Focal adhesions are controlled by microtubules through local contractility regulation.

Microtubules regulate cell polarity and migration via local activation of focal adhesion turnover, but the mechanism of this process is insufficiently understood. Molecular complexes containing KANK family proteins connect microtubules with talin, the major component of focal adhesions. Here, local optogenetic activation of KANK1-mediated microtubule/talin linkage promoted microtubule targeting to an individual focal adhesion and subsequent withdrawal, resulting in focal adhesion centripetal sliding and rapid disassembly. This sliding is preceded by a local increase of traction force due to accumulation of myosin-II and actin in the proximity of the focal adhesion. Knockdown of the Rho activator GEF-H1 prevented development of traction force and abolished sliding and disassembly of focal adhesions upon KANK1 activation. Other players participating in microtubule-driven, KANK-dependent focal adhesion disassembly include kinases ROCK, PAK, and FAK, as well as microtubules/focal adhesion-associated proteins kinesin-1, APC, and αTAT. Based on these data, we develop a mathematical model for a microtubule-driven focal adhesion disruption involving local GEF-H1/RhoA/ROCK-dependent activation of contractility, which is consistent with experimental data.

Engineering of a Biologically Active Glycosylated Glucagon-Like Peptide-1 Analogue.

Glucagon-like peptide receptor (GLP-1R) agonists (e.g., semaglutide, liraglutide, etc.) are efficient treatment options for people with type 2 diabetes and obesity. The manufacturing method to produce semaglutide, a blockbuster GLP-1 drug on the market, involves multistep synthesis. The large peptide has a hydrophobic fatty acid side chain that makes it sparingly soluble, and its handling, purification, and large-scale production difficult. The growing demand for semaglutide that the manufacturer is not capable of addressing immediately triggered a worldwide shortage. Thus, we have developed a potential alternative analogue to semaglutide by replacing the hydrophobic fatty acid with a hydrophilic human complex-type biantennary oligosaccharide. Our novel glycoGLP-1 analogue was isolated in an ∼10-fold higher yield compared with semaglutide. Importantly, our glycoGLP-1 analogue possessed a similar GLP-1R activation potency to semaglutide and was biologically active in vivo in reducing glucose levels to a similar degree as semaglutide.

OrgaSegment: deep-learning based organoid segmentation to quantify CFTR dependent fluid secretion.

Epithelial ion and fluid transport studies in patient-derived organoids (PDOs) are increasingly being used for preclinical studies, drug development and precision medicine applications. Epithelial fluid transport properties in PDOs can be measured through visual changes in organoid (lumen) size. Such organoid phenotypes have been highly instrumental for the studying of diseases, including cystic fibrosis (CF), which is characterized by genetic mutations of the CF transmembrane conductance regulator (CFTR) ion channel. Here we present OrgaSegment, a MASK-RCNN based deep-learning segmentation model allowing for the segmentation of individual intestinal PDO structures from bright-field images. OrgaSegment recognizes spherical structures in addition to the oddly-shaped organoids that are a hallmark of CF organoids and can be used in organoid swelling assays, including the new drug-induced swelling assay that we show here. OrgaSegment enabled easy quantification of organoid swelling and could discriminate between organoids with different CFTR mutations, as well as measure responses to CFTR modulating drugs. The easy-to-apply label-free segmentation tool can help to study CFTR-based fluid secretion and possibly other epithelial ion transport mechanisms in organoids.

Single-atom nanozymes with peroxidase-like activity: A review.

Single-atom nanozymes (SANs) are nanomaterials-based nanozymes with atomically dispersed enzyme-like active sites. SANs offer improved as well as tunable catalytic activity. The creation of extremely effective SANs and their potential uses have piqued researchers' curiosity due to their advantages of cheap cost, variable catalytic activity, high stability, and large-scale production. Furthermore, SANs with uniformly distributed active centers and definite coordination structures offer a distinctive opportunity to investigate the structure-activity correlation and control the geometric and electrical features of metal centers. SANs have been extensively explored in photo-, thermal-, and electro-catalysis. However, SANs suffer from the following disadvantages, such as efficiency, non-mimicking of the 3-D complexity of natural enzymes, limited and narrow range of artificial SANs, and biosafety aspects. Among a quite limited range of artificial SANs, the peroxidase action of SANs has attracted significant research attention in the last five years with the aim of producing reactive oxygen species for use in cancer therapy, and water treatment among many other applications. In this review, we explore the recent progress of different SANs as peroxidase mimics, the role of the metal center in enzymatic activity, possible prospects, and underlying limitations in real-time applications.

CFTR Function Restoration upon Elexacaftor/Tezacaftor/Ivacaftor Treatment in Patient-Derived Intestinal Organoids with Rare CFTR Genotypes.

Cystic fibrosis (CF) is caused by mutations in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene. The combination of the CFTR modulators elexacaftor, tezacaftor, and ivacaftor (ETI) enables the effective rescue of CFTR function in people with the most prevalent F508del mutation. However, the functional restoration of rare CFTR variants remains unclear. Here, we use patient-derived intestinal organoids (PDIOs) to identify rare CFTR variants and potentially individuals with CF that might benefit from ETI. First, steady-state lumen area (SLA) measurements were taken to assess CFTR function and compare it to the level observed in healthy controls. Secondly, the forskolin-induced swelling (FIS) assay was performed to measure CFTR rescue within a lower function range, and to further compare it to ETI-mediated CFTR rescue in CFTR genotypes that have received market approval. ETI responses in 30 PDIOs harboring the F508del mutation served as reference for ETI responses of 22 PDIOs with genotypes that are not currently eligible for CFTR modulator treatment, following European Medicine Agency (EMA) and/or U.S. Food and Drug Administration (FDA) regulations. Our data expand previous datasets showing a correlation between in vitro CFTR rescue in organoids and corresponding in vivo ppFEV1 improvement upon a CFTR modulator treatment in published clinical trials, and suggests that the majority of individuals with rare CFTR variants could benefit from ETI. CFTR restoration was further confirmed on protein levels using Western blot. Our data support that CFTR function measurements in PDIOs with rare CFTR genotypes can help to select potential responders to ETI, and suggest that regulatory authorities need to consider providing access to treatment based on the principle of equality for people with CF who do not have access to treatment.

Increasing compliance with international pandemic law: international relations and new global health agreements.

Across multiple pandemics, global health governance institutions have struggled to secure the compliance of states with international legal and political commitments, ranging from data sharing to observing WHO guidance to sharing vaccines. In response, governments are negotiating a new pandemic treaty and revising the International Health Regulations. Achieving compliance remains challenging, but international relations and international law research in areas outside of health offers insights. This Health Policy analyses international relations research on the reasons why states comply with international law, even in the absence of sanctions. Drawing on human rights, trade, finance, tobacco, and environmental law, we categorise compliance mechanisms as police patrol, fire alarm, or community organiser models. We show that, to date, current and proposed global health law incorporates only a few of the mechanisms that have shown to be effective in other areas. We offer six specific, politically feasible mechanisms for new international agreements that, together, could create compliance pressures to shift state behaviour.

Maximum mutational robustness in genotype-phenotype maps follows a self-similar blancmange-like curve.

Phenotype robustness, defined as the average mutational robustness of all the genotypes that map to a given phenotype, plays a key role in facilitating neutral exploration of novel phenotypic variation by an evolving population. By applying results from coding theory, we prove that the maximum phenotype robustness occurs when genotypes are organized as bricklayer's graphs, so-called because they resemble the way in which a bricklayer would fill in a Hamming graph. The value of the maximal robustness is given by a fractal continuous everywhere but differentiable nowhere sums-of-digits function from number theory. Interestingly, genotype-phenotype maps for RNA secondary structure and the hydrophobic-polar (HP) model for protein folding can exhibit phenotype robustness that exactly attains this upper bound. By exploiting properties of the sums-of-digits function, we prove a lower bound on the deviation of the maximum robustness of phenotypes with multiple neutral components from the bricklayer's graph bound, and show that RNA secondary structure phenotypes obey this bound. Finally, we show how robustness changes when phenotypes are coarse-grained and derive a formula and associated bounds for the transition probabilities between such phenotypes.

Cross-modal autoencoder framework learns holistic representations of cardiovascular state.

A fundamental challenge in diagnostics is integrating multiple modalities to develop a joint characterization of physiological state. Using the heart as a model system, we develop a cross-modal autoencoder framework for integrating distinct data modalities and constructing a holistic representation of cardiovascular state. In particular, we use our framework to construct such cross-modal representations from cardiac magnetic resonance images (MRIs), containing structural information, and electrocardiograms (ECGs), containing myoelectric information. We leverage the learned cross-modal representation to (1) improve phenotype prediction from a single, accessible phenotype such as ECGs; (2) enable imputation of hard-to-acquire cardiac MRIs from easy-to-acquire ECGs; and (3) develop a framework for performing genome-wide association studies in an unsupervised manner. Our results systematically integrate distinct diagnostic modalities into a common representation that better characterizes physiologic state.

The feasibility, safety, and efficacy of lower limb garment-integrated blood flow restriction training in healthy adults.

OBJECTIVES: Explore the feasibility of lower-limb garment-integrated BFR-training. DESIGN: Observational study. SETTING: Human performance laboratory. PARTICIPANTS: Healthy males with no experience of BFR-training. MAIN OUTCOME MEASURES: Feasibility was determined by a priori thresholds for recruitment, adherence, and data collection. Safety was determined by measuring BFR torniquet pressure and the incidence of side effects. Efficacy was determined by measuring body anthropometry and knee isokinetic dynamometry. Feasibility and safety outcomes were reported descriptively or as a proportion with 95% confidence intervals (95% CI), with mean change, 95% CIs, and effect sizes for efficacy outcomes. RESULTS: Twelve participants (mean age 24.8 years [6.5]) were successfully recruited; 11 completed the study. 134/136 sessions were completed (adherence = 98.5%) and 100% of data were collected. There was one event of excessive pain during exercise (0.7%, 95% CI 0.0%, 4.0%), two events of excessive pain post-exercise (1.5%, 95% CI 0.4%, 5.5%), and one event of persistent paraesthesia post-exercise (0.7%, 95% CI 0.0%, 4.0%). Mean maximal BFR torniquet pressure was <200 mmHg. We observed an increase in knee extension peak torque (mean change 12.4 Nm), but no notable changes in body anthropometry. CONCLUSIONS: Lower-limb garment-integrated BFR-training is feasible, has no signal of important harm, and could be used independently.

Benefits of living closer to kin vary by genealogical relationship in a territorial mammal.

While cooperative interactions among kin are a key building block in the societies of group-living species, their importance for species with more variable social environments is unclear. North American red squirrels (Tamiasciurus hudsonicus) defend individual territories in dynamic neighbourhoods and are known to benefit from living among familiar conspecifics, but not relatives. However, kin-directed behaviours may be restricted to specific genealogical relationships or strongly mediated by geographical distance, masking their influence at broader scales. Using distance between territories as a proxy for the ability of individuals to interact, we estimated the influence of primary kin (parents, offspring, siblings) on the annual survival and reproductive success of red squirrels. This approach revealed associations between fitness and access to kin, but only for certain genealogical relationships and fitness components. For example, females had enhanced annual survival when living closer to their daughters, though the reverse was not true. Most surprising was the finding that males had higher annual reproductive success when living closer to their father, suggesting possible recognition and cooperation among fathers and sons. Together, these findings point to unexpected nuance in the fitness consequences of kinship dynamics for a species that is territorial and largely solitary.

ANALYSES OF SOME CALL FACTORS AFFECTING SAR LEVELS OF GSM MOBILE PHONES USED IN GHANA.

In response to mounting radiofrequency health concerns, this study was constituted to provide critical scientific data and assess any potential exposure from global system for mobile communication mobile phones. Specific absorption rate (SAR) from phones approved by the regulator and untested/unapproved phones were measured with a ComoSAR system. The maximum 10 g SAR (0.51 W/kg) and 1 g SAR (0.99 W/kg) measured were 25 and 62% of the International Commission on Non-Ionizing Radiation Protection and Federal Communication Commission limits, respectively. The approved phone produced statistically significant higher SAR values relative to the untested phone. SAR values of the right ear were relatively higher. All maximum SAR values were recorded on the right ear. The regulatory approval status of the phone, phone's orientation to the head, operating frequency channel and in which ear (right or left) the phone is used influenced the SAR measured. The SAR values of the approved phone compared favourably with similar studies while the unapproved phone does not.

Drug Repurposing for Cystic Fibrosis: Identification of Drugs That Induce CFTR-Independent Fluid Secretion in Nasal Organoids.

Individuals with cystic fibrosis (CF) suffer from severe respiratory disease due to a genetic defect in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which impairs airway epithelial ion and fluid secretion. New CFTR modulators that restore mutant CFTR function have been recently approved for a large group of people with CF (pwCF), but ~19% of pwCF cannot benefit from CFTR modulators Restoration of epithelial fluid secretion through non-CFTR pathways might be an effective treatment for all pwCF. Here, we developed a medium-throughput 384-well screening assay using nasal CF airway epithelial organoids, with the aim to repurpose FDA-approved drugs as modulators of non-CFTR-dependent epithelial fluid secretion. From a ~1400 FDA-approved drug library, we identified and validated 12 FDA-approved drugs that induced CFTR-independent fluid secretion. Among the hits were several cAMP-mediating drugs, including ß2-adrenergic agonists. The hits displayed no effects on chloride conductance measured in the Ussing chamber, and fluid secretion was not affected by TMEM16A, as demonstrated by knockout (KO) experiments in primary nasal epithelial cells. Altogether, our results demonstrate the use of primary nasal airway cells for medium-scale drug screening, target validation with a highly efficient protocol for generating CRISPR-Cas9 KO cells and identification of compounds which induce fluid secretion in a CFTR- and TMEM16A-indepent manner.

The structure of genotype-phenotype maps makes fitness landscapes navigable.

Fitness landscapes are often described in terms of 'peaks' and 'valleys', indicating an intuitive low-dimensional landscape of the kind encountered in everyday experience. The space of genotypes, however, is extremely high dimensional, which results in counter-intuitive structural properties of genotype-phenotype maps. Here we show that these properties, such as the presence of pervasive neutral networks, make fitness landscapes navigable. For three biologically realistic genotype-phenotype map models-RNA secondary structure, protein tertiary structure and protein complexes-we find that, even under random fitness assignment, fitness maxima can be reached from almost any other phenotype without passing through fitness valleys. This in turn indicates that true fitness valleys are very rare. By considering evolutionary simulations between pairs of real examples of functional RNA sequences, we show that accessible paths are also likely to be used under evolutionary dynamics. Our findings have broad implications for the prediction of natural evolutionary outcomes and for directed evolution.

Identifying cellular cancer mechanisms through pathway-driven data integration.

MOTIVATION: Cancer is a genetic disease in which accumulated mutations of driver genes induce a functional reorganization of the cell by reprogramming cellular pathways. Current approaches identify cancer pathways as those most internally perturbed by gene expression changes. However, driver genes characteristically perform hub roles between pathways. Therefore, we hypothesize that cancer pathways should be identified by changes in their pathway-pathway relationships. RESULTS: To learn an embedding space that captures the relationships between pathways in a healthy cell, we propose pathway-driven non-negative matrix tri-factorization. In this space, we determine condition-specific (i.e. diseased and healthy) embeddings of pathways and genes. Based on these embeddings, we define our 'NMTF centrality' to measure a pathway's or gene's functional importance, and our 'moving distance', to measure the change in its functional relationships. We combine both measures to predict 15 genes and pathways involved in four major cancers, predicting 60 gene-cancer associations in total, covering 28 unique genes. To further exploit driver genes' tendency to perform hub roles, we model our network data using graphlet adjacency, which considers nodes adjacent if their interaction patterns form specific shapes (e.g. paths or triangles). We find that the predicted genes rewire pathway-pathway interactions in the immune system and provide literary evidence that many are druggable (15/28) and implicated in the associated cancers (47/60). We predict six druggable cancer-specific drug targets. AVAILABILITY AND IMPLEMENTATION: The code and data are available at: https://gitlab.bsc.es/swindels/pathway_driven_nmtf. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Causation, not collinearity: Identifying sources of bias when modelling the evolution of brain size and other allometric traits.

Many biological traits covary with body size, resulting in an allometric relationship. Identifying the evolutionary drivers of these traits is complicated by possible relationships between a candidate selective agent and body size itself, motivating the widespread use of multiple regression analysis. However, the possibility that multiple regression may generate misleading estimates when predictor variables are correlated has recently received much attention. Here, we argue that a primary source of such bias is the failure to account for the complex causal structures underlying brains, bodies, and agents. When brains and bodies are expected to evolve in a correlated manner over and above the effects of specific agents of selection, neither simple nor multiple regression will identify the true causal effect of an agent on brain size. This problem results from the inclusion of a predictor variable in a regression analysis that is (in part) a consequence of the response variable. We demonstrate these biases with examples and derive estimators to identify causal relationships when traits evolve as a function of an existing allometry. Model mis-specification relative to plausible causal structures, not collinearity, requires further consideration as an important source of bias in comparative analyses.

Genetic factors and shared environment contribute equally to objective singing ability.

Singing ability is a complex human skill influenced by genetic and environmental factors, the relative contributions of which remain unknown. Currently, genetically informative studies using objective measures of singing ability across a range of tasks are limited. We administered a validated online singing tool to measure performance across three everyday singing tasks in Australian twins (n = 1189) to explore the relative genetic and environmental influences on singing ability. We derived a reproducible phenotypic index for singing ability across five performance measures of pitch and interval accuracy. Using this index we found moderate heritability of singing ability (h 2 = 40.7%) with a striking, similar contribution from shared environmental factors (c 2 = 37.1%). Childhood singing in the family home and being surrounded by music early in life both significantly predicted the phenotypic index. Taken together, these findings show that singing ability is equally influenced by genetic and shared environmental factors.

Cross-modal perception of identity by sound and taste in bottlenose dolphins.

While studies have demonstrated concept formation in animals, only humans are known to label concepts to use them in mental simulations or predictions. To investigate whether other animals use labels comparably, we studied cross-modal, individual recognition in bottlenose dolphins (Tursiops truncatus) that use signature whistles as labels for conspecifics in their own communication. First, we tested whether dolphins could use gustatory stimuli and found that they could distinguish between water and urine samples, as well as between urine from familiar and unfamiliar individuals. Then, we paired playbacks of signature whistles of known animals with urine samples from either the same dolphin or a different, familiar animal. Dolphins investigated the presentation area longer when the acoustic and gustatory sample matched than when they mismatched. This demonstrates that dolphins recognize other individuals by gustation alone and can integrate information from acoustic and taste inputs indicating a modality independent, labeled concept for known conspecifics.

Multiple Mechanistically Distinct Timescales of Neocortical Plasticity Occur During Habituation.

Recognizing familiar but innocuous stimuli and suppressing behavioral response to those stimuli are critical steps in dedicating cognitive resources to significant elements of the environment. Recent work in the visual system has uncovered key neocortical mechanisms of this familiarity that emerges over days. Specifically, exposure to phase-reversing gratings of a specific orientation causes long-lasting stimulus-selective response potentiation (SRP) in layer 4 of mouse primary visual cortex (V1) as the animal's behavioral responses are reduced through habituation. This plasticity and concomitant learning require the NMDA receptor and the activity of parvalbumin-expressing (PV+) inhibitory neurons. Changes over the course of seconds and minutes have been less well studied in this paradigm, so we have here characterized cortical plasticity occurring over seconds and minutes, as well as days, to identify separable forms of plasticity accompanying familiarity. In addition, we show evidence of interactions between plasticity over these different timescales and reveal key mechanistic differences. Layer 4 visual-evoked potentials (VEPs) are potentiated over days, and they are depressed over minutes, even though both forms of plasticity coincide with significant reductions in behavioral response. Adaptation, classically described as a progressive reduction in synaptic or neural activity, also occurs over the course of seconds, but appears mechanistically separable over a second as compared to tens of seconds. Interestingly, these short-term forms of adaptation are modulated by long-term familiarity, such that they occur for novel but not highly familiar stimuli. Genetic knock-down of NMDA receptors within V1 prevents all forms of plasticity while, importantly, the modulation of short-term adaptation by long-term familiarity is gated by PV+ interneurons. Our findings demonstrate that different timescales of adaptation/habituation have divergent but overlapping mechanisms, providing new insight into how the brain is modified by experience to encode familiarity.

Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution.

SignificanceWhy does evolution favor symmetric structures when they only represent a minute subset of all possible forms? Just as monkeys randomly typing into a computer language will preferentially produce outputs that can be generated by shorter algorithms, so the coding theorem from algorithmic information theory predicts that random mutations, when decoded by the process of development, preferentially produce phenotypes with shorter algorithmic descriptions. Since symmetric structures need less information to encode, they are much more likely to appear as potential variation. Combined with an arrival-of-the-frequent mechanism, this algorithmic bias predicts a much higher prevalence of low-complexity (high-symmetry) phenotypes than follows from natural selection alone and also explains patterns observed in protein complexes, RNA secondary structures, and a gene regulatory network.