title: Anti-GD2 antibody disrupts GD2:Siglec-7 interactions and synergizes with CD47 blockade to mediate tumor eradication

abstract: The disialoganglioside GD2 is consistently overexpressed in neuroblastoma and osteosarcoma, and is variably expressed in other sarcomas, gliomas, neuroendocrine tumors, and epithelial cancers. Anti-GD2 antibodies have improved the survival rates of patients with neuroblastoma only when administered as part of intense chemotherapy-based cytotoxic regimens, which are associated with debilitating late effects including hearing loss, growth retardation, and secondary leukemias. Despite broad expression of GD2 on osteosarcoma, anti-GD2 antibody has not mediated significant antitumor activity in that disease or any other GD2+ cancers. CD47 is a checkpoint molecule overexpressed on tumor cells that inhibits macrophage activity, and CD47 blockade has demonstrated promising clinical activity in early human trials. We investigated whether anti-CD47 antibody could enhance the efficacy of anti-GD2 antibody in neuroblastoma and other GD2+ malignancies. We demonstrate substantial synergy of these two agents, resulting in the recruitment of tumor associated macrophages (TAMs) to mediate robust and durable anti-tumor responses. The responses are driven by GD2-specific factors that reorient the balance of macrophage activity towards phagocytosis of tumor cells, including disruption of a newly described GD2:Siglec-7 axis. These results demonstrate the unique synergy of combining anti-GD2 with anti-CD47, which has the potential to significantly enhance outcomes for children with neuroblastoma and osteosarcoma and will soon be investigated in a first-in-human clinical trial.


title: Predicting potentially permissive substitutions that improve the fitness of A(H1N1)pdm09 viruses bearing the H275Y NA substitution

abstract:
Oseltamivir-resistant influenza viruses arise due to amino-acid mutations in key residues, but these changes often reduce their replicative and transmission fitness. Widespread oseltamivir-resistance has not yet been observed in A(H1N1)pdm09 viruses. However, it is known that permissive mutations in the neuraminidase (NA) of former seasonal A(H1N1) viruses from 2007-2009 buffered the detrimental effect of the NA H275Y mutation, resulting in fit oseltamivir-resistant viruses that circulated widely. This study explored two approaches to predict permissive mutations that may enable a fit H275Y A(H1N1)pdm09 variant to arise.

A computational approach used phylogenetic and in silico protein stability analyses to predict potentially permissive mutations, which were then evaluated by in vitro NA enzyme activity and expression analysis, followed by in vitro replication. The second approach involved the generation of a virus library which encompassed all possible individual 2.9 x 104 codon mutations in the NA whilst keeping H275Y fixed. To select for variant viruses with the greatest fitness, the virus library was serially passaged in ferrets (via contact and aerosol transmission) and resultant viruses were deep sequenced.

The computational approach predicted three NA permissive mutations, and even though they only offset the in vitro impact of H275Y on NA enzyme expression by 10%, they could restore replication fitness of the H275Y variant in A549 cells. In our experimental approach, a diverse virus library (97% of 8911 possible single amino-acid substitutions were sampled) was successfully transmitted through ferrets, and sequence analysis of resulting virus pools in nasal washes identified three mutations that improved virus transmissibility. Of these, one NA mutation, I188T, has been increasing in frequency since 2017 and is now present in 90% of all circulating A(H1N1)pdm09 viruses.

Overall, this study provides valuable insights into the evolution of the influenza NA protein and identified several mutations that may potentially facilitate the emergence of a fit H275Y A(H1N1)pdm09 variant.

category: microbiology


title: Acriflavine, a clinically aproved drug, inhibits SARS-CoV-2 and other betacoronaviruses

abstract: SO_SCPLOWUMMARYC_SCPLOWThe COVID-19 pandemic caused by SARS-CoV-2 has been socially and economically devastating. Despite an unprecedented research effort, effective therapeutics are still missing to limit severe disease and mortality. Using high-throughput screening, we identified acriflavine as a potent papain-like protease (PLpro) inhibitor. NMR titrations and a co-crystal structure confirm that acriflavine blocks the PLpro catalytic pocket in an unexpected binding mode. We show that the drug inhibits viral replication at nanomolar concentration in cellular models, in vivo in mice and ex vivo in human airway epithelia, with broad range activity against SARS-CoV-2 and other betacoronaviruses. Considering that acriflavine is an inexpensive drug approved in some countries, it may be immediately tested in clinical trials and play an important role during the current pandemic and future outbreaks.


title: Gastruloids as in vitro models of embryonic blood development with spatial and temporal resolution

abstract: Gastruloids are three-dimensional embryonic organoids that reproduce key features of early mammalian development in vitro with unique scalability, accessibility, and spatiotemporal similarity to real embryos. Recently, we adapted gastruloid culture conditions to promote cardiovascular development. In this work, we extended these conditions to capture features of embryonic blood development through a combination of immunophenotyping, detailed transcriptomics analysis, and identification of blood stem/progenitor cell potency. We uncovered the emergence of blood progenitor and erythroid-like cell populations in late gastruloids and showed the multipotent clonogenic capacity of these cells, both in vitro and after transplantation into irradiated mice. We also identified the spatial localization near a vessel-like plexus in the anterior of gastruloids with similarities to the emergence of blood stem cells in the embryo. These results highlight the potential and applicability of gastruloids to the in vitro study of complex processes in embryonic blood development with spatiotemporal fidelity.

category: developmental biology


title: Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns

abstract: Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortant-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different treespaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable treespaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the least conservation by host species. Bayesian skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to common host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.

category: evolutionary biology


title: Thiamin-Diphosphate Enzymes Are an Ancient Family of Repeat Proteins

abstract: A repeating sequence and structure pattern that is highly similar to the canonical cofactor binding motif has been identified in the thiamin-diphosphate dependent (ThDP) enzyme family. We have identified more than a thousand of these repeats in a non-redundant set (N = 58) of ThDP enzyme structures. The repeating element has a helix-turn-strand secondary structure which typically begins with an [G/A]{X(1,2)}[G/A] sequence motif with a typical length of 29 residues. The catalytically important diphosphate and aminopyrimidine interacting domains are comprised of a set of six of these repeats in a conserved architecture with a flavodoxin-like 213465 strand order. The canonical ThDP binding motif is the fourth repeat in the ThDP binding domain, while the conserved aminopyrimidine interacting glutamate is part of the second repeat in its domain. The third and fourth repeats form a contact between the functional domains, while the fifth repeat in the N-terminal domain forms an inter-chain contact. The conservation of these functional properties highlights the role of these repeats in the function and structure of this well-studied enzyme family and agrees with the principle of modular assembly in protein ancestry.

category: biophysics


title: Combined Inhibition of SHP2 and CXCR1/2 Promotes Anti-Tumor T Cell Response in NSCLC

abstract:
Clinical trials of SHP2 inhibitors (SHP2i) alone and in various combinations are ongoing for multiple tumors with over-activation of the RAS/ERK pathway. SHP2 plays critical roles in normal cell signaling; hence, SHP2is could influence the tumor microenvironment. We found that SHP2i treatment depleted alveolar and M2-like macrophages and promoted B and T lymphocyte infiltration in Kras- and Egfr-mutant non-small cell lung cancer (NSCLC). However, treatment also increased intratumor gMDSCs via tumor-intrinsic, NF-kB-dependent production of CXCR2 ligands. Other RAS/ERK pathway inhibitors also induced CXCR2 ligands and gMDSC influx in mice, and CXCR2 ligands were induced in tumors from patients on KRASG12C-inhibitor trials. Combined SHP2(SHP099)/CXCR1/2(SX682) inhibition depleted a specific cluster of S100a8/9high gMDSCs, generated Klrg1+ CD8+ effector T cells with a strong cytotoxic phenotype but expressing the checkpoint receptor NKG2A, and enhanced survival in Kras-and Egfr-mutant models. Our results argue for testing RAS/ERK pathway/CXCR1/2/NKG2A inhibitor combinations in NSCLC patients.

Statement of SignificanceOur study shows that inhibiting the SHP2/RAS/ERK pathway triggers NF-kB-dependent up-regulation of CXCR2 ligands and recruitment of S100A8high gMDSCs, which suppress T cells in NSCLC. Combining SHP2 and CXCR2 inhibitors blocks this gMDSC immigration, resulting in enhanced Th1 polarization, induction of CD8+ KLRG1+ effector T cells with high cytotoxic activity and improved survival in multiple NSCLC models.

category: cancer biology


title: Bacterial-type plant ferroxidases tune local phosphate sensing in root development

abstract: Fluctuating bioavailability of inorganic phosphate (Pi), often caused by complex Pi-metal interactions, guide root tip growth and root system architecture for maximizing the foraged soil volume. Two interacting genes in Arabidopsis thaliana, PDR2 (P5-type ATPase) and LPR1 (multicopper oxidase), are central to external Pi monitoring by root tips, which is modified by iron (Fe) co-occurrence. Upon Pi deficiency, the PDR2-LPR1 module facilitates cell type-specific Fe accumulation and cell wall modifications in root meristems, inhibiting intercellular communication and thus root growth. LPR1 executes local Pi sensing, whereas PDR2 restricts LPR1 function. We show that native LPR1 displays specific ferroxidase activity and requires a conserved acidic triad motif for high-affinity Fe2+ binding and root growth inhibition under limiting Pi. Our data indicate that substrate availability tunes LPR1 function and implicate PDR2 in maintaining Fe homeostasis. LPR1 represents the prototype of an ancient ferroxidase family, which evolved very early upon bacterial colonization of land. During plant terrestrialization, horizontal gene transfer transmitted LPR1-type ferroxidase from soil bacteria to the common ancestor of Zygnematophyceae algae and embryophytes, a hypothesis supported by homology modeling, phylogenomics, and activity assays of bacterial LPR1-type multicopper oxidases.

category: plant biology


title: Prediction errors for aversive events shape long-term memory formation through a distinct neural mechanism

abstract: Prediction errors (PEs) have been known for decades to guide associative learning, but their role in episodic memory formation has been discovered only recently. Using an encoding task in which participants learned to predict which stimuli are followed by aversive shocks, combined with univariate, multivoxel, and large-scale network analyses of fMRI data, we show that enhanced memory for events associated with negative PEs was linked to reduced hippocampal responses to PEs and increased crosstalk between the  salience network and a frontoparietal network commonly implicated in memory formation for events that are in line with prior expectation. These PE-related effects could not be explained by mere changes in physiological arousal or the prediction itself. Our results suggest that superior memory for events associated with high PEs is driven by a distinct neural mechanism that might serve to set memories of high PE events apart from those with expected outcomes.

category: neuroscience


title: Human gaze is precisely aligned with the foveolar cone topography of both eyes

abstract: The small physical depression of the human retina, the fovea, is the retinal locus of prime visual resolution, achieved by a peaking topography of the light sensitive cone photoreceptor outer segments 1-3 and a post-receptor wiring scheme preserving high-density sampling 4,5. Humans dynamically direct their gaze such that the retinal images of objects of interest fall onto the foveola, the central one-degree diameter of the fovea 6-8, but it is yet unclear if a relationship between the individual photoreceptor topography at this location and visual fixation behavior exists 9,10. By employing adaptive optics in vivo imaging and micro-stimulation 11-13, we created topographical maps of the complete foveolar cone mosaics in both eyes of 20 healthy participants while simultaneously recording the retinal location of a fixated visual object in a psychophysical experiment with cellular resolution. We found that the locus of fixation was systematically shifted away from the topographical centers towards a naso-superior quadrant on the retina, about 5 minutes of arc of visual angle on average, with a mirror symmetrical trend between fellow eyes. In cyclopean view, the topographical centers were superior to the fixated target, corresponding to areas in the visual field usually more distant 14,15 and thus containing higher spatial frequencies. Given the large variability in foveal topography between individuals, and the surprising precision with which fixation is repeatedly directed to just a small bouquet of cones in the foveola, these findings demonstrate a finely tuned, functionally relevant link between the development of the cellular mosaic of photoreceptors and visual behavior.


title: Human gaze is systematically offset from the center of cone topography


title: The E3 ubiquitin ligase RNF216/TRIAD3 is a central regulator of the hypothalamic-pituitary-gonadal axis

abstract:
RNF216/TRIAD3 is an E3 ligase that ubiquitinates substrates in the nervous system. Recessive mutations in RNF216/TRIAD3 cause Gordon Holmes syndrome (GHS), where hypogonadotropic hypogonadism is a core phenotype. However, the functions of RNF216/TRIAD3 within the neuroendocrine system are not well-understood. Here, we used the CRISPR-Cas9 system to knock out Rnf216/Triad3 in GT1-7 cells, a GnRH immortalized cell line derived from mouse hypothalamus. Rnf216/Triad3 knockout cells had decreased steady state Gnrh and reduced calcium transient frequency. To address functions of RNF216/TRIAD3 in vivo, we generated a Rnf216/Triad3 constitutive knockout (KO) mouse. KO mice of both sexes showed reductions in GnRH and soma size. Furthermore, KO mice exhibited sex-specific phenotypes with males showing gonadal impairment and derangements in gonadotropin release compared to KO females, which only had irregular estrous cyclicity. Our work shows that dysfunction of RNF216/TRIAD3 affects the HPG axis in a sex-dependent manner, implicating sex-specific therapeutic interventions for GHS.

HighlightsO_LIRnf216/Triad3 controls Gnrh and intrinsic hypothalamic cell activity
C_LIO_LIRnf216/Triad3 knockout male mice have greater reproductive impairments than females
C_LIO_LIRnf216/Triad3 controls the HPG axis at multiple levels
C_LI


title: Fusion of the N-terminal 119 amino acids with the RelA-CTD renders its growth inhibitory effects (p)ppGpp-dependent

abstract: The guanosine nucleotide derivatives ppGpp and pppGpp, are central to the remarkable capacity of bacteria to adapt to fluctuating environment and metabolic perturbations. These alarmones are synthesized by two proteins, RelA and SpoT in E. coli and the activities of each of the two enzymes are highly regulated for homeostatic control of (p)ppGpp levels in the cell. Although the domain structure and function of RelA are well defined, the findings of this study unfold the regulatory aspect of RelA that is possibly relevant in vivo. We uncover here the importance of the N-terminal 1-119 amino acids of the enzymatically compromised (p)ppGpp hydrolytic domain (HD) of monofunctional RelA for the (p)ppGpp mediated regulation of RelA-CTD function. We find that even moderate level expression of RelA appreciably reduces growth when the basal levels of (p)ppGpp in the cells are higher than in the wild type, an effect independent of its ability to synthesize (p)ppGpp. This is evidenced by the growth inhibitory effects of oversynthesis of the RelA-CTD in the relA+ strain but not in relA null mutant, suggesting the requirement of the functional RelA protein for basal level synthesis of (p)ppGpp, accordingly corroborated by the restoration of the growth inhibitory effects of the RelA-CTD expression in the relA1 spoT202 mutant. The N-terminal 119 amino acids of RelA fused in-frame with the RelA-CTD, both from 406-744 amino acids (including TGS) and from 454-744 amino acids (sans TGS) caused growth inhibition only in spoT1 and spoT202 relA1 mutants, uncovering the hitherto unrealized (p)ppGpp-dependent regulation of RelA-CTD function. An incremental rise in the (p)ppGpp levels is proposed to progressively modulate the interaction of RelA-CTD with the ribosomes, with possible implications in the feedback regulation of the N-terminal (p)ppGpp synthesis function, a proposal that best explains the nonlinear relationship between (p)ppGpp synthesis and increased ratio of RelA:ribosomes, both in vitro as well as in vivo.


title: Constructing phylogenetic relationship based on the independent selection law of genome sequences

abstract: Exploring the composition and evolution regularity of genome sequences and constructing phylogenetic relationship by alignment-free method in genome level are high-profile topics. Our previous researches discovered the CG and TA independent selection law s existed in genome sequences by analysis on the spectral features of 8-mer subsets of 920 eukaryote and prokaryote genomes. We found that the evolution state of genomes is determined by the intensity of the two independent selections and the degree of the mutual inhibition between them. In this study, the two independent selection patterns of 22 primate and 28 insect genome sequences were analyzed further. The two complete 8-mer motif sets containing CG or TA dinucleotide and their feature of relative frequency are proposed. We found that the two 8-mer sets and their feature are related directly to sequence evolution of genomes. According to the relative frequency of two 8-mer sets, phylogenetic trees were constructed respectively for the given primate and insect genomes. Through analysis and comparison, we found that our phylogenetic trees are more consistent with the known conclusions. The two kinds of phylogenetic relationships constructed by CG 8-mer set and TA 8-mer set are similar in insect genomes, but the phylogenetic relationship constructed by CG 8-mer set reflect the evolution state of genomes in current age and phylogenetic relationship constructed by TA 8-mer set reflect the evolution state of genomes in a slight earlier period. We thought it is the result that the TA independent selection is repressed by the CG independent selection in the process of genome evolution. Our study provides a theoretical approach to construct more objective evolution relationships in genome level.


title: Genetic characteristics of Apodemus speciosus at Akiyoshidai Quasi-National Park in Yamaguchi Prefecture

abstract: The large Japanese field mouse (Apodemus speciosus) is a small rodent endemic to Japan. The mice have a genetic characteristic in which the number of chromosomes differs between those from western Japan and those from eastern Japan. A. spesiosus, found throughout Japan, is used as a model animal for geogenetics and monitoring of radiation effects of wildlife. In this present study, to elucidate the genetic characteristics of the mice Akiyoshidai Quasi-National Park in Yamaguchi Prefecture, we investigated mitochondrial DNA and chromosome numbers. As a result, A. speciosus from Yamaguchi Prefecture were classified into the Honshu-Shikoku-Kyushu group and had a western Japan-type chromosome set of 2n=46; however, some Yamaguchi Prefecture mice formed a genetic cluster in Yamaguchi Prefecture, suggesting that continuous monitoring is needed to reveal the dynamics of genetic diversity.

category: genetics


title: Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease

abstract: The gastrointestinal (GI) tract is inhabited by a complex microbial community, which contributes to its homeostasis. Disrupted microbiome can cause GI-related diseases, including inflammatory bowel disease, therefore identifying host-microbe interactions is crucial for better understanding gut health. Bacterial extracellular vesicles (BEVs), released into the gut lumen, can cross the mucus layer and access underlying immune cells. To study cross-kingdom communication between BEVs and host, we focused on the influence of BEVs, generated by Bacteroides thetaiotaomicron (VPI-5482), on host immune cells. Using single-cell RNA sequencing data and host-microbe protein-protein interaction networks, we examined the potential effect of BEVs on dendritic cells, macrophages and monocytes with particular focus on the Toll-like receptor (TLR) pathway. We identified biological processes affected in each immune cell type, and also cell-type specific processes (e.g myeloid cell differentiation). The TLR pathway analysis highlighted that BEV targets differ among cells and even between the same cells in healthy versus disease (ulcerative colitis) conditions. Our in silico findings were validated in BEV-monocyte co-cultures demonstrating the requirement for TLR4 in BEV-elicited NF-{kappa} B activation. This study demonstrates that both cell-type and health condition influence BEV-host communication. The results and the pipeline can facilitate BEV-based therapy development for the treatment of IBD.

category: bioinformatics


title: The Geometry of Concept Learning

abstract: Understanding the neural basis of the remarkable human cognitive capacity to learn novel concepts from just one or a few sensory experiences constitutes a fundamental problem. We propose a simple, biologically plausible, mathematically tractable, and computationally powerful neural mechanism for few-shot learning of naturalistic concepts. We posit that the concepts that can be learnt from few examples are defined by tightly circumscribed manifolds in the neural firing rate space of higher order sensory areas. We further posit that a single plastic downstream readout neuron learns to discriminate new concepts based on few examples using a simple plasticity rule. We demonstrate the computational power of our proposal by showing it can achieve high few-shot learning accuracy on natural visual concepts using both macaque inferotemporal cortex representations and deep neural network models of these representations, and can even learn novel visual concepts specified only through linguistic descriptors. Moreover, we develop a mathematical theory of few-shot learning that links neurophysiology to behavior by delineating several fundamental and measurable geometric properties of high-dimensional neural representations that can accurately predict the few-shot learning performance of naturalistic concepts across all our numerical simulations. We discuss testable predictions of our theory for psychophysics and neurophysiological experiments.


title: From atoms to cells: bridging the gap between potency, efficacy, and safety of small molecules directed at a membrane protein

abstract: Membrane proteins constitute a substantial fraction of the human proteome, thus representing a vast source of therapeutic drug targets. Indeed, newly devised technologies now allow targeting "undruggable" regions of membrane proteins to modulate protein function in the cell. Despite the advances in technology, the rapid translation of basic science discoveries into potential drug candidates targeting transmembrane protein domains remains challenging. We address this issue by harmonizing single molecule-based and ensemble-based atomistic simulations of ligand-membrane interactions with patient-derived induced pluripotent stem cell (iPSC)-based experiments to gain insights into drug delivery, cellular efficacy, and safety of molecules directed at membrane proteins. In this study, we interrogated the pharmacological activation of the cardiac Ca2+ pump (Sarcoplasmic reticulum Ca2+-ATPase, SERCA2a) in human iPSC-derived cardiac cells as a proof-of-concept model. The combined computational-experimental approach serves as a platform to explain the differences in the cell-based activity of candidates with similar functional profiles, thus streamlining the identification of drug-like candidates that directly target SERCA2a activation in human cardiac cells. Systematic cell-based studies further showed that a direct SERCA2a activator does not induce cardiotoxic pro-arrhythmogenic events in human cardiac cells, demonstrating that pharmacological stimulation of SERCA2a activity is a safe therapeutic approach targeting the heart. Overall, this novel platform encompasses organ-specific drug potency, efficacy, and safety, and opens new avenues to accelerate the bench-to-patient research aimed at designing effective therapies directed at membrane protein domains.

category: pharmacology and toxicology


title: Two interacting transcriptional coactivators cooperatively control plant immune responses

abstract: The phytohormone salicylic acid (SA) plays a pivotal role in plant defense against biotrophic and hemibiotrophic pathogens. Genetic studies have identified NPR1 and EDS1 as two central hubs in plant local and systemic immunity. However, it is unclear how NPR1 orchestrates gene regulation and whether EDS1 directly participates in transcriptional reprogramming. Here we show that NPR1 and EDS1 synergistically activate Pathogenesis-Related (PR) genes and plant defenses by forming a protein complex and co-opting with Mediator. In particular, we discover that EDS1 functions as an autonomous transcriptional coactivator with intrinsic transactivation domains and physically interacts with the CDK8 subunit of Mediator. Upon SA induction, EDS1 is directly recruited by NPR1 onto the PR1 promoter via physical NPR1-EDS1 interactions, thereby potentiating PR1 activation. We further demonstrate that EDS1 stabilizes NPR1 protein and NPR1 transcriptionally upregulates EDS1 in plant-pathogen interactions. Our results reveal an elegant interplay of key coactivators with Mediator and elucidate novel molecular mechanisms for activating transcription during immune responses.


title: Comparative repeat profiling of two closely related conifers (Larix decidua and Larix kaempferi) reveals high genome similarity with only one fast-evolving satellite DNA

abstract: In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 gigabasepairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers accumulative genome evolution mode. For this, we applied low coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carriere and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.


title: Kupeantha yabassi (Coffeeae- Rubiaceae), a new Critically Endangered shrub species of the Ebo Forest area, Littoral Region, Cameroon

abstract: A new species to science of evergreen forest shrub, Kupeantha yabassi (Coffeeae - Rubiaceae), is described, illustrated, mapped, and compared morphologically with the closely similar species K. pentamera. Restricted so far to a single site in evergreen lowland forest near the Ebo Forest, Yabassi, Littoral Region, Cameroon, this species is Critically Endangered using the IUCN 2012 standard due to habitat clearance driven mainly by agriculture, adding to the growing list of threatened species resulting from anthropogenic pressure on Cameroon forests. A revised key to the six species of Kupeantha is presented. Two distinct geographical and ecological species groupings within the genus are identified and discussed. Notes are given on other narrowly endemic and threatened species in the Ebo forest area, a threatened centre of diversity important for conservation in Littoral Region.


title: dCas9 targeted chromatin and histone enrichmentfor mass spectrometry (Catchet-MS) identifies IKZF1as a novel drug-able target for HIV-1 latency reversal

abstract:
A major pharmacological strategy toward HIV cure aims to reverse latency in infected cells as a first step leading to their elimination. While the unbiased identification of molecular targets physically associated with the latent HIV-1 provirus would be highly valuable to unravel the molecular determinants of HIV-1 transcriptional repression and latency reversal, due to technical limitations, this has not been possible. Here we use a dCas9 targeted chromatin and histone enrichment strategy coupled to mass spectrometry (Catchet-MS) to describe the protein composition of the latent and activated HIV-1 5LTR. Catchet-MS identified known and novel latent 5LTR-associated host factors. Among these, IKZF1 is a novel HIV-1 transcriptional repressor, required for Polycomb Repressive Complex 2 recruitment to the LTR. We find the clinically advanced thalidomide analogue iberdomide, and the FDA approved analogues lenalidomide and pomalidomide, to be novel LRAs that, by targeting IKZF1 for degradation, reverse HIV-1 latency in CD4+T-cells isolated from virally suppressed people living with HIV-1.

One Sentence SummarydCas9 targeted chromatin and histone enrichment for mass spectrometry (Catchet-MS) led to the identification of IKZF1-targeting thalidomide analogues as novel HIV-1 latency reversal agents

category: molecular biology


title: Catchet-MS identifies IKZF1-targeting Thalidomide analogues as novel HIV-1 latency reversal agents


title: The effects of experimental floral resource removal on plant-pollinator interactions

abstract: Pollination is essential for ecosystem functioning, yet our understanding of the empirical consequences of species loss for plant-pollinator interactions remains limited. It is hypothesized that the loss of abundant and generalized (well-connected) species from a pollination network will have a large effect on the remaining species and their interactions. However, to date, relatively few studies have experimentally removed species from their natural setting to address this hypothesis. We investigated the consequences of losing an abundant, well-linked species from a series of plant-pollinator networks by experimentally removing the flowers of Helianthella quinquenervis (Asteraceae) from half of a series of 10 paired plots (15 m diameter) within a subalpine ecosystem. We then asked how the localized loss of this species influenced pollinator visitation patterns, floral visitor composition, and interaction network structure. The experimental removal of Helianthella flowers led to an overall decline in plot-level pollinator visitation rates and shifts in pollinator composition. Species-level responses to floral removal differed between the two other abundant, co-flowering plants in our experiment: Potentilla pulcherrima received higher visitation rates, whereas Erigeron speciosus visitation rates did not change. Experimental floral removal altered the structural properties of the localized plant-pollinator networks such that they were more specialized, less nested, and less robust to further species loss. Such changes to interaction structure were consistently driven more by species turnover than by interaction rewiring. Our findings suggest that the local loss of an abundant, well-linked, generalist plant can bring about diverse responses within pollination networks, including potential competitive and facilitative effects for individual species, changes to network structure that may render them more sensitive to future change, but also numerous changes to interactions that may also suggest flexibility in response to species loss.

category: ecology


title: Naked mole-rats (Heterocephalus glaber) do not specialise on cooperative tasks

abstract: It has been proposed that naked mole-rat (Heterocephalus glaber) societies resemble those of eusocial insects by showing a division of labour among non-breeding individuals. Earlier studies suggested that non-breeders belong to distinct castes that specialise permanently or temporarily on specific cooperative tasks. In contrast, recent research on naked mole-rats has shown that behavioural phenotypes are continuously distributed across non-breeders and that mole-rats exhibit considerable behavioural plasticity suggesting that individuals may not specialise permanently on work tasks. However, it is currently unclear whether individuals specialise temporarily and whether there is a sex bias in cooperative behaviour among non-breeders. Here we show that non-breeding individuals vary in overall cooperative investment, but do not specialise on specific work tasks. Within individuals, investment into specific cooperative tasks such as nest building, food carrying and burrowing are positively correlated, and there is no evidence that individuals show trade-offs between these cooperative behaviours. Non-breeding males and females do not differ in their investment in cooperative behaviours and show broadly similar age and body mass related differences in cooperative behaviours. Our results suggest that non-breeding naked mole-rats vary in their overall contribution to cooperative behaviours and that some of this variation may be explained by differences in age and body mass. Our data provide no evidence for temporary specialisation, as found among some eusocial insects, and suggests that the behavioural organisation of naked mole-rats resembles that of other cooperatively breeding vertebrates more than that of eusocial insect species.

category: animal behavior and cognition


title: Optical Nanosensors for Real-time Feedback on Insulin Secretion by β-Cells

abstract: Quantification of insulin is essential for diabetes research in general, and for the study of pancreatic {beta}-cell function in particular. Herein, fluorescent single-walled carbon nanotubes (SWCNT) are used for the recognition and real-time quantification of insulin. Two approaches for rendering the SWCNT sensors for insulin are compared, using surface functionalization with either a natural insulin aptamer with known affinity to insulin, or a synthetic PEGylated-lipid (C16-PEG(2000Da)-Ceramide), both of which show a modulation of the emitted fluorescence in response to insulin. Although the PEGylated-lipid has no prior affinity to insulin, the response of C16-PEG(2000Da)-Ceramide-SWCNTs to insulin is more stable and reproducible compared to the insulin aptamer-SWCNTs. The C16-PEG(2000Da)-Ceramide-SWCNTs optical response is excitation-wavelength dependent, where resonant excitation leads to a larger fluorescence decrease in response to insulin. The SWCNT sensors successfully detect insulin secreted by {beta}-cells within the complex environment of the conditioned media. The insulin is quantified by comparing the SWCNTs fluorescence response to a standard calibration curve, and the results are found to be in agreement with an enzyme-linked immunosorbent assay (ELISA). This novel analytical tool for real time quantification of insulin secreted by {beta}-cells provides new opportunities for rapid assessment of {beta}-cell function, with the ability to push forward many aspects of diabetes research.

category: bioengineering


title: Population-specific genome graphs improve high-throughput sequencing data analysis: A case study on the Pan-African genome

abstract: Graph-based genome reference representations have seen significant development, motivated by the inadequacy of the current human genome reference to represent the diverse genetic information from different human populations and its inability to maintain the same level of accuracy for non-European ancestries. While there have been many efforts to develop computationally efficient graph-based toolkits for NGS read alignment and variant calling, methods to curate genomic variants and subsequently construct genome graphs remains an understudied problem that inevitably determines the effectiveness of the overall bioinformatics pipeline. In this study, we discuss obstacles encountered during graph construction and propose methods for sample selection based on population diversity, graph augmentation with structural variants and resolution of graph reference ambiguity caused by information overload. Moreover, we present the case for iteratively augmenting tailored genome graphs for targeted populations and demonstrate this approach on the whole-genome samples of African ancestry. Our results show that population-specific graphs, as more representative alternatives to linear or generic graph references, can achieve significantly lower read mapping errors and enhanced variant calling sensitivity, in addition to providing the improvements of joint variant calling without the need of computationally intensive post-processing steps.


title: SPART, a versatile and standardized data exchange format for species partition information

abstract: A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of SD under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the "inferred species". The syntax also allows to optionally report support values, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.


title: Dihydropyrimidinase-like 2 (DPYSL2) regulates breast cancer migration via a JAK/STAT3/vimentin axis

abstract:
The intricate neuronal wiring during development requires cytoskeletal reorganization orchestrated by signaling cues. Considering that cytoskeletal remodeling is a hallmark of cell migration, we inquired whether metastatic cancer cells exploit the axon guidance proteins to migrate. Indeed, in breast cancer patients, we found a significant correlation between the mesenchymal markers and the expression of dihydropyrimidinase-like 2 (DPYSL2), a regulator of cytoskeletal dynamics in growing axons. Strikingly, DPYSL2 knockout in mesenchymal-like cells profoundly inhibited cell migration, invasion, stemness features, tumor growth rate, and metastasis. Next, we aimed to decode the molecular mechanism underlying this phenomenon and revealed an interaction between DPYSL2 and Janus kinase 1 (JAK1). This binding is crucial for triggering signal transducer and activator of transcription 3 (STAT3) and subsequently expressing vimentin, the pro-migratory intermediate filament. Collectively, we identified DPYSL2 as a molecular link between oncogenic signaling pathways and cytoskeletal reorganization in migrating breast cancer cells.

Statement of significanceThis study shows that the axon guidance adaptor protein DPYSL2 is essential for promoting breast cancer migration. Specifically, this protein interacts with JAK1 to govern STAT3 signaling and subsequently vimentin expression.


title: Unilateral corneal insult in Zebrafish results in a bilateral cell shape and identity modification, supporting wound closure

abstract: Most of terrestrial and aquatic vertebrates are equipped with camera-type eyes, offering a focused and clear sight. This apparatus is rendered inefficient if its most superficial and transparent element, the cornea, is opaque. This structure, prone to environmental aggressions, bears excellent wound healing capabilities to preserve vision. Up to date, most of the corneal wound healing studies are made on mammals. Here, for the first time, zebrafish is used as model to study wound closure of corneal epithelium after abrasion. Our study demonstrates a swift wound closure after corneal insult. Interestingly, a unilateral wound induces a bilateral response. While cell proliferation is increased during wound closure, this parameter is not crucial, and cell rearrangements seems to be the driving force. Furthermore, we discovered a profound change in epithelial cell transcriptomic signature after abrasion, reflecting a modulation of cell identity and increase of phenotypic plasticity. The latter seems to unlock terminally differentiated cell capacities for wound healing, which could be the key for a speed up organ regeneration. Our results prove that zebrafish cornea is a powerful model to investigate, not only corneal wound healing, but ectodermal organ pathophysiology.

category: physiology


title: Molecular features of RNA silencing against phloem-restricted polerovirus TuYV enable amplification of silencing signal from host transcripts

abstract: In plants and some animal lineages, RNA silencing is an efficient and adaptable defense mechanism against viruses. To counter it, viruses encode suppressor proteins that interfere with RNA silencing. Phloem-restricted viruses are spreading at an alarming rate and cause substantial reduction of crop yield, but how they interact with their hosts at the molecular level is still insufficiently understood. Here, we investigate the antiviral response against phloem-restricted turnip yellows virus (TuYV) in the model plant Arabidopsis thaliana. Using a combination of genetics, deep sequencing, and mechanical vasculature enrichment, we show that the main axis of silencing active against TuYV involves 22-nt vsiRNA production by DCL2, and their preferential loading into AGO1. Unexpectedly, and despite the viral encoded VSR P0 previously shown to mediate degradation of AGO proteins, vascular AGO1 undergoes specific post-translational stabilization during TuYV infection. We also identify vascular novel secondary siRNA produced from conserved plant transcripts and initiated by DCL2-processed AGO1-loaded vsiRNA, supporting a viral strategy to modulate host response. Collectively, our work uncovers the complexity of antiviral RNA silencing against phloem-restricted TuYV and prompts a re-assessment of the role of its suppressor of silencing P0 during genuine infection.


title: Neural Representation of the Relational Self from Infancy to Adulthood

abstract:
Investigations into the neural underpinnings of the "self" highlight its complexity and multi-dimensionality and emphasize that various aspects of the self are sustained by different neural systems. Here, we focused on the Relational Self, a dimension denoting the self-within-attachment-relationships that taps the continuity of attachment across individual development and affiliative bonds. Mothers and children were followed across two decades and videotaped in naturalistic interactions at three ages: infancy (3-6 months), childhood (9-12 years), and young adulthood (18-24 years). During fMRI scanning, young adults were exposed to videos of their own mother-child interactions from the three ages versus matched unfamiliar interactions. Relational Self-stimuli elicited greater activations across preregistered nodes of the human caregiving network, including thalamus-to-brainstem, amygdala, hippocampus, ACC, insula, and temporal cortex. Critically, Relational Self-stimuli were age-invariant in most regions of interest despite large variability of stimuli across multiple self-related features, such as similarity, temporal distance, affect, or mentalization, and Bayesian analysis indicated strong evidence for lack of age-related differences. PPI analysis demonstrated that Relational Self-stimuli elicited tighter connectivity between the ACC and insula. Greater child social engagement during interaction with mother correlated with higher ACC and insula response to Relational Self-stimuli. Findings highlight an important novel dimension in the neural representation of the self, suggest that the Relational Self may be sustained by a paralimbic interface integrating exteroceptive and interoceptive self-related signals, and demonstrate overlap in the attachment network of parents and children, lending support to perspectives on the continuity of attachment and self across the individuals developmental history.

Significance StatementDescribing the neural underpinnings of the "self" is inherently complex due to the multi-dimensionality of the construct. Following mothers and children from infancy to adulthood, we focused on the Relational Self, a dimension denoting the self-within-attachment-relationships, and exposed young adults to own versus unfamiliar mother-child interactions across their relational history. Relational Self stimuli triggered greater activations in the human caregiving network, including thalamus-to-brainstem, amygdala, hippocampus, ACC, insula, and temporal cortex, were age-invariant, and elicited tighter connectivity between ACC and insula, creating a paralimbic interface of interoception-exteroception sustaining the Relational Self. Findings highlight a novel dimension in the neural representation of the self and lend support to perspectives emphasizing the cross-generational transmission of attachment and its continuity across the individuals developmental history.


title: Convergence of clinically relevant manipulations on dopamine-regulated prefrontal activity underlying stress-coping responses

abstract:
BackgroundDepression is a pleiotropic condition that can be produced or ameliorated by diverse genetic, environmental, and pharmacological manipulations. In this context, identifying patterns of circuit activity on which many of these manipulations converge would be important, because studying these patterns could reveal underlying biological processes related to depression and/or new therapies. In particular, the prefrontal cortex and dopaminergic signaling have both been implicated in depression. Nevertheless, how dopamine influences disease-relevant patterns of prefrontal circuit activity remains unknown.

MethodsWe used calcium imaging in brain slices to identify depression-relevant patterns of activity in prefrontal microcircuits, and measure how these are modulated by dopamine D2 receptors (D2Rs). Then, we used optogenetic and genetic manipulations to test how dopamine and D2Rs contribute to stress-coping behavior in a paradigm commonly used to assay how manipulations promote or ameliorate depression-like states.

ResultsPatterns of correlated activity in prefrontal microcircuits are enhanced by D2R stimulation as well as by two mechanistically distinct antidepressants: ketamine and fluoxetine. Conversely, this D2R-driven effect was disrupted in two etiologically distinct models of depression: a genetic susceptibility model and chronic social defeat. Phasic stimulation of dopamine afferents to prefrontal cortex increased effortful responses to tail suspension stress. Conversely, deleting prefrontal D2R receptors reduced the duration of individual struggling episodes.

ConclusionsCorrelated prefrontal microcircuit activity represents a point of convergence for multiple depression-related manipulations. Prefrontal D2Rs enhance this activity. Through this mechanism, prefrontal dopamine signaling may promote network states associated with antidepressant actions that manifest as effortful responses to stress.


title: The impact of brain lesions on tDCS-induced electric field magnitude

abstract:
BackgroundTranscranial direct current stimulation (tDCS) has been used to enhance motor and language rehabilitation following a stroke. However, improving the effectiveness of clinical tDCS protocols depends on understanding how lesions may influence tDCS-induced current flow through the brain.

ObjectiveWe systematically investigated the effect of brain lesions on the magnitude of electric fields (e-mag) induced by tDCS, and how to overcome lesion-induced inter-individual variability in e-mag.

MethodsWe simulated the effect of 630 different lesions - by varying lesion location, distance from the target region of interest (ROI), size and conductivity - on tDCS-induced e-mag in the brains of two participants. Current flow modelling was conducted for two tDCS montages commonly used in clinical applications, which target either primary motor cortex (M1) or Brocas area (BA44), respectively. We further explored how the inherent variability in e-mag that is introduced by inter-lesion differences can be overcome by individualising tDCS protocols.

ResultsThe effect on absolute e-mag was highly dependent on lesion size, conductance and the distance from the target ROI. Larger lesions, with high conductivity, closer to the ROI caused e-mag changes of more than 30%. The sign of this change was determined by the location of the lesion. Specifically, lesions located in-line with the predominant direction of current flow increased e-mag in the ROI, whereas lesions located in the opposite direction caused a decrease. Lesions had a large impact on the optimal electrode configuration if attempting to maximise for the total e-mag in the ROI, but little impact if only the component of e-mag flowing radially inward to the cortex was maximised. Knowing the effect of a given lesion on e-mag also allows for individualising tDCS intensity to reduce variability.

ConclusionsThese results demonstrate that tDCS-induced electric fields are profoundly influenced by lesion characteristics, and further exacerbate the known variability in e-mag across individuals. Additionally, the dependence of these results on the assigned conductance of the lesion underlines the need for improved estimates of lesion conductivity for current flow models. Our results highlight the need for individualised dose control of tDCS in the lesioned brain to overcome the substantial inter-individual variability in electric fields delivered to a cortical target region.

Highlights- Lesions can alter tDCS-induced electric field magnitude (e-mag) in a target by 30%
- Lesions can cause increases or decreases to e-mag
- Direction of change depends on the position of the lesion relative to current flow
- Lesion conductivity - the true value for which is unknown - also impacts change
- E-mag variability can be reduced by individualising montage and stimulation intensity


title: Automated long-term two-photon imaging in head-fixed walking Drosophila

abstract:
The brain of Drosophila shows dynamics at multiple timescales, from the millisecond range of fast voltage or calcium transients to functional and structural changes occurring over multiple days. To relate such dynamics to behavior requires monitoring neural circuits across these multiple timescales in behaving animals.

Here, we develop a technique for automated long-term two-photon imaging in fruit flies, during wakefulness and sleep, navigating in virtual reality over up to seven days. The method is enabled by laser surgery, a microrobotic arm for controlling forceps for dissection assistance, an automated feeding robot, as well as volumetric, simultaneous multiplane imaging. The approach is validated in the flys head direction system.

Imaging in behaving flies over multiple timescales will be useful for understanding circadian activity, learning and long-term memory, or sleep.


title: Gambling on an empty stomach: Hunger modulates preferences for learned but not described risks

abstract: We assess risks differently when they are explicitly described, compared to when we learn directly from experience, suggesting dissociable decision-making systems. Our needs, such as hunger, could globally affect our risk preferences, but do they affect described and learned risks equally? On one hand, explicit decision-making is often considered flexible and contextsensitive, and might therefore be modulated by metabolic needs. On the other hand, implicit preferences learned through reinforcement might be more strongly coupled to biological drives. To answer this, we asked participants to choose between two options with different risks, where the probabilities of monetary outcomes were either described or learned. In agreement with previous studies, rewarding contexts induced risk-aversion when risks were explicitly described, but risk-seeking when they were learned through experience. Crucially, hunger attenuated these contextual biases, but only for learned risks. The results suggest that our metabolic state determines risk-taking biases when we lack explicit descriptions.


title: Evolution of MEG: a first MEG-feasible fluxgate magnetometer

abstract: In the current article we present a first solid-state sensor feasible for magnetoencephalography (MEG), and working at room temperature. The sensor is a fluxgate magnetometer based on yttrium-iron garnet films (YIGM). In this feasibility study we prove the concept of usage the YIGM in terms of MEG by registering a simple brain induced field: the human alpha rhythm 1. All the experiments and results are validated with usage of another kind of high-sensitive magnetometers - optically pumped magnetometer (OPM), which currently appears to be well-established in terms of MEG.


title: Identification of biomarkers and candidate regulators for multiple myeloma under the knockout of AURKA

abstract: Multiple myeloma (MM) is a plasma cell malignancy that is characterized by the overabundance of monoclonal paraprotein. Aurora kinase A (AURKA) was upregulated in patients with high-risk MM. AURKA inhibitors were used to inhibit MM cell proliferation by inducing cell apoptosis and injury. In our study, we aim to identify biological processes and pathways of MM cells under the knockout of AURKA (AURKA KO) by using a bioinformatics method to elucidate their potential pathogenesis. The gene expression profiles of the GSE163589 dataset were originally produced by using the high-throughput BGISEQ-500 (Homo sapiens). The biological categories and pathways were analyzed by the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG), Gene Ontology (GO), and Reactom enrichment. KEGG and GO results indicated the biological pathways related to the immune responses and cancer activities were mostly affected in the development of MM with AURKA KO. Moreover, we identified several genes including GNG5, UBE2D1, and BUB1B were involved in the regulation of cancer genesis. We further predicted novel regulators that had the ability to affect the progression of MM with AURKA KO based on the L1000fwd analysis. Therefore, this study provides further insights into the mechanism of MM under AURKA inhibitor treatments.

category: immunology


title: Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin

abstract: Osteocytes use an elaborate network of dendritic connections to control bone remodeling. Some osteoblasts embed within mineralized bone matrix, change shape, and become osteocytes. The molecular circuitry that drives dendrite formation during "osteocytogenesis" is poorly understood. Here we show that deletion of Sp7, a gene linked to rare and common skeletal disease, in mature osteoblasts and osteocytes causes severe defects in osteocyte dendrites. Unbiased profiling of Sp7 target genes and binding sites reveals unexpected repurposing of this transcription factor to drive dendrite formation. Osteocrin is a Sp7 target gene that promotes osteocyte dendrite formation and rescues phenotypic and molecular defects in Sp7-deficient mice. Single-cell RNA-sequencing demonstrates overt defects in osteocyte maturation in vivo in the absence of Sp7. Sp7-dependent gene networks enriched in developing osteocytes are associated with rare and common human skeletal traits. Moreover, humans homozygous for the osteogenesis imperfecta-causing SP7R316C mutation show dramatic defects in osteocyte morphology. Genes that mark osteocytes in vivo and that are regulated by Sp7 in vitro are highly enriched in neurons, highlighting shared features between osteocytic and neuronal connectivity. Taken together, these findings reveal a crucial role for Sp7 and its target gene Osteocrin in osteocytogenesis, demonstrating that pathways that control osteocyte development influence human bone diseases.


title: Computational modeling of C-terminal tails to predict the calcium-dependent secretion of ER resident proteins

abstract: The lumen of the endoplasmic reticulum (ER) has resident proteins that are critical to perform the various tasks of the ER such as protein maturation and lipid metabolism. These ER resident proteins typically have a carboxy-terminal ER retention sequence (ERS). The canonical ERS is Lys-Asp-Glu-Leu (KDEL) and when an ER resident protein moves from the ER to the Golgi, KDEL receptors (KDELRs) in the Golgi recognize the ERS and return the protein to the ER lumen. Depletion of ER calcium leads to the mass departure of ER resident proteins in a process termed exodosis, which is also regulated by KDELRs. Here, by combining computational prediction with machine learning-based models and experimental validation, we identify carboxy tail sequences of ER resident proteins divergent from the canonical "KDEL" ERS. Using molecular modeling and simulations, we demonstrated that two representative non-canonical ERS can stably bind to the KDELR. Collectively, we developed a method to predict whether a carboxy-terminal sequence acts as a putative ERS that would undergo secretion in response to ER calcium depletion and interact with the KDELRs. Identification of proteins that undergo exodosis will further our understanding of changes in ER proteostasis under physiological and pathological conditions where ER calcium is depleted.

category: cell biology


title: piRNA pathway is essential for generating functional oocytes in golden hamster

abstract: Piwi-interacting RNAs (piRNAs) are small RNAs predominantly expressed in germ cells that are critical for gametogenesis in various species. However, PIWI-deficient female mice are fertile and mouse oocytes express a panel of small RNAs that do not appear widely representative of mammals, and piRNA function in the oogenesis of other mammals has therefore remained elusive. Recent studies revealed the small RNA and PIWI transcriptional profiles in golden hamster oocytes more closely resemble that of humans than mice. Herein, we generated PIWIL1-, PLD6- and MOV10L1-deficient golden hamsters and found that all female mutants were sterile, with embryos arrested at the two-cell stage. In PIWIL1 mutant oocytes, we observed transposon accumulation and broad transcriptomic dysregulation, while zygotic gene activation was impaired in early embryos. Intriguingly, PIWIL1-piRNAs exhibited a unique, preferential silencing of endogenous retroviruses (ERVs), whereas silencing LINE1s depended on both PIWIL1- and PIWIL3-piRNAs. Moreover, we showed that piRNAs participate in the degradation of maternal mRNAs in MII oocytes and embryos via partially complementary targets. Together, our findings demonstrate that piRNAs are indispensable for generating functional oocytes in golden hamster, and show the informative value of this model for functional and mechanistic investigations of piRNAs, especially those related to female infertility.


title: Stochasticity-induced stabilization weakens in diverse communities.

abstract: Environmental stochasticity and the temporal variations of demographic rates associated with it are ubiquitous in nature. The ability of these fluctuations to stabilize a coexistence state of competing populations (sometimes known as the storage effect) is a counterintuitive feature that has aroused much interest. Here we consider the performance of environmental stochasticity as a stabilizer in diverse communities. We review the results of previous studies which suggest that the stabilizing effects of stochasticity weaken as the number of species increases, provide a systematic numerical exploration of the phenomenon and identify the relevant parameter regimes. Of particular importance is the ratio between the dwell time of the environment and the generation time: we show that stochasticity promotes diversity only when this ratio is smaller than the inverse of the fundamental biodiversity parameter. In an opposite regime, when stochasticity impedes coexistence and lowers the species richness, its effect is determined by the ratio between the strength of environmental variations and the rate at which new types are added to the community via speciation, mutation or immigration.


title: Lower Vibrio spp. abundances in Zostera marina leaf canopies suggest a novel ecosystem function for temperate seagrass beds

abstract: Seagrasses, a polyphyletic group of about 60 marine angiosperm species, are the foundation of diverse and functionally important marine habitats along sheltered sedimentary coasts. As a novel ecological function with high societal relevance, a role of the leaf canopy for reducing potentially harmful bacteria has recently been hypothesized. Accordingly, we tested whether or not the abundance of general bacteria and more specifically, those belonging to the genus Vibrio were reduced within temperate Zostera marina (eelgrass) meadows compared to adjacent sand flats and sampled 5 sites in the south-western Baltic Sea using SCUBA. Compared to non-vegetated area, we found an average reduction of 39% for all Vibrio and 63% for the potentially harmful V. vulnificus/cholerae subtype based on robust plate counting data on Vibrio selective agar. The underlying mechanism is currently elusive and clearly merits further study. Our results underline the critical importance of seagrasses in maintaining shallow water ecosystem functioning including water quality and provide further motivation for their protection and restoration.


title: Minimal clustering and species delimitation based on multi-locus alignments vs SNPs: the case of the Seriphium plumosum L. complex (Gnaphalieae: Asteraceae)

abstract: We applied species delimitation methods based on the Multi-Species Coalescent (MSC) model to 500+ loci derived from genotyping-by-sequencing on the South African Seriphium plumosum (Asteraceae) species complex. The loci were represented either as multiple sequence alignments or single nucleotide polymorphisms (SNPs), and analysed by the STACEY and Bayes Factor Delimitation (BFD)/SNAPP methods, respectively. Both methods supported species taxonomies where virtually all of the 32 sampled individuals, each representing its own geographical population, were identified as separate species. Computational efforts required to achieve adequate mixing of MCMC chains were considerable, and the species/minimal cluster trees identified similar strongly supported clades in replicate runs. The resolution was, however, higher in the STACEY trees than in the SNAPP trees, which is consistent with the higher information content of full sequences. The computational efficiency, measured as effective sample sizes of likelihood and posterior estimates per time unit, was consistently higher for STACEY. A random subset of 56 alignments had similar resolution to the 524-locus SNP data set. The STRUCTURE-like sparse Non-negative Matrix Factorisation (sNMF) method was applied to six individuals from each of 48 geographical populations and 28023 SNPs. Significantly fewer (13) clusters were identified as optimal by this analysis compared to the MSC methods. The sNMF clusters correspond closely to clades consistently supported by MSC methods, and showed evidence of admixture, especially in the western Cape Floristic Region. We discuss the significance of these findings, and conclude that it is important to a priori consider the kind of species one wants to identify when using genome-scale data, the assumptions behind the parametric models applied, and the potential consequences of model violations may have.


title: Genomic architecture and evolutionary dynamics of a social niche polymorphism in the California harvester ant, Pogonomyrmex californicus

abstract: Social insects vary considerably in their social organization both between and within species. In the California harvester ant, Pogonomyrmex californicus (Buckley 1867), colonies are commonly founded and headed by a single queen (haplometrosis, primary monogyny). However, in some populations in California (USA), unrelated queens cooperate not only during founding (pleometrosis) but throughout the life of the colony (primary polygyny). The genetic architecture and evolutionary dynamics of this complex social niche polymorphism (haplometrosis vs pleometrosis) have remained unknown. Here, we provide a first analysis of its genomic basis and evolutionary history. We discover a recently evolved (< 200 k years), 8 Mb non-recombining region segregating with the observed social niche polymorphism, showing characteristics of a supergene comparable to those underlying social polymorphisms in other ant species. However, we also find remarkable differences to the other so far described social supergenes. Particularly, four additional genomic regions not in linkage with the supergene show signatures of a selective sweep in the pleometrotic population. Within these regions, we find for example genes crucial for epigenetic regulation via histone modification (chameau) and DNA methylation (dnmt1). Our results suggest that social morph in this species is a polygenic trait including an incipient supergene that evolved less than 200 000 years ago.


title: The Pogonomyrmex californicus social niche polymorphism is a polygenic trait involving a young supergene


title: Somewhere I Belong: Phylogenetic Comparative Methods and Machine Learning to Investigate the Evolution of a Species-Rich Lineage of Parasites

abstract: AO_SCPLOWBSTRACTC_SCPLOWA substantial portion of biodiversity evolved through adaptive radiation. However, the effects of explosive speciation on species interactions remain poorly understood. Metazoan parasites infecting radiating host lineages could improve our knowledge because of their intimate host relationships. Yet limited molecular, phenotypic, and ecological data discourage multivariate analyses of evolutionary patterns and encourage the use of discrete characters. Here, we assemble new molecular, morphological, and host range data widely inferred from a species-rich lineage of parasites (Cichlidogyrus, Platyhelminthes: Monogenea) infecting cichlid fishes to address data scarcity. We infer a multi-marker (28S/18S rDNA, ITS1, COI mtDNA) phylogeny of 58/137 species and characterise major lineages through synapomorphies inferred from mapping morphological characters. We predict the phylogenetic position of species without DNA data through shared character states, a combined molecular-morphological phylogenetic analysis, and a classification analysis with support vector machines. Based on these predictions and a cluster analysis, we assess the systematic informativeness of continuous characters, search for continuous equivalents for discrete characters, and suggest new characters for morphological traits not analysed to date. We also model the attachment/reproductive organ and host range evolution using the data of 136/137 described species and multivariate phylogenetic comparative methods (PCMs). We show that discrete characters can mask phylogenetic signals but can be key for characterising species groups. Regarding the attachment organ morphology, a divergent evolutionary regime for at least one lineage was detected and a limited morphological variation indicates host and environmental parameters affecting its evolution. However, moderate success in predicting phylogenetic positions, and a low systematic informativeness and high multicollinearity of morphological characters call for a revaluation of characters included in species characterisations.


title: Somewhere I belong: phylogenetic comparative methods and machine learning to investigate the evolution of a species-rich lineage of parasites


title: Somewhere I belong: phylogeny and morphological evolution in a species-rich lineage of ectoparasitic flatworms infecting cichlid fishes


title: Avoiding attack: How dune wasps leverage colour and motion to detect their cryptic spider predators

abstract: Ambush predators depend on cryptic body colouration, stillness and a suitable hunting location to optimise the probability of prey capture. Detection of cryptic predators, such as crab spiders, by flower seeking wasps may also be hindered by wind induced movement of the flowers themselves. In a beach dune habitat, Microbembex nigrifrons wasps approaching flowerheads of the Palafoxia lindenii plant need to evaluate the flowers to avoid spider attack. Wasps may detect spiders through colour and movement cues. We tracked the flight trajectories of dune wasps as they approached occupied and unoccupied flowers under two movement conditions; when the flowers were still or moving. We simulated the appearance of the spider and the flower using psychophysical visual modelling techniques and related it to the decisions made by the wasp to land or avoid the flower. Wasps could discriminate spiders only at a very close range, and this was reflected in the shape of their trajectories. Wasps were more prone to making errors in threat assessment when the flowers are moving. Our results suggest that dune wasp predation risk is augmented by abiotic conditions such as wind and compromises their early detection capabilities.


title: Song complexity in relation to repertoire size and phonological syntax in the breeding song of Purple Sunbird

abstract: There are multiple measures for bird song complexity such as repertoire size, phonological or compositional syntax and complex vocal mechanism (CVM). We examined these in an old-world passerine, Purple Sunbird. First, we identified and acoustically characterised the repertoire size (of notes and phrases). We then assessed positional fidelity and ordering of notes within phrases. We found 23 distinct notes by aural-visual inspection of spectrograms which was validated using a Classification and Regression Tree based on 5 acoustic parameters. These notes combined in different iterations to form 30 different phrases. Phrases comprised of an overall structure with an introductory note (prefix) at the onset, followed by notes occurring at specific positions within the phrase body, and terminated with a trill (suffix syllable(s)). Prefix was present in 93% of phrases whereas suffix syllable(s) occurred in 27% of phrases only. We found that notes exhibited positional fidelity and combined in specific order to form a phrase. This is indicative of underlying phonological syntax that limits the ways in which notes combine to form phrase and offers insights to song complexity. Finally, we found that suffix syllables exhibit the presence of mini-breath (very short inter-note interval) which are known to be produced by CVM.


title: Identification of regulatory networks associated with anti-HIV/AIDS genes via integrated transcriptome, epigenome and proteome analyses

abstract: There are individuals naturally resistant to HIV. To identify anti-HIV genes and regulatory networks that enable the native ability to resist HIV, we reanalyzed the transcriptome of HIV resistant and susceptible individuals based on previous efforts, and performed regulatory network prediction using HIV-infection related DNA methylation, miRNA and Chip-SEQ data. We totally found 25 potential anti-HIV genes and 23 of them are newly identified. They are enriched in pathways of immunity, neurological system and cell signaling. 4 anti-HIV genes show DNA hypermethylation signatures and 4 are possibly bounded by the HIV-1 Trans-Activator of Transcription protein (Tat). We found a potential HIV-resistance correlated miRNA hsa-miR-3074-5p possibly regulating an anti-HIV hub gene JUN. Our findings provide novel insights for AIDS treatments and approaches to HIV vaccine design.


title: MAAPER: model-based analysis of alternative polyadenylation using 3' end-linked reads

abstract: Most eukaryotic genes harbor multiple cleavage and polyadenylation sites (PASs), leading to expression of alternative polyadenylation (APA) isoforms. APA regulation has been implicated in a diverse array of physiological and pathological conditions. While RNA sequencing tools that generate reads containing the PAS, named onSite reads, have been instrumental in identifying PASs, they have not been widely used. By contrast, a growing number of methods generate reads that are close to the PAS, named nearSite reads, including the 3 end counting strategy commonly used in single cell analysis. How these nearSite reads can be used for APA analysis, however, is poorly studied. Here, we present a computational method, named model-based analysis of alternative polyadenylation using 3 end-linked reads (MAAPER), to examine APA using nearSite reads. MAAPER uses a probabilistic model to predict PASs for nearSite reads with high accuracy and sensitivity, and examines different types of APA events, including those in 3UTRs and introns, with robust statistics. We show MAAPERs accuracy with data from both bulk and single cell RNA samples and its applicability in unpaired or paired experimental designs. Our result also highlights the importance of using well annotated PASs for nearSite read analysis.


title: Information-Efficient, Off-Center Sampling Results in Improved Precision in 3D Single Particle Tracking Microscopy

abstract: In this work, we present a 3D single-particle tracking system that can apply tailored sampling patterns to selectively extract photons that yield the most information for particle localization. We demonstrate that off-center sampling at locations predicted by Fisher information utilizes photons most efficiently. When performing localization in a single dimension, optimized off-center sampling patterns gave doubled precision compared to uniform sampling. A ~20% increase in precision compared to uniform sampling can be achieved when a similar off-center pattern is used in 3D localization. Here we systematically investigated the photon efficiency of different emission patterns in a diffraction-limited system and achieved higher precision than uniform sampling. The ability to maximize information from the limited number of photons demonstrated here is critical for particle tracking applications in biological samples, where photons may be limited.


title: Fast ATP-dependent subunit rotation in reconstituted FoF1-ATP synthase trapped in solution

abstract:
FoF1-ATP synthases are ubiquitous membrane-bound, rotary motor enzymes that can catalyze ATP synthesis and hydrolysis. Their enzyme kinetics are controlled by internal subunit rotation, by substrate and product concentrations, by mechanical inhibitory mechanisms, but also by the electrochemical potential of protons across the membrane. Single-molecule Forster resonance energy transfer (smFRET) has been used to detect subunit rotation within FoF1-ATP synthases embedded in freely diffusing liposomes. We now report that kinetic monitoring of functional rotation can be prolonged from milliseconds to seconds by utilizing an Anti-Brownian electrokinetic trap (ABEL trap). These extended observation times allowed us to observe fluctuating rates of functional rotation for individual FoF1-liposomes in solution. Broad distributions of ATP-dependent catalytic rates were revealed. The buildup of an electrochemical potential of protons was confirmed to limit the maximum rate of ATP hydrolysis. In the presence of ionophores or uncouplers, the fastest subunit rotation speeds measured in single reconstituted FoF1-ATP synthases were 180 full rounds per second. This was much faster than measured by biochemical ensemble averaging, but not as fast as the maximum rotational speed reported previously for isolated single F1 complexes uncoupled from the membrane-embedded Fo complex. Further application of ABEL trap measurements should help resolve the mechanistic causes of such fluctuating rates of subunit rotation.

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title: Fast ATP-dependent Subunit Rotation in reconstituted FoF1-ATP synthase trapped in Solution


title: Fast ATP-dependent Subunit Rotation in Reconstituted FoF1-ATP Synthase Trapped in Solution


title: Coupling between protrusion dynamics and polarized trafficking steers persistent cell migration

abstract: Migrating cells present a variety of paths, from random to highly directional ones. While random movement can be explained by basal intrinsic activity, persistent movement requires stable polarization. Here, we quantitatively address emergence of persistent migration in RPE1 cells over long timescales. By live-cell imaging and dynamic micropatterning, we demonstrate that the Nucleus-Golgi axis aligns with direction of migration leading to efficient cell movement. We show that polarized trafficking is directed towards protrusions with a 20 min delay, and that migration becomes random after disrupting internal cell organization. Eventually, we prove that localized optogenetic Cdc42 activation orients the Nucleus-Golgi axis. Our work suggests that polarized trafficking stabilizes the protrusive activity of the cell, while protrusive activity orients this polarity axis, leading to persistent cell migration. Using a minimal physical model, we show that this feedback is sufficient to recapitulate the quantitative properties of cell migration in the timescale of hours.


title: Persistent cell migration emerges from a coupling between protrusion dynamics and polarized trafficking


title: A metabolomics insight into the Cyclic Nucleotide Monophosphate signaling cascade in tomato under non-stress and salinity conditions

abstract:
Cyclic Nucleotides Monophosphate (cNMP) are key signalling compounds whose role in plant cell signal transduction is till poorly understood. In this work we used sildenafil, a phosphodiesterase (PDE) inhibitor used in human, to amplify the signal cascade triggered by cNMP using tomato as model plant. Metabolomics was then used, together with plant growth and root architecture parameters, to unravel the changes elicited by PDE inhibition either under non-stress and 100 mM NaCl salinity conditions.

The PDE inhibitor elicited a significant increase in biomass (+62%) and root length (+56%) under no stress conditions, and affected root architecture in terms of distribution over diameter classes. Together with cGMP, others cNMP were modulated by the treatment. Moreover, PDE inhibition triggered a broad metabolic reprogramming involving photosynthesis and secondary metabolism. A complex crosstalk network of phytohormones and other signalling compounds could be observed in treated plants. Nonetheless, metabolites related to redox imbalance processes and NO signalling could be highlighted in tomato following PDE application. Despite salinity damped down the growth-promoting effects of sildenafil, interesting implications in plant mitigation to stress-related detrimental effects could be observed.

HIGHLIGHTThe role of Cyclic Nucleotides Monophosphate in plant cell signal transduction involves regulation of plant growth and architecture, together with a broad biochemical reprogramming of metabolism.


title: Endosperm turgor pressure both promotes and restricts seed growth and size

abstract: Organ size depends on complex biochemical and mechanical interactions between cells and tissues. Here, we investigate the control of seed size, a key agronomic trait, by mechanical interactions between two compartments: the endosperm and the testa. By combining experiments with computational modelling, we tested an incoherent mechanical feedforward loop hypothesis in which pressure-induced stresses play two antagonistic roles; directly driving seed growth, but indirectly inhibiting it through mechanosensitive stiffening of the seed coat. We show that our model can recapitulate wild type growth patterns and explain the small seed phenotype of the haiku2 mutant. Our work further reveals that the developmental regulation of endosperm pressure is needed to prevent a precocious reduction of seed growth rate induced by force-dependent seed coat stiffening.


title: A Class of Simple Biomolecular Antithetic Proportional-Integral-Derivative Controllers

abstract: Proportional-Integral-Derivative (PID) feedback controllers have been the most widely used controllers in industry for almost a century due to their good performance, simplicity, and ease of tuning. Motivated by their success in various engineering disciplines, PID controllers recently found their way into synthetic biology, where the design of feedback molecular control systems has been identified as an important goal. In this paper, we consider the mathematical realization of PID controllers via biomolecular interactions. We propose an array of topologies that offer a compromise between simplicity and high performance. We first demonstrate that different Proportional-Integral (PI) controllers exhibit different capabilities for enhancing the dynamics and reducing variance (cell-to-cell variability). Next, we introduce several derivative controllers that are realized based on incoherent feedforward loops acting in a feedback configuration. Alternatively, we show that differentiators can be realized by placing molecular integrators in a negative feedback loop--an arrangement that can then be augmented by PI components to yield PID feedback controllers. We demonstrate that the derivative component can be exploited for enhancing system stability, dramatically increasing the molecular control systems dynamic performance, and for reducing the noise effect on the output of interest. The PID controller features are established through various deterministic and stochastic analyses as well as numerical simulations. Finally, we provide an experimental demonstration using a recently developed hybrid setup, the cyberloop, where the controller is implemented in silico to control a biological genetic circuit in vivo. The large array of novel biomolecular PID controllers introduced here forms a basis for the design and construction of advanced high-performance biomolecular control systems that robustly regulate the dynamics of living systems.

category: synthetic biology


title: A Hierarchy of Biomolecular Proportional-Integral-Derivative Feedback Controllers for Robust Perfect Adaptation and Dynamic Performance


title: Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator

abstract:
Bacteria must balance the different needs for substrate assimilation, growth functions, and resilience in order to thrive in their environment. Of all cellular macromolecules, the bacterial proteome is by far the most important resource and its size is limited. Here, we investigated how the highly versatile  knallgas bacterium Cupriavidus necator reallocates protein resources when grown on different limiting substrates and with different growth rates. We determined protein quantity by mass spectrometry and estimated enzyme utilization by resource balance analysis modeling. We found that C. necator invests a large fraction of its proteome in functions that are hardly utilized. Of the enzymes that are utilized, many are present in excess abundance. One prominent example is the strong expression of CBB cycle genes such as Rubisco during growth on fructose. Modeling and mutant competition experiments suggest that CO2-reassimilation through Rubisco does not provide a fitness benefit for heterotrophic growth, but is rather an investment in readiness for autotrophy.

HighlightsO_LIA large fraction of the C. necator proteome is not utilized and not essential
C_LIO_LIHighly utilized enzymes are more abundant and less variable
C_LIO_LIAutotrophy related enzymes are largely underutilized
C_LIO_LIRe-assimilation of CO2 via the CBB cycle is unlikely to provide a fitness benefit
C_LI

category: systems biology


title: Motion extrapolation in the flash-lag effect depends on perceived, rather than physical speed

abstract: In the flash-lag effect (FLE), a flash in spatiotemporal alignment with a moving object is misperceived as lagging behind the moving object. One proposed explanation for this illusion is based on predictive motion extrapolation of trajectories. In this interpretation, the diverging effects of velocity on the perceived position of the moving object suggest that FLE might be based on the neural representation of perceived, rather than physical, velocity. By contrast, alternative explanations based on differential latency or temporal averaging would predict that the FLE does not rely on such a representation of perceived velocity. Here we examined whether the FLE is sensitive to illusory changes in perceived speed that result in changes to perceived velocity, while physical speed is constant. The perceived speed of the moving object was manipulated using revolving wedge stimuli with variable pattern textures (Experiment 1) and luminance contrast (Experiment 2). The motion extrapolation interpretation would predict that the changes in FLE magnitude should correspond to the changes in the perceived speed of the moving object. In the current study, two experiments demonstrated that perceived speed and FLE magnitude increased in the dynamic pattern relative to the static pattern conditions, and that the same effect was found in the low contrast compared to the high contrast conditions. These results showed that manipulations of texture and contrast that are known to alter judgments of perceived speed also modulate perceived position. We interpret this as a consequence of motion extrapolation mechanisms and discuss possible explanations for why we observed no cross-effect correlation.


title: Modulation of pulsatile GnRH dynamics across the ovarian cycle: the role of excitability within the arcuate kisspeptin network

abstract: Pulsatile GnRH release is essential for normal reproductive function. Kisspeptin secreting neurons found in the arcuate nucleus, known as KNDy neurons for co-expressing neurokinin B, and dynorphin, drive pulsatile GnRH release. Furthermore, gonadal steroids regulate GnRH pulsatile dynamics across the ovarian cycle by altering KNDy neurons signalling properties. However, the precise mechanism of regulation remains mostly unknown. To better understand these mechanisms we start by perturbing the KNDy system at different stages of the estrous cycle using optogenetics. We find that optogenetic stimulation of KNDy neurons stimulates pulsatile GnRH/LH secretion in estrous mice but inhibits it in diestrous mice. These in-vivo results in combination with mathematical modelling suggest that the transition between estrus and diestrus is underpinned by well-orchestrated changes in neuropeptide signalling and in the excitability of the KNDy population controlled via glutamate signalling. Guided by model predictions, we show that blocking glutamate signalling in diestrous animals inhibits LH pulses, and that optic stimulation of the KNDy population mitigates this inhibition. In estrous mice, disruption of glutamate signalling inhibits pulses generated via sustained low-frequency optic stimulation of the KNDy population, supporting the idea that the level of network excitability is critical for pulse generation. Our results reconcile previous puzzling findings regarding the estradiol-dependent effect that several neuromodulators have on the GnRH pulse generator dynamics. Therefore, we anticipate our model to be a cornerstone for a more quantitative understanding of the pathways via which gonadal steroids regulate GnRH pulse generator dynamics. Finally, our results could inform useful repurposing of drugs targeting the glutamate system in reproductive therapy.


title: Modulation of pulsatile GnRH dynamics across the ovarian cycle: the role of glutamatergic transmission in the arcuate kisspeptin network.


title: Replicative senescence dictates the emergence of disease-associated microglia and contributes to Abeta pathology

abstract: The sustained proliferation of microglia is a key hallmark of Alzheimers disease (AD), accelerating its progression. Here, we sought to understand the long-term impact of the early and prolonged microglial proliferation observed in AD, hypothesising that extensive and repeated cycling would engender a distinct transcriptional and phenotypic trajectory. We found that the early and sustained microglial proliferation seen in an AD-like model promotes replicative senescence, characterised by increased {beta}gal activity, a senescence-associated transcriptional signature and telomere shortening, correlating with the appearance of disease-associated microglia (DAM) and senescent microglial profiles in human post-mortem AD cases. Prevention of early microglial proliferation hindered the development of senescence and DAM, impairing the accumulation of A{beta} and associated neuritic damage. Overall, our results support that excessive microglial proliferation leads to the generation of senescent DAM, which contribute to early A{beta} pathology in AD.


title: Sex-specific life extension in tauopathy mice by CSF1R inhibition causing selective microglial depletion and suppressed pathogenesis

abstract: Microglia are a fundamental component of pathogenesis in many neurological conditions and have specialized functions that vary by disease stage or specific pathology. Drugs targeting colony-stimulating factor-1 receptor (CSF1R) to block microglial proliferation in preclinical disease models have shown mixed outcomes, thus the therapeutic potential of this approach remains unclear. Here, we evaluated CSF1R inhibitors in tauopathy mice using multiple dosing schemes, drug analogs, and longitudinal measurements in the brain and plasma. In both spontaneous disease and in tau fibril inoculation models, we found a region-dependent reduction in insoluble phosphorylated tau and replication-competent tau in mice treated with CSF1R inhibitors. Surprisingly, despite greater drug exposure and microglial depletion in male mice, we observed a rescue of aberrant behavior, reduced plasma neurofilament light chain, and extended survival in female mice only. Gene expression patterns in CSF1R inhibitor-treated tauopathy mice reverted toward a normal wildtype signature, and in vivo imaging revealed suppressed astrogliosis. However, we observed drug dose-dependent upregulation of immediate early genes in male mice only, indicating excitotoxicity, which may have masked functional benefits. Drug-resilient microglia in tauopathy mice exhibited a ramified morphology similar to wildtype microglia but with greater territory occupied per cell, and their transcriptome was neither disease-associated nor homeostatic, suggesting a unique microglial subtype. Our data argue that complete or continuous microglial ablation is neither required nor desired for neuroprotection, and that selective depletion of detrimental, tauopathy-activated microglia may be achieved by precise timing and dosing of CSF1R inhibitors. Importantly, therapeutics targeting microglia must consider sex-dependent effects on functional outcomes when weighing their translational potential for neurological disease.


title: Explicit and implicit depth-cue integration: evidence of systematic biases with real objects

abstract: In a previous series of experiments using virtual stimuli, we found evidence that 3D shape estimation agrees to a superadditivity rule of depth-cue combination. According to this rule, adding depth cues leads to greater perceived depth magnitudes and, in principle, to depth overestimation. The mechanism underlying the superadditivity effect can be fully accounted for by a normative theory of cue integration, through the adaptation of a model of cue integration termed the Intrinsic Constraint (IC) model. As for its nature, it remains unclear whether superadditivity is a byproduct of the artificial nature of virtual environments, causing explicit reasoning to infiltrate behavior and inflate the depth judgments when a scene is richer in depth cues, or the genuine output of the process of depth-cue integration. In the present study, we addressed this question by testing whether the IC models prediction of superadditivity generalizes beyond VR environments to real world situations. We asked participants to judge the perceived 3D shape of cardboard prisms through a matching task. To assay the potential influence of explicit control over those perceptual estimates, we also asked participants to reach and hold the same objects with their fingertips and we analyzed the in-flight grip size during the reaching. Using physical objects ensured that all visual information was fully consistent with the stimulis 3D structure without computer-generated artifacts. We designed a novel technique to carefully control binocular and monocular 3D cues independently from one another, allowing to add or remove depth information from the scene seamlessly. Even with real objects, participants exhibited a clear superadditivity effect in both explicit and implicit tasks. Furthermore, the magnitude of this effect was accurately predicted by the IC model. These results confirm that superadditivity is an inherent feature of depth estimation.


title: Single dose of amphetamine induces delayed subregional attenuation of striatal cholinergic interneuron activity

abstract:
Psychostimulants such as amphetamine target dopamine neuron synapses to engender drug-induced plasticity. While dopamine neurons modulate the activity of striatal cholinergic interneurons (ChIs) with regional heterogeneity, how amphetamine affects ChI activity has not been elucidated. Here, we applied quantitative fluorescence imaging approaches to map the dose-dependent effects of a single dose of amphetamine on ChI activity at 2.5 and 24 hours after injection across the mouse striatum using the activity-dependent marker phosphorylated ribosomal protein S6 (p-rpS6). We found that amphetamine did not induce neurotoxic effects on ChIs, as their distribution and morphology were not affected. While low- or high-dose amphetamine did not affect ChI activity after 2.5 hours, ChI activity was significantly reduced in all striatal subregions after 24 hours, with a dose-dependent effect in the nucleus accumbens. Thus, our findings suggest that a single dose of amphetamine has delayed regionally heterogeneous effects on ChI activity.

Significance statementUsing the activity dependent marker phosphorylated ribosomal protein S6 (p-rpS6), we mapped amphetamine effects on the activity of cholinergic interneurons (ChIs) across the striatum. Amphetamine caused a delayed attenuation of ChI activity in all striatal subregions, and a dose-dependent effect in the ventral striatum/nucleus accumbens, a critical site of psychostimulant action.