The many facets of brain aging
Applying big-data analytic techniques to brain images from 18,707 individuals is shedding light on the influence of aging on the brain. (Source: eLife)
Source: eLife - April 16, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Correction: Blockade of the LRP16-PKR-NF- κB signaling axis sensitizes colorectal carcinoma cells to DNA-damaging cytotoxic therapy
(Source: eLife)
Source: eLife - April 16, 2020 Category: Biomedical Science Tags: Cancer Biology Cell Biology Source Type: research

Charting the native architecture of < i > Chlamydomonas < /i > thylakoid membranes with single-molecule precision
Thylakoid membranes scaffold an assortment of large protein complexes that work together to harness the energy of light. It has been a longstanding challenge to visualize how the intricate thylakoid network organizes these protein complexes to finely tune the photosynthetic reactions. Previously, we used in situ cryo-electron tomography to reveal the native architecture of thylakoid membranes (Engel et al., 2015). Here, we leverage technical advances to resolve the individual protein complexes within these membranes. Combined with a new method to visualize membrane surface topology, we map the molecular landscapes of thyla...
Source: eLife - April 16, 2020 Category: Biomedical Science Tags: Plant Biology Structural Biology and Molecular Biophysics Source Type: research

RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia
In hypoxic stress conditions, glycolysis enzymes assemble into singular cytoplasmic granules called glycolytic (G) bodies. G body formation in yeast correlates with increased glucose consumption and cell survival. However, the physical properties and organizing principles that define G body formation are unclear. We demonstrate that glycolysis enzymes are non-canonical RNA binding proteins, sharing many common mRNA substrates that are also integral constituents of G bodies. Targeting nonspecific endoribonucleases to G bodies reveals that RNA nucleates G body formation and maintains its structural integrity. Consistent with...
Source: eLife - April 16, 2020 Category: Biomedical Science Tags: Cell Biology Source Type: research

Telomere dysfunction cooperates with epigenetic alterations to impair murine embryonic stem cell fate commitment
The precise relationship between epigenetic perturbations and telomere dysfunction is an extant question. Previously, we showed that telomere dysfunction leads to differentiation instability in murine embryonic stem cells (mESCs) via perturbations in DNA methylation at pluripotency-factor promoters. Here, we uncovered that telomerase reverse transcriptase null (Tert-/-) mESCs exhibit genome-wide perturbations in chromatin accessibility and gene expression during differentiation. These changes were accompanied by an increase of H3K27me3 globally, an altered chromatin landscape at thePou5f1/Oct4pluripotency gene promoter, an...
Source: eLife - April 16, 2020 Category: Biomedical Science Tags: Chromosomes and Gene Expression Source Type: research

Enhancer architecture sensitizes cell-specific responses to < i > Notch < /i > gene dose via a bind and discard mechanism
Notch pathway haploinsufficiency can cause severe developmental syndromes with highly variable penetrance. Currently, we have a limited mechanistic understanding of phenotype variability due to gene dosage. Here, we unexpectedly found that inserting an enhancer containing pioneer transcription factor sites coupled to Notch dimer sites can induce a subset ofNotch haploinsufficiency phenotypes inDrosophila with wild typeNotch gene dose. UsingDrosophila genetics, we show that this enhancer induces Notch phenotypes in a Cdk8-dependent, transcription-independent manner. We further combined mathematical modeling with quantitativ...
Source: eLife - April 16, 2020 Category: Biomedical Science Tags: Developmental Biology Source Type: research

The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression program to control neurite outgrowth
The mitotic deacetylase complex (MiDAC) is a recently identified histone deacetylase (HDAC) complex. While other HDAC complexes have been implicated in neurogenesis, the physiological role of MiDAC remains unknown. Here, we show that MiDAC constitutes an important regulator of neural differentiation. We demonstrate that MiDAC functions as a modulator of a neurodevelopmental gene expression program and binds to important regulators of neurite outgrowth. MiDAC upregulates gene expression of pro-neural genes such as those encoding the secreted ligands SLIT3 and NETRIN1 (NTN1) by a mechanism suggestive of H4K20ac removal on pr...
Source: eLife - April 16, 2020 Category: Biomedical Science Tags: Chromosomes and Gene Expression Source Type: research

Single-molecule observation of ATP-independent SSB displacement by RecO in < i > Deinococcus radiodurans < /i >
Deinococcus radiodurans (DR) survives in the presence of hundreds of double-stranded DNA (dsDNA) breaks by efficiently repairing such breaks. RecO, an essential protein for the extreme radioresistance of DR, is one of the major recombination mediator proteins in the RecA-loading process in the RecFOR pathway. However, how RecO participates in the RecA-loading process is still unclear. In this work, we investigated the function of drRecO using single-molecule techniques. We found that drRecO competes with the ssDNA binding protein (drSSB) for binding to the freely exposed ssDNA and efficiently displaces drSSB from ssDNA wit...
Source: eLife - April 16, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

A molecular view on the escape of lipoplexed DNA from the endosome
The use of non-viral vectors forin vivo gene therapy could drastically increase safety, whilst reducing the cost of preparing the vectors. A promising approach to non-viral vectors makes use of DNA/cationic liposome complexes (lipoplexes) to deliver the genetic material. Here we use coarse-grained molecular dynamics simulations to investigate the molecular mechanism underlying efficient DNA transfer from lipoplexes. Our computational fusion experiments of lipoplexes with endosomal membrane models show two distinct modes of transfection: parallel and perpendicular. In the parallel fusion pathway, DNA aligns with the membran...
Source: eLife - April 16, 2020 Category: Biomedical Science Tags: Computational and Systems Biology Source Type: research

Limited Dishevelled/Axin oligomerization determines efficiency of Wnt/ β-catenin signal transduction
In Wnt/ β-catenin signaling, the transcriptional coactivator β-catenin is regulated by its phosphorylation in a complex that includes the scaffold protein Axin and associated kinases. Wnt binding to its coreceptors activates the cytosolic effector Dishevelled (Dvl), leading to the recruitment of Axin and the inhibition of β-catenin phosphorylation. This process requires interaction of homologous DIX domains present in Dvl and Axin, but is mechanistically undefined. We show that Dvl DIX forms antiparallel, double-stranded oligomersin vitro, and that Dvl in cells forms oligomers typically
Source: eLife - April 16, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

Stretching the skin immediately enhances perceived stiffness and gradually enhances the predictive control of grip force
When manipulating objects, we use kinesthetic and tactile information to form an internal representation of their mechanical properties for cognitive perception and for preventing their slippage using predictive control of grip force. A major challenge in understanding the dissociable contributions of tactile and kinesthetic information to perception and action is the natural coupling between them. Unlike previous studies that addressed this question by focusing on impaired sensory processing in patients or via local anesthesia, we used a behavioral study with a programmable mechatronic device that stretches the skin of th...
Source: eLife - April 15, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Cortical anchoring of the microtubule cytoskeleton is essential for neuron polarity
The development of a polarized neuron relies on the selective transport of proteins to axons and dendrites. Although it is well known that the microtubule cytoskeleton has a central role in establishing neuronal polarity, how its specific organization is established and maintained is poorly understood. Using the in vivo model systemCaenorhabditis elegans, we found that the highly conserved UNC-119 protein provides a link between the membrane-associated Ankyrin (UNC-44) and the microtubule-associated CRMP (UNC-33). Together they form a periodic membrane-associated complex that anchors axonal and dendritic microtubule bundle...
Source: eLife - April 15, 2020 Category: Biomedical Science Tags: Cell Biology Neuroscience Source Type: research

Antagonism of PP2A is an independent and conserved function of HIV-1 Vif and causes cell cycle arrest
The seminal description of the cellular restriction factor APOBEC3G and its antagonism by HIV-1 Vif has underpinned two decades of research on the host-virus interaction. We recently reported that HIV-1 Vif is also able to degrade the PPP2R5 family of regulatory subunits of key cellular phosphatase PP2A (PPP2R5A-E; Greenwood et al., 2016; Naamati et al., 2019). We now identify amino acid polymorphisms at positions 31 and 128 of HIV-1 Vif which selectively regulate the degradation of PPP2R5 family proteins. These residues covary across HIV-1 virusesin vivo, favouring depletion of PPP2R5A-E. Through analysis of point mutants...
Source: eLife - April 15, 2020 Category: Biomedical Science Tags: Microbiology and Infectious Disease Source Type: research

Determinants of MDA impact and designing MDAs towards malaria elimination
Malaria remains at the forefront of scientific research and global political and funding agendas. Malaria models have consistently oversimplified how mass interventions are implemented. Here, we present an individual based, spatially explicit model ofP. falciparum malaria transmission that includes all the programmatic implementation details of mass drug administration (MDA) campaigns. We uncover how the impact of MDA campaigns is determined by the interaction between implementation logistics, patterns of human mobility and how transmission risk is distributed over space. Our results indicate that malaria elimination is on...
Source: eLife - April 15, 2020 Category: Biomedical Science Tags: Epidemiology and Global Health Source Type: research

The metalloproteinase Papp-aa controls epithelial cell quiescence-proliferation transition
Human patients carryingPAPP‐A2 inactivating mutations have low bone mineral density. The underlying mechanisms for this reduced calcification are poorly understood. Using a zebrafish model, we report that Papp-aa regulates bone calcification by promoting Ca2+-transporting epithelial cell (ionocyte) quiescence-proliferation transition. Ionocytes, which are normally quiescent, re-enter the cell cycle under low [Ca2+] stress. Genetic deletion of Papp-aa, but not the closely related Papp-ab, abolished ionocyte proliferation and reduced calcified bone mass. Loss of Papp-aa expression or activity resulted in diminished IGF1 re...
Source: eLife - April 15, 2020 Category: Biomedical Science Tags: Developmental Biology Source Type: research

Linking mitochondria to the immune response
A gene associated with Parkinson ’s disease regulates mitochondrial homeostasis, thus affecting innate immunity. (Source: eLife)
Source: eLife - April 15, 2020 Category: Biomedical Science Tags: Immunology and Inflammation Microbiology and Infectious Disease Source Type: research

STK25 suppresses Hippo signaling by regulating SAV1-STRIPAK antagonism
The MST-LATS kinase cascade is central to the Hippo pathway that controls tissue homeostasis, development, and organ size. The PP2A complex STRIPAKSLMAP blocks MST1/2 activation. The GCKIII family kinases associate with STRIPAK, but the functions of these phosphatase-associated kinases remain elusive. We previously showed that the scaffolding protein SAV1 promotes Hippo signaling by counteracting STRIPAK (Bae et al. 2017). Here, we show that the GCKIII kinase STK25 promotes STRIPAK-mediated inhibition of MST2 in human cells. Depletion of STK25 enhances MST2 activation without affecting the integrity of STRIPAKSLMAP. STK25 ...
Source: eLife - April 15, 2020 Category: Biomedical Science Tags: Cell Biology Source Type: research

Reinforcement biases subsequent perceptual decisions when confidence is low: a widespread behavioral phenomenon
Learning from successes and failures often improves the quality of subsequent decisions. Past outcomes, however, should not influence purely perceptual decisions after task acquisition is complete since these are designed so that only sensory evidence determines the correct choice. Yet, numerous studies report that outcomes can bias perceptual decisions, causing spurious changes in choice behavior without improving accuracy. Here we show that the effects of reward on perceptual decisions are principled: past rewards bias future choices specifically when previous choice was difficult and hence decision confidence was low. W...
Source: eLife - April 14, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Cryo-EM structure of the potassium-chloride cotransporter KCC4 in lipid nanodiscs
Cation-chloride-cotransporters (CCCs) catalyze transport of Cl- with K+ and/or Na+ across cellular membranes. CCCs play roles in cellular volume regulation, neural development and function, audition, regulation of blood pressure, and renal function. CCCs are targets of clinically important drugs including loop diuretics and their disruption has been implicated in pathophysiology including epilepsy, hearing loss, and the genetic disorders Andermann, Gitelman, and Bartter syndromes. Here we present the structure of a CCC, theMus musculus K+-Cl- cotransporter (KCC) KCC4, in lipid nanodiscs determined by cryo-EM. The structure...
Source: eLife - April 14, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

The natverse, a versatile toolbox for combining and analysing neuroanatomical data
To analyse neuron data at scale, neuroscientists expend substantial effort reading documentation, installing dependencies and moving between analysis and visualisation environments. To facilitate this, we have developed a suite of interoperable open-source R packages called the natverse. The natverse allows users to read local and remote data, perform popular analyses including visualisation and clustering and graph-theoretic analysis of neuronal branching. Unlike most tools, the natverse enables comparison across many neurons of morphology and connectivity after imaging or co-registration within a common template space. T...
Source: eLife - April 14, 2020 Category: Biomedical Science Tags: Computational and Systems Biology Neuroscience Source Type: research

Kin discrimination in social yeast is mediated by cell surface receptors of the Flo11 adhesin family
Microorganisms have evolved specific cell surface molecules that enable discrimination between cells from the same and from a different kind. Here, we investigate the role of Flo11-type cell surface adhesins from social yeasts in kin discrimination. We measure the adhesion forces mediated by Flo11A-type domains using single-cell force spectroscopy, quantify Flo11A-based cell aggregation in populations and determine the Flo11A-dependent segregation of competing yeast strains in biofilms. We find that Flo11A domains from diverse yeast species confer remarkably strong adhesion forces by establishing homotypic interactions bet...
Source: eLife - April 14, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

Chloride channels regulate differentiation and barrier functions of the mammalian airway
In this study, we systematically characterized the developmental landscape of the mouse airway using single-cell RNA sequencing and identified remarkably conserved cellular programs operating during human fetal development. We demonstrated that in mouse, genetic inactivation of chloride channelAno1/Tmem16acompromises airway barrier function, results in early signs of inflammation, and alters the airway cellular landscape by depleting epithelial progenitors. MouseAno1-/- mutants exhibited mucus obstruction and abnormal mucociliary clearance that resemble the airway defects associated with cystic fibrosis. The data reveal cr...
Source: eLife - April 14, 2020 Category: Biomedical Science Tags: Developmental Biology Source Type: research

Confidence-guided updating of choice bias during perceptual decisions is a widespread behavioral phenomenon
We report a novel form of reinforcement learning during perceptual decisions: past rewards bias future perceptual choices specifically when the previous stimulus was difficult to judge , and the confidence in obtaining the reward was low. We identified this phenomenon in six datasets from four laboratories, across mice, rats and humans, and sensory modalities from olfaction and audition to vision. We show that reinforcement learning models incorporating decision confidence into th eir teaching signal explain this choice updating. Thus, reinforcement learning mechanisms are continually engaged to produce systematic adjustme...
Source: eLife - April 14, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate
Taking control of the cellular apparatus for protein production is a requirement for virus progression. To ensure this control, diverse strategies of cellular mimicry and/or ribosome hijacking evolved. The initiation stage of translation is specially targeted as it involves multiple steps and the engagement of numerous initiation factors. The use of structured RNA sequences, calledInternalRibosomalEntrySites (IRES) in viral RNAs is a widespread strategy for the exploitation of eukaryotic initiation. Using a combination of electron cryo-microscopy (cryo-EM) and reconstituted translation initiation assays with native compone...
Source: eLife - April 14, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

The sifting of visual information in the superior colliculus
Much of the early visual system is devoted to sifting the visual scene for the few bits of behaviorally relevant information. In the visual cortex of mammals a hierarchical system of brain areas leads eventually to the selective encoding of important features, like faces and objects. Here we report that a similar process occurs in the other major visual pathway, the superior colliculus. We investigate the visual response properties of collicular neurons in the awake mouse with large-scale electrophysiology. Compared to the superficial collicular layers, neuronal responses in the deeper layers become more selective for beha...
Source: eLife - April 14, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment
Bone marrow mesenchymal lineage cells are a heterogeneous cell population involved in bone homeostasis and diseases such as osteoporosis. While it is long postulated that they originate from mesenchymal stem cells, the true identity of progenitors and their in vivo bifurcated differentiation routes into osteoblasts and adipocytes remain poorly understood. Here, by employing large scale single cell transcriptome analysis, we computationally defined mesenchymal progenitors at different stages and delineated their bi-lineage differentiation paths in young, adult and aging mice. One identified subpopulation is a unique cell ty...
Source: eLife - April 14, 2020 Category: Biomedical Science Tags: Cell Biology Source Type: research

Cryo-EM structure < i > in situ < /i > reveals a molecular switch that safeguards virus against genome loss
The portal protein is a key component of many double-stranded DNA viruses, governing capsid assembly and genome packaging. Twelve subunits of the portal protein define a tunnel, through which DNA is translocated into the capsid. It is unknown how the portal protein functions as a gatekeeper, preventing DNA slippage, whilst allowing its passage into the capsid, and how these processes are controlled. A cryo-EM structure of the portal protein of thermostable virus P23-45, determinedin situin its procapsid-bound state, indicates a mechanism that naturally safeguards the virus against genome loss. This occurs via an inversion ...
Source: eLife - April 14, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital
Multidrug-resistant bacteria pose a serious health threat, especially in hospitals. Horizontal gene transfer (HGT) of mobile genetic elements (MGEs) facilitates the spread of antibiotic resistance, virulence, and environmental persistence genes between nosocomial pathogens. We screened the genomes of 2173 bacterial isolates from healthcare-associated infections from a single hospital over 18 months, and identified identical nucleotide regions in bacteria belonging to distinct genera. To further resolve these shared sequences, we performed long-read sequencing on a subset of isolates and generated highly contiguous genomes....
Source: eLife - April 14, 2020 Category: Biomedical Science Tags: Epidemiology and Global Health Microbiology and Infectious Disease Source Type: research

Retromer subunit, VPS29, regulates synaptic transmission and is required for endolysosomal function in the aging brain
Retromer, including Vps35, Vps26, and Vps29, is a protein complex responsible for recycling proteins within the endolysosomal pathway. Although implicated in both Parkinson's and Alzheimer's disease, our understanding of retromer function in the adult brain remains limited, in part becauseVps35andVps26are essential for development. InDrosophila, we find thatVps29 is dispensable for embryogenesis but required for retromer function in aging adults, including for synaptic transmission, survival, and locomotion. Unexpectedly, inVps29mutants, Vps35 and Vps26 proteins are normally expressed and associated, but retromer is misloc...
Source: eLife - April 14, 2020 Category: Biomedical Science Tags: Cell Biology Neuroscience Source Type: research

Cre-assisted fine-mapping of neural circuits using orthogonal split inteins
Existing genetic methods of neuronal targeting do not routinely achieve the resolution required for mapping brain circuits. New approaches are thus necessary. Here, we introduce a method for refined neuronal targeting that can be applied iteratively. Restriction achieved at the first step can be further refined in a second step, if necessary. The method relies on first isolating neurons within a targeted group (i.e. Gal4 pattern) according to their developmental lineages, and then intersectionally limiting the number of lineages by selecting only those in which two distinct neuroblast enhancers are active. The neuroblast e...
Source: eLife - April 14, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

CNGA3 acts as a cold sensor in hypothalamic neurons
We report that, in comparison to squirrels, mice have a larger proportion of cold-sensitive neurons in the POA. We further show that mouse cold-sensitive neurons express the cyclic nucleotide-gated ion channel CNGA3, and that mouse, but not squirrel, CNGA3 is potentiated by cold. Our data reveal CNGA3 as a hypothalamic cold sensor and a molecular marker to interrogate the neuronal circuitry underlying thermoregulation. (Source: eLife)
Source: eLife - April 9, 2020 Category: Biomedical Science Tags: Evolutionary Biology Neuroscience Source Type: research

Differential expression of MAGEA6 toggles autophagy to promote pancreatic cancer progression
The melanoma-associated antigen family A (MAGEA) antigens are expressed in a wide variety of malignant tumors but not in adult somatic cells, rendering them attractive targets for cancer immunotherapy. Here we show that a number of cancer-associated MAGEA mutants that undergo proteasome-dependent degradationin vitro could negatively impact their utility as immunotherapeutic targets. Importantly, in pancreatic ductal adenocarcinoma cell models, MAGEA6 suppresses macroautophagy (autophagy). The inhibition of autophagy is released upon MAGEA6 degradation, which can be induced by nutrient deficiency or by acquisition of cancer...
Source: eLife - April 9, 2020 Category: Biomedical Science Tags: Cancer Biology Genetics and Genomics Source Type: research

Cooperative enzymatic control of N-acyl amino acids by PM20D1 and FAAH
The N-acyl amino acids are a family of bioactive lipids with pleiotropic physiologic functions, including in energy homeostasis. Their endogenous levels are regulated by an extracellular mammalian N-acyl amino acid synthase/hydrolase called PM20D1 (peptidase M20 domain containing 1). Using an activity-guided biochemical approach, we report the molecular identification of fatty acid amide hydrolase (FAAH) as a second intracellular N-acyl amino acid synthase/hydrolase. In vitro, FAAH exhibits a more restricted substrate scope compared to PM20D1. In mice, genetic ablation or selective pharmacological inhibition of FAAH bidire...
Source: eLife - April 9, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Source Type: research

High-phytate/low-calcium diet is a risk factor for crystal nephropathies, renal phosphate wasting, and bone loss
Phosphate overload contributes to mineral bone disorders that are associated with crystal nephropathies. Phytate, the major form of phosphorus in plant seeds, is known as an indigestible and of negligible nutritional value in humans. However, the mechanism and adverse effects of high-phytate intake on Ca2+ and phosphate absorption and homeostasis are unknown. Here, we show that excessive intake of phytate along with a low-Ca2+ diet fed to rats contributed to the development of crystal nephropathies, renal phosphate wasting, and bone loss through tubular dysfunction secondary to dysregulation of intestinal calcium and phosp...
Source: eLife - April 9, 2020 Category: Biomedical Science Tags: Human Biology and Medicine Source Type: research

The social life of Norway rats ( < i > Rattus norvegicus < /i > )
The Norway rat has important impacts on our life. They are amongst the most used research subjects, resulting in ground-breaking advances. At the same time, wild rats live in close association with us, leading to various adverse interactions. In face of this relevance, it is surprising how little is known about their natural behaviour. While recent laboratory studies revealed their complex social skills, little is known about their social behaviour in the wild. An integration of these different scientific approaches is crucial to understand their social life, which will enable us to design more valid research paradigms, de...
Source: eLife - April 9, 2020 Category: Biomedical Science Tags: Ecology Neuroscience Source Type: research

The axonal actin-spectrin lattice acts as a tension buffering shock absorber
Axons span extreme distances and are subjected to significant stretch deformations during limb movements or sudden head movements, especially during impacts. Yet, axon biomechanics, and its relation to the ultrastructure that allows axons to withstand mechanical stress, is poorly understood. Using a custom developed force apparatus, we demonstrate that chick dorsal root ganglion axons exhibit a tension buffering or strain-softening response, where its steady state elastic modulus decreases with increasing strain. We then explore the contributions from the various cytoskeletal components of the axon to show that the recentl...
Source: eLife - April 8, 2020 Category: Biomedical Science Tags: Physics of Living Systems Source Type: research

Structural basis for ion selectivity in TMEM175 K < sup > + < /sup > channels
The TMEM175 family constitutes recently discovered K+ channels that are important for autophagosome turnover and lysosomal pH regulation and are associated with the early onset of Parkinson Disease. TMEM175 channels lack a P-loop selectivity filter, a hallmark of all known K+ channels, raising the question how selectivity is achieved. Here, we report the X-ray structure of a closed bacterial TMEM175 channel in complex with a nanobody fusion-protein disclosing bound K+ ions. Our analysis revealed that a highly conserved layer of threonine residues in the pore conveys a basal K+selectivity. An additional layer comprising two...
Source: eLife - April 8, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

Direct ETTIN-auxin interaction controls chromatin states in gynoecium development
Hormonal signalling in animals often involves direct transcription factor-hormone interactions that modulate gene expression1,2. In contrast, plant hormone signalling is most commonly based on de-repression via the degradation of transcriptional repressors3-5. Recently, we uncovered a non-canonical signalling mechanism for the plant hormone auxin whereby auxin directly affects the activity of the atypical auxin response factor (ARF), ETTIN towards target genes without the requirement for protein degradation6,7. Here we show that ETTIN directly binds auxin, leading to dissociation from co-repressor proteins of the TOPLESS/T...
Source: eLife - April 8, 2020 Category: Biomedical Science Tags: Developmental Biology Plant Biology Source Type: research

Top-down machine learning approach for high-throughput single-molecule analysis
Single-molecule approaches provide enormous insight into the dynamics of biomolecules, but adequately sampling distributions of states and events often requires extensive sampling. Although emerging experimental techniques can generate such large datasets, existing analysis tools are not suitable to process the large volume of data obtained in high-throughput paradigms. Here, we present a new analysis platform (DISC) that accelerates unsupervised analysis of single-molecule trajectories. By merging model-free statistical learning with the Viterbi algorithm, DISC idealizes single-molecule trajectories up to three orders of ...
Source: eLife - April 8, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

Single-molecule functional anatomy of endogenous HER2-HER3 heterodimers
Human epidermal growth factor receptors (HERs) are the primary targets of many directed cancer therapies. However, the reason a specific dimer of HERs generates a stronger proliferative signal than other permutations remains unclear. Here, we used single-molecule immunoprecipitation to develop a biochemical assay for endogenously-formed, entire HER2-HER3 heterodimers. We observed unexpected, large conformational fluctuations in juxta-membrane and kinase domains of the HER2-HER3 heterodimer. Nevertheless, the individual HER2-HER3 heterodimers catalyze tyrosine phosphorylation at an unusually high rate, while simultaneously ...
Source: eLife - April 8, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Source Type: research

The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts
This study highlights the complex interactions among adaptive physiology, animal-bacterial symbiosis, and ecological context. (Source: eLife)
Source: eLife - April 7, 2020 Category: Biomedical Science Tags: Evolutionary Biology Source Type: research

Stress-mediated exit to quiescence restricted by increasing persistence in CDK4/6 activation
Mammalian cells typically start the cell-cycle entry program by activating cyclin-dependent protein kinase 4/6 (CDK4/6). CDK4/6 activity is clinically relevant as mutations, deletions, and amplifications that increase CDK4/6 activity contribute to the progression of many cancers. However, when CDK4/6 is activated relative to CDK2 remained incompletely understood. Here we developed a reporter system to simultaneously monitor CDK4/6 and CDK2 activities in single cells and found that CDK4/6 activity increases rapidly before CDK2 activity gradually increases, and that CDK4/6 activity can be active after mitosis or inactive for...
Source: eLife - April 7, 2020 Category: Biomedical Science Tags: Cell Biology Source Type: research

Lipid polarity gradient formed by ω-hydroxy lipids in tear film prevents dry eye disease
Meibum lipids form a lipid layer on the outermost side of the tear film and function to prevent water evaporation and reduce surface tension. (O-Acyl)- ω-hydroxy fatty acids (OAHFAs), a subclass of these lipids, are thought to be involved in connecting the lipid and aqueous layers in tears, although their actual function and synthesis pathway have to date remained unclear. Here, we reveal that the fatty acid ω-hydroxylaseCyp4f39 is involved in OAHFA production.Cyp4f39-deficient mice exhibited damaged corneal epithelium and shortening of tear film break-up time, both indicative of dry eye disease. In addition, t...
Source: eLife - April 7, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Source Type: research

Post-translational regulation of retinal IMPDH1 in vivo to adjust GTP synthesis to illumination conditions
We report the in vivo regulation of Inosine-5 ´-monophosphate dehydrogenase 1 (IMPDH1) in the retina. IMPDH1 catalyzes the rate-limiting step in the de novo synthesis of guanine nucleotides, impacting the cellular pools of GMP, GDP and GTP. Guanine nucleotide homeostasis is central to photoreceptor cells, where cGMP is the signal transducing m olecule in the light response. Mutations in IMPDH1 lead to inherited blindness. We unveil a light-dependent phosphorylation of retinal IMPDH1 at Thr159/Ser160 in the Bateman domain that desensitizes the enzyme to allosteric inhibition by GDP/GTP. When exposed to bright light, l...
Source: eLife - April 7, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Neuroscience Source Type: research

Condensin I subunit Cap-G is essential for proper gene expression during the maturation of post-mitotic neurons
Condensin complexes are essential for mitotic chromosome assembly and segregation during cell divisions, however, little is known about their functions in post-mitotic cells. Here we report a role for the condensin I subunit Cap-G in Drosophila neurons. We show that, despite not requiring condensin for mitotic chromosome compaction, post-mitotic neurons express Cap-G. Knockdown of Cap-G specifically in neurons (from their birth onwards) results in developmental arrest, behavioural defects, and dramatic gene expression changes, including reduced expression of a subset of neuronal genes and aberrant expression of genes that ...
Source: eLife - April 7, 2020 Category: Biomedical Science Tags: Developmental Biology Source Type: research

Evolution of multifunctionality through a pleiotropic substitution in the innate immune protein S100A9
Multifunctional proteins are evolutionary puzzles: how do proteins evolve to satisfy multiple functional constraints? S100A9 is one such multifunctional protein. It potently amplifies inflammation via Toll-like receptor 4 and is antimicrobial as part of a heterocomplex with S100A8. These two functions are seemingly regulated by proteolysis: S100A9 is readily degraded, while S100A8/S100A9 is resistant. We take an evolutionary biochemical approach to show that S100A9 evolved both functions and lost proteolytic resistance from a weakly proinflammatory, proteolytically resistant amniote ancestor. We identify a historical subst...
Source: eLife - April 7, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Evolutionary Biology Source Type: research

Separable gain control of ongoing and evoked activity in the visual cortex by serotonergic input
Controlling gain of cortical activity is essential to modulate weights between internal ongoing communication and external sensory drive. Here, we show that serotonergic input has separable suppressive effects on the gain of ongoing and evoked visual activity. We combined optogenetic stimulation of the dorsal raphe nucleus (DRN) with wide-field calcium imaging, extracellular recordings, and iontophoresis of serotonin (5-HT) receptor antagonists in the mouse visual cortex. 5-HT1A receptors promote divisive suppression of spontaneous activity, while 5-HT2A receptors act divisively on visual response gain and largely account ...
Source: eLife - April 7, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Independent evolution of ancestral and novel defenses in a genus of toxic plants ( < i > Erysimum < /i > , Brassicaceae)
Phytochemical diversity is thought to result from coevolutionary cycles as specialization in herbivores imposes diversifying selection on plant chemical defenses. Plants in the speciose genusErysimum (Brassicaceae) produce both ancestral glucosinolates and evolutionarily novel cardenolides as defenses. Here we test macroevolutionary hypotheses on co-expression, co-regulation, and diversification of these potentially redundant defenses across this genus. We sequenced and assembled the genome ofE. cheiranthoides and foliar transcriptomes of 47 additionalErysimum species to construct a phylogeny from 9,869 orthologous genes, ...
Source: eLife - April 7, 2020 Category: Biomedical Science Tags: Evolutionary Biology Plant Biology Source Type: research

A highly accurate platform for clone-specific mutation discovery enables the study of active mutational processes
Bulk whole genome sequencing (WGS) enables the analysis of tumor evolution but, because of depth limitations, can only identify old mutational events. The discovery of current mutational processes for predicting the tumor's evolutionary trajectory requires dense sequencing of individual clones or single cells. Such studies, however, are inherently problematic because of the discovery of excessive false positive mutations when sequencing picogram quantities of DNA. Data pooling to increase the confidence in the discovered mutations, moves the discovery back in the past to a common ancestor. Here we report a robust whole gen...
Source: eLife - April 7, 2020 Category: Biomedical Science Tags: Cancer Biology Genetics and Genomics Source Type: research

Cell and molecular transitions during efficient dedifferentiation
Dedifferentiation is a critical response to tissue damage, yet is not well understood, even at a basic phenomenological level. DevelopingDictyosteliumcells undergo highly efficient dedifferentiation, completed by most cells within 24 hours. We use this rapid response to investigate the control features of dedifferentiation, combining single cell imaging with high temporal resolution transcriptomics. Gene expression during dedifferentiation was predominantly a simple reversal of developmental changes, with expression changes not following this pattern primarily associated with ribosome biogenesis. Mutation of genes induced ...
Source: eLife - April 7, 2020 Category: Biomedical Science Tags: Developmental Biology Stem Cells and Regenerative Medicine Source Type: research