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Probiotics are widely used for their health promoting effects, though a lot remain to be discovered, particularly on their mechanisms of action at the molecular level. The functional genomic approach is an appropriate method to decipher how probiotics may influence human cell fate and therefore contribute to their health benefit. In the present work, we focused on Shouchella clausii (formerly named Bacillus then Alkalihalobacillus clausii), a spore-forming bacterium that is commercially available as a probiotic for the prevention and the treatment of intestinal dysbiosis and related gastrointestinal disorders, such as diarrhoea. Several studies have demonstrated that S. clausii treatment modulated inflammatory and immune responses, as well as gut barrier functions. A functional genomic strategy was implemented to decipher the mechanisms by which S. clausii exerts its probiotic effects on human intestinal epithelial cells. To do so, a large genomic DNA fragment library was constructed for each of the four strains: O/C, N/R, SIN and T. A high throughput in vitro screening in human epithelial cells was then conducted, using the reporter gene strategy, targeting the nuclear factor kappa B (NF-κB) pathway and interleukin-10 (IL-10) gene expression. After an exhaustive in vitro screening of approximately a thousand clones per library, several clones modulating the NF-κB pathway in the HT-29 reporter cell line were identified. Among clone lysates, 1.1% (O/C), 1.4% (N/R), 2.0% (SIN), and 1.2% (T) were identified as biologically active on immune reporter systems (NF-κB and IL-10 expression). After transposon mutagenesis and a new set of screening and sequencing, 23 coding sequences (CDS) were identified, including one encoding for the glutamine synthetase, associated with NF-κB modulation, and six CDS for IL-10 modulation. The functional genomic strategy that was applied to S. clausii was an original approach to identify gene candidates that may explain the mechanisms of action of probiotics. However, further work is needed to validate the identified leads.

This study assessed the impact of on-site field-simulated oil spills at the International Institute for Sustainable Development-Experimental Lakes Area (IISD-ELA) on a freshwater boreal lake. Low total petroleum hydrocarbons (TPH) values were obtained in water and sediments from the locations without direct oil loading across the 6-year monitoring program. Biogenic n-alkanes and pyrogenic polycyclic aromatic hydrocarbons (PAHs) were predominant pre- and post-spill. No petroleum biomarkers were detected in the water, but trace levels appeared in a few sediments. Most TPH and PAH levels were within acceptable limits set by the Canadian Council of Ministers of the Environment (CCME) and Ontario regulations, though some PAHs exceeded guidelines. However, the frequency of exceedances did not change significantly before and after the spill. These results suggest that the spilled oil was contained effectively during the experiment period, and the environment recovered to near-background levels afterward with appropriate precautions and remediation operations., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Termination factor Rho, responsible for the main factor-dependent pathway of transcription termination and the major inhibitor of antisense transcription, is an emerging regulator of various physiological processes in microorganisms. In Gram-positive bacterium Bacillus subtilis, Rho is involved in the control of cell adaptation to starvation and, in particular, in the control of sporulation, a complex differentiation program leading to the formation of a highly resistant dormant spore. While the initiation of sporulation requires a decrease in Rho protein levels during the transition to stationary phase, the mechanisms regulating the expression of rho gene throughout the cell cycle remain largely unknown. Here we show that a drop in the activity of the vegetative SigA-dependent rho promoter causes the inhibition of rho expression in stationary phase. However, after the initiation of sporulation, rho gene is specifically reactivated in two compartments of the sporulating cell using distinct mechanisms. In the mother cell, rho expression occurs by read-through transcription initiated at the SigH-dependent promoter of the distal spo0F gene. In the forespore, rho gene is transcribed from the intrinsic promoter recognized by the alternative sigma factor SigF. These regulatory elements ensure the activity of Rho during sporulation, which appears important for the proper formation of spores. We provide experimental evidence that disruption of the spatiotemporal expression of rho during sporulation affects the resistance properties of spores, their morphology, and the ability to return to vegetative growth under favorable growth conditions., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Respiratory dysfunction is an important contributor to morbidity and mortality in advanced Parkinson's disease (PD), but it is unclear what parameters are sensitive to diagnose and monitor respiratory dysfunction across disease phases., Objectives: We aimed to characterize respiratory dysfunction in mild to moderate PD., Methods: In 20 individuals without cardiopulmonary comorbidity, pulmonary and inspiratory muscle function testing were performed ON-medication. Subsequently, the acute ventilatory response to hypoxia (HVR) was assessed by gradually decreasing F I O 2 from 0.209 (room air) to 0.127, which was compared to eight age- and sex-matched healthy controls under arterial blood gas monitoring. Lastly, on different days, the same 20 individuals with PD underwent six blinded exposures to 45-min normobaric hypoxia at FiO2 0.163 and 0.127 or placebo OFF-medication to assess breathing responses., Results: At rest, individuals with greatest PD severity had a lower tidal volume (pairwise comparisons: 0.59 vs. 0.74, P = 0.038-0.050) and tended to have a higher breathing frequency (17.7 vs. 14.4, P = 0.076), despite normal pulmonary function. A 45-min exposure to hypoxia induced a significantly lower acute HVR in individuals with PD compared to controls (-0.0489 vs. 0.133 L.min/%, P = 0.0038). Acute HVR was reduced regardless of disease severity. Subacute HVR in individuals with milder disease tended to be higher compared to those with more advanced disease (P = 0.079)., Conclusions: Respiratory dysfunction is present in individuals with PD, including those with relatively mild disease severity, and is characterized by altered breathing patterns at rest, as well as a lower HVR, despite normal pulmonary and inspiratory muscle function testing., (© 2024 The Author(s). Movement Disorders Clinical Practice published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.)

There is a group of beta (β)-thalassemia trait 'carriers' (with heterozygous mutations) who should be asymptomatic with minor abnormalities in their hematological parameters, but experience more severe disease manifestations than predicted based solely on their β-globin genotype. This review focuses on literature describing trans-acting genetic modifiers outside of the α- and β-globin gene clusters that could cause this phenomenon. These genetic modifiers are categorized into: mutations affecting the quantity of alpha-globin products, non-globin mutations affecting erythropoiesis, membranopathies, enzymopathies and erythrocyte-independent modifiers of complications relating to β-thalassemia. Although some genetic determinants seem to correlate more directly with β-thalassemia trait severity, such as mutations in SUPT5H, PIEZO1 and hereditary elliptocytosis, the difficulties of linking the contribution of other modulating factors are elucidated in this review. Targeted next generation sequencing of hemolytic anemias can be helpful but also raises another quandary in interpreting variants of uncertain significance. The accrual of knowledge, along with the increased availability of genetic testing for genetic modifiers has considerable potential for clinical applications such as genetic counselling, decision-making for clinical interventions and prognostication, and perhaps generating new therapeutic targets., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Peptidoglycan synthesis is an essential driver of bacterial growth and division. The final steps of this crucial process involve the activity of SEDS family glycosyltransferases that polymerize glycan strands and class B penicillin-binding protein (bPBP) transpeptidases that cross-link them. While most bacteria encode multiple bPBPs that perform specialized roles during specific cellular processes, some bPBPs can play redundant roles that are important for resistance against certain cell wall stresses. Our understanding of these compensatory mechanisms, however, remains incomplete. Endospore-forming bacteria typically encode multiple bPBPs that drive morphological changes required for sporulation. The sporulation-specific bPBP, SpoVD, is important for synthesizing the asymmetric division septum and spore cortex peptidoglycan during sporulation in the pathogen Clostridioides difficile . Although SpoVD catalytic activity is essential for cortex synthesis, we show that it is unexpectedly dispensable for SpoVD to mediate asymmetric division. The dispensability of SpoVD's catalytic activity requires the presence of its SEDS partner, SpoVE, and is facilitated by the catalytic activity of another sporulation-specific bPBP, PBP3. Our data further suggest that PBP3 interacts with components of the asymmetric division machinery, including SpoVD. These findings suggest a possible mechanism by which bPBPs can be functionally redundant in diverse bacteria and facilitate antibiotic resistance.

Firefighters can be exposed to complex mixtures of airborne substances, including hazardous substances released during structural fires. This study employed silicone wristbands (SWBs) as passive samplers to investigate potential exposure to polycyclic aromatic hydrocarbons (PAHs) and flame retardants (FRs). SWBs were deployed at different areas of four fire stations, in four truck cabins, and at an office control location; they were also donned outside the jackets of 18 firefighters who responded to fire calls. Overall, office areas had significantly lower PAHs than fire station areas. Vehicle bays and truck cabins had significantly higher concentrations of low molecular weight (LMW) PAHs than sleeping and living room areas. For organophosphate ester flame retardants (OPFRs), tri-n-butyl phosphate (TnBP) and tris(1-chloro-2-propyl) phosphate (TCPP) were detected in all the samples; 2-ethylhexyl diphenyl phosphate (EHDPP) was more frequently detected in the fire station areas. Triphenyl phosphate (TPP) concentrations were highest in the truck cabin and office areas, and tris(1,3-dichloro-2-propyl)phosphate (TDCPP) was highest in truck cabins. Thirteen of 16 PAHs and nine of 36 OPFRs were detected in all the SWBs worn by firefighters, and tris (2-butoxyethyl) phosphate (TBEP) was the predominant OPFR. Levels of LMW PAHs were significantly lower when firefighters did not enter the fire. LMW PAHs, HMW (high molecular weight) PAHs, and EHDPP were significantly elevated when heavy smoke was reported. This work highlights the potential for occupational exposure to PAHs and flame retardants in some fire station areas; moreover, factors that may influence exposure during fire suppression. Whilst firefighters' occupational exposure to PAHs is likely related to fire suppression and exposure to contaminated gear and trucks, exposure to OPFRs may be more related to their presence in truck interiors and electronics.

Rationale and Objective: Avoidance of opioid withdrawal plays a key role in human opioid addiction. Here, we present a procedure for studying operant negative reinforcement in rats that was inspired by primate procedures where opioid-dependent subjects lever-press to prevent naloxone infusions., Methods: In Experiment 1, we trained rats (n = 30, 15 females) to lever-press to escape and then avoid mild footshocks (0.13-0.27 mA) for 35 days (30 trials/d). Next, we catheterized them and implanted minipumps containing methadone (10 mg/kg/day) or saline. We then paired (4 times, single session) a light cue (20-s) with a naloxone infusion (20 µg/kg, i.v) that precipitated opioid withdrawal. Next, we trained the rats to escape naloxone injections for 10 days (30 trials/d). Each trial started with the onset of the opioid-withdrawal cue. After 20-s, the lever extended, and an infusion of naloxone (1 to 2.2 µg/kg/infusion) began; a lever-press during an 11-s window terminated the withdrawal-paired cue and the infusion. In Experiment 2, we trained rats (n = 34, 17 females) on the same procedure but decreased the footshock escape/avoidance training to 20 days., Results: All rats learned to lever-press to escape or avoid mild footshocks. In both experiments, a subset, 56% (10/18) and 33% (8/24) of methadone-dependent rats learned to lever-press to escape naloxone infusions., Conclusions: We introduce an operant negative reinforcement procedure where a subset of opioid-dependent rats learned to lever-press to escape withdrawal-inducing naloxone infusions. The procedure can be used to study mechanisms of individual differences in opioid negative reinforcement-related behaviors in opioid-dependent rats., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Levothyroxine is one of the most prescribed drugs in the western world. Dosing is challenging due to high-interindividual differences in effective dosage and the narrow therapeutic window. Model-informed precision dosing (MIPD) using machine learning could assist general practitioners (GPs), but no such models exist for primary care. Furthermore, introduction of decision-support algorithms in healthcare is limited due to the substantial gap between developers and clinicians' perspectives. We report the development, validation, and a clinical simulation trial of the first MIPD application for primary care. Stable maintenance dosage of levothyroxine was the model target. The multiclass model generates predictions for individual patients, for different dosing classes. Random forest was trained and tested on a national primary care database (n = 19,004) with a final weighted AUC across dosing options of 0.71, even in subclinical hypothyroidism. TSH, fT4, weight, and age were most predictive. To assess the safety, feasibility, and clinical impact of MIPD for levothyroxine, we performed clinical simulation studies in GPs and compared MIPD to traditional prescription. Fifty-one GPs selected starting dosages for 20 primary hypothyroidism cases without and then with MIPD 2 weeks later. Overdosage and underdosage were defined as higher and lower than 12.5 μg relative to stable maintenance dosage. MIPD decreased overdosage in number (30.5 to 23.9%, P < 0.01) and magnitude (median 50 to 37.5 μg, P < 0.01) and increased optimal starting dosages (18.3 to 30.2%, P < 0.01). GPs considered lab results more often with MIPD and most would use the model frequently. This study demonstrates the clinical relevance, safety, and effectiveness of MIPD for levothyroxine in primary care., (© 2024 The Authors. Clinical Pharmacology & Therapeutics published by Wiley Periodicals LLC on behalf of American Society for Clinical Pharmacology and Therapeutics.)

The case report details the adaptive radiotherapy management of a 75-year-old female diagnosed with high-grade endometrial carcinoma. The patient, who was known to be hypertensive with no other comorbidities and no family history of cancer, presented with a complaint of bleeding per vagina for six months. Following extensive investigations, she underwent a laparoscopic radical hysterectomy. Postoperative histopathology confirmed endometrial adenocarcinoma International Federation of Gynecology and Obstetrics (FIGO) stage IA, grade III. The adjuvant treatment plan included adjuvant chemoradiotherapy to the postoperative tumor bed and draining lymph nodes. On planning computed tomography (CT), the patient's lymphocele responded remarkably to radiation therapy, an unusual outcome that underscores the potential efficacy of adaptive radiotherapy in complex cases., Competing Interests: Human subjects: Consent was obtained or waived by all participants in this study. Conflicts of interest: In compliance with the ICMJE uniform disclosure form, all authors declare the following: Payment/services info: All authors have declared that no financial support was received from any organization for the submitted work. Financial relationships: All authors have declared that they have no financial relationships at present or within the previous three years with any organizations that might have an interest in the submitted work. Other relationships: All authors have declared that there are no other relationships or activities that could appear to have influenced the submitted work., (Copyright © 2024, Weerarathna et al.)

Squamous cells in the cervix can develop into a type of cervical cancer. Cervical squamous cells are the cells that line the outside of the cervix. These thin, flat cells have a striking resemblance to fish scales under a microscope. Squamous cell carcinomas (SCCs) are the most common type of cervical cancer. We report the case of a 60-year-old woman with SCC devoid of a family history of cancer or related diseases. Following a biopsy confirming SCC, the patient's contrast-enhanced computed tomography scan revealed a somewhat enlarged cervix along with a white discharge per vagina. The patient underwent a Wertheim hysterectomy and was diagnosed with microinvasive SCC, adenomyosis, and negative lymph nodes. Two years after being free from disease, the issue reappeared even with routine follow-ups. The patient underwent six rounds of chemotherapy, followed by chemoradiation and interstitial brachytherapy. The multimodality therapy method applied to an aged female patient experiencing recurrent SCC of the cervix is demonstrated in this case study. It underlines how crucial regular follow-ups and multimodal therapy are to control recurrent cervical cancer., Competing Interests: Human subjects: Consent was obtained or waived by all participants in this study. Conflicts of interest: In compliance with the ICMJE uniform disclosure form, all authors declare the following: Payment/services info: All authors have declared that no financial support was received from any organization for the submitted work. Financial relationships: All authors have declared that they have no financial relationships at present or within the previous three years with any organizations that might have an interest in the submitted work. Other relationships: All authors have declared that there are no other relationships or activities that could appear to have influenced the submitted work., (Copyright © 2024, Jules et al.)

Regulatory T cells (Treg) play a prominent role in utero tolerating non-inherited maternal antigens and in regulating immune responses against pathogens at birth. This study investigates Treg immunity in newborns in West Africa, where sepsis remains a major public health problem. Treg phenotypes on neonates subgroups with early-onset sepsis (EOS), presumed sepsis, and healthy newborn with and without prenatal risk factors were evaluated. Treg phenotypes varied according to prenatal conditions, with increase in Treg frequency and Foxp3 expression in healthy newborns with prenatal risk factors compared to those with none risk. Compared to healthy newborns with prenatal risk factors, EOS neonates had a significantly reduced frequency of Treg and Foxp3 expression. In the Treg pool, higher frequency of activated Treg was observed in EOS neonates, suggesting an in-utero activation upstream of the sepsis onset. Their migration to the infection site may explain the reduced frequency of circulating Integrin α4β1 + Treg suggestive of homing to the endothelial tissue. EOS neonates show increases expression of CTLA-4, PD-1 and CD39 on Treg, which negatively regulate the activation of effector T cells (Teff) corroborating by the lower frequency of Teff in EOS neonates. The higher frequency of CD39 + Treg and the lower frequency of integrinα4β1 + Treg in EOS non-survivor suggests that Treg exhaustement and endothelial homing are associated with outcome severity. Neonates developing EOS are born with an altered Treg phenotypic profile. Treg expression of CTLA-4, PD-1, CD39, and integrinα4β1 cell markers can be considered as early warning or diagnostic markers of EOS., Competing Interests: Authors AP, LG, and KB-P were employed by the company bioMérieux. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The authors declare that this study received funding from bioMerieux. The funder had the following involvement in the study: design, analysis, interpretation of data, the writing of this article., (Copyright © 2024 Sossou, Ezinmegnon, Agbota, Gbedande, Accrombessi, Massougbodji, d’Almeida, Alao, Dossou-Dagba, Pachot, Vachot, Brengel-Pesce, Cottrell, Yessoufou, Briand, Tissières and Fievet.)

Digital biomarkers that remotely monitor symptoms have the potential to revolutionize outcome assessments in future disease-modifying trials in Parkinson's disease (PD), by allowing objective and recurrent measurement of symptoms and signs collected in the participant's own living environment. This biomarker field is developing rapidly for assessing the motor features of PD, but the non-motor domain lags behind. Here, we systematically review and assess digital biomarkers under development for measuring non-motor symptoms of PD. We also consider relevant developments outside the PD field. We focus on technological readiness level and evaluate whether the identified digital non-motor biomarkers have potential for measuring disease progression, covering the spectrum from prodromal to advanced disease stages. Furthermore, we provide perspectives for future deployment of these biomarkers in trials. We found that various wearables show high promise for measuring autonomic function, constipation and sleep characteristics, including REM sleep behavior disorder. Biomarkers for neuropsychiatric symptoms are less well-developed, but show increasing accuracy in non-PD populations. Most biomarkers have not been validated for specific use in PD, and their sensitivity to capture disease progression remains untested for prodromal PD where the need for digital progression biomarkers is greatest. External validation in real-world environments and large longitudinal cohorts remains necessary for integrating non-motor biomarkers into research, and ultimately also into daily clinical practice., (© 2024. The Author(s).)

Archaeological studies of pre-historic Arctic cultures are often limited to artefacts and architecture; such records may be incomplete and often do not provide a continuous record of past occupation. Here, we used lake sediment archives to supplement archaeological evidence to explore the history of Thule and Dorset populations on Somerset Island, Nunavut (Canada). We examined biomarkers in dated sediment cores from two ponds adjacent to abandoned Thule settlements (PaJs-3 and PaJs-13) and compared these to sediment cores from two ponds without past human occupation. Coprostanol and epicoprostanol, δ 15 N measurements, sedimentary chlorophyll a and the ratio of diatom valves to chrysophyte cysts were elevated in the dated sediment profiles at both sites during Thule and Dorset occupations. Periods of pronounced human impact during the Thule occupation of the site were corroborated by 14 C-dated caribou bones found at both sites that identified intense caribou hunting between ca 1185 and 1510 CE. Notably, these sediment core data show evidence of the Dorset occupation from ca 200 to 500 CE at sites where archaeological evidence was heretofore lacking. We highlight the utility of lake sediments in assisting archaeological studies to better establish the timings, peak occupations and even lifestyle practices of the Dorset and Thule Arctic peoples.

Background: Parkinson's disease (PD) is a neurodegenerative disease for which no disease-modifying therapies exist. Preclinical and clinical evidence suggest that repeated exposure to intermittent hypoxia might have short- and long-term benefits in PD. In a previous exploratory phase I trial, we demonstrated that in-clinic intermittent hypoxia exposure is safe and feasible with short-term symptomatic effects on PD symptoms. The current study aims to explore the safety, tolerability, feasibility, and net symptomatic effects of a four-week intermittent hypoxia protocol, administered at home, in individuals with PD., Methods/design: This is a two-armed double-blinded randomized controlled trial involving 40 individuals with mild to moderate PD. Participants will receive 45 min of normobaric intermittent hypoxia (fraction of inspired oxygen 0.16 for 5 min interspersed with 5 min normoxia), 3 times a week for 4 weeks. Co-primary endpoints include nature and total number of adverse events, and a feasibility-tolerability questionnaire. Secondary endpoints include Movement Disorders Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) part II and III scores, gait tests and biomarkers indicative of hypoxic dose and neuroprotective pathway induction., Discussion: This trial builds on the previous phase I trial and aims to investigate the safety, tolerability, feasibility, and net symptomatic effects of intermittent hypoxia in individuals with PD. Additionally, the study aims to explore induction of relevant neuroprotective pathways as measured in plasma. The results of this trial could provide further insight into the potential of hypoxia-based therapy as a novel treatment approach for PD., Trial Registration: ClinicalTrials.gov Identifier: NCT05948761 (registered June 20th, 2023)., (© 2024. The Author(s).)

The role of the intestinal microbiota in host health is increasingly revealed in its contributions to disease states. The host-microbiome interaction is multifactorial and dynamic. One of the factors that has recently been strongly associated with host physiological responses is peptidoglycan from bacterial cell walls. Peptidoglycan from gut commensal bacteria activates peptidoglycan sensors in human cells, including the nucleotide-binding oligomerization domain-containing protein 2. When present in the gastrointestinal tract, both the polymeric form (sacculi) and depolymerized fragments can modulate host physiology, including checkpoint anticancer therapy efficacy, body temperature and appetite, and postnatal growth. To utilize this growing area of biology toward therapeutic prescriptions, it will be critical to directly analyze a key feature of the host-microbiome interaction from living hosts in a reproducible and noninvasive way. Here we show that metabolically labeled peptidoglycan/sacculi can be readily isolated from fecal samples collected from both mice and humans. Analysis of fecal samples provided a noninvasive route to probe the gut commensal community including the metabolic synchronicity with the host circadian clock. Together, these results pave the way for noninvasive diagnostic tools to interrogate the causal nature of peptidoglycan in host health and disease.

Animal psychophysics can generate rich behavioral datasets, often comprised of many 1000s of trials for an individual subject. Gradient-boosted models are a promising machine learning approach for analyzing such data, partly due to the tools that allow users to gain insight into how the model makes predictions. We trained ferrets to report a target word's presence, timing, and lateralization within a stream of consecutively presented non-target words. To assess the animals' ability to generalize across pitch, we manipulated the fundamental frequency (F0) of the speech stimuli across trials, and to assess the contribution of pitch to streaming, we roved the F0 from word token to token. We then implemented gradient-boosted regression and decision trees on the trial outcome and reaction time data to understand the behavioral factors behind the ferrets' decision-making. We visualized model contributions by implementing SHAPs feature importance and partial dependency plots. While ferrets could accurately perform the task across all pitch-shifted conditions, our models reveal subtle effects of shifting F0 on performance, with within-trial pitch shifting elevating false alarms and extending reaction times. Our models identified a subset of non-target words that animals commonly false alarmed to. Follow-up analysis demonstrated that the spectrotemporal similarity of target and non-target words rather than similarity in duration or amplitude waveform was the strongest predictor of the likelihood of false alarming. Finally, we compared the results with those obtained with traditional mixed effects models, revealing equivalent or better performance for the gradient-boosted models over these approaches., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Griffiths et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Parkinson's disease (PD) has a long, heterogeneous, pre-diagnostic phase, during which pathology insidiously accumulates. Increasing evidence suggests that environmental and lifestyle factors in early life contribute to disease risk and progression. Thanks to the extensive study of this pre-diagnostic phase, the first prevention trials of PD are being designed. However, the highly heterogenous evolution of the disease across the life course is not yet sufficiently taken into account. This could hamper clinical trial success in the advent of biological disease definitions. In an interdisciplinary patient-clinician study group, we discussed how an approach that incorporates the lifetime evolution of PD may benefit the design of disease-modifying trials by impacting population, target and outcome selection. We argue that the timepoint of exposure to risk and protective factors plays a critical role in PD subtypes, influencing population selection. In addition, recent developments in differential disease mechanisms, aided by biological disease definitions, could impact optimal treatment targets. Finally, multimodal biomarker panels using this lifetime approach will likely be most sensitive as progression markers for more personalized trials. We believe that the lifetime evolution of PD should be considered in the design of clinical trials, and that such initiatives could benefit from more patient-clinician partnerships.

Objectives: Peptidoglycan (PG) is an arthritogenic bacterial cell wall component whose role in human osteoarthritis is poorly understood. The purpose of this study was to determine if PG is present in synovial tissue of osteoarthritis patients at the time of primary total knee arthroplasty (TKA), and if its presence is associated with inflammation and patient reported outcomes., Methods: Intraoperative synovial tissue and synovial fluid samples were obtained from 56 patients undergoing primary TKA, none of whom had history of infection. PG in synovial tissue was detected by immunohistochemistry (IHC) and immunofluorescence microscopy (IFM). Synovial tissue inflammation and fibrosis were assessed by histopathology and synovial fluid cytokine quantification. Primary human fibroblasts isolated from arthritis synovial tissue were stimulated with PG to determine inflammatory cytokine response., Results: A total of 33/56 (59%) of primary TKA synovial tissue samples were positive for PG by IHC, and PG staining colocalized with markers of synovial macrophages and fibroblasts by IFM. Synovial tissue inflammation and elevated IL-6 in synovial fluid positively correlated with PG positivity. Primary human fibroblasts stimulated with PG secreted high levels of IL-6, consistent with ex vivo findings. Interestingly, we observed a significant inverse correlation between PG and age at time of TKA, indicating younger age at time of TKA was associated with higher PG levels., Conclusion: Peptidoglycan is commonly found in synovial tissue from patients undergoing TKA. Our data indicate that PG may play an important role in inflammatory synovitis, particularly in patients who undergo TKA at a relatively younger age., (© 2024. The Author(s).)

Algal bioindicators, such as diatoms, often show subdued responses to eutrophication in Arctic lakes because climate-related changes (e.g., ice cover) tend to be the overriding factors influencing assemblage composition. Here, we examined how sub-Arctic ponds historically receiving high nutrient inputs from nesting seabirds have responded to recent climate change. We present diatom data obtained from 12 sediment cores in seaduck-affected ponds located on islands through Hudson Strait, Canada. All study cores show consistently elevated values of sedimentary ẟ 15 N, an established proxy for tracking marine-derived nutrients, indicating seabirds have been present on these islands for at least the duration of the sediment records (~100 to 400 years). We document diverse epiphytic diatom assemblages to the base of all sediment cores, which is in marked contrast to seabird-free Arctic ponds-these oligotrophic sites typically record epilithic diatom flora prior to recent warming. Diatoms are likely responding indirectly to seabird nutrients via habitat as nutrients promote the growth of mosses supporting epiphytic diatom communities. This masks the typical diatom response to increased warming in the Arctic, which also results in habitat changes and the growth of mosses around the pond edges. Changes in sedimentary chlorophyll a were not consistently synchronous with large changes in ẟ 15 N values, suggesting that primary production in ponds is not responding linearly to changes in seabird-derived nitrogen. Across all ponds, we recorded shifts in diatom epiphytic assemblages (e.g., increases in % relative abundance of many Nitzschia species) that often align with increases in chlorophyll a . The changes in diatoms and chlorophyll a , although variable, are most likely driven by climate change as they are generally consistent with longer ice-free conditions and growing seasons. Together, our results show that to effectively use diatoms in animal population reconstructions across the sub-Arctic and Arctic, a strong understanding of eutrophication and climate change, based on supplementary proxies, is also required., Competing Interests: The authors have no conflicts of interest to declare., (© 2024 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Parkinson's disease (PD) is a progressive neurodegenerative disorder for which only symptomatic treatments are available. Both preclinical and clinical studies suggest that moderate hypoxia induces evolutionarily conserved adaptive mechanisms that enhance neuronal viability and survival. Therefore, targeting the hypoxia response pathway might provide neuroprotection by ameliorating the deleterious effects of mitochondrial dysfunction and oxidative stress, which underlie neurodegeneration in PD. Here, we review experimental studies regarding the link between PD pathophysiology and neurophysiological adaptations to hypoxia. We highlight the mechanistic differences between the rescuing effects of chronic hypoxia in neurodegeneration and short-term moderate hypoxia to improve neuronal resilience, termed "hypoxic conditioning". Moreover, we interpret these preclinical observations regarding the pharmacological targeting of the hypoxia response pathway. Finally, we discuss controversies with respect to the differential effects of hypoxia response pathway activation across the PD spectrum, as well as intervention dosing in hypoxic conditioning and potential harmful effects of such interventions. We recommend that initial clinical studies in PD should focus on the safety, physiological responses, and mechanisms of hypoxic conditioning, as well as on repurposing of existing pharmacological compounds. © 2023 International Parkinson and Movement Disorder Society., (© 2023 International Parkinson and Movement Disorder Society.)

Mercury (Hg) contamination in aquatic systems can lead to adverse human and environmental health outcomes. Yellowknife, a city in Canada's Northwest Territories, is a historic mining community, with two large gold mines (Giant Mine and Con Mine) that used Hg amalgamation methods to extract gold between ∼1938 and 1960. We analyzed dated sediment cores from 20 small lakes to investigate the spatial and temporal Hg deposition patterns within 50 km of Giant Mine. Breakpoint analysis of the within-lake z-score normalized anthropogenic Hg flux indicates two significant time periods of changing emission rates. The first is a significant increase in Hg deposition rate (∼1925) during the time of gold exploration in the region and onset of Hg amalgamation (1938) and the second is a significant decrease in deposition rate that begins around the time of the cessation of Hg amalgamation at Giant Mine (∼1959). Sediment Hg concentrations exceeded the Canadian Council for Ministers of the Environment Interim Sediment Quality Guideline (ISQG) for Hg (0.17 mg/kg dw) in 55% of the lakes (n = 11) during mining (1948-1999). All lakes within 5 km of the Giant Mine roaster stack exceeded CCME ISQG during mining (n = 8), with a 4-fold increase in total Hg concentration observed during mining at these near-field (<5 km from stack) sites. We observed evidence of enriched Hg in near-field, mid-field, and far-field sites. The elevated sedimentary Hg concentrations during mining in near-field sites would have posed a hazard to human and wildlife health during the height of emissions, however the significant decrease in Hg concentrations since the closure of mines in the region demonstrate the potential for recovery in these aquatic ecosystems., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Ltd.)

Firefighters experience exposures to carcinogenic and mutagenic substances, including polycyclic aromatic hydrocarbons (PAHs). Silicone wristbands (SWBs) have been used as passive samplers to assess firefighters' exposures over the course of a shift but their utility in measuring short term exposures, source of exposure, and correlations with other measurements of exposure have not yet been investigated. In this study, SWBs were used to measure the concentrations of 16 priority PAHs inside and outside of firefighters' personal protective equipment (PPE) while firefighting. SWBs were placed on the wrist and jacket of 20 firefighters conducting live fire training. Correlations were made with matching data from a sister project that measured urinary concentrations of PAH metabolites and PAH concentrations from personal air samples from the same participants. Naphthalene, acenaphthylene and phenanthrene had the highest geometric mean concentrations in both jacket and wrist SWB, with 1040, 320, 180 ng/g SWB for jacket and 55.0, 4.9, and 6.0 ng/g SWB for wrist, respectively. Ratios of concentrations between the jacket and wrist SWBs were calculated as worker protection factors (WPFs) and averaged 40.1 for total PAHs and ranged from 2.8 to 214 for individual PAHs, similar to previous studies. Several significant correlations were observed between PAHs in jacket SWBs and air samples (e.g., total and low molecular weight PAHs, r = 0.55 and 0.59, p < 0.05, respectively). A few correlations were found between PAHs from SWBs worn on the wrist and jacket, and urinary concentrations of PAH metabolites and PAH concentrations in air samples. The ability of the SWBs to accurately capture exposures to various PAHs was likely influenced by short sampling time, high temperatures, and high turbulence. Future work should further examine the limitations of SWBs for PAH exposures in firefighting, and other extreme environments., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Inc. All rights reserved.)

The genetic engineering of genome fragments larger than 100 kbp is challenging and requires both specific methods and cloning hosts. The yeast Saccharomyces cerevisiae is considered as a host of choice for cloning and engineering whole or partial genomes from viruses, bacteria, and algae. Several methods are now available to perform these manipulations, each with its own limitations. In order to extend the range of yeast cloning strategies, a new approach combining two already described methods, Fusion cloning and CReasPy-Cloning, was developed. The CReasPy-Fusion method allows the simultaneous cloning and engineering of megabase-sized genomes in yeast by the fusion of bacterial cells with yeast spheroplasts carrying the CRISPR-Cas9 system. With this new approach, we demonstrate the feasibility of cloning and editing whole genomes from several Mycoplasma species belonging to different phylogenetic groups. We also show that CReasPy-Fusion allows the capture of large genome fragments with high efficacy, resulting in the successful cloning of selected loci in yeast. We finally identify bacterial nuclease encoding genes as barriers for CReasPy-Fusion by showing that their removal from the donor genome improves the cloning efficacy.

A new sensitive method to determine polonium-210 ( 210 Po) and lead-210 ( 210 Pb) in a diversity of environmental samples was developed. For fresh and marine waters, Po was pre-concentrated using a titanium (III) hydroxide (Ti(OH) 3 ) co-precipitation. Solid environmental samples were digested with nitric acid (HNO 3 ) and hydrogen peroxide (H 2 O 2 ). The alpha thin layer source was prepared using CuS micro-precipitation and 210 Po was measured by alpha spectrometry. Lead-210 was left to decay for up to a year and indirectly measured via its progeny, 210 Po. The chemical recoveries for 210 Po and 210 Pb were high, 90% and 97%, respectively, for a large variety of samples and a very low minimum detectable activity (MDA) was obtained. The method was validated using standardized solutions and certified reference materials., (© 2023. The Author(s).)

Eutrophication, which remains one of the greatest threats to water quality worldwide, is particularly acute in agricultural areas. Here we assessed long-term drivers of potential pollution inputs to lakes in southwest Nova Scotia (Canada), a region marked by fur farming (mainly mink) and other agricultural activities. We used a BACI (before-after-control-impact) study design with sediment cores collected from 14 lakes selected based on their proximity to mink farms. We combined economic data, mink faecal samples, and a series of geochemical markers in dated sediment cores, including sterols, δ 15 N, visible reflectance spectroscopy (VRS)-inferred chlorophyll-a, and heavy metals, to relate changes in sediment geochemistry to the growth of mink farms in the region. Sterol biomarkers (cholesterol and β-sitosterol) measured in a range of samples (i.e. mink faeces and feed, aquaculture feed), were elevated where mink farms were located close to each study lake. Mink-related sterols (cholesterol, β-sitoserol), δ 15 N measurements, VRS chlorophyll-a, and heavy metals As, Cu, Sr increased in the 1980s coeval with a ∼400% increase of mink farms in the region, especially near Nowlans Lake. Agricultural impacts were subtler in other lakes. Our study expands on prior applications of geochemical fingerprinting in forensic paleolimnology when direct monitoring data are incomplete. This multi-proxy approach has promising applications for environmental pollution assessments in other lake ecosystems experiencing water quality issues., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

The role of the intestinal microbiota in host health is increasingly revealed in its contributions to disease states. The host-microbiome interaction is multifactorial and dynamic. One of the factors that has recently been strongly associated with host physiological responses is peptidoglycan from bacterial cell walls. Peptidoglycan from gut commensal bacteria activate peptidoglycan sensors in human cells, including the Nucleotide-binding oligomerization domain containing protein 2 (NOD2). When present in the gastrointestinal tract, both the polymeric form (sacculi) and de-polymerized fragments can modulate host physiology, including checkpoint anticancer therapy efficacy, body temperature and appetite, and postnatal growth. To leverage this growing area of biology towards therapeutic prescriptions, it will be critical to directly analyze a key feature of the host-microbiome interaction from living hosts in a reproducible and non-invasive way. Here we show that metabolically labeled peptidoglycan/sacculi can be readily isolated from fecal samples collected from both mice and humans. Analysis of fecal samples provided a non-invasive route to probe the gut commensal community including the metabolic synchronicity with the host circadian clock. Together, these results pave the way for non-invasive diagnostic tools to interrogate the causal nature of peptidoglycan in host health and disease.

Plasmodium vivax is the second-most common malaria pathogen globally, but is considered very rare in the predominantly Duffy-negative sub-Saharan African population. In 259 malaria patients from highland southern Rwanda, we assessed Plasmodium species and Duffy blood group status by polymerase chain reaction (PCR). Plasmodium falciparum, P. vivax, Plasmodium malariae, and Plasmodium ovale were seen in 90.7%, 8.1%, 11.6%, and 5.0%, respectively. Plasmodium vivax occurred more frequently as a monoinfection than in combination with P. falciparum. All P. vivax-infected individuals showed heterozygous Duffy positivity, whereas this was the case for only 3.1% of patients with P. falciparum monoinfection and malaria-negative control subjects (P < 0.01). Based on PCR diagnosis, P. vivax is not rare in southern Rwanda. All episodes of P. vivax were observed in heterozygous Duffy-positive patients, whereas elsewhere in Africa, P. vivax is also reported in Duffy-negative individuals. Refined mapping of Plasmodium species is required to establish control and elimination strategies including all malaria species.

Following an oil spill into water, bacteria can biodegrade petroleum hydrocarbons which could lead to petrogenic carbon assimilation by aquatic biota. We used changes in the isotope ratios of radio- (Δ 14 C) and stable (δ 13 C) carbon to examine the potential for assimilation of petrogenic carbon into a freshwater food web following experimental spills of diluted bitumen (dilbit) into a boreal lake in northwestern Ontario, Canada. Different volumes (1.5, 2.9, 5.5, 18, 42, 82, and 180 L) of Cold Lake Winter Blend (a heavy crude blend of bitumen and condensate) dilbit were applied to seven 10-m diameter littoral limnocorrals (approximate volume of 100 m 3 ), and two additional limnocorrals had no added dilbit to serve as controls. Particulate organic matter (POM) and periphyton from oil-treated limnocorrals had lower δ 13 C (up to 3.2‰ and 2.1‰ for POM and periphyton, respectively) than the control at every sampled interval (3, 6 and 10 weeks for POM and 6, 8 and 10 weeks for periphyton). Dissolved organic and inorganic carbon (DOC and DIC, respectively) had lower Δ 14 C in the oil-treated limnocorrals relative to the control (up to 122‰ and 440‰ lower, respectively). Giant floater mussel (Pyganodon grandis) housed for 25 days in aquaria containing oil-contaminated water from the limnocorrals did not show significant changes in δ 13 C values of muscle tissue compared to mussels housed in control water. Overall, the changes in δ 13 C and Δ 14 C observed indicated small amounts (up to 11% in DIC) of oil carbon incorporation into the food web. The combined δ 13 C and Δ 14 C data provide evidence for minimal incorporation of dilbit into the food web of this oligotrophic lake, suggesting that microbial degradation and subsequent incorporation of oil C into the food web may play a relatively small role in the ultimate fate of oil in this type of ecosystem., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Ltd.)

Due to the sudden nature of oil spills, few controlled studies have documented how oil weathers immediately following accidental release into a natural lake environment. Here, we evaluated the weathering patterns of Cold Lake Winter Blend, a diluted bitumen (dilbit) product, by performing a series of controlled spills into limnocorrals installed in a freshwater lake in Northern Ontario, Canada. Using a regression-based design, we added seven different dilbit volumes, ranging from 1.5 to 180 L, resulting in oil-to-water ratios between 1:71,000 (v/v) and 1:500 (v/v). We monitored changes in the composition of various petroleum hydrocarbons (PHCs), including n -alkanes, polycyclic aromatic hydrocarbons (PAHs), and oil biomarkers in dilbit over time, as it naturally weathered for 70 days. Depletion rate constants ( k D ) of n -alkanes and PAHs ranged from 0.0009 to 0.41 d -1 and 0.0008 to 0.38 d -1 , respectively. There was no significant relationship between k D and spill volume, suggesting that spill size did not influence the depletion of petroleum hydrocarbons from the slick. Diagnostic ratios calculated from concentrations of n -alkanes, isoprenoids, and PAHs indicated that evaporation and photooxidation were major processes contributing to dilbit weathering, whereas dissolution and biodegradation were less important. These results demonstrate the usefulness of large scale field studies carried out under realistic environmental conditions to elucidate the role of different weathering processes following a dilbit spill.

Because they mimic cells while offering an accessible and controllable environment, lysate-based cell-free systems (CFS) have emerged as valuable biotechnology tools for synthetic biology. Historically used to uncover fundamental mechanisms of life, CFS are nowadays used for a multitude of purposes, including protein production and prototyping of synthetic circuits. Despite the conservation of fundamental functions in CFS like transcription and translation, RNAs and certain membrane-embedded or membrane-bound proteins of the host cell are lost when preparing the lysate. As a result, CFS largely lack some essential properties of living cells, such as the ability to adapt to changing conditions, to maintain homeostasis and spatial organization. Regardless of the application, shedding light on the black-box of the bacterial lysate is necessary to fully exploit the potential of CFS. Most measurements of the activity of synthetic circuits in CFS and in vivo show significant correlations because these only require processes that are preserved in CFS, like transcription and translation. However, prototyping circuits of higher complexity that require functions that are lost in CFS (cell adaptation, homeostasis, spatial organization) will not show such a good correlation with in vivo conditions. Both for prototyping circuits of higher complexity and for building artificial cells, the cell-free community has developed devices to reconstruct cellular functions. This mini-review compares bacterial CFS to living cells, focusing on functional and cellular process differences and the latest developments in restoring lost functions through complementation of the lysate or device engineering., Competing Interests: The authors declare that they have no affiliations with or involvement in any organization or entity with any financial interest in the subject matter or materials discussed in this manuscript., (© 2023 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.)

Understanding how animals respond to large-scale environmental changes is difficult to achieve because monitoring data are rarely available for more than the past few decades, if at all. Here, we demonstrate how a variety of palaeoecological proxies (e.g. isotopes, geochemistry and DNA) from an Andean Condor ( Vultur gryphus ) guano deposit from Argentina can be used to explore breeding site fidelity and the impacts of environmental changes on avian behaviour. We found that condors used the nesting site since at least approximately 2200 years ago, with an approximately 1000-year nesting frequency slowdown from ca 1650 to 650 years before the present (yr BP). We provide evidence that the nesting slowdown coincided with a period of increased volcanic activity in the nearby Southern Volcanic Zone, which resulted in decreased availability of carrion and deterred scavenging birds. After returning to the nest site ca 650 yr BP, condor diet shifted from the carrion of native species and beached marine animals to the carrion of livestock (e.g. sheep and cattle) and exotic herbivores (e.g. red deer and European hare) introduced by European settlers. Currently, Andean Condors have elevated lead concentrations in their guano compared to the past, which is associated with human persecution linked to the shift in diet.

Objectives: Peptidoglycan (PG) is an arthritogenic bacterial cell wall component whose role in human osteoarthritis is poorly understood. The purpose of this study was to determine if PG is present in synovial tissue of osteoarthritis patients at the time of primary total knee arthroplasty (TKA), and if its presence is associated with inflammation and patient reported outcomes., Methods: Intraoperative synovial tissue and synovial fluid samples were obtained from 56 patients undergoing primary TKA, none of whom had history of infection. PG in synovial tissue was detected by immunohistochemistry (IHC). Synovial tissue inflammation and fibrosis were assessed by histopathology and synovial fluid cytokine quantification. Primary human fibroblasts isolated from arthritis synovial tissue were stimulated with PG to determine inflammatory cytokine response., Results: A total of 33/56 (59%) of primary TKA synovial tissue samples were positive for PG by IHC, with mean 8 PG occurrences per 10 mm 2 of tissue in PG-positive samples. Synovial tissue inflammation and elevated IL-6 in synovial fluid positively correlated with PG positivity. Primary human fibroblasts stimulated with PG secreted high levels of IL-6, consistent with ex vivo findings. Interestingly, we observed a significant inverse correlation between PG and age at time of TKA, indicating younger age at time of TKA was associated with higher PG levels., Conclusion: Peptidoglycan is commonly found in synovial tissue from patients undergoing TKA. Our data indicate that PG may play an important role in inflammatory synovitis, particularly in patients who undergo TKA at a relatively younger age., Competing Interests: Competing interests The authors declare that they have no competing interests.

Background: There is no systematic insight into the effect of case management on common complications of chronic diseases, including depressive symptoms and symptoms of anxiety. This is a significant knowledge gap, given that people with a chronic disease such as Parkinson Disease or Alzheimer's Disease have identified care coordination as one of their highest priorities. Furthermore, it remains unclear whether the putative beneficial effects of case management would vary by crucial patient characteristics, such as their age, gender, or disease characteristics. Such insights would shift from "one size fits all" healthcare resource allocation to personalized medicine., Objective: We systematically examined the effectiveness of case management interventions on two common complications associated PD and other chronic health conditions: Depressive symptoms and symptoms of anxiety., Methods: We identified studies published until November 2022 from PubMed and Embase databases using predefined inclusion criteria. For each study, data were extracted independently by two researchers. First, descriptive and qualitative analyses of all included studies were performed, followed by random-effects meta-analyses to assess the impact of case management interventions on anxiety and depressive symptoms. Second, meta-regression was performed to analyze potential modifying effects of demographic characteristics, disease characteristics and case management components., Results: 23 randomized controlled trials and four non-randomized studies reported data on the effect of case management on symptoms of anxiety (8 studies) or depressive symptoms (26 studies). Across meta-analyses, we observed a statistically significant effect of case management on reducing symptoms of anxiety (Standardized Mean Difference [SMD] = - 0.47; 95% confidence interval [CI]: -0.69, -0.32) and depressive symptoms (SMD = - 0.48; CI: -0.71, -0.25). We found large heterogeneity in effect estimates across studies, but this was not explained by patient population or intervention characteristics., Conclusions: Among people with chronic health conditions, case management has beneficial effects on symptoms of depressive symptoms and symptoms of anxiety. Currently, research on case management interventions are rare. Future studies should assess the utility of case management for potentially preventative and common complications, focusing on the optimal content, frequency, and intensity of case management., Competing Interests: The authors have declared that no competing interests exists., (Copyright: © 2023 Geerlings et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Genome-scale engineering enables rational removal of dispensable genes in chassis genomes. Deviating from this approach, we applied greedy accumulation of deletions of large dispensable regions in the Bacillus subtilis genome, yielding a library of 298 strains with genomes reduced up to 1.48 Mb in size. High-throughput physiological phenotyping of these strains confirmed that genome reduction is associated with substantial loss of cell fitness and accumulation of synthetic-sick interactions. Transcriptome analysis indicated that <15% of the genes conserved in our genome-reduced strains exhibited a twofold or higher differential expression and revealed a thiol-oxidative stress response. Most transcriptional changes can be explained by loss of known functions and by aberrant transcription at deletion boundaries. Genome-reduced strains exhibited striking new phenotypes relative to wild type, including a very high resistance (increased >300-fold) to the DNA-damaging agent mitomycin C and a very low spontaneous mutagenesis (reduced 100-fold). Adaptive laboratory evolution failed to restore cell fitness, except when coupled with a synthetic increase of the mutation rate, confirming low evolvability. Although mechanisms underlying this emergent phenotype are not understood, we propose that low evolvability can be leveraged in an engineering strategy coupling reductive cycles with evolutive cycles under induced mutagenesis., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Transcription termination factor Rho is known for its ubiquitous role in suppression of pervasive, mostly antisense, transcription. In the model Gram-positive bacterium Bacillus subtilis, de-repression of pervasive transcription by inactivation of rho revealed the role of Rho in the regulation of post-exponential differentiation programs. To identify other aspects of the regulatory role of Rho during adaptation to starvation, we have constructed a B. subtilis strain (Rho+) that expresses rho at a relatively stable high level in order to compensate for its decrease in the wild-type cells entering stationary phase. The RNAseq analysis of Rho+, WT and Δrho strains (expression profiles can be visualized at http://genoscapist.migale.inrae.fr/seb&#95;rho/) shows that Rho over-production enhances the termination efficiency of Rho-sensitive terminators, thus reducing transcriptional read-through and antisense transcription genome-wide. Moreover, the Rho+ strain exhibits global alterations of sense transcription with the most significant changes observed for the AbrB, CodY, and stringent response regulons, forming the pathways governing the transition to stationary phase. Subsequent physiological analyses demonstrated that maintaining rho expression at a stable elevated level modifies stationary phase-specific physiology of B. subtilis cells, weakens stringent response, and thereby negatively affects the cellular adaptation to nutrient limitations and other stresses, and blocks the development of genetic competence and sporulation. These results highlight the Rho-specific termination of transcription as a novel element controlling stationary phase. The release of this control by decreasing Rho levels during the transition to stationary phase appears crucial for the functionality of complex gene networks ensuring B. subtilis survival in stationary phase., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Bidnenko et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Firefighters are exposed to carcinogenic and mutagenic combustion emissions, including polycyclic aromatic hydrocarbons (PAHs). Fire service and firefighter cancer advocacy groups recommend skin cleaning using wipes or washing with detergent and water after exposure to smoke, although these strategies have not been proven to reduce exposures to harmful combustion products such as PAHs. This study assessed dermal decontamination methods to reduce PAH exposures by firefighters participating in live fire training scenarios. Study participants ( n  = 88) were randomly assigned to an intervention group (i.e., two types of commercial skin wipes, detergent and water, or a control group who did not use any skin decontamination). PAHs were measured in personal air (during the fire) and dermal wipe samples (before and after fire suppression and after dermal decontamination). PAH metabolites and mutagenicity were measured in urine samples before and after fire suppression. Airborne PAH concentrations during the fire ranged between 200 and 3,970 μg/m 3 (mean = 759 μg/m 3 , SD  = 685 μg/m 3 ). Firefighters had higher total PAHs and high-molecular-weight PAHs on their skin after the fire compared to before (1.3- and 2.2-fold, respectively, p  < 0.01). Urinary PAH metabolites increased significantly following exposure to the training fires by 1.7 to 2.2-fold (depending on the metabolite, p  < 0.001). Urinary mutagenicity did not differ significantly between pre- and post-fire for any of the decontamination methods. Detergent and water was the only intervention that removed a significant amount of total PAHs from the skin (0.72 ng/cm 2 preintervention vs. 0.38 ng/cm 2 postintervention, p  < 0.01). However, fold changes in urinary PAH metabolites (i.e., pre- vs. post-exposure levels) did not differ among any of the dermal decontamination methods or the control group. These data suggest that despite on-site attempts to remove PAHs from firefighters' skin, the examined interventions did not reduce the internal dose of PAHs. Future work should investigate preventing initial exposure using other interventions, such as improved personal protective equipment.

Syphilis, caused by the spirochete Treponema pallidum subsp. pallidum (hereafter called T. pallidum ), is re-emerging as a worldwide sexually transmitted infection. A single intramuscular dose of benzathine penicillin G is the preferred syphilis treatment option. Both supply shortage concerns and the potential for acquired antibiotic resistance further the need to broaden the repertoire of syphilis therapeutics. We reasoned that other β-lactams may be equally or more effective at targeting the disease-causing agent, Treponema pallidum , but have yet to be discovered due to a previous lack of a continuous in vitro culture system. Recent technical advances with respect to in vitro T. pallidum propagation allowed us to conduct a high-throughput screen of almost 100 β-lactams. Using several molecular and cellular approaches that we developed or adapted, we identified and confirmed the efficacy of several β-lactams that were similar to or outperformed the current standard, benzathine penicillin G. These options are either currently used to treat bacterial infections or are synthetic derivatives of naturally occurring compounds. Our studies not only identified additional potential therapeutics in the resolution of syphilis, but provide techniques to study the complex biology of T. pallidum -a spirochete that has plagued human health for centuries., Competing Interests: Competing interestsThe authors declare no competing interests., (© The Author(s) 2023.)

Pipelines carrying diluted bitumen (dilbit) traverse North America and may result in dilbit release into sensitive freshwater ecosystems. To better understand the potential effects of a freshwater oil release, the Boreal-lake Oil Release Experiment by Additions to Limnocorrals project at the International Institute for Sustainable Development-Experimental Lakes Area (Ontario, Canada) modeled seven dilbit spills contained within a 10-m diameter of littoral limnocorrals in a boreal lake. Wild finescale dace (Phoxinus neogaeus) were released in the limnocorrals 21 days after oil addition and remained there for 70 days. Dilbit volumes covered a large range representing a regression of real spill sizes and total polycyclic aromatic compounds (TPAC) between 167 ng L -1  day -1 and 1989 ng L -1  day -1 . We report the effects of chronic exposure on reproductive potential as well as physiological responses in the gallbladder and liver. In exposures >1000 ng L -1  day -1 , there was a significant decrease in fish retrieval, culminating in zero recapture from the three highest treatments. Among the fish from the limnocorrals with lower levels of TPAC (<500 ng L -1  day -1 ), effects were inconsistent. Gallbladder bile fluorescence for a naphthalene metabolite was significantly different in fish from the oil-exposed limnocorrals when compared to the lake and reference corral, indicating that fish in these lower exposures were interacting with dilbit-derived polycyclic aromatic compounds. There were no significant differences in condition factor, somatic indices, or hepatocyte volume indices. There were also no significant changes in the development of testes or ovaries of exposed dace. The results from the present study may serve to orient policymakers and emergency responders to the range of TPAC exposures that may not significantly affect wild fish. Environ Toxicol Chem 2022;41:2745-2757. © 2022 SETAC., (© 2022 SETAC.)

Oil spills constitute a major risk to the environment and the bioaccumulation potential of the derived oil constituents will influence their impact on aquatic biota. Here we determined the bioaccumulation potential and toxicokinetic parameters of polycyclic aromatic compounds (PACs) and various selected metals in the giant floater mussels (Pyganodon grandis) following experimental oil spills in a freshwater lake. Specifically, these mussels were exposed ex situ for 25 days to water contaminated with naturally weathered diluted bitumen (dilbit), a form of oil commonly transported through pipelines. We detected greater concentrations of total PAC in mussels (∑PAC 44 ) exposed to dilbit-contaminated water (25.92-27.79 μg g -1 lipid, n = 9, at day 25 of the uptake phase) compared to mussels from a control with no exposure to dilbit (average of 2.62 ± 1.95 μg g -1 lipid; ±SD, n = 17). This study demonstrates the importance of including alkylated PACs when assessing the impacts of an oil spill as the concentration of alkylated PACs in mussel tissue were an order of magnitude higher than their parent counterparts. However, metal accumulation in dilbit-exposed mussels did not exceed the unexposed controls, suggesting no excess metal accumulation by mussels from a 25-day dilbit exposure. From first-order one-compartment models, mean uptake rate constants (0.78-18.11 L g -1 day -1 , n = 29) and bioconcentration factors (log values from 4.02 to 5.92 L kg -1 , n = 87) for the 29 individual PACs that accumulated in mussels demonstrated that some alkylated PACs had greater bioaccumulation potential compared to their parent PAC counterpart but for the most part, alkylated and parent PACs had comparable BCF values. Results from this study also demonstrated that giant floater mussels could be used to biomonitor PAC contamination following oil spills as PACs accumulated in mussel tissue and some were still detectable following the 16-day depuration phase. This study provides the largest, most comprehensive set of toxicokinetic and bioaccumulation parameters for PACs and their alkylated counterparts (44 analytes) in freshwater mussels obtained to date., Competing Interests: Declaration of Competing Interest The authors declare no conflicts of interest., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Arsenic (As) and sulfate pollution are often found co-occurring as a result of smelting metal ores. Previous studies showed that sulfate reducing microbes (SRMs) can use As(V) as a terminal electron acceptor, while others reported that SRMs are the main mercury (Hg) methylators in freshwater systems. However, we have yet to fully explore how As(V) can affect methylmercury (MeHg) production. In this study, we examined whether additions of As(V) and sulfate in freshwater sediments collected near a major gold mine with a history of S and As emissions affect Hg methylation. First, we show that Hg methylation in lake sediments was primarily limited by carbon substrate availability rather than by that of sulfate as terminal electron acceptors. Then, under conditions where carbon is not limiting, sulfate addition to the system significantly increased Hg methylation rate constants. Finally, we show that MeHg production rates in sediments significantly decreased with increasing As(V) concentrations, regardless of the sulfate concentration amended to sediments. This work underscores the apparent antagonistic effects of As(V) on the one hand, and carbon and sulfate on the other hand on the kinetics of Hg methylation. Arsenic controls on Hg methylation are complex and a combination of direct impact on the methylators' fitness, the formation of As-bearing mineral phases affecting Hg bioavailability, or changes in the microbial community structures over increasing As concentrations should be the focus of additional investigations.

The contamination of lakes by industrial emissions is an issue of international concern. Traditional paleolimnology examines sedimentary micro-fossils to infer the biological response to natural and anthropogenic stressors over time. Here, we calculate a theoretical biological effect for historic sediment sections using Probable Effect Concentration Quotient (PEC-Q) and arsenic specific quotient methods and develop novel time-constrained sediment toxicity test methods using a cultured Daphnia sp. combined with a whole cell microbial biosensor to assess the toxicity of past industrial contamination with modern testing methods. These methods were developed using sediments collected from Pocket Lake (Northwest Territories, Canada), a lake known to have exhibited a significant ecological shift following input from nearby gold smelter emissions during the mid 20th century. We then applied these methods to near-, mid-, and far-field sites to assess the response of Daphnia sp. to varying contaminant load. Daphnia sp. mortality exposed to dated sediments indicated a strong concordance with the timing of mining activities, and a strong concordance with PEC-Q and arsenic specific toxicity quotients. In contrast, a decrease in Daphnia mortality was observed during pre-, and post-mining periods when the contaminant burden was lower. Initial assessments of bioavailability using a microbial biosensor indicated that arsenic in porewater is 72-96% bioavailable, and limited evidence that oxidative stress may contribute to the Daphnia sp. toxic response. These results indicate that lake sediment archives can be used to infer missing biomonitoring data in sites of legacy anthropogenic influence, which will be useful for those seeking to conduct cost-effective and efficient preliminary environmental risk assessments., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The prevalence of Parkinson disease (PD) is growing fast, amplifying the quest for disease-modifying therapies in early disease phases where pathology is still limited. Lifestyle interventions offer a promising avenue for preventing progression from prodromal to manifest PD. We illustrate this primarily for 1 specific lifestyle intervention, namely aerobic exercise because the case for the other main lifestyle factor (dietary interventions) to modify the course of prodromal PD is currently less persuasive. Various observations have hinted at the disease-modifying potential of exercise. First, studies in rodents with experimental parkinsonism showed that exercise elicits adaptive neuroplasticity in basal ganglia circuitries. Second, exercise is associated with a reduced risk of developing PD, suggesting a disease-modifying potential. Third, 2 large trials in persons with manifest PD indicate that exercise can help to stabilize motor parkinsonism, although this could also reflect a symptomatic effect. In addition, exercise seems to be a feasible intervention, given its minimal risk of side effects. Theoretical risks include an increase in fall incidents and cardiovascular complications, but these concerns seem to be acceptably low. Innovative approaches using gamification elements indicate that adequate long-term compliance with regular exercise programs can be achieved, although more work remains necessary to demonstrate enduring adherence for multiple years. Advances in digital technology can be used to deliver the exercise intervention in the participant's own living environment and also to measure the outcomes remotely, which will help to further boost long-term compliance. When delivering exercise to prodromal participants, outcome measures should focus not just on phenoconversion to manifest PD (which may well take many years to occur) but also on measurable intermediate outcomes, such as physical fitness or prodromal nonmotor symptoms. Taken together, there seems to be sufficient evidence to advocate the first judicious attempt of investigating exercise as a disease-modifying treatment in prodromal PD., (Copyright © 2022 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.)

Background: Parkinson's disease (PD) is a neurodegenerative disease, for which no disease-modifying therapies exist. Preclinical and clinical evidence suggest that hypoxia-based therapy might have short- and long-term benefits in PD. We present the contours of the first study to assess the safety, feasibility and physiological and symptomatic impact of hypoxia-based therapy in individuals with PD., Methods/design: In 20 individuals with PD, we will investigate the safety, tolerability and short-term symptomatic efficacy of continuous and intermittent hypoxia using individual, double-blind, randomized placebo-controlled N-of-1 trials. This design allows for dose finding and for including more individualized outcomes, as each individual serves as its own control. A wide range of exploratory outcomes is deployed, including the Movement Disorders Society Unified Parkinson's Disease Rating scale (MDS-UPDRS) part III, Timed Up & Go Test, Mini Balance Evaluation Systems (MiniBES) test and wrist accelerometry. Also, self-reported impression of overall symptoms, motor and non-motor symptoms and urge to take dopaminergic medication will be assessed on a 10-point Likert scale. As part of a hypothesis-generating part of the study, we also deploy several exploratory outcomes to probe possible underlying mechanisms of action, including cortisol, erythropoietin and platelet-derived growth factor β. Efficacy will be assessed primarily by a Bayesian analysis., Discussion: This evaluation of hypoxia therapy could provide insight in novel pathways that may be pursued for PD treatment. This trial also serves as a proof of concept for deploying an N-of-1 design and for including individualized outcomes in PD research, as a basis for personalized treatment approaches., Trial Registration: ClinicalTrials.gov Identifier: NCT05214287 (registered January 28, 2022)., (© 2022. The Author(s).)

Rationale and Objective: Social factors play a critical role in drug addiction. We recently showed that rats will abstain from methamphetamine, cocaine, heroin, and remifentanil self-administration when given a choice between the addictive drug and operant social interaction. Here, we further characterized operant social interaction by determining the effects of access duration, effort, peer familiarity, and housing conditions. We also determined choice between social interaction vs. palatable food or remifentanil., Methods: We first trained single-housed male and female rats to lever-press for social interaction with a sex- and age-matched peer. Next, we determined effects of access duration (3.75 to 240 s), effort (increasing fixed-ratio schedule requirements or progressive ratio schedule), peer familiarity (familiar vs. unfamiliar), and housing conditions (single vs. paired housing) on social self-administration. We also determined choice between social interaction vs. palatable food pellets or intravenous remifentanil (0, 1, 10 µg/kg/infusion)., Results: Increasing access duration to a peer decreased social self-administration under fixed ratio but not progressive ratio schedule; the rats showed similar preference for short vs. long access duration. Social self-administration under different fixed ratio requirements was higher in single-housed than in paired-housed rats and higher for a familiar vs. unfamiliar partner in single-housed but not paired-housed rats. Response rates of food-sated rats under increasing fixed-ratio requirements were higher for palatable food than for social interaction. The rats strongly preferred palatable food over social interaction and showed dose-dependent preference for social interaction vs. remifentanil., Conclusions: We identified parameters influencing the reinforcing effects of operant social interaction and introduce a choice procedure sensitive to remifentanil self-administration dose., (© 2022. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.)

Seabird population size is intimately linked to the physical, chemical, and biological processes of the oceans. Yet, the overall effects of long-term changes in ocean dynamics on seabird colonies are difficult to quantify. Here, we used dated lake sediments to reconstruct ~10,000-years of seabird dynamics in the Northwest Atlantic to determine the influences of Holocene-scale climatic oscillations on colony size. On Baccalieu Island (Newfoundland and Labrador, Canada)-where the world's largest colony of Leach's storm-petrel (Hydrobates leucorhous Vieillot 1818) currently breeds-our data track seabird colony growth in response to warming during the Holocene Thermal Maximum (ca. 9000 to 6000 BP). From ca. 5200 BP to the onset of the Little Ice Age (ca. 550 BP), changes in colony size were correlated to variations in the North Atlantic Oscillation (NAO). By contrasting the seabird trends from Baccalieu Island to millennial-scale changes of storm-petrel populations from Grand Colombier Island (an island in the Northwest Atlantic that is subjected a to different ocean climate), we infer that changes in NAO influenced the ocean circulation, which translated into, among many things, changes in pycnocline depth across the Northwest Atlantic basin where the storm-petrels feed. We hypothesize that the depth of the pycnocline is likely a strong bottom-up control on surface-feeding storm-petrels through its influence on prey accessibility. Since the Little Ice Age (LIA), the effects of ocean dynamics on seabird colony size have been altered by anthropogenic impacts. Subsequently, the colony on Baccalieu Island grew at an unprecedented rate to become the world's largest resulting from favorable conditions linked to climate warming, increased vegetation (thereby nesting habitat), and attraction of recruits from other colonies that are now in decline. We show that although ocean dynamics were an important driver of seabird colony dynamics, its recent influence has been modified by human interference., (© 2022 John Wiley & Sons Ltd.)