title: Longitudinal effects of using and discontinuing CNS medications on cognitive functioning

abstract:
BackgroundMedications acting on the central nervous system (CNS) have been associated with accelerated cognitive decline and increased risk of dementia. However, results are inconsistent and the longitudinal effects of CNS medications on cognitive performance are still not known.

MethodsUsing longitudinal cognitive data from healthy adults aged 25-100 years (N = 2,475) from four test waves five years apart, we investigated both the link between use of CNS medications (opioids, antidepressants, anxiolytics, hypnotics and sedatives) on cognitive task performance (episodic memory, semantic memory, visuospatial ability) across 15 years, and the effect of discontinuing these medications in linear mixed effects models.

ResultsWe found that opioid use was associated with decline in visuospatial ability, whereas antidepressant use was associated with decline in semantic memory over 15 years. A link between drug discontinuation and cognitive improvement was seen for opioids, antidepressants as well as for anxiolytics, hypnotics and sedatives.

ConclusionsAlthough our results may be confounded by subjacent conditions, they suggest that long-term use of CNS medications may have domain-specific negative effects on cognitive performance over time, whereas the discontinuation of these medications may partly reverse these effects. These results open up for future studies that address subjacent conditions on cognition to develop a more complete understanding of the cognitive effects of CNS medications.


title: Investigation of a derived adverse outcome pathway (AOP) network for endocrine-mediated perturbations

abstract: An adverse outcome pathway (AOP) is a compact representation of the available mechanistic information on observed adverse effects upon environmental exposure. Sharing of events across individual AOPs has led to the emergence of AOP networks. Since AOP networks are expected to be functional units of toxicity prediction, there is current interest in their development tailored to specific research question or regulatory problem. To this end, we have developed a detailed workflow to construct a comprehensive endocrine-specific AOP (ED-AOP) network. Connectivity analysis of the ED-AOP network comprising 48 AOPs reveals 7 connected components and 12 isolated AOPs. Subsequently, we apply standard network measures to perform an in-depth analysis of the two largest connected components of the ED-AOP network. Notably, the graph-theoretic analyses led to the identification of important events including points of convergence or divergence in the ED-AOP network. Detailed analysis of the largest component in the ED-AOP network gives insights on the systems-level perturbations caused by endocrine disruption, emergent paths, and stressor-event associations. In sum, the derived ED-AOP network can be used to address the current knowledge gaps in the existing regulatory framework and aid in better risk assessment of environmental chemicals.

category: pharmacology and toxicology


title: Compounds enhancing human sperm motility identified using a high-throughput phenotypic screening platform

abstract:
Study questionCan a high-throughput screening platform facilitate male fertility drug discovery?

Summary answerA high-throughput screening platform identified a large number of compounds that enhanced sperm motility.

What is known alreadySeveral efforts to find small molecules modulating sperm function have been performed but not using high-throughput technology.

Study design, size, durationHealthy donor semen samples were used and samples were pooled (3-5 donors per pool). Primary screening was performed in singlicate; dose-response screening was performed in duplicate (independent donor pools).

Participants/materials, setting, methodsSpermatozoa isolated from healthy donors were prepared by density gradient centrifugation and incubated in 384-well plates with compounds (6.25 uM) to identify those compounds with enhancing effects on motility. A total of [~]17,000 compounds from the following libraries: ReFRAME, Prestwick, Tocris, LOPAC, CLOUD and MMV Pathogen Box were screened. Dose response experiments of screening hits were performed to confirm the enhancing effect on sperm motility. Experiments were performed in a University setting.

Main results and the role of chanceFrom our primary single concentration screening, 105 compounds elicited an enhancing effect on sperm motility compared to DMSO treated wells. Confirmed enhancing compounds were grouped based on their annotated targets/target classes. A major target class, phosphodiesterase inhibitors, were identified in particular PDE10A inhibitors as well as number of compounds not previously identified/known to enhance human sperm motility such as those related to GABA signaling.

Limitations, reasons for cautionCompounds have been tested with prepared donor spermatozoa and only incubated for a short period of time. Therefore, the effect of compounds on whole semen or with longer incubation time may be different. All experiments were performed in vitro.

Wider implications of the findingsThis phenotypic screening assay identified a large number of compounds that increased sperm motility. In addition to furthering our understanding of human sperm function, for example identifying new avenues for discovery, we highlight potential inhibitors as promising start-point for a medicinal chemistry programme for potential enhancement of male infertility. Moreover, with disclosure of the results of screening we present a substantial resource to inform further work in the field

Study funding/competing interest(s)This study was supported by the Bill and Melinda Gates Foundation and Scottish Funding Council and Scottish Universities Life Science Alliance.

category: physiology


title: Dry heat sterilization as a method to recycle N95 respirator masks: the importance of fit

abstract: In times of crisis, including the current COVID-19 pandemic, the supply chain of filtering facepiece respirators, such as N95 respirators, are disrupted. To combat shortages of N95 respirators, many institutions were forced to decontaminate and reuse respirators. While several reports have evaluated the impact on filtration as a measurement of preservation of respirator function after decontamination, the equally important fact of maintaining proper fit to the users face has been understudied. In the current study, we demonstrate the complete inactivation of SARS-CoV-2 and preservation of fit test performance of N95 respirators following treatment with dry heat. We apply scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDS), X-ray diffraction (XRD) measurements, Raman spectroscopy, and contact angle measurements to analyze filter material changes as a consequence of different decontamination treatments. We further compared the integrity of the respirator after autoclaving versus dry heat treatment via quantitative fit testing and found that autoclaving, but not dry heat, causes the fit of the respirator onto the users face to fail, thereby rendering the decontaminated respirator unusable. Our findings highlight the importance to account for both efficacy of disinfection and mask fit when reprocessing respirators to for clinical redeployment.

category: scientific communication and education


title: Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania

abstract: Aneuploidy causes system-wide disruptions in the stochiometric balances of transcripts, proteins, and metabolites, often resulting in detrimental effects for the organism. The protozoan parasite Leishmania has an unusually high tolerance for aneuploidy, but its molecular consequences remain poorly understood. Here, we present the first integrated analysis of the genome, transcriptome, proteome, and metabolome of highly aneuploid Leishmania donovani strains. Our analysis unambiguously establishes that, despite this tolerance, aneuploidy in Leishmania globally and proportionally impacts the transcriptome and proteome of affected chromosomes, ultimately explaining the degree of metabolic differences between strains. This impact was present in both proliferative and infectious life stages. Protein complex subunits, secreted proteins, and non-cytoplasmic proteins, responded less or even not at all to aneuploidy-induced dosage changes. In contrast to other Eukaryotes, widespread transcript regulation modulating aneuploidy-related stress was absent. Further, the majority of regulated proteins was encoded by non-aneuploid chromosomes and had no underlying transcript change, suggesting that aneuploidy induces extensive post-transcriptional protein-level modulation. This makes Leishmania a unique Eukaryotic model for elucidating post-transcriptional protein-abundance modulation in the context of aneuploidy.

category: systems biology


title: The Paradox of the Plankton: Coexistence of Structured Microbial Communities

abstract:
In the framework of resource-competition models, it has been argued that the number of species stably coexisting in an ecosystem cannot exceed the number of shared resources. However, plankton seems to be an exception of this so-called "competitive-exclusion principle". In planktic ecosystems, a large number of different species stably coexist in an environment with limited resources. This contradiction between theoretical expectations and empirical observations is often referred to as "The Paradox of the Plankton". This project aims to investigate biophysical models that can account for the large biodiversity observed in real ecosystems in order to resolve this paradox. A model is proposed that combines classical resource competition models, metabolic trade-offs and stochastic ecosystem assembly. Simulations of the model match empirical observations, while relaxing some unrealistic assumptions from previous models.

Paradox: from Greek para: "distinct from", and doxa: opinion. Sainsbury (1995) defines a paradox as "an apparently unacceptable conclusion derived by apparently acceptable reasoning from apparently acceptable premises". Paradoxes are useful research tools as they suggest logical inconsistencies. In order to spot the flaw, the validity of all the premises has to be carefully assessed.

Plankton: refers to the collection of organisms that spend part or all of their lives in suspension in water (Reynolds 2006). Plankton, or plankters, are "organisms that have velocities significantly smaller than oceanic currents and thus are considered to travel with the water parcel they occupy" (Lombard et al. 2019). Phytoplankters refer to the members of the plankton that perform photosynthesis.


title: GABA and IA Independently Regulate rNST Responses to Afferent Input

abstract: Taste responses in the rostral nucleus of the solitary tract (rNST) influence motivated ingestive behavior via ascending pathways, and consummatory reflex behavior via local, brainstem connections. Modifications to the afferent signal within the rNST include changes in gain (the overall rate of neuron activity) and changes in gustatory tuning (the degree to which individual neurons respond to divergent gustatory qualities). These alterations of the sensory signal derive from both synaptic interactions within the nucleus and the constitutive cellular membrane properties of rNST neurons. GABA neurons are well represented within the rNST, as is expression of KV4.3, a channel for a rapidly inactivating outward K+ current (IA). GABAergic synapses suppress rNST responses to afferent input and previous studies showed that this suppression is greater in cells expressing IA, suggesting a possible interaction. Here, we examine the potential interaction between GABAergic inhibition and IA channels in a series of patch clamp experiments. Optogenetic release of GABA suppressed rNST responses to afferent (electrical) stimulation and this effect was greater in cells with IA, confirming an earlier report. We further observed that the composite inhibitory postsynaptic potential was larger in IA positive cells, suggesting one mechanism for the greater afferent suppression. Blocking IA with the channel blocker AmmTX3, enhanced the response to afferent stimulation, suggesting a suppressive role for this channel in regulating afferent input at rest. However, pharmacologic blockade of IA did not suppress GABAergic inhibition, indicating that IA and GABA independently regulate excitatory afferent input.

category: neuroscience


title: The calcium sensor synaptotagmin-1 is critical for phasic axonal dopamine release in the striatum and mesencephalon, but is dispensable for basic motor behaviors in mice

abstract: Midbrain dopamine (DA) neurons, a population of cells that are critical for motor control, motivated behaviors and cognition, release DA via an exocytotic mechanism from both their axonal terminals and their somatodendritic (STD) compartment. In Parkinsons disease (PD), it is striking that motor dysfunctions only become apparent after extensive loss of DA innervation. Although it has been hypothesized that this resilience is due to the ability of many motor behaviors to be sustained through a basal tone of DA and diffuse transmission, experimental evidence for this is limited. Here we conditionally deleted the calcium sensor synaptotagmin-1 (Syt1) in DA neurons (cKODA mice) to abrogate most activity-dependent axonal DA release in the striatum and mesencephalon, leaving STD DA release intact. Strikingly, Syt1 cKODA mice showed intact performance in multiple unconditioned DA-dependent motor tasks, suggesting that activity-dependent DA release is dispensable for such basic motor functions. Basal extracellular levels of DA in the striatum were unchanged, suggesting that a basal tone of extracellular DA is sufficient to sustain basic movement. We also found multiple adaptations in the DA system of cKODA mice, similar to those happening at early stages of PD. Taken together, our findings reveal the striking resilience of DA-dependent motor functions in the context of a near-abolition of phasic DA release, shedding new light on why extensive loss of DA innervation is required to reveal motor dysfunctions in PD.


title: Chronic sodium bromide treatment relieves autistic-like behavioral deficits in three mouse models of autism

abstract: Autism Spectrum Disorders (ASD) are neurodevelopmental disorders whose diagnosis relies on deficient social interaction and communication together with repetitive behavior. To date, no pharmacological treatment has been approved that ameliorates social behavior in patients with ASD. Based on the excitation/inhibition imbalance theory of autism, we hypothesized that bromide ions, long used as an antiepileptic medication, could relieve core symptoms of ASD. We evaluated the effects of chronic sodium bromide (NaBr) administration on autistic-like symptoms in three genetic mouse models of autism: Oprm1-/- , Fmr1-/- and Shank3{Delta}ex13-16-/- mice. We showed that chronic NaBr treatment relieved autistic-like behaviors in these three models. In Oprm1-/- mice, these beneficial effects were superior to those of chronic bumetanide administration. At transcriptional level, chronic NaBr in Oprm1 null mice was associated with increased expression of genes coding for chloride ions transporters, GABAA receptor subunits, oxytocin and mGlu4 receptor. Lastly, we uncovered synergistic alleviating effects of chronic NaBr and a positive allosteric modulator (PAM) of mGlu4 receptor on autistic-like behavior in Oprm1-/- mice. We evidenced in heterologous cells that bromide ions behave as PAMs of mGlu4, providing a molecular mechanism for such synergy. Our data reveal the therapeutic potential of bromide ions, alone or in combination with a PAM of mGlu4 receptor, for the treatment of ASDs.


title: Gli1 regulates the postnatal acquisition of peripheral nerve architecture

abstract:
Peripheral nerves are organized into discrete cellular compartments. Axons, Schwann cells (SCs), and endoneurial fibroblasts (EFs) reside within the endoneurium and are surrounded by the perineurium - a cellular sheath comprised of layers of perineurial glia (PNG). SC secretion of Desert Hedgehog (Dhh) regulates this organization. In Dhh nulls, the perineurium is deficient and the endoneurium is subdivided into small compartments termed minifascicles. Human Dhh mutations cause a peripheral neuropathy with similar defects. Here we examine the role of Gli1, a canonical transcriptional effector of hedgehog signaling, in regulating peripheral nerve organization. We identify PNG, EFs, and pericytes as Gli1-expressing cells by genetic fate mapping. Although expression of Dhh by SCs and Gli1 in target cells is coordinately regulated with myelination, Gli1 expression unexpectedly persists in Dhh null EFs. Thus, Gli1 is expressed in EFs non-canonically i.e., independent of hedgehog signaling. Gli1 and Dhh also have non-redundant activities. In contrast to Dhh nulls, Gli1 nulls have a normal perineurium. Like Dhh nulls, Gli1 nulls form minifascicles, which we show likely arise from EFs. Thus, Dhh and Gli1 are independent signals: Gli1 is dispensable for perineurial development but functions cooperatively with Dhh to drive normal endoneurial development. During development, Gli1 also regulates endoneurial extracellular matrix production, nerve vascular organization, and has modest, non-autonomous effects on SC sorting and myelination of axons. Finally, in adult nerves, induced deletion of Gli1 is sufficient to drive minifascicle formation. Thus, Gli1 regulates the development and is required to maintain the endoneurial architecture of peripheral nerves.

SIGNIFICANCE STATEMENTPeripheral nerves are organized into distinct cellular/ECM compartments: the epineurium, perineurium and endoneurium. This organization, with its associated cellular constituents, are critical for the structural and metabolic support of nerves and their response to injury. Here, we show Gli1 - a transcription factor normally expressed downstream of hedgehog signaling - is required for the proper organization of the endoneurium but not the perineurium. Unexpectedly, Gli1 expression by endoneurial cells is independent of, and functions non-redundantly with, Schwann Cell-derived Desert Hedgehog in regulating peripheral nerve architecture. These results further delineate how peripheral nerves acquire their distinctive organization during normal development and highlight mechanisms that may regulate their reorganization in pathologic settings including peripheral neuropathies and nerve injury.


title: Dynamic and stable brain connectivity during movie watching as revealed by functional MRI

abstract: Spatially remote brain regions show synchronized activity as typically revealed by correlated functional MRI (fMRI) signals. An emerging line of research has focused on the temporal fluctuations of connectivity; however, its relationships with stationary connectivity have not been clearly illustrated. We examined dynamic and stationary connectivity when the participants watched four different movie clips. We calculated point-by-point multiplication between two regional time series to estimate the time-resolved dynamic connectivity, and estimated the inter-individual consistency of the dynamic connectivity time series. Widespread consistent dynamic connectivity was observed for each movie clip, which also showed differences between the clips. For example, a cartoon movie clip, Wall-E, showed more consistent of dynamic connectivity with the posterior cingulate cortex and supramarginal gyrus, while a court drama clip, A Few Good Men, showed more consistent of dynamic connectivity with the auditory cortex and temporoparietal junction, which might suggest the involvement of specific brain processing for different movie contents. In contrast, the stationary connectivity as measured by the correlations between regional time series was highly similar among the movie clips, and showed fewer statistically significant differences. The patterns of consistent dynamic connectivity could be used to classify different movie clips with higher accuracy than the stationary connectivity and regional activity. These results support the functional significance of dynamic connectivity in reflecting functional brain changes, which could provide more functionally relevant information than stationary connectivity.


title: Dynamic and stationary brain connectivity during movie watching as revealed by functional MRI


title: Defective endosome-TGN retrograde transport promotes NLRP3 inflammasome activation

abstract: Inflammasome complexes are pivotal in the innate immune response to pathogens and other danger signals1-4. The NLRP3 inflammasome is activated in response to a broad variety of cellular stressors. Most of the stimuli act in a potassium efflux-dependent manner but a primary and converging sensing mechanism by the NLRP3 receptor initiating inflammasome assembly remains ill-defined. Here we show that NLRP3 activators disrupt endosome-TGN retrograde transport (ETRT) and lead to localization of NLRP3 to endosomal vesicles. Genetic and pharmacologic perturbation of ETRT leads to accumulation of phosphoinositol-4-phosphate (PI4P) in endosomes to which NLRP3 is recruited. Disruption of ETRT potentiates NLRP3 inflammasome activation in murine and human macrophages in vitro. Mice with defects in ETRT in the myeloid compartment are more susceptible to LPS-induced sepsis showing enhanced mortality and IL-1{beta} serum levels as compared to control animals. Our study thus uncovers that changes in endocytic trafficking mediate NLRP3-dependent inflammatory responses.

category: immunology


title: The creation of ghost forests is driven by physical, ecological, and disturbance factors but remains a rare phenomenon

abstract: Marine transgression and the landward migration of coastlines in response to sea-level rise will determine the future of coastal ecosystems and species worldwide, yet no complete model of these processes exist. Ghost forests, areas where coastal forest has been killed by saltwater inundation, are an attention-grabbing early indicator of marine transgression. Research on marine transgression to date has largely been limited to place-based studies that, due to logistical constraints and foci of expertise, investigate subsets of the potential drivers of marine transgression. Here I take advantage of new open source datasets to provide the first systematic analysis of marine transgression across large scales, focusing on the creation of ghost forests across a region of ecological and scientific importance, the northeast U.S. My analysis provides the first synthesis of the physical, ecological, and disturbance factors that influence marine transgression. It also provides crucial regional context for more intensive studies that have a limited geographic scope. I found that ghost forests are a rare phenomenon in the landscape context: 95% of recent forest loss is concentrated in less than 3.86% of marshes, and between 2000 and 2018, only 0.88% of the entire forested area of the transgression zone experienced loss. As a result of this rarity, regional variation in marine transgression is largely driven by opportunities for rare events, which are more numerous when suitable conditions, such as shallow slopes, cover extensive areas. Quantifying recent trends in the rate of forest loss found little evidence of acceleration, with evidence instead suggesting that fewer ghost forests are being created. I also found that physical, ecological, and disturbance factors, including hurricane impacts, were all important for understanding recent trends in forest loss, suggesting that an interdisciplinary approach is warranted for future analyses and modeling of marine transgression. Such interdisciplinary research is urgently needed, as the current rate of marine transgression points to the likelihood of near-term losses of coastal wetlands, with dire implications for the species that depend on them.

category: ecology


title: Size-selective mortality fosters ontogenetic changes in collective risk-taking behaviour in zebrafish, Danio rerio

abstract: Size-selective mortality is common in fish populations and can operate either in a positive size-selective fashion or be negatively size-selective. Through various mechanisms (like genetic correlations among behaviour and life-history traits or direct selection on behaviour co-varying with growth rate or size-at-maturation), both positive- and negative size-selection can result in evolutionary changes in behavioural traits. Theory suggests that size-selection alone favours boldness, but little experimental evidence exists about whether and to what extent size-selection can trigger its evolution. Here we investigated the impact of size-selective mortality on boldness across ontogeny using three experimental lines of zebrafish (Danio rerio) generated through positive (large-harvested), negative (small-harvested) and random (control line) size-selective mortality for five generations. We measured risk-taking during feeding (boldness) under simulated aerial predation threat and in presence of a live cichlid. We found that boldness decreased with ontogenetic age under aerial predation threat, and the small-harvested line was consistently bolder than controls. Collective personality emerged post larval stages among the selection lines. In presence of a cichlid, the large-harvested line was bolder at the highest risk of predation. The large-harvested line showed higher variability and plasticity in boldness across life stages and predation risks. Collectively, our results demonstrate that size-selective harvesting may evolutionarily alter risk-taking tendency. Size-selection alone favours boldness when selection acts on small fish. Selection typical of fisheries operating on large fish favours boldness at the highest risk of predation and increases behavioural variability and plasticity. There was no evidence for positive size-selection favouring evolution of shyness.


title: Identifying synergies and antagonisms between plant defense traits in Asclepias syriaca

abstract: As a general rule, plants defend against herbivores with multiple traits. The defense synergy hypothesis posits that some traits are more potent when co-expressed with others, compared to their independent potency. However, this hypothesis has rarely been tested outside of synergies within a class of particular phytochemicals, and seldom under field conditions. We tested for synergies between multiple defense traits of common milkweed (Asclepias syriaca) by assaying the performance of two specialist herbivores on plants in natural populations. We employed both standard regression and exploratory analysis using a novel application of Random Forests that allowed us to detect synergies between defense traits. In hypothesis testing, we found the first empirical evidence for a previously hypothesized synergy between one pair of co-expressed defense traits (latex and cardenolides), but not another (latex and trichomes). When exploring all potential interactions between pairs of traits we found eight synergies and five antagonisms in predicting herbivore performance. Half of the identified synergies involved carbon, which is the basis of several defenses including chemical and physical barriers to feeding, and also essential nutrients. Our findings suggest that defense synergies could explain co-expression of latex and cardenolides in milkweeds. This synergy may be common among the diverse plant species that employ latex as a defense. Future studies should test carbon-based synergies, which our work suggests are prevalent, as well as the other synergies identified in our exploratory analysis. Our analytic approach provides a general, flexible framework for more broadly discovering and predicting the coexpression of traits through their synergistic function.


title: Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time

abstract:
AimWe tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene.

LocationSolimoes River, Western Amazon, South America

TaxonMyrmoborus lugubris, Thamnophilus cryptoleucus and Myrmotherula assimilis Methods: We analyzed thousands of UltraConserved Elements to explore spatial patterns of genetic diversity and connectivity between individuals. Range expansions were tested with alternative methods. We quantified habitat preference for the analyzed species in order to test if the occupation of dynamic habitats could predict spatial patterns of genetic diversity.

ResultsOur study did not support shared population range expansions related to historical regionalized changes in habitat availability. We found considerable variation in the spatial distribution of the genetic diversity between studied taxa, and that species with higher levels of specialization to dynamic environments have a more heterogeneous distribution of genetic diversity and reduced levels of gene flow across space.

Main conclusionsOur results suggest that demographic expansions along the Solimoes River might be linked to geographic homogeneous oscillation in the distribution of floodplain environments, promoting effective population size changes but not range expansion. We found that habitat specificity might be a good predictor of population connectivity along the Amazonian floodplains.

category: evolutionary biology


title: Weak selection and the separation of eco-evo time scales using perturbation analysis

abstract: We show that under the assumption of weak frequency-dependent selection a wide class of population dynamical models can be analysed using perturbation theory. The inner solution corresponds to the ecological dynamics, where to zeroth order, the genotype frequencies remain constant. The outer solution provides the evolutionary dynamics and corresponds, to zeroth order, to a generalisation of the replicator equation. We apply this method to a model of public goods dynamics and construct, using matched asymptotic expansions, a composite solution valid for all times. We also analyse a Lotka-Volterra model of predator competition and show that to zeroth order the fraction of wild-type predators follows a replicator equation with a constant selection coefficient given by the predator death rate. For both models we investigate how the error between approximate solutions and the solution to the full model depend on the order of the approximation, and show using numerical comparison, for k = 1 and 2, that the error scales according to{varepsilon} k+1, where{varepsilon} is the strength of selection and k is the order of the approximation.


title: High-quality genome assembly of Cinnamomum burmami (chvar. Borneol) provides insights into the natural borneol biosynthesis

abstract: Cinnamomum burmannii (chvar. Borneol) is a well-known medicinal and industrial plant cultivated in the Lingnan region of China. It is the key source from organism of natural borneol (D-borneol), one of the precious and widely used Chinese herbal medicines with a variety of medicinal effects. Here, we report a high-quality chromosome-scale genome assembly of C. burmannii (chvar. Borneol) using Pacbio single-molecule sequencing and Hi-C technology. The assembled genome size was 1.14 GB with a scaffold N50 of 94.30 Mb, while 98.77% of the assembled sequences were anchored on 12 pseudochromosomes including 41549 protein-coding genes. Genomic evolution analysis revealed C. burmannii and C. micranthum shared two Lauraceae unique ancestral whole-genome duplication (WGD) events. Likewise, comparative genomic analysis showed strong collinearity between these two species. Besides, the analysis for Long Terminal Repeat Retrotransposons (LTR-RTs) indicated the outbreak of LTR-RTs insertion made a great contribution to the size difference of genomes between C. burmannii and C. micranthum. Furthermore, the candidate genes in pathway associated with natural borneol synthesis were identified on the genome and their differential expressions were analyzed in various biological tissues. We considered that several of genes in Mevalonate (MVA) Methylerythritol Phosphate (MEP) pathways or in downstream pathway have the potential to be the key factors in the biosynthesis of D-borneol. We also constructed the genome database (CAMD; http://www.cinnamomumdatabase.com/) of Cinnamomum species for a better data utilization in the future. All these results will enrich the genomic data of Lauraceae plants and facilitate genetic improvement of this commercially important plant.

category: genomics


title: High-quality genome assembly of Cinnamomum burmannii (chvar. Borneol) provides insights into the natural borneol biosynthesis


title: Social modulation of oogenesis and egg-laying in Drosophila melanogaster

abstract:
Being part of a group facilitates cooperation between group members, but also creates competition for limited resources. This conundrum is problematic for gravid females who benefit from being in a group, but whose future offspring may struggle for access to nutrition in larger groups. Females should thus modulate their reproductive output depending on their social context. Although social-context dependent modulation of reproduction is documented in a broad range of species, its underlying mechanisms and functions are poorly understood. In the fruit fly Drosophila melanogaster, females actively attract conspecifics to lay eggs on the same resources, generating groups in which individuals may cooperate or compete. The tractability of the genetics of this species allows dissecting the mechanisms underlying physiological adaptation to their social context.

Here, we show that females produce eggs increasingly faster as group size increases. By laying eggs faster in group than alone, females appear to reduce competition between offspring and increase their likelihood of survival. In addition, females in a group lay their eggs during the light phase of the day, while isolated females lay them during the night. We show that responses to the presence of others are determined by vision through the motion detection pathway and that flies from any sex, mating status or species can trigger these responses. The mechanisms of this modulation of egg-laying by group is connected to a lifting of the inhibition of light on oogenesis and egg-laying by stimulating hormonal pathways involving juvenile hormone. Because modulation of reproduction by social context is a hallmark of animals with higher levels of sociality, our findings represent a protosocial mechanism in a species considered solitary that may have been the target of selection for the evolution of more complex social systems.

category: animal behavior and cognition


title: 3D Microenvironment-Specific Mechanosensing Regulates Neural Stem Cell Lineage Commitment

abstract: While extracellular matrix (ECM) mechanics strongly regulate stem cell commitment, the fields mechanistic understanding of this phenomenon largely derives from simplified two-dimensional (2D) culture substrates. Here we found a three-dimensional (3D) matrix-specific mechanoresponsive mechanism for neural stem cell (NSC) differentiation. NSC lineage commitment in 3D is maximally stiffness-sensitive in the range of 0.1-1.2 kPa, a narrower and more brain-mimetic range than we had previously identified in 2D (0.75 - 75 kPa). Transcriptomics revealed stiffness-dependent upregulation of early growth response 1 (Egr1) in 3D but not in 2D. Egr1 knockdown enhanced neurogenesis in stiff ECMs by driving {beta}-catenin nuclear localization and activity in 3D, but not in 2D. Mechanical modeling and experimental studies under osmotic pressure indicate that stiff 3D ECMs are likely to stimulate Egr1 via increases in confining stress during cell volumetric growth. To our knowledge, Egr1 represents the first 3D-specific stem cell mechanoregulatory factor.

category: bioengineering


title: Potential Key Genes Associated with Stroke types and its subtypes: A Computational Approach

abstract: To investigate prospective key genes and pathways associated with the pathogenesis and prognosis of stroke types along with subtypes. Human genes using genome assembly build 38 patch release 13 with known gene symbols through NCBI gene database (https://www.ncbi.nlm.nih.gov/gene) were fetched. PubMed advanced queries were constructed using stroke-related keywords and associations were calculated using Normalized pointwise mutual information (nPMI) between each gene symbol and queries. Genes related with stroke risk within their types and subtypes were investigated in order to discover genetic markers to predict individuals who are at the risk of developing stroke with their subtypes. A total of 2,785 (9.4%) genes were found to be linked to the risk of stroke. Based on stroke types, 1,287 (46.2%) and 376 (13.5%) genes were found to be related with IS and HS respectively. Further stratification of IS based on TOAST classification, 86 (6.6%) genes were confined to Large artery atherosclerosis; 131 (10.1%) and 130 (10%) genes were related with the risk of small vessel disease and Cardioembolism subtypes of IS. Besides, a prognostic panel of 9 genes signature consisting of CYP4A11, ALOX5P, NOTCH, NINJ2, FGB, MTHFR, PDE4D, HDAC9, and ZHFX3 can be treated as a diagnostic marker to predict individuals who are at the risk of developing stroke with their subtypes.

category: bioinformatics


title: Effect of SFX-01 on proliferation of human glioblastoma cell lines

abstract: Glioblastoma (GBM) is the most aggressive and lethal of brain tumours and there is a clear need for novel therapies. SFX-01, a stabilised formu of sulforaphane (SFN) that is complexed with -cyclodextrin, is being investigated as a potential anticancer drug. And as part of this investigation we have determined its effect on the proliferation of a series of tumour cell lines. Growth-inhibitory concentrations (IC50 values) of SFX-01 and reference SFN were highly correlated but showed a divergence at higher drug concentrations that is likely to reflect drug binding to -cyclodextrin complexes. Because SFN is redox-sensitive, we also compared the effects of these drugs on four GBM lines that had been derived and cultured under physiological oxygen (5%) conditions. Comparisons were also made using a three-dimensional spheroid model, used to mimic the in vivo state of glioblastomas and to simulate barriers to drug delivery in vivo. SFX-01 and reference SFN and inhibited proliferation of four GBM cell lines in monolayers as well as in spheroids; -cyclodextrin alone had no significant effect. Our results are consistent with the hypothesis that SFN is liberated from SFX-01 at concentrations sufficient to inhibit cell growth. We envision that SFX-01 will have improved pharmacokinetic properties in vivo, warranting further pre-clinical investigation and clinical development.

category: cancer biology


title: Identification of a discrete neuronal circuit that relays insulin signaling into the brain to regulate glucose homeostasis

abstract:
26RFa (QRFP) is a biologically active peptide that regulates glucose homeostasis by acting as an incretin and by increasing insulin sensitivity at the periphery. 26RFa is also produced by a neuronal population localized in the hypothalamus. In the present study, we have investigated whether the 26RFa neurons may be involved in the hypothalamic regulation of glucose homeostasis. Our data indicate that 26RFa, i.c.v. injected, induces a robust antihyperglycemic effect associated with an increase of insulin production by the pancreatic islets. In addition, we found that insulin strongly stimulates 26RFa expression and secretion by the hypothalamus. RNAscope experiments revealed that neurons expressing 26RFa in the lateral hypothalamic area and the ventromedial hypothalamic nucleus also express the insulin receptor and that insulin induces the expression of 26RFa in these neurons. Concurrently, we show that the central antihyperglycemic effect of insulin is abolished in presence of a 26RFa receptor (GPR103) antagonist as well as in mice deficient for 26RFa. Finally, our data indicate that the hypothalamic 26RFa neurons are not involved in the central inhibitory effect of insulin on hepatic glucose production, but mediate the central effects of the hormone on its own peripheral production.

To conclude, in the present study we have identified a novel actor of the hypothalamic regulation of glucose homeostasis, the 26RFa/GPR103 system and we provide the evidence that this neuronal peptidergic system is a key relay for the central regulation of glucose metabolism by insulin.


title: Muscle weakness precedes atrophy during cancer cachexia and is associated with muscle-specific mitochondrial stress

abstract: Muscle weakness and wasting are defining features of cancer-induced cachexia. Mitochondrial stress occurs before atrophy in certain muscles, but distinct responses between muscles and across time remains unclear. We aimed to determine the time-dependent and muscle-specific responses to Colon-26 (C26) cancer-induced cachexia in mice. At 2 weeks post-inoculation, the presence of small tumours did not alter body or muscle mass but decreased force production in the quadriceps and diaphragm. Pyruvate-supported mitochondrial respiration was lower in quadriceps while mitochondrial H2O2 emission was elevated in diaphragm. At 4 weeks, large tumours corresponded to lower body mass, muscle mass, and cross-sectional area of fibers in quadriceps and diaphragm. Force production in quadriceps was unchanged but remained lower in diaphragm vs control. Mitochondrial respiration was increased while H2O2 emission was unchanged in both muscles vs control. Mitochondrial creatine sensitivity was compromised in quadriceps. These findings indicate muscle weakness precedes atrophy in quadriceps and diaphragm but is linked to heterogeneous mitochondrial alterations. Eventual muscle-specific restorations in force and bioenergetics highlight how the effects of cancer on one muscle do not predict the response in another muscle. Exploring heterogeneous responses of muscles to cancer may reveal new mechanisms underlying distinct sensitivities, or resistance, to cancer cachexia.


title: A graph-based framework for multi-scale modeling of physiological transport

abstract:
Trillions of chemical reactions occur in the human body every second, where the generated products are not only consumed locally but also transported to various locations in a systematic manner to sustain homeostasis. Current solutions to model these biological phenomena are restricted in computability and scalability due to the use of continuum approaches where it is practically impossible to encapsulate the complexity of the physiological processes occurring at diverse scales. Here we present a discrete modeling framework defined on an interacting graph that offers the flexibility to model multiscale systems by translating the physical space into a metamodel. We discretize the graph-based metamodel into functional units composed of well-mixed volumes with vascular and cellular subdomains; the operators defined over these volumes define the transport dynamics. We predict glucose drift governed by advective-dispersive transport in the vascular subdomains of an islet vasculature and cross-validate the flow and concentration fields with finite-element based COMSOL simulations. Vascular and cellular subdomains are coupled to model the nutrient exchange occurring in response to the gradient arising out of reaction and perfusion dynamics. The application of our framework for modeling biologically relevant test systems shows how our approach can assimilate both multi-omics data from in vitro - in vivo studies and vascular topology from imaging studies for examining the structure-function relationship of complex vasculatures. The framework can advance simulation of whole-body networks at user-defined levels and is expected to find major use in personalized medicine and drug discovery.

GRAPHICAL ABSTRACT

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title: Microbench: Automated metadata management for systems biology benchmarking and reproducibility in Python

abstract:
MotivationComputational systems biology analyses typically make use of multiple software and their dependencies, which often run across heterogeneous compute environments. This can introduce differences in performance and reproducibility. Capturing metadata (e.g. package versions, GPU model) currently requires repetitious code and is difficult to store centrally for analysis. Even where virtual environments and containers are used, updates over time mean that versioning metadata should still be captured within analysis pipelines to guarantee reproducibility.

ResultsMicrobench is a simple and extensible Python package to automate metadata capture to a file or Redis database. Captured metadata can include execution time, software package versions, environment variables, hardware information, Python version, and more, with plugins. We present three case studies demonstrating Microbench usage to benchmark code execution and examine environment metadata for reproducibility purposes.

AvailabilityInstall from the Python Package Index using pip install microbench. Source code is available from https://github.com/alubbock/microbench.

Contactc.lopez@vanderbilt.edu


title: Divergent encoding of active avoidance behavior in corticostriatal and corticolimbic projections

abstract: Active avoidance behavior, in which an animal performs an action to avoid a stressor, is crucial for survival and may provide insight into avoidance behaviors seen in anxiety disorders. Active avoidance requires the dorsomedial prefrontal cortex (dmPFC), which is thought to regulate avoidance via downstream projections to the striatum and amygdala. However, the endogenous activity of projection-defined dmPFC subpopulations during active avoidance learning remains unexplored. Here we utilized fiber photometry to record from the dmPFC and its downstream projections to the dorsomedial striatum (DMS) and the basolateral amygdala (BLA) during active avoidance learning in mice. We examined neural activity during conditioned stimulus (CS) presentations, active avoidance, and cued freezing. Both prefrontal projections showed learning-related increases in activity during CS onset throughout active avoidance training. The dmPFC as a whole showed increased activity during avoidance and decreased activity during cued freezing. Finally, dmPFC-DMS and dmPFC-BLA projections showed divergent encoding of active avoidance behavior, with the dmPFC-DMS projection showing increased activity and the dmPFC-BLA showing decreased activity during active avoidance. Our results identify differential prefrontal encoding of active and passive coping behaviors in the same behavioral paradigm and demonstrate divergent encoding of active avoidance in projection-specific dmPFC subpopulations.


title: Crocin inhibited amyloid-beta (Aβ) generation via promoting non-amyloidogenic APP processing and suppressed ER stress UPR signaling in N2a/APP cells

abstract:
BackgroundCrocin is a major active component of saffron (Crocus sativus) with many beneficial effects. More recently, crocin has been proposed for management of neurodegenerative diseases such as Alzheimers disease (AD). Here, we demonstrated for the first time that crocin reduced amyloid-beta (A{beta}) generation through promoting -cleavage of APP processing and inhibited ER stress by attenuating UPR signaling in N2a/APP cells.

MethodologyMouse neuroblastoma N2a cells stably transfected with the Swedish mutant APP (N2a/APP) was used as a cellular model for AD pathogenesis. Vector transfected cells (N2a/vector) were employed to serve as control. The toxicity of crocin was first evaluated and non-toxic treatment of crocin (>30 {micro}M for 24 h) was used for further investigations. A{beta} levels were determined by ELISA. Expression levels of UPR signaling proteins were determined by using Western blot.

ResultsCrocin significantly inhibited the protein expression of total APP in N2a/APP cells and promoted -cleavage of APP processing to increase sAPP generation, but only modestly reduced BACE-1 and PS1, suggesting A{beta} reduction by crocin was mainly associated with the non-amyloidogenic APP processing. Further investigation on ER stress related protein expressions showed that GRP78, CHOP, p-PERK, p-eIF2, p-IRE1, XBP1, ATF6 and PDI were all significantly elevated in N2a/APP cells compared to N2a/vector. Crocin effectively reduced the levels of GRP78 and CHOP, and significantly inhibited p-PERK/p-eIF2 amd AT6 while slightly reduced p-IRE1.

ConclusionThe present study showed that crocin was effective at blocking A{beta} generation and inhibiting ER stress associated overactivation of UPR signaling in AD cell model N2a/APP. The results provided evidence for crocin as useful natural product for the treatment of AD.


title: Reward enhances memory via age-varying online and offline neural mechanisms across development

abstract: Reward motivation enhances memory through interactions between mesolimbic, hippocampal, and cortical systems -- both during and after encoding. Developmental changes in these distributed neural circuits may lead to age-related differences in reward-motivated memory and the underlying neural mechanisms. Converging evidence from cross-species studies suggests that subcortical dopamine signaling is increased during adolescence, which may lead to stronger memory representations of rewarding, relative to mundane, events and changes in the contributions of underlying subcortical and cortical brain mechanisms across age. Here, we used fMRI to examine how reward motivation influences the "online" encoding and "offline" post-encoding brain mechanisms that support long-term associative memory from childhood to adulthood. We found that reward motivation led to both age-invariant as well as adolescent-specific enhancements in associative memory after 24 hours. Furthermore, reward-related memory benefits were linked to age-varying neural mechanisms. During encoding, interactions between the prefrontal cortex and ventral tegmental area (VTA) were associated with better high-reward memory to a greater degree with increasing age. Pre-to post-encoding changes in functional connectivity between the anterior hippocampus and VTA were also associated with better high-reward memory, but more so at younger ages. Our findings suggest that there may be developmental shifts -- from offline subcortical to online cortical processes -- in the brain mechanisms supporting reward-motivated memory.


title: Identification of the safe harbor locus, AAVS1, from porcine genome and site-specific integration of recombinase-mediated cassette exchange system in porcine fibroblasts using CRISPR/Cas9

abstract: Gene integration at site-specific loci, such as safe harbor regions for stable expression via transgenesis, is a critical approach for understanding the function of a gene in cells or animals. The AAVS1 locus is a well-known safe harbor site for human and mouse studies. In the present study, we found an AAVS1-like sequence in the porcine genome using the UCSC Genome Browser and designed TALEN and CRISPR/Cas9 to target AAVS1. The efficiency of CRISPR/Cas9 for targeting the AAVS1 locus in porcine cells was superior to that of TALEN. An AAVS1-targeting donor vector containing GFP was designed and cloned. We added a loxP-lox2272 cassette sequence to the donor vector for further exchange of various transgenes in the AAVS1-targeted cell line. The donor vector and CRISPR/Cas9 components targeting AAVS1 were transfected into a porcine fibroblast cell line. Targeted cells of CRISPR/Cas9-mediated homologous recombination were identified by antibiotic selection. Gene knock-in at the AAVS1 locus was confirmed by PCR analysis. To induce recombinase-mediated cassette exchange (RMCE), another donor vector containing the loxP-lox2272 cassette and inducible (Tet-on) Cre recombinase was cloned. The Cre-donor vector was transfected into the AAVS1-targeted cell line, and RMCE was induced by adding doxycycline to the culture medium. RMCE in porcine fibroblasts was confirmed using PCR analysis. In conclusion, gene targeting at the AAVS1 locus and RMCE in porcine fibroblasts was successful. This technology will be useful for future porcine transgenesis studies and the generation of stable transgenic pigs.

category: molecular biology


title: The future impact of climate and land-use changes on Anatolian ground squirrels under different scenarios

abstract: Climate and land-use changes are among the most important drivers of biodiversity loss and, moreover, their impacts on biodiversity are expected to increase further in the 21st century. In this study, the future impact of climate and land-use changes on Anatolian ground squirrels was assessed. Accordingly, a hierarchical approach with two steps was used. First, ecological niche modelling was used to assess the impact of climate change in areas accessible to Anatolian ground squirrels through dispersal (i.e. the impact of climate change). Second, based on the habitat preferences of ground squirrels, land-use data were used to assess the impact of land-use change in suitable bioclimatic areas for Anatolian ground squirrels under present and future conditions (i.e. the combined impact of both changes). Also, priority areas for the conservation of Anatolian ground squirrels were identified based on in-situ climate change refugia. This study represents a first attempt to combine niche modelling and land-use data for a species in Anatolia, one of the most vulnerable regions to the drivers of biodiversity loss, because it is the region where three of biodiversity hotspots meet, and interact. Habitat availability (i.e. suitable habitats across suitable bioclimatic areas) was projected to decline by 19-69% in the future (depending on the scenario), mainly due to the loss of suitable bioclimatic areas (47-77%, depending on the scenario) at lower elevations and in the western part of the central Anatolia and in the eastern Anatolia, suggesting that Anatolian ground squirrels will contract their range in the future, mainly due to climate change. Thus, in-situ climate change refugia were projected mainly in the eastern and southeastern parts of the central Anatolia, suggesting these regions as priority areas for the conservation of Anatolian ground squirrels.


title: The genetic basis of tail-loss evolution in humans and apes

abstract: The loss of the tail is one of the main anatomical evolutionary changes to have occurred along the lineage leading to humans and to the "anthropomorphous apes"1,2. This morphological reprogramming in the ancestral hominoids has been long considered to have accommodated a characteristic style of locomotion and contributed to the evolution of bipedalism in humans3-5. Yet, the precise genetic mechanism that facilitated tail-loss evolution in hominoids remains unknown. Primate genome sequencing projects have made possible the identification of causal links between genotypic and phenotypic changes6-8, and enable the search for hominoid-specific genetic elements controlling tail development9. Here, we present evidence that tail-loss evolution was mediated by the insertion of an individual Alu element into the genome of the hominoid ancestor. We demonstrate that this Alu element - inserted into an intron of the TBXT gene (also called T or Brachyury10-12) - pairs with a neighboring ancestral Alu element encoded in the reverse genomic orientation and leads to a hominoid-specific alternative splicing event. To study the effect of this splicing event, we generated a mouse model that mimics the expression of human TBXT products by expressing both full-length and exon-skipped isoforms of the mouse TBXT ortholog. We found that mice with this genotype exhibit the complete absence of a tail or a shortened tail, supporting the notion that the exon-skipped transcript is sufficient to induce a tail-loss phenotype, albeit with incomplete penetrance. We further noted that mice homozygous for the exon-skipped isoforms exhibited embryonic spinal cord malformations, resembling a neural tube defect condition, which affects [~]1/1000 human neonates13. We propose that selection for the loss of the tail along the hominoid lineage was associated with an adaptive cost of potential neural tube defects and that this ancient evolutionary trade-off may thus continue to affect human health today.


title: Integrating Transcriptomics, Genomics, and Imaging in Alzheimer's Disease: A Federated Model

abstract: Alzheimers disease (AD) affects more than 1 in 9 people age 65 and older and becomes an urgent public health concern as the global population ages. In clinical practice, structural magnetic resonance imaging (sMRI) is the most accessible and widely used diagnostic imaging modality. Additionally, genome-wide association studies (GWAS) and transcriptomics - the study of gene expression - also play an important role in understanding AD etiology and progression. Sophisticated imaging genetics systems have been developed to discover genetic factors that consistently affect brain function and structure. However, most studies to date focused on the relationships between brain sMRI and GWAS or brain sMRI and transcriptomics. To our knowledge, few methods have been developed to discover and infer multimodal relationships among sMRI, GWAS, and transcriptomics. To address this, we propose a novel federated model, Genotype-Expression-Imaging Data Integration (GEIDI), to identify genetic and transcriptomic influences on brain sMRI measures. The relationships between brain imaging measures and gene expression are allowed to depend on a persons genotype at the single-nucleotide polymorphism (SNP) level, making the inferences adaptive and personalized. We performed extensive experiments on publicly available Alzheimers Disease Neuroimaging Initiative (ADNI) dataset. Experimental results demonstrated our proposed method outperformed state-of-the-art expression quantitative trait loci (eQTL) methods for detecting genetic and transcriptomic factors related to AD and has stable performance when data are integrated from multiple sites. Our GEIDI approach may offer novel insights into the relationship among image biomarkers, genotypes, and gene expression and help discover novel genetic targets for potential AD drug treatments.


title: Long-term in vivo imaging of mouse spinal cord through an optically cleared intervertebral window

abstract: Spinal cord, as part of the central nervous system, accounts for the main communication pathway between the brain and the peripheral nervous system. Spinal cord injury is a devastating and largely irreversible neurological trauma, and can result in lifelong disability and paralysis with no available cure. In vivo spinal cord imaging in mouse models without introducing immunological artifacts is critical to understand spinal cord pathology and discover effective treatments. We developed a minimal-invasive intervertebral window by retaining ligamentum flavum to protect the underlying spinal cord. By introducing an optical clearing method, we achieved repeated two-photon fluorescence and stimulated Raman scattering imaging at subcellular resolution with up to 16 imaging sessions over 167 days and observed no inflammatory response. Using this optically cleared intervertebral window, we studied the neuron-glia dynamics following laser axotomy and observed strengthened contact of microglia with the nodes of Ranvier during axonal degeneration. By enabling long-term, repetitive, stable, high-resolution and inflammation-free imaging of mouse spinal cord, our method provides a reliable platform in the research aiming at understanding and treatment of spinal cord pathology.


title: A model of preferential pairing between epithelial and dendritic cells in thymic antigen transfer

abstract: Medullary thymic epithelial cells (mTECs) which produce and present self-antigens are essential for the establishment of central tolerance. Since mTEC numbers are limited, their function is complemented by thymic dendritic cells (DCs), which transfer mTEC-produced self-antigens via cooperative antigen transfer (CAT). While CAT is required for effective T cell selection, many aspects remain enigmatic. Given the recently described heterogeneity of mTECs and DCs, it is unclear whether the antigen acquisition from a particular TEC subset is mediated by preferential pairing with specific subset of DCs. Using several relevant Cre-based mouse models controlling the expression of fluorescent proteins, we found that in regards to CAT, each subset of thymic DCs preferentially targets distinct mTEC subset(s) and importantly, XCR1+ activated DCs represented the most potent subset in CAT. Interestingly, one thymic DC can acquire antigen repetitively and of these, monocyte-derived DCs (moDC) were determined to be the most efficient in repetitive CAT. moDCs also represented the most potent DC subset in the acquisition of antigen from other DCs. These findings suggest a preferential pairing model for the distribution of mTEC-derived antigens among distinct populations of thymic DCs.


title: Anti-SARS-CoV-2 IgG and IgA antibodies in COVID-19 convalescent plasma do not facilitate antibody-dependent enhance of viral infection.

abstract: The novel coronavirus SARS-CoV2, which causes COVID-19, has resulted in the death of nearly 4 million people within the last 18 months. While preventive vaccination and monoclonal antibody therapies have been rapidly developed and deployed, early in the pandemic the use of COVID-19 convalescent plasma (CCP) was a common means of passive immunization, with the theoretical risk of antibody-dependent enhancement (ADE) of viral infection remaining undetermined. Though vaccines elicit a strong and protective immune response, and transfusion of CCP with high titers of neutralization activity are correlated with better clinical outcomes, the question of whether antibodies in CCP can enhance infection of SARS-CoV2 has not been directly addressed. In this study, we analyzed for and observed passive transfer of neutralization activity with CCP transfusion. Furthermore, to specifically understand if antibodies against the spike protein (S) enhance infection, we measured the anti-S IgG, IgA, and IgM responses and adapted retroviral-pseudotypes to measure virus neutralization with target cells expressing the ACE2 virus receptor and the Fc alpha receptor (FcR) or Fc gamma receptor IIA (Fc{gamma}RIIA). Whereas neutralizing activity of CCP correlated best with higher titers of anti-S IgG antibodies, the neutralizing titer was not affected when Fc receptors were present on target cells. These observations support the absence of antibody-dependent enhancement of infection (ADE) by IgG and IgA isotypes found in CCP. The results presented, therefore, support the clinical use of currently available antibody-based treatment including the continued study of CCP transfusion strategies.


title: Antifungal activity of fibrate-based compounds and substituted pyrroles inhibiting the enzyme 3-hydroxy-methyl-glutaryl-CoA reductase of Candida glabrata (CgHMGR), and decreasing yeast viability and ergosterol synthesis

abstract:
Due to the emergence of multi-drug resistant strains of yeasts belonging to the Candida genus, there is an urgent need to discover antifungal agents directed at alternative molecular targets. The aim of the current study was to evaluate the capacity of synthetic compounds to inhibit the Candida glabrata enzyme denominated 3-hydroxy-methyl-glutaryl-CoA reductase (CgHMGR), and thus affect ergosterol synthesis and yeast viability. One series of synthetic antifungal compounds were analogues to fibrates, a second series had substituted 1,2-dihydroquinolines and the third series included substituted pyrroles. -asarone-related compounds 1c and 5b with a pyrrolic core were selected as the best antifungal candidates. Both inhibited the growth of fluconazole-resistant C. glabrata 43 and fluconazole-susceptible C. glabrata CBS 138. A yeast growth rescue experiment based on the addition of exogenous ergosterol showed that the compounds act by inhibiting the mevalonate synthesis pathway. A greater recovery of yeast growth occurred for the C. glabrata 43 strain and after the 1c (versus 5b) treatment. Given that the compounds decreased the ergosterol concentration in the yeast strains, they probably target the ergosterol synthesis. According to the docking analysis, the inhibitory effect of the 1c and 5b could possibly be mediated by their interaction with the amino acid residues of the catalytic site of CgHMGR. Since 1c displayed higher binding energy than -asarone and 5b, it is a good candidate for further research, which should include structural modifications to increase its specificity and potency as well as in vivo studies on its effectiveness at a therapeutic dose.

HIGHLIGHTSO_LIFibrate-based and pyrrole-containing compounds were tested as C. glabrata inhibitors.
C_LIO_LIThe best inhibitor from fibrate was 1c and from pyrroles was 5b.
C_LIO_LIThese agents inhibited C. glabrata growth better than the reference antifungals.
C_LIO_LIThey also inhibited ergosterol synthesis by the two C. glabrata strains tested. Experimental
C_LI

category: microbiology


title: Exploring the effects of CO2 elevation on seedlings' growth of Acacia senegal in the era of changes

abstract: Acacia senegal is a priority and important C3 tree species in drylands of Sudan and across the gum belt. Investigation of its seedlings response to elevated carbon dioxide (eCO2) is important as atmospheric ([CO2]) has increased and predicted to continue to rise. Many studies showed that eCO2 causes increased photosynthesis in plants, which leads to greater production of carbohydrates and biomass, and increased soil organic matter and carbon content. This study investigated the effects of eCO2 on A. senegal seedlings grown in sand and silt soils under irrigation intervals of every day and every two days. Seven days old seedlings were assigned to the treatments in Split - spilt plot design for 4 weeks. The main plot is eCO2 (600-800 ppm) and ambient ([≤]400 ppm) under Free Air CO2 Enrichment (FACE) system. Subplots are irrigation intervals and soil types. Seedling height and number of leaves were measured weekly, and seedlings were harvested after 4 weeks where growth parameters and soil properties were measured. The eCO2 showed no effect on the measured parameters except the significant increase in tap-root length. However, the irrigation every day showed significant increase than every two days in seedlings height, number of leaves, root length and seedlings dry weight but not seedlings and soil C% & N%. Soil treatment showed effects on stem height, leaf number, seedlings dry weight, leaves and root N% and soil C% but not root length, seedling C% and soil N%. The results indicate the importance of soil moisture, physical and chemical properties that reflects adaptation of the species to its dry land environment.


title: Fitting deterministic population models tostochastic data: from trajectory matching tostate-space models

abstract:
O_LIPopulation and community ecology traditionally has a very strong theoretical foundation with well-known models, such as the logistic and its many variations, and many modification of the classical Lotka-Volterra predator-prey and interspecific competition models. More and more, these classical models are confronted to data via fitting to empirical time-series for purposes of projections or for estimating model parameters of interest. However, the interface between mathematical population or community models and data, provided by a statistical model, is far from trivial.
C_LIO_LIIn order to help empiricists, especially researchers working with experimental laboratory populations in micro- and mesocosms, make informed decisions, we here ask which error structure one should use when fitting classical deterministic ODE models to empirical data, from single species to community dynamics and trophic interactions. We use both realistically simulated data and empirical data from microcosms to answer this question in a Bayesian framework.
C_LIO_LIWe find that many model parameters can be estimated precisely with an appropriate choice of error structure using pure observation error or state-space models, if observation errors are not too high. However, Allee effect models are typically hard to identify and state-space models should be preferred with when model complexity increases.
C_LIO_LIOur work shows that, at least in the context of experimental laboratory populations, deterministic models can be used to describe stochastic population dynamics that include process variability and observation error. Also, many scenarios do not require a complex state-space model formulation and simpler trajectory matching is sufficient for accurate parameter estimates. Finally, we provide a comprehensive tutorial for fitting these models in R.
C_LI


title: Confronting population models with experimental microcosm data: from trajectory matching to state-space models


title: A root for massive crown-of-thorns starfish outbreaks in the Pacific Ocean

abstract: Recurring outbreaks of crown-of-thorns starfish (COTS) severely damage healthy corals in the Western Pacific Ocean. To determine the source of outbreaking COTS larvae and their dispersal routes across the Western Pacific, complete mitochondrial genomes were sequenced from 243 individuals collected in 11 reef regions. Our results indicate that Pacific COTS comprise two major clades, an East-Central Pacific clade (ECP-C) and a Pan-Pacific clade (PP-C). The ECP-C consists of COTS from French Polynesia (FP), Fiji, Vanuatu and the Great Barrier Reef (GBR), and does not appear prone to outbreaks. In contrast, the PP-C, which repeatedly spawns outbreaks, is a large clade comprising COTS from FP, Fiji, Vanuatu, GBR, Papua New Guinea, Vietnam, the Philippines, Japan, Micronesia, and the Marshall Islands. Given the nature of Pacific Ocean currents, the vast area encompassing FP, Fiji, Vanuatu, and the GBR likely supplies larvae for repeated outbreaks, exacerbated by anthropogenic environmental changes, such as eutrophication.


title: Testing for heterogeneous rates of discrete character evolution on phylogenies

abstract: Many hypotheses in the field of phylogenetic comparative biology involve specific changes in the rate or process of trait evolution. We present a method designed to test whether the rate of evolution of a discrete character has changed in one or more clades, lineages, or time periods. This method differs from other related approaches (such as the  covarion model) in that the  regimes in which the rate or process is postulated to have changed are specified a priori by the user, rather than inferred from the data. Similarly, it differs from methods designed to model a correlation between two binary traits in that the regimes mapped onto the tree are fixed. We apply our method to investigate the rate of dewlap color and/or caudal vertebra number evolution in Caribbean and mainland clades of the diverse lizard genus Anolis. We find little evidence to support any difference between mainland and island evolution in either character. We also examine the statistical properties of the method more generally and show that it has acceptable type I error, parameter estimation, and power. Finally, we discuss the relationship of our method to existing models of heterogeneity in the rate of discrete character evolution on phylogenies.


title: Little hope for the polyploid endemic Pyrenean Larkspur (Delphinium montanum): evidences from population genomics and Ecological Niche Modelling

abstract: Species endemic to restricted geographical ranges represent a particular conservation issue, be it for their heritage interest. In a context of global change, this is particularly the case for plants which belong to high-mountain ecosystems and, because of their ecological requirements, are doomed to survive or disappear on their  sky islands. The Pyrenean Larkspur (Delphinium montanum, Ranunculaceae) is endemic to the Eastern part of the Pyrenees (France and Spain). It is now only observable at a dozen of localities and some populations show signs of decline, such as a recurrent lack of flowering. Implementing population genomic approach (e.g. RAD-seq like) is particularly useful to understand genomic patterns of diversity and differentiation in order to provide recommendations in term of conservation. However, it remains challenging for species such as D. montanum that are autotetraploid with a large genome size (1C-value > 10 pg) as most methods currently available were developed for diploid species. A Bayesian framework able to call genotypes with uncertainty allowed us to assess genetic diversity and population structure in this system. Our results show evidence for inbreeding (mean GIS = 0.361) within all the populations and substantial population structure (mean GST = 0.403) at the metapopulation level. In addition to a lack of connectivity between populations, spatial projections of Ecological Niche Modelling analyses under different climatic scenarios predict a dramatic decrease of suitable habitat for D. montanum in the future. Based on these results, we discuss the relevance and feasibility of different conservation measures.


title: Ancient genomes redate the extinction of Sussemionus, a subgenus of Equus, to late Holocene

abstract: The exceptionally-rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses and zebras represent three extant subgenus of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in Pleistocene. We sequenced 26 archaeological specimens from northern China in Holocene showing morphological features reminiscent of Equus ovodovi, a species representative of Sussemionus, and further confirmed them as this species by genetic analyses. Thus, we present the first high-quality complete genome of the Sussemionus that we sequenced to 12.0x depth-of-coverage and demonstrate that it survived until [~]3,500 years ago, despite the continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree, and found Sussemionus diverged from the ancestor of non-caballine equids [~]2.3-2.7 Million years ago and admixture events could have taken place between them. Our works suggest the small genetic diversity but not the enhanced inbreeding mainly limited the chances of survival of the species, and illustrates how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.


title: Refractive-index matching enhanced polarization-sensitive optical coherence tomography quantification in human brain tissue

abstract: The importance of polarization-sensitive optical coherence tomography (PS-OCT) has been increasingly recognized in human brain imaging. Despite the recent progress of PS-OCT in revealing white matter architecture and orientation, quantification of fine-scale fiber tracts in the human brain cortex has been a challenging problem, due to a low birefringence in the gray matter. In this study, we investigated the effect of refractive index matching by 2,2-thiodiethanol (TDE) immersion on the improvement of PS-OCT measurements in ex vivo human brain tissue. We obtain the cortical fiber orientation maps in the gray matter, which reveals the radial fibers in the gyrus, the U-fibers along the sulcus, as well as distinct layers of fiber axes exhibiting laminar organization. Further analysis shows that index matching reduces the noise in axis orientation measurements by 56% and 39%, in white and gray matter, respectively. Index matching also enables precise measurements of apparent birefringence, which was underestimated in the white matter by 82% but overestimated in the gray matter by 16% prior to TDE immersion. Mathematical simulations show that the improvements are primarily attributed to the reduction in the tissue scattering coefficient, leading to an enhanced signal-to-noise ratio in deeper tissue regions, which could not be achieved by conventional noise reduction methods.


title: Dinosaur bonebed amber from an original swamp forest soil

abstract: Dinosaur bonebeds with amber content, yet scarce, offer a superior wealth and quality of data on ancient terrestrial ecosystems. However, the preserved palaeodiversity and/or taphonomic characteristics of these exceptional localities had hitherto limited their palaeobiological potential. Here we describe the amber from the Lower Cretaceous dinosaur bonebed of Arino (Teruel, Spain) using a multidisciplinary approach. Amber is found in both a root layer with amber strictly in situ and a litter layer namely composed of aerial pieces unusually rich in bioinclusions, encompassing 11 insect orders, arachnids, and a few plant and vertebrate remains, including a feather. Additional palaeontological data - charophytes, palynomorphs, ostracods- are provided. Arino arguably represents the most prolific and palaeobiologically diverse locality in which fossiliferous amber and a dinosaur bonebed have been found in association, and the only one known where the vast majority of the palaeontological assemblage suffered no or low-grade pre-burial transport. That has enabled unlocking unprecedentedly complete and reliable palaeoecological data out of two complementary windows of preservation from the same site.

category: paleontology


title: A G-protein-biased S1P1 agonist, SAR247799, improved LVH and diastolic function in a rat model of metabolic syndrome

abstract:
AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSAimC_ST_ABSHeart failure with preserved ejection fraction (HFpEF) is a major cause of death worldwide with no approved treatment. Left ventricular hypertrophy (LVH) and diastolic dysfunction represent the structural and functional components of HFpEF, respectively. Endothelial dysfunction is prevalent in HFpEF and predicts cardiovascular events. We investigated if SAR247799, a G-protein-biased sphingosine-1-phosphate receptor 1 (S1P1) agonist with endothelial-protective properties, could improve cardiac and renal functions in a rat model of metabolic syndrome LVH and diastolic function.

Methods31- and 65-week-old obese ZSF1 (Ob-ZSF1) rats, representing young and old animals with LVH and diastolic dysfunction, were randomized to a chow diet containing 0.025% (w/w) of SAR247799, or control (CTRL) chow for 4 weeks. Age-matched lean ZSF1 (Le-ZSF1) rats were fed control chow. Echocardiography, telemetry, biochemical and histological analysis were performed to evaluate the effect of SAR247799.

ResultsEchocardiography revealed that Ob-ZSF1 rats, in contrast to Le-ZSF1 rats, developed progressive diastolic dysfunction and cardiac hypertrophy with age. SAR247799 blunted the progression of diastolic dysfunction in young and old animals: in young animals E/e was evaluated at 21.8 {+/-} 1.4 for Ob-ZSF1-CTRL, 19.5 {+/-} 1.2 for Ob-ZSF1-SAR247799 p<0.01, and 19.5 {+/-} 2.3 for Le-ZSF1-CTRL (median {+/-} IQR). In old animals E/e was evaluated at 23.15 {+/-} 4.45 for Ob-ZSF1-CTRL, 19.5 {+/-} 5 for Ob-ZSF1-SAR247799 p<0.01, and 16.69 {+/-} 1.7 for Le-ZSF1-CTRL, p<0.01 (median {+/-} IQR). In old animals, SAR247799 reduced cardiac hypertrophy (mean {+/-} SEM of heart weight/tibia length 0.053 {+/-} 0.001 for Ob-ZSF1-CTRL vs 0.046 {+/-} 0.002 for Ob-ZSF1-SAR247799 p<0.01, Le-ZSF1-CTRL 0.035 {+/-} 0.001) and myocardial perivascular collagen content (p<0.001), independently of any changes in microvascular density. In young animals, SAR247799 improved endothelial function as assessed by the very low frequency bands of systolic blood pressure variability (mean {+/-} SEM 67.8 {+/-} 3.41 for Ob-ZSF1-CTRL 55.8 {+/-} 4.27 or Ob-ZSF1-SAR247799, p<0.05 and 57.3 {+/-} 1.82 Le-ZSF1-CTRL), independently of any modification of arterial blood pressure. In old animals, SAR247799 reduced urinary protein/creatinine ratio, an index of glomerular injury, (10.3 {+/-} 0.621 vs 8.17 {+/-} 0.231 for Ob-ZSF1-CTRL vs Ob-ZSF1-SAR247799, respectively, p<0.05 and 0.294 {+/-} 0.029 for Le-ZSF1-CTRL, mean {+/-} SEM) and the fractional excretion of electrolytes. Circulating lymphocytes were not decreased by SAR247799, confirming lack of S1P1 desensitization.

ConclusionsThese experimental findings suggest that S1P1 activation with SAR247799 could improve LVH, cardiac diastolic and renal function in HFpEF patients.


title: Addition of a carboxy terminal tail to the normally tailless gonadotropin-releasing hormone receptor impairs fertility in female mice

abstract: Gonadotropin-releasing hormone (GnRH) is the primary neuropeptide controlling reproduction in vertebrates. GnRH stimulates follicle-stimulating hormone (FSH) and luteinizing hormone (LH) synthesis via a G protein-coupled receptor, GnRHR, in the pituitary gland. In mammals, GnRHR lacks a C-terminal cytosolic tail (Ctail) and does not exhibit homologous desensitization. This might be an evolutionary adaptation that enables LH surge generation and ovulation. To test this idea, we fused the chicken GnRHR Ctail to the endogenous murine GnRHR in a transgenic model. The LH surge was blunted, but not blocked in these mice. In contrast, they showed reductions in FSH production, ovarian follicle development, and fertility. Addition of the Ctail altered the nature of agonist-induced calcium signaling required for normal FSH production. The loss of the GnRHR Ctail during mammalian evolution is unlikely to have conferred a selective advantage by enabling the LH surge. The adaptive significance of this specialization remains to be determined.


title: A genetic trap in yeast for inhibitors of SARS-CoV-2 main protease

abstract:
The ongoing COVID-19 pandemic urges searches for antiviral agents that can block infection or ameliorate its symptoms. Using dissimilar search strategies for new antivirals will improve our overall chances of finding effective treatments. Here, we have established an experimental platform for screening of small molecule inhibitors of SARS-CoV-2 main protease in Saccharomyces cerevisiae cells, genetically engineered to enhance cellular uptake of small molecules in the environment. The system consists of a fusion of the E. coli toxin MazF and its antitoxin MazE, with insertion of a protease cleavage site in the linker peptide connecting the MazE and MazF moieties. Expression of the viral protease confers cleavage of the MazEF fusion, releasing the MazF toxin from its antitoxin, resulting in growth inhibition. In the presence of a small molecule inhibiting the protease, cleavage is blocked and the MazF toxin remains inhibited, promoting growth. The system thus allows positive selection for inhibitors. The engineered yeast strain is tagged with a fluorescent marker protein, allowing precise monitoring of its growth in the presence or absence of inhibitor. We detect an established main protease inhibitor down to 10 M by a robust growth increase. The system is suitable for robotized large-scale screens. It allows in vivo evaluation of drug candidates, and is rapidly adaptable for new variants of the protease with deviant site specificities.

IMPORTANCEThe COVID-19 pandemic may continue several years before vaccination campaigns can put an end it globally. Thus, the need for discovery of new antiviral drug candidates will remain. We have engineered a system in yeast cells for detection of small molecule inhibitors of one attractive drug target of SARS-CoV-2, its main protease which is required for viral replication. To detect inhibitors in live cells brings the advantage that only compounds capable of entering the cell and remain stable there, will score in the system. Moreover, by its design in yeast, the system is rapidly adaptable for tuning of detection level, eventual modification of protease cleavage site in case of future mutant variants of the SARS-CoV-2 main protease, or even for other proteases.

category: synthetic biology


title: Analysis of Multisensory-Motor Integration in Olfactory Navigation of Silkmoth, Bombyx mori, using Virtual Reality System

abstract: Most animals survive and thrive due to navigation behavior to reach their destinations. In order to navigate, it is important for animals to integrate information obtained from multisensory inputs and use that information to modulate their behavior. In this study, by using a virtual reality (VR) system for an insect, we investigated how an adult silkmoth integrates visual and wind direction information during female search behavior (olfactory behavior). According to the behavioral experiments using the VR system, the silkmoth had the highest navigation success rate when odor, vision, and wind information were correctly provided. However, we found that the success rate of the search significantly reduced if wind direction information was provided that was incorrect from the direction actually detected. This indicates that it is important to acquire not only odor information, but also wind direction information correctly. In other words, Behavior was modulated by the degree of co-incidence between the direction of arrival of the odor and the direction of arrival of the wind, and posture control (angular velocity control) was modulated by visual information. We mathematically modeled the modulation of behavior using multisensory information and evaluated it by simulation. As a result, the mathematical model not only succeeded in reproducing the actual female search behavior of the silkmoth, but can also improve search success relative to the conventional odor source search algorithm.


title: In silico investigation of biomechanical response of a human subjected to primary blast

abstract: The response of the brain to the explosion induced primary blast waves is actively sought. Over the past decade, reasonable progress has been made in the fundamental understanding of bTBI using head surrogates and animal models. Yet, the current understanding of how blast waves interact with the human is in nascent stages, primarily due to lack of data in humans. The biomechanical response in human is critically required so that connection to the aforementioned bTBI models can be faithfully established. Here, using a detailed, full-body human model, we elucidate the biomechanical cascade of the brain under a primary blast. The input to the model is incident overpressure as achieved by specifying charge mass and standoff distance through ConWep. The full-body model allows to holistically probe short- (<5 ms) and long-term (200 ms) brain biomechanical responses. The full-body model has been extensively validated against impact loading in the past. In this work, we validate the head model against blast loading. We also incorporate structural anisotropy of the brain white matter. Blast wave human interaction is modeled using a conventional weapon modeling approach. We demonstrate that the blast wave transmission, linear and rotational motion of the head are dominant pathways for the biomechanical loading of the brain, and these loading paradigms generate distinct biomechanical fields within the brain. Blast transmission and linear motion of the head govern the volumetric response, whereas the rotational motion of the head governs the deviatoric response. We also observe that blast induced head rotation alone produces a diffuse injury pattern in white matter fiber tracts. Lastly, we find that the biomechanical response under blast is comparable to the impact event. These insights will augment laboratory and clinical investigations of bTBI and help devise better blast mitigation strategies.


title: Gram-negative bacterial infection increases lung cancer metastasis via Toll-like receptor 1 activation and increased cancer cell proliferation post-tumor adhesion

abstract:
BackgroundLung cancer is a leading cause of death partially due to high recurrence rates after surgical resection. Clinical data suggest that post-operative infections may increase the risk of recurrence. Our previous work indicated that increased adhesion of circulating tumors in the context of infection is partially responsible for this phenotype. However, cancer metastasis is a multi-step process, and it is likely that other events following tumor adhesion also play a role.

MethodsIn vivo intrasplenic injection of murine lung cancer cells into wild type (WT) and Toll-like receptor 4 knockout (TLR4-/-) mice followed by cecal-ligation and puncture (CLP) as a model of post-operative infection or sham surgery were used. H&E staining and immunohistochemistry analysis of Ki67+ cells in the livers of those mice were performed. In vitro proliferation assays were performed on human lung cancer cells using combinations of TLR blockade.

ResultsWe found a 5-fold increase in hepatic metastases in WT CLP mice compared to WT sham mice. TLR4-/- CLP mice had a significant decreased tumor burden compared to WT CLP mice. This indicated an important mechanistic role for the TLR4-initiated host response to gram negative infection post-tumor cell adhesion. By analyzing the livers of those mice, we observed an increase in proliferation of tumor micrometastases in vivo in WT CLP mice as compared to WT sham mice. Here again, CLP TLR4 -/- mice had significantly fewer replicating micrometastases than CLP WT mice. Indeed, we found that direct stimulation of lung cancer cells with heat-inactivated E.Coli resulted in increased proliferation of tumor growth in vitro. These effects were partially abrogated by tumor TLR4 blockade; combined TLR2, 4 and 5 blockades led to a more prominent decrease. Conditioned media from bronchoalveolar epithelial cells treated with lipopolysaccharide lead to increased lung cancer proliferation; these changes were reversed with TLR blockade, indicating that the host response to infection is TLR mediated.

ConclusionsOverall, these results imply a more complex mechanistic role of post-operative infection in metastasis. From a clinical standpoint, this evidence strengthens the case for the use of TLR blockade as a potential therapeutic target in the prevention of metastasis.


title: VGLL2-NCOA2 leverages developmental programs for pediatric sarcomagenesis

abstract: Clinical sequencing efforts are uncovering numerous fusion genes in childhood solid tumors, yet few methods exist to delineate fusion-oncogenes from structural changes of unknown significance. One such novel fusion gene is VGLL2-NCOA2, which was described by us and others in patients with congenital sarcomas but has lacked functional validation. To determine if this fusion is an oncogene, and how it is driving disease, we developed a vertebrate zebrafish model and mouse allograft model of human VGLL2-NCOA2 driven sarcomagenesis. We found that VGLL2-NCOA2 is indeed an oncogene and is sufficient to generate mesenchymal tumors that recapitulate the human disease at the histological and transcriptional level. Zebrafish VGLL2-NCOA2 tumors display features of arrested skeletal muscle development, and a subset transcriptionally cluster with somitogenesis in developing embryos. By comparing tumor and embryonic gene expression signatures, we identified developmentally regulated targets that VGLL2-NCOA2 potentially leverages for tumorigenesis. These targets highlight the core biology of the disease and could represent therapeutic opportunities. Specifically, a RAS family GTPase, arf6/ARF6, involved in actin remodeling and rapid cycling of endocytic vesicles at the plasma membrane, is highly expressed during zebrafish somitogenesis and in VGLL2-NCOA2 tumors. In zebrafish tumors, arf6 protein is highly expressed and is absent from mature skeletal muscle. In VGLL2-NCOA2 mouse allograft models and patient tumors, ARF6 mRNA is overexpressed as compared to skeletal muscle or normal controls. More broadly, ARF6 is overexpressed in adult and pediatric sarcoma subtypes as compared to mature skeletal muscle. Overall, our cross-species comparative oncology approach provides evidence that VGLL2-NCOA2 is an oncogene which leverages developmental programs for tumorigenesis, and that one of these programs, the reactivation or persistence of arf6/ARF6, could represent a therapeutic opportunity.


title: PL1 Peptide Engages Acidic Surfaces on Tumor-Associated Fibronectin and Tenascin Isoforms to Trigger Cellular Uptake.

abstract:
Tumor extracellular matrix (ECM) is a high-capacity and genetically stable target for the precision delivery of affinity ligand-guided drugs and imaging agents. Recently, we developed a PL1 peptide (sequence: PPRRGLIKLKTS) for systemic targeting of malignant ECM. Here we map the dynamics of PL1 binding to its receptors Fibronectin Extra Domain B (FN-EDB) and Tenascin C C-isoform (TNC-C) by computational modeling and cell-free binding studies on mutated receptor proteins, and study cellular binding and internalization of PL1 nanoparticles in cultured cells. Molecular dynamics simulation and docking analysis suggested that the engagement of PL1 peptide with both receptors is primarily driven by electrostatic interactions. Substituting acidic amino acid residues with neutral amino acids at predicted PL1 binding sites in FN-EDB (D52N-D49N-D12N) and TNC-C (D39N-D45N) resulted in the loss of binding of PL1 nanoparticles. Remarkably, PL1-functionalized nanoparticles (NPs) were not only deposited on the target ECM but bound the cells and initiated a robust cellular uptake via a pathway resembling macropinocytosis. Our studies establish the mode of engagement of the PL1 peptide with its receptors and suggest applications for intracellular delivery of nanoscale payloads. The outcomes of this work can be used for the development of PL1-derived peptides with improved stability, affinity and specificity for precision targeting of the tumor ECM and malignant cells.

One Sentence SummaryPL1 peptide is recruited to the acidic surfaces on oncofetal fibronectin EDB and tenascin C-C isoform, triggering cellular uptake of PL1-functionalized nanoparticles.


title: Construction of a solid Cox model for AML patients based on multiomics bioinformatic analysis

abstract: Acute myeloid leukemia (AML) is a highly heterogeneous hematological malignancy. The bone marrow (BM) microenvironment in AML plays an important role in leukemogenesis, drug resistance and leukemia relapse. In this study, we aimed to identify reliable immune-related biomarkers for AML prognosis by multiomics analysis. We obtained expression profiles from The Cancer Genome Atlas (TCGA) database and constructed a LASSO-Cox regression model to predict the prognosis of AML using multiomics bioinformatic analysis data. This was followed by independent validation of the model in the GSE106291 (n=251), GSE12417 (n=163) and GSE37642 (n=137) datasets and mutated genes in clinical samples for predicting overall survival (OS). Molecular docking was performed to predict the most optimal ligands to these hub genes. The single-cell RNA sequence dataset GSE116256 was used to clarify the expression of the hub genes in different immune cell types. According to their significant differences in immune gene signatures and survival trends, we concluded that the immune infiltration-lacking subtype (IL type) is associated with better prognosis than the immune infiltration-rich subtype (IR type). Using the LASSO model, we built a classifier based on 5 hub genes to predict the prognosis of AML (risk score = -0.086xADAMTS3 + 0.180xCD52 + 0.472xCLCN5 - 0.356xHAL + 0.368xICAM3). In summary, we constructed a prognostic model of AML using integrated multiomics bioinformatic analysis that could serve as a therapeutic classifier.


title: MICAL1 activation by PAK1 mediates actin filament disassembly

abstract: The MICAL1 monooxygenase has emerged as an important regulator of filamentous actin (F-actin) structures that contribute to numerous processes including nervous system development, cell morphology, motility, viability and cytokinesis [1-4]. Activating MICAL1 mutations have been linked with autosomal-dominant lateral temporal epilepsy, a genetic syndrome characterized by focal seizures with auditory symptoms [5], emphasizing the need for tight control of MICAL1 activity. F-actin binding to MICAL1 stimulates catalytic activity, resulting in the oxidation of actin methionine residues that promote F-actin disassembly [6, 7]. Although MICAL1 has been shown to be regulated via interactions of the autoinhibitory carboxyl-terminal coiled-coil region [8] with RAB8, RAB10 and RAB35 GTPases [9-12], or Plexin transmembrane receptors [13, 14], a mechanistic link between the RHO GTPase signaling pathways that control actin cytoskeleton dynamics and the regulation of MICAL1 activity had not been established. Here we show that the CDC42 GTPase effector PAK1 serine/threonine kinase associates with and phosphorylates MICAL1 on serine 817 (Ser817) and 960 (Ser960) residues, leading to accelerated F-actin disassembly. Deletion analysis mapped PAK1 binding to the amino-terminal catalytic monooxygenase and calponin domains, distinct from the carboxyl-terminal proteinprotein interaction domain. Stimulation of cells with extracellular ligands including basic fibroblast growth factor (FGF2) led to significant PAK-dependent Ser960 phosphorylation, thus linking extracellular signals to MICAL1 phosphorylation. Moreover, mass spectrometry analysis revealed that co-expression of MICAL1 with CDC42 and active PAK1 resulted in hundreds of proteins increasing their association with MICAL1, including the previously described MICAL1-interacting protein RAB10 [15]. These results provide the first insight into a redox-mediated actin disassembly pathway linking extracellular signals to cytoskeleton regulation via a RHO GTPase family member, and reveal a novel means of communication between RHO and RAB GTPase signaling pathways.

category: cell biology