Cryogenic Optical Position Encoders for Mechanisms in the JWST Optical Telescope Element Simulator (OSIM)

The JWST Optical Telescope Element Simulator (OSIM) is a configurable, cryogenic, optical stimulus for high fidelity ground characterization and calibration of JWST's flight instruments. OSIM and its associated Beam Image Analyzer (BIA) contain several ultra-precise, cryogenic mechanisms that enable OSIM to project point sources into the instruments according to the same optical prescription as the flight telescope images stars - correct in focal surface position and chief ray angle. OSIM's and BIA's fifteen axes of mechanisms navigate according to redundant, cryogenic, absolute, optical encoders - 32 in all operating at or below 100 K. OSIM's encoder subsystem, the engineering challenges met in its development, and the encoders' sub-micron and sub-arcsecond performance are discussed

SARS Antibody Testing in Children: Development of Oral Fluid Assays for IgG Measurements.

Seroepidemiological studies to monitor antibody kinetics are important for assessing the extent and spread of SARS-CoV-2 in a population. Noninvasive sampling methods are advantageous for reducing the need for venipuncture, which may be a barrier to investigations, particularly in pediatric populations. Oral fluids are obtained by gingiva-crevicular sampling from children and adults and are very well accepted. Enzyme immunoassays (EIAs) based on these samples have acceptable sensitivity and specificity compared to conventional serum-based antibody EIAs and are suitable for population-based surveillance. We describe the development and evaluation of SARS-CoV-2 IgG EIAs using SARS-CoV-2 viral nucleoprotein (NP) and spike (S) proteins in IgG isotype capture format and an indirect receptor-binding-domain (RBD) IgG EIA, intended for use in children as a primary endpoint. All three assays were assessed using a panel of 1,999 paired serum and oral fluids from children and adults participating in school SARS-CoV-2 surveillance studies during and after the first and second pandemic wave in the United Kingdom. The anti-NP IgG capture assay was the best candidate, with an overall sensitivity of 75% (95% confidence interval [CI]: 71 to 79%) and specificity of 99% (95% CI: 78 to 99%) compared with paired serum antibodies. Sensitivity observed in children (80%, 95% CI: 71 to 88%) was higher than that in adults (67%, CI: 60% to 74%). Oral fluid assays (OF) using spike protein and RBD antigens were also 99% specific and achieved reasonable but lower sensitivity in the target population (78%, 95% CI [68% to 86%] and 53%, 95% CI [43% to 64%], respectively). IMPORTANCE We report on the first large-scale assessment of the suitability of oral fluids for detection of SARS-CoV-2 antibody obtained from healthy children attending school. The sample type (gingiva-crevicular fluid, which is a transudate of blood but is not saliva) can be self collected. Although detection of antibodies in oral fluids is less sensitive than that in blood, our study suggests an optimal format for operational use. The laboratory methods we have developed can reliably measure antibodies in children, who are able to take their own samples. Our findings are of immediate practical relevance for use in large-scale seroprevalence studies designed to measure exposure to infection, as they typically require venipuncture. Overall, our data indicate that OF assays based on the detection of SARS-CoV-2 antibodies are a tool suitable for population-based seroepidemiology studies in children and highly acceptable in children and adults, as venipuncture is no longer necessary

Biofilm dynamics : linking in situ biofilm biomass and metabolic activity measurements in real-time under continuous flow conditions

CITATION: Klopper, K. B., et al. Biofilm dynamics : linking in situ biofilm biomass and metabolic activity measurements in real-time under continuous flow conditions. npj Biofilms and Microbiomes, 6:42, doi:10.1038/s41522-020-00153-9.The original publication is available at https://www.nature.comPublication of this article was funded by the Stellenbosch University Open Access FundThe tools used to study biofilms generally involve either destructive, end-point analyses or periodic measurements. The advent of the internet of things (IoT) era allows circumvention of these limitations. Here we introduce and detail the development of the BioSpec; a modular, nondestructive, real-time monitoring system, which accurately and reliably track changes in biofilm biomass over time. The performance of the system was validated using a commercial spectrophotometer and produced comparable results for variations in planktonic and sessile biomass. BioSpec was combined with the previously developed carbon dioxide evolution measurement system (CEMS) to allow simultaneous measurement of biofilm biomass and metabolic activity and revealed a differential response of these interrelated parameters to changing environmental conditions. The application of this system can facilitate a greater understanding of biofilm mass–function relationships and aid in the development of biofilm control strategies.https://www.nature.com/articles/s41522-020-00153-9Publisher's versio

Specific Variants in the MLH1 Gene Region May Drive DNA Methylation, Loss of Protein Expression, and MSI-H Colorectal Cancer

Background: We previously identified an association between a mismatch repair gene, MLH1, promoter SNP (rs1800734) and microsatellite unstable (MSI-H) colorectal cancers (CRCs) in two samples. The current study expanded on this finding as we explored the genetic basis of DNA methylation in this region of chromosome 3. We hypothesized that specific polymorphisms in the MLH1 gene region predispose it to DNA methylation, resulting in the loss of MLH1 gene expression, mismatch-repair function, and consequently to genome-wide microsatellite instability. Methodology/Principal Findings: We first tested our hypothesis in one sample from Ontario (901 cases, 1,097 controls) and replicated major findings in two additional samples from Newfoundland and Labrador (479 cases, 336 controls) and from Seattle (591 cases, 629 controls). Logistic regression was used to test for association between SNPs in the region of MLH1 and CRC, MSI-H CRC, MLH1 gene expression in CRC, and DNA methylation in CRC. The association between rs1800734 and MSI-H CRCs, previously reported in Ontario and Newfoundland, was replicated in the Seattle sample. Two additional SNPs, in strong linkage disequilibrium with rs1800734, showed strong associations with MLH1 promoter methylation, loss of MLH1 protein, and MSI-H CRC in all three samples. The logistic regression model of MSI-H CRC that included MLH1-promotermethylation status and MLH1 immunohisotchemistry status fit most parsimoniously in all three samples combined. When rs1800734 was added to this model, its effect was not statistically significant (P-value = 0.72 vs. 2.361024 when the SNP was examined alone). Conclusions/Significance: The observed association of rs1800734 with MSI-H CRC occurs through its effect on the MLH1 promoter methylation, MLH1 IHC deficiency, or both

Logistic regression model results for MSI status with various predictor combinations in the combined data.

<p>Age at diagnosis, sex, and location are covariates common to all the models described above. IHC refers to the MLH1 immunohistochemical staining variable, CH3 refers to the <i>MLH1</i> promoter methylation variable, AIC  =  Akaike's information criterion. Logistic regression models for each SNP per study population and for the combined data are shown in <b>Supplementary <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013314#pone.0013314.s003" target="_blank">File S3</a></b>.</p><p>The role of three SNPs of interest, rs1800734, rs749072, and rs13098279, is explored.</p

Region of chromosome 3 examined with genes and 3 SNPs.

<p>A total of 99 polymorphisms were examined in the Ontario samples across a 500kb region of chromosome 3 surrounding the <i>MLH1</i> gene. Genes in this region are outlined (top panel) along with their transcriptional directionality (bottom panel). The three polymorphisms of interest are indicated. Modified from Ensembl (<a href="http://www.ensembl.org" target="_blank">www.ensembl.org</a>).</p

Proposed model for genetic susceptibility to DNA methylation in sporadic MSI-H CRCs.

<p>Specific SNPs predispose the region, including the <i>MLH1</i> gene promoter, to methylation, which results in promoter silencing and loss of <i>MLH1</i> gene expression that is measured by immunohistochemical staining. Loss of the <i>MLH1</i> gene expression leads to genome-wide microsatellite instability and MSI-H colorectal cancer.</p

Single marker analysis in the combined data for 3 SNPs for CRC cases versus controls, <i>MLH1</i> promoter methylation, MLH1 IHC staining and MSI tumor status.

<p>Analyses of CRC cases versus controls are adjusted for age, sex, and site.</p><p>OR  =  odds ratio, CI  =  confidence interval.</p><p>Single marker results for the above SNPs for each study population are shown in <b>Supplementary <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013314#pone.0013314.s002" target="_blank">File S2</a></b>.</p