Search Results (78)

Beneficial interactions between nitrogen-fixing soil bacteria and legumes offer a solution to increase crop yield on Earth and potentially in future Martian colonies. Paraburkholderia phymatum is a nitrogen-fixing beta-rhizobium, which enters symbiosis with more than 50 legumes and can survive in acidic or aluminium-rich soils. In a previous RNA-sequencing study, we showed that the beta-rhizobium P. phymatum grows well in simulated microgravity and identified phymabactin as the only siderophore produced by this strain. Here, the growth of the beta-rhizobium P. phymatum was assessed in Martian simulant soil using Enhanced Mojave Mars Simulant 2 (MMS-2), which contains a high amount of iron (18.4 percent by weight) and aluminium (13.1 percent by weight). While P. phymatum wild-type’s growth was not affected by exposure to MMS-2, a mutant strain impaired in siderophore biosynthesis (ΔphmJK) grew less than P. phymatum wild-type on gradient plates in the presence of a high concentration of MMS-2 or aluminium. This result suggests that the P. phymatum siderophore phymabactin alleviates aluminium-induced heavy metal stress. Ultra-high performance liquid chromatography–mass spectrometry (UHPLC-MS) showed that phymabactin can bind to aluminium more efficiently than iron. These results not only deepen our understanding of the behaviour of rhizobia in simulated extraterrestrial environments but also provide new insights into the potential use of P. phymatum for bioremediation of aluminium-rich soils and the multiple roles of the siderophore phymabactin. Full article

The objective of this study is to analyse the principles of educational buildings in the First National Architectural style in Turkey by examining the works of Ernst A. Egli, who is considered one of the pioneers of the modernisation process during the National Architecture Period. To this end, shape grammar was selected as the most appropriate method, as it offers the potential to analyse design languages and produce similar or hybrid designs within this language. The method was first developed by Stiny and Gips in the 1970s with the objective of defining design rules through an algorithmic process. In line with this methodological framework, the study employed a typological analysis of Egli’s educational buildings to derive shape grammar rules. These rules were then presented as input to the design process, with a hybrid application that explores potential design alternatives in accordance with Egli’s design approach by adopting parametric modelling methodology. The findings of the study are discussed comparatively with the buildings of other architects of the period. In this context, the analysis of Egli’s buildings reveals that his designs are compatible with the contemporary architects of his period. Accordingly, a design language that reflects the characteristic features of the First National Architecture Period is presented. Full article

Background: Central facial palsy (CFP) is a common condition following stroke, typically affecting the lower face and causing symptoms such as drooling, dysarthria, and facial asymmetry. Despite available rehabilitation methods, the evidence supporting their effectiveness is limited. Electromyography (EMG)-triggered Functional Electrical Stimulation (FES) has shown promise in neurorehabilitation for motor impairments, but its application to CFP remains unclear. Methods: This case report explores the use of EMG-triggered FES in a 77-year-old patient with CFP following a severe ischemic stroke of the middle cerebral artery (MCA). Therapy, focused on stimulating the orbicularis oris muscle to address persistent drooling and improve facial symmetry, was alongside usual care. The stimulation duration was 5–15 min, frequency 35 Hz, and pulse duration 300 µs, applied 5 times a week. Stimulation duration was adjusted based on the patient’s progress. Results: The patient underwent 16 sessions of EMG-triggered FES over four weeks. Post-therapy reassessment with the Sunnybrook Facial Grading System (SFGS) showed an improvement in facial motor function, with the score increasing from 58/100 to 78/100. Reassessment of the Facial Disability Index (FDI) revealed significant improvement in physical function (55 to 85 points), though the social function score slightly decreased (76 to 64 points). Improvements in dysarthria and the complete resolution of drooling were reflected in the physical function domain of the FDI and the Allensbach Dysarthria Severity Scale. Conclusions: The results highlight that EMG-triggered FES was well tolerated and effectively supported therapy, contributing to the resolution of drooling, improved facial symmetry, and enhanced speech function. Future research should focus on randomized controlled trials to confirm its effectiveness and determine optimal therapy parameters. Full article

Biofilm formation on orthopedic joint implants complicates diagnosis of periprosthetic joint infections (PJIs). Sonication of explanted orthopedic implants for diagnostic enhances pathogen detection, but it shows limitations in sensitivity and handling. We investigated whether the biosurfactant saponin could improve bacterial recovery from orthopaedic implants and thereby enhance infection diagnosis ex vivo. Orthopaedic material discs of 1 cm diameter were contaminated with different clinical bacterial PJI isolates. Biofilms of Staphylococcus epidermidis, Staphylococcus aureus, Escherichia coli, Cutibacterium avidum, and Cutibacterium acnes were grown on the discs, which were then treated with either saline solution or various concentrations of saponin. Next, the discs were vortexed or sonicated. Colony-forming units (CFUs) enumeration and time-to-positivity of liquid cultures were determined. Additionally, a novel 3D PJI soft tissue in vitro model was established to validate these findings in a more representative scenario. Median CFU enumeration showed that 0.001% (w/v) saponin as compared to saline solution increased CFUs recovery by 2.2 log₁₀ for S. epidermidis, 0.6 log₁₀ for S. aureus, 0.6 log₁₀ for C. avidum, 1.1 log₁₀ for C. acnes, and 0.01 log₁₀ for E. coli. Furthermore, saponin treatment resulted in a >1 log₁₀ increase in S. epidermidis CFU recovery from implants in the 3D tissue model compared to standard saline sonication. With that, we propose a novel two-component kit, consisting of a saponin solution and a specialized transportation box, for the efficient collection, transportation, and processing of potentially infected implants. Our data suggest that biosurfactants can enhance bacterial recovery from artificially contaminated orthopedic implants, potentially improving the diagnosis of PJIs. Full article

The double-stranded RNA editing enzyme ADAR1 connects two forms of genetic programming, one based on codons and the other on flipons. ADAR1 recodes codons in pre-mRNA by deaminating adenosine to form inosine, which is translated as guanosine. ADAR1 also plays essential roles in the immune defense against viruses and cancers by recognizing left-handed Z-DNA and Z-RNA (collectively called ZNA). Here, we review various aspects of ADAR1 biology, starting with codons and progressing to flipons. ADAR1 has two major isoforms, with the p110 protein lacking the p150 Zα domain that binds ZNAs with high affinity. The p150 isoform is induced by interferon and targets ALU inverted repeats, a class of endogenous retroelement that promotes their transcription and retrotransposition by incorporating Z-flipons that encode ZNAs and G-flipons that form G-quadruplexes (GQ). Both p150 and p110 include the Zβ domain that is related to Zα but does not bind ZNAs. Here we report strong evidence that Zβ binds the GQ that are formed co-transcriptionally by ALU repeats and within R-loops. By binding GQ, ADAR1 suppresses ALU-mediated alternative splicing, generates most of the reported nonsynonymous edits and promotes R-loop resolution. The recognition of the various alternative nucleic acid conformations by ADAR1 connects genetic programming by flipons with the encoding of information by codons. The findings suggest that incorporating G-flipons into editmers might improve the therapeutic editing efficacy of ADAR1. Full article

Objective: The clinical diagnosis of respiratory tract infections (RTIs) may result in unnecessary antibiotic treatment due to clinical exams’ low sensitivity and specificity to differentiate viral from bacterial infections and costly diagnostic work-ups. Unnecessary antibiotic consumption drives antibiotic resistance. We explored whether a rapid influenza-specific polymerase chain reaction (PCR) assay reduced antibiotic use in an emergency room before the COVID-19 pandemic. Methods: We conducted an observational retrospective study of patients with RTI symptoms treated in the ER of the University Hospital Basel from September 2014 to June 2015. We evaluated the impact of rapid diagnostic results, such as an influenza-specific PCR, blood sample results, and radiological imaging, on antibiotic prescription rates. Patient-related confounding factors were included since a patient’s clinical condition affects doctors’ clinical decision-making. Results: We included 607 patients with RTIs, tested with PCR for influenza A or B. Logistic regression showed that the odds ratio (OR) of being treated with antibiotics was significantly reduced by more than two-thirds in patients with a positive influenza PCR result (OR = 0.37; 95% CI, 0.22–0.59; p < 0.001). Increasing C-reactive protein (CRP) levels by tenfold (OR = 5.14; 95% CI, 3.34–8.12; p < 0.001) or suspected chest infection on a radiograph (OR = 5.81; 95% CI, 3.23–10.89; p < 0.001) increased the OR of antibiotic treatment by fivefold. The highest OR for antibiotic prescription was due to increased procalcitonin level by tenfold (OR = 10.13; 95% CI, 4.79–23.4; p < 0.001). Conclusions: Our study provides real-world evidence from a pre-COVID-19 ER setting of diagnostic tools used for RTI evaluation and their impact on antibiotic prescriptions. Rapid influenza-specific PCR results may affect the prescription rate of antibiotics but should be seen as part of a comprehensive diagnostic approach to guide clinical decision-making. Full article

Classical preoperative skin antisepsis is insufficient in completely eliminating bacterial skin colonization for arthroplasty. In contrast, photodynamic therapy (PDT) with red light and methyl-aminolevulinate (MAL), combined with skin antisepsis, led to the absence of bacterial growth in healthy participants, though with local skin erythema, posing an obstacle for orthopedic surgery. Therefore, we explored whether artificial daylight PDT (PDT-DL) was superior to red light. Twenty healthy participants were allocated to either 5-aminolevulinic acid-(5-ALA) PDT-DL (n = 10) or MAL-PDT-DL (n = 10) before antisepsis with povidone-iodine/alcohol. Skin swabs from the groin were taken to cultivate bacteria at baseline, after PDT-DL, and after the subsequent antisepsis. Additional swabs were taken on day 4 before and after antisepsis without PDT. The contralateral groin of each participant and of ten additional healthy volunteers served as the control (n = 30). In selected participants, 16S rRNA-based amplicon deep sequencing was performed. All participants showed a baseline bacterial colonization. After a PDT-DL with skin antisepsis, bacterial growth occurred in three (30%) and in one (10%) participants with 5-ALA and MAL, respectively, compared to the sixteen (55%) participants in the control group. On day 4, three (30%) participants per group showed positive cultures post antisepsis. Adverse effects were reported in six (60%) and zero (0%) participants for 5-ALA- and MAL-PDT-DL, respectively. The skin bacteriome changes correlated with the bacterial culture results. The MAL-PDT-DL with skin antisepsis significantly increased bacterial reduction on the skin without adverse effects. This offers an opportunity to prevent infections in arthroplasty patients and reduce antibiotic use, thus contributing to antibiotic stewardship goals emphasized in the One Health approach. Full article

This study investigates the application of neural networks to the evaluation of minimum-time low-thrust transfers in low Earth orbit. The findings demonstrate the effectiveness of utilizing costates to regularize the training loss, significantly enhancing the accuracy of the predictions of the neural networks, even when working with limited datasets. Remarkably precise estimates of transfer times are achieved by training the regularized networks on datasets comprising one million samples. The incorporation of a warm-started guess strategy, involving simpler neural networks to provide transfer time and costates predictions for new transfers, accelerates the data collection process, making this approach highly practical for real-world applications. Overall, the methodology employed in this research study holds significant promise for low-thrust space missions, particularly when the evaluation of multiple minimum-time transfers is necessary in mission planning. In fact, the trained neural networks significantly speed up convergence when solving optimal control problems with indirect optimization methods. Furthermore, the remarkable accuracy in estimating both minimum transfer times and costates provides the flexibility of relying entirely on neural networks for determining minimum time. Full article

This study aimed to determine cefazolin target attainment in patients with invasive Staphylococcus aureus (S. aureus) infections and to develop a population pharmacokinetic (PK) model. Adult patients with invasive S. aureus infections treated with cefazolin bolus infusions were included. Unbound and total trough and mid-dose cefazolin concentrations were measured, and strain-specific MICs were determined. The primary outcome was the proportion of patients attaining 100% fT_>MIC at all time points evaluated. A population PK model was developed, using non-linear mixed-effects modelling. Overall, 51 patients were included, with a total of 226 unbound and total cefazolin concentrations measured (mean: 4.4 per patient). The median daily dosage in patients with an estimated glomerular filtration rate of >60 mL/min/m² was 8 g. The median age was 74 years (interquartile range (IQR) 57–82) and 26% were female. A history of chronic kidney disease and acute kidney injury were present in 10/51 (19.6%) and 6/51 (11.7%), respectively. Achievement of 100% fT_>MIC occurred in 86% of the patients and decreased to 45% when a target of 100% fT_>4xMIC was evaluated. The mean unbound cefazolin fraction was 27.0% (standard deviation (SD) 13.4). Measured and estimated mean cefazolin trough concentrations differed significantly [13.1 mg/L (SD 23.5) vs. 7.4 mg/L (SD 7.9), p < 0.001]. In the population PK model, elevated estimated creatinine clearance and bolus instead of continuous application were covariates for target non-attainment. In conclusion, cefazolin target achievement was high, and the measurement of the unbound cefazolin concentration may be favored. The Monte Carlo simulations indicated that target attainment was significantly improved with continuous infusion. Full article

Aging clocks are predictive models of biological age derived from age-related changes, such as epigenetic changes, blood biomarkers, and, more recently, the microbiome. Gut and skin microbiota regulate more than barrier and immune function. Recent studies have shown that human microbiomes may predict aging. In this narrative review, we aim to discuss how the gut and skin microbiomes influence aging clocks as well as clarify the distinction between chronological and biological age. A literature search was performed on PubMed/MEDLINE databases with the following keywords: “skin microbiome” OR “gut microbiome” AND “aging clock” OR “epigenetic”. Gut and skin microbiomes may be utilized to create aging clocks based on taxonomy, biodiversity, and functionality. The top contributing microbiota or metabolic pathways in these aging clocks may influence aging clock predictions and biological age. Furthermore, gut and skin microbiota may directly and indirectly influence aging clocks through the regulation of clock genes and the production of metabolites that serve as substrates or enzymatic regulators. Microbiome-based aging clock models may have therapeutic potential. However, more research is needed to advance our understanding of the role of microbiota in aging clocks. Full article

Hyperparathyroidism (HPT) with hypercalcemia, often deemed irreversible and detrimental to graft survival post-kidney transplantation (KT), prompts pre-transplant parathyroidectomy in hypercalcemic patients. In this retrospective analysis of 1212 kidney transplant recipients (KTRs) between 2006 and 2019, the incidence and effect of persistent HPT and hypercalcemia on graft and patient survival, and risk factors for persistence were analyzed until 60 months of follow up (FU). At KT, 5.7% (n = 69) had no HPT, 32.7% (n = 396) had HPT without hypercalcemia and 37.0% (n = 448) had HPT with hypercalcemia. At 2 years FU, 26.4% (n = 320) of patients had no HPT and 6% (n = 73) had HPT with hypercalcemia. Dialysis and dialysis duration were linked to HPT development, while dialysis, KT waiting time and donor type correlated with persisting hypercalcemia after KT. KTRs with normalized PTH and recovered hypercalcemia had improved death-censored graft survival (p < 0.001) and overall patient survival (p < 0.001). HPT with hypercalcemia is frequent at time of KT with normalization of PTH and calcium in a substantial proportion of patients after a KT. These findings question the routine pre-KT parathyroidectomy for suspected parathyroid autonomy. Persisting HPT, especially with hypercalcemia, adversely affects graft and patient survival, suggesting the need for more aggressive treatment of HPT, especially in cases of persisting hypercalcemia. Full article

Microbial factories, including microalgae biofactories, have the enormous potential to produce biochemicals for manufacturing diverse bioproducts. A strategic approach to biofactories is maintaining cultures in bioreactors with sufficient resource inputs to optimize biochemical precursors for manufacturing bioproducts. Exploiting synergies that use the waste output from a bioreactor containing one microbial culture as a resource input to another bioreactor with a different microbe can lead to overall efficiencies in biofactories. In this paper, two synergies are evaluated. The first is between yeast and algae bioreactors, where data are presented on oxygen (O₂) uptake by aerobic yeast cultures and their production of carbon dioxide (CO₂) and the uptake of CO₂ by algae and their production of O₂. The second focuses on a carbon capture reactor, which is utilized to increase CO₂ levels to promote higher algal production. This approach of waste as a resource for bioreactor cultures is a novel synergy that can be important to bioreactor designs and, ultimately, to the production of bioproducts. Full article

During the SARS-CoV-2 pandemic, the Dr. Risch medical group employed the multiplex TaqPath^TM COVID-19 CE-IVD RT-PCR Kit for large-scale routine diagnostic testing in Switzerland and the principality of Liechtenstein. The TaqPath Kit is a widely used multiplex assay targeting three genes (i.e., ORF1AB, N, S). With emergence of the B.1.1.7 (Alpha) variant, a diagnostic flaw became apparent as the amplification of the S-gene target was absent in these samples due to a deletion (ΔH69/V70) in the Alpha variant genome. This S-gene target failure (SGTF) was the earliest indication of a new variant emerging and was also observed in subsequent variants such as Omicron BA.1 and BA4/BA.5. The Delta variant and Omicron BA.2 did not present with SGTF. From September 2020 to November 2022, we investigated the applicability of the SGTF as a surrogate marker for emerging variants such as B.1.1.7, B.1.617.2 (Delta), and Omicron BA.1, BA.2, and BA.4/BA.5 in samples with cycle threshold (Ct) values < 30. Next to true SGTF-positive and SGTF-negative samples, there were also samples presenting with delayed-type S-gene amplification (higher Ct value for S-gene than ORF1ab gene). Among these, a difference of 3.8 Ct values between the S- and ORF1ab genes was found to best distinguish between “true” SGTF and the cycle threshold variability of the assay. Samples above the cutoff were subsequently termed partial SGTF (pSGTF). Variant confirmation was performed by whole-genome sequencing (Oxford Nanopore Technology, Oxford, UK) or mutation-specific PCR (TIB MOLBIOL). In total, 17,724 (7.4%) samples among 240,896 positives were variant-confirmed, resulting in an overall sensitivity and specificity of 93.2% [92.7%, 93.7%] and 99.3% [99.2%, 99.5%], respectively. Sensitivity was increased to 98.2% [97.9% to 98.4%] and specificity lowered to 98.9% [98.6% to 99.1%] when samples with pSGTF were included. Furthermore, weekly logistic growth rates (α) and sigmoid’s midpoint (t₀) were calculated based on SGTF data and did not significantly differ from calculations based on comprehensive data from GISAID. The SGTF therefore allowed for a valid real-time estimate for the introduction of all dominant variants in Switzerland and Liechtenstein. Full article

Cancer is defined as a group of diseases characterized by abnormal cell growth, expansion, and progression with metastasis. Various signaling pathways are involved in its development. Malignant tumors exhibit a high morbidity and mortality. Cancer research increased our knowledge about some of the underlying mechanisms, but to this day, our understanding of this disease is unclear. High throughput omics technology and bioinformatics were successful in detecting some of the unknown cancer mechanisms. However, novel groundbreaking research and ideas are necessary. A stay in orbit causes biochemical and molecular biological changes in human cancer cells which are first, and above all, due to microgravity (µg). The µg-environment provides conditions that are not reachable on Earth, which allow researchers to focus on signaling pathways controlling cell growth and metastasis. Cancer research in space already demonstrated how cancer cell-exposure to µg influenced several biological processes being involved in cancer. This novel approach has the potential to fight cancer and to develop future cancer strategies. Space research has been shown to impact biological processes in cancer cells like proliferation, apoptosis, cell survival, adhesion, migration, the cytoskeleton, the extracellular matrix, focal adhesion, and growth factors, among others. This concise review focuses on publications related to genetic, transcriptional, epigenetic, proteomic, and metabolomic studies on tumor cells exposed to real space conditions or to simulated µg using simulation devices. We discuss all omics studies investigating different tumor cell types from the brain and hematological system, sarcomas, as well as thyroid, prostate, breast, gynecologic, gastrointestinal, and lung cancers, in order to gain new and innovative ideas for understanding the basic biology of cancer. Full article

At the end of 2021, we observed an increase in N-gene target failures (NGTF) with the TaqPathTM COVID-19 CE-IVD RT-PCR Kit from Thermo Fisher Scientific (TaqPath). We subsequently used whole-genome sequencing (Oxford Nanopore Technology) to identify potential issues with N-gene PCR efficacy. Among 168,101 positive samples with a cycle threshold (CT) value <30 from August 2021 to May 2022, 194 specimens without N-gene amplification by PCR were identified (0.12%). Most NGTF samples originated from a wave of infection attributable to the Delta variant (B.1.617.2) and its sublineages. Sequencing revealed the nucleotide substitution G28922T (A217S) in 151 samples (88.8%). The substitution G215C, a hallmark mutation for Delta lineages, was concurrently present in all of these samples. Ten samples (5.9%) carried the deletion 28,913–28,918 (del214/215), eight samples (4.7%) the deletion 28,913–28,915 (del214) and one sample (0.6%) the deletion 28,892–28,930 (del207–219). Samples showing intact N-gene amplification by PCR lacked these specific mutations, but delayed-type amplification (i.e., partial or pNGTF) was attributable to the exclusive presence of A217S. As the N gene is a common target in many RT-PCR methods for SARS-CoV-2, an in-depth analysis of single-target failures using a combination with viral whole genome sequencing may allow for the identification of diagnostic flaws and eventual new variants. Full article