Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations
Evolutionary adaptation to a constant environment is driven by the accumulation of mutations which can have a range of unrealized pleiotropic effects in other environments. These pleiotropic consequences of adaptation can influence the emergence of specialists or generalists, and are critical for evolution in temporally or spatially fluctuating environments. While many experiments have examined the pleiotropic effects of adaptation at a snapshot in time, very few have observed the dynamics by which these effects emerge and evolve. Here, we propagated hundreds of diploid and haploid laboratory budding yeast populations in e...
Source: eLife - October 1, 2021 Category: Biomedical Science Tags: Evolutionary Biology Source Type: research

Bazooka/Par3 cooperates with Sanpodo for the assembly of Notch clusters following asymmetric division of < i > Drosophila < /i > sensory organ precursor cells
In multiple cell lineages, Delta-Notch signalling regulates cell fate decisions owing to unidirectional signalling between daughter cells. InDrosophila pupal sensory organ lineage, Notch regulates the intra-lineage pIIa/pIIb fate decision at cytokinesis. Notch and Delta that localise apically and basally at the pIIa-pIIb interface are expressed at low levels and their residence time at the plasma membrane is in the order of minutes. How Delta can effectively interact with Notch to trigger signalling from a large plasma membrane area remains poorly understood. Here, we report that the signalling interface possesses a unique...
Source: eLife - October 1, 2021 Category: Biomedical Science Tags: Cell Biology Developmental Biology Source Type: research

Proof of concept for multiple nerve transfers to a single target muscle
This study describes a novel experimental model to investigate the neurophysiological effects of peripheral double nerve transfers. For this purpose, we developed a forelimb model to enable tension-free transfer of one or two donor nerves in the upper extremity. Anatomic dissections were performed to design the double nerve transfer model (n=8). In 62 male Sprague-Dawley rats the ulnar nerve of the antebrachium alone (n=30) or together with the anterior interosseus nerve (n=32) was transferred to reinnervate the long head of the biceps brachii. Before neurotization, the motor branch to the biceps ’ long head was tran...
Source: eLife - October 1, 2021 Category: Biomedical Science Tags: Neuroscience Source Type: research

HIF1 α stabilization in hypoxia is not oxidant-initiated
Hypoxic adaptation mediated by HIF transcription factors requires mitochondria, which have been implicated in regulating HIF1 α stability in hypoxia by distinct models that involve consuming oxygen or alternatively converting oxygen into the second messenger peroxide. Here, we use a ratiometric, peroxide reporter, HyPer to evaluate the role of peroxide in regulating HIF1α stability. We show that antioxidant enzymes are n either homeostatically induced nor are peroxide levels increased in hypoxia. Additionally, forced expression of diverse antioxidant enzymes, all of which diminish peroxide, had disparate effect...
Source: eLife - October 1, 2021 Category: Biomedical Science Tags: Cell Biology Neuroscience Source Type: research

microRNA-mediated regulation of microRNA machinery controls cell fate decisions
microRNAs associate with Argonaute proteins, forming the microRNA-induced silencing complex (miRISC), to repress target gene expression post-transcriptionally. Although microRNAs are critical regulators in mammalian cell differentiation, our understanding of how microRNA machinery, such as the miRISC, are regulated during development is still limited. We previously showed that repressing the production of one Argonaute protein, Ago2, by Trim71 is important for mouse embryonic stem cells (mESC) self-renewal (Liu et al., 2021). Here we show that among the four Argonaute proteins in mammals, Ago2 is the major developmentally ...
Source: eLife - October 1, 2021 Category: Biomedical Science Tags: Cell Biology Chromosomes and Gene Expression Source Type: research

Principles of mRNA targeting via the Arabidopsis m < sup > 6 < /sup > A-binding protein ECT2
Specific recognition ofN6-methyladenosine (m6A) in mRNA by RNA-binding proteins containing a YT521-B homology (YTH) domain is important in eukaryotic gene regulation. The Arabidopsis YTH-domain protein ECT2 is thought to bind to mRNA at URU(m6A)Y sites, yet RR(m6A)CH is the canonical m6A consensus site in all eukaryotes and ECT2 functions require m6A binding activity. Here, we apply iCLIP (individual-nucleotide resolution cross-linking and immunoprecipitation) and HyperTRIBE (targets of RNA-binding proteins identified by editing) to define high-quality target sets of ECT2, and analyze the patterns of enriched sequence moti...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Genetics and Genomics Plant Biology Source Type: research

Members of the ELMOD protein family specify formation of distinct aperture domains on the < i > Arabidopsis < /i > pollen surface
Pollen apertures, the characteristic gaps in pollen wall exine, have emerged as a model for studying the formation of distinct plasma membrane domains. In each species, aperture number, position, and morphology are typically fixed; across species they vary widely. During pollen development, certain plasma membrane domains attract specific proteins and lipids and become protected from exine deposition, developing into apertures. However, how these aperture domains are selected is unknown. Here, we demonstrate that patterns of aperture domains inArabidopsis are controlled by the members of the ancient ELMOD protein family, w...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Cell Biology Plant Biology Source Type: research

Mutational analysis to explore long-range allosteric couplings involved in a pentameric channel receptor pre-activation and activation
Pentameric ligand-gated ion channels (pLGICs) mediate chemical signaling through a succession of allosteric transitions that are yet not completely understood as intermediate states remain poorly characterized by structural approaches. In a previous study on the prototypic bacterial proton-gated channel GLIC, we generated several fluorescent sensors of the protein conformation that report a fast transition to a pre-active state, which precedes the slower process of activation with pore opening. Here, we explored the phenotype of a series of allosteric mutations, using paralleled steady-state fluorescence and electrophysiol...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Neuroscience Structural Biology and Molecular Biophysics Source Type: research

A MET-PTPRK kinase-phosphatase rheostat controls ZNRF3 and Wnt signalling
Zinc and ring finger 3 (ZNRF3) is a transmembrane E3 ubiquitin ligase that targets Wnt receptors for ubiquitination and lysosomal degradation. Previously we showed that dephosphorylation of an endocytic tyrosine motif (4Y motif) in ZNRF3 by protein tyrosine phosphatase receptor-type kappa (PTPRK) promotes ZNRF3 internalization and Wnt receptor degradation (Chang et al. 2020). However, a responsible protein tyrosine kinase(s) (PTK) phosphorylating the 4Y motif remained elusive. Here we identify the proto-oncogene MET (mesenchymal-epithelial transition factor) as a 4Y kinase. MET binds to ZNRF3 and induces 4Y phosphorylation...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Cell Biology Source Type: research

The YTHDF proteins ECT2 and ECT3 bind largely overlapping target sets and influence target mRNA abundance, not alternative polyadenylation
Gene regulation viaN6-methyladenosine (m6A) in mRNA involves RNA-binding proteins that recognize m6A via a YT521-B homology (YTH) domain. The plant YTH domain proteins ECT2 and ECT3 act genetically redundantly in stimulating cell proliferation during organogenesis, but several fundamental questions regarding their mode of action remain unclear. Here, we use HyperTRIBE (targets of RNA-binding proteins identified by editing) to show that most ECT2 and ECT3 targets overlap, with only few examples of preferential targeting by either of the two proteins. HyperTRIBE in different mutant backgrounds also provides direct views of r...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Genetics and Genomics Plant Biology Source Type: research

Structure of mycobacterial CIII < sub > 2 < /sub > CIV < sub > 2 < /sub > respiratory supercomplex bound to the tuberculosis drug candidate telacebec (Q203)
The imidazopyridine telacebec, also known as Q203, is one of only a few new classes of compounds in more than fifty years with demonstrated antituberculosis activity in humans. Telacebec inhibits the mycobacterial respiratory supercomplex composed of complexes III and IV (CIII2CIV2). In mycobacterial electron transport chains, CIII2CIV2 replaces canonical CIII and CIV, transferring electrons from the intermediate carrier menaquinol to the final acceptor, molecular oxygen, while simultaneously transferring protons across the inner membrane to power ATP synthesis. We show that telacebec inhibits the menaquinol:oxygen oxidore...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

Adaptation and compensation in a bacterial gene regulatory network evolving under antibiotic selection
In this study, we discover that the early evolutionary response ofEscherichia coli to the antibiotic trimethoprim involves derepression of PhoPQ signaling, an Mg2+-sensitive two-component system, by inactivation of the MgrB feedback-regulatory protein. We report that derepression of PhoPQ confers trimethoprim-tolerance toE. coli by hitherto unrecognized transcriptional upregulation of dihydrofolate reductase (DHFR), target of trimethoprim. As a result, mutations inmgrB precede and facilitate the evolution of drug resistance. Using laboratory evolution, genome sequencing, and mutation re-construction, we show that populatio...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Genetics and Genomics Microbiology and Infectious Disease Source Type: research

Localization of KRAS downstream target ARL4C to invasive pseudopods accelerates pancreatic cancer cell invasion
Pancreatic cancer has a high mortality rate due to metastasis. Whereas KRAS is mutated in most pancreatic cancer patients, controlling KRAS or its downstream effectors has not been succeeded clinically. ARL4C is a small G protein whose expression is induced by the Wnt and EGF-RAS pathways. In the present study, we found that ARL4C is frequently overexpressed in pancreatic cancer patients and showed that its localization to invasive pseudopods is required for cancer cell invasion. IQGAP1 was identified as a novel interacting protein for ARL4C. ARL4C recruited IQGAP1 and its downstream effector, MMP14, to invasive pseudopods...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Cancer Biology Cell Biology Source Type: research

Adult stem cells and niche cells segregate gradually from common precursors that build the adult Drosophila ovary during pupal development
Production of proliferative Follicle Cells (FCs) and quiescent Escort Cells (ECs) by Follicle Stem Cells (FSCs) in adult Drosophila ovaries is regulated by niche signals from anterior (Cap Cells, ECs) and posterior (polar FCs) sources. Here we show that ECs, FSCs and FCs develop from common pupal precursors, with different fates acquired by progressive separation of cells along the AP axis and a graded decline in anterior cell proliferation. ECs, FSCs and most FCs derive from Intermingled Cell (IC) precursors interspersed with germline cells. Precursors also accumulate posterior to ICs before engulfing a naked germline cys...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Developmental Biology Stem Cells and Regenerative Medicine Source Type: research

First-principles model of optimal translation factors stoichiometry
Enzymatic pathways have evolved uniquely preferred protein expression stoichiometry in living cells, but our ability to predict the optimal abundances from basic properties remains underdeveloped. Here we report a biophysical, first-principles model of growth optimization for core mRNA translation, a multi-enzyme system that involves proteins with a broadly conserved stoichiometry spanning two orders of magnitude. We show that predictions from maximization of ribosome usage in a parsimonious flux model constrained by proteome allocation agree with the conserved ratios of translation factors. The analytical solutions, witho...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Computational and Systems Biology Physics of Living Systems Source Type: research

The LRRK2 G2019S mutation alters astrocyte-to-neuron communication via extracellular vesicles and induces neuron atrophy in a human iPSC-derived model of Parkinson's disease
This study focuses on the effects of the PD-related mutation LRRK2 G2019S in astrocytes generated from patient-derived induced pluripotent stem cells. We report the alteration of extracellular vesicle (EV) biogenesis in astrocytes, and we identify the abnormal accumulation of key PD-related proteins within multi vesicular bodies (MVBs). We found that dopaminergic neurons internalize astrocyte-secreted EVs and that LRRK2 G2019S EVs are abnormally enriched in neurites and fail to provide full neurotrophic support to dopaminergic neurons. Thus, dysfunctional astrocyte-to-neuron communication via altered EV biological properti...
Source: eLife - September 30, 2021 Category: Biomedical Science Tags: Cell Biology Neuroscience Source Type: research

Competitive binding of MatP and topoisomerase IV to the MukB hinge domain
Structural Maintenance of Chromosomes (SMC) complexes have ubiquitous roles in compacting DNA linearly, thereby promoting chromosome organization-segregation. Interaction between theEscherichia coli SMC complex, MukBEF, andmatS-bound MatP in the chromosome replication termination region,ter, results in depletion of MukBEF fromter, a process essential for efficient daughter chromosome individualisation and for preferential association of MukBEF with the replication origin region. Chromosome-associated MukBEF complexes also interact with topoisomerase IV (ParC2E2), so that their chromosome distribution mirrors that of MukBEF...
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Chromosomes and Gene Expression Source Type: research

Lying in a 3T MRI scanner induces neglect-like spatial attention bias
The static magnetic field of MRI scanners can induce a magneto-hydrodynamic stimulation of the vestibular organ (MVS). In common fMRI settings, this MVS effect leads to a vestibular ocular reflex (VOR). We asked whether – beyond inducing a VOR – putting a healthy subject in a 3T MRI scanner would also alter goal-directed spatial behavior, as is known from other types of vestibular stimulation. We investigated 17 healthy volunteers, all of which exhibited a rightward VOR inside the MRI-scanner as compared to out side-MRI conditions. More importantly, when probing the distribution of overt spatial attention insid...
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Neuroscience Source Type: research

Autonomous clocks that regulate organelle biogenesis, cytoskeletal organization, and intracellular dynamics
How do cells perceive time? Do cells use temporal information to regulate the production/degradation of their enzymes, membranes, and organelles? Does controlling biological time influence cytoskeletal organization and cellular architecture in ways that confer evolutionary and physiological advantages? Potential answers to these fundamental questions of cell biology have historically revolved around the discussion of ‘master’ temporal programs, such as the principal cyclin-dependent kinase/cyclin cell division oscillator and the circadian clock. In this review, we provide an overview of the recent evidence supp...
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Cell Biology Physics of Living Systems Source Type: research

Exposure to landscape fire smoke reduced birthweight in low- and middle-income countries: findings from a siblings-matched case-control study
Landscape fire smoke (LFS) has been associated with reduced birthweight, but evidence from low- and middle-income countries (LMICs) is rare. Here, we present a sibling-matched case-control study of 227,948 newborns to identify an association between fire-sourced fine particulate matter (PM2.5) and birthweight in 54 LMICs from 2000 to 2014. We selected mothers from the geocoded Demographic and Health Survey with at least two children and valid birthweight records. Newborns affiliated with the same mother were defined as a family group. Gestational exposure to LFS was assessed in each newborn using the concentration of fire-...
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Epidemiology and Global Health Source Type: research

Predicting cancer risk based on family history
A new software package provides more accurate cancer risk prediction profiles and has the ability to integrate more genes and cancer types in the future. (Source: eLife)
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Cancer Biology Genetics and Genomics Source Type: research

3'HS1 CTCF binding site in human β-globin locus regulates fetal hemoglobin expression
Mutations in the adult β-globin gene can lead to a variety of hemoglobinopathies, including sickle cell disease and β-thalassemia. An increase in fetal hemoglobin expression throughout adulthood, a condition named Hereditary Persistence of Fetal Hemoglobin (HPFH), has been found to ameliorate hemoglobinopathies. Deletio nal HPFH occurs through the excision of a significant portion of the 3' end of the β-globin locus, including a CTCF binding site termed 3'HS1. Here, we show that the deletion of this CTCF site alone induces fetal hemoglobin expression in both adult CD34+ hematopoietic stem and progenitor cell...
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Chromosomes and Gene Expression Genetics and Genomics Source Type: research

Differentiation of mouse fetal lung alveolar progenitors in serum-free organotypic cultures
Lung epithelial progenitors differentiate into alveolar type 1 (AT1) and type 2 (AT2) cells. These cells form the air-blood interface and secrete surfactant, respectively, and are essential for lung maturation and function. Current protocols to derive and culture alveolar cells do not faithfully recapitulate the architecture of the distal lung, which influences cell fate patterns in vivo. Here, we report serum-free conditions that allow for growth and differentiation of mouse distal lung epithelial progenitors. We find that Collagen I promotes the differentiation of flattened, polarized AT1 cells. Using these organoids, we...
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Developmental Biology Source Type: research

mRNA vaccination in people over 80 years of age induces strong humoral immune responses against SARS-CoV-2 with cross neutralisation of P.1 Brazilian variant
Age is the major risk factor for mortality after SARS-CoV-2 infection and older people have received priority consideration for COVID-19 vaccination. However vaccine responses are often suboptimal in this age group and few people over the age of 80 years were included in vaccine registration trials. We determined the serological and cellular response to spike protein in 100 people aged 80-96 years at 2 weeks after second vaccination with the Pfizer BNT162b2 mRNA vaccine. Antibody responses were seen in every donor with high titres in 98%. Spike-specific cellular immune responses were detectable in only 63% and correlated w...
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Microbiology and Infectious Disease Source Type: research

Neural basis for regulation of vasopressin secretion by anticipated disturbances in osmolality
Water balance, tracked by extracellular osmolality, is regulated by feedback and feedforward mechanisms. Feedback regulation is reactive, occurring as deviations in osmolality aredetected. Feedforward or presystemic regulation is proactive, occurring when disturbances in osmolality areanticipated. Vasopressin (AVP) is a key hormone regulating water balance and is released during hyperosmolality to limit renal water excretion. AVP neurons are under feedback and feedforward regulation. Not only do they respond to disturbances in blood osmolality, but they are also rapidly suppressed and stimulated, respectively, by drinking ...
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Medicine Neuroscience Source Type: research

Phosphorylation of luminal region of the SUN-domain protein Mps3 promotes nuclear envelope localization during meiosis
During meiosis, protein ensembles in the nuclear envelope (NE) containing SUN- and KASH-domain proteins, called linker nucleocytoskeleton and cytoskeleton (LINC) complex, promote the chromosome motion. Yeast SUN-domain protein, Mps3, forms multiple meiosis-specific ensembles on NE, which show dynamic localisation for chromosome motion; however, the mechanism by which these Mps3 ensembles are formed during meiosis remains largely unknown. Here, we showed that the cyclin-dependent protein kinase (CDK) and Dbf4-dependent Cdc7 protein kinase (DDK) regulate meiosis-specific dynamics of Mps3 on NE, particularly by mediating the ...
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Chromosomes and Gene Expression Source Type: research

Profiling sensory neuron microenvironment after peripheral and central axon injury reveals key pathways for neural repair
This study provides a map of the distinct DRG mic roenvironment responses to peripheral and central injuries at the single-cell level and highlights that manipulating non-neuronal cells could lead to avenues to promote functional recovery after CNS injuries or disease. (Source: eLife)
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Neuroscience Source Type: research

< i > APOE4 < /i > is associated with elevated blood lipids and lower levels of innate immune biomarkers in a tropical Amerindian subsistence population
In post-industrial settings, apolipoproteinE4 (APOE4) is associated with increased cardiovascular and neurological disease risk. However, the majority of human evolutionary history occurred in environments with higher pathogenic diversity and low cardiovascular risk. We hypothesize that in high-pathogen and energy-limited contexts, theAPOE4 allele confers benefits by reducing innate inflammation when uninfected, while maintaining higher lipid levels that buffer costs of immune activation during infection. Among Tsimane forager-farmers of Bolivia (N = 1266, 50% female),APOE4 is associated with 30% lower C-reactive protein, ...
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Evolutionary Biology Medicine Source Type: research

Total parasite biomass but not peripheral parasitaemia is associated with endothelial and haematological perturbations in < i > Plasmodium vivax < /i > patients
In this study we investigate associations between both peripheral and total parasite biomass and host response in vivax malaria. We analysed parasite and host signatures in a cohort of uncomplicated vivax malaria patients from Manaus, Brazil, combining clinical and parasite parameters, multiplexed analysis of host responses andex vivo assays. Patterns of clinical features, parasite burden and host signatures measured in plasma across the patient cohort were highly heterogenous. Further data deconvolution revealed two patient clusters, here termed Vivaxlow and Vivaxhigh. These patient subgroups were defined based on differe...
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Microbiology and Infectious Disease Source Type: research

A morphological transformation in respiratory syncytial virus leads to enhanced complement deposition
The complement system is a critical host defense against infection, playing a protective role that can also enhance disease if dysregulated. Although many consequences of complement activation during viral infection are well established, mechanisms that determine the extent to which viruses activate complement remain elusive. Here, we investigate complement activation by human respiratory syncytial virus (RSV), a filamentous respiratory pathogen that causes significant morbidity and mortality. By engineering a strain of RSV harboring tags on the surface glycoproteins F and G, we are able to monitor opsonization of single R...
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Microbiology and Infectious Disease Physics of Living Systems Source Type: research

Pain or gain?
The 3D structures of a membrane protein called TMEM120A suggest that it may act as an enzyme in fat metabolism rather than as an ion channel that senses mechanical pain. (Source: eLife)
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Neuroscience Structural Biology and Molecular Biophysics Source Type: research

Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy
Removal of damaged organelles via the process of selective autophagy constitutes a major form of cellular quality control. Damaged organelles are recognized by a dedicated surveillance machinery, leading to the assembly of an autophagosome around the damaged organelle, prior to fusion with the degradative lysosomal compartment. Lysosomes themselves are also prone to damage and are degraded through the process of lysophagy. While early steps involve recognition of ruptured lysosomal membranes by glycan-binding Galectins and ubiquitylation of transmembrane lysosomal proteins, many steps in the process, and their inter-relati...
Source: eLife - September 29, 2021 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Cell Biology Source Type: research

History of winning and hierarchy landscape influence stress susceptibility in mice
Social hierarchy formation is strongly evolutionarily conserved. Across species, rank within social hierarchy has large effects on health and behavior. To investigate the relationship between social rank and stress susceptibility, we exposed ranked male and female mice to social and non-social stressors and manipulated social hierarchy position. We found that rank predicts same sex social stress outcomes: dominance in males and females confers resilience while subordination confers susceptibility. Pre-existing rank does not predict non-social stress outcomes in females and weakly does so in males, but rank emerging under s...
Source: eLife - September 28, 2021 Category: Biomedical Science Tags: Neuroscience Source Type: research

Dietary nitrate supplementation prevents radiotherapy-induced xerostomia
Management of salivary gland hypofunction caused by irradiation (IR) therapy for head and neck cancer remains lack of effective treatments. Salivary glands, especially the parotid gland, actively uptake dietary nitrate and secrete it into saliva. Here, we investigated the effect of dietary nitrate on the prevention and treatment of IR-induced parotid gland hypofunction in miniature pigs, and elucidated the underlying mechanism in human parotid gland cells (hPGCs). We found that nitrate administration prevented IR-induced parotid gland damage in a dose-dependent manner, by maintaining the function of irradiated parotid glan...
Source: eLife - September 28, 2021 Category: Biomedical Science Tags: Cell Biology Source Type: research

Mutation analysis links angioimmunoblastic T-cell lymphoma to clonal hematopoiesis and smoking
(Source: eLife)
Source: eLife - September 28, 2021 Category: Biomedical Science Tags: Cancer Biology Medicine Source Type: research

Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants
High-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission. While single-nucleotide variations (SNVs) are commonly considered as driving virus adaption, RNA recombination events that delete or insert nucleic acid sequences are also critical. Whole genome targeting sequencing of SARS-CoV-2 is typically achieved using pairs of primers to generate cDNA amplicons suitable for next-generation sequencing (NGS). However, paired-primer approaches impose constraints on where primers can be designed, how many amplicons are synthesized and ...
Source: eLife - September 28, 2021 Category: Biomedical Science Tags: Genetics and Genomics Microbiology and Infectious Disease Source Type: research

Mechanically transduced immunosorbent assay to measure protein-protein interactions
Measuring protein-protein interaction (PPI) affinities is fundamental to biochemistry. Yet, conventional methods rely upon the law of mass action and cannot measure many PPIs due to a scarcity of reagents and limitations in the measurable affinity ranges. Here, we present a novel technique that leverages the fundamental concept of friction to produce a mechanical signal that correlates to binding potential. The mechanically transduced immunosorbent (METRIS) assay utilizes rolling magnetic probes to measure PPI interaction affinities. METRIS measures the translational displacement of protein-coated particles on a protein-fu...
Source: eLife - September 28, 2021 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Physics of Living Systems Source Type: research

Age-dependent changes in protein incorporation into collagen-rich tissues of mice by in vivo pulsed SILAC labelling
We report dynamic turnover of the matrisome, the proteins of the extracellular matrix, in bone and cartilage during skeletal maturation, which was markedly reduced after skeletal maturity. Comparing young adult with older adult mice, new protein incorporation was reduced in all tissues. STRING clustering revealed changes in epigenetic modulators across all tissues, a decline in chondroprotective growth factors such as FGF2 and TGF β in cartilage, and clusters indicating mitochondrial dysregulation and reduced collagen synthesis in bone. Several pathways were implicated in age-related disease. Fewer changes were observ...
Source: eLife - September 28, 2021 Category: Biomedical Science Tags: Cell Biology Source Type: research

An open label randomized controlled trial of tamoxifen combined with amphotericin B and fluconazole for cryptococcal meningitis
Background: Cryptococcal meningitis has high mortality. Flucytosine is a key treatment but is expensive and rarely available. The anti-cancer agent tamoxifen has synergistic anti-cryptococcal activity with amphotericin in vitro. It is off-patent, cheap, and widely available. We performed a trial to determine its therapeutic potential. (Source: eLife)
Source: eLife - September 28, 2021 Category: Biomedical Science Tags: Medicine Microbiology and Infectious Disease Source Type: research

Deep evolutionary origin of gamete-directed zygote activation by KNOX/BELL transcription factors in green plants
KNOX and BELL transcription factors regulate distinct steps of diploid development in plants. In the green algaChlamydomonas reinhardtii, KNOX and BELL proteins are inherited by gametes of the opposite mating types and heterodimerize in zygotes to activate diploid development. By contrast, in land plants such asPhyscomitrium patens andArabidopsis thaliana, KNOX and BELL proteins function in meristem maintenance and organogenesis during the later stages of diploid development. However, whether the contrasting functions of KNOX and BELL were acquired independently in algae and land plants is currently unknown. Here, we show ...
Source: eLife - September 28, 2021 Category: Biomedical Science Tags: Developmental Biology Evolutionary Biology Source Type: research

PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans
Many software solutions are available for proteomics and glycomics studies, but none are ideal for the structural analysis of peptidoglycan (PG), the essential and major component of bacterial cell envelopes. It icomprises glycan chains and peptide stems, both containing unusual amino acids and sugars. This has forced the field to rely on manual analysis approaches, which are time-consuming, labour-intensive, and prone to error. The lack of automated tools has hampered the ability to perform high-throughput analyses and prevented the adoption of a standard methodology. Here, we describe a novel tool called PGFinder for the...
Source: eLife - September 28, 2021 Category: Biomedical Science Tags: Microbiology and Infectious Disease Source Type: research

A state space modeling approach to real-time phase estimation
Brain rhythms have been proposed to facilitate brain function, with an especially important role attributed to the phase of low frequency rhythms. Understanding the role of phase in neural function requires interventions that perturb neural activity at a target phase, necessitating estimation of phase in real-time. Current methods for real-time phase estimation rely on bandpass filtering, which assumes narrowband signals and couples the signal and noise in the phase estimate, adding noise to the phase and impairing detections of relationships between phase and behavior. To address this, we propose a state space phase estim...
Source: eLife - September 27, 2021 Category: Biomedical Science Tags: Neuroscience Source Type: research

Phase response analyses support a relaxation oscillator model of locomotor rhythm generation in < i > Caenorhabditis elegans < /i >
Neural circuits coordinate with muscles and sensory feedback to generate motor behaviors appropriate to an animal ’s environment. InC. elegans,the mechanisms by which the motor circuit generates undulations and modulates them based on the environment are largely unclear. We quantitatively analyzedC. eleganslocomotion during free movement and during transient optogenetic muscle inhibition. Undulatory movements were highly asymmetrical with respect to the duration of bending and unbending during each cycle. Phase response curves induced by brief optogenetic inhibition of head muscles showed gradual increases and rapid ...
Source: eLife - September 27, 2021 Category: Biomedical Science Tags: Computational and Systems Biology Neuroscience Source Type: research

Single-molecule imaging reveals the concerted release of myosin from regulated thin filaments
Regulated thin filaments (RTFs) tightly control striated muscle contraction through calcium binding to troponin, which enables tropomyosin to expose myosin-binding sites on actin. Myosin binding holds tropomyosin in an open position, exposing more myosin-binding sites on actin, leading to cooperative activation. At lower calcium levels, troponin and tropomyosin turn off the thin filament; however, this is antagonised by the high local concentration of myosin, questioning how the thin filament relaxes. To provide molecular details of deactivation, we used single-molecule imaging of green fluorescent protein (GFP)-tagged myo...
Source: eLife - September 27, 2021 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Structural Biology and Molecular Biophysics Source Type: research

Conformational changes in twitchin kinase in vivo revealed by FRET imaging of freely moving < i > C. elegans < /i >
The force-induced unfolding and refolding of proteins is speculated to be a key mechanism in the sensing and transduction of mechanical signals in the living cell. Yet, little evidence has been gathered for its existencein vivo. Prominently, stretch-induced unfolding is postulated to be the activation mechanism of the twitchin/titin family of autoinhibited sarcomeric kinases linked to the mechanical stress response of muscle. To test the occurrence of mechanical kinase activation in living working muscle, we generated transgenicC. elegans expressing twitchin containing FRET moieties flanking the kinase domain and developed...
Source: eLife - September 27, 2021 Category: Biomedical Science Tags: Physics of Living Systems Structural Biology and Molecular Biophysics Source Type: research

Quantifying the relationship between SARS-CoV-2 viral load and infectiousness
The relationship between SARS-CoV-2 viral load and infectiousness is poorly known. Using data from a cohort of cases and high-risk contacts, we reconstructed viral load at the time of contact and inferred the probability of infection. The effect of viral load was larger in household contacts than in non-household contacts, with a transmission probability as large as 48% when the viral load was greater than 1010 copies per mL. The transmission probability peaked at symptom onset, with a mean probability of transmission of 29%, with large individual variations. The model also projects the effects of variants on disease trans...
Source: eLife - September 27, 2021 Category: Biomedical Science Tags: Microbiology and Infectious Disease Source Type: research

A parameter-free statistical test for neuronal responsiveness
Neurophysiological studies depend on a reliable quantification of whether and when a neuron responds to stimulation. Simple methods to determine responsiveness require arbitrary parameter choices, such as binning size, while more advanced model-based methods require fitting and hyperparameter tuning. These parameter choices can change the results, which invites bad statistical practice and reduces the replicability. New recording techniques that yield increasingly large numbers of cells would benefit from a test for cell-inclusion that requires no manual curation. Here, we present the parameter-free ZETA-test, which outper...
Source: eLife - September 27, 2021 Category: Biomedical Science Tags: Neuroscience Source Type: research

Characterization and prediction of clinical pathways of vulnerability to psychosis through graph signal processing
Causal interactions between specific psychiatric symptoms could contribute to the heterogenous clinical trajectories observed in early psychopathology. Current diagnostic approaches merge clinical manifestations that co-occur across subjects and could significantly hinder our understanding of clinical pathways connecting individual symptoms. Network analysis techniques have emerged as alternative approaches that could help shed light on the complex dynamics of early psychopathology. The present study attempts to address the two main limitations that have in our opinion hindered the application of network approaches in the ...
Source: eLife - September 27, 2021 Category: Biomedical Science Tags: Medicine Source Type: research

TRPM7 is critical for short-term synaptic depression by regulating synaptic vesicle endocytosis
TRPM7 contributes to a variety of physiological and pathological processes in many tissues and cells. With a widespread distribution in the nervous system, TRPM7 is involved in animal behaviors and neuronal death induced by ischemia. However, the physiological role of TRPM7 in CNS neuron remains unclear. Here, we identify endocytic defects in neuroendocrine cells and neurons from TRPM7 knockout (KO) mice, indicating a role of TRPM7 in synaptic vesicle endocytosis. Our experiments further pinpoint the importance of TRPM7 as an ion channel in synaptic vesicle endocytosis. Ca2+ imaging detects a defect in presynaptic Ca2+ dyn...
Source: eLife - September 27, 2021 Category: Biomedical Science Tags: Cell Biology Neuroscience Source Type: research

Convergent and divergent brain structural and functional abnormalities associated with developmental dyslexia
Brain abnormalities in the reading network have been repeatedly reported in individuals with developmental dyslexia (DD); however, it is still not totally understood where the structural and functional abnormalities are consistent/inconsistent across languages. In the current multimodal meta-analysis, we found convergent structural and functional alterations in the left superior temporal gyrus across languages, suggesting a neural signature of DD. We found greater reduction in grey matter volume and brain activation in the left inferior frontal gyrus in morpho-syllabic languages (e.g. Chinese) than in alphabetic languages,...
Source: eLife - September 27, 2021 Category: Biomedical Science Tags: Neuroscience Source Type: research