Functional and structural characterization of an IclR family transcription factor for the development of dicarboxylic acid biosensors.

Prokaryotic transcription factors (TFs) regulate gene expression in response to small molecules, thus representing promising candidates as versatile small molecule-detecting biosensors valuable for synthetic biology applications. The engineering of such biosensors requires thorough in vitro and in vivo characterization of TF ligand response as well as detailed molecular structure information. In this work, we functionally and structurally characterize the Pca regulon regulatory protein (PcaR) transcription factor belonging to the IclR transcription factor family. Here, we present in vitro functional analysis of the ligand profile of PcaR and the construction of genetic circuits for the characterization of PcaR as an in vivo biosensor in the model eukaryote Saccharomyces cerevisiae. We report the crystal structures of PcaR in the apo state and in complex with one of its ligands, succinate, which suggests the mechanism of dicarboxylic acid recognition by this transcription factor. This work contributes key structural and functional insights enabling the engineering of PcaR for dicarboxylic acid biosensors, in addition to providing more insights into the IclR family of regulators.

Prevalence in Potato of 'Candidatus Arsenophonus Phytopathogenicus' and 'Candidatus Phytoplasma Solani' and Their Transmission via Adult Pentastiridius leporinus.

The planthopper Pentastiridius leporinus (Hempiptera: Cixiidae) is the main vector of two bacterial pathogens: the γ-proteobacterium 'Candidatus Arsenophonus phytopathogenicus' and the stolbur phytoplasma 'Candidatus Phytoplasma solani'. These pathogens cause the disease syndrome basses richesses (SBR) in sugar beet (Beta vulgaris), which reduces the yields and sugar content. In 2022, potato (Solanum tuberosum) fields were found to be colonized by P. leporinus, and the transmission of Arsenophonus was confirmed, resulting in symptoms like wilting, yellow leaves, and rubbery tubers. We monitored both pathogens in Southwest Germany in 2022 and 2023. This revealed their widespread presence in potato tubers, although there were differences in regional prevalence. The broad prevalence of Arsenophonus was maintained in 2023, whereas the prevalence of stolbur increased in most locations. We confirmed that P. leporinus adults can transmit both pathogens to potatoes, but neither pathogen reduced the germination rate of tubers, and no plants showed abnormal growth after germination. Arsenophonus was not detected in germinated shoots, but 5.4% contained stolbur, emphasizing the need for plant material testing to maintain phytosanitary conditions.

Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies.

Endogenous tags have become invaluable tools to visualize and study native proteins in live cells. However, generating human cell lines carrying endogenous tags is difficult due to the low efficiency of homology-directed repair. Recently, an engineered split mNeonGreen protein was used to generate a large-scale endogenous tag library in HEK293 cells. Using split mNeonGreen for large-scale endogenous tagging in human iPSCs would open the door to studying protein function in healthy cells and across differentiated cell types. We engineered an iPS cell line to express the large fragment of the split mNeonGreen protein (mNG21-10) and showed that it enables fast and efficient endogenous tagging of proteins with the short fragment (mNG211). We also demonstrate that neural network-based image restoration enables live imaging studies of highly dynamic cellular processes such as cytokinesis in iPSCs. This work represents the first step towards a genome-wide endogenous tag library in human stem cells.

The human body contains around 20,000 different proteins that perform a myriad of essential roles. To understand how these proteins work in healthy individuals and during disease, we need to know their precise locations inside cells and how these locations may change in different situations. Genetic tools known as fluorescent proteins are often used as tags to study the location of specific proteins of interest within cells. When exposed to light, the fluorescent proteins emit specific colours of light that can be observed using microscopes. In a fluorescent protein system known as split mNeonGreen, researchers insert the DNA encoding two fragments of a fluorescent protein (one large, one small) separately into cells. The large fragment can be found throughout the cell, while the small fragment is attached to specific host proteins. When the two fragments meet, they assemble into the full mNeonGreen protein and can fluoresce. Researchers can use split mNeonGreen and other similar systems to generate large libraries of cells where the small fragment of a fluorescent protein is attached to thousands of different host proteins. However, so far these libraries are restricted to a handful of different types of cells. To address this challenge, Husser et al. inserted the DNA encoding the large fragment of mNeonGreen into human cells known as induced pluripotent stem cells, which are able to give rise to any other type of human cell. This then enabled the team to quickly and efficiently generate a library of stem cells that express the small fragment of mNeonGreen attached to different host proteins. Further experiments studied the locations of host proteins in the stem cells just before they divided into two cells. This suggested that there are differences between how induced pluripotent stem cells and other types of cells divide. In the future, the cells and the method developed by Husser et al. may be used by other researchers to create atlases showing where human proteins are located in many other types of cells.

Enzymatic Assembly of Small Synthetic Genes with Repetitive Elements.

Gene synthesis efficiency has greatly improved in recent years but is limited when it comes to repetitive sequences, which results in synthesis failure or delays by DNA synthesis vendors. This represents a major obstacle for the development of synthetic biology since repetitive elements are increasingly being used in the design of genetic circuits and design of biomolecular nanostructures. Here, we describe a method for the assembly of small synthetic genes with repetitive elements: First, a gene of interest is split in silico into small synthons of up to 80 base pairs flanked by Golden-Gate-compatible overhangs. Then, synthons are made by oligo extension and finally assembled into a synthetic gene by Golden Gate Assembly. We demonstrate the method by constructing eight challenging genes with repetitive elements, e.g., multiple repeats of RNA aptamers and RNA origami scaffolds with multiple identical aptamers. The genes range in size from 133 to 456 base pairs and are assembled with fidelities of up to 87.5%. The method was developed to facilitate our own specific research but may be of general use for constructing challenging and repetitive genes and, thus, a valuable addition to the molecular cloning toolbox.

Sleepiness should be reinvestigated through the lens of clinical neurophysiology: A mixed expertal and big-data Natural Language Processing approach.

Historically, the field of sleep medicine has revolved around electrophysiological tools. However, the use of these tools as a neurophysiological method of investigation seems to be underrepresented today, from both international recommendations and sleep centers, in contrast to behavioral and psychometric tools. The aim of this article is to combine a data-driven approach and neurophysiological and sleep medicine expertise to confirm or refute the hypothesis that neurophysiology has declined in favor of behavioral or self-reported dimensions in sleep medicine for the investigation of sleepiness, despite the use of electrophysiological tools. Using Natural Language Processing methods, we analyzed the abstracts of the 18,370 articles indexed by PubMed containing the terms 'sleepiness' or 'sleepy' in the title, abstract, or keywords. For this purpose, we examined these abstracts using two methods: a lexical network, enabling the identification of concepts (neurophysiological or clinical) related to sleepiness in these articles and their interconnections; furthermore, we analyzed the temporal evolution of these concepts to extract historical trends. These results confirm the hypothesis that neurophysiology has declined in favor of behavioral or self-reported dimensions in sleep medicine for the investigation of sleepiness. In order to bring sleepiness measurements closer to brain functioning and to reintroduce neurophysiology into sleep medicine, we discuss two strategies: the first is reanalyzing electrophysiological signals collected during the standard sleep electrophysiological test; the second takes advantage of the current trend towards dimensional models of sleepiness to situate clinical neurophysiology at the heart of the redefinition of sleepiness.

Objective evaluation of excessive daytime sleepiness.

Excessive daytime sleepiness (EDS) is multifactorial. It combines, among other things, an excessive propensity to fall asleep ("physiological sleepiness") and a continuous non-imperative sleepiness (or drowsiness/hypo-arousal) leading to difficulties remaining awake and maintaining sustained attention and vigilance over the long term ("manifest sleepiness"). There is no stand-alone biological measure of EDS. EDS measures can either capture the severity of physiological sleepiness, which corresponds to the propensity to fall asleep, or the severity of manifest sleepiness, which corresponds to behavioral consequences of sleepiness and reduced vigilance. Neuropsychological tests (The psychomotor vigilance task (PVT), Oxford Sleep Resistance Test (OSLeR), Sustained Attention to Response Task (SART)) explore manifest sleepiness through several sustained attention tests but the lack of normative values and standardized protocols make the results difficult to interpret and use in clinical practice. Neurophysiological tests explore the two main aspects of EDS, i.e. the propensity to fall asleep (Multiple sleep latency test, MSLT) and the capacity to remain awake (Maintenance of wakefulness test, MWT). The MSLT and the MWT are widely used in clinical practice. The MSLT is recognized as the "gold standard" test for measuring the severity of the propensity to fall asleep and it is a diagnostic criterion for narcolepsy. The MWT measures the ability to stay awake. The MWT is not a diagnostic test as it is recommended only to evaluate the evolution of EDS and efficacy of EDS treatment. Even if some efforts to standardize the protocols for administration of these tests have been ongoing, MSLT and MWT have numerous limitations: age effect, floor or ceiling effects, binding protocol, no normal or cutoff value (or determined in small samples), and no or low test-retest values in some pathologies. Moreover, the recommended electrophysiological set-up and the determination of sleep onset using the 30­sec epochs scoring rule show some limitations. New, more precise neurophysiological techniques should aim to detect very brief periods of physiological sleepiness and, in the future, the brain local phenomenon of sleepiness likely to underpin drowsiness, which could be called "physiological drowsiness".

Symptom content analysis of OSA questionnaires: time to identify and improve relevance of diversity of OSA symptoms?

STUDY OBJECTIVES: Obstructive sleep apnea (OSA) is a heterogeneous condition covering many clinical phenotypes in terms of the diversity of symptoms. Patient-based OSA screening questionnaires used in routine practice contain significantly varying contents that can impact the reliability and validity of the screening. We investigated to what extent common patient-based OSA screening questionnaires differ or overlap in their item content by conducting a rigorous, methodical, and quantified content overlap analysis. METHODS: We conducted an item content analysis of 11 OSA screening questionnaires validated in adult populations and characterized their overlap using a four-step approach: i) selection of OSA screening questionnaires; ii) item extraction and selection; iii) extraction of symptoms from items; iv) assessment of content overlap with the Jaccard Index (from 0: no overlap to 1: full overlap). RESULTS: We extracted 72 items that provided 25 distinct symptoms from 11 selected OSA questionnaires. The overlap between them was weak (mean Jaccard Index 0.224, ranging from 0.138 to 0.329). All questionnaires contained symptoms of the "OSA symptom" dimension (e.g., snoring or witnessed apneas). The STOP-BANG (0.329) and the Berlin (0.280) questionnaires exhibited the highest overlap content. Ten symptoms (40%) were investigated in only one questionnaire. CONCLUSIONS: The heterogeneity of content and the low overlap across these questionnaires reflect the challenges of screening OSA. The different OSA questionnaires potentially capture varying aspects of the disorder, with the risk of biased results in studies. Suggestions are made for better OSA screening and refinement of clinical OSA phenotypes.

Effects of a Cycling versus Running HIIT Program on Fat Mass Loss and Gut Microbiota Composition in Men with Overweight/Obesity.

PURPOSE: High-intensity interval training (HIIT) can efficiently decrease total and (intra-)abdominal fat mass (FM); however, the effects of running versus cycling HIIT programs on FM reduction have not been compared yet. In addition, the link between HIIT-induced FM reduction and gut microbiota must be better investigated. The aim of this study was to compare the effects of two 12-wk HIIT isoenergetic programs (cycling vs running) on body composition and fecal microbiota composition in nondieting men with overweight or obesity. METHODS: Sixteen men (age, 54.2 ± 9.6 yr; body mass index, 29.9 ± 2.3 kg·m -2 ) were randomly assigned to the HIIT-BIKE (10 × 45 s at 80%-85% of maximal heart rate, 90-s active recovery) or HIIT-RUN (9 × 45 s at 80%-85% of maximal heart rate, 90-s active recovery) group (3 times per week). Dual-energy x-ray absorptiometry was used to determine body composition. Preintervention and postintervention fecal microbiota composition was analyzed by 16S rRNA gene sequencing, and diet was controlled. RESULTS: Overall, body weight, and abdominal and visceral FM decreased over time ( P < 0.05). No difference was observed for weight, total body FM, and visceral FM between groups (% change). Conversely, abdominal FM loss was greater in the HIIT-RUN group (-16.1% vs -8.3%; P = 0.050). The α-diversity of gut microbiota did not vary between baseline and intervention end and between groups, but was associated with abdominal FM change ( r = -0.6; P = 0.02). The baseline microbiota profile and composition changes were correlated with total and abdominal/visceral FM losses. CONCLUSIONS: Both cycling and running isoenergetic HIIT programs improved body composition in men with overweight/obesity. Baseline intestinal microbiota composition and its postintervention variations were correlated with FM reduction, strengthening the possible link between these parameters. The mechanisms underlying the greater abdominal FM loss in the HIIT-RUN group require additional investigations.

Is Physical Activity an Efficient Strategy to Control the Adverse Effects of Persistent Organic Pollutants in the Context of Obesity? A Narrative Review.

Obesity affects nearly 660 million adults worldwide and is known for its many comorbidities. Although the phenomenon of obesity is not fully understood, science regularly reveals new determinants of this pathology. Among them, persistent organic pollutants (POPs) have been recently highlighted. Mainly lipophilic, POPs are normally stored in adipose tissue and can lead to adverse metabolic effects when released into the bloodstream. The main objective of this narrative review is to discuss the different pathways by which physical activity may counteract POPs' adverse effects. The research that we carried out seems to indicate that physical activity could positively influence several pathways negatively influenced by POPs, such as insulin resistance, inflammation, lipid accumulation, adipogenesis, and gut microbiota dysbiosis, that are associated with the development of obesity. This review also indicates how, through the controlled mobilization of POPs, physical activity could be a valuable approach to reduce the concentration of POPs in the bloodstream. These findings suggest that physical activity should be used to counteract the adverse effects of POPs. However, future studies should accurately assess its impact in specific situations such as bariatric surgery, where weight loss promotes POPs' blood release.

Fe-Ni-based alloys as highly active and low-cost oxygen evolution reaction catalyst in alkaline media.

NiFe-based oxo-hydroxides are highly active for the oxygen evolution reaction but require complex synthesis and are poorly durable when deposited on foreign supports. Herein we demonstrate that easily processable, Earth-abundant and cheap Fe-Ni alloys spontaneously develop a highly active NiFe oxo-hydroxide surface, exsolved upon electrochemical activation. While the manufacturing process and the initial surface state of the alloys do not impact the oxygen evolution reaction performance, the growth/composition of the NiFe oxo-hydroxide surface layer depends on the alloying elements and initial atomic Fe/Ni ratio, hence driving oxygen evolution reaction activity. Whatever the initial Fe/Ni ratio of the Fe-Ni alloy (varying between 0.004 and 7.4), the best oxygen evolution reaction performance (beyond that of commercial IrO2) and durability was obtained for a surface Fe/Ni ratio between 0.2 and 0.4 and includes numerous active sites (high NiIII/NiII capacitive response) and high efficiency (high Fe/Ni ratio). This knowledge paves the way to active and durable Fe-Ni alloy oxygen-evolving electrodes for alkaline water electrolysers.

Mechanisms of type I interferon production by chicken TLR21.

The innate immune response relies on the ability of host cells to rapidly detect and respond to microbial nucleic acids. Toll-like receptors (TLRs), a class of pattern recognition receptors (PRRs), play a fundamental role in distinguishing self from non-self at the molecular level. In this study, we focused on TLR21, an avian TLR that recognizes DNA motifs commonly found in bacterial genomic DNA, specifically unmethylated CpG motifs. TLR21 is believed to act as a functional homologue to mammalian TLR9. By analysing TLR21 signalling in chickens, we sought to elucidate avian TLR21 activation outputs in parallel to that of other nucleic acid species. Our analyses revealed that chicken TLR21 (chTLR21) triggers the activation of NF-κB and induces a potent type-I interferon response in chicken macrophages, similar to the signalling cascades observed in mammalian TLR9 activation. Notably, the transcription of interferon beta (IFNB) by chTLR21 was found to be dependent on both NF-κB and IRF7 signalling, but independent of the TBK1 kinase, a distinctive feature of mammalian TLR9 signalling. These findings highlight the conservation of critical signalling components and downstream responses between avian TLR21 and mammalian TLR9, despite their divergent evolutionary origins. These insights into the evolutionarily conserved mechanisms of nucleic acid sensing contribute to the broader understanding of host-pathogen interactions across species.

Combined Endurance and Strength or Only Endurance Training? Effects of Training Mode on Neuromuscular Characteristics and Functional Abilities in Obese Adolescent Girls Enrolled in a Weight-Reduction Program.

The aim of the present study was to examine whether combining strength and endurance training would promote better improvements in neuromuscular characteristics and functional abilities than endurance training alone in obese adolescent girls enrolled in a weight-reduction program. Twenty-four obese adolescent girls (12-15 years) volunteered to participate in a 9-month training program. Participants were allocated into two groups following either (i) combined training (endurance + strength; E+ST) or (ii) endurance training (ET) program. Absolute and specific maximal torque, muscle size, and maximal voluntary activation level (VA) of the knee extensor (KE) and plantar flexor (PF) muscles were assessed. Moreover, functional abilities such as balance and fatigability during a maximal isometric intermittent contraction test of the KE muscles were measured before and after the intervention. The force of the adductor pollicis (AP) muscles was used as a control to account for any effect of growth or mechanical unloading on neuromuscular properties and muscle size. While absolute and specific torque of the KE (+14.7 ± 12.1% and +14.4 ± 15.5%; p < 0.05) and PF (+19.2 ± 16.7% and +18.3 ± 17.5%; p < 0.001) muscles increased in the E+ST group, PF torque decreased, and KE torque did not change in the ET group (-22.6 ± 10.5% and -15.0 ± 17.2%; p < 0.001). Moreover, the VA of the KE muscles increased for the E+ST (+6.1 ± 5.6%; p < 0.01) group and decreased for the ET group (-5.4 ± 5.4%; p < 0.05). In contrast, VA remained similar in the PF muscles for both groups. The number of repetitions during the fatigability test increased in the ET group (38.4 ± 22.3 vs. 84.1 ± 33.3; p = 0.032) and was unchanged in the E+ST group (50.8 ± 14.1 vs. 54.2 ± 37.8), but it was associated with a higher force level. Moreover, balance improved in the E+ST group, but not in the ET group. To conclude, physical training combining strength and endurance training promoted larger improvement in neuromuscular characteristics and functional abilities than endurance training alone in obese adolescent girls. Greater neuromuscular adaptations resulting from the E+ST training may be beneficial for preserving or even increasing functional abilities and possibly induce greater engagement in the active lifestyle of obese adolescents. However, the endurance component seems necessary in training programs to reduce fatigability during daily living activities.

Sex-Related Neuromuscular Adaptations to Youth Obesity: Force, Muscle Mass, and Neural Issues.

Young obese are generally stronger than their typically developing counterparts. Strength differences could be partly ascribed to nervous adaptations, due to the loading effect of carrying overweight. We hypothesized that central adaptations of the muscles highly involved in weight bearing, i.e., plantar flexors (PF) and knee extensors (KE) could be greater in girls than boys due to their reduced potential for muscle hypertrophy. Furthermore, it is possible that neuromuscular adaptations in weight-bearing muscles will be greater compared to the unloaded muscles such as the adductor pollicis (AP).Twenty-four non-obese and 21 obese (body mass index: 33 ± 4 kg·m-2) adolescent girls and boys (12-15 years) performed maximal voluntary isometric contractions (MVC) of the PF and KE muscles. Voluntary activation (VA), assessed with the twitch interpolation technique, the antagonist co-activation (Co-Act) level, and the normalized root-mean-square value (RMS) of the agonist muscles were measured to account for central adaptations.The results revealed a weight status effect (p < 0.001) on the absolute MVC torque and VA of both KE and PF muscles. Moreover, these differences were also related to the sex of the participants (p < 0.05) for the PF muscles. While the VA, absolute, and specific MVC torque were greater in obese compared with non-obese girls, no difference was found between boys. A similar Co-Act level was observed between groups, whatever the sex and muscle group considered. Finally, no significant differences were found for the AP regarding peripheral and neural factors.This study highlighted a favorable effect of obesity on the central mechanisms (i.e., VA) responsible for force production within the lower limb muscles. However, obesity-related central adaptation was only observed in girls for the PF muscles. Thus, the excess of body mass supported by the muscles involved in weight-bearing could act as a chronic training stimulus responsible for these adaptations in obese adolescents but mostly in girls.

Neuromuscular and Metabolic Responses during Repeated Bouts of Loaded Downhill Walking.

INTRODUCTION: The aim of this study was to compare vastus lateralis (VL) and rectus femoris (RF) muscles for their nervous and mechanical adaptations during two bouts of downhill walking (DW) with load carriage performed 2 wk apart. Moreover, we investigated cardiometabolic and perceived exertion responses during both DW bouts. METHODS: Seventeen participants performed two 45-min sessions of loaded DW (30% of body mass; slope, -25%; speed, 4.5 km·h -1 ) separated by 2 wk. Rating of perceived exertion, cost of walking, heart rate, and EMG activity of thigh muscles were assessed during the DW. Muscle shear elastic modulus ( µ ) of RF and VL were assessed before each exercise bout. Maximal voluntary contraction torque was assessed before (PRE), immediately after (POST), and 24 and 48 h after the two exercise bouts. RESULTS: Maximal voluntary contraction torque decreased from POST (-23.7% ± 9.2%) to 48 h (-19.2% ± 11.9%) after the first exercise (Ex1), whereas it was significantly reduced only at POST (-14.6% ± 11.0%) after the second exercise (Ex2; P < 0.001). Rating of perceived exertion (Ex1: 12.3 ± 1.9; Ex2: 10.8 ± 2.0), heart rate (Ex1: 156 ± 23 bpm; Ex2: 145 ± 25 bpm), cost of walking (Ex1: 4.5 ± 0.9 J·m -1 ·kg -1 ; Ex2: 4.1 ± 0.7 J·m -1 ·kg -1 ), and RF EMG activity (Ex1: 0.071 ± 0.028 mV; Ex2: 0.041 ± 0.014 mV) were significantly decreased during Ex2 compared with Ex1 ( P < 0.01). RF µ was significantly greater in Ex2 (0.44 ± 0.18) compared with Ex1 (0.56 ± 0.27; P < 0.001). CONCLUSIONS: The RF muscle displayed specific mechanical and nervous adaptations to repeated DW bouts as compared with VL. Moreover, the muscle adaptations conferred by the first bout of DW could have induced greater exercise efficiency, inducing lesser perceived exertion and cardiometabolic demand when the same exercise was repeated 2 wk later.

Exploring Serum Biomarkers for Neuropathic Pain in Rat Models of Chemotherapy-Induced Peripheral Neuropathy: A Comparative Pilot Study with Oxaliplatin, Paclitaxel, Bortezomib, and Vincristine.

Blood biomarkers, including neurofilament light chain (NfL), have garnered attention as potential indicators for chemotherapy-induced peripheral neuropathy (CIPN), a dose-limiting adverse effect of neurotoxic anticancer drugs. However, no blood biomarker has been established for routine application or translational research. This pilot study aimed to evaluate a limited panel of blood biomarkers in rat models of CIPN and their correlations with neuropathic pain. CIPN models were induced through repeated injections of oxaliplatin, paclitaxel, bortezomib, and vincristine. Electronic von Frey testing was used to assess tactile allodynia. Post anticancer injections, serum concentrations of 31 proteins were measured. Allodynia thresholds decreased in anticancer-treated animals compared to controls. No consistent modifications were observed in the biomarkers across CIPN models. The most noteworthy biomarkers with increased concentrations in at least two CIPN models were NfL (paclitaxel, vincristine), MCP-1, and RANTES (oxaliplatin, vincristine). Vincristine-treated animals exhibited strong correlations between LIX, MCP-1, NfL, and VEGF concentrations and tactile allodynia thresholds. No single biomarker can be recommended as a unique indicator of CIPN-related pain. Because of the study limitations (single dose of each anticancer drug, young animals, and single time measurement of biomarkers), further investigations are necessary to define the kinetics, specificities, and sensitivities of MCP-1, RANTES, and NfL.

The 68 symptoms of the clinical high risk for psychosis: Low similarity among fourteen screening questionnaires.

The Clinical High Risk for psychosis (CHR) is a heterogeneous condition with multiple symptoms. CHR screening is challenging in routine care, as a wide variety of questionnaires exists. We propose to explore the extent to which these questionnaires differ or overlap in item content. We performed a systematic and quantitative analysis of item content in a set of widely-used CHR screening questionnaires. Items were extracted from questionnaires and reworded according to the Structured Interview for Psychosis-Risk Syndromes (SIPS). Then, symptoms were generated from individual items. The Jaccard Index was calculated to assess content overlap. The 14 analysed questionnaires were composed of 347 items, from which 198 symptoms were generated and, in turn, collapsed into 68 distinct symptoms. Positive symptoms were the most commonly represented. The overall overlap across questionnaires showed weak similarity (Jaccard = 0.19±0.50). CHR screening questionnaires might evaluate the same broad clinical construct, but have different scopes within that construct, and may be more or less comprehensive than one another. Clinicians and researchers should be mindful of the specific features of each instrument for optimal CHR screening.

Content analysis of insomnia questionnaires: A step to better evaluate the complex and multifaceted construct of insomnia disorder.

Insomnia disorder is a mental disorder that includes various types of symptoms (e.g., insomnia initiating, worries, mood disturbances) and impairments (e.g., distress related to sleep alterations). Self-report questionnaires are the most common method for assessing insomnia but no systematic quantified analysis of their content and overlap has been carried out. We used content analysis and a visualization method to better identify the different types of clinical manifestations that are investigated by nine commonly used insomnia questionnaires for adults and the Jaccard index to quantify the degree to which they overlap. Content analysis found and visualized 16 different clinical manifestations classified into five dimensions ("Insomnia symptoms", "Insomnia-related symptoms", "Daytime symptoms", "Insomnia-related impairments", "Sleep behaviors"). The average Jaccard Index was 0.409 (moderate overlap in content). There is a lack of distinction between symptoms and impairments, and the assessment of sleep duration and hyperarousal symptoms remains overlooked. This preliminary analysis makes it possible to visualize the content of each of the nine questionnaires and to select the most appropriate questionnaire based on the issue to be addressed. Suggestions are made regarding the development of future questionnaires to better distinguish symptoms and impairments, and the different phenotypes of insomnia disorder.

Genome sequencing of 15 acid-tolerant yeasts.

We report draft genome sequences for 15 non-conventional Saccharomycotina yeast strains obtained from public culture repositories. Included in our collection are eight strains of Pichia with broad tolerance to dicarboxylic acids. The genome sequences of these strains will enable comparative genomics of acid-tolerant phenotypes and strain engineering of non-conventional hosts.

Risk factors for migraine disease progression: a narrative review for a patient-centered approach.

BACKGROUND: In individuals with migraine, attacks may increase in frequency, severity, or both. Preventing migraine progression has emerged as a treatment goal in headache subspecialty practice, but there may be less awareness in general neurology or primary care settings where most people with migraine who seek treatment consult. Herein, we review the definition of and risk factors for migraine progression and consider strategies that could reduce its risk. METHODS: A group of headache expert healthcare professionals, clinicians, and researchers reviewed published evidence documenting factors associated with increased or decreased rates of migraine progression and established expert opinions for disease management recommendations. Strength of evidence was rated as good, moderate, or based solely on expert opinion, using modified criteria for causation developed by AB Hill. RESULTS: Migraine progression is commonly operationally defined as the transition from ≤ 15 to ≥ 15 monthly headache days among people with migraine; however, this does not necessarily constitute a fundamental change in migraine biology and other definitions should be considered. Established and theoretical key risk factors for migraine progression were categorized into five domains: migraine disease characteristics, treatment-related factors, comorbidities, lifestyle/exogenous factors, and demographic factors. Within these domains, good evidence supports the following risk factors: poorly optimized acute headache treatment, cutaneous allodynia, acute medication overuse, selected psychiatric symptoms, extra-cephalic chronic pain conditions, metabolism-related comorbidities, sleep disturbances, respiratory conditions, former/current high caffeine intake, physical inactivity, financial constraints, tobacco use, and personal triggers as risk factors. Protective actions that may mitigate migraine progression are sparsely investigated in published literature; our discussion of these factors is primarily based on expert opinion. CONCLUSIONS: Recognizing risk factors for migraine progression will allow healthcare providers to suggest protective actions against migraine progression (Supplementary Fig. 1). Intervention studies are needed to weight the risk factors and test the clinical benefit of hypothesized mitigation strategies that emerge from epidemiological evidence.

CRAPS: Chromosomal-Repair-Assisted Pathway Shuffling in Yeast.

A fundamental challenge of metabolic engineering involves assembling and screening vast combinations of orthologous enzymes across a multistep biochemical pathway. Current pathway assembly workflows involve combining genetic parts ex vivo and assembling one pathway configuration per tube or well. Here, we present CRAPS, Chromosomal-Repair-Assisted Pathway Shuffling, an in vivo pathway engineering technique that enables the self-assembly of one pathway configuration per cell. CRAPS leverages the yeast chromosomal repair pathway and utilizes a pool of inactive, chromosomally integrated orthologous gene variants corresponding to a target multistep pathway. Supplying gRNAs to the CRAPS host activates the expression of one gene variant per pathway step, resulting in a unique pathway configuration in each cell. We deployed CRAPS to build more than 1000 theoretical combinations of a four-step carotenoid biosynthesis network. Sampling the CRAPS pathway space yielded strains with distinct color phenotypes and carotenoid product profiles. We anticipate that CRAPS will expedite strain engineering campaigns by enabling the generation and sampling of vast biochemical spaces.