A structurally conserved helix enables leader-independent tyramine splicing of proteins.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are natural products that feature diverse modifications. They show a wide range of biological activities and are therefore of great interest for drug discovery and protein engineering. An unusual modification found in spliceotide RiPPs is the installation of ß-amino acid residues with diverse side chains, generated by backbone excision of a tyramine moiety derived from tyrosine. We have previously shown that the modification can be adapted to protein engineering to greatly expand the set of amino acid residues and to introduce unique reaction centers for site-directed modification. To understand requirements for splicease-substrate interactions, we investigated the role of a RiPP recognition element (RRE) in spliceotide biosynthesis and provide evidence that it acts as an activator and enables leader-independent protein splicing. We leveraged this knowledge to engineer a simplified splicease system derived from Rheinheimera aquimaris B26 that processes splice tags introduced into proteins with high efficiency. This work expands the toolbox for peptide and protein engineering and contributes to an understanding of substrate recognition in RiPP biosynthesis.

Targeting CDC42 reduces skeletal degeneration after hematopoietic stem cell transplantation.

Osteopenia and osteoporosis are common long-term complications of the cytotoxic conditioning regimen for hematopoietic stem cell transplantation (HSCT). We examined mesenchymal stem and progenitor cells (MSPCs) that include skeletal progenitors from mice undergoing HSCT. Such MSPCs showed reduced CFU-F frequency, increased DNA damage and enhanced occurrence of cellular senescence, while there was a reduced bone volume in animals that underwent HSCT. This reduced MSPC function correlated with elevated activation of the small RhoGTPAse Cdc42, disorganized F-actin distribution, mitochondrial abnormalities and impaired mitophagy in MSPCs. Changes and defects similar to those in mice were also observed in MSPCs from humans undergoing HSCT. A pharmacological treatment that attenuated the elevated activation of CDC42 restored F-actin fiber alignment, mitochondrial function, and mitophagy in MSPCs in vitro. Finally, targeting CDC42 activity in vivo in animals undergoing transplants improved MSPC quality to increase both bone volume and trabecular bone thickness. Our study shows that attenuation of CDC42 activity is sufficient to attenuate reduced function of MSPCs in a BM transplant setting.

Mid-infrared tunable filter based on a femtosecond-written silica volume Bragg grating.

A silica volume Bragg grating (VBG) is used to filter the light of a mid-infrared (mid-IR) supercontinuum laser. The VBG with a 7 µm period was inscribed with 800 nm pulses with a 100 fs duration and the phase-mask technique over a glass thickness of 3 mm. Despite silica's absorption, the VBG allows obtaining a narrowband light source tunable from 2.9 to 4.2 µm with a full width at half maximum (FWHM) of 29 nm. This demonstrates the great potential of using femtosecond-written VBGs as highly tunable, yet selective, spectral filters in the mid-IR.

[Thyroid nodules as an incidental finding : Value of sonography and scintigraphy in primary diagnostics]. / Zufallsbefund Schilddrüsenknoten : Stellenwert der Sonographie und Szintigraphie in der Primärdiagnostik.

Due to the widespread use of high-resolution sonography, numerous thyroid nodules are diagnosed, often as incidental findings. The challenge lies in evaluating various criteria such as size, shape, and echogenicity to assess the nodules' malignancy risk. Risk stratification systems have been developed to enable systematic assessment as well as to avoid unnecessary medical interventions and malignant findings being overlooked. This article provides an overview of the current diagnostic standards in primary assessment of thyroid nodules.

Brainstem raphe hypoechogenicity is an independent predictor of post-stroke depression.

PURPOSE: Post-stroke depression (PSD) is a common complication after stroke and has a substantial effect on the quality of life of patients. Nevertheless, reliable individual prediction of PSD is not possible. As depressive symptoms have been associated with brainstem raphe (BR) hypoechogenicity on transcranial sonography (TCS), we aimed to explore the association of BR hypoechogenicity and the occurrence of PSD. MATERIALS AND METHODS: The Prognostic Markers of Post-Stroke Depression (PROMoSD) study is a prospective, observational, single-center, investigator-initiated study that included patients with acute ischemic stroke (AIS) to investigate the presence of BR hypoechogenicity by TCS early after symptom onset. The primary outcome was the presence of PSD assessed at the three-month follow-up investigation by a blinded psychiatrist and defined according to the fifth version of the Diagnostic and Statistical Manual of Mental Disorders (DSM-V criteria). RESULTS: From 105 included AIS patients, 99 patients completed the study. AIS patients with a hypoechogenic BR developed a PSD at three months more frequently compared to patients with normal echogenicity (48.0% versus 4.1%, P <0.001). After adjustment for confounders (sex, mRS at follow-up, previous depressive episode), a hypoechogenic BR remained independently associated with a substantial increase in the appearance of PSD (adjusted OR: 6.371, 95%-CI: 1.181-34.362). CONCLUSION: A hypoechogenic BR is a strong and independent predictor of PSD at three months after AIS. TCS could be a routine tool to assess PSD risk in clinical practice, thereby streamlining diagnostic and therapeutic algorithms.

Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes.

Two common approaches to study the composition of environmental protist communities are metabarcoding and metagenomics. Raw metabarcoding data are usually processed into Operational Taxonomic Units (OTUs) or amplicon sequence variants (ASVs) through clustering or denoising approaches, respectively. Analogous approaches are used to assemble metagenomic reads into metagenome-assembled genomes (MAGs). Understanding the correspondence between the data produced by these two approaches can help to integrate information between the datasets and to explain how metabarcoding OTUs and MAGs are related with the underlying biological entities they are hypothesised to represent. MAGs do not contain the commonly used barcoding loci, therefore sequence homology approaches cannot be used to match OTUs and MAGs. We made an attempt to match V9 metabarcoding OTUs from the 18S rRNA gene (V9 OTUs) and MAGs from the Tara Oceans expedition based on the correspondence of their relative abundances across the same set of samples. We evaluated several metrics for detecting correspondence between features in these two datasets and developed controls to filter artefacts of data structure and processing. After selecting the best-performing metrics, ranking the V9 OTU/MAG matches by their proportionality/correlation coefficients and applying a set of selection criteria, we identified candidate matches between V9 OTUs and MAGs. In some cases, V9 OTUs and MAGs could be matched with a one-to-one correspondence, implying that they likely represent the same underlying biological entity. More generally, matches we observed could be classified into 4 scenarios: one V9 OTU matches many MAGs; many V9 OTUs match many MAGs; many V9 OTUs match one MAG; one V9 OTU matches one MAG. Notably, we found some instances in which different OTU-MAG matches from the same taxonomic group were not classified in the same scenario, with all four scenarios possible even within the same taxonomic group, illustrating that factors beyond taxonomic lineage influence the relationship between OTUs and MAGs. Overall, each scenario produces a different interpretation of V9 OTUs, MAGs and how they compare in terms of the genomic and ecological diversity they represent.

Novel types of RiPP-modifying enzymes.

Novel discoveries in natural product biosynthesis reveal hidden bioactive compounds and expand our knowledge in enzymology. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a rapidly growing class of natural products featuring diverse non-canonical amino acids introduced by maturation enzymes as a class-defining characteristic. Underexplored RiPP sources, such as the human microbiome, the oceans, uncultured microorganisms, and plants are rich hunting grounds for novel enzymology. Unusual α- and ß-amino acids, peptide cleavages, lipidations, diverse macrocyclizations, and other features expand the range of chemical groups that are installed in RiPPs by often promiscuous enzymes. This review highlights the search for novelty in RiPP enzymology in the past two years, with respect to the discovery of new biochemical modifications but also towards novel applications.

Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions.

Ancestral reconstruction is a widely used technique that has been applied to understand the evolutionary history of gain and loss of gene families. Ancestral gene content can be reconstructed via different phylogenetic methods, but many current and previous studies employ Dollo parsimony. We hypothesize that Dollo parsimony is not appropriate for ancestral gene content reconstruction inferences based on sequence homology, as Dollo parsimony is derived from the assumption that a complex character cannot be regained. This premise does not accurately model molecular sequence evolution, in which false orthology can result from sequence convergence or lateral gene transfer. The aim of this study is to test Dollo parsimony's suitability for ancestral gene content reconstruction and to compare its inferences with a maximum likelihood-based approach that allows a gene family to be gained more than once within a tree. We first compared the performance of the two approaches on a series of artificial data sets each of 5,000 genes that were simulated according to a spectrum of evolutionary rates without gene gain or loss, so that inferred deviations from the true gene count would arise only from errors in orthology inference and ancestral reconstruction. Next, we reconstructed protein domain evolution on a phylogeny representing known eukaryotic diversity. We observed that Dollo parsimony produced numerous ancestral gene content overestimations, especially at nodes closer to the root of the tree. These observations led us to the conclusion that, confirming our hypothesis, Dollo parsimony is not an appropriate method for ancestral reconstruction studies based on sequence homology.

The evolution of acute stroke care in Germany from 2019 to 2021: analysis of nation-wide administrative datasets.

BACKGROUND: The treatment of ischemic stroke (IS) has changed considerably in recent years. Particularly the advent of mechanical thrombectomy (MTE) has revolutionized the available treatment options. Most patients in developed countries have access to intravenous thrombolysis (IVT). However access to MTE remains restricted in some regions despite efforts to increase its availability. We performed an evaluation of national datasets to monitor improvements made in access to revascularization therapies for IS patients in Germany. METHODS: We analyzed national datasets on German Diagnosis-Related Groups and structured quality reports by extracting information of patients admitted with stroke with and without IVT and MTE for the period of 2019-2021. Data from 2016 and limited data for 2022 were also included for comparison. RESULTS: Admissions with ischemic stroke declined during the years of the COVID 19 pandemic by 4.5% from 227,258 in 2019 to 216,923 in 2021. IVT rates were stable with 16.3% being treated with IVT in 2019 and 2021. MTE rates continued to increase from 7.1 to 8.4% and the number of MTE centers increased by 14.8% in the same period. Over 87.3% of MTEs were performed in centers with a case volume exceeding 50 cases per year in 2021. The largest increase in the relative share of MTEs was seen in large MTE centers (n ≥ 200). Patient age for MTEs surpassed the age for IVTs in 2019 and the proportion of patients ≥ 80 years receiving MTE continued to increase. The proportion of regions in Germany with poor MTE rates (≤ 4.1%) decreased significantly from 2019 (12.3%) to 2021 (5.3%) (p < 0.001). CONCLUSIONS: We found strong evidence that while IVT rates reached a temporary ceiling effect, both the absolute number of and access to MTEs continued to increase in Germany. Regional disparities have become less significant and the majority of MTEs are performed in centers with medium or high case volumes.

The protist cultural renaissance.

Protists are key players in the biosphere. Here, we provide a perspective on integrating protist culturing with omics approaches, imaging, and high-throughput single-cell manipulation strategies, concluding with actions required for a successful return of the golden age of protist culturing.

Risk stratification of thyroid nodules: Assessing the suitability of ChatGPT for text-based analysis.

PURPOSE: Accurate risk stratification of thyroid nodules is essential for optimal patient management. This study aimed to assess the suitability of ChatGPT for risk stratification of thyroid nodules using a text-based evaluation. METHODS: A dataset was compiled comprising 50 anonymized clinical reports and associated risk assessments for thyroid nodules. The Chat Generative Pre-trained Transformer (ChatGPT) was used to classify sonographic patterns in accordance with the Thyroid Imaging Reporting and Data System (TI-RADS). The model's performance was assessed using various criteria, including sensitivity, specificity, and accuracy. A comparative analysis was conducted, evaluating the model against investigator-based risk stratification as well as histology. RESULTS: With an overall agreement rate of 42 % in comparison with examiner-based evaluation (TI-RADS 1-5), the results show that ChatGPT has moderate potential for predicting the risk of malignancy in thyroid nodules using text-based reports. The chatbot model achieved a sensitivity of 86.7 %, a specificity of 10.7 %, and an overall accuracy of 68 % when distinguishing between low-risk (TI-RADS 2 and 3) and high-risk (TI-RADS 4 and 5) categories. Interrater reliability was calculated with a Cohen's kappa of 0.686. CONCLUSION: This study highlights the potential of ChatGPT in assisting clinicians with risk stratification of thyroid nodules. The results suggest that ChatGPT can facilitate personalized treatment decisions, although the agreement rate is still low. Further research and validation studies are necessary to establish the clinical applicability and generalizability of ChatGPT in routine practice. The integration of ChatGPT into clinical workflows has the potential to enhance thyroid nodule risk assessment and improve patient care.

The primacy of temporal dynamics in driving spatial self-organization of soil iron redox patterns.

This study investigates mechanisms that generate regularly spaced iron-rich bands in upland soils. These striking features appear in soils worldwide, but beyond a generalized association with changing redox, their genesis is yet to be explained. Upland soils exhibit significant redox fluctuations driven by rainfall, groundwater changes, or irrigation. Pattern formation in such systems provides an opportunity to investigate the temporal aspects of spatial self-organization, which have been heretofore understudied. By comparing multiple alternative mechanisms, we found that regular iron banding in upland soils is explained by coupling two sets of scale-dependent feedbacks, the general principle of Turing morphogenesis. First, clay dispersion and coagulation in iron redox fluctuations amplify soil Fe(III) aggregation and crystal growth to a level that negatively affects root growth. Second, the activation of this negative root response to highly crystalline Fe(III) leads to the formation of rhythmic iron bands. In forming iron bands, environmental variability plays a critical role. It creates alternating anoxic and oxic conditions for required pattern-forming processes to occur in distinctly separated times and determines durations of anoxic and oxic episodes, thereby controlling relative rates of processes accompanying oxidation and reduction reactions. As Turing morphogenesis requires ratios of certain process rates to be within a specific range, environmental variability thus modifies the likelihood that pattern formation will occur. Projected changes of climatic regime could significantly alter many spatially self-organized systems, as well as the ecological functioning associated with the striking patterns they present. This temporal dimension of pattern formation merits close attention in the future.

Legacies of Pre-1960s Municipal Waste Incineration in the Pb of City Soils.

A 1937 street map of Durham, North Carolina, located four city-run waste incinerators that we recognized to be sites of contemporary city parks. We obtained city permission to sample three park's soils, developed a sampling design for geospatial mapping of hypothetical incinerator-ash contamination of park soils, and queried online Durham newspapers to understand histories of incinerator operations, ash disposal, and incinerator-to-park conversions. In 2021-2022, seven decades after parks were created, two parks had soil-Pb > 400 mgPb/kg, EPA's threshold for safe soil in play areas. At Walltown Park, six of 97 surface samples ranged from 416 to 1338 mg Pb/kg within meters of a basketball court and a park path. East Durham Park had a hectare-sized area where 12 samples averaged 1294 mgPb/kg (median 1335 mg/kg). Engineering surveys of United States and Canadian cities in 1941 and 1958 suggest that half incinerated solid wastes. Many records describe how incinerator ash was dumped with little regard for health or environmental hazards. Legacy soil contaminations of incinerator ash can be identified, as we have done in Durham, from historical records of city-waste incinerator operations, online access to newspaper archives that describe incinerator-to-park conversions, and a XRF to screen for soil-Pb contamination.

Software- and TDM-Guided Dosing of Meropenem Promises High Rates of Target Attainment in Critically Ill Patients.

Various studies have reported insufficient beta-lactam concentrations in critically ill patients. The optimal dosing strategy for beta-lactams in critically ill patients, particularly in septic patients, is an ongoing matter of discussion. This retrospective study aimed to evaluate the success of software-guided empiric meropenem dosing (CADDy, Calculator to Approximate Drug-Dosing in Dialysis) with subsequent routine meropenem measurements and expert clinical pharmacological interpretations. Adequate therapeutic drug exposure was defined as concentrations of 8-16 mg/L, whereas concentrations of 16-24 mg/L were defined as moderately high and concentrations >24 mg/L as potentially harmful. A total of 91 patients received meropenem as a continuous infusion (229 serum concentrations), of whom 60% achieved 8-16 mg/L, 23% achieved 16-24 mg/L, and 10% achieved unnecessarily high and potentially harmful meropenem concentrations >24 mg/L in the first 48 h using the dosing software. No patient showed concentrations <2 mg/L using the dosing software in the first 48 h. With a subsequent TDM-guided dose adjustment, therapeutic drug exposure was significantly (p ≤ 0.05) enhanced to 70%. No patient had meropenem concentrations >24 mg/L with TDM-guided dose adjustments. The combined use of dosing software and consecutive TDM promised a high rate of adequate therapeutic drug exposures of meropenem in patients with sepsis and septic shock.

Site-specific bioorthogonal protein labelling by tetrazine ligation using endogenous ß-amino acid dienophiles.

The tetrazine ligation is an inverse electron-demand Diels-Alder reaction widely used for bioorthogonal modifications due to its versatility, site specificity and fast reaction kinetics. A major limitation has been the incorporation of dienophiles in biomolecules and organisms, which relies on externally added reagents. Available methods require the incorporation of tetrazine-reactive groups by enzyme-mediated ligations or unnatural amino acid incorporation. Here we report a tetrazine ligation strategy, termed TyrEx (tyramine excision) cycloaddition, permitting autonomous dienophile generation in bacteria. It utilizes a unique aminopyruvate unit introduced by post-translational protein splicing at a short tag. Tetrazine conjugation occurs rapidly with a rate constant of 0.625 (15) M-1 s-1 and was applied to produce a radiolabel chelator-modified Her2-binding Affibody and intracellular, fluorescently labelled cell division protein FtsZ. We anticipate the labelling strategy to be useful for intracellular studies of proteins, as a stable conjugation method for protein therapeutics, as well as other applications.

Inpatient care of neuromyelitis optica spectrum disorder in Germany: Nationwide analysis from 2010 to 2021.

Background: Despite tremendous development in the treatment of neuromyelitis optica spectrum disorder (NMOSD), less is known about the characteristics of hospitalized patients and inpatient care utilization. Objective: To investigate the development of inpatient NMOSD case numbers and implemented immunotherapies in the last decade in Germany. Methods: We conducted a nationwide retrospective study using an administrative database of all hospitalized NMOSD patients between 2010 and 2021. We evaluated yearly data on case numbers, demographics, treatment regimens, and seasonal variations of apheresis therapy as a surrogate marker of severe relapse incidence. Results: During the observational period case number of inpatients substantially increased (2010:n = 463, 2021:n = 992). The mean age was 48.1 ± 2.5 years (74% females). The pooled yearly rate of plasmapheresis/immunoadsorption was 14% (95% CI [13-15%]), without seasonal variations. Its application peaked in 2013 (18%, 95% CI [15-21%]) with decreasing trend since. Predominant immunotherapy was rituximab (40%, 95% CI [34-45%]), followed by tocilizumab (4%, 95% CI [3-5%]) since 2013 and eculizumab (4%, 95% CI [3-5%]) since 2020. Inpatient mortality ranged between 0% and 1% per year. Conclusions: Inpatient case numbers of NMOSD substantially increased during the past decade, probably reflecting improving disease awareness. In parallel with the administration of highly effective therapies rate of apheresis therapies decreased. A stable apheresis rate over the year makes seasonal variations of the steroid-refractive relapses unlikely.

First steps in the development of next-generation chirped volume Bragg gratings by means of fs laser inscription in fused silica.

The first steps towards the development and characterization of next-generation chirped volume Bragg gratings (CVBGs) by means of fs laser inscription were made. Based on the phase mask inscription technique we realized CVBGs in fused silica with a 3 × 3 mm2 aperture and a length of almost 12 mm with a chirp rate of ∼190 ps/nm around a central wavelength of 1030.5 nm. Strong mechanical stresses induced serious polarization and phase distortions of the radiation. We show a possible approach to solution of this problem. The change in the linear absorption coefficient associated with local modification of fused silica is quite small, enabling utilization of this type of gratings in high average power lasers.

Cortical blindness as a sign of delayed post-hypoxic encephalopathy: a case report.

We present a case of a 67-year-old female patient, who presented with acute cortical blindness five days after a successful resuscitation from cardiac arrest. The magnetic resonance tomography revealed a mild FLAIR signal increase of the bilateral occipital cortex. A lumbar puncture revealed considerably elevated tau protein levels, in the presence of normal phospho-tau, as a marker of brain injury, whilst neuron-specific enolase levels were normal. The diagnosis of delayed post-hypoxic encephalopathy was set. We hereby describe a rare clinical manifestation after initially successful resuscitation and encourage the studying of tau protein as a potential marker of this disease entity.

Regulatory and coding sequences of TRNP1 co-evolve with brain size and cortical folding in mammals.

Brain size and cortical folding have increased and decreased recurrently during mammalian evolution. Identifying genetic elements whose sequence or functional properties co-evolve with these traits can provide unique information on evolutionary and developmental mechanisms. A good candidate for such a comparative approach is TRNP1, as it controls proliferation of neural progenitors in mice and ferrets. Here, we investigate the contribution of both regulatory and coding sequences of TRNP1 to brain size and cortical folding in over 30 mammals. We find that the rate of TRNP1 protein evolution (ω) significantly correlates with brain size, slightly less with cortical folding and much less with body size. This brain correlation is stronger than for >95% of random control proteins. This co-evolution is likely affecting TRNP1 activity, as we find that TRNP1 from species with larger brains and more cortical folding induce higher proliferation rates in neural stem cells. Furthermore, we compare the activity of putative cis-regulatory elements (CREs) of TRNP1 in a massively parallel reporter assay and identify one CRE that likely co-evolves with cortical folding in Old World monkeys and apes. Our analyses indicate that coding and regulatory changes that increased TRNP1 activity were positively selected either as a cause or a consequence of increases in brain size and cortical folding. They also provide an example how phylogenetic approaches can inform biological mechanisms, especially when combined with molecular phenotypes across several species.