Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments.

For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least seven and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways.

Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii.

Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Nearly all (96%) of the events were associated with deletions, duplications, or more complex rearrangements of genomic DNA at the sites of plasmid insertion, and together with deletions that were unassociated with a plasmid insertion, 1470 genes were identified to be affected. Functional annotations of these genes were enriched in those related to photosynthesis, signaling, and tetrapyrrole synthesis as would be expected from a library enriched for photosynthesis mutants. Systematic manual analysis of the disrupted genes for each mutant generated a list of 253 higher-confidence candidate photosynthesis genes, and we experimentally validated two genes that are essential for photoautotrophic growth, CrLPA3 and CrPSBP4. The inventory of candidate genes includes 53 genes from a phylogenomically defined set of conserved genes in green algae and plants. Altogether, 70 candidate genes encode proteins with previously characterized functions in photosynthesis in Chlamydomonas, land plants, and/or cyanobacteria; 14 genes encode proteins previously shown to have functions unrelated to photosynthesis. Among the remaining 169 uncharacterized genes, 38 genes encode proteins without any functional annotation, signifying that our results connect a function related to photosynthesis to these previously unknown proteins. This mutant library, with genome sequences that reveal the molecular extent of the chromosomal lesions and resulting higher-confidence candidate genes, will aid in advancing gene discovery and protein functional analysis in photosynthesis.

Army Combat Fitness Test Scores Moderate Cognitive Function Improvements After a Ruck March: A Hierarchical Linear Model Approach.

ABSTRACT: Sax van der Weyden, M, Merrigan, JJ, Newman, K, Hahn, J, and Martin, J. Army Combat Fitness Test scores moderate cognitive function improvements after a ruck march: A hierarchical linear model approach. J Strength Cond Res 38(7): 1314-1320, 2024-Heavy load carriage is a common task for military personnel and can lead to undue physical and mental fatigue. The purpose of this study was to assess effects of load carriage on cognitive function (CF) and the role individual characteristics play in CF responses. Anthropometrics/body composition, demographics, and Army Combat Fitness Test (ACFT) scores were gathered from 47 Reserve Officers' Training Corps cadets. Cadets' CF was assessed through the concentration task grid (CTG) before (preruck), immediately after (postruck), and 3 weeks after (follow-up) a 16.09- to 19.31-km ruck march. Hierarchical linear modeling was used, with α < 0.05. The final model revealed growth, or improvement, in CF from preruck to postruck with growth decelerating, but still improved, at follow-up. The load carriage bout improved CF in most cadets, with average growth from 5.67- to 7.20-grid squares found. However, postruck CF did not return to the same level as a controlled follow-up (9.69). Sex (2.46, female), familiarity with the CTG (1.99), ACFT total scores (0.009), and relative ruck mass (-0.09) were all significant predictors of postruck CF. Army Combat Fitness Test scores (0.008) were also significant predictors of the slope between preruck and postruck, such that an ACFT score 59 points above average would result in a 1-grid square greater improvement in CF postruck. The significance of ACFT scores, lower relative ruck mass, and familiarization highlights the importance physical and mental preparation for desirable CF outcomes after occupational tasks.

Impact of Attentional Focus on Dance Performance: A Critically Appraised Topic.

CLINICAL SCENARIO: Dancing is a demanding esthetic activity with dancers having an 85% annual injury incident rate when performing complex dance motor skills. Teachers and clinicians use a combination of external and internal attentional cues when teaching dancers motor skills and when working on rehabilitation programs with injured dancers, respectively. External attentional focus (ie, focusing on movement outcome) reportedly results in superior performance than internal attentional focus (ie, focus on body movements). Interestingly, dancers reportedly often adopt an internal focus when dancing. Still, limited literature exists examining the effects of attentional focus on dancers' performance. CLINICAL QUESTION: How does attentional focus (external or internal) impact performance in dancers? SUMMARY OF KEY FINDINGS: Four original quasi-experimental studies met inclusion criteria. In the current examination, we found mixed results about the impact of attentional focus in dancers. Specifically, using an external attentional focus resulted in better performance in 2 studies, but these findings were limited to lesser experienced dancers. Experienced dancers did not have any physical performance differences when using external or internal focus. Internal focus also did not negatively affect dancers' performance in 2 studies. Some authors noted positive motivational effects (eg, increased perceived competence) when dancers used external focus. CLINICAL BOTTOM LINE: Low-quality evidence exists supporting the notion that in less experienced dance students, external focus improves performance. In experienced dancers, the type of attentional focus did not impact performance. External focus provides positive mental effects. Thus, clinicians working with dancers can integrate individualized feedback according to dancer level, with a preference toward external focus due to positive mental effects, to design optimal training and rehabilitation programs. STRENGTH OF RECOMMENDATION: Grade B evidence exists supporting the notion that an external attentional focus improves performance in less experienced dance students and also has positive mental effects. Internal attentional focus does not impede experienced dancers' performance.

Silencing of Dicer-like protein 2a restores the resistance phenotype in the rice mutant, sxi4 (suppressor of Xa21-mediated immunity 4).

The rice immune receptor XA21 confers resistance to Xanthomonas oryzae pv. oryzae (Xoo), and upon recognition of the RaxX21-sY peptide produced by Xoo, XA21 activates the plant immune response. Here we screened 21 000 mutant plants expressing XA21 to identify components involved in this response, and reported here the identification of a rice mutant, sxi4, which is susceptible to Xoo. The sxi4 mutant carries a 32-kb translocation from chromosome 3 onto chromosome 7 and displays an elevated level of DCL2a transcript, encoding a Dicer-like protein. Silencing of DCL2a in the sxi4 genetic background restores resistance to Xoo. RaxX21-sY peptide-treated leaves of sxi4 retain the hallmarks of XA21-mediated immune response. However, WRKY45-1, a known negative regulator of rice resistance to Xoo, is induced in the sxi4 mutant in response to RaxX21-sY peptide treatment. A CRISPR knockout of a short interfering RNA (TE-siRNA815) in the intron of WRKY45-1 restores the resistance phenotype in sxi4. These results suggest a model where DCL2a accumulation negatively regulates XA21-mediated immunity by altering the processing of TE-siRNA815.

Individual responses to the implementation of mandatory fitness testing within a fire department.

OBJECTIVES: To examine the effects of implementing a consequential fitness assessment (pull-ups, curl-ups, push-ups, 3 min step test) in a fire department on an individual level. METHODS: We used a repeated-measures design to analyse fitness assessment data from 2019 to 2020 in Northern Virginia. A total of 631 professional firefighters completed the fitness assessment in both years. Repeated measures analysis of variances (ANOVAs) and multiple regression modelling were used to examine the effects of the fitness assessment and factors associated with changes in fitness, respectively. RESULTS: Overall all aspects of fitness improved over the first year of implementation with a majority of firefighters improved on all components of the fitness assessment except for pull-ups (16.1% improved). Greater levels of baseline fitness and being female were negatively associated with changes in all fitness measures. Older firefighters had smaller changes in pull-up, curl-up and push-up performance. CONCLUSIONS: During the first year of fitness assessment implementation, the fire department generally improved. The findings suggest that fire departments which enforce mandatory fitness assessments must establish policies for dealing with inadequate performance and offer resources to aid individual firefighters.

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.

Simulated Tibiofemoral Joint Reaction Forces for Three Previously Studied Gait Modifications in Healthy Controls.

Gait modifications, such as lateral trunk lean (LTL), medial knee thrust (MKT), and toe-in gait (TIG), are frequently investigated interventions used to slow the progression of knee osteoarthritis. The Lerner knee model was developed to estimate the tibiofemoral joint reaction forces (JRF) in the medial and lateral compartments during gait. These models may be useful for estimating the effects on the JRF in the knee as a result of gait modifications. We hypothesized that all gait modifications would decrease the JRF compared to normal gait. Twenty healthy individuals volunteered for this study (26.7 ± 4.7 years, 1.75 ± 0.1 m, 73.4 ± 12.4 kg). Ten trials were collected for normal gait as well as for the three gait modifications: LTL, MKT, and TIG. The data were used to estimate the JRF in the first and second peaks for the medial and lateral compartments of the knee via opensim using the Lerner knee model. No significant difference from baseline was found for the first peak in the medial compartment. There was a decrease in JRF in the medial compartment during the loading phase of gait for TIG (6.6%) and LTL (4.9%) and an increasing JRF for MKT (2.6%). but none was statistically significant. A significant increase from baseline was found for TIG (5.8%) in the medial second peak. We found a large variation in individual responses to gait interventions, which may help explain the lack of statistically significant results. Possible factors influencing these wide ranges of responses to gait modifications include static alignment and the impacts of variation in muscle coordination strategies used, by participants, to implement gait modifications.

PySilSub: An open-source Python toolbox for implementing the method of silent substitution in vision and nonvisual photoreception research.

The normal human retina contains several classes of photosensitive cell-rods for low-light vision, three cone classes for daylight vision, and intrinsically photosensitive retinal ganglion cells (ipRGCs) expressing melanopsin for non-image-forming functions, including pupil control, melatonin suppression, and circadian photoentrainment. The spectral sensitivities of the photoreceptors overlap significantly, which means that most lights will stimulate all photoreceptors to varying degrees. The method of silent substitution is a powerful tool for stimulating individual photoreceptor classes selectively and has found much use in research and clinical settings. The main hardware requirement for silent substitution is a spectrally calibrated light stimulation system with at least as many primaries as there are photoreceptors under consideration. Device settings that will produce lights to selectively stimulate the photoreceptor(s) of interest can be found using a variety of analytic and algorithmic approaches. Here we present PySilSub (https://github.com/PySilentSubstitution/pysilsub), a novel Python package for silent substitution featuring flexible support for individual colorimetric observer models (including human and mouse observers), multiprimary stimulation devices, and solving silent substitution problems with linear algebra and constrained numerical optimization. The toolbox is registered with the Python Package Index and includes example data sets from various multiprimary systems. We hope that PySilSub will facilitate the application of silent substitution in research and clinical settings.

Effects of Law Enforcement Load Carriage Systems on Muscle Activity and Coordination during Walking: An Exploratory Study.

Law enforcement officers (LEOs) commonly wear a duty belt (DB) or tactical vest (TV) and from prior findings, these forms of load carriage (LC) likely alter muscular activity. However, studies on the effects of LEO LC on muscular activity and coordination are limited in the current literature. The present study examined the effects of LEO load carriage on muscular activity and coordination. Twenty-four volunteers participated in the study (male = 13, age = 24.5 ± 6.0 years). Surface electromyography (sEMG) sensors were placed on the vastus lateralis, biceps femoris, multifidus, and lower rectus abdominus. Participants completed treadmill walking for two load carriage conditions (duty belt and tactical vest) and a control condition. Mean activity, sample entropy and Pearson correlation coefficients were computed for each muscle pair during the trials. The duty belt and tactical vest resulted in an increase in muscle activity in several muscles; however, no differences between the duty belt and tactical vest were found. Consistently across the conditions, the largest correlations were observed between the left and right multifidus (r = 0.33-0.68) and rectus abdominus muscles (0.34-0.55). There were statistically small effects (p < 0.05, η2 = 0.031 to 0.076) of the LC on intermuscular coordination. No effect (p > 0.05) of the LC on sample entropy was found for any muscle. The findings indicate that LEO LC causes small differences in muscular activity and coordination during walking. Future research should incorporate heavier loads and longer durations.

Pupillometry and the vigilance decrement: Task-evoked but not baseline pupil measures reflect declining performance in visual vigilance tasks.

Baseline and task-evoked pupil measures are known to reflect the activity of the nervous system's central arousal mechanisms. With the increasing availability, affordability and flexibility of video-based eye tracking hardware, these measures may one day find practical application in real-time biobehavioural monitoring systems to assess performance or fitness for duty in tasks requiring vigilant attention. But real-world vigilance tasks are predominantly visual in their nature and most research in this area has taken place in the auditory domain. Here, we explore the relationship between pupil size-both baseline and task-evoked-and behavioural performance measures in two novel vigilance tasks requiring visual target detection: (1) a traditional vigilance task involving prolonged, continuous and uninterrupted performance (n = 28) and (2) a psychomotor vigilance task (n = 25). In both tasks, behavioural performance and task-evoked pupil responses declined as time spent on task increased, corroborating previous reports in the literature of a vigilance decrement with a corresponding reduction in task-evoked pupil measures. Also in line with previous findings, baseline pupil size did not show a consistent relationship with performance measures. Our data offer novel insights into the complex interplay of brain systems involved in vigilant attention and question the validity of the assumption that baseline (prestimulus) pupil size and task-evoked (poststimulus) pupil measures reflect the tonic and phasic firing modes of the locus coeruleus.

Association between Self-Reported Prior Night's Sleep and Single-Task Gait in Healthy, Young Adults: A Study Using Machine Learning.

Failure to obtain the recommended 7−9 h of sleep has been associated with injuries in youth and adults. However, most research on the influence of prior night's sleep and gait has been conducted on older adults and clinical populations. Therefore, the objective of this study was to identify individuals who experience partial sleep deprivation and/or sleep extension the prior night using single task gait. Participants (n = 123, age 24.3 ± 4.0 years; 65% female) agreed to participate in this study. Self-reported sleep duration of the night prior to testing was collected. Gait data was collected with inertial sensors during a 2 min walk test. Group differences (<7 h and >9 h, poor sleepers; 7−9 h, good sleepers) in gait characteristics were assessed using machine learning and a post-hoc ANCOVA. Results indicated a correlation (r = 0.79) between gait parameters and prior night's sleep. The most accurate machine learning model was a Random Forest Classifier using the top 9 features, which had a mean accuracy of 65.03%. Our findings suggest that good sleepers had more asymmetrical gait patterns and were better at maintaining gait speed than poor sleepers. Further research with larger subject sizes is needed to develop more accurate machine learning models to identify prior night's sleep using single-task gait.

Is the OUTPUT Sports Unit Reliable and Valid When Estimating Back Squat and Bench Press Concentric Velocity?

ABSTRACT: Merrigan, JJ and Martin, JR. Is the OUTPUT sports unit reliable and valid when estimating back squat and bench press concentric velocity? J Strength Cond Res 36(8): 2069-2076, 2022-This study evaluated the reliability and concurrent validity of the OUTPUT sports inertial unit to measure concentric velocity of free-weight back squat and bench press exercises. Eleven men and women performed back squat and bench press 1 repetition maximum (1RM) testing. One week later, subjects performed 3 repetitions of each exercise with 35, 45, 55, 65, 75, and 85% 1RM (18 total repetitions). The OUTPUT and 4 cable extension transducers (criterion) simultaneously recorded the mean and peak velocity. The OUTPUT had acceptable reliability for all loads except 85% 1RM for back squat and bench press (intraclass correlation coefficient = 0.72-0.96, coefficient of variation = 0.03-0.12). High systematic biases existed for the mean and peak velocity for the back squat and bench press, according to Bland-Altman plot's wide limits of agreement and ordinary least products regressions. According to Bland-Altman plots, OUTPUT tended to overestimate bench press velocity and overestimate back squat velocity at slower velocities. Least products regression analyses determined proportional bias existed for the mean and peak velocity of the back squat and peak velocity of the bench press. In conclusion, researchers and practitioners are advised not to compare velocity estimates of the OUTPUT unit with criterion devices because these methods cannot be used interchangeably. However, because of the demonstrated reliability when estimating the mean and peak velocity, strength and conditioning practitioners may find the OUTPUT unit valuable for monitoring performance of the back squat and bench press exercises. Yet, caution should be taken when evaluating loads ≥85% 1RM.

PyPlr: A versatile, integrated system of hardware and software for researching the human pupillary light reflex.

We introduce PyPlr-a versatile, integrated system of hardware and software to support a broad spectrum of research applications concerning the human pupillary light reflex (PLR). PyPlr is a custom Python library for integrating a research-grade video-based eye-tracker system with a light source and streamlining stimulus design, optimisation and delivery, device synchronisation, and extraction, cleaning, and analysis of pupil data. We additionally describe how full-field, homogenous stimulation of the retina can be realised with a low-cost integrating sphere that serves as an alternative to a more complex Maxwellian view setup. Users can integrate their own light source, but we provide full native software support for a high-end, commercial research-grade 10-primary light engine that offers advanced control over the temporal and spectral properties of light stimuli as well as spectral calibration utilities. Here, we describe the hardware and software in detail and demonstrate its capabilities with two example applications: (1) pupillometer-style measurement and parametrisation of the PLR to flashes of white light, and (2) comparing the post-illumination pupil response (PIPR) to flashes of long and short-wavelength light. The system holds promise for researchers who would favour a flexible approach to studying the PLR and the ability to employ a wide range of temporally and spectrally varying stimuli, including simple narrowband stimuli.

Does Blood Flow Restriction Resistance Training Improve Knee-Extensor Strength, Function, and Reduce Patient-Reported Pain? A Critically Appraised Topic.

Clinical Scenario: Knee pathologies often require rehabilitation to address the loss of knee-extensor (KE) strength, function, and heightened pain. However, in the early stages of rehabilitation, higher loads may be contraindicated. Blood flow restriction (BFR) resistance training does not require high loads and has been used clinically to promote strength improvements in a variety of injured populations. BFR resistance training may be an effective alternative to high-intensity resistance training during early rehabilitation of knee pathologies. Clinical Question: Following a knee injury, does BFR resistance training improve KE strength and function, and reduce patient-reported pain? Summary of Key Findings: Four randomized controlled trial studies met the inclusion criteria. Each included study evaluated the use of BFR resistance training on knee pathologies and the effects on KE strength, functional outcomes, and pain compared with high- or low-load resistance training. All 4 studies reported significant improvements in KE strength, function, and pain through a variety of outcome measures, following BFR resistance training use as the treatment. Clinical Bottom Line: There is consistent evidence to support the use of BFR resistance training as a treatment intervention following knee injury and as a means to improve KE strength and function and to reduce pain. Strength of Recommendation: Grade A evidence supporting the use of BFR resistance training for improvement in KE strength and function, and the reduction of patient-reported pain following an acute or chronic knee pathology.

Quantitative single-cell analysis of immunofluorescence protein multiplex images illustrates biomarker spatial heterogeneity within breast cancer subtypes.

BACKGROUND: The extent of cellular heterogeneity in breast cancer could have potential impact on diagnosis and long-term outcome. However, pathology evaluation is limited to biomarker immunohistochemical staining and morphology of the bulk cancer. Inter-cellular heterogeneity of biomarkers is not usually assessed. As an initial evaluation of the extent of breast cancer cellular heterogeneity, we conducted quantitative and spatial imaging of Estrogen Receptor (ER), Progesterone Receptor (PR), Epidermal Growth Factor Receptor-2 (HER2), Ki67, TP53, CDKN1A (P21/WAF1), CDKN2A (P16INK4A), CD8 and CD20 of a tissue microarray (TMA) representing subtypes defined by St. Gallen surrogate classification. METHODS: Quantitative, single cell-based imaging was conducted using an Immunofluorescence protein multiplexing platform (MxIF) to study protein co-expression signatures and their spatial localization patterns. The range of MxIF intensity values of each protein marker was compared to the respective IHC score for the TMA core. Extent of heterogeneity in spatial neighborhoods was analyzed using co-occurrence matrix and Diversity Index measures. RESULTS: On the 101 cores from 59 cases studied, diverse expression levels and distributions were observed in MxIF measures of ER and PR among the hormonal receptor-positive tumor cores. As expected, Luminal A-like cancers exhibit higher proportions of cell groups that co-express ER and PR, while Luminal B-like (HER2-negative) cancers were composed of ER+, PR- groups. Proliferating cells defined by Ki67 positivity were mainly found in groups with PR-negative cells. Triple-Negative Breast Cancer (TNBC) exhibited the highest proliferative fraction and incidence of abnormal P53 and P16 expression. Among the tumors exhibiting P53 overexpression by immunohistochemistry, a group of TNBC was found with much higher MxIF-measured P53 signal intensity compared to HER2+, Luminal B-like and other TNBC cases. Densities of CD8 and CD20 cells were highest in HER2+ cancers. Spatial analysis demonstrated variability in heterogeneity in cellular neighborhoods in the cancer and the tumor microenvironment. CONCLUSIONS: Protein marker multiplexing and quantitative image analysis demonstrated marked heterogeneity in protein co-expression signatures and cellular arrangement within each breast cancer subtype. These refined descriptors of biomarker expressions and spatial patterns could be valuable in the development of more informative tools to guide diagnosis and treatment.

Increased Trunk Kinetics Observed During Dose-Specific Trunk Lean Gait Modification.

Trunk modification is associated with knee abduction moment reduction in both healthy groups and individuals with knee osteoarthritis. Ambulatory-related changes in trunk kinematics have been implicated in increased trunk moment. The purpose of this study was to investigate the effect of dose-specific lateral trunk lean on trunk kinetics during ipsilateral and contralateral stance phases. Nineteen healthy participants completed 10 baseline walking trials, followed by 10 trials employing lateral trunk lean. Trunk modification magnitudes were determined based on the average baseline trunk angle. Five trials of both small and large trunk modification magnitudes were completed. Visual real-time biofeedback was projected as a line graph displaying the trunk angle during stance, and a highlighted bandwidth was designated the target range. A 1-factor repeated-measures analysis of variance or Friedman test was used to assess differences between the conditions (P < .05) in trunk dependent measures. Trunk kinetics displayed significant increases, even during modest modifications to the trunk angle. The participants experienced increased peak frontal plane trunk moment and angular impulse during ipsilateral stance. The observed increase in the peak lateral joint reaction force is suggestive of a compromised loading environment at the spine. Implementing trunk modification might result in unintended secondary changes along the kinetic chain, but further investigation is required.

The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies.

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.

Dual blockade of IL-4 and IL-13 with dupilumab, an IL-4Rα antibody, is required to broadly inhibit type 2 inflammation.

BACKGROUND: Dupilumab, a fully human monoclonal antibody that binds IL-4Rα and inhibits signaling of both IL-4 and IL-13, has shown efficacy across multiple diseases with underlying type 2 signatures and is approved for treatment of asthma, atopic dermatitis, and chronic sinusitis with nasal polyposis. We sought to provide a comprehensive analysis of the redundant and distinct roles of IL-4 and IL-13 in type 2 inflammation and report dupilumab mechanisms of action. METHODS: Using primary cell assays and a mouse model of house dust mite-induced asthma, we compared IL-4 vs IL-13 vs IL-4Rα blockers. RESULTS: Intranasal administration of either IL-4 or IL-13 confers an asthma-like phenotype in mice by inducing immune cell lung infiltration, including eosinophils, increasing cytokine/chemokine expression and mucus production, thus demonstrating redundant functions of these cytokines. We further teased out their respective contributions using human in vitro culture systems. Then, in a mouse asthma model by comparing in head-to-head studies, either IL-4 or IL-13 inhibition to dual IL-4/IL-13 inhibition, we demonstrate that blockade of both IL-4 and IL-13 is required to broadly block type 2 inflammation, which translates to protection from allergen-induced lung function impairment. Notably, only dual IL-4/IL-13 blockade prevented eosinophil infiltration into lung tissue without affecting circulating eosinophils, demonstrating that tissue, but not circulating eosinophils, contributes to disease pathology. CONCLUSIONS: Overall, these data support IL-4 and IL-13 as key drivers of type 2 inflammation and help provide insight into the therapeutic mechanism of dupilumab, a dual IL-4/IL-13 blocker, in multiple type 2 diseases.

Component processes in free-viewing visual search: Insights from fixation-aligned pupillary response averaging.

Pupil size changes during a visual search may reflect cognitive processes, such as effort and memory accumulation, but methodological confounds and the general lack of literature in this area leave the reliability of findings open to question. We used a novel synthesis of experimental methods and averaging techniques to explore how cognitive processing unfolds during free-viewing visual search for multiple targets. Twenty-seven participants completed 152 searches across two separate 1-hour sessions. The number of targets present (Targets: 0, 1, 2, and 3) in each trial was the main manipulation and the task was to "find all of the targets" and report the total via mouse-click at the end of the trial. Search time lasted for 10 seconds or until the participant purported to have found all of the targets, in which case they could terminate the search via keypress. Whole-trial pupil analysis revealed a significant effect of button pressing as well as a significant main effect of targets for trials that were not self-terminated via button press. Fixation-aligned pupil responses revealed transient modulations in pupil size following initial fixations on targets but not distractors and refixations on both targets and distractors. Owing to rigorous control over experimental confounds and a detailed analysis and correction of eye-movement-related measurement error, we confidently discuss these findings in terms of task-related processing and underlying brain activity.