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1.
Eur Urol Focus ; 2024 Sep 03.
Article in English | MEDLINE | ID: mdl-39232906

ABSTRACT

Chronic urinary infection may have implications for disease because of reactivation of toxins in the urine or damage to bladder defences. Exploration of these possibilities requires a scrupulous scientific approach.

2.
Nucleic Acids Res ; 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-39217469

ABSTRACT

The efficiency of translation termination is determined by the nature of the stop codon as well as its context. In eukaryotes, recognition of the A-site stop codon and release of the polypeptide are mediated by release factors eRF1 and eRF3, respectively. Translation termination is modulated by other factors which either directly interact with release factors or bind to the E-site and modulate the activity of the peptidyl transferase center. Previous studies suggested that the Saccharomyces cerevisiae ABCF ATPase New1 is involved in translation termination and/or ribosome recycling, however, the exact function remained unclear. Here, we have applied 5PSeq, single-particle cryo-EM and readthrough reporter assays to provide insight into the biological function of New1. We show that the lack of New1 results in ribosomal stalling at stop codons preceded by a lysine or arginine codon and that the stalling is not defined by the nature of the C-terminal amino acid but rather by the identity of the tRNA isoacceptor in the P-site. Collectively, our results suggest that translation termination is inefficient when ribosomes have specific tRNA isoacceptors in the P-site and that the recruitment of New1 rescues ribosomes at these problematic termination contexts.

3.
mSystems ; : e0062624, 2024 Sep 17.
Article in English | MEDLINE | ID: mdl-39287382

ABSTRACT

In the global efforts to combat antimicrobial resistance and reduce antimicrobial use in pig production, there is a continuous search for methods to prevent and/or treat infections. Within this scope, we explored the relationship between the developing piglet nasal microbiome and (zoonotic) bacterial pathogens from birth until 10 weeks of life. The nasal microbiome of 54 pigs was longitudinally studied over 16 timepoints on 9 farms in 3 European countries (Germany, Ireland, and the Netherlands) using amplicon sequencing targeting the V3-V4 16S rRNA region as well as the tuf gene for its staphylococcal discrimination power. The piglets' age, the farm, and the litter affected the nasal microbiome, with piglets' age explaining 19% of the variation in microbial composition between samples. Stabilization of the microbiome occurred around 2 weeks post-weaning. Notably, while opportunistic pathogens were ubiquitously present, they did not cause disease. The piglet nasal microbiome often carried species associated with gut, skin, or vagina, which suggests that contact with the vaginal and fecal microbiomes shapes the piglet nasal microbiome. We identified bacterial co-abundance groups of species that were present in the nasal microbiomes in all three countries over time. Anti-correlation between these species and known bacterial pathogens identified species that might be exploited for pathogen reduction. Further experimental evidence is required to confirm these findings. Overall, this study advances our understanding of the piglet nasal microbiome, the factors influencing it, and its longitudinal development, providing insights into its role in health and disease. IMPORTANCE: Our study on the nasal microbiota development in piglets across farms in three European countries found that the microbiomes developed similarly in all locations. Additionally, we observed that the colonization of porcine pathogens was either positively or negatively associated with the presence of other bacterial species. These findings enhance our knowledge of co-colonizing species in the nasal cavity and the identified microbial interactions that can be explored for the development of interventions to control pathogens in porcine husbandry.

4.
RNA ; 2024 Sep 25.
Article in English | MEDLINE | ID: mdl-39322276

ABSTRACT

Uridine residues present at the wobble position of eukaryotic cytosolic tRNAs often carry a 5-carbamoylmethyl (ncm5), 5-methoxycarbonylmethyl (mcm5), or 5-methoxycarbonylhydroxymethyl (mchm5) side-chain. The presence of these side-chains allows proper pairing with cognate codons and they are particularly important in tRNA species where the U34 residue is also modified with a 2-thio (s2) group. The first step in synthesis of the ncm5, mcm5, and mchm5 side-chains is dependent on the six-subunit Elongator complex, whereas the thiolation of the 2-position is catalyzed by the Ncs6/Ncs2 complex. In both yeast and metazoans, allelic variants of Elongator subunit genes show genetic interactions with mutant alleles of SOD1, which encodes the cytosolic Cu,Zn-superoxide dismutase. However, the cause of these genetic interactions remains unclear. Here, we show that yeast sod1 null mutants are impaired in the formation of 2-thio-modified U34 residues. In addition, the lack of Sod1 induces a defect in the biosynthesis of wybutosine, which is a modified nucleoside found at position 37 of tRNAPhe Our results suggest that these tRNA modification defects are caused by superoxide-induced inhibition of the iron-sulfur cluster-containing Ncs6/Ncs2 and Tyw1 enzymes. Since mutations in Elongator subunit genes generate strong negative genetic interactions with mutant ncs6 and ncs2 alleles, our findings at least partially explain why the activity of Elongator can modulate the phenotypic consequences of SOD1/sod1 alleles. Collectively, our results imply that tRNA hypomodification may contribute to impaired proteostasis in Sod1-deficient cells.

5.
Eur Urol Focus ; 2024 Sep 24.
Article in English | MEDLINE | ID: mdl-39322455

ABSTRACT

Urinary tract infection (UTI) is among the most common human bacterial infections. In the context of increasing antibiotic resistance, there are many research efforts to improve the pathophysiological understanding, diagnosis, and treatment of UTI. Despite the high clinical relevance of UTI, there is high variability in definitions in the literature, making interpretation and comparison of research studies difficult, and even impossible in some cases. A recent Delphi consensus study generated a new reference standard definition for UTI that incorporates symptoms, pyuria, and urine culture results. This definition allows for designation of systemic involvement, and no longer categorizes UTIs as complicated or uncomplicated. The definition aligns with guidance from regulatory bodies for approval of UTI drugs. Implementation of a reference standard definition in the design and reporting of future investigations will allow better research design and interpretability within and outside the urology field. The new reference standard resolves some issues and offers a suitable way to unify methodology, and hence increase the potential strength of research in this area. There are some limitations and challenges for implementation, such as difficulties in establishing sensitivity and specificity values for the various settings in which the definition will be used. The inclusion of "probable" and "possible" UTI categories could be a problem in studies that require dichotomous outcomes. Nonetheless, the reference standard should be recommended until new developments become available, notably a more specific UTI biomarker than pyuria. Approaches to standardized diagnosis of catheter-associated UTIs remain unresolved. PATIENT SUMMARY: A new research definition for urinary tract infection (UTI) has been developed. Use of a single standardized definition in research will help in better design of research studies and comparison of results. Although the new definition will help in reducing the variability in UTI research reports, it has some limitations and there may be challenges to overcome before it is widely used.

6.
bioRxiv ; 2024 Sep 23.
Article in English | MEDLINE | ID: mdl-39345367

ABSTRACT

Mechanisms that restrict class switch recombination (CSR) to IgE limit the subsequent production of IgE antibodies and therefore the development of allergic disease. Mice with impaired B cell receptor (BCR) signaling have significantly increased IgE responses, consistent with a role for BCR signaling in IgE regulation. While prior work focused on BCR signaling in IgE-expressing cells to explain these findings, it has been reported that BCR signaling can reduce CSR. Therefore, we investigated the possibility that IgE CSR might be particularly sensitive to inhibition by BCR signaling in unswitched B cells. We found that immunization of mice with high-affinity antigen resulted in reduced representation of IgE-expressing cells among germinal center B cells and plasma cells relative to a low-affinity antigen. Mechanistic experiments with cultured mouse B cells demonstrated that BCR ligands selectively inhibited IgE CSR in a dose-, affinity-, and avidity-dependent manner. Signaling via Syk was required for the inhibition of IgE CSR following BCR stimulation, whereas inhibition of the PI3K subunit p110δ increased IgE CSR independently of BCR ligation. The inhibition of IgE CSR by BCR ligands synergized with IL-21 or TGFß1. BCR ligation also inhibited CSR to IgE in human tonsillar B cells, and this inhibition was also synergistic with IL-21. These findings establish that IgE CSR is uniquely susceptible to inhibition by BCR signaling in mouse and human B cells, with important implications for the regulation and pathogenesis of allergic disease.

7.
bioRxiv ; 2024 Sep 18.
Article in English | MEDLINE | ID: mdl-39345495

ABSTRACT

Hypercholesterolemia has long been implicated in endothelial cell (EC) dysfunction, but the mechanisms by which excess cholesterol causes vascular pathology are incompletely understood. Here we used a cholesterol-mimetic probe to map cholesterol-protein interactions in primary human ECs and discovered that cholesterol binds to and stabilizes the adhesion molecule VCAM-1. We show that accessible plasma membrane (PM) cholesterol in ECs is acutely responsive to inflammatory stimuli and that the nonvesicular cholesterol transporter Aster-A regulates VCAM-1 stability in activated ECs by controlling the size of this pool. Deletion of Aster-A in ECs increases VCAM-1 protein, promotes immune cell recruitment to vessels, and impairs pulmonary immune homeostasis. Conversely, depleting cholesterol from the endothelium in vivo dampens VCAM-1 induction in response to inflammatory stimuli. These findings identify cholesterol binding to VCAM-1 as a key step during EC activation and provide a biochemical explanation for the ability of excess membrane cholesterol to promote immune cell recruitment to the endothelium.

8.
Immunity ; 2024 Sep 15.
Article in English | MEDLINE | ID: mdl-39305904

ABSTRACT

Existing antibodies (Abs) have varied effects on humoral immunity during subsequent infections. Here, we leveraged in vivo systems that allow precise control of antigen-specific Abs and B cells to examine the impact of Ab dose, affinity, and specificity in directing B cell activation and differentiation. Abs competing with the B cell receptor (BCR) epitope showed affinity-dependent suppression. By contrast, Abs targeting a complementary epitope, not overlapping with the BCR, shifted B cell differentiation toward Ab-secreting cells. Such Abs allowed for potent germinal center (GC) responses to otherwise poorly immunogenic sites by promoting antigen capture and presentation by low-affinity B cells. These mechanisms jointly diversified the B cell repertoire by facilitating the recruitment of high- and low-affinity B cells into Ab-secreting cell, GC, and memory B cell fates. Incorporation of small amounts of monoclonal Abs into protein- or mRNA-based vaccines enhanced immunogenicity and facilitated sustained immune responses, with implications for vaccine design and our understanding of protective immunity.

9.
J Clin Anesth ; 99: 111565, 2024 Sep 23.
Article in English | MEDLINE | ID: mdl-39316931

ABSTRACT

STUDY OBJECTIVE: Male sex has inconsistently been associated with the development of postoperative pulmonary complications (PPCs). These studies were different in size, design, population and preoperative risk. We reanalysed the database of 'Local ASsessment of Ventilatory management during General Anaesthesia for Surgery study' (LAS VEGAS) to evaluate differences between females and males with respect to PPCs. DESIGN, SETTING AND PATIENTS: Post hoc unmatched and matched analysis of LAS VEGAS, an international observational study in patients undergoing intraoperative ventilation under general anaesthesia for surgery in 146 hospitals across 29 countries. The primary endpoint was a composite of PPCs in the first 5 postoperative days. Individual PPCs, hospital length of stay and mortality were secondary endpoints. Propensity score matching was used to create a similar cohort regarding type of surgery and epidemiological factors with a known association with development of PPCs. MAIN RESULTS: The unmatched cohort consisted of 9697 patients; 5342 (55.1%) females and 4355 (44.9%) males. The matched cohort consisted of 6154 patients; 3077 (50.0%) females and 3077 (50.0%) males. The incidence in PPCs was neither significant between females and males in the unmatched cohort (10.0 vs 10.7%; odds ratio (OR) 0.93 [0.81-1.06]; P = 0.255), nor in the matched cohort (10.5 vs 10.0%; OR 1.05 [0.89-1.25]; P = 0.556). New invasive ventilation occurred less often in females in the unmatched cohort. Hospital length of stay and mortality were similar between females and males in both cohorts. CONCLUSIONS: In this conveniently-sized worldwide cohort of patients receiving intraoperative ventilation under general anaesthesia for surgery, the PPC incidence was not significantly different between sexes. REGISTRATION: LAS VEGAS was registered at clinicaltrial.gov (study identifier NCT01601223).

10.
World Neurosurg ; 2024 Sep 24.
Article in English | MEDLINE | ID: mdl-39326664

ABSTRACT

OBJECTIVE: Cauda equina syndrome (CES) is a serious neurological injury that can result in permanent disability. Our objective was to review the evidence for rehabilitation strategies for CES in a scoping review. METHODS: A scoping review of the literature to identify rehabilitation strategies and their outcomes was performed. The search strategy used was: (Cauda equina syndrome) AND (treatment OR management OR intervention OR physio* OR bladder* OR neuro* OR stem cell OR repair OR rehab*) AND ("post?operat* OR post?surgical OR surgery"). MEDLINE, CINHAL, Prospero, Cochrane, ClinicalTrials.gov, EMBASE, Web of Science, PEDro, and eThos were searched. RESULTS: Eight studies of rehabilitation for CES were identified which assessed general rehabilitation, active rehabilitation in a spinal cord injury unit, multidisciplinary team involvement and follow-up, spinal manipulation, spinal cord stimulation and sacral nerve stimulation. Outcome measures used were inconsistent, study quality was low, and it was difficult to draw conclusions regarding the effectiveness of rehabilitation strategies. CONCLUSION: Despite the risk of devastating injury and a recent GIRFT pathway recommending rehabilitation post CES surgery, there is very limited literature on rehabilitation for CES. Future high-quality rehabilitation trials following CES surgery are needed to guide treatment decisions and optimise post-surgical outcomes.

11.
Eur Urol Focus ; 2024 Sep 27.
Article in English | MEDLINE | ID: mdl-39341718

ABSTRACT

BACKGROUND AND OBJECTIVE: Bacteriuria is anticipated in long-term indwelling catheter (IDC) use, and urinary tract infections (UTIs) and related issues are common. Defence mechanisms against infection are undermined by the presence of a Foley catheter, and adjustments to design could influence UTI risk. METHODS: We reviewed the various aspects of IDCs and ureteric stent designs to discuss potential impact on UTI risk. KEY FINDINGS AND LIMITATIONS: Design adaptations have focussed on reducing the sump of undrained urine, potential urinary tract trauma, and bacterial adherence. Experimental and computational studies on ureteral stents found an interplay between urine flow, bacterial microcolony formation, and accumulation of encrusting particles. The most critical regions for biofilm and crystal accumulation are associated with low shear stress. The full drainage system is the functioning unit, not just the IDC in isolation. This means reliably keeping the drainage system closed and considering whether a valve is preferred to a collection bag. Other developments may include one-way valves, obstacles to "bacterial swimming", and ultrasound techniques. Preventing or clearing IDC blockage can exploit access via the lumen or retaining balloon. Progress in computational fluid dynamics, energy delivery, and soft robotics may increase future options. Clinical data on the effectiveness of IDC design features are lacking, which is partly due to reliance on proxy measures and the challenges of undertaking trials. CONCLUSIONS AND CLINICAL IMPLICATIONS: Design changes are legitimate lines of development, but are only indirect for UTI prevention. Modifications may be advantageous, but might potentially bring problems in other ways. Education of health care professionals can improve UTIs and should be prioritised. PATIENT SUMMARY: Catheters used to help bladder drainage can cause urinary infections, and improvements in design might reduce the risk. Several approaches are described in this review. However, proving that these approaches work is a challenge. Training professionals in the key aspects of catheter care is important.

12.
RNA ; 2024 Aug 29.
Article in English | MEDLINE | ID: mdl-39209556

ABSTRACT

Caenorhabditis elegans is an important model organism for human health and disease, with foundational contributions to the understanding of gene expression and tissue patterning in animals. An invaluable tool in modern gene expression research is the presence of a high-resolution ribosome structure, though no such structure exists for C. elegans. Here we present a high-resolution single-particle cryogenic electron microscopy (cryoEM) reconstruction and molecular model of a C. elegans ribosome, revealing a significantly streamlined animal ribosome. Many facets of ribosome structure are conserved in C. elegans, including overall ribosomal architecture and the mechanism of cycloheximide, while other facets such as expansion segments and eL28 are rapidly evolving. We identify uL5 and uL23 as two instances of tissue-specific ribosomal protein paralog expression conserved in Caenorhabditis, suggesting that C. elegans ribosomes vary across tissues. The C. elegans ribosome structure will provide a basis for future structural, biochemical, and genetic studies of translation in this important animal system.

13.
BMJ Med ; 3(1): e000731, 2024.
Article in English | MEDLINE | ID: mdl-39184567

ABSTRACT

Objectives: To describe the effect of multimorbidity on adverse patient centred outcomes in people attending emergency department. Design: Population based cohort study. Setting: Emergency departments in NHS Lothian in Scotland, from 1 January 2012 to 31 December 2019. Participants: Adults (≥18 years) attending emergency departments. Data sources: Linked data from emergency departments, hospital discharges, and cancer registries, and national mortality data. Main outcome measures: Multimorbidity was defined as at least two conditions from the Elixhauser comorbidity index. Multivariable logistic or linear regression was used to assess associations of multimorbidity with 30 day mortality (primary outcome), hospital admission, reattendance at the emergency department within seven days, and time spent in emergency department (secondary outcomes). Primary analysis was stratified by age (<65 v ≥65 years). Results: 451 291 people had 1 273 937 attendances to emergency departments during the study period. 43 504 (9.6%) had multimorbidity, and people with multimorbidity were older (median 73 v 43 years), more likely to arrive by emergency ambulance (57.8% v 23.7%), and more likely to be triaged as very urgent (23.5% v 9.2%) than people who do not have multimorbidity. After adjusting for other prognostic covariates, multimorbidity, compared with no multimorbidity, was associated with higher 30 day mortality (8.2% v 1.2%, adjusted odds ratio 1.81 (95% confidence interval (CI) 1.72 to 1.91)), higher rate of hospital admission (60.1% v 20.5%, 1.81 (1.76 to 1.86)), higher reattendance to an emergency department within seven days (7.8% v 3.5%, 1.41 (1.32 to 1.50)), and longer time spent in the department (adjusted coefficient 0.27 h (95% CI 0.26 to 0.27)). The size of associations between multimorbidity and all outcomes were larger in younger patients: for example, the adjusted odds ratio of 30 day mortality was 3.03 (95% CI 2.68 to 3.42) in people younger than 65 years versus 1.61 (95% CI 1.53 to 1.71) in those 65 years or older. Conclusions: Almost one in ten patients presenting to emergency department had multimorbidity using Elixhauser index conditions. Multimorbidity was strongly associated with adverse outcomes and these associations were stronger in younger people. The increasing prevalence of multimorbidity in the population is likely to exacerbate strain on emergency departments unless practice and policy evolve to meet the growing demand.

14.
Bioorg Med Chem ; 112: 117873, 2024 Oct 01.
Article in English | MEDLINE | ID: mdl-39180860

ABSTRACT

In these days of information overload and high-throughput analysis, it is easy to lose focus on the study of individual proteins. It is our conjecture that such investigations are still crucially important and offer uniquely penetrative insights. We thus present a discussion of biophysical methods to allow readers to get to know their protein of interest better. Although this perspective is not written with the expert in mind, we hope that for interdisciplinary scientists, or researchers who do not routinely perform biophysical analyses, the content will be helpful and inspiring.


Subject(s)
Proteins , Proteins/chemistry , Proteins/metabolism , Biophysics , Humans
15.
Crit Care ; 28(1): 269, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-39217380

ABSTRACT

This review explores the complex interactions between sedation and invasive ventilation and examines the potential of volatile anesthetics for lung- and diaphragm-protective sedation. In the early stages of invasive ventilation, many critically ill patients experience insufficient respiratory drive and effort, leading to compromised diaphragm function. Compared with common intravenous agents, inhaled sedation with volatile anesthetics better preserves respiratory drive, potentially helping to maintain diaphragm function during prolonged periods of invasive ventilation. In turn, higher concentrations of volatile anesthetics reduce the size of spontaneously generated tidal volumes, potentially reducing lung stress and strain and with that the risk of self-inflicted lung injury. Taken together, inhaled sedation may allow titration of respiratory drive to maintain inspiratory efforts within lung- and diaphragm-protective ranges. Particularly in patients who are expected to require prolonged invasive ventilation, in whom the restoration of adequate but safe inspiratory effort is crucial for successful weaning, inhaled sedation represents an attractive option for lung- and diaphragm-protective sedation. A technical limitation is ventilatory dead space introduced by volatile anesthetic reflectors, although this impact is minimal and comparable to ventilation with heat and moisture exchangers. Further studies are imperative for a comprehensive understanding of the specific effects of inhaled sedation on respiratory drive and effort and, ultimately, how this translates into patient-centered outcomes in critically ill patients.


Subject(s)
Anesthetics, Inhalation , Diaphragm , Respiration, Artificial , Humans , Diaphragm/drug effects , Anesthetics, Inhalation/administration & dosage , Anesthetics, Inhalation/pharmacology , Respiration, Artificial/methods , Lung/drug effects , Lung/physiology
16.
Intensive Care Med ; 50(9): 1411-1425, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39102027

ABSTRACT

PURPOSE: Veno-venous extracorporeal membrane oxygenation (VV-ECMO) is an integral part of the management algorithm of patients with severe respiratory failure refractory to evidence-based conventional treatments. Right ventricular injury (RVI) pertaining to abnormalities in the dimensions and/or function of the right ventricle (RV) in the context of VV-ECMO significantly influences mortality. However, in the absence of a universally accepted RVI definition and evidence-based guidance for the management of RVI in this very high-risk patient cohort, variations in clinical practice continue to exist. METHODS: Following a systematic search of the literature, an international Steering Committee consisting of eight healthcare professionals involved in the management of patients receiving ECMO identified domains and knowledge gaps pertaining to RVI definition and management where the evidence is limited or ambiguous. Using a Delphi process, an international panel of 52 Experts developed Expert position statements in those areas. The process also conferred RV-centric overarching open questions for future research. Consensus was defined as achieved when 70% or more of the Experts agreed or disagreed on a Likert-scale statement or when 80% or more of the Experts agreed on a particular option in multiple-choice questions. RESULTS: The Delphi process was conducted through four rounds and consensus was achieved on 31 (89%) of 35 statements from which 24 Expert position statements were derived. Expert position statements provided recommendations for RVI nomenclature in the setting of VV-ECMO, a multi-modal diagnostic approach to RVI, the timing and parameters of diagnostic echocardiography, and VV-ECMO settings during RVI assessment and management. Consensus was not reached on RV-protective driving pressure thresholds or the effect of prone positioning on patient-centric outcomes. CONCLUSION: The proposed definition of RVI in the context of VV-ECMO needs to be validated through a systematic aggregation of data across studies. Until further evidence emerges, the Expert position statements can guide informed decision-making in the management of these patients.


Subject(s)
Delphi Technique , Extracorporeal Membrane Oxygenation , Extracorporeal Membrane Oxygenation/methods , Extracorporeal Membrane Oxygenation/standards , Humans , Adult , Respiratory Insufficiency/therapy , Respiratory Insufficiency/etiology , Ventricular Dysfunction, Right/etiology , Ventricular Dysfunction, Right/therapy , Ventricular Dysfunction, Right/physiopathology , Consensus , Heart Ventricles/physiopathology , Heart Ventricles/injuries , Heart Ventricles/diagnostic imaging
18.
Magn Reson Med ; 92(6): 2392-2403, 2024 Dec.
Article in English | MEDLINE | ID: mdl-39136249

ABSTRACT

PURPOSE: Advancing the development of 7 T MRI for spinal cord imaging is crucial for the enhanced diagnosis and monitoring of various neurodegenerative diseases and traumas. However, a significant challenge at this field strength is the transmit field inhomogeneity. Such inhomogeneity is particularly problematic for imaging the small, deep anatomical structures of the cervical spinal cord, as it can cause uneven signal intensity and elevate the local specific absorption ratio, compromising image quality. This multisite study explores several RF shimming techniques in the cervical spinal cord. METHODS: Data were collected from 5 participants between two 7 T sites with a custom 8Tx/20Rx parallel transmission coil. We explored two radiofrequency (RF) shimming approaches from an MRI vendor and four from an open-source toolbox, showcasing their ability to enhance transmit field and signal homogeneity along the cervical spinal cord. RESULTS: The circularly polarized (CP), coefficient of variation (CoV), and specific absorption rate (SAR) efficiency shim modes showed the highest B1 + efficiency, and the vendor-based "patient" and "volume" modes showed the lowest B1 + efficiency. The coefficient of variation method produced the highest CSF/spinal cord contrast on T2*-weighted scans (ratio of 1.27 ± 0.03), and the lowest variation of that contrast along the superior-inferior axis. CONCLUSION: The study's findings highlight the potential of RF shimming to advance 7 T MRI's clinical utility for central nervous system imaging by enabling more homogenous and efficient spinal cord imaging. Additionally, the research incorporates a reproducible Jupyter Notebook, enhancing the study's transparency and facilitating peer verification.


Subject(s)
Cervical Cord , Magnetic Resonance Imaging , Radio Waves , Humans , Magnetic Resonance Imaging/methods , Cervical Cord/diagnostic imaging , Male , Female , Adult , Image Processing, Computer-Assisted/methods , Spinal Cord/diagnostic imaging , Algorithms
19.
ACS Synth Biol ; 13(9): 2833-2843, 2024 Sep 20.
Article in English | MEDLINE | ID: mdl-39158169

ABSTRACT

Genetic code expansion has enabled cellular synthesis of proteins containing unique chemical functional groups to allow the understanding and modulation of biological systems and engineer new biotechnology. Here, we report the development of efficient methods for site-specific incorporation of structurally diverse noncanonical amino acids (ncAAs) into proteins expressed in the electroactive bacterium Shewanella oneidensis MR-1. We demonstrate that the biosynthetic machinery for ncAA incorporation is compatible and orthogonal to the endogenous pathways of S. oneidensis MR-1 for protein synthesis, maturation of c-type cytochromes, and protein secretion. This allowed the efficient synthesis of a c-type cytochrome, MtrC, containing site-specifically incorporated ncAA in S. oneidensis MR-1 cells. We demonstrate that site-specific replacement of surface residues in MtrC with ncAAs does not influence its three-dimensional structure and redox properties. We also demonstrate that site-specifically incorporated bioorthogonal functional groups could be used for efficient site-selective labeling of MtrC with fluorophores. These synthetic biology developments pave the way to expand the chemical repertoire of designer proteins expressed in S. oneidensis MR-1.


Subject(s)
Genetic Code , Shewanella , Shewanella/genetics , Shewanella/metabolism , Shewanella/enzymology , Cytochrome c Group/metabolism , Cytochrome c Group/genetics , Cytochrome c Group/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Amino Acids/metabolism , Oxidation-Reduction
20.
Respir Res ; 25(1): 312, 2024 Aug 17.
Article in English | MEDLINE | ID: mdl-39153979

ABSTRACT

BACKGROUND: Ventilation management may differ between COVID-19 ARDS (COVID-ARDS) patients and patients with pre-COVID ARDS (CLASSIC-ARDS); it is uncertain whether associations of ventilation management with outcomes for CLASSIC-ARDS also exist in COVID-ARDS. METHODS: Individual patient data analysis of COVID-ARDS and CLASSIC-ARDS patients in six observational studies of ventilation, four in the COVID-19 pandemic and two pre-pandemic. Descriptive statistics were used to compare epidemiology and ventilation characteristics. The primary endpoint were key ventilation parameters; other outcomes included mortality and ventilator-free days and alive (VFD-60) at day 60. RESULTS: This analysis included 6702 COVID-ARDS patients and 1415 CLASSIC-ARDS patients. COVID-ARDS patients received lower median VT (6.6 [6.0 to 7.4] vs 7.3 [6.4 to 8.5] ml/kg PBW; p < 0.001) and higher median PEEP (12.0 [10.0 to 14.0] vs 8.0 [6.0 to 10.0] cm H2O; p < 0.001), at lower median ΔP (13.0 [10.0 to 15.0] vs 16.0 [IQR 12.0 to 20.0] cm H2O; p < 0.001) and higher median Crs (33.5 [26.6 to 42.1] vs 28.1 [21.6 to 38.4] mL/cm H2O; p < 0.001). Following multivariable adjustment, higher ΔP had an independent association with higher 60-day mortality and less VFD-60 in both groups. Higher PEEP had an association with less VFD-60, but only in COVID-ARDS patients. CONCLUSIONS: Our findings show important differences in key ventilation parameters and associations thereof with outcomes between COVID-ARDS and CLASSIC-ARDS. TRIAL REGISTRATION: Clinicaltrials.gov (identifier NCT05650957), December 14, 2022.


Subject(s)
COVID-19 , Pneumonia , Respiration, Artificial , Respiratory Distress Syndrome , Adult , Aged , Female , Humans , Male , Middle Aged , COVID-19/mortality , COVID-19/therapy , Respiratory Distress Syndrome/mortality , Respiratory Distress Syndrome/therapy , Treatment Outcome , Pneumonia/complications
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