bluuebunny/crossref_metadata_2025 huggingface dataset:
The aftermath of a trophic cascade: Increased anoxia following species invasion of a eutrophic lake
Authors: Rohwer Robin R. , Ladwig Robert , Dugan Hilary A. , Hanson Paul C. , Walsh Jake R. , Zanden M. Jake Vander
Published: January 2023

Species invasions can disrupt aquatic ecosystems by re-wiring food webs. A trophic cascade triggered by the invasion of the predatory zooplankter spiny water flea (Bythotrephes cederströmii) resulted in increased phytoplankton due to decreased zooplankton grazing. Here, we show that increased phytoplankton biomass led to an increase in lake anoxia. The temporal and spatial extent of anoxia experienced a step change increase coincident with the invasion. Anoxia was driven by phytoplankton biomass and stratification changes, and anoxic factor increased by 10 days. In particular, anoxia established more quickly following spring stratification. A shift in spring phytoplankton phenology encompassed both abundance and community composition. Diatoms (Bacillaryophyta) drove the increase in spring phytoplankton biomass, but not all phytoplankton community members increased, shifting the community composition. We infer that increased phytoplankton biomass increased labile organic matter and drove hypolimnetic oxygen consumption. These results demonstrate how a species invasion can shift lake phenology and biogeochemistry.

Scientific significance statement

Invasive species can affect aquatic ecosystems, often by disrupting food webs. We investigated whether the invasive predatory zooplankton spiny water flea could additionally impact the biogeochemistry of a lake, specifically hypolimnetic anoxia dynamics. Using 24 years of observations spanning a spiny water flea invasion that triggered a food web-mediated increase in phytoplankton, we found that increased spring phytoplankton coincided with an earlier onset of anoxia, thereby drawing a connection between a species invasion and a shift in lake oxygen dynamics.

Data availability statement

All data is publicly available through the Environmental Data Initiative via identifiers referenced in the methods. Scripts and data to reproduce the results are available on GitHub (https://github.com/robertladwig/spinyAnoxia) and in Rohwer et al. (2023).

Author contributions

RRR and RL co-led the entire manuscript effort and contributed equally. RL and RRR came up with the research question and conducted the statistical and numerical analyses: RL analysed the anoxia dynamics and related water quality variables, RRR analysed the phytoplankton community dynamics. RL, RRR, and HAD created figures and visualizations. PCH, JW and JVZ provided essential feedback to the analyses and the discussion of ecosystem implications. RRR and RL co-wrote the paper.
Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13
Authors: Kim Sun Kyung , Dickinson Miles Sasha , Finer-Moore Janet , Guan Ziqiang , Kaake Robyn M. , Echeverria Ignacia , Chen Jen , Pulido Ernst H. , Sali Andrej , Krogan Nevan J. , Rosenberg Oren S. , Stroud Robert M.
Published: January 2023

Mycobacterium tuberculosisis currently the leading cause of death by any bacterial infection1. The mycolic acid layer of the cell wall is essential for viability and virulence, and the enzymes responsible for its synthesis are therefore front line targets for antimycobacterial drug development2,3. Polyketide synthase 13 (Pks13) is a module comprised of a closely symmetric parallel dimer of chains, each encoding several enzymatic and transport functions, that carries out the condensation of two different very long chain fatty acids to produce mycolic acids that are essential components of the mycobacterial cell wall. Consequently individual enzymatic domains of Pks13 are targets for antimycobacterial drug development4. To understand this machinery, we sought to determine the structure and domain trajectories of the dimeric multi-enzyme Pks13, a 2×198,426 Dalton complex, from protein purified endogenously from mycobacteria under normal growth conditions, to capture it with normal substrates bound trapped ‘in action’.

Structures of the multi-domain assembly revealed by cryogenic electron microscopy (cryoEM) define the ketosynthase (KS), linker, and acyltransferase (AT) domains, each at atomic resolution (1.8Å), with bound substrates defined at 2.4Å and 2.9Å resolution. Image classification reveals two distinct structures with alternate locations of the N-terminal acyl carrier protein (termed ACP1a, ACP1b) seen at 3.6Å and 4.6Å resolution respectively. These two structures suggest plausible intermediate states, related by a ~60Å movement of ACP1, on the pathway for substrate delivery from the fatty acyl-ACP ligase (FadD32) to the ketosynthase domain. The linking sequence between ACP1 and the KS includes an 11 amino acid sequence with 6 negatively charged side chains that lies in different positively charged grooves on the KS in ACP1a versus ACP1b structures. This charge complementarity between the extended chain and the grooves suggests some stabilization of these two distinct orientations. Other domains are visible at lower resolution and indicate flexibility relative to the KS-AT core. The chemical structures of three bound endogenous long chain fatty acid substrates with their proximal regions defined in the structures were determined by electrospray ionization mass spectrometry.

The domain proximities were probed by chemical cross-linking and identified by mass spectrometry. These were incorporated into integrative structure modeling to define multiple domain configurations that transport the very long fatty acid chains throughout the multistep Pks13 mediated synthetic pathway.
The nuclear receptor LRH-1 discriminates between ligands using distinct allosteric signaling circuits
Authors: Mays Suzanne G. , Hercules David , Ortlund Eric A. , Okafor C. Denise
Published: January 2023

Nuclear receptors (NRs) are transcription factors that regulate essential biological processes in response to cognate ligands. An important part of NR function involves ligand-induced conformational changes that recruit coregulator proteins to the activation function surface (AFS), ~15 Å away from the ligand binding pocket. Ligands must communicate with the AFS to recruit appropriate coregulators and elicit different transcriptional outcomes, but this communication is poorly understood. These studies illuminate allosteric communication networks underlying activation of liver receptor homolog-1 (LRH-1), a NR that regulates development, metabolism, cancer progression and intestinal inflammation. Using >100 microseconds of all-atom molecular dynamics simulations involving 69 LRH-1 complexes, we identify distinct signaling circuits used by active and inactive ligands for AFS communication. Inactive ligands communicate via strong, coordinated motions along paths through the receptor to the AFS. Activating ligands disrupt the “inactive” circuit by inducing connectivity elsewhere. Ligand-contacting residues in helix 7 help mediate the switch between circuits, suggesting new avenues for developing LRH-1-targeted therapeutics. We also elucidate aspects of coregulator signaling, showing that localized, destabilizing fluctuations are induced by inappropriate ligand-coregulator pairings. These studies have uncovered novel features of LRH-1 allostery, and the quantitative approach used to analyze many simulations provides a framework to study allosteric signaling in other receptors.
pA regulator: a system for controlling mammalian gene expression via the modulation of polyA signal cleavage
Authors: Luo Liming , Jea Jocelyn Duen-Ya , Wang Yan , Chao Pei-Wen , Yen Laising
Published: January 2023

The ability to control the expression of a therapeutic gene or a transgene in mammalian cells is crucial for safe and efficacious gene and cell therapy, as well as for elucidating the function of a specific gene product. Yet current mammalian gene regulation systems either evoke harmful immune responses in hosts or lack the required regulatory efficiency. Here we describe a highly responsive RNA-based molecular switch, the pA regulator, that harnesses the power of polyA signal cleavage within the 5’ UTR to control mammalian gene expression. The pA regulator is governed by a ‘dual mechanism’ to ensure maximal control of gene expression: (1) aptamer clamping of polyA signal via drug binding and (2) drug-induced alternative splicing that removes the polyA signal. The metholology achieves an induction efficiency up to 900-fold with an EC50of 0.5μg/ml Tetracycline, a drug concentration that falls well within the FDA-approved dose range. The pA regulator circumvents the immune responses that plague other systems by eliminating the use of a regulatory foreign protein and the need to change transgene coding sequences. Furthermore, it is not dependent on any specific promoter, therefore the system is simple to implement in a single non-viral or viral vector. In a mouse study using AAV-mediated gene transfer, we showed that the pA regulator controlled transgene expression in a “dose-dependent’ and “reversible” manner and exhibited long-term stabilityin vivo, in which both features are crucial for effective therapeutics. The pA regulator is the first non-immunogenic system that demonstrates an EC50at a drug concentration approved by FDA, making it a clinically relevant gene regulation system that could open a new window of opportunity in clinical applications as well as biological studies.
Social Isolation Causes Cortical and Trabecular Bone Loss in Adult Male, but not Female, C57BL/6J Mice
Authors: Mountain Rebecca V. , Langlais Audrie L. , Hu Dorothy , Baron Roland , Lary Christine W. , Motyl Katherine J.
Published: January 2023

Social isolation is a potent form of psychosocial stress and is a growing public health concern, particularly among older adults. Even prior to the onset of the COVID-19 pandemic, which has significantly increased the prevalence of isolation and loneliness, researchers have been concerned about a rising “epidemic” of loneliness. Isolation is associated with an increased risk for many physical and mental health disorders and increased overall mortality risk. In addition to social isolation, older adults are also at greater risk for osteoporosis and related fractures. While researchers have investigated the negative effects of other forms of psychosocial stress on bone, including depression and PTSD, the effects of social isolation on bone have not been thoroughly investigated. The aim of this study was to test the hypothesis that social isolation would lead to bone loss in male and female C57BL/6J mice. 16-week-old mice were randomized into social isolation (1 mouse/cage) or grouped housing (4 mice/cage) for four weeks (N=16/group). Social isolation significantly decreased trabecular (BV/TV, BMD, Tb. N., Tb. Th.) and cortical bone (Ct.Th., Ct.Ar., Ct.Ar./Tt.Ar., pMOI, Ct.Por.) parameters in male, but not female mice. Isolated male mice had signs of reduced bone remodeling represented by reduced osteoblast numbers, osteoblast-related gene expression and osteoclast-related gene expression. However, isolated females had increased bone resorption-related gene expression, without any change in bone mass. Overall, our data suggest that social isolation has negative effects on bone in males, but not females, although females showed suggestive effects on bone resorption. These results provide critical insight into the effects of isolation on bone and have key clinical implications as we grapple with the long-term health impacts of the rise in social isolation related to the COVID-19 pandemic.
HAT:de novovariant calling for highly accurate short-read and long-read sequencing data
Authors: Ng Jeffrey K. , Turner Tychele N.
Published: January 2023

Motivation

de novovariant (DNV) calling is challenging from parent-child sequenced trio data. We developedHareAndTortoise (HAT) to work as an automated workflow to detect DNVs in highly accurate short-read and long-read sequencing data. Reliable detection of DNVs is important for human genetics studies (e.g., autism, epilepsy).

Results

HAT is a workflow to detect DNVs from short-read and long read sequencing data. This workflow begins with aligned read data (i.e., CRAM or BAM) from a parent-child sequenced trio and outputs DNVs. HAT detects high-quality DNVs from short-read whole-exome sequencing, short-read wholegenome sequencing, and highly accurate long-read sequencing data.

Availability

https://github.com/TNTurnerLab/HAT

Contact

tychele@wustl.edu

Supplementary information

Supplementary data are available at bioRxiv.
Identification of potent and selectiveN-myristoyltransferase inhibitors ofPlasmodium vivaxliver stage hypnozoites and schizonts
Authors: Rodríguez-Hernández Diego , Vijayan Kamalakannan , Zigweid Rachael , Fenwick Michael K. , Sankaran Banumathi , Roobsoong Wanlapa , Sattabongkot Jetsumon , Glennon Elizabeth K.K. , Myler Peter J. , Sunnerhagen Per , Staker Bart L. , Kaushansky Alexis , Grøtli Morten
Published: January 2023

New drugs targeting multiple stages of the malaria-causing parasite,Plasmodium, are needed to reduce and eliminate malaria worldwide.N-Myristoyltransferase (NMT) is an essential eukaryotic enzyme, and a validated chemically tractable drug target for malaria. Previous efforts have failed to target NMT owing to the low selectivity for thePlasmodiumenzyme compared with human NMTs. Herein, we applied a structure-guided approach using previously reported NMT inhibitors as scaffolds to develop a new generation ofPlasmodium vivaxNMT (PvNMT) targeting compounds. We report a series of compounds with IC50values in the nM range and an order of magnitude improved selectivity toPlasmodiumNMT over human NMT (HsNMT). X-ray co-crystallization ofPvNMT with a representative lead compound,12b, supported the prevailing hypothesis that a conformational difference in a key tyrosine residue ofPvNMT andHsNMT drives the selectivity between these enzymes. The compounds were triaged based on their selectivity forPvNMT. They significantly decreasedP. falciparumblood-stage parasite load, with IC50values ranging from 0.36 μM to 1.25 μM. The compounds exhibited a dose-dependent inhibition ofP. vivaxliver stage schizont and hypnozoite infection, consistently, in three differentP. vivaxisolates with IC50values ranging from 2.2 μM to 6 μM and from 1.2 μM to 12 μM. Our data provide evidence that NMT inhibitors could be multistage antimalarials, targeting both dormant and developing liver stage parasites, which is essential for malaria elimination.

One Sentence Summary

Potent and selectiveN-myristoyltransferase inhibitors ofPlasmodium vivaxhypnozoites and schizonts were synthesized and tested.
Humans adaptively select different computational strategies in different learning environments
Authors: Verbeke Pieter , Verguts Tom
Published: January 2023

The Rescorla-Wagner rule remains the most popular tool to describe human behavior in reinforcement learning tasks. Nevertheless, it cannot fit human learning in complex environments. Previous work proposed several hierarchical extensions of this learning rule. However, it remains unclear when a flat (non-hierarchical) versus a hierarchical strategy is adaptive, or when it is implemented by humans. To address this question, current work applies a nested modelling approach to evaluate multiple models in multiple reinforcement learning environments both computationally (which approach performs best) and empirically (which approach fits human data best). We consider ten empirical datasets (N= 407) divided over three reinforcement learning environments. Our results demonstrate that different environments are best solved with different learning strategies; and that humans adaptively select the learning strategy that allows best performance. Specifically, while flat learning fitted best in less complex stable learning environments, humans employed more hierarchically complex models in more complex environments.
Accumulation of TCR signaling from self-antigens in naive CD8 T cells mitigates early responsiveness
Authors: Eggert Joel , Zinzow-Kramer Wendy M. , Hu Yuesong , Tsai Yuan-Li , Weiss Arthur , Salaita Khalid , Scharer Christopher D. , Au-Yeung Byron B.
Published: January 2023

The cumulative effects of T cell receptor (TCR) signal transduction over extended periods of time influences T cell biology, such as the positive selection of immature thymocytes or the proliferative responses of naive T cells. Naive T cells experience recurrent TCR signaling in response to self-antigens in the steady state. However, how these signals influence the responsiveness of naive CD8+T cells to subsequent agonist TCR stimulation remains incompletely understood. We investigated how naive CD8+T cells that experienced relatively low or high levels of TCR signaling in response to self-antigens respond to stimulation with foreign antigens. A transcriptional reporter ofNr4a1(Nur77-GFP) revealed substantial heterogeneity of the amount of TCR signaling naive CD8+T cells accumulate in the steady state. Nur77-GFPHIcells exhibited diminished T cell activation and secretion of IFNγ and IL-2 relative to Nur77-GFPLOcells in response to agonist TCR stimulation. Differential gene expression analyses revealed upregulation of genes associated with acutely stimulated T cells in Nur77-GFPHIcells but also increased expression of negative regulators such as the phosphatase Sts1. Responsiveness of Nur77-GFPHIcells to TCR stimulation was partially restored at the level of IFNγ secretion by deficiency of Sts1 or the ubiquitin ligase Cbl-b. Our data suggest that extensive accumulation of TCR signaling during steady state conditions induces a recalibration of the responsiveness of naive CD8+T cells through gene expression changes and negative regulation, at least in part, dependent on Sts1 and Cbl-b. This cell-intrinsic negative feedback loop may allow the immune system to limit the autoreactive potential of highly self-reactive naive CD8+T cells.
Perturbation Variability Does Not Influence Implicit Sensorimotor Adaptation
Authors: Wang Tianhe , Avraham Guy , Tsay Jonathan S. , Abram Sabrina J. , Ivry Richard B.
Published: January 2023

Cerebellar-dependent implicit adaptation has been regarded as a rigid process that automatically operates in response to movement errors in order to keep the sensorimotor system calibrated. This hypothesis has been challenged by recent evidence suggesting flexibility in this learning process. One compelling line of evidence comes from work suggesting that this form of learning is context-dependent, with the rate of learning modulated by error history. Specifically, learning was attenuated in the presence of perturbations exhibiting high variance compared to when the perturbation is fixed. However, these findings are confounded by the fact that the adaptation system corrects for errors of different magnitudes in a non-linear manner, with the adaptive response increasing in a proportional manner to small errors and saturating to large errors. Through simulations, we show that this non-linear motor correction function is sufficient to explain the effect of perturbation variance without referring to an experience-dependent change in error sensitivity. Moreover, by controlling the distribution of errors experienced during training, we provide empirical evidence showing that there is no measurable effect of perturbation variance on implicit adaptation. As such, we argue that the evidence to date remains consistent with the rigidity assumption.
Cup is essential foroskarmRNA translational repression during earlyDrosophilaoogenesis
Authors: Bayer Livia V. , Milano Samantha , Formel Stephen K. , Kaur Harpreet , Ravichandran Rishi , Cambeiro Juan A. , Slinko Lizaveta , Catrina Irina E. , Bratu Diana P.
Published: January 2023

The proper timing of mRNA translation is crucial across many biological systems for processes such as intercellular communication, body pattern formation, and morphogenesis. The mainD. melanogasterposterior determinant,oskar, is maternally transcribed, but only translated when properly localized at the oocyte’s posterior cortex. Bruno 1 and Cup are two effector proteins known to participate in multiple aspects ofoskarmRNA regulation. Current model describes a mechanism in which Bruno 1 is necessary for Cup’s recruitment tooskarmRNA, and Bruno 1 is indispensable for its translational repression. Here, we reveal that the Bruno 1-Cup interaction, as well as their interdependent influence on each other’s mRNA and protein expression, lead to preciseoskarmRNA regulation during early oogenesis. We show that these factors stably associate with theoskarmRNAin vivo, but surprisingly, Bruno 1’s stable association withoskarmRNA depends on Cup, while Bruno 1 is not necessary for Cup association tooskarmRNA. During early oogenesis, Cup, not Bruno 1, is the essential factor foroskarmRNA repression. Cup is a crucial P-body member that maintains proper P-body morphology during oogenesis, as well as it is necessary foroskarmRNA’s association with P-bodies, thus driving the translational repression and stability ofoskarmRNA. Our experimental results collectively suggest a regulatory mechanism where a feedback loop between Bruno 1 and Cup coordinatesoskarmRNA regulation in the egg chamber allowing for proper development to occur.
Sperm-contributed centrioles segregate stochastically into blastomeres of 4-cell stageC. elegansembryos
Authors: Gönczy Pierre , Balestra Fernando R.
Published: January 2023

Whereas both sperm and egg similarly contribute nuclear genetic material to the zygote of metazoan organisms, the inheritance of other cellular constituents is unequal between the two gametes. Thus, the centriole organelle is contributed solely by the sperm to the zygote in most systems. Whereas centrioles can have a stereotyped distribution during some asymmetric divisions, whether sperm-contributed centrioles are distributed in a stereotyped manner in the resulting embryo is not known. Here, we addressed this question inCaenorhabditis elegansusing marked mating experiments, whereby the presence of sperm-contributed centrioles is monitored in the resulting embryos using the stable centriolar component SAS-4::GFP, as well as GFP::SAS-7. Our analysis demonstrates that the distribution of sperm-contributed centrioles is stochastic in 4-cell stage embryos. Moreover, using sperm fromzyg-1mutant males that harbor a single centriole, we show that the older sperm-contributed centriole is also distributed stochastically in the resulting embryo. Overall, we conclude that in contrast to the situation during some asymmetric cell divisions, centrioles contributed by the male germ line are distributed stochastically in embryos ofC. elegans.
In situ modeling of acquired resistance to RTK/RAS pathway targeted therapies
Authors: Sealover Nancy E. , Theard Patricia T. , Linke Amanda J. , Hughes Jacob M. , Daley Brianna R. , Kortum Robert L.
Published: January 2023

Intrinsic and acquired resistance limit the window of effectiveness for oncogene-targeted cancer therapies. Preclinical studies that identify synergistic combinations enhance therapeutic efficacy to target intrinsic resistance, however, methods to study acquired resistance in cell culture are lacking. Here, we describe anin situresistance assay (ISRA), performed in a 96-well culture format, that models acquired resistance to RTK/RAS pathway targeted therapies. Using osimertinib resistance inEGFR-mutated lung adenocarcinoma (LUAD) as a model system, we show acquired resistance can be reliably modeled across cell lines with objectively defined osimertinib doses. We further show that acquired osimertinib resistance can be significantly delayed by inhibition of proximal RTK signaling using two distinct SHP2 inhibitors. Similar to patient populations, isolated osimertinib-resistant populations showed resistance via enhanced activation of multiple parallel RTKs so that individual RTK inhibitors did not re-sensitize cells to osimertinib. In contrast, inhibition of proximal RTK signaling using the SHP2 inhibitor RMC-4550 both re-sensitized resistant populations to osimertinib. Similar, objectively defined drug doses were used to model resistance to additional RTK/RAS pathway targeted therapies including the KRASG12Cinhibitors adagrasib and sotorasib, the MEK inhibitor trametinib, and the farnesyl transferase inhibitor tipifarnib. These studies highlight the tractability of in situ resistance assays to model acquired resistance to targeted therapies and provide a framework for assessing the extent to which synergistic drug combinations can target acquired drug resistance.

Highlights

Acquired resistance to RTK/RAS pathway members can be modeled in situ

SHP2 inhibitors reduce the development of acquired osimertinib resistance

Isolated osimertinib-resistant populations show hyperactivation of multiple RTKs

SHP2 inhibitors re-sensitize resistant populations to osimertinib treatment
Bridging model and experiment in systems neuroscience with Cleo: the Closed-Loop, Electrophysiology, and Optophysiology simulation testbed
Authors: Johnsen Kyle A. , Cruzado Nathanael A. , Menard Zachary C. , Willats Adam A. , Charles Adam S. , Markowitz Jeffrey E. , Rozell Christopher J.
Published: January 2023

Systems neuroscience has experienced an explosion of new tools for reading and writing neural activity, enabling exciting new experiments such as all-optical or closed-loop control that effect powerful causal interventions. At the same time, improved computational models are capable of reproducing behavior and neural activity with increasing fidelity. Unfortunately, these advances have drastically increased the complexity of integrating different lines of research, resulting in the missed opportunities and untapped potential of suboptimal experiments. Experiment simulation can help bridge this gap, allowing model and experiment to better inform each other by providing a low-cost testbed for experiment design, model validation, and methods engineering. Specifically, this can be achieved by incorporating the simulation of the experimental interface into our models, but no existing tool integrates optogenetics, two-photon calcium imaging, electrode recording, and flexible closed-loop processing with neural population simulations. To address this need, we have developed Cleo: the Closed-Loop, Electrophysiology, and Optophysiology experiment simulation testbed. Cleo is a Python package enabling injection of recording and stimulation devices as well as closed-loop control with realistic latency into a Brian spiking neural network model. It is the only publicly available tool currently supporting two-photon and multi-opsin/wavelength optogenetics. To facilitate adoption and extension by the community, Cleo is open-source, modular, tested, and documented, and can export results to various data formats. Here we describe the design and features of Cleo, validate output of individual components and integrated experiments, and demonstrate its utility for advancing optogenetic techniques in prospective experiments using previously published systems neuroscience models.
Large polyacrylamide hydrogels for large-batch cell culture and mechanobiological studies
Authors: Shi Xuechen , Janmey Paul
Published: January 2023

The rigidity of a cell’s substrate or extracellular matrix plays a vital role in regulating cell and tissue functions. Polyacrylamide (PAAm) hydrogels are one of the most widely used cell culture substrates that provide a physiologically relevant range of stiffness. However, it is still arduous and time-consuming to prepare PAAm substrates in large batches for high-yield or multi-scale cell cultures. Here we present a simple method to prepare PAAm hydrogels with less time cost and easily accessible materials. The hydrogel is mechanically uniform and supports cell culture in a large batch. We further show that the stiffness of the hydrogel covers a large range of Young’s modulus and is sensed by cells, regulating various cell features including changes in cell morphology, proliferation, and contractility. This method improves reproducibility of mechanobiology studies and can be easily applied for mechanobiology research requiring large numbers of cells or experimental groups.
Role of Strong Localized vs. Weak Distributed Interactions in Disordered Protein Phase Separation
Authors: Rekhi Shiv , Devarajan Dinesh Sundaravadivelu , Howard Michael P. , Kim Young C. , Nikoubashman Arash , Mittal Jeetain
Published: January 2023

Interaction strength and localization are critical parameters controlling the single-chain and condensed-state properties of intrinsically disordered proteins (IDPs). Here, we decipher these relationships using coarse-grained heteropolymers comprised of hydrophobic (H) and polar (P) monomers as model IDPs. We systematically vary the fraction of P monomersXPand employ two distinct particle-based models that include either strong localized attractions between only H–H pairs (HP model) or weak distributed attractions between both H–H and H–P pairs (HP+ model). To compare different sequences and models, we first carefully tune the attraction strength for all sequences to match the single-chain radius of gyration. Interestingly, we find that this procedure produces similar conformational ensembles, nonbonded potential energies, and chain-level dynamics for single chains of almost all sequences in both models, with some deviations for the HP model at largeXP. However, we observe a surprisingly rich phase behavior for the sequences in both models that deviates from the expectation that similarity at the single-chain level will translate to similar phase-separation propensity. Coexistence between dilute and dense phases is only observed up to a model-dependentXPdespite the presence of favorable interchain interactions, which we quantify using the second virial coefficient. Instead, the limited number of attractive sites (H monomers) leads to the self-assembly of finite-sized clusters of different sizes depending onXP. Our findings strongly suggest that models with distributed interactions favor the formation of liquid-like condensates over a much larger range of sequence compositions compared to models with localized interactions.
ChIP-MS reveals the local chromatin composition by label-free quantitative proteomics
Authors: Yong Wai Khang , Rane Grishma , Zaal Anuar Nurkaiyisah , Shao Xiaoman , Goh Chai Yeen , Khanchandani Vartika , Kuan Vivian L. S. , Jeitany Maya , Koeffler H. Phillip , Deng Lih-Wen , Sanda Takaomi , Kappei Dennis
Published: January 2023

Chromatin immunoprecipitation (ChIP) has been a cornerstone for epigenetic analyses over the last decades, but even coupled to sequencing approaches (ChIP-seq), it is ultimately limited to one protein at a time. In a complementary effort, we here combined ChIP with label-free quantitative (LFQ) mass spectrometry (ChIP-MS) to interrogate local chromatin compositions. We demonstrate the versatility of our approach at telomeres, with transcription factors, in tissue and by dCas9-driven locus-specific enrichment.
Biological and structural analysis of new potent Integrase-LEDGF allosteric HIV-1 inhibitors
Authors: Le Rouzic Erwann , Bonnard Damien , Le Strat Frédéric , Batisse Claire , Batisse Julien , Amadori Céline , Chasset Sophie , Emiliani Stéphane , Ledoussal Benoit , Ruff Marc , Moreau François , Benarous Richard
Published: January 2023

LEDGF/p75 (LEDGF) main cellular cofactor of HIV-1 integrase (IN), acts as tethering factor to target integration of HIV in actively transcribed genes. Recently a class of IN inhibitors based on inhibition of LEDGF-IN interaction has been developed. We describe here a new series of IN-LEDGF allosteric inhibitors (INLAIs), with potent anti-HIV-1 activity in the one-digit nanomolar range. These compounds inhibited IN-LEDGF interaction while enhancing IN-IN aberrant multimerization by allosteric mechanism. Compounds of this series were fully active on HIV-1 mutants resistant to IN strand transfer inhibitors (INSTIs) and other class of anti-HIV drugs, confirming that they belong to a new class of antiretrovirals. These compounds displayed most potent antiretroviral activity at post-integration due to aberrant IN polymerization responsible of infectivity defect of viral particles produced. INLAI-resistant mutants were selected by dose escalation method and the most detrimental mutation found was T174I. The impact of these resistance mutations was analyzed by fold shift EC50with regard to wild type virus and the replication capacity of mutated viruses were determined. Crystal structure of BDM-2, the lead compound of this series in complex with IN catalytic core domain (CCD) was elucidated. No antagonism was observed between BDM-2 and a panel of 16 antiretroviral drugs from different classes. In conclusion, the overall virologic profile of BDM-2 warrants the recently completed single ascending dose phase I trial (ClinicalTrials.govId:NCT03634085) and supports further clinical investigation for potential use in combination with other antiretroviral drugs.

Author summary

Integrase-LEDGF allosteric inhibitors are a new class of antiretrovirals recently developed that target the interaction of HIV-1 Integrase with its cellular cofactor LEDGF/p75 required for HIV-1 integration in actively transcribed genes. The great interest of developing such new class of antiretroviral is to add to the anti-HIV drug arsenal compounds that are fully active on resistant viruses to all other classes of drugs currently used in clinic. However, none of these inhibitors are currently in clinical use or in late clinical trials. Here we describe a series of highly potent Integrase allosteric inhibitors that can be considered as precursors of a new class of antiretroviral drugs, with fully conserved activity on viruses resistant to currently used anti-HIV drugs, and a lead compound that has no antagonism with a large panel of present anti-HIV drugs and that was successfully validated in a phase I clinical trial.
The biology of aging in a social world: insights from free-ranging rhesus macaques
Authors: Newman Laura E. , Testard Camille , DeCasien Alex R. , Chiou Kenneth L. , Watowich Marina M. , Janiak Mareike C. , Pavez-Fox Melissa A. , Sanchez Rosado Mitchell R. , Cooper Eve B. , Costa Christina E. , Petersen Rachel M. , Montague Michael J. , Platt Michael L. , Brent Lauren J.N. , Snyder-Mackler Noah , Higham James P.
Published: January 2023

Social adversity can increase the age-associated risk of disease and death, yet the biological mechanisms that link social adversities to aging remain poorly understood. Long-term naturalistic studies of nonhuman animals are crucial for integrating observations of social behavior throughout an individual’s life with detailed anatomical, physiological, and molecular measurements. Here, we synthesize the body of research from one such naturalistic study system, Cayo Santiago Island, which is home to the world’s longest continuously monitored free-ranging population of rhesus macaques. We review recent studies of age-related variation in morphology, gene regulation, microbiome composition, and immune function. We also discuss ecological and social modifiers of age-markers in this population. In particular, we summarize how a major natural disaster, Hurricane Maria, affected rhesus macaque physiology and social structure and highlight the context-dependent and domain-specific nature of aging modifiers. Finally, we conclude by providing directions for future study, on Cayo Santiago and elsewhere, that will further our understanding of aging across different domains and how social adversity modifies aging processes.
Hub architecture of the human structural connectome: Links to aging and processing speed
Authors: Li Xin , Salami Alireza , Persson Jonas
Published: January 2023

The human structural brain network, or connectome, has a rich-club organization with a small number of brain regions showing high network connectivity, called hubs. Hubs are centrally located in the network, energy costly, and critical for human cognition. Aging has been associated with changes in brain structure, function, and cognitive decline, such as processing speed. At a molecular level, the aging process is a progressive accumulation of oxidative damage, which leads to subsequent energy depletion in the neuron and causes cell death. However, it is still unclear how age affects hub connections in the human connectome. The current study aims to address this research gap by utilizing a novel measure of structural connectivity strength, fiber bundle capacity (FBC), which is derived from Constrained Spherical Deconvolution (CSD) modeling of white-matter fiber bundles. FBC represents the capacity of a fiber bundle to transfer information and is a less biased measure for quantifying connection strength within biological pathways. We found that hubs exhibit longer-distance connections and higher metabolic rates compared to peripheral brain regions, suggesting that hubs are biologically costly. Although the landscape of structural hubs was relatively age-invariant, there were wide-spread age effects on FBC in the connectome. Critically, these age effects were larger in connections within hub compared to peripheral brain connections. These findings were supported by both a cross-sectional sample with wide age-range (N=137) and a longitudinal sample across 5 years (N=83). Moreover, our results demonstrated that associations between FBC and processing speed were more concentrated in hub connections than chance level, and FBC in hub connections mediated the age-effects on processing speed. Overall, our findings indicate that structural connections of hubs, which demonstrate greater energy demands, are particular vulnerable to aging. The vulnerability may contribute to age-related impairments in processing speed among older adults.
Investigating the impact of introduced crabs on the distribution and morphology of littorinid snails: Implications for the survival of the snailLittorina saxatilis
Authors: Wells Christopher D. , Van Volkom Kaitlin S. , Edquist Sara , Marovelli Sinead , Marovelli John
Published: January 2023

Introduced species can have profound impacts on communities by displacing and consuming native species. The intertidal communities in the Gulf of Maine have been radically altered through a suite of invasions including the herbivorous snailLittorina littoreaand the omnivorous crabCarcinus maenasleading to morphological and spatial distribution changes in two native gastropod grazers (Littorina saxatilisandLittorina obtusata). Subsequently, another intertidal omnivorous crabHemigrapsus sanguineushas become abundant in the intertidal, occurring in areas which were once refuges from crab predation. In order to quantify the potential impact ofH. sanguineuson native snails, we conducted bothinandex situexperiments, testing the susceptibility of different sized snails to predation by introduced crabs. Additionally, we measured the distribution, abundance, and morphology of intertidal snails and crabs. Smaller snails of all species were the most susceptible to predation, although susceptibility differed among snail species.Littorina saxatiliswas the most vulnerable to predation, with 73 and 64% of the population susceptible to largeH. sanguineusand smallC. maenas, respectively, while more than 89% of theL. littoreapopulation was resistant to predation.Littorina saxatilishas been relegated to the high intertidal where there is high abiotic stress and poor-quality food, but until the invasion ofH. sanguineus, there was little predation risk. Now, it seems thatL. saxatilisis at the most risk of all three snail species, and may be at threat of local extirpation at locations with high populations ofH. sanguineus.
MIIP downregulation promotes colorectal cancer progression via inducing adjacent adipocytes browning
Authors: Wang Qinhao , Su Yuanyuan , Sun Ruiqi , Xiong Xin , Guo Kai , Wei Mengying , Ru Yi , Yang Guodong , Zhang Zhengxiang , Qiao Qing , Li Xia
Published: January 2023

The enrichment of peri-cancerous adipocytes is one of the distinctive features of colorectal cancer (CRC), which accelerates the disease progression and worsens the prognosis. The communication between tumor cells and adjacent adipocytes plays an important role in this process. However, the detailed mechanisms remain largely unknown. Here we demonstrated MIIP is downregulated in high-grade CRC, and revealed its role and mechanism in tumor cell-adipocyte communication. By detecting MIIP expression in CRC tissues and adjacent normal tissues, we found MIIP was significantly decreased in CRC, and was closely related to adjacent adipocytes browning. In detail, MIIP reduction altered the N-linked glycosylation modification of AZGP1 and thus alleviated the inhibition of secretion. AZGP1, a critical lipid mobilization factor, led to the intensification of adipocytes browning and the release of free fatty acids (FFAs), which in turn fueled for CRC progression. Our data demonstrate that MIIP plays a key regulatory role in the communication between CRC and neighboring adipocytes by mediating AZGP1 secretion, and MIIP reduction leads to adipose browning-induced cancer rapid progression and poor prognosis.
Audiovisual integration is preserved in older adults across the cortical hierarchy
Authors: Jones Samuel A. , Noppeney Uta
Published: January 2023

Effective interactions with the environment rely on integration of multisensory signals: our brains must efficiently combine signals that share a common source, and segregate those that do not. Healthy ageing can change or impair this process. This functional magnetic resonance imaging study assessed the neural mechanisms underlying age differences in the integration of auditory and visual spatial cues. Participants were presented with synchronous audiovisual signals at various degrees of spatial disparity and indicated their perceived sound location. Behaviourally, older adults were able to maintain localisation accuracy, albeit with longer response times. At the neural level, they integrated auditory and visual cues into spatial representations along dorsal auditory and visual processing pathways similarly to their younger counterparts, but showed greater activations in a widespread system of frontal, temporal and parietal areas. According to multivariate Bayesian decoding, these areas encoded critical stimulus information beyond that which was encoded in the brain areas commonly activated by both groups. Surprisingly, however, the boost in information provided by these areas with age-related activation increases was comparable across the two age groups.

This dissociation—between comparable response accuracy and information encoded in brain activity patterns across the two age groups, but age-related increases in response times and regional activations—suggests that older participants accumulate noisier sensory evidence for longer, to maintain reliable neural encoding of stimulus-relevant information and thus preserve localisation accuracy.
Germline TFAM levels regulate mitochondrial DNA copy number and mutant heteroplasmy inC. elegans
Authors: Schwartz Aaron Z.A. , Nance Jeremy
Published: January 2023

The mitochondrial genome (mtDNA) is packaged into discrete protein-DNA complexes called nucleoids. mtDNA packaging factor TFAM (mitochondrial transcription factor-A) promotes nucleoid compaction and is required for mtDNA replication. Here, we investigate how changing TFAM levels affects mtDNA in theCaenorhabditis elegansgerm line. We show that increasing germline TFAM activity boosts mtDNA number and significantly increases the relative proportion of a selfish mtDNA mutant,uaDf5. We conclude that TFAM levels must be tightly controlled to ensure appropriate mtDNA composition in the germ line.
Myeloperoxidase enhances the migration of human choriocarcinoma JEG-3 cells1
Authors: Mihalic ZN. , Kloimböck T. , Cosic-Mujkanovic N. , Valadez-Cosmes P. , Maitz K. , Kindler O. , Wadsack C. , Heinemann A. , Marsche G. , Gauster M. , Pollheimer J. , Kargl J.
Published: January 2023

Myeloperoxidase (MPO) is one of the most abundant proteins in neutrophil granules. It catalyzes the production of reactive oxygen species, which are important in inflammation and immune defense. MPO also binds to several proteins, lipids, and DNA to alter their function. MPO is present at the feto-maternal interface during pregnancy, where neutrophils are abundant. In this study, we determined the effect of MPO on JEG-3 human choriocarcinoma cells as a model of extravillous trophoblasts (EVTs) during early pregnancy. We found that MPO was internalized by JEG-3 cells and localized to the cytoplasm and nuclei. MPO internalization and activity enhanced JEG-3 cell migration, whereas this effect was impaired by pre-treating cells with heparin, to block cellular uptake, and MPO-activity inhibitor 4-ABAH. This study identifies a novel mechanism for the effect of MPO on EVT function during normal pregnancy and suggests a potential role of MPO in abnormal pregnancies.

GRAPHICAL ABSTRACT
Axonal transport of autophagosomes is regulated by dynein activators JIP3/JIP4 and ARF/RAB GTPases
Authors: Cason Sydney E. , Holzbaur Erika L.F.
Published: January 2023

Neuronal autophagosomes, “self-eating” degradative organelles, form at presynaptic sites in the distal axon and are transported to the soma to recycle their cargo. During transit, autophagic vacuoles (AVs) mature through fusion with lysosomes to acquire the enzymes necessary to breakdown their cargo. AV transport is driven primarily by the microtubule motor cytoplasmic dynein in concert with dynactin and a series of activating adaptors that change depending on organelle maturation state. The transport of mature AVs is regulated by the scaffolding proteins JIP3 and JIP4, both of which activate dynein motility in vitro. AV transport is also regulated by ARF6 in a GTP-dependent fashion. While GTP-bound ARF6 promotes the formation of the JIP3/4-dynein-dynactin complex, RAB10 competes with the activity of this complex by increasing kinesin recruitment to axonal AVs and lysosomes. These interactions highlight the complex coordination of motors regulating organelle transport in neurons.

Mature autophagosomes in the axon are transported by the microtubule motor dynein, activated by JNK-interacting proteins 3 and 4 (JIP3/4). This motility is regulated by the small GTPases ARF6 and RAB10. The tight regulation of autolysosomal transport is essential for intracellular recycling to maintain neuronal homeostasis.
Cell fate specification and conversion generate foveolar cone subtype patterning in human retinal organoids
Authors: Hussey Katarzyna A. , Eldred Kiara , Guy Brian , Santiago Clayton , Glass Ian , Reh Thomas A. , Blackshaw Seth , Goff Loyal A. , Johnston Robert J.
Published: January 2023

The mechanisms that generate patterns of cell types unique to humans are poorly understood. In the central region of the human retina, the high-acuity foveola is notable, in part, for its dense packing of green (M) and red (L) cones and absence of blue (S) cones. To identify mechanisms that promote M/L and suppress S cone patterning in the foveola, we examined human fetal retinas and differentiated human retinal organoids. During development, sparse S-opsin-expressing cones are initially observed in the foveola. Later in fetal development, the foveola contains a mix of cones that either co-express S- and M/L-opsins or exclusively express M/L-opsin. In adults, only M/L cones are present. Two signaling pathway regulators are highly and continuously expressed in the central retina: Cytochrome P450 26 subfamily A member 1 (CYP26A1), which degrades retinoic acid (RA) and Deiodinase 2 (DIO2), which promotes thyroid hormone (TH) signaling. BothCYP26A1null mutant organoids and high RA conditions increased the number of S cones and reduced the number of M/L cones in human retinal organoids. In contrast, sustained TH signaling promoted the generation of M/L-opsin-expressing cones and induced M/L-opsin expression in S-opsin-expressing cones, showing that cone fate is plastic. Our data suggest that CYP26A1 degrades RA to specify M/L cones and limit S cones and that continuous DIO2 expression sustains high levels of TH to convert S cones into M/L cones, resulting in the foveola containing only M/L cones. Since the foveola is highly susceptible to impairment in diseases such as macular degeneration, a leading cause of vision loss, our findings inform organoid design for potential therapeutic applications.