Aerosol measurement identifies SARS-CoV 2 PCR positive adults compared with healthy controls.

BACKGROUND: SARS-CoV-2 is spread primarily through droplets and aerosols. Exhaled aerosols are generated in the upper airways through shear stress and in the lung periphery by 'reopening of collapsed airways'. Aerosol measuring may detect highly contagious individuals ("super spreaders or super-emitters") and discriminate between SARS-CoV-2 infected and non-infected individuals. This is the first study comparing exhaled aerosols in SARS-CoV-2 infected individuals and healthy controls. DESIGN: A prospective observational cohort study in 288 adults, comprising 64 patients testing positive by SARS CoV-2 PCR before enrollment, and 224 healthy adults testing negative (matched control sample) at the University Hospital Frankfurt, Germany, from February to June 2021. Study objective was to evaluate the concentration of exhaled aerosols during physiologic breathing in SARS-CoV-2 PCR-positive and -negative subjects. Secondary outcome measures included correlation of aerosol concentration to SARS-CoV-2 PCR results, change in aerosol concentration due to confounders, and correlation between clinical symptoms and aerosol. RESULTS: There was a highly significant difference in respiratory aerosol concentrations between SARS-CoV-2 PCR-positive (median 1490.5/L) and -negative subjects (median 252.0/L; p < 0.0001). There were no significant differences due to age, sex, smoking status, or body mass index. ROC analysis showed an AUC of 0.8918. CONCLUSIONS: Measurements of respiratory aerosols were significantly elevated in SARS-CoV-2 positive individuals, which helps to understand the spread and course of respiratory viral infections, as well as the detection of highly infectious individuals.

De Novo Variants in TAOK1 Cause Neurodevelopmental Disorders.

De novo variants represent a significant cause of neurodevelopmental delay and intellectual disability. A genetic basis can be identified in only half of individuals who have neurodevelopmental disorders (NDDs); this indicates that additional causes need to be elucidated. We compared the frequency of de novo variants in patient-parent trios with (n = 2,030) versus without (n = 2,755) NDDs. We identified de novo variants in TAOK1 (thousand and one [TAO] amino acid kinase 1), which encodes the serine/threonine-protein kinase TAO1, in three individuals with NDDs but not in persons who did not have NDDs. Through further screening and the use of GeneMatcher, five additional individuals with NDDs were found to have de novo variants. All eight variants were absent from gnomAD (Genome Aggregation Database). The variant carriers shared a non-specific phenotype of developmental delay, and six individuals had additional muscular hypotonia. We established a fibroblast line of one mutation carrier, and we demonstrated that reduced mRNA levels of TAOK1 could be increased upon cycloheximide treatment. These results indicate nonsense-mediated mRNA decay. Further, there was neither detectable phosphorylated TAO1 kinase nor phosphorylated tau in these cells, and mitochondrial morphology was altered. Knockdown of the ortholog gene Tao1 (Tao, CG14217) in Drosophila resulted in delayed early development. The majority of the Tao1-knockdown flies did not survive beyond the third instar larval stage. When compared to control flies, Tao1 knockdown flies revealed changed morphology of the ventral nerve cord and the neuromuscular junctions as well as a decreased number of endings (boutons). Furthermore, mitochondria in mutant flies showed altered distribution and decreased size in axons of motor neurons. Thus, we provide compelling evidence that de novo variants in TAOK1 cause NDDs.

Quantitative Depth Profiling Using Online-Laser Ablation of Solid Samples in Liquid (LASIL) to Investigate the Oxidation Behavior of Transition Metal Borides.

The increased demand for sustainability requires, among others, the development of new materials with enhanced corrosion resistance. Transition metal diborides are exceptional candidates, as they exhibit fascinating mechanical and thermal properties. However, at elevated temperatures and oxidizing atmospheres, their use is limited due to the fact of their inadequate oxidation resistance. Recently, it was found that chromium diboride doped with silicon can overcome this limitation. Further improvement of this protective coating requires detailed knowledge regarding the composition of the forming oxide layer and the change in the composition of the remaining thin film. In this work, an analytical method for the quantitative measurement of depth profiles without using matrix-matched reference materials was developed. Using this approach, based on the recently introduced online-LASIL technique, it was possible to achieve a depth resolution of 240 nm. A further decrease in the ablation rate is possible but demands a more sensitive detection of silicon. Two chromium diboride samples with different Si contents suffering an oxidation treatment were used to demonstrate the capabilities of this technique. The concentration profiles resembled the pathway of the formed oxidation layers as monitored with transmission electron microscopy. The stoichiometry of the oxidation layers differed strongly between the samples, suggesting different processes were taking place. The validity of the LASIL results was cross-checked with several other analytical techniques.

[Development of specific guidance for the safe opening and operation of recreational destinations under pandemic conditions]. / Entwicklung konkreter Handlungsoptionen für die sichere Öffnung und den Betrieb von Freizeitdestinationen unter Pandemiebedingungen.

Background: The SARS-CoV­2 pandemic led to the closure of leisure and recreation facilities worldwide. As part of a model study funded by the Baden-Wuerttemberg Ministry of Social Affairs, Health and Integration, it was possible to demonstrate how a hygiene and safety concept can be successfully implemented in practice using the example of the opening and operation of an amusement park in Baden-Wuerttemberg (Germany) under scientific supervision. Objective: The aim of the model project was, besides the verification of a possible infection event through a visit to the amusement park, to develop and review a recommended course of action for the safe opening and operation of leisure facilities under pandemic conditions, which can be transferred to other destinations. Methods: A variety of data sources were used for this project: Recurrent expert rounds of multidisciplinary teams (business administration, healthcare research, sociology and medicine), aerosol measurement data, observation protocols, official infection statistics and interview data from visitor surveys. Results: The action plan developed in this project provides guidance and recommendations for operators of recreation and leisure facilities to implement measures that enhance staff and guest safety, allowing facilities to operate under pandemic conditions. Conclusion: This study sets a precedent using the example of a recreational park in Baden-Wuerttemberg (Germany) to serve as a guide for other facilities; however, operations in the leisure and tourism sector are unique and measures are accordingly difficult to transfer directly. The recommended action plan is further intended to support policy makers in future pandemic situations regarding measures to close, open and operate such facilities.

Activation of Apoptosis in a ßB1-CTGF Transgenic Mouse Model.

To reveal the pathomechanisms of glaucoma, a common cause of blindness, suitable animal models are needed. As previously shown, retinal ganglion cell and optic nerve degeneration occur in ßB1-CTGF mice. Here, we aimed to determine possible apoptotic mechanisms and degeneration of different retinal cells. Hence, retinae were processed for immunohistology (n = 5-9/group) and quantitative real-time PCR analysis (n = 5-7/group) in 5- and 10-week-old ßB1-CTGF and wildtype controls. We noted significantly more cleaved caspase 3+ cells in ßB1-CTGF retinae at 5 (p = 0.005) and 10 weeks (p = 0.02), and a significant upregulation of Casp3 and Bax/Bcl2 mRNA levels (p < 0.05). Furthermore, more terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL+) cells were detected in transgenic mice at 5 (p = 0.03) and 10 weeks (p = 0.02). Neurofilament H staining (p = 0.01) as well as Nefh (p = 0.02) and Tubb3 (p = 0.009) mRNA levels were significantly decreased at 10 weeks. GABAergic synapse intensity was lower at 5 weeks, while no alterations were noted at 10 weeks. The glutamatergic synapse intensity was decreased at 5 (p = 0.007) and 10 weeks (p = 0.01). No changes were observed for bipolar cells, photoreceptors, and macroglia. We conclude that apoptotic processes and synapse loss precede neuronal death in this model. This slow progression rate makes the ßB1-CTGF mice a suitable model to study primary open-angle glaucoma.

Loss of retinal ganglion cells in a new genetic mouse model for primary open-angle glaucoma.

Primary open-angle glaucoma (POAG) is one of the most common causes for blindness worldwide. Although an elevated intraocular pressure (IOP) is the main risk factor, the exact pathology remained indistinguishable. Therefore, it is necessary to have appropriate models to investigate these mechanisms. Here, we analysed a transgenic glaucoma mouse model (ßB1-CTGF) to elucidate new possible mechanisms of the disease. Therefore, IOP was measured in ßB1-CTGF and wildtype mice at 5, 10 and 15 weeks of age. At 5 and 10 weeks, the IOP in both groups were comparable (P > 0.05). After 15 weeks, a significant elevated IOP was measured in ßB1-CTGF mice (P < 0.001). At 15 weeks, electroretinogram measurements were performed and both the a- and b-wave amplitudes were significantly decreased in ßB1-CTGF retinae (both P < 0.01). Significantly fewer Brn-3a+ retinal ganglion cells (RGCs) were observed in the ßB1-CTGF group on flatmounts (P = 0.02), cross-sections (P < 0.001) and also via quantitative real-time PCR (P = 0.02). Additionally, significantly more cleaved caspase 3+ RGCs were seen in the ßB1-CTGF group (P = 0.002). Furthermore, a decrease in recoverin+ cells was observable in the ßB1-CTGF animals (P = 0.004). Accordingly, a significant down-regulation of Recoverin mRNA levels were noted (P < 0.001). Gfap expression, on the other hand, was higher in ßB1-CTGF retinae (P = 0.023). Additionally, more glutamine synthetase signal was noted (P = 0.04). Although no alterations were observed regarding photoreceptors via immunohistology, a significant decrease of Rhodopsin (P = 0.003) and Opsin mRNA (P = 0.03) was noted. We therefore assume that the ßB1-CTGF mouse could serve as an excellent model for better understanding the pathomechanisms in POAG.

Development of an evidence-based algorithm that optimizes sensitivity and specificity in ES-based diagnostics of a clinically heterogeneous patient population.

PURPOSE: Next-generation sequencing (NGS) is rapidly replacing Sanger sequencing in genetic diagnostics. Sensitivity and specificity of NGS approaches are not well-defined, but can be estimated from applying NGS and Sanger sequencing in parallel. Utilizing this strategy, we aimed at optimizing exome sequencing (ES)-based diagnostics of a clinically diverse patient population. METHODS: Consecutive DNA samples from unrelated patients with suspected genetic disease were exome-sequenced; comparatively nonstringent criteria were applied in variant calling. One thousand forty-eight variants in genes compatible with the clinical diagnosis were followed up by Sanger sequencing. Based on a set of variant-specific features, predictors for true positives and true negatives were developed. RESULTS: Sanger sequencing confirmed 81.9% of ES-derived variants. Calls from the lower end of stringency accounted for the majority of the false positives, but also contained ~5% of the true positives. A predictor incorporating three variant-specific features classified 91.7% of variants with 100% specificity and 99.75% sensitivity. Confirmation status of the remaining variants (8.3%) was not predictable. CONCLUSIONS: Criteria for variant calling in ES-based diagnostics impact on specificity and sensitivity. Confirmatory sequencing for a proportion of variants, therefore, remains a necessity. Our study exemplifies how these variants can be defined on an empirical basis.

Predicting Visual Acuity by Using Machine Learning in Patients Treated for Neovascular Age-Related Macular Degeneration.

PURPOSE: To predict, by using machine learning, visual acuity (VA) at 3 and 12 months in patients with neovascular age-related macular degeneration (AMD) after initial upload of 3 anti-vascular endothelial growth factor (VEGF) injections. DESIGN: Database study. PARTICIPANTS: For the 3-month VA forecast, 653 patients (379 female) with 738 eyes and an average age of 74.1 years were included. The baseline VA before the first injection was 0.54 logarithm of the minimum angle of resolution (logMAR) (±0.39). A total of 456 of these patients (270 female, 508 eyes, average age: 74.2 years) had sufficient follow-up data to be included for a 12-month VA prediction. The baseline VA before the first injection was 0.56 logMAR (±0.42). METHODS: Five different machine-learning algorithms (AdaBoost.R2, Gradient Boosting, Random Forests, Extremely Randomized Trees, and Lasso) were used to predict VA in patients with neovascular AMD after treatment with 3 anti-VEGF injections. Clinical data features came from a data warehouse (DW) containing electronic medical records (41 features, e.g., VA) and measurement features from OCT (124 features, e.g., central retinal thickness). The VA of patient eyes excluded from machine learning was predicted and compared with the ground truth, namely, the actual VA of these patients as recorded in the DW. MAIN OUTCOME MEASURES: Difference in logMAR VA after 3 and 12 months upload phase between prediction and ground truth as defined. RESULTS: For the 3-month VA forecast, the difference between the prediction and ground truth was between 0.11 logMAR (5.5 letters) mean absolute error (MAE)/0.14 logMAR (7 letters) root mean square error (RMSE) and 0.18 logMAR (9 letters) MAE/0.2 logMAR (10 letters) RMSE. For the 12-month VA forecast, the difference between the prediction and ground truth was between 0.16 logMAR (8 letters) MAE/0.2 logMAR (10 letters) RMSE and 0.22 logMAR (11 letters) MAE/0.26 logMAR (13 letters) RMSE. The best performing algorithm was the Lasso protocol. CONCLUSIONS: Machine learning allowed VA to be predicted for 3 months with a comparable result to VA measurement reliability. For a forecast after 12 months of therapy, VA prediction may help to encourage patients adhering to intravitreal therapy.

COMPLIANCE AND ADHERENCE OF PATIENTS WITH DIABETIC MACULAR EDEMA TO INTRAVITREAL ANTI-VASCULAR ENDOTHELIAL GROWTH FACTOR THERAPY IN DAILY PRACTICE.

PURPOSE: We assessed differences in compliance and adherence (lateness of patients, visual acuity, reasons for abstaining) between patients with diabetic macular edema (DME) and patients with age-related macular degeneration (AMD), both under anti-vascular endothelial growth factor therapy. METHODS: We included 136 patients with DME (36% women, 65 years, 22 visits, 13.9 injections, and 29.9 months of follow-up) and 109 patients with AMD (59% women, 76 years, 20 visits, 14.7 injections, and 22.3 months of follow-up) (minimum follow-up of 12 months and at least 5 injections). We assessed missed appointments (lateness >14 days) and therapy break-offs (lateness >100 days). All delayed patients were called and interviewed for abstaining reasons. RESULTS: Forty-six percent of patients with DME and 22% of patients with AMD had at least one break-off. Thirty-five percent of patients with DME and 50% of patients with AMD were always on schedule. In patients with DME, there was significant correlation (P = 0.017) between the number of break-offs and change of visual acuity. In 60% DME and 38% AMD of break-off cases, visual acuity was worse than the before break-off. The most common reason for abstaining was comorbidities (33% AMD and 20% DME). CONCLUSION: There are significant differences between patients with AMD and DME regarding compliance and adherence, which also affects outcome. Strategies to tie patients with DME to costly intravitreal therapy need to be developed to improve outcomes and efficacy.

Prediction uncertainty estimates elucidate the limitation of current NSCLC subtype classification in representing mutational heterogeneity.

The heterogeneous pathogenesis and treatment response of non-small cell lung cancer (NSCLC) has led clinical treatment decisions to be guided by NSCLC subtypes, with lung adenocarcinoma and lung squamous cell carcinoma being the most common subtypes. While histology-based subtyping remains challenging, NSCLC subtypes were found to be distinct at the transcriptomic level. However, unlike genomic alterations, gene expression is generally not assessed in clinical routine. Since subtyping of NSCLC has remained elusive using mutational data, we aimed at developing a neural network model that simultaneously learns from adenocarcinoma and squamous cell carcinoma samples of other tissue types and is regularized using a neural network model trained from gene expression data. While substructures of the expression-based manifold were captured in the mutation-based manifold, NSCLC classification accuracy did not significantly improve. However, performance was increased when rejecting inconclusive samples using an ensemble-based approach capturing prediction uncertainty. Importantly, SHAP analysis of misclassified samples identified co-occurring mutations indicative of both NSCLC subtypes, questioning the current NSCLC subtype classification to adequately represent inherent mutational heterogeneity. Since our model captures mutational patterns linked to clinical heterogeneity, we anticipate it to be suited as foundational model of genomic data for clinically relevant prognostic or predictive downstream tasks.

The clinically relevant triple mutation in the mtND1 gene inactivates Escherichia coli complex I.

NADH:ubiquinone oxidoreductase (respiratory complex I) plays a major role in cellular energy metabolism. Complex I deficiencies are the most common cause of mitochondrial dysfunction. Patients suffering from a variety of neurodegenerative diseases carry numerous mutations in the mitochondrially encoded subunits of the complex. The biochemical consequences of these mutations are largely unknown because these genes are difficult to access experimentally. Here, we use Escherichia coli as a model system to characterize the effect of a 7 bps inversion in mtND1 (m.3902-3908inv7) that results in a triple mutation. The triple mutant grew poorly but contained a normal amount of the stably assembled variant. The variant showed no enzymatic activity, which might contribute to the deleterious effect of the mutation in humans.

Elemental mapping of fluorine by means of molecular laser induced breakdown spectroscopy.

The growing importance of fluoropolymers in high-tech applications and green technologies results in the rising need for their characterization. In contrast to conventional methods used for this task, laser-induced breakdown spectroscopy (LIBS) provides the advantage of a spatially resolved analysis. Nevertheless, the high excitation energy of fluorine results in low sensitivity of the atomic F(I) lines, which limits the feasibility of its LIBS-based analysis. This work presents a novel approach for quantitative mapping of fluorine in fluoropolymer samples. It bases on monitoring of molecular emission bands (CuF or CaF) arising from fluorine containing molecules. These species were generated during later stages of the LIBS plasma by a recombination of fluorine atoms originating from fluoropolymer sample with a molecule-forming partner (Cu or Ca) stemming from a surface coating. This approach enables F detection limits in the parts per million (µg g-1) range and elemental imaging using single shot measurements. The elements required for molecular formation are deposited on the sample surface prior to analysis. We evaluate two techniques - spray coating and sputter coating - with regards to their effects on sensitivity and spatial resolution in elemental mapping. Overall, both methods proved to be suitable for a spatially resolved analysis of fluorine: whereas sputter-coating of copper yielded a better sensitivity, spray coating of calcium provided a higher spatial resolution.

Performance modulation through selective, homogenous surface doping of lanthanum strontium ferrite electrodes revealed by in situ PLD impedance measurements.

Accelerating the oxygen reduction kinetics of solid oxide fuel cell (SOFC) cathodes is crucial to improve their efficiency and thus to provide the basis for an economically feasible application of intermediate temperature SOFCs. In this work, minor amounts of Pt were doped into lanthanum strontium ferrite (LSF) thin film electrodes to modulate the material's oxygen exchange performance. Surprisingly, Pt was found to be incorporated on the B-site of the perovskite electrode as non metallic Pt4+. The polarization resistance of LSF thin film electrodes with and without additional Pt surface doping was compared directly after film growth employing in situ electrochemical impedance spectroscopy inside a PLD chamber (i-PLD). This technique enables observation of the polarization resistance of pristine electrodes unaltered by degradation or any external contamination of the electrode surface. Moreover, growth of multi-layers of materials with different compositions on the very same single crystalline electrolyte substrate combined with in situ impedance measurements allow excellent comparability of different materials. Even a 5 nm layer of Pt doped LSF (1.5 at% Pt), i.e. a Pt loading of 80 ng cm-2, improved the polarization resistance by a factor of about 2.5. In addition, p(O2) and temperature dependent impedance measurements on both pure and Pt doped LSF were performed in situ and obtained similar activation energies and p(O2) dependence of the polarization resistance, which allow us to make far reaching mechanistic conclusions indicating that Pt4+ introduces additional active sites.

In situ techniques reveal the true capabilities of SOFC cathode materials and their sudden degradation due to omnipresent sulfur trace impurities.

In this study, five different mixed conducting cathode materials were grown as dense thin films by pulsed laser deposition (PLD) and characterized via in situ impedance spectroscopy directly after growth inside the PLD chamber (i-PLD). This technique enables quantification of the oxygen reduction kinetics on pristine and contaminant-free mixed conducting surfaces. The measurements reveal excellent catalytic performance of all pristine materials with polarization resistances being up to two orders of magnitude lower than those previously reported in the literature. For instance, on dense La0.6Sr0.4CoO3-δ thin films, an area specific surface resistance of ∼0.2 Ω cm2 at 600 °C in synthetic air was found, while values usually >1 Ω cm2 are measured in conventional ex situ measurement setups. While surfaces after i-PLD measurements were very clean, ambient pressure X-ray photoelectron spectroscopy (AP-XPS) measurements found that all samples measured in other setups were contaminated with sulfate adsorbates. In situ impedance spectroscopy during AP-XPS revealed that already trace amounts of sulfur present in high purity gases accumulate quickly on pristine surfaces and lead to strongly increased surface polarization resistances, even before the formation of a SrSO4 secondary phase. Accordingly, the inherent excellent catalytic properties of this important class of materials were often inaccessible so far. As a proof of concept, the fast kinetics observed on sulfate-free surfaces were also realized in ex situ measurements with a gas purification setup and further reduces the sulfur concentration in the high purity gas.

Exhaled Aerosols in SARS-CoV-2 Polymerase Chain Reaction-Positive Children and Age-Matched-Negative Controls.

Background: Children and adolescents seem to be less affected by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease in terms of severity, especially until the increasing spread of the omicron variant in December 2021. Anatomical structures and lower number of exhaled aerosols may in part explain this phenomenon. In a cohort of healthy and SARS-CoV-2 infected children, we compared exhaled particle counts to gain further insights about the spreading of SARS-CoV-2. Materials and Methods: In this single-center prospective observational trial, a total of 162 children and adolescents (age 6-17 years), of whom 39 were polymerase chain reaction (PCR)-positive for SARS-CoV-2 and 123 PCR-negative, were included. The 39 PCR-positive children were compared to 39 PCR-negative age-matched controls. The data of all PCR-negative children were analyzed to determine baseline exhaled particle counts in children. In addition, medical and clinical history was obtained and spirometry was measured. Results: Baseline exhaled particle counts were low in healthy children. Exhaled particle counts were significantly increased in SARS-CoV-2 PCR-positive children (median 355.0/L; range 81-6955/L), compared to age-matched -negative children (median 157.0/L; range 1-533/L; p < 0.001). Conclusion: SARS-CoV-2 PCR-positive children exhaled significantly higher levels of aerosols than healthy children. Overall children had low levels of exhaled particle counts, possibly indicating that children are not the major driver of the SARS-CoV-2 pandemic. Trial Registration: [ClinicalTrials.gov], Identifier [NCT04739020].

Revisited: Comparison of Empirical Methods to Evaluate Visualizations Supporting Crafting and Assembly Purposes.

Ubiquitous, situated, and physical visualizations create entirely new possibilities for tasks contextualized in the real world, such as doctors inserting needles. During the development of situated visualizations, evaluating visualizations is a core requirement. However, performing such evaluations is intrinsically hard as the real scenarios are safety-critical or expensive to test. To overcome these issues, researchers and practitioners adapt classical approaches from ubiquitous computing and use surrogate empirical methods such as Augmented Reality (AR), Virtual Reality (VR) prototypes, or merely online demonstrations. This approach's primary assumption is that meaningful insights can also be gained from different, usually cheaper and less cumbersome empirical methods. Nevertheless, recent efforts in the Human-Computer Interaction (HCI) community have found evidence against this assumption, which would impede the use of surrogate empirical methods. Currently, these insights rely on a single investigation of four interactive objects. The goal of this work is to investigate if these prior findings also hold for situated visualizations. Therefore, we first created a scenario where situated visualizations support users in do-it-yourself (DIY) tasks such as crafting and assembly. We then set up five empirical study methods to evaluate the four tasks using an online survey, as well as VR, AR, laboratory, and in-situ studies. Using this study design, we conducted a new study with 60 participants. Our results show that the situated visualizations we investigated in this study are not prone to the same dependency on the empirical method, as found in previous work. Our study provides the first evidence that analyzing situated visualizations through different empirical (surrogate) methods might lead to comparable results.

Depletion of Boric Acid and Cobalt from Cultivation Media: Impact on Recombinant Protein Production with Komagataella phaffii.

The REACH regulation stands for "Registration, Evaluation, Authorization and Restriction of Chemicals" and defines certain substances as harmful to human health and the environment. This urges manufacturers to adapt production processes. Boric acid and cobalt dichloride represent such harmful ingredients, but are commonly used in yeast cultivation media. The yeast Komagataella phaffii (Pichia pastoris) is an important host for heterologous protein production and compliance with the REACH regulation is desirable. Boric acid and cobalt dichloride are used as boron and cobalt sources, respectively. Boron and cobalt support growth and productivity and a number of cobalt-containing enzymes exist. Therefore, depletion of boric acid and cobalt dichloride could have various negative effects, but knowledge is currently scarce. Herein, we provide an insight into the impact of boric acid and cobalt depletion on recombinant protein production with K. phaffii and additionally show how different vessel materials affect cultivation media compositions through leaking elements. We found that boric acid could be substituted through boron leakiness from borosilicate glassware. Furthermore, depletion of boric acid and cobalt dichloride neither affected high cell density cultivation nor cell morphology and viability on methanol. However, final protein quality of three different industrially relevant enzymes was affected in various ways.

Novel pathogenic variants and multiple molecular diagnoses in neurodevelopmental disorders.

BACKGROUND: Rare denovo variants represent a significant cause of neurodevelopmental delay and intellectual disability (ID). METHODS: Exome sequencing was performed on 4351 patients with global developmental delay, seizures, microcephaly, macrocephaly, motor delay, delayed speech and language development, or ID according to Human Phenotype Ontology (HPO) terms. All patients had previously undergone whole exome sequencing as part of diagnostic genetic testing with a focus on variants in genes implicated in neurodevelopmental disorders up to January 2017. This resulted in a genetic diagnosis in 1336 of the patients. In this study, we specifically searched for variants in 14 recently implicated novel neurodevelopmental disorder (NDD) genes. RESULTS: We identified 65 rare, protein-changing variants in 11 of these 14 novel candidate genes. Fourteen variants in CDK13, CHD4, KCNQ3, KMT5B, TCF20, and ZBTB18 were scored pathogenic or likely pathogenic. Of note, two of these patients had a previously identified cause of their disease, and thus, multiple molecular diagnoses were made including pathogenic/likely pathogenic variants in FOXG1 and CDK13 or in TMEM237 and KMT5B. CONCLUSIONS: Looking for pathogenic variants in newly identified NDD genes enabled us to provide a molecular diagnosis to 14 patients and their close relatives and caregivers. This underlines the relevance of re-evaluation of existing exome data on a regular basis to improve the diagnostic yield and serve the needs of our patients.

Clinical exome sequencing: results from 2819 samples reflecting 1000 families.

We report our results of 1000 diagnostic WES cases based on 2819 sequenced samples from 54 countries with a wide phenotypic spectrum. Clinical information given by the requesting physicians was translated to HPO terms. WES processes were performed according to standardized settings. We identified the underlying pathogenic or likely pathogenic variants in 307 families (30.7%). In further 253 families (25.3%) a variant of unknown significance, possibly explaining the clinical symptoms of the index patient was identified. WES enabled timely diagnosing of genetic diseases, validation of causality of specific genetic disorders of PTPN23, KCTD3, SCN3A, PPOX, FRMPD4, and SCN1B, and setting dual diagnoses by detecting two causative variants in distinct genes in the same patient. We observed a better diagnostic yield in consanguineous families, in severe and in syndromic phenotypes. Our results suggest that WES has a better yield in patients that present with several symptoms, rather than an isolated abnormality. We also validate the clinical benefit of WES as an effective diagnostic tool, particularly in nonspecific or heterogeneous phenotypes. We recommend WES as a first-line diagnostic in all cases without a clear differential diagnosis, to facilitate personal medical care.

Next-generation sequencing of the BRCA1 and BRCA2 genes for the genetic diagnostics of hereditary breast and/or ovarian cancer.

Genetic testing for hereditary breast and/or ovarian cancer mostly relies on laborious molecular tools that use Sanger sequencing to scan for mutations in the BRCA1 and BRCA2 genes. We explored a more efficient genetic screening strategy based on next-generation sequencing of the BRCA1 and BRCA2 genes in 210 hereditary breast and/or ovarian cancer patients. We first validated this approach in a cohort of 115 samples with previously known BRCA1 and BRCA2 mutations and polymorphisms. Genomic DNA was amplified using the Ion AmpliSeq BRCA1 and BRCA2 panel. The DNA Libraries were pooled, barcoded, and sequenced using an Ion Torrent Personal Genome Machine sequencer. The combination of different robust bioinformatics tools allowed detection of all previously known pathogenic mutations and polymorphisms in the 115 samples, without detecting spurious pathogenic calls. We then used the same assay in a discovery cohort of 95 uncharacterized hereditary breast and/or ovarian cancer patients for BRCA1 and BRCA2. In addition, we describe the allelic frequencies across 210 hereditary breast and/or ovarian cancer patients of 74 unique definitely and likely pathogenic and uncertain BRCA1 and BRCA2 variants, some of which have not been previously annotated in the public databases. Targeted next-generation sequencing is ready to substitute classic molecular methods to perform genetic testing on the BRCA1 and BRCA2 genes and provides a greater opportunity for more comprehensive testing of at-risk patients.