Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions
Human cytomegalovirus (HCMV) extensively modulates host cells, downregulating>900 human proteins during viral replication and degrading ≥133 proteins shortly after infection. The mechanism of degradation of most host proteins remains unresolved, and the functions of many viral proteins are incompletely characterised. We performed a mass spectrometry-based interactome analysis of 169 tagged, stably-expressed canonical strain Merlin HCMV proteins, and two non-canonical HCMV proteins, in infected cells. This identified a network of>3,400 virus-host and>150 virus-virus protein interactions, providing insights into ...
Source: eLife - December 24, 2019 Category: Biomedical Science Tags: Computational and Systems Biology Microbiology and Infectious Disease Source Type: research

Spinal signaling of C-fiber mediated pleasant touch in humans
C-tactile afferents form a distinct channel that encodes pleasant tactile stimulation. Prevailing views indicate they project, as with other unmyelinated afferents, in lamina I-spinothalamic pathways. However, we found that spinothalamic ablation in humans, whilst profoundly impairing pain, temperature and itch, had no effect on pleasant touch perception. Only discriminative touch deficits were seen. These findings preclude privileged C-tactile-lamina I-spinothalamic projections and imply integrated hedonic and discriminative spinal processing from the body. (Source: eLife)
Source: eLife - December 24, 2019 Category: Biomedical Science Tags: Human Biology and Medicine Neuroscience Source Type: research

Unstructured regions in IRE1 α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR
We report that enforced loading of endogenous BiP onto endogenous IRE1 α repressed UPR signalling in CHO cells and deletions in the IRE1α locus that de-repressed the UPR in cells, encode flexible regions of IRE1LD that mediated BiP ‑induced monomerisation in vitro. Changes in the hydrogen exchange mass spectrometry profile of IRE1LD induced by ERdj4 and BiP confirmed monomerisation and were consistent with active destabilisation of the IRE1LD dimer. Together, these observations support a competition model whereby waning ER stress passively partitions ERdj4 and BiP to IRE1LD to initiate active repression of UP...
Source: eLife - December 24, 2019 Category: Biomedical Science Tags: Cell Biology Source Type: research

Siglec1-expressing subcapsular sinus macrophages provide soil for melanoma lymph node metastasis
Lymph nodes (LNs) are a common site of metastasis in solid cancers, and cutaneous melanomas show inherent properties of LN colonization. However, interactions between LN stroma and pioneer metastatic cells during metastatic colonization remain largely uncharacterized. Here we studied mice implanted with GFP-expressing melanoma cells to decipher early LN colonization events. We show that Siglec1-expressing subcapsular sinus (SCS) macrophages provide anchorage to pioneer metastatic cells. We performed in vitro co-culture to demonstrate that interactions between hypersialylated cancer cells and Siglec1 drive the proliferation...
Source: eLife - December 24, 2019 Category: Biomedical Science Tags: Cancer Biology Source Type: research

Resolving homology in the face of shifting germ layer origins: Lessons from a major skull vault boundary
The vertebrate skull varies widely in shape, accommodating diverse strategies of feeding and predation. The braincase is composed of several flat bones that meet at flexible joints called sutures. Nearly all vertebrates have a prominent ‘coronal’ suture that separates the front and back of the skull. This suture can develop entirely within mesoderm-derived tissue, neural crest-derived tissue, or at the boundary of the two. Recent paleontological findings and genetic insights in non-mammalian model organisms serve to revise fund amental knowledge on the development and evolution of this suture. Growing evidence ...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Developmental Biology Evolutionary Biology Source Type: research

Metabolic modulation regulates cardiac wall morphogenesis in zebrafish
During cardiac development, cardiomyocytes form complex inner wall structures called trabeculae. Despite significant investigation into this process, the potential role of metabolism has not been addressed. Using single cell resolution imaging in zebrafish, we find that cardiomyocytes seeding the trabecular layer actively change their shape while compact layer cardiomyocytes remain static. We show that Erbb2 signaling, which is required for trabeculation, activates glycolysis to support changes in cardiomyocyte shape and behavior. Pharmacological inhibition of glycolysis impairs cardiac trabeculation, and cardiomyocyte-spe...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Cell Biology Developmental Biology Source Type: research

Robust cullin-RING ligase function is established by a multiplicity of poly-ubiquitylation pathways
The cullin-RING ligases (CRLs) form the major family of E3 ubiquitin ligases. The prototypic CRLs in yeast, called SCF enzymes, employ a single E2 enzyme, Cdc34, to build poly-ubiquitin chains required for degradation. In contrast, six different human E2 and E3 enzyme activities, including Cdc34 orthologs UBE2R1 and UBE2R2, appear to mediate SCF-catalyzed substrate polyubiquitylationin vitro. The combinatorial interplay of these enzymes raises questions about genetic buffering of SCFs in human cells and challenges the dogma that E3s alone determine substrate specificity. To enable the quantitative comparisons of SCF-depend...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Cell Biology Source Type: research

Indirect sexual selection drives rapid sperm protein evolution in abalone
Sexual selection can explain the rapid evolution of fertilization proteins, yet sperm proteins evolve rapidly even if not directly involved in fertilization. In the marine mollusk abalone, sperm secrete enormous quantities of two rapidly evolving proteins, lysin and sp18, that are stored at nearly molar concentrations. We demonstrate that this extraordinary packaging is achieved by associating into Fuzzy Interacting Transient Zwitterion (FITZ) complexes upon binding the intrinsically disordered FITZ Anionic Partner (FITZAP). FITZ complexes form at intracellular ionic strengths, and upon exocytosis into seawater, lysin and ...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Evolutionary Biology Structural Biology and Molecular Biophysics Source Type: research

A role for phagocytosis in inducing cell death during thymocyte negative selection
Autoreactive thymocytes are eliminated during negative selection in the thymus, a process important for establishing self-tolerance. Thymic phagocytes serve to remove dead thymocytes, but whether they play additional roles during negative selection remains unclear. Here, using a murine thymic slice model in which thymocytes undergo negative selectionin situ, we demonstrate that phagocytosis promotes negative selection, and provide evidence for the escape of autoreactive CD8 T cells to the periphery when phagocytosis in the thymus is impaired. We also show that negative selection is more efficient when the phagocyte also pr...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Cell Biology Immunology and Inflammation Source Type: research

Single-cell analysis uncovers that metabolic reprogramming by ErbB2 signaling is essential for cardiomyocyte proliferation in the regenerating heart
While the heart regenerates poorly in mammals, efficient heart regeneration occurs in zebrafish. Studies in zebrafish have resulted in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. To identify which processes occur in proliferating cardiomyocytes we have used a single-cell RNA-sequencing approach. We uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the nonproliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover, these cells have reduced expression of mitochondr...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Developmental Biology Stem Cells and Regenerative Medicine Source Type: research

Relaxation of synaptic inhibitory events as a compensatory mechanism in fetal SOD spinal motor networks
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease affecting motor neurons (MNs) during late adulthood. Here, with the aim of identifying early changes underpinning ALS neurodegeneration, we analyzed the GABAergic/glycinergic inputs to E17.5 fetal MNs from SOD1G93A (SOD) mice in parallel with chloride homeostasis. Our results show that IPSCs are less frequent in SOD animals in accordance with a reduction of synaptic VIAAT-positive terminals. SOD MNs exhibited an EGABAAR 10 mV more depolarized than in WT MNs associated with a KCC2 reduction. Interestingly, SOD GABAergic/glycinergic IPSCs and evok...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Neuroscience Source Type: research

Homeostatic regulation of perisynaptic MMP9 activity in the amblyopic visual cortex
Dark exposure (DE) followed by light reintroduction (LRx) reactivates robust synaptic plasticity in adult mouse V1, which allows recovery from amblyopia. Previously we showed that LRx-induced perisynaptic proteolysis of extracellular matrix (ECM) by MMP9 mediates the enhanced plasticity in binocular adult mice (Murase et al., 2017). However, it is unknown if a visual system compromised by amblyopia could engage this pathway. Here we show that LRx to adult amblyopic mice induces perisynaptic MMP2/9 activity and ECM degradation in the deprived and non-deprived V1. LRx restricted to the amblyopic eye induces equally robust MM...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Neuroscience Source Type: research

Acute cerebellar knockdown of Sgce reproduces salient features of Myoclonus-dystonia (DYT11) in mice
Myoclonus dystonia (DYT11) is a movement disorder caused by loss-of-function mutations inSGCE and characterized by involuntary jerking and dystonia that frequently improve after drinking alcohol. Existing transgenic mouse models of DYT11 exhibit only mild motor symptoms, possibly due to rodent-specific developmental compensation mechanisms, which have limited the study of neural mechanisms underlying DYT11. To circumvent potential compensation, we used short hairpin RNA (shRNA) to acutely knock down Sgce in the adult mouse and found that this approach produced dystonia and repetitive, myoclonic-like, jerking movements in m...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Neuroscience Source Type: research

C-Mannosylation supports folding and enhances stability of thrombospondin repeats
Previous studies demonstrated importance of C-mannosylation for efficient protein secretion. To study its impact on protein folding and stability, we analyzed both C-mannosylated and non-C-mannosylated thrombospondin type 1 repeats (TSRs) of netrin receptor UNC-5. In absence of C-mannosylation, UNC-5 TSRs could only be obtained at low temperature and a significant proportion displayed incorrect intermolecular disulfide bridging, which was hardly observed when C-mannosylated. Glycosylated TSRs exhibited higher resistance to thermal and reductive denaturation processes and the presence of C-mannoses promoted the oxidative fo...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Cell Biology Source Type: research

MeCP2 nuclear dynamics in live neurons results from low and high affinity chromatin interactions
Methyl-CpG-binding-Protein 2 (MeCP2) is an abundant nuclear protein highly enriched in neurons. Here we report live-cell single-molecule imaging studies of the kinetic features of mouse MeCP2 at high spatial-temporal resolution. MeCP2 displays dynamic features that are distinct from both highly mobile transcription factors and immobile histones. Stable binding of MeCP2 in living neurons requires its methyl-binding domain and is sensitive to DNA modification levels. Diffusion of unbound MeCP2 is strongly constrained by weak, transient interactions mediated primarily by its AT-hook domains, and varies with the level of chrom...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Neuroscience Structural Biology and Molecular Biophysics Source Type: research

Down but not out
A new study in monkeys suggests that treating HIV infection early with antiretroviral therapy reduces the number of latent viruses, but has little impact on viral reactivation when treatment stops. (Source: eLife)
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Microbiology and Infectious Disease Source Type: research

From single neurons to behavior in the jellyfish < i > Aurelia aurita < /i >
Jellyfish nerve nets provide insight into the origins of nervous systems, as both their taxonomic position and their evolutionary age imply that jellyfish resemble some of the earliest neuron-bearing, actively-swimming animals. Here we develop the first neuronal network model for the nerve nets of jellyfish. Specifically, we focus on the moon jellyAurelia aurita and the control of its energy-efficient swimming motion. The proposed single neuron model disentangles the contributions of different currents to a spike. The network model identifies factors ensuring non-pathological activity and suggests an optimization for the t...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Computational and Systems Biology Neuroscience Source Type: research

Regulation of zebrafish melanocyte development by ligand-dependent BMP signaling
Preventing terminal differentiation is important in the development and progression of many cancers including melanoma. Recent identification of the BMP ligandGDF6 as a novel melanoma oncogene showedGDF6-activated BMP signaling suppresses differentiation of melanoma cells. Previous studies have identified roles forGDF6 orthologs during early embryonic and neural crest development, but have not identified direct regulation of melanocyte development by GDF6. Here, we investigate the BMP ligandgdf6a, a zebrafish ortholog of humanGDF6, during the development of melanocytes from the neural crest. We establish that the loss ofgd...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Cancer Biology Developmental Biology Source Type: research

Aberrant calcium channel splicing drives defects in cortical differentiation in Timothy Syndrome
The syndromic autism spectrum disorder (ASD) Timothy Syndrome (TS) is caused by a point mutation in the alternatively spliced exon 8A of the calcium channel Cav1.2. Using mouse brain and human induced pluripotent stem cells (iPSCs), we provide evidence that the TS mutation prevents a normal developmental switch in Cav1.2 exon utilization, resulting in persistent expression of gain-of-function mutant channels during neuronal differentiation. In iPSC models, the TS mutation reduces the abundance of SATB2-expressing cortical projection neurons, leading to excess CTIP2+ neurons. We show that expression of TS-Cav1.2 channels in...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Neuroscience Stem Cells and Regenerative Medicine Source Type: research

Activation of a nucleotide-dependent RCK domain requires binding of a cation cofactor to a conserved site
RCK domains regulate the activity of K+ channels and transporters in eukaryotic and prokaryotic organisms by responding to ions or nucleotides. The mechanisms of RCK activation by Ca2+ in the eukaryotic BK and bacterial MthK K+ channels are well understood. However, the molecular details of activation in nucleotide-dependent RCK domains are not clear. Through a functional and structural analysis of the mechanism of ATP activation in KtrA, a RCK domain from theB. subtilis KtrAB cation channel, we have found that activation by nucleotide requires binding of cations to an intra-dimer interface site in the RCK dimer. In partic...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

VEGF/VEGFR2 signaling regulates hippocampal axon branching during development
Axon branching is crucial for proper formation of neuronal networks. Although originally identified as an angiogenic factor, VEGF also signals directly to neurons to regulate their development and function. Here we show that VEGF and its receptor VEGFR2 (also known as KDR or FLK1) are expressed in mouse hippocampal neurons during development, with VEGFR2 locally expressed in the CA3 region. Activation of VEGF/VEGFR2 signaling in isolated hippocampal neurons results in increased axon branching. Remarkably, inactivation of VEGFR2 also results in increased axon branching in vitro and in vivo. The increased CA3 axon branching ...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Developmental Biology Source Type: research

Development, calibration, and validation of a novel human ventricular myocyte model in health, disease, and drug block
In this study, we present the design, development, calibration and independent validation of a human-based ventricular model (ToR-ORd) for simulations of electrophysiology and excitation-contraction coupling, from ionic to whole-organ dynamics, including the electrocardiogram. Validation based on substantial multiscale simulations supports the credibility of the ToR-ORd model under healthy and key disease conditions, as well as drug blockade. In addition, the process uncovers new theoretical insights into the biophysical properties of the L-type calcium current, which are critical for sodium and calcium dynamics. These ins...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Cell Biology Computational and Systems Biology Source Type: research

EphrinB2 regulates VEGFR2 during dendritogenesis and hippocampal circuitry development
Vascular endothelial growth factor (VEGF) is an angiogenic factor that play important roles in the nervous system, although it is still unclear which receptors transduce those signals in neurons. Here, we show that in the developing hippocampus VEGFR2 (also known as KDR or FLK1) is expressed specifically in the CA3 region and it is required for dendritic arborization and spine morphogenesis in hippocampal neurons. Mice lacking VEGFR2 in neurons (Nes-cre Kdrlox/-) show decreased dendritic arbors and spines as well as a reduction in long-term potentiation (LTP) at the associational-commissural – CA3 synapses. Mechanist...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Developmental Biology Neuroscience Source Type: research

A multilayer circuit architecture for the generation of distinct locomotor behaviors in < i > Drosophila < /i >
Animals generate diverse motor behaviors, yet how the same motor neurons (MNs) generate two distinct or antagonistic behaviors remains an open question. Here we characterizeDrosophila larval muscle activity patterns and premotor/motor circuits to understand how they generate forward and backward locomotion. We show that all body wall MNs are activated during both behaviors, but a subset of MNs change recruitment timing for each behavior. We used TEM to reconstruct a full segment of all 60 MNs and 236 premotor neurons (PMNs), including differentially-recruited MNs. Analysis of this comprehensive connectome identified PMN-MN...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Neuroscience Source Type: research

Sensing of nutrients by CPT1C regulates late endosome/lysosome anterograde transport and axon growth
Anterograde transport of late endosomes or lysosomes (LE/Lys) is crucial for proper axon growth. However, the role of energetic nutrients has been poorly explored. Malonyl-CoA is a precursor of fatty acids, and its intracellular levels highly fluctuate depending on glucose availability or the energy sensor AMP-activated protein kinase (AMPK). We demonstrate in HeLa cells that carnitine palmitoyltransferase 1C (CPT1C) senses malonyl-CoA and enhances LE/Lys anterograde transport by interacting with the endoplasmic reticulum protein protrudin and facilitating the transfer of Kinesin-1 from protrudin to LE/Lys. In cultured mou...
Source: eLife - December 23, 2019 Category: Biomedical Science Tags: Cell Biology Neuroscience Source Type: research

Pathway-, layer- and cell-type-specific thalamic input to mouse barrel cortex
Mouse primary somatosensory barrel cortex (wS1) processes whisker sensory information, receiving input from two distinct thalamic nuclei. The first-order ventral posterior medial (VPM) somatosensory thalamic nucleus most densely innervates layer 4 (L4) barrels, whereas the higher-order posterior thalamic nucleus (medial part, POm) most densely innervates L1 and L5A. We optogenetically stimulated VPM or POm axons, and recorded evoked excitatory postsynaptic potentials (EPSPs) in different cell-types across cortical layers in wS1. We found that excitatory neurons and parvalbumin-expressing inhibitory neurons received the lar...
Source: eLife - December 20, 2019 Category: Biomedical Science Tags: Neuroscience Source Type: research

FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory
Loss of the RNA binding protein FMRP causes Fragile X Syndrome (FXS), the most common cause of inherited intellectual disability, yet it is unknown how FMRP function varies across brain regions and cell types and how this contributes to disease pathophysiology. Here we use conditional tagging of FMRP and CLIP (FMRP cTag CLIP) to examine FMRP mRNA targets in hippocampal CA1 pyramidal neurons, a critical cell type for learning and memory relevant to FXS phenotypes. Integrating these data with analysis of ribosome-bound transcripts in these neurons revealed CA1-enriched binding of autism-relevant mRNAs, and CA1-specific regul...
Source: eLife - December 20, 2019 Category: Biomedical Science Tags: Neuroscience Source Type: research

Single-molecule turnover dynamics of actin and membrane coat proteins in clathrin-mediated endocytosis
Actin dynamics generate forces to deform the membrane and overcome the cell's high turgor pressure during clathrin-mediated endocytosis (CME) in yeast, but precise molecular details are still unresolved. Our previous models predicted that actin filaments of the endocytic meshwork continually polymerize and disassemble, turning over multiple times during an endocytic event, similar to other actin systems. We applied single-molecule speckle tracking in live fission yeast to directly measure molecular turnover within CME sites for the first time. In contrast with the overall ~20-sec lifetimes of actin and actin-associated pro...
Source: eLife - December 19, 2019 Category: Biomedical Science Tags: Cell Biology Physics of Living Systems Source Type: research

Large-scale state-dependent membrane remodeling by a transporter protein
That channels and transporters can influence the membrane morphology is increasingly recognized. Less appreciated is that the extent and free-energy cost of these deformations likely varies among different functional states of a protein, and thus, that they might contribute significantly to defining its mechanism. We consider the trimeric Na+-aspartate symporter GltPh, a homolog of an important class of neurotransmitter transporters, whose mechanism entails one of the most drastic structural changes known. Molecular simulations indicate that when the protomers become inward-facing, they cause deep, long-ranged, and yet mut...
Source: eLife - December 19, 2019 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

TLE3 loss confers AR inhibitor resistance by facilitating GR-mediated human prostate cancer cell growth
Androgen receptor (AR) inhibitors represent the mainstay of prostate cancer treatment. In a genome-wide CRISPR-Cas9 screen using LNCaP prostate cancer cells, loss of co-repressorTLE3 conferred resistance to AR antagonists apalutamide and enzalutamide. Genes differentially expressed uponTLE3loss share AR as the top transcriptional regulator, andTLE3 loss rescued the expression of a subset of androgen-responsive genes upon enzalutamide treatment. GR expression was strongly upregulated upon AR inhibition in aTLE3-negative background. This was consistent with binding of TLE3 and AR at theGR locus. Furthermore, GR binding was o...
Source: eLife - December 19, 2019 Category: Biomedical Science Tags: Cancer Biology Source Type: research

The Fml1-MHF complex suppresses inter-fork strand annealing in fission yeast
Previously we reported that a process called inter-fork strand annealing (IFSA) causes genomic deletions during the termination of DNA replication when an active replication fork converges on a collapsed fork (Morrow et al., 2017). We also identified the FANCM-related DNA helicase Fml1 as a potential suppressor of IFSA. Here, we confirm that Fml1 does indeed suppress IFSA, and show that this function depends on its catalytic activity and ability to interact with Mhf1-Mhf2 via its C-terminal domain. Finally, a plausible mechanism of IFSA suppression is demonstrated by the finding that Fml1 can catalyse regressed fork restor...
Source: eLife - December 19, 2019 Category: Biomedical Science Tags: Chromosomes and Gene Expression Source Type: research

Common activation mechanism of class A GPCRs
Class A G protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology. Understanding receptor activation mechanism is critical for discovering novel therapeutics since about one-third of all marketed drugs target members of this family. GPCR activation is an allosteric process that couples agonist binding to G protein recruitment, with the hallmark outward movement of transmembrane helix 6 (TM6). However, what leads to TM6 movement and the key residue level changes of this movement remain less well understood. Here, we report a framework to quantify conformational changes. By analyzing the confor...
Source: eLife - December 19, 2019 Category: Biomedical Science Tags: Computational and Systems Biology Structural Biology and Molecular Biophysics Source Type: research

GC content shapes mRNA storage and decay in human cells
In this study, we combined our recent P-body transcriptome with transcriptomes obtained following silencing of broadly acting mRNA decay and repression factors, and with available CLIP and related data. This revealed the central role of GC content in mRNA fate, in terms of P-body localization, mRNA translation and mRNA stability: P-bodies contain mostly AU-rich mRNAs, which have a particular codon usage associated with a low protein yield; AU-rich and GC-rich transcripts tend to follow distinct decay pathways; and the targets of sequence-specific RBPs and miRNAs are also biased in terms of GC content. Altogether, these res...
Source: eLife - December 19, 2019 Category: Biomedical Science Tags: Chromosomes and Gene Expression Source Type: research

Length-dependent disassembly maintains four different flagellar lengths in < i > Giardia < /i >
With eight flagella of four different lengths, the parasitic protistGiardia is an ideal model to evaluate flagellar assembly and length regulation. To determine how four different flagellar lengths are maintained, we used live-cell quantitative imaging and mathematical modeling of conserved components of intraflagellar transport (IFT)-mediated assembly and kinesin-13-mediated disassembly in different flagellar pairs. Each axoneme has a long cytoplasmic region extending from the basal body, and transitions to a canonical membrane-bound flagellum at the 'flagellar pore'. We determined that each flagellar pore is the site of ...
Source: eLife - December 19, 2019 Category: Biomedical Science Tags: Cell Biology Microbiology and Infectious Disease Source Type: research

Uncovering the functional anatomy of the human insula during speech
The contribution of insular cortex to speech production remains unclear and controversial given diverse findings from functional neuroimaging and lesional data. To create a precise spatiotemporal map of insular activity, we performed a series of experiments: single-word articulations of varying complexity, non-speech orofacial movements and speech listening, in a cohort of 27 patients implanted with penetrating intracranial electrodes. The posterior insula was robustly active bilaterally, but after the onset of articulation, during listening to speech and during production of non-speech mouth movements. Preceding articulat...
Source: eLife - December 19, 2019 Category: Biomedical Science Tags: Neuroscience Source Type: research

De novo design of a homo-trimeric amantadine-binding protein
The computational design of a symmetric protein homo-oligomer that binds a symmetry-matched small molecule larger than a metal ion has not yet been achieved. We used de novo protein design to create a homo-trimeric protein that binds the C3 symmetric small molecule drug amantadine with each protein monomer making identical interactions with each face of the small molecule. Solution NMR data show that the protein has regular three-fold symmetry and undergoes localized structural changes upon ligand binding. A high-resolution X-ray structure reveals a close overall match to the design model with the exception of water molecu...
Source: eLife - December 19, 2019 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

Too hip for two sacral vertebrae
A complex pelvic morphology has been discovered in the fossils of one of the largest crocodylians. (Source: eLife)
Source: eLife - December 19, 2019 Category: Biomedical Science Tags: Evolutionary Biology Source Type: research

Inferring synaptic inputs from spikes with a conductance-based neural encoding model
Descriptive statistical models of neural responses generally aim to characterize the mapping from stimuli to spike responses while ignoring biophysical details of the encoding process. Here, we introduce an alternative approach, the conductance-based encoding model (CBEM), which describes amapping fromstimuli to excitatory and inhibitory synaptic conductances governing the dynamics of sub-threshold membrane potential. Remarkably, we show that the CBEM can be fit to extracellular spike train data and then used to predict excitatory and inhibitory synaptic currents. We validate these predictions with intracellular recordings...
Source: eLife - December 18, 2019 Category: Biomedical Science Tags: Neuroscience Source Type: research

Catecholaminergic modulation of meta-learning
The remarkable expedience of human learning is thought to be underpinned by meta-learning, whereby slow accumulative learning processes are rapidly adjusted to the current learning environment. To date, the neurobiological implementation of meta-learning remains unclear. A burgeoning literature argues for an important role for the catecholamines dopamine and noradrenaline in meta-learning. Here we tested the hypothesis that enhancing catecholamine function modulates the ability to optimise a meta-learning parameter (learning rate) as a function of environmental volatility. 102 participants completed a task which required l...
Source: eLife - December 18, 2019 Category: Biomedical Science Tags: Neuroscience Source Type: research

HIV restriction factor APOBEC3G binds in multiple steps and conformations to search and deaminate single-stranded DNA
APOBEC3G (A3G), an enzyme expressed in primates with the potential to inhibit human immunode ficiency virus type 1 (HIV-1) infectivity, is a single-stranded DNA (ssDNA) deoxycytidine deaminase with two domains, a catalytically active, weakly ssDNA binding C-terminal domain (CTD) and a catalytically inactive, strongly ssDNA binding N-terminal domain (NTD). Using optical tweezers, we measure A3G binding a single, long ssDNA substrate under various applied forces to characterize the binding interaction. A3G binds ssDNA in multiple steps and in two distinct conformations, distinguished by degree of ssDNA contraction. A3G stab...
Source: eLife - December 18, 2019 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

The follicle epithelium in the ​ < i > Drosophila ​ < /i > ovary is maintained by a small number of stem cells
The follicle stem cells (FSCs) in the Drosophila ovary are an important experimental model for the study of epithelial stem cell biology. Although decades of research support the conclusion that there are two FSCs per ovariole, a recent study used a novel clonal marking system to conclude that there are 15-16 FSCs per ovariole. We performed clonal analysis using both this novel clonal marking system and standard clonal marking systems, and identified several problems that may have contributed to the overestimate of FSC number. In addition, we developed new methods for accurately measuring clone size, and found that FSC clo...
Source: eLife - December 18, 2019 Category: Biomedical Science Tags: Stem Cells and Regenerative Medicine Source Type: research

Crl activates transcription by stabilizing active conformation of the master stress transcription initiation factor
In this study, we determined a 3.80 Å cryo-EM structure of anEscherichia coli transcription activation complex (E. coli Crl-TAC) comprisingE. coliσS-RNA polymerase ( σS-RNAP) holoenzyme, Crl, and a nucleic-acid scaffold. The structure reveals that Crl interacts with domain 2 of σS ( σS2) and the RNAP core enzyme, but does not contact promoter DNA. Results from subsequent hydrogen-deuterium exchange mass spectrometry (HDX-MS) indicate that Crl stabilizes key structural motifs within σS2 to promote the assembly of the σS-RNAP holoenzyme and also to facilitate formation of an RNA poly...
Source: eLife - December 17, 2019 Category: Biomedical Science Tags: Chromosomes and Gene Expression Source Type: research

Default mode-visual network hypoconnectivity in an autism subtype with pronounced social visual engagement difficulties
Social visual engagement difficulties are hallmark early signs of autism (ASD) and are easily quantified using eye tracking methods. However, it is unclear how these difficulties are linked to atypical early functional brain organization in ASD. With resting state fMRI data in a large sample of ASD toddlers and other non-ASD comparison groups, we find ASD-related functional hypoconnnectivity between ‘social brain’ circuitry such as the default mode network (DMN) and visual and attention networks. An eye tracking-identified ASD subtype with pronounced early social visual engagement difficulties (GeoPref ASD) is ...
Source: eLife - December 17, 2019 Category: Biomedical Science Tags: Human Biology and Medicine Neuroscience Source Type: research

Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones
Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here we combine complementary theoretical approaches to elucidate the structural and thermodynamic details of the chaperone-induced expansion of a substrate protein, with a particular emphasis on the critical role played by ATP hydrolysis. We first determine the conformational free-energy cost of the substrate expansion due to the binding of multiple chaperones using coarse-grained molecular simulations. We then exploit this result to implement a ...
Source: eLife - December 17, 2019 Category: Biomedical Science Tags: Physics of Living Systems Source Type: research

Combining genomics and epidemiology to analyse bi-directional transmission of < i > Mycobacterium bovis < /i > in a multi-host system
Quantifying pathogen transmission in multi-host systems is difficult, as exemplified in bovine tuberculosis (bTB) systems, but is crucial for control. The agent of bTB,Mycobacterium bovis, persists in cattle populations worldwide, often where potential wildlife reservoirs exist. However, the relative contribution of different host species to bTB persistence is generally unknown. In Britain, the role of badgers in infection persistence in cattle is highly contentious, despite decades of research and control efforts. We applied Bayesian phylogenetic and machine-learning approaches to bacterial genome data to quantify the rol...
Source: eLife - December 17, 2019 Category: Biomedical Science Tags: Epidemiology and Global Health Microbiology and Infectious Disease Source Type: research

Rethinking research into metastasis
The partial success of an attempt to repeat findings in cancer biology highlights the need to improve study designs for preclinical research into metastasis and the targeting of cancer cells. (Source: eLife)
Source: eLife - December 17, 2019 Category: Biomedical Science Tags: Cancer Biology Source Type: research

Replication Study: Biomechanical remodeling of the microenvironment by stromal caveolin-1 favors tumor invasion and metastasis
As part of theReproducibility Project: Cancer Biology we published a Registered Report (Fiering et al., 2015) that described how we intended to replicate selected experiments from the paper ‘Biomechanical remodeling of the microenvironment by stromal caveolin-1 favors tumor invasion and metastasis’ (Goetz et al., 2011). Here we report the results. Primary mouse embryonic fibroblasts (pMEFs) expressing caveolin 1 (Cav1WT) demonstrated increased extracellular matrix remodelingin vitro compared to Cav1 deficient (Cav1KO) pMEFs, similar to the original study (Goetz et al., 2011).In vivo, we found higher levels of i...
Source: eLife - December 17, 2019 Category: Biomedical Science Tags: Cancer Biology Source Type: research

Primary cilia deficiency in neural crest cells models Anterior Segment Dysgenesis in mouse
Defects affecting tissues of the anterior segment (AS) of the eye lead to a group of highly debilitating disorders called Anterior Segment Dysgenesis (ASD). Despite the identification of some causative genes, the pathogenesis of ASD remains unclear. Interestingly, several ciliopathies display conditions of the AS. Using conditional targeting ofIft88 withWnt1-Cre, we show that primary cilia of neural crest cells (NCC), precursors of most AS structures, are indispensable for normal AS development and their ablation leads to ASD conditions including abnormal corneal dimensions, defective iridocorneal angle, reduced anterior c...
Source: eLife - December 17, 2019 Category: Biomedical Science Tags: Developmental Biology Source Type: research

< i > Har-P < /i > , a short < i > P < /i > -element variant, weaponizes < i > P < /i > -transposase to severely impair < i > Drosophila < /i > development
Without transposon-silencing Piwi-interacting RNAs (piRNAs), transposition causes an ovarian atrophy syndrome inDrosophila called gonadal dysgenesis (GD).Harwich (Har) strains withP-elements cause severe GD in F1 daughters whenHar fathers mate with mothers lackingP-element-piRNAs (i.e.ISO1 strain). To address the mystery of whyHar induces severe GD, we bred hybridDrosophila withHar genomic fragments into theISO1 background to createHISR-D or HISR-N lines that still causeDysgenesis or areNon-dysgenic, respectively. In these lines, we discovered a highly truncatedP-element variant we named ‘Har-P’ as the most fre...
Source: eLife - December 17, 2019 Category: Biomedical Science Tags: Chromosomes and Gene Expression Genetics and Genomics Source Type: research

Compensatory sequence variation between < i > trans < /i > -species small RNAs and their target sites
Trans-species small regulatory RNAs (sRNAs) are delivered to host plants from diverse pathogens and parasites and can target host mRNAs. Howtrans-species sRNAs can be effective on diverse hosts has been unclear. Multiple species of the parasitic plantCuscuta producetrans-species sRNAs that collectively target many host mRNAs. Confirmed target sites are nearly always in highly conserved, protein-coding regions of host mRNAs.Cuscuta trans-species sRNAs can be grouped into superfamilies that have variation in a three-nucleotide period. These variants compensate for synonymous-site variation in host mRNAs. By targeting host mR...
Source: eLife - December 17, 2019 Category: Biomedical Science Tags: Plant Biology Source Type: research