julilili42/papers huggingface dataset:
Ancient DNA reveals interstadials as a main driver of the temperate common vole (Microtus arvalis) population dynamics during the Last Glacial Period
2024-01-31

The common vole is a temperate rodent widespread across Europe. Phylogeographic studies of its extant populations suggested the Last Glacial Maximum (LGM) as one of the main drivers of the species’ population history. However, analyses based solely on extant genetic diversity may not recover the full complexity of Late Pleistocene population dynamics. To reconstruct the population history of the common vole through the Last Glacial Period, we analysed a 4.2 kb-long fragment of mitochondrial DNA of 148 ancient and 51 modern specimens, sampled from across Europe, and covering the last 60 thousand years (ka). We estimate the time to the most recent common ancestor of Last Glacial common vole lineages to 90 ka ago and the diversification of the main extant lineages to between 55 and 40 ka ago, substantially earlier than previously estimated. Our data suggests multiple lineage turnovers in Europe at the end of Marine Isotope Stage (MIS) 3 and around the Pleistocene/Holocene transition. Conversely, data from the Western Carpathians suggest continuity throughout the LGM. This further suggests that climate amelioration during MIS 2 had little impact on common voles and that the main driver of population dynamics was the reduction of open habitats during the interstadial periods.
Structural insights in the GTP-driven monomerization and activation of a bacterial LRRK2 homologue using allosteric nanobodies
2024-01-31

Abstract The Roco proteins are a family of GTPases, characterized by the conserved presence of a Roc-COR tandem domain. These proteins entered the limelight after mutations in human LRRK2 were identified as a major cause of familial Parkinson’s disease. LRRK2 is a large and complex protein combining a GTPase and protein kinase activity, and disease mutation increase the kinase activity, while presumably decreasing the GTPase activity. Although a cross-communication between both catalytic activities has been suggested, the underlying mechanisms and the regulatory role of the GTPase domain remain unknown. Recently, several structures of LRRK2 have been reported, but so far structures of Roco proteins in their activated GTP-bound state are lacking. Here, we use single particle cryo-EM to solve the structure of a simpler bacterial Roco protein (CtRoco) in its GTP-bound state, aided by the use of two conformation-specific nanobodies: NbRoco1 and NbRoco2. This structure presents CtRoco in an active monomeric state, featuring very significant conformational changes compared to the previously solved nucleotide-free dimer structure. In particular, the structure shows a very large GTP-induced conformational change of the LRR domain, unleashing it from the Roc-COR domains, using the Roc-LRR linker as a hinge. Furthermore, this structure shows how NbRoco1 and NbRoco2 collaborate to activate CtRoco in an allosteric way. Altogether, our data provides important new insights in the activation mechanism of Roco proteins, with relevance to LRRK2 regulation, and suggest new routes for the allosteric modulation of their GTPase activity.
The choice of ultra‐low attachment plates impacts primary human and primary canine hepatocyte spheroid formation, phenotypes, and function
2024-02-01

Abstract Organotypic three‐dimensional liver spheroid cultures in which hepatic cells retain their molecular phenotype and functionality have emerged as powerful tools for preclinical drug development. In recent years a multitude of culture systems have been developed; however, a thorough side‐by‐side benchmarking of the different methods is lacking. Here, we compared the performance of ten different 96‐ and 384‐well microplate types to support spheroid formation and long‐term culture. Specifically, we evaluated differences in spheroid formation kinetics, viability, functionality, expression patterns, and their utility for hepatotoxicity assessments using primary human hepatocytes (PHH) and primary canine hepatocytes (PCH). All 96‐well plates enabled formation of PHH liver spheroids, albeit with differences between plates in spheroid size, geometry, and reproducibility. Performance of different 384‐wells was less consistent. Only 6/10 microplates supported the formation of PCH aggregates. Interestingly, even if PCH aggregates in these six microplates were more loosely packed than PHH spheroids, they maintained their function and were compatible with long‐term pharmacological and toxicological assays. Overall, Corning and Biofloat plates showed the best performance in the formation of both human and canine liver spheroids with highest viability, most physiologically relevant phenotypes, superior CYP activity and lowest coefficient of variation in toxicity assays. The presented data constitutes a valuable resource that demonstrates the impacts of current ultra‐low attachment plates on liver spheroid metrics and can guide evidence‐based plate selection. Combined, these results have important implications for the cross‐comparison of different studies and can facilitate the standardization and reproducibility of three‐dimensional liver culture experiments.
ISG15 blocks cardiac glycolysis and ensures sufficient mitochondrial energy production during Coxsackievirus B3 infection
2024-02-01

Abstract Aims Virus infection triggers inflammation and, may impose nutrient shortage to the heart. Supported by type I interferon (IFN) signalling, cardiomyocytes counteract infection by various effector processes, with the IFN-stimulated gene of 15 kDa (ISG15) system being intensively regulated and protein modification with ISG15 protecting mice Coxsackievirus B3 (CVB3) infection. The underlying molecular aspects how the ISG15 system affects the functional properties of respective protein substrates in the heart are unknown. Methods and results Based on the protective properties due to protein ISGylation, we set out a study investigating CVB3-infected mice in depth and found cardiac atrophy with lower cardiac output in ISG15−/− mice. By mass spectrometry, we identified the protein targets of the ISG15 conjugation machinery in heart tissue and explored how ISGylation affects their function. The cardiac ISGylome showed a strong enrichment of ISGylation substrates within glycolytic metabolic processes. Two control enzymes of the glycolytic pathway, hexokinase 2 (HK2) and phosphofructokinase muscle form (PFK1), were identified as bona fide ISGylation targets during infection. In an integrative approach complemented with enzymatic functional testing and structural modelling, we demonstrate that protein ISGylation obstructs the activity of HK2 and PFK1. Seahorse-based investigation of glycolysis in cardiomyocytes revealed that, by conjugating proteins, the ISG15 system prevents the infection-/IFN-induced up-regulation of glycolysis. We complemented our analysis with proteomics-based advanced computational modelling of cardiac energy metabolism. Our calculations revealed an ISG15-dependent preservation of the metabolic capacity in cardiac tissue during CVB3 infection. Functional profiling of mitochondrial respiration in cardiomyocytes and mouse heart tissue by Seahorse technology showed an enhanced oxidative activity in cells with a competent ISG15 system. Conclusion Our study demonstrates that ISG15 controls critical nodes in cardiac metabolism. ISG15 reduces the glucose demand, supports higher ATP production capacity in the heart, despite nutrient shortage in infection, and counteracts cardiac atrophy and dysfunction.
Challenging old microbiological treasures for natural compound biosynthesis capacity
2024-02-01

Strain collections are a treasure chest of numerous valuable and taxonomically validated bioresources. The Leibniz Institute DSMZ is one of the largest and most diverse microbial strain collections worldwide, with a long tradition of actinomycetes research. Actinomycetes, especially the genus Streptomyces , are renowned as prolific producers of antibiotics and many other bioactive natural products. In light of this, five Streptomyces strains, DSM 40971 T , DSM 40484 T , DSM 40713 T , DSM 40976 T , and DSM 40907 T , which had been deposited a long time ago without comprehensive characterization, were the subject of polyphasic taxonomic studies and genome mining for natural compounds based on in vitro and in silico analyses. Phenotypic, genetic, and phylogenomic studies distinguished the strains from their closely related neighbors. The digital DNA–DNA hybridization and average nucleotide identity values between the five strains and their close, validly named species were below the threshold of 70% and 95%–96%, respectively, determined for prokaryotic species demarcation. Therefore, the five strains merit being considered as novel Streptomyces species, for which the names Streptomyces kutzneri sp. nov., Streptomyces stackebrandtii sp. nov. , Streptomyces zähneri sp. nov. , Streptomyces winkii sp. nov., and Streptomyces kroppenstedtii sp. nov. are proposed. Bioinformatics analysis of the genome sequences of the five strains revealed their genetic potential for the production of secondary metabolites, which helped identify the natural compounds cinerubin B from strain DSM 40484 T and the phosphonate antibiotic phosphonoalamide from strain DSM 40907 T and highlighted strain DSM 40976 T as a candidate for regulator-guided gene cluster activation due to the abundance of numerous “ Streptomyces antibiotic regulatory protein” (SARP) genes.
First Detection of Polarization in X-Rays for PSR B0540-69 and Its Nebula
2024-02-01

Abstract We report on X-ray polarization measurements of the extragalactic Crab-like PSR B0540-69 and its Pulsar Wind Nebula (PWN) in the Large Magellanic Cloud, using a ∼850 ks Imaging X-ray Polarimetry Explorer (IXPE) exposure. The PWN is unresolved by IXPE. No statistically significant polarization is detected for the image-averaged data, giving a 99% confidence polarization upper limit (MDP 99 ) of 5.3% in the 2–8 keV energy range. However, a phase-resolved analysis detects polarization for both the nebula and pulsar in the 4–6 keV energy range. For the PWN defined as the off-pulse phases, the polarization degree (PD) of (24.5 ± 5.3)% and polarization angle (PA) of (78.1 ± 6.2)° is detected at 4.6 σ significance level, consistent with the PA observed in the optical band. In a single on-pulse window, a hint of polarization is measured at 3.8 σ with PD of (50.0 ± 13.1)% and PA of (6.2 ± 7.4)°. A “simultaneous” PSR/PWN analysis finds two bins at the edges of the pulse exceeding 3 σ PD significance, with PD of (68 ± 20)% and (62 ± 20)%; intervening bins at 2–3 σ significance have lower PD, hinting at additional polarization structure.
Three-Minute Enantioselective Amino Acid Analysis by Ultra-High-Performance Liquid Chromatography Drift Tube Ion Mobility-Mass Spectrometry Using a Chiral Core–Shell Tandem Column Approach
2024-02-01

Fast liquid chromatography (LC) amino acid enantiomer separation of 6-aminoquinolyl-<i>N</i>-hydroxysuccinimidyl carbamate (AQC) derivatives using a chiral core-shell particle tandem column with weak anion exchange and zwitterionic-type quinine carbamate selectors in less than 3 min was achieved. Enantiomers of all AQC-derivatized proteinogenic amino acids and some isomeric ones (24 in total plus achiral glycine) were baseline separated (<i>R</i><sub>s</sub> > 1.5 except for glutamic acid with <i>R</i><sub>s</sub> = 1.3), while peaks of distinct amino acids and structural isomers (constitutional isomers and diastereomers of leucine and threonine) of the same configuration overlapped to various degrees. For this reason, drift tube ion mobility-mass spectrometry was added (i.e., LC-IM-MS) as an additional selectivity filter without extending run time. The IM separation dimension in combination with high-resolution demultiplexing enabled confirmation of threonine isomers (threonine, <i>allo</i>-threonine, homoserine), while leucine, isoleucine, and <i>allo</i>-isoleucine have almost identical collisional cross-section (<i><sup>DT</sup>CCS<sub>N2</sub></i>) values and added no selectivity to the partial LC separation. Density functional theory (DFT) calculations show that IM separation of threonine isomers was possible due to conformational stabilization by hydrogen bond formation between the hydroxyl side chain and the urea group. Generally, the CCS<sub>N2</sub> of protonated ions increased uniformly with addition of the AQC label, while outliers could be explained by consideration of intramolecular interactions and additional structural analysis. Preliminary validation of the enantioselective LC-IM-MS method for quantitative analysis showed compliance of accuracy and precision with common limits in bioanalytical methods, and applicability to a natural lipopeptide and a therapeutic synthetic peptide could be demonstrated.
Prospective study of complications and sequelae of glucocorticoid therapy in ANCA-associated vasculitis
2024-02-01

Objective Glucocorticoids (GC) are a cornerstone in treating antineutrophil cytoplasmic antibodies-associated vasculitides (AAV), however, they add to morbidity and mortality. To date, GC toxicity in AAV has rarely been systematically investigated. Methods Patients with a confirmed AAV were included in this monocentric prospective study. GC toxicity was assessed by structured interviews, clinical examination and electronic medical record analysis. The Glucocorticoid Toxicity Index (GTI) consisting of the Aggregate Improvement Score (GTI-AIS) and the Cumulative Worsening Score (GTI-CWS) was assessed at two time points (t1 baseline, t2 6 months later). We used regression analyses to assess the relationship between GTI and GC exposure, toxicity, and disease activity, and a receiver operating characteristic analysis to calculate a GC threshold dose beyond which toxicity is expected to occur. Results We included 138 patients with AAV. The median cumulative GC dose was 9014.0 mg. The most frequent adverse events were skin atrophy, osteoporosis and myopathy. GC exposure and toxicity were significantly correlated (p&lt;0.001). GTI-AIS was significantly higher in active disease compared with patients in remission (p&lt;0.001). GTI-CWS scored significantly higher in long-standing diseases (p=0.013) with high cumulative GC doses (p=0.003). Patients with a cumulative GC dose of 935 mg or more showed an 80% likelihood for a clinically meaningful change in GTI scoring. Conclusion The GTI is capable of capturing GC toxicity in AAV and identifies patients at increased risk for GC side effects. Our data support efforts to limit GC exposure in patients with AAV.
Image‐guided metabolomics and transcriptomics reveal tumour heterogeneity in luminal A and B human breast cancer beyond glucose tracer uptake
2024-02-01

Abstract Background Breast cancer is a metabolically heterogeneous disease, and although the concept of heterogeneous cancer metabolism is known, its precise role in human breast cancer is yet to be fully elucidated. Methods We investigated in an explorative approach a cohort of 42 primary mamma carcinoma patients with positron emission tomography/magnetic resonance imaging (PET/MR) prior to surgery, followed by histopathology and molecular diagnosis. From a subset of patients, which showed high metabolic heterogeneity based on tracer uptake and pathology classification, tumour centre and periphery specimen tissue samples were further investigated by a targeted breast cancer gene expression panel and quantitative metabolomics by nuclear magnetic resonance (NMR) spectroscopy. All data were analysed in a combinatory approach. Results [ 18 F]FDG (2‐deoxy‐2‐[fluorine‐18]fluoro‐ d ‐glucose) tracer uptake confirmed dominance of glucose metabolism in the breast tumour centre, with lower levels in the periphery. Additionally, we observed differences in lipid and proliferation related genes between luminal A and B subtypes in the centre and periphery. Tumour periphery showed elevated acetate levels and enrichment in lipid metabolic pathways genes especially in luminal B. Furthermore, serine was increased in the periphery and higher expression of thymidylate synthase (TYMS) indicated one‐carbon metabolism increased in tumour periphery. The overall metabolic activity based on [ 18 F]FDG uptake of luminal B subtype was higher than that of luminal A and the difference between the periphery and centre increased with tumour grade. Conclusion Our analysis indicates variations in metabolism among different breast cancer subtypes and sampling locations which details the heterogeneity of the breast tumours. Correlation analysis of [ 18 F]FDG tracer uptake, transcriptome and tumour metabolites like acetate and serine facilitate the search for new candidates for metabolic tracers and permit distinguishing luminal A and B. This knowledge may help to differentiate subtypes preclinically or to provide patients guide for neoadjuvant therapy and optimised surgical protocols based on individual tumour metabolism.
Long-term Follow-up and Safety of Patients after an Upfront Therapy with Letrozole for Early Breast Cancer in Routine Clinical Care – The PreFace Study
2024-02-01

Abstract Adjuvant treatment of patients with early-stage breast cancer (BC) should include an aromatase inhibitor (AI). Especially patients with a high recurrence risk might benefit from an upfront therapy with an AI for a minimum of five years. Nevertheless, not much is known about the patient selection for this population in clinical practice. Therefore, this study analyzed the prognosis and patient characteristics of postmenopausal patients selected for a five-year upfront letrozole therapy. From 2009 to 2011, 3529 patients were enrolled into the adjuvant phase IV PreFace clinical trial (NCT01908556). Postmenopausal hormone receptor-positive BC patients, for whom an upfront five-year therapy with letrozole (2.5 mg/day) was indicated, were eligible. Disease-free survival (DFS), overall survival (OS) and safety in relation to patient and tumor characteristics were assessed. 3297 patients started letrozole therapy. The majority of patients (n = 1639, 57%) completed the five-year treatment. 34.5% of patients continued with endocrine therapy after the mandated five-year endocrine treatment. Five-year DFS rates were 89% (95% CI: 88–90%) and five-year OS rates were 95% (95% CI: 94–96%). In subgroup analyses, DFS rates were 83%, 84% and 78% for patients with node-positive disease, G3 tumor grading, and pT3 tumors respectively. The main adverse events (any grade) were pain and hot flushes (66.8% and 18.3% of patients). The risk profile of postmenopausal BC patients selected for a five-year upfront letrozole therapy showed a moderate recurrence and death risk. However, in subgroups with unfavorable risk factors, prognosis warrants an improvement, which might be achieved with novel targeted therapies.
Danger Zones of the Gluteal Anatomy: Improving the Safety Profile of the Gluteal Fat Grafting
2024-02-01

Abstract Introduction Knowledge of the vascular anatomy is critical to performing safe gluteal surgery. To date, only the course of the main blood vessels within the muscles has been outlined. These findings are based on MRI and CTA images that do not conform to a topographically standardized and normalized probability distribution. Objectives The aim of this study was to develop a three-dimensional mapping of the gluteal zones of high vascular density in relation to anatomical landmarks. Materials and Methods This single-center retrospective cohort analysis comprised all consecutive patients who underwent cone-beam computed tomography (CBCT) scans between January 2016 and October 2021. The location of blood vessels in the gluteal region was allometrically normalized in relation to anatomical landmarks. Moreover, the caliber and area of the blood vessels were assessed. Results CBCT scans of 32 patients with an average age of 64 ± 12 years (range 34–87 years) were included. Fifty-three percent were female. The median [IQR] caliber of the intramuscular gluteal vessels was 1.47 [1.15–1.88] mm, significantly greater than that of the subcutaneous vessels 1.09 [0.72–1.44] mm ( p &lt; 0.001). Vascular density was higher intramuscularly, as 4.5% of the area of the muscle was occupied by blood vessels, as opposed to 0.3% in the adipose tissue. Conclusion The analysis of the CBCT scans showed a higher vascular density and larger vessels intramuscularly. We, therefore, recommend the injection of autologous fat merely to the subcutaneous plane. Level of Evidence II This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .
Innate immune response to SARS‐CoV‐2 infection contributes to neuronal damage in human iPSC‐derived peripheral neurons
2024-02-01

Abstract Severe acute respiratory coronavirus 2 (SARS‐CoV‐2) causes neurological disease in the peripheral and central nervous system (PNS and CNS, respectively) of some patients. It is not clear whether SARS‐CoV‐2 infection or the subsequent immune response are the key factors that cause neurological disease. Here, we addressed this question by infecting human induced pluripotent stem cell‐derived CNS and PNS neurons with SARS‐CoV‐2. SARS‐CoV‐2 infected a low number of CNS neurons and did not elicit a robust innate immune response. On the contrary, SARS‐CoV‐2 infected a higher number of PNS neurons. This resulted in expression of interferon (IFN) λ1, several IFN‐stimulated genes and proinflammatory cytokines. The PNS neurons also displayed alterations characteristic of neuronal damage, as increased levels of sterile alpha and Toll/interleukin receptor motif‐containing protein 1, amyloid precursor protein and α‐synuclein, and lower levels of cytoskeletal proteins. Interestingly, blockade of the Janus kinase and signal transducer and activator of transcription pathway by Ruxolitinib did not increase SARS‐CoV‐2 infection, but reduced neuronal damage, suggesting that an exacerbated neuronal innate immune response contributes to pathogenesis in the PNS. Our results provide a basis to study coronavirus disease 2019 (COVID‐19) related neuronal pathology and to test future preventive or therapeutic strategies.
Influence of open-source virtual-reality based gaze training on navigation performance in Retinitis pigmentosa patients in a crossover randomized controlled trial
2024-02-01

Methods A group of RP patients (n = 8, aged 20-60) participated in a study consisting of two 4-week-phases, both carried out by the same patient group in randomized order: In the ‘training phase’, participants carried out a Virtual-Reality gaze training for 30 minutes per day; In the ‘control phase’, no training occurred. Before and after each phase, participants were tasked to move through a randomized real-world obstacle course. Navigation performance in the obstacle course as well as eye-tracking data during the trials were evaluated. The study is registered at the German Clinical Trials Register (DRKS) with the ID DRKS00032628. Results On average, the time required to move through the obstacle course decreased by 17.0% after the training phase, the number of collisions decreased by 50.0%. Both effects are significantly higher than those found in the control phase ( p &lt; 0.001 for required time, p = 0.0165 for number of collisions), with the required time decreasing by 5.9% and number of collisions decreasing by 10.4% after the control phase. The average visual area observed by participants increases by 4.41% after training, however the effect is not found to be significantly higher than in the control phase ( p = 0.394). Conclusion The performance increase over the training phase significantly surpasses the natural learning effect found in the control phase, suggesting that Virtual-Reality based gaze training can have a positive effect on real-world navigation tasks for patients with RP. The training is available as work-in-progress open-source software.