mapping and complementation experiments. From these studies and experiments by others, we conclude that the most potent general mutator mutations in E. coli occur in a single gene, dnaQ. To define further the role of the dnaQ gene, we have used two-dimensional gel electrophoresis to compare the labeled dnaQ gene product with purified polymerase III holoenzyme. The dnaQ product comigrates with the epsilon-subunit, a 25-kilodalton protein of the polymerase III "core" enzyme. We conclude that the epsilon-subunit of polymerase III holoenzyme has a special role in defining the accuracy of DNA replication, probably through control of the 3' leads to 5' exonuclease activity.