High-dimensional analysis of 16 SARS-CoV-2 vaccine combinations reveals lymphocyte signatures correlating with immunogenicity.

The range of vaccines developed against severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) provides a unique opportunity to study immunization across different platforms. In a single-center cohort, we analyzed the humoral and cellular immune compartments following five coronavirus disease 2019 (COVID-19) vaccines spanning three technologies (adenoviral, mRNA and inactivated virus) administered in 16 combinations. For adenoviral and inactivated-virus vaccines, heterologous combinations were generally more immunogenic compared to homologous regimens. The mRNA vaccine as the second dose resulted in the strongest antibody response and induced the highest frequency of spike-binding memory B cells irrespective of the priming vaccine. Priming with the inactivated-virus vaccine increased the SARS-CoV-2-specific T cell response, whereas boosting did not. Distinct immune signatures were elicited by the different vaccine combinations, demonstrating that the immune response is shaped by the type of vaccines applied and the order in which they are delivered. These data provide a framework for improving future vaccine strategies against pathogens and cancer.

Stress-triggered hematopoietic stem cell proliferation relies on PrimPol-mediated repriming.

Stem cell division is linked to tumorigenesis by yet-elusive mechanisms. The hematopoietic system reacts to stress by triggering hematopoietic stem and progenitor cell (HSPC) proliferation, which can be accompanied by chromosomal breakage in activated hematopoietic stem cells (HSCs). However, whether these lesions persist in their downstream progeny and induce a canonical DNA damage response (DDR) remains unclear. Inducing HSPC proliferation by simulated viral infection, we report that the associated DNA damage is restricted to HSCs and that proliferating HSCs rewire their DDR upon endogenous and clastogen-induced damage. Combining transcriptomics, single-cell and single-molecule assays on murine bone marrow cells, we found accelerated fork progression in stimulated HSPCs, reflecting engagement of PrimPol-dependent repriming, at the expense of replication fork reversal. Ultimately, competitive bone marrow transplantation revealed the requirement of PrimPol for efficient HSC amplification and bone marrow reconstitution. Hence, fine-tuning replication fork plasticity is essential to support stem cell functionality upon proliferation stimuli.

Histone Ubiquitination by the DNA Damage Response Is Required for Efficient DNA Replication in Unperturbed S Phase.

Chromatin ubiquitination by the ubiquitin ligase RNF168 is critical to regulate the DNA damage response (DDR). DDR deficiencies lead to cancer-prone syndromes, but whether this reflects DNA repair defects is still elusive. We identified key factors of the RNF168 pathway as essential mediators of efficient DNA replication in unperturbed S phase. We found that loss of RNF168 leads to reduced replication fork progression and to reversed fork accumulation, particularly evident at repetitive sequences stalling replication. Slow fork progression depends on MRE11-dependent degradation of reversed forks, implicating RNF168 in reversed fork protection and restart. Consistent with regular nucleosomal organization of reversed forks, the replication function of RNF168 requires H2A ubiquitination. As this novel function is shared with the key DDR players ATM, γH2A.X, RNF8, and 53BP1, we propose that double-stranded ends at reversed forks engage classical DDR factors, suggesting an alternative function of this pathway in preventing genome instability and human disease.

Replication Fork Slowing and Reversal upon DNA Damage Require PCNA Polyubiquitination and ZRANB3 DNA Translocase Activity.

DNA damage tolerance during eukaryotic replication is orchestrated by PCNA ubiquitination. While monoubiquitination activates mutagenic translesion synthesis, polyubiquitination activates an error-free pathway, elusive in mammals, enabling damage bypass by template switching. Fork reversal is driven in vitro by multiple enzymes, including the DNA translocase ZRANB3, shown to bind polyubiquitinated PCNA. However, whether this interaction promotes fork remodeling and template switching in vivo was unknown. Here we show that damage-induced fork reversal in mammalian cells requires PCNA ubiquitination, UBC13, and K63-linked polyubiquitin chains, previously involved in error-free damage tolerance. Fork reversal in vivo also requires ZRANB3 translocase activity and its interaction with polyubiquitinated PCNA, pinpointing ZRANB3 as a key effector of error-free DNA damage tolerance. Mutations affecting fork reversal also induced unrestrained fork progression and chromosomal breakage, suggesting fork remodeling as a global fork slowing and protection mechanism. Targeting these fork protection systems represents a promising strategy to potentiate cancer chemotherapy.

Formation of Peroxynitrite, [O-N-O-O]-, via a Cascade of Reactions between Ozonide and Ammonia.

We report on an unexpected reaction between ammonia and potassium ozonide dissolved in liq. NH3 resulting in the formation of peroxynitrite, [ONOO]-, which exclusively happens in the presence of a specific partially fluorinated aniline-based ammonium cation. High-resolution structural data of the peroxynitrite anion in cis-conformation have been obtained. We further studied this molecule anion by single crystal Raman spectroscopy. The cis and trans isomers of peroxynitrite were analysed computationally with respect to their relative energies, the cis-trans transition barrier and their decomposition pathways to the nitrate anion. By experimentally examining cations decorated with fluorine ligands to different degrees, we demonstrate that fluorine specific interactions play a crucial role in the unexpected formation of peroxynitrite and as a conspicuously structure directing factor for the underlying crystalline solid phases, exhibiting distinct micro-separations of fluorine and hydrogen enriched regions.

Radical C-H Trifluoromethoxylation of (Hetero)arenes with Bis(trifluoromethyl)peroxide.

Trifluoromethoxylated (hetero)arenes are of great interest for several disciplines, especially in agro- and medicinal chemistry. Radical C-H trifluoromethoxylation of (hetero)arenes represents an attractive approach to prepare such compounds, but the high cost and low atom economy of existing . OCF3 radical sources make them unsuitable for the large-scale synthesis of trifluoromethoxylated building blocks. Herein, we introduce bis(trifluoromethyl)peroxide (BTMP, CF3 OOCF3 ) as a practical and efficient trifluoromethoxylating reagent that is easily accessible from inexpensive bulk chemicals. Using either visible light photoredox or TEMPO catalysis, trifluoromethoxylated arenes could be prepared in good yields under mild conditions directly from unactivated aromatics. Moreover, TEMPO catalysis allowed for the one-step synthesis of valuable pyridine derivatives, which have been previously prepared via multi-step approaches.

Generative adversarial networks for the design of acoustic metamaterials.

Metamaterials are attracting increasing interest in the field of acoustics due to their sound insulation effects. By periodically arranged structures, acoustic metamaterials can influence the way sound propagates in acoustic media. To date, the design of acoustic metamaterials relies primarily on the expertise of specialists since most effects are based on localized solutions and interference. This paper outlines a deep learning-based approach to extend current knowledge of metamaterial design in acoustics. We develop a design method by using conditional generative adversarial networks. The generative network proposes a cell candidate regarding a desired transmission behavior of the metamaterial. To validate our method, numerical simulations with the finite element method are performed. Our study reveals considerable insight into design strategies for sound insulation tasks. By providing design directives for acoustic metamaterials, cell candidates can be inspected and tailored to achieve desirable transmission characteristics.

Acoustics Apps: Interactive simulations for digital teaching and learning of acoustics.

This paper presents the Acoustics Apps, an e-learning platform that offers an interactive and playful environment for teaching and learning the principles of acoustics and vibration. The Acoustics Apps address the increasing demand for digitized teaching methods, which might be suitable for home schooling or as a complement to physical experiments by adding interactive simulation. The apps combine learning by experimenting, observing, and exploring using state-of-the-art scientific methods and numerical simulations. The ability to visualize and control acoustic phenomena facilitates understanding of the relevant physical principles. The apps are designed to be used intuitively and can be tailored to suit the existing knowledge of the user. As such, a wide range of users can benefit from this learning aid. It has been developed to allow barrier-free access to modern educational tools, requiring only a device with a browser and Internet access. The necessary computing power is provided by an external server using the COMSOL ServerTM technology. The Acoustics Apps are freely available for academic and teaching purposes at apps.vib.mw.tum.de.

Spatial reconstruction of the sound field in a room in the modal frequency range using Bayesian inference.

Spatial characterization of the sound field in a room is a challenging task, as it usually requires a large number of measurement points. This paper presents a probabilistic approach for sound field reconstruction in the modal frequency range for small and medium-sized rooms based on Bayesian inference. A plane wave expansion model is used to decompose the sound field in the examined domain. The posterior distribution for the amplitude of each plane wave is inferred based on a uniform prior distribution with limits based on the maximum sound pressure observed in the measurements. Two different application cases are studied, namely a numerically computed sound field in a non-rectangular two-dimensional (2D) domain and a measured sound field in a horizontal evaluation area of a lightly damped room. The proposed reconstruction method provides an accurate reconstruction for both examined cases. Further, the results of Bayesian inference are compared to the reconstruction with a deterministic compressive sensing framework. The most significant advantage of the Bayesian method over deterministic reconstruction approaches is that it provides a probability distribution of the sound pressure at every reconstruction point, and thus, allows quantifying the uncertainty of the recovered sound field.

Identification and comparison of two closely related dextransucrases released by water kefir borne Lactobacillus hordei TMW 1.1822 and Lactobacillus nagelii TMW 1.1827.

Dextransucrases are extracellular enzymes, which are exclusively expressed by lactic acid bacteria (LAB) and produce α-1→6 linked glucose polymers from sucrose. In this study, two dextransucrases derived from water kefir borne Lactobacillus hordei TMW 1.1822 and Lactobacillus nagelii TMW 1.1827 were identified and comparatively investigated. Differences between both proteins mainly arise from an additional C-terminal glucan-binding domain and the presence of a signal motif in the L. nagelii TMW 1.1827 dextransucrase. L. hordei TMW 1.1822 released the enzyme only in the presence of its substrate sucrose in contrast to L. nagelii TMW 1.1827, while both strains functionally expressed the dextransucrases independently of sucrose. Both enzymes could be recovered as crude protein extracts in culture supernatants, as they are not covalently bound to the cell surface. This enabled the formation of dextrans at equal reaction conditions as well as their subsequent structural analysis in terms of molecular structure and molecular weight. The volumetric transglycosylation and hydrolysis activities were distinctly different for both enzymes, which produced O3-branched dextrans with a comparable degree of branching. Moreover, identical oligosaccharides were obtained for both dextrans upon endo-dextranase digestion, while some differences in the polysaccharide fine structures could be identified from the varying portions of certain oligosaccharides. Dextrans synthesized by the dextransucrase released by L. nagelii exhibited an averaged molecular weight (Mw) of 7.9×107 Da, while those produced by the dextransucrase released by L. hordei exhibited an Mw of 6.1×107 Da. Moreover, glycosylation of glucansucrases by LAB was identified for the first time for the released dextransucrase of L. nagelii TMW 1.1827. Our study therefore reveals new molecular insights into how dextransucrases released by water kefir borne L. hordei TMW 1.1822 and L. nagelii TMW 1.1827 contribute to the complex formation of the traditional beverage water kefir.

A systematic approach to study the pH-dependent release, productivity and product specificity of dextransucrases.

BACKGROUND: Dextransucrases are extracellular enzymes, which catalyze the formation of α-1→6-linked glucose polymers from sucrose. These enzymes are exclusively expressed by lactic acid bacteria, which commonly acidify the extracellular environment due to their physiology. Dextransucrases are thus confronted with steadily changing reaction conditions in regards to the environmental pH, which can further affect the amount of released dextransucrases. In this work, we studied the effect of the environmental pH on the release, the productivity and the product specificity of the dextransucrase expressed by Lactobacillus (L.) hordei TMW 1.1822. Dextransucrases were recovered as crude extracts at pH 3.5-pH 6.5 and then again used to produce dextrans at these pH values. The respectively produced dextran amounts and sizes were determined and the obtained results finally systematically correlated. RESULTS: Maximum dextran amounts were produced at pH 4.0 and pH 4.5, while the productivity of the dextransucrases significantly decreased at pH 3.5 and pH 6.5. The distribution of dextran amounts produced at different pH most likely reflects the pH dependent activity of the dextransucrases released by L. hordei, since different transglycosylation rates were determined at different pH using the same dextransucrase amounts. Moreover, similar hydrolysis activities were detected at all tested conditions despite significant losses of transglycosylation activities indicating initial hydrolysis prior to transglycosylation reactions. The molar masses and rms radii of dextrans increased up to pH 5.5 independently of the stability of the enzyme. The gelling properties of dextrans produced at pH 4.0 and pH 5.5 were different. CONCLUSIONS: The presented methodological approach allows the controlled production of dextrans with varying properties and could be transferred and adapted to other microbes for systematic studies on the release and functionality of native sucrases or other extracellular enzymes.

Accuracy and tracing time of cephalometric analyses on a tablet or desktop computer : A prospective study.

BACKGROUND: This prospective study aimed to evaluate the influence of the computer type (tablet or desktop) on accuracy and tracing time of cephalometric analyses. METHODS: Dental students used a web-based application specifically developed for this purpose to perform cephalometric analyses on tablet and desktop computers. Landmark locations and timestamps were exported to measure the accuracy, successful detection rate and tracing time. Reference landmarks were established by six experienced orthodontists. Statistical analysis included reliability assessment, descriptive statistics, and linear mixed effect models. RESULTS: Over a period of 8 semesters a total of 277 cephalometric analyses by 161 students were included. The interrater reliability of the orthodontists establishing the reference coordinates was excellent (ICC > 0.9). For the students, the mean landmark deviation was 2.05 mm and the successful detection rate for the clinically acceptable threshold of 2 mm suggested in the literature was 68.6%, with large variations among landmarks. No effect of the computer type on accuracy and tracing time of the cephalometric analyses could be found. CONCLUSION: The use of tablet computers for cephalometric analyses can be recommended.

Quality of occlusal outcome in adult class II patients after maxillary total arch distalization with interradicular mini-screws.

BACKGROUND: The aim of the investigation was to evaluate if a Class II malocclusion in adult patients can be successfully corrected by maxillary total arch distalization with interradicular mini-screws in combination with completely customized lingual appliances (CCLA). METHODS: Two patient groups were matched for age and gender to determine differences in the quality of final treatment outcome. The treatment results of 40 adult patients with a Class I malocclusion (Group 1) were compared with those of 40 adult patients with a moderate to severe Class II malocclusion (Group 2). All patients had completed treatment with a CCLA (WIN, DW Lingual Systems, Bad Essen, Germany) without overcorrection in the individual treatment plan defined by a target set-up. To compare the treatment results of the two groups, 7 measurements using the American Board of Orthodontics Model Grading System (ABO MGS) and linear measurements for anterior-posterior (AP) and vertical dimensions were assessed at the start of lingual treatment (T1), after debonding (T2B), and compared to the individual target set-up (T2A). RESULTS: A statistically significant AP correction (mean 4.5 mm, min/max 2.1/8.6, SD 1.09) was achieved in Group 2, representing 99% of the planned amount. The planned overbite correction was fully achieved in both the Class I and Class II groups. There was a statistically significant improvement in the ABO scores in both groups (Group 1: 39.4 to 17.7, Group 2: 55.8 to 17.1), with no significant difference between the two groups at T2B. 95% of the adult patients in Group 1 and 95% in Group 2 would meet the ABO standards after maxillary total arch distalization with a CCLA and interradicular mini-screws. CONCLUSIONS: CCLAs in combination with interradicular mini-screws for maxillary total arch distalization can successfully correct moderate to severe Class II malocclusions in adult patients. The quality of the final occlusal outcome is high and the amount of the sagittal correction can be predicted by the individual target set-up.

H2AX promotes replication fork degradation and chemosensitivity in BRCA-deficient tumours.

Histone H2AX plays a key role in DNA damage signalling in the surrounding regions of DNA double-strand breaks (DSBs). In response to DNA damage, H2AX becomes phosphorylated on serine residue 139 (known as γH2AX), resulting in the recruitment of the DNA repair effectors 53BP1 and BRCA1. Here, by studying resistance to poly(ADP-ribose) polymerase (PARP) inhibitors in BRCA1/2-deficient mammary tumours, we identify a function for γH2AX in orchestrating drug-induced replication fork degradation. Mechanistically, γH2AX-driven replication fork degradation is elicited by suppressing CtIP-mediated fork protection. As a result, H2AX loss restores replication fork stability and increases chemoresistance in BRCA1/2-deficient tumour cells without restoring homology-directed DNA repair, as highlighted by the lack of DNA damage-induced RAD51 foci. Furthermore, in the attempt to discover acquired genetic vulnerabilities, we find that ATM but not ATR inhibition overcomes PARP inhibitor (PARPi) resistance in H2AX-deficient tumours by interfering with CtIP-mediated fork protection. In summary, our results demonstrate a role for H2AX in replication fork biology in BRCA-deficient tumours and establish a function of H2AX separable from its classical role in DNA damage signalling and DSB repair.

The Position of the Virtual Hinge Axis in Relation to the Maxilla in Digital Orthognathic Surgery Planning-A k-Means Cluster Analysis.

The aim of this study was to investigate a possible relation between skeletal phenotypes and virtual mounting data in orthognathic surgery patients. A retrospective cohort study including 323 female (26.1 ± 8.7 years) and 191 male (27.9 ± 8.3 years) orthognathic surgery patients was conducted. A k-means cluster analysis was performed on the mounting parameters: the angle α between the upper occlusal plane (uOP) and the axis orbital plane (AOP); the perpendicular distance (AxV) from the uOP to the hinge axis; and the horizontal length (AxH) of the uOP from upper incisor edge to AxV, with subsequent statistical analysis of related cepalometric values. Three clusters of mounting data were identified, representing three skeletal phenotypes: (1) balanced face with marginal skeletal class II or III and α=8∘, AxV = 36 mm and AxH = 99 mm; (2) vertical face with skeletal class II and α=11∘, AxV = 27 mm and AxH = 88 mm; (3) horizontal face with class III and α=2∘, AxV = 36 mm and AxH = 86 mm. The obtained data on the position of the hinge axis can be applied to any digital planning in orthognathic surgery using CBCT or a virtual articulator, provided that the case can be clearly assigned to one of the calculated clusters.

Non-Surgical Transversal Dentoalveolar Compensation with Completely Customized Lingual Appliances versus Surgically Assisted Rapid Palatal Expansion in Adults-Tipping or Translation in Posterior Crossbite Correction?

The aim of this study was to investigate buccolingual tooth movements (tipping/translation) in surgical and nonsurgical posterior crossbite correction. A total of 43 patients (f/m 19/24; mean age 27.6 ± 9.5 years) treated with surgically assisted rapid palatal expansion (SARPE) and 38 patients (f/m 25/13; mean age 30.4 ± 12.9 years) treated with dentoalveolar compensation using completely customized lingual appliances (DC-CCLA) were retrospectively included. Inclination was measured on digital models at canines (C), second premolars (P2), first molars (M1), and second molars (M2) before (T0) and after (T1) crossbite correction. There was no statistically significant difference (p > 0.05) in absolute buccolingual inclination change between both groups, except for the upper C (p < 0.05), which were more tipped in the surgical group. Translation, i.e., bodily tooth movements that cannot be explained by pure uncontrolled tipping, could be observed with SARPE in the maxilla and with DC-CCLA in both jaws. Dentoalveolar transversal compensation with completely customized lingual appliances does not cause greater buccolingual tipping compared to SARPE.

Direct visualization of transcription-replication conflicts reveals post-replicative DNA:RNA hybrids.

Transcription-replication collisions (TRCs) are crucial determinants of genome instability. R-loops were linked to head-on TRCs and proposed to obstruct replication fork progression. The underlying mechanisms, however, remained elusive due to the lack of direct visualization and of non-ambiguous research tools. Here, we ascertained the stability of estrogen-induced R-loops on the human genome, visualized them directly by electron microscopy (EM), and measured R-loop frequency and size at the single-molecule level. Combining EM and immuno-labeling on locus-specific head-on TRCs in bacteria, we observed the frequent accumulation of DNA:RNA hybrids behind replication forks. These post-replicative structures are linked to fork slowing and reversal across conflict regions and are distinct from physiological DNA:RNA hybrids at Okazaki fragments. Comet assays on nascent DNA revealed a marked delay in nascent DNA maturation in multiple conditions previously linked to R-loop accumulation. Altogether, our findings suggest that TRC-associated replication interference entails transactions that follow initial R-loop bypass by the replication fork.

Anion-assisted amidinium exchange and metathesis.

Dynamic covalent chemistry has become an invaluable tool for the design and preparation of adaptable yet robust molecular systems. Herein we explore the scope of a largely overlooked dynamic covalent reaction - amidinium exchange - and report on conditions that allow formal amidinium metathesis reactions.

Non-Surgical Transversal Dentoalveolar Compensation with Completely Customized Lingual Appliances versus Surgically Assisted Rapid Palatal Expansion in Adults-The Amount of Posterior Crossbite Correction.

The aim of this study was to compare the crossbite correction of a group (n = 43; f/m 19/24; mean age 27.6 ± 9.5 years) with surgically assisted rapid palatal expansion (SARPE) versus a non-surgical transversal dentoalveolar compensation (DC) group (n = 38; f/m 25/13; mean age 30.4 ± 12.9 years) with completely customized lingual appliances (CCLA). Arch width was measured on digital models at the canines (C), second premolars (P2), first molars (M1) and second molars (M2). Measurements were obtained before treatment (T0) and at the end of lingual treatment (T1) or after orthodontic alignment prior to a second surgical intervention for three-dimensional bite correction. There was no statistically significant difference (p > 0.05) in the amount of total crossbite correction between the SARPE and DC-CCLA group at C, P2, M1 and M2. Maxillary expansion was greater in the SARPE group and mandibular compression was greater in the DC-CCLA group. Crossbite correction in the DC-CCLA group was mainly a combination of maxillary expansion and mandibular compression. Dentoalveolar compensation with CCLAs as a combination of maxillary expansion and mandibular compression seems to be a clinically effective procedure to correct a transverse maxillo-mandibular discrepancy without the need for surgical assistance.