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Harnessing the Anti-Cancer Natural Product Nimbolide for Targeted Protein Degradation

Nimbolide, a terpenoid natural product derived from the Neem tree, impairs cancer pathogenicity across many types of human cancers; however, the direct targets and mechanisms by which nimbolide exerts its effects are poorly understood. Here, we used activity-based protein profiling (ABPP) chemoproteomic platforms to discover that nimbolide reacts with a novel functional cysteine crucial for substrate recognition in the E3 ubiquitin ligase RNF114. Nimbolide impairs breast cancer cell proliferation by disrupting RNF114 substrate recognition, leading to inhibition of ubiquitination and degradation of the tumor-suppressor p21, resulting in its rapid stabilization. We further demonstrate that nimbolide can be harnessed to recruit RNF114 as an E3 ligase in targeted protein degradation applications and show that synthetically simpler scaffolds are also capable of accessing this unique reactive site. Our study highlights the utility of ABPP platforms in uncovering unique druggable modalities accessed by natural products for cancer therapy and drug discovery applications.

cancer biology

Individuals with 22q11.2 deletion syndrome show intact prediction but reduced adaptation in responses to repeated sounds: evidence from Bayesian mapping

Background: One of the most common copy number variants, the 22q11.2 microdeletion, confers a increased risk for schizophrenia. Since schizophrenia has been associated with an aberrant neural response to repeated stimuli through both reduced adaptation and prediction, we here hypothesized that this may also be the case in nonpsychotic individuals with a 22q11.2 deletion. Methods: We recorded high-density EEG from 19 individuals with 22q11.2 deletion syndrome (12-25 years), as well as 27 healthy volunteers with comparable age and sex distribution, while they listened to a sequence of sounds arranged in a roving oddball paradigm. Using posterior probability maps and dynamic causal modelling we tested three different models accounting for repetition dependent changes in cortical responses as well as in effective connectivity; namely an adaptation model, a prediction model, and a model including both adaptation and prediction. Results: Repetition-dependent changes were parametrically modulated by a combination of adaptation and prediction and were apparent in both cortical responses and in the underlying effective connectivity. This effect was reduced in individuals with a 22q11.2 deletion and was negatively correlated with negative symptom severity. Follow-up analysis showed that the reduced effect of the combined adaptation and prediction model seen in individuals with 22q11.2 deletion was driven by reduced adaptation rather than prediction failure. Conclusions: Our findings suggest that adaptation is reduced in individuals with a 22q11.2 deletion, which can be interpreted in light of the framework of predictive coding as a failure to suppress prediction errors.

neuroscience

Deep structural brain lesions associated with consciousness impairment early after haemorrhagic stroke

BackgroundThe significance of deep structural lesions on level of consciousness early after intracerebral haemorrhage (ICH) is largely unknown.\n\nMethodsWe studied a consecutive series of patients with spontaneous ICH that underwent MRI within 7 days of the bleed. We assessed consciousness by testing for command following from time of MRI to hospital discharge, and determined 3-months functional outcomes using the Glasgow Outcome Scale-Extended (GOS-E). ICH and oedema volumes, intraventricular haemorrhage (IVH), and midline shift (MLS) were quantified. Presence of blood and oedema in deep brain regions previously implicated in consciousness were assessed. A machine learning approach using logistic regression with elastic net regularization was applied to identify parameters that best predicted consciousness at discharge controlling for confounders.\n\nResultsFrom 158 ICH patients that underwent MRI, 66% (N=105) were conscious and 34% (N=53) unconscious at the time of MRI. Almost half of unconscious patients (49%, N= 26) recovered consciousness by ICU discharge. Focal lesions within subcortical structures predicted persistent impairment of consciousness at discharge together with MLS, IVH, and ICH and oedema volumes (AUC 0.74; 95%-CI 0.73-0.75). Caudate nucleus, midbrain peduncle, and pontine tegmentum were implicated as critical structures. Unconscious patients predicted to recover consciousness had better 3-month functional outcomes than those predicted to remain unconscious (35% vs 0% GOS-E [≥]4; p-value=0.02).\n\nConclusionMRI lesions within key subcortical structures together with measures reflecting the mass effect of the haemorrhage (lesion volumes, IVH, MLS) obtained within one week of ICH can help predict early recovery of consciousness and 3-month functional outcome.

neuroscience

Degron tagging to label membrane-wrapped objects and probe membrane topology

Visualization of specific organelles in tissues over background fluorescence can be challenging, especially when reporters localize to multiple structures. Instead of trying to identify proteins enriched in specific membrane-wrapped structures, we used a selective degradation approach to remove reporters from the cytoplasm or nucleus of C. elegans embryos and mammalian cells. We demonstrate specific labelling of organelles using degron-tagged reporters, including extracellular vesicles, as well as individual neighbouring membranes. These degron-tagged reporters facilitate long-term tracking of released cell debris and cell corpses, even during uptake and phagolysosomal degradation. We further show that degron protection assays can probe the topology of the nuclear envelope and plasma membrane during cell division, giving insight into protein and organelle dynamics. As endogenous and heterologous degrons are used in bacteria, yeast, plants, and animals, degron approaches can enable the specific labelling and tracking of proteins, vesicles, organelles, cell fragments, and cells in many model systems.

cell biology

Root Anatomy based on Root Cross-Section Image Analysis with Deep Learning

Aboveground plant efficiency has improved significantly in recent years, and the improvement has led to a steady increase in global food production. The improvement of belowground plant efficiency has potential to further increase food production. However, belowground plant roots are harder to study, due to inherent challenges presented by root phenotyping. Several tools for identifying root anatomical features in root cross-section images have been proposed. However, the existing tools are not fully automated and require significant human effort to produce accurate results. To address this limitation, we use a fully automated approach, specifically, the Faster Region-based Convolutional Neural Network (Faster R-CNN), to identify anatomical traits in root cross-section images. By training Faster R-CNN models on root cross-section images, we can detect objects such as root, stele and late metaxylem, and predict rectangular bounding boxes around such objects. Subsequently, the bounding boxes can be used to estimate the root diameter, stele diameter, late metaxylem number, and average diameter. Experimental evaluation using standard object detection metrics, such as intersection-over-union and mean average precision, has shown that the Faster R-CNN models trained on rice root cross-section images can accurately detect root, stele and late metaxylem objects. Furthermore, the results have shown that the measurements estimated based on predicted bounding boxes have small root mean square error when compared with the corresponding ground truth values, suggesting that Faster R-CNN can be used to accurately detect anatomical features. A webserver for performing root anatomy using the Faster R-CNN models trained on rice images is available at https://rootanatomy.org, together with a link to a GitHub repository that contains a copy of the Faster R-CNN code. The labeled images used for training and evaluating the Faster R-CNN models are also available from the GitHub repository.

bioinformatics

Long-range phase synchronization of high-gamma activity in human cortex

Inter-areal synchronization of neuronal oscillations below 100 Hz is ubiquitous in cortical circuitry and thought to regulate neuronal communication. In contrast, faster activities are generally considered to be exclusively local-circuit phenomena. We show with human intracerebral recordings that 100-300 Hz high-gamma activity (HGA) may be synchronized between widely distributed regions. HGA synchronization was not attributable to artefacts or to epileptic pathophysiology. Instead, HGA synchronization exhibited a reliable cortical connectivity and community structures, and a laminar profile opposite to that of lower frequencies. Importantly, HGA synchronization among functional brain systems during non-REM sleep was distinct from that in resting state. Moreover, HGA synchronization was transiently enhanced for correctly inhibited responses in a Go/NoGo task. These findings show that HGA synchronization constitutes a new, functionally significant form of neuronal spike-timing relationships in brain activity. We suggest that HGA synchronization reflects the temporal microstructure of spiking-based neuronal communication per se in cortical circuits.

neuroscience

Microridges are apical projections formed of branched F-actin networks that organize the glycan layer

Apical projections are integral functional units of epithelial cells. Microvilli and stereocilia are cylindrical apical projections that are formed of bundled actin. Microridges on the other hand, grow laterally long, forming labyrinthine patterns on surfaces of various kinds of squamous epithelial cells. So far, the structural organization and functions of microridges have remained elusive. We have analyzed microridges on zebrafish epidermal cells using confocal and electron microscopy methods including electron tomography, to show that a microridge is formed of a network of F-actin and requires the function of the Arp2/3 complex for its maintenance. During development, microridges begin as F-actin punctae showing signatures of branching and requiring an active Arp2/3 complex. Using inhibitors of actin polymerization and the Arp2/3 complex, we show that microridges organize the surface glycan layer. Our analyses have unraveled the F-actin organization supporting the most abundant and evolutionarily conserved apical projection, which functions in glycan organization.

cell biology

Transitions in paternal dominance regulate offspring growth and metabolic transcription

Parental effects are an important source of adaptive traits. By contrast, parental effects failing to regulate offspring phenotype to fit current conditions could be deleterious. Although adaptive parental responses to single cues have been identified, we lack an understanding of the reversibility of parental effects across breeding cycles in a fluctuating environment. Social status of parents can occasionally fluctuate and, in turn, influence high-fitness pathways available to offspring. We show that social competition status results in robust parental effects on growth in mice. Dominant males produce faster growing offspring because of status related cues, not genetic associations. The timing, effect-size, and sex-specificity of this paternal effect are modulated by maternal experience. We experimentally demonstrate that status-ascending males produce heavier sons than before, and status-descending males produce lighter sons than before. Paternal status predicts genome-wide transcription in the liver, including transcriptional networks controlling xenobiotic and fatty acid metabolism, and oxidative phosphorylation. Our study demonstrates that paternal social status reversibly conditions offspring growth in naturalistic environments.

evolutionary biology

Identification of a simple and novel cut-point based CSF and MRI signature for predicting Alzheimer disease progression that reinforces the 2018 NIA-AA research framework

The 2018 NIA-AA research framework proposes a classification system with beta-Amyloid deposition, pathologic Tau, and neurodegeneration (ATN) for the diagnosis and staging of Alzheimers Disease (AD). Data from the ADNI (AD neuroimaging initiative) database can be utilized to identify diagnostic signatures for predicting AD progression, and to determine the utility of this NIA-AA research framework. Profiles of 320 peptides from baseline cerebrospinal fluid (CSF) samples of 287 normal, mild cognitive impairment (MCI) and AD subjects followed over a 3-10 year period were measured via multiple reaction monitoring (MRM) mass spectrometry. CSF A{beta}42, total-Tau (tTau), phosphorylated-Tau (pTau-181) and hippocampal volume were also measured. From these candidate markers, optimal diagnostic signatures with decision thresholds to separate AD and normal subjects were first identified via unbiased regression and tree-based algorithms. The best performing signature determined via cross-validation was then tested in an independent group of MCI subjects to predict future progression. This multivariate analysis yielded a simple diagnostic signature comprising CSF pTau-181 to A{beta}42 ratio, MRI hippocampal volume and a novel PTPRN peptide, with a decision threshold on each marker. When applied to a separate MCI group at baseline, subjects meeting this signature criteria experience 4.3-fold faster progression to AD compared to a 2.2-fold faster progression using only conventional markers. This novel 4-marker signature represents an advance over the current diagnostics based on widely used marker, and is much easier to use in practice than recently published complex signatures. In addition, this signature reinforces the ATN construct from the 2018 NIA-AA research framework.\n\nDisclosuresViswanath Devanarayan is an employee of Charles River Laboratories, and as such owns equity in, receives salary and other compensation from Charles River Laboratories.\n\nData collection and sharing for this project was funded by the Alzheimers Disease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904) and DOD ADNI (Department of Defense award number W81XWH-12-2-0012). ADNI is funded by the National Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering, and through generous contributions from the following: AbbVie, Alzheimers Association; Alzheimers Drug Discovery Foundation; Araclon Biotech; BioClinica, Inc.;Biogen; Bristol-Myers Squibb Company; CereSpir, Inc.; Eisai Inc.; Elan Pharmaceuticals, Inc.; Eli Lilly and Company; EuroImmun; F. Hoffmann-La Roche Ltd and its affiliated company Genentech, Inc.; Fujirebio; GE Healthcare; IXICO Ltd.; Janssen Alzheimer Immunotherapy Research & Development, LLC.; Johnson & Johnson Pharmaceutical Research & Development LLC.; Lumosity; Lundbeck; Merck & Co., Inc.; Meso Scale Diagnostics, LLC.; NeuroRx Research; Neurotrack Technologies; Novartis Pharmaceuticals Corporation; Pfizer Inc.; Piramal Imaging; Servier; Takeda Pharmaceutical Company; and Transition Therapeutics. The Canadian Institutes of Health Research is providing funds to support ADNI clinical sites in Canada. Private sector contributions are facilitated by the Foundation for the National Institutes of Health (www.fnih.org). The grantee organization is the Northern California Institute for Research and Education, and the study is coordinated by the Alzheimers Disease Cooperative Study at the University of California, San Diego. ADNI data are disseminated by the Laboratory for Neuro Imaging at the University of Southern California.

neuroscience

Redundancy in the central tachykinin systems safeguards puberty onset and fertility

The tachykinin neurokinin B (NKB, Tac2) is critical for GnRH release. NKB signaling deficiency leads to infertility in humans. However, some patients reverse this hypogonadism resembling the fertile phenotype of Tac2KO and Tacr3KO (encoding NKB receptor, NK3R) mice despite the absence of NKB signaling. Here, we demonstrate that in the absence of NKB signaling, other tachykinins (substance P and neurokinin A [NKA], encoded by Tac1) may take over to preserve fertility. The complete absence of tachykinins in Tac1/Tac2KO mice leads to delayed puberty onset in both sexes and infertility in 80% of females (but not males), in contrast to the 100% fertile phenotype of Tac1KO and Tac2KO mice separately. Furthermore, we demonstrate that NKA controls puberty onset and LH release through NKB-independent mechanisms in the presence of sex steroids and NKB-dependent mechanisms in their absence. In summary, tachykinins interact in a coordinated manner to ensure reproductive success in female mice.

physiology

Attention explores space periodically at the theta frequency

Voluntary attention is at the core of cognitive functions. Attention can be sustained at a location, or reoriented in space to allow processing at other locations, critical in an ever-changing environment. Numerous studies have investigated attentional orienting in time and space but little is known about the spatio-temporal dynamics of attentional reorienting. Here, we explicitly manipulated attentional reorienting using a cueing procedure in a 2-AFC orientation discrimination task. At various delays during the task, we interrogated attentional deployment by flashing two probe stimuli. Then, solving a second-degree equation to estimate the report probability at each probe location, we demonstrated that attention reorients periodically at ~4 Hz (theta) between the two stimulus locations. We further observed that each stimulus location is sampled at ~11 Hz (alpha). Finally, we support our mathematical approach using simulations and show that this method is sufficiently powered making it a valuable tool for studying the spatio-temporal dynamics of attention.

neuroscience

Intravascular arrest of circulating tumor cells is a two-step process exploiting their adhesion repertoire.

Cancer metastasis is a process whereby a primary tumor spreads to distant organs. We have previously demonstrated that blood flow controls the intravascular arrest of circulating tumor cells (CTCs), through stable adhesion to endothelial cells. We now aim at defining the contribution of cell adhesive potential and at identifying adhesion receptors at play. Early arrest is mediated by the formation of weak adhesion depending on CD44 and integrin v{beta}3. Stabilization of this arrest uses integrin 5{beta}1-dependent adhesions with higher adhesion strength, which allows CTCs to stop in vascular regions with lower shear forces. Moreover, blood flow favors luminal deposition of fibronectin on endothelial cells, an integrin 5{beta}1 ligand. Finally, we show that only receptors involved in stable adhesion are required for subsequent extravasation and metastasis. In conclusion, we identified the molecular partners that are sequentially exploited by CTCs to arrest and extravasate in vascular regions with permissive flow regimes.

cancer biology

Cell Mechanics at the Rear Act To Steer the Direction of Cell Migration

Motile cells navigate complex environments by changing their direction of travel, generating left-right asymmetries in their mechanical subsystems to physically turn. Currently little is known about how external directional cues are propagated along the length scale of the whole cell and integrated with its force-generating apparatus to steer migration mechanically. We examine the mechanics of spontaneous cell turning in fish epidermal keratocytes and find that the mechanical asymmetries responsible for turning behavior predominate at the rear of the cell, where there is asymmetric centripetal actin flow. Using experimental perturbations we identify two linked feedback loops connecting myosin II contractility, adhesion strength and actin network flow in turning cells that are sufficient to recreate observed cell shapes and trajectories in a computational model. Surprisingly, asymmetries in actin polymerization at the cell leading edge play only a minor role in the mechanics of cell turning - that is, cells steer from the rear.\n\nHighlightsO_LIFish keratocytes can migrate with persistent angular velocity, straight or in circles.\nC_LIO_LIAsymmetry in protrusion at the leading edge is not sufficient to generate persistent turning.\nC_LIO_LIAsymmetries in myosin II contraction, actin flow and adhesion at the cell rear cause turns.\nC_LIO_LIOur new computational model of migration predicts observed cell trajectories.\nC_LI

cell biology

Non-functional and weak alleles of FRIGIDA and FLOWERING LOCUS C reduce lifetime water-use independent of leaf-level water-use-efficiency traits in Arabidopsis thaliana

Natural selection driven by water availability has resulted in considerable variation for traits associated with drought tolerance and leaf level water-use efficiency (WUE). In Arabidopsis, little is known about the variation of whole-plant water use (PWU) and whole-plant WUE (TE). To investigate the genetic basis of PWU, we developed a novel proxy trait by combining flowering time and rosette water use to estimate lifetime PWU. We validated its usefulness for large scale screening of mapping populations in a subset of ecotypes. This parameter subsequently facilitated the screening of water-use but also drought tolerance traits in a recombinant inbred line population derived from two Arabidopsis accessions with distinct water use strategies, namely C24 (low PWU) and Col-0 (high PWU). Subsequent quantitative trait loci (QTL) mapping and validation through near-isogenic lines identified two causal QTLs, which showed that a combination of weak and non-functional alleles of the FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) genes substantially reduced plant water-use without penalising reproductive performance. Drought tolerance traits, stomatal conductance, intrinsic water use efficiency ({delta}13C) and rosette water-use were independent of allelic variation at FRI and FLC, suggesting that flowering is critical in determining life-time plant water use, but not leaf-level traits.

plant biology

The genetics of morphological and behavioral island traits in deer mice

Animals on islands often exhibit dramatic differences in morphology and behaviour compared to mainland individuals, a phenomenon known as the \"island syndrome\". These differences are thought to be adaptations to island environments, but the extent to which they have a genetic basis or instead represent plastic responses to environmental extremes is often unknown. Here, we revisit a classic case of island syndrome in deer mice (Peromyscus maniculatus) from British Columbia. We first show that Saturna Island mice and those from neighbouring islands are [~]35% ([~]5g) heavier than mainland mice and diverged approximately 10 thousand years ago. We then established laboratory colonies and find that Saturna Island mice are heavier both because they are longer and have disproportionately more lean mass. These trait differences are maintained in second-generation captive-born mice raised in a common environment. In addition, island-mainland hybrids reveal a maternal genetic effect on body weight. Using behavioural testing in the lab, we also find that wild-caught island mice are less aggressive than mainland mice; however, lab-raised mice born to these founders do not differ in aggression. Together, our results reveal that these mice respond differently to environmental conditions on islands - evolving both heritable changes in a morphological trait and also expressing a plastic phenotypic response in a behavioural trait.

evolutionary biology

Characterisation of the faecal virome of captive and wild Tasmanian devils using virus-like particles metagenomics and meta-transcriptomics

BackgroundThe Tasmanian devil is an endangered carnivorous marsupial threatened by devil facial tumour disease (DFTD). While research on DFTD has been extensive, little is known about the viruses present in devils, and whether any of these are of potential conservation relevance for this endangered species.\n\nMethodsUsing both metagenomics based on virus-like particle (VLP) enrichment and sequence-independent amplification (VLP metagenomics), and meta-transcriptomics based on bulk RNA sequencing, we characterised and compared the faecal viromes of captive and wild Tasmanian devils.\n\nResultsA total of 54 devil faecal samples collected from captive (n = 2) and wild (n = 4) populations were processed for virome characterisation using both approaches. We detected many novel, highly divergent viruses, including vertebrate viruses, bacteriophage and other dietary associated plant and insect viruses. In total, 18 new vertebrate viruses, including novel sapelovirus, astroviruses, bocaviruses, papillomaviruses and gammaherpesvirus were identified, as well as known mammalian pathogens including rabbit haemorrhagic disease virus 2 (RHDV2). Captive devils showed significantly lower levels of viral diversity than wild devils. Comparison of the two methodological approaches revealed substantial differences in the number and types of viruses detected, with meta-transcriptomics mainly identifying RNA viruses, and VLP metagenomics largely identifying DNA viruses.\n\nConclusionThis study has greatly expanded our knowledge of eukaryotic viruses in the Tasmanian devil and provides important baseline information that will contribute to the conservation and captive management of this endangered species. In addition, our results showed that a combination of VLP metagenomics and meta-transcriptomics may be a more comprehensive approach to virome characterisation than either method alone.

molecular biology

Hopanoid composition mediates bacterial ethanol tolerance

Hopanoids are abundant membrane lipids found in diverse bacterial lineages, but their physiological roles are not well understood. The ethanol fermenter Zymomonas mobilis features the highest measured concentration of hopanoids, leading to the hypothesis that these lipids can protect against bacterial solvent toxicity. However, the lack of genetic tools for manipulating hopanoid composition in vivo has limited their further functional analysis. Because of polyploidy (> 50 genome copies per cell), we found that disruptions of essential hopanoid biosynthesis (hpn) genes in Z. mobilis act as genetic knockdowns, reliably modulating the abundance of different hopanoid species. Using a set of hpn transposon mutants, we demonstrate that both reduced hopanoid content and modified hopanoid head group composition mediate growth and survival in ethanol. In contrast, the amount of hopanoids, but not their polar group composition, contributes to fitness at low pH. Spectroscopic analysis of model membranes showed that hopanoids protect against several ethanol-driven phase transitions in membrane structure, including lipid interdigitation and bilayer dissolution. We propose that hopanoids act through a combination of hydrophobic and inter-lipid hydrogen bonding interactions to stabilize bacterial membranes against solvent stress.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=196 HEIGHT=200 SRC=\"FIGDIR/small/443473v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (57K):\norg.highwire.dtl.DTLVardef@119f9adorg.highwire.dtl.DTLVardef@5701bcorg.highwire.dtl.DTLVardef@330bfaorg.highwire.dtl.DTLVardef@1574d44_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology

An intrinsic neural eye tracker in primary visual cortex

Humans and other primates rely on eye movements to explore visual scenes and to track moving objects. As a result, the image that is projected onto the retina - and propagated throughout the visual cortical hierarchy - is almost constantly changing and makes little sense without taking into account the momentary direction of gaze. How is this achieved in the visual system? Here we show that in primary visual cortex (V1), the earliest stage of cortical vision, neural representations carry an embedded \"eye tracker\" that signals the direction of gaze associated with each image. Using chronically implanted multi-electrode arrays, we recorded the activity of neurons in V1 during tasks requiring fast (exploratory) and slow (pursuit) eye movements. Neurons were stimulated with flickering, full-field luminance noise at all times. As in previous studies 1-4, we observed neurons that were sensitive to gaze direction during fixation, despite comparable stimulation of their receptive fields. We trained a decoder to translate neural activity into metric estimates of (stationary) gaze direction. This decoded signal not only tracked the eye accurately during fixation, but also during fast and slow eye movements, even though the decoder had not been exposed to data from these behavioural states. Moreover, this signal lagged the real eye by approximately the time it took for new visual information to travel from the retina to cortex. Using simulations, we show that this V1 eye position signal could be used to take into account the sensory consequences of eye movements and map the fleeting positions of objects on the retina onto their stable position in the world.

neuroscience