bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of an IntelliCage based Cognitive Bias Test for Mice
Authors: Kahnau Pia , Jaap Anne , Urmersbach Birk , Diederich Kai , Lewejohann Lars
Published: October 2022

The cognitive bias test is used to measure the emotional state of animals with regard to future expectations. Thus, the test offers a unique possibility to assess animal welfare with regard to housing and testing conditions of laboratory animals. So far, however, the performance of such a test is time consuming and requires the presence of an experimenter. Therefore, we developed an automated and home-cage based cognitive bias test based on the IntelliCage system. We present several developmental steps to improve the experimental design leading to a successful measurement of cognitive bias in group-housed female C57BL/6J mice. The automated and home-cage based test design allows to obtain individual data from group-housed mice, to test the mice in their familiar environment, and during their active phase. By connecting the test-cage to the home-cage via a gating system, the mice participated in the test on a self-chosen schedule, indicating high motivation to actively participate in the experiment. We propose that this should have a positive effect on the animals themselves as well as on the data. Unexpectedly, the mice showed an optimistic cognitive bias after enrichment was removed and additional restraining. An optimistic expectation of the future as a consequence of worsening environmental conditions, however, can also be interpreted as an active coping strategy in which a potential profit is sought to be maximized through a higher willingness to take risks.
Novel husbandry practices result in rapid rates of growth and sexual maturation without impacting adult behavior in the blind Mexican cavefish
Authors: Kozol Robert A. , Yuiska Anders , Han Ji Heon , Tolentino Bernadeth , Lopatto Arthur , Lewis Peter , Paz Alexandra , Keene Alex C. , Kowalko Johanna E. , Duboué Erik R
Published: October 2022

The development of animal model systems is dependent on the standardization of husbandry protocols that increase fecundity and reduce generation time. The blind Mexican tetra,Astyanax mexicanus, is an emerging genetic vertebrate model for evolution and biomedical research. Surface and cave populations ofA. mexicanushave independently evolved, providing a model system for studying the genetic basis of divergent biological traits. While a rapid increase in the use ofA. mexicanushas led to the generation of genetic tools including gene-editing and transgenesis, a slow and inconsistent growth rate remains a major limitation to the expanded application ofA. mexicanus. The optimization of husbandry protocols that maximizes high-nutrient feed, smaller tank densities and larger tank sizes across development, would facilitate faster growth and expand the use of this model. Here, we describe standardized husbandry practices that optimize growth through a high protein diet, increased feeding, growth sorting of larvae and juveniles, and tank size transitions based on standard length. These changes to husbandry had a significant effect on growth rates and decreased the age of sexual maturity in comparison to our previous protocols. To determine whether our nutritional change and increased feeding impacted behavior, we tested fish in exploration and schooling assays. We found that a change in diet had no effect on the behaviors we tested, suggesting that increased feeding and rapid growth will not impact the natural variation in behavioral traits. Taken together, this standardized husbandry protocol will accelerate the development ofA. mexicanusas a genetic model.
MSBooster: Improving Peptide Identification Rates using Deep Learning-Based Features
Authors: Yang Kevin L , Yu Fengchao , Teo Guo Ci , Demichev Vadim , Ralser Markus , Nesvizhskii Alexey I
Published: October 2022

Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments relies on computational algorithms for matching acquired MS/MS spectra against sequences of candidate peptides using database search tools, such as MSFragger. Here, we present a new tool, MSBooster, for rescoring peptide-to-spectrum matches using additional features incorporating deep learning-based predictions of peptide properties, such as LC retention time, ion mobility, and MS/MS spectra. We demonstrate the utility of MSBooster, in tandem with MSFragger and Percolator, in several different workflows, including nonspecific searches (immunopeptidomics), direct identification of peptides from data independent acquisition data, single-cell proteomics, and data generated on an ion mobility separation-enabled timsTOF MS platform. MSBooster is fast, robust, and fully integrated into the widely used FragPipe computational platform.
Retention time prediction to facilitate molecular structure identification with tandem mass spectrometry
Authors: Friedlos Patrik , Gasser Lilian , Harris Eliza
Published: October 2022

Comparing measured and predicted chromatographic retention time can improve molecular structure assignment in applications such as coupled liquid chromatography-tandem mass spectrometry. We assess a range of different machine learning methods to predict hydrophobicity, a molecular property that can be used as a proxy for retention time. The performance of the models is evaluated on the benchmark Martel and SAMPL7 datasets. We find that more powerful models perform better when predicting in-sample but not necessarily when generalizing to out-of-sample molecular families. We also find that ensemble methods can outperform individual models. Additionally, a multitask learning model shows promise for improving the generalization ability of graph neural networks for hydrophobicity prediction. Finally, we discuss how the ability of graph neural networks to generalize for molecular property prediction could be improved further.
mRNA therapy restores ureagenesis and corrects glutathione metabolism in argininosuccinic aciduria
Authors: Gurung Sonam , Timmermand Oskar V. , Perocheau Dany , Gil-Martinez Ana Luisa , Minnion Magdalena , Touramanidou Loukia , Fang Sherry , Messina Martina , Khalil Youssef , Barber Abigail R. , Edwards Richard S. , Finn Patrick F. , Cavedon Alex , Siddiqui Summar , Rice Lisa , Martini Paolo G.V. , Mills Philippa B. , Waddington Simon N. , Gissen Paul , Eaton Simon , Ryten Mina , Feelisch Martin , Frassetto Andrea , Witney Timothy H. , Baruteau Julien
Published: October 2022

Argininosuccinate lyase (ASL) is a key enzyme integral to the hepatic urea cycle which is required for ammonia detoxification, and the citrulline-nitric oxide (NO) cycle for NO production. ASL deficient patients present with argininosuccinic aciduria (ASA), an inherited metabolic disease with hyperammonaemia and a chronic systemic phenotype with neurocognitive impairment and chronic liver disease. ASL deficiency as an inherited model of systemic NO deficiency, shows enhanced nitrosative and oxidative stress. Here, we describe the dysregulation of glutathione biosynthesis and upstream cysteine utilization in ASL-deficient patients and mice using targeted metabolomics andin vivopositron emission tomography (PET) imaging using (S)-4-(3-18F-fluoropropyl)-L-glutamate ([18F]FSPG). Upregulation of cysteine metabolism contrasted with glutathione depletion and down-regulated antioxidant pathways.hASLmRNA encapsulated in lipid nanoparticles corrected and rescued the neonatal and adult Asl-deficient mouse phenotypes, respectively, enhancing ureagenesis and glutathione metabolism and ameliorating chronic liver disease. We further present [18F]FSPG PET as a novel non-invasive diagnostic tool to assess liver disease and therapeutic efficacy in ASA. These findings support clinical translation of mRNA therapy for ASA.
The IRE1α-XBP1 signaling axis promotes glycolytic reprogramming in response to inflammatory stimuli
Authors: English Bevin C. , Savage Hannah P. , Mahan Scott P. , Diaz-Ochoa Vladimir E. , Young Briana M. , Abuaita Basel H. , Sule Gautam , Knight Jason S. , O’Riordan Mary X. , Bäumler Andreas J. , Tsolis Renée M.
Published: October 2022

Immune cells must be able to adjust their metabolic programs to effectively carry out their effector functions. Here, we show that the ER stress sensor IRE1α and its downstream transcription factor XBP1 enhance the upregulation of glycolysis in classically activated macrophages (CAM). The IRE1α-XBP1 signaling axis supports this glycolytic switch in macrophages when activated by LPS stimulation or infection with the intracellular bacterial pathogenBrucella abortus. Importantly, these different inflammatory stimuli have distinct mechanisms of IRE1α activation; while TLR4 supports glycolysis under both conditions, TLR4 is required for activation of IRE1α in response to LPS treatment but notB. abortusinfection. Though IRE1α and XBP1 are necessary for maximal induction of glycolysis in CAM, activation of this pathway is not sufficient to increase the glycolytic rate of macrophages, indicating that the cellular context in which this pathway is activated ultimately dictates the cell’s metabolic response and that IRE1α activation may be a way to fine-tune metabolic reprogramming.

IMPORTANCE

The immune system must be able to tailor its response to different types of pathogens in order to eliminate them and protect the host. When confronted with bacterial pathogens, macrophages, frontline defenders in the immune system, switch to a glycolysis-driven metabolism to carry out their antibacterial functions. Here, we show that IRE1α, a sensor of ER stress, and its downstream transcription factor XBP1 support glycolysis in macrophages during infection withBrucella abortusor challenge withSalmonellaLPS. Interestingly, these stimuli activate IRE1α by independent mechanisms. While the IRE1α-XBP1 signaling axis promotes the glycolytic switch, activation of this pathway is not sufficient to increase glycolysis in macrophages. This study furthers our understanding of the pathways that drive macrophage immunometabolism and highlights a new role for IRE1α and XBP1 in innate immunity.
Dual receptive fields underlying target and wide-field motion sensitivity in looming sensitive descending neurons
Authors: Nicholas Sarah , Ogawa Yuri , Nordström Karin
Published: October 2022

Responding rapidly to visual stimuli is fundamental for many animals. For example, predatory birds and insects alike have amazing target detection abilities, with incredibly short neural and behavioral delays, enabling efficient prey capture. Similarly, looming objects need to be rapidly avoided to ensure immediate survival, as these could represent approaching predators. MaleEristalis tenaxhoverflies are non-predatory, highly territorial insects, that perform high-speed pursuits of conspecifics and other territorial intruders. During the initial stages of the pursuit the retinal projection of the target is very small, but grows to a larger object before physical interaction. Supporting such behaviors,E. tenaxand other insects have both target-tuned and loom-sensitive neurons in the optic lobes and the descending pathways. We here show that these visual stimuli are not necessarily encoded in parallel. Indeed, we describe a class of descending neurons that respond to small targets, to looming and to widefield stimuli. We show that these neurons have two distinct receptive fields where the dorsal receptive field is sensitive to the motion of small targets and the ventral receptive field responds to larger objects or widefield stimuli. Our data suggest that the two receptive fields have different pre-synaptic input, where the inputs are not linearly summed. This novel and unique arrangement could support different behaviors, including obstacle avoidance, flower landing, target pursuit or capture.

Significance Statement

If you are playing baseball, when the ball is far away, it appears as a very small object on your retina. However, as the ball gets closer, its image becomes a rapidly expanding object. Here, we show that within the hoverfly visual system, a single neuron could respond to both of these images. Indeed, we found a class of descending neurons with dual sensitivity, separated into two distinct parts of the visual field. The neurons have a more dorsal receptive field that is sensitive to small targets and a more ventral receptive field that is sensitive to larger objects.
Predictive Network Analysis IdentifiesJMJD6and Other Novel Key Drivers in Alzheimer’s Disease
Authors: Merchant Julie P. , Zhu Kuixi , Henrion Marc Y.R. , Zaidi Syed S.A. , Branden Lau , Moein Sara , Alamprese Melissa L. , Pearse Richard V. , Bennett David A. , Ertekin-Taner Nilüfer , Young-Pearse Tracy L. , Chang Rui
Published: October 2022

Despite decades of genetic studies on late onset Alzheimer’s disease (LOAD), the molecular mechanisms of Alzheimer’s disease (AD) remain unclear. Furthermore, different cell types in the central nervous system (CNS) play distinct roles in the onset and progression of AD pathology. To better comprehend the complex etiology of AD, we used an integrative approach to build robust predictive (causal) network models which were cross-validated over multiple large human multi-omics datasets in AD. We employed a published method to delineate bulk-tissue gene expression into single cell-type gene expression and integrated clinical and pathologic traits of AD, single nucleotide variation, and deconvoluted gene expression for the construction of predictive network models for each cell type in AD. With these predictive causal models, we are able to identify and prioritize robust key drivers of the AD-associated network state. In this study, we focused on neuron-specific network models and prioritized 19 predicted key drivers modulating AD pathology. These targets were validated via shRNA knockdown in human induced pluripotent stem cell (iPSC) derived neurons (iNs), in which 10 out of the 19 neuron-related targets (JMJD6, NSF, NUDT2, YWHAZ, RBM4, DCAF12, NDRG4, STXBP1, ATP1B1, andFIBP) significantly modulated levels of amyloid-beta and/or phosphorylated tau peptides in the postmitotic iNs. Most notably, knockdown ofJMJD6significantly altered the neurotoxic ratios of Aβ42 to 40 and p231-tau to total tau, indicating its potential therapeutic relevance to both amyloid and tau pathology in AD. Molecular validation by RNA sequencing (RNAseq) in iNs further confirmed the network structure, showing significant enrichment in differentially expressed genes after knockdown of the validated targets. Interestingly, our network model predicts that these 10 key drivers are upstream regulators of REST and VGF, two recently identified key regulators of AD pathogenesis.
Mating activates neuroendocrine pathways signaling hunger inDrosophilafemales
Authors: Laturney Meghan , Sterne Gabriella R. , Scott Kristin
Published: October 2022

Mated females reallocate resources to offspring production, causing changes in nutritional requirements and challenges to energy homeostasis. Although observed in most species, the neural and endocrine mechanisms that regulate the nutritional needs of mated females are not well understood. Here, we investigate the neural circuitry that regulates sugar appetite in matedDrosophila melanogasterfemales. During copulation, a male-derived sex peptide is transferred to females, silencing the mating status circuit to elicit many postmating behavioral changes1-3. We find that increased sucrose consumption is a postmated female behavior and show that it is mediated by the mating status circuit. We discovered that sexually dimorphic insulin receptor (Lgr3) neurons integrate mating status and nutritional state signals to adjust sucrose consumption. Lgr3+ cells receive inhibitory input from the mating status circuit via female specific pCd-2 neurons. In mated females, the inhibition of Lgr3 cells from pCd-2 is attenuated, transforming the mated signal into a long-term hunger signal that promotes sugar intake. Our results thus demonstrate that the mating circuit alters nutrient sensing centers in females to promote sugar consumption, providing a mechanism to increase intake in anticipation of the energetic costs associated with reproduction.
Genomic underpinnings of convergent adaptation to high altitudes for alpine plants
Authors: Zhang Xu , Kuang Tianhui , Dong Wenlin , Qian Zhihao , Zhang Huajie , Landis Jacob B. , Feng Tao , Li Lijuan , Sun Yanxia , Huang Jinling , Deng Tao , Wang Hengchang , Sun Hang
Published: October 2022

Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection. However, genomic evidence for convergent adaptation to extreme environments remains scarce. The Himalaya-Hengduan Mountains represent the world’s most species-rich temperate alpine biota, providing an ideal “natural laboratory” for studying convergent adaptation to high altitudes. Here, we generate reference genomes for two alpine plants,Saussurea obvallata(Asteraceae) andRheum alexandrae(Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes, we investigate genomic signatures of convergent adaptation to the hostile environments of high altitudes. We show that alpine genomes tend to mitigate their genetic load by contracting genes functioning in the immune system to survive such harsh environments with few pathogens present. We detect signatures of convergent positive selection on a set of genes involved in reproduction and development and reveal that molecular convergence has acted on genes involved in self-incompatibility, cell wall modification, DNA repair and stress resistance, which underlie adaptation to extremely cold, high UV radiation and hypoxia environments. Using gene expression profiles, we further demonstrate that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding lights on the genetic mechanisms of the adaptive ‘greenhouse’ morphology. Our integrative data provide genomic insights into the convergent evolution at higher-taxonomic levels, aiding in deep understanding of genetic adaptation to complex environments.
Reprogramming M2-polarized patient-derived glioblastoma associated microglia/macrophages via CSF1R inhibition
Authors: Fermi Valentina , Warta Rolf , Rapp Carmen , Knoll Maximilian , Jungwirth Gerhard , Jungk Christine , Dao Trong Philip , von Deimling Andreas , Abdollahi Amir , Unterberg Andreas , Herold-Mende Christel
Published: October 2022

Targeting immunosuppressive and protumorigenic glioblastoma-associated macrophages and microglial cells (GAMs) holds great potential to improve patient outcomes. Although CSF1R has emerged as a promising target to reprogram anti-inflammatory M2-like GAMs, relevant treatment data on human, tumor-educated GAMs and innovative patient-derived 3D tumor organoid models to study the influence on adaptive immunity and the effectiveness of treatment in a complex and entirely autologous setting are largely lacking. We performed a comprehensive phenotypical, transcriptional and functional analysis of primary, patient-derived GAMs upon treatment with the CSF1R-targeting drugs PLX3397, BLZ945, and GW2580. The most effective reprogramming of GAMs was observed upon GW2580 treatment, which led to a downregulation of M2-related markers and signaling pathways, while M1-like markers, phagocytosis, and T-cell killing were substantially increased. Moreover, treatment of patient-derived glioblastoma organoids with GW2580 confirmed successful reprogramming together with reduced tumor cell proliferation, indicating that treatment with GW2580 could be an important pillar in the future therapy of GBM.
Modulation of functional networks related to the serotonin neurotransmitter system by citalopram: evidence from a multimodal neuroimaging study
Authors: Boucherie Daphne E , Reneman Liesbeth , Booij Jan , Martins Daniel , Dipasquale Ottavia , Schrantee Anouk
Published: October 2022

Background

Selective serotonin reuptake inhibitors (SSRIs) potentiate serotonergic neurotransmission by blocking the serotonin transporter (5-HTT), but the functional brain response to SSRIs involves neural circuits beyond regions with high 5-HTT expression. Currently, it is unclear whether and how changes in 5-HTT availability after SSRI administration modulate brain function of key serotoninergic circuits, including those characterized by high availability of serotonin 1A receptors (5-HT1AR).

Aim

We investigated the association between 5-HTT availability and 5-HTT- and 5-HT1AR-enriched functional connectivity (FC) after an acute citalopram challenge.

Methods

We analyzed multimodal data from a dose-response, placebo-controlled, double-blind study, in which 45 healthy women were randomized into three groups receiving placebo, a low (4 mg), or high (16 mg) oral dose of citalopram. Receptor-Enhanced Analysis of functional Connectivity by Targets was used to estimate 5-HTT- and 5-HT1AR-enriched FC from resting-state and task-based fMRI. 5-HTT availability was determined using [123I]FP-CIT single-photon emission computerized tomography.

Results

5-HTT availability was negatively correlated with resting-state 5-HTT-enriched FC, and with task-dependent 5-HT1AR-enriched FC. Our exploratory analyses revealed lower 5-HT1AR-enriched FC in the low dose group compared to the high dose group at rest and the placebo group during the task.

Conclusions

Taken together, our findings provide evidence for differential links between 5-HTT availability and brain function within 5-HTT and 5-HT1AR pathways and in context- and dose-dependent manner. As such, they support a potential pivotal role of the 5-HT1AR in the effects of citalopram on the brain and add to its potential as a therapeutic avenue for mood and anxiety disturbances.
Species-specific roles for the MAFA and MAFB transcription factors in regulating islet β cell identity
Authors: Cha Jeeyeon , Tong Xin , Walker Emily , Dahan Tehila , Cochrane Veronica , Ashe Sudipta , Russell Ronan , Osipovich Anna , Mawla Alex , Guo Min , Liu Jin-hua , Huising Mark , Magnuson Mark , Hebrok Matthias , Dor Yuval , Stein Roland
Published: October 2022

Type 2 diabetes (T2D) is associated with compromised identity of insulin-producing pancreatic islet beta (β) cells, characterized by inappropriate production of other islet cell-enriched hormones. Here we examined how hormone misexpression was influenced by the MAFA and MAFB transcription factors, closely related proteins that maintain islet cell function. Mice specifically lacking MafA in β cells demonstrated broad, population-wide changes in hormone gene expression with an overall gene signature closely resembling islet gastrin (Gast)-positive cells generated under conditions of chronic hyperglycemia and obesity. A human β cell line deficient in MAFB, but not one lacking MAFA, also produced a gastrin (GAST)-positive gene expression pattern. In addition, GAST was detected in human T2D β cells with low levels of MAFB. Moreover, evidence is provided that human MAFB can directly repressGASTgene transcription. These results support a novel, species-specific role for MafA and MAFB in maintaining adult mouse and human β cell identity, respectively, by repressing expression of Gast/GAST and other non-β cell hormones.
CWLP and PRP940 form plasma-membrane nanodomain complexes with aquaporins, interact with PP2A and contribute to dehydration tolerance
Authors: Honig Arik , Eilenberg Haviva , Zuther Ellen , Avisar Dror , Erster Oran , Eshkol Gad , Stein Hanan , Reznik Noam , Schuster Silvia , Belausov Eduard , Abu-Abied Muhammad , Hotta Takashi , Lee Yuh-Ru Julie , Liu Bo , Sadot Einat , Koncz Csaba , Zilberstein Aviah , Fichman Yosef
Published: October 2022

The C-type hybrid-proline-rich protein (HyPRP) AtCWLP and its homolog AtPRP940 are referred as cell wall (CW)-plasma-membrane (PM) linker proteins, but little is known about their functions. Here we show that N-terminal proline-rich domains of CWLP and PRP940, containing glycosylated hydroxyproline residues, contact the CW, while their C-terminal 8CM domains function as PM-scaffolds. Both proteins are detected in PM nanodomains (PM-ND) and show co-localization and co-immunoprecipitation with aquaporins PIP2;1 and PIP2;7. Inhibition of actin polymerization by latrunculin B promotes CWLP-endosome appearance, while blocking the actomyosin-based transport by a truncated form of myosin XI-K relaxes lateral boundaries of CWLP-PIP2;1 PD-NDs. Mass spectrometry data indicate that CWLP co-purifies with dynamins implicated in fission of endocytic PD-ND invaginations. Lack of co-localization and co-immunoprecipitation with aquaporin-binding flotillin (FLOT2) indicates that CWLP and PRP940 mark a new distinct type of PM-ND. Yeast two-hybrid and co-immunoprecipitation assays demonstrate that CWLP and PRP940 interact with multiple aquaporins and several protein phosphatase PP2A-B’’ regulatory subunits. By preventing irreversible separation of CW and PM, and likely assisting PP2A-mediated dephosphorylation of aquaporins and closure of their water channels, overexpression of CWLP confers tolerance to plasmolysis, dehydration and freezing in Arabidopsis and to water shortage in potato plants.

Summary Statement

Arabidopsis Hybrid-Proline-Rich Proteins CWLP and PRP940 occur in association with dynamins, recruit PP2A protein phosphatases to aquaporin water channels in plasma-membrane (PM) nanodomains and elevate tolerance to cellular dehydration.
The priming effect of rewarding brain stimulation in rats depends on both the cost and strength of reward but survives blockade of D2-like dopamine receptors
Authors: Evangelista Czarina , Mehrez Norhan , Boisvert Esthelle Ewusi , Brake Wayne G. , Shizgal Peter
Published: October 2022

Receipt of an intense reward boosts motivation to work for more of that reward. This phenomenon is called thepriming effect of rewards. Using a novel measurement method, we show that the priming effect of rewarding electrical brain stimulation depends on the cost, as well as on the strength, of the anticipated reward. Previous research on the priming effect of electrical brain stimulation utilized a runway paradigm in which running speed serves as the measure of motivation. In the present study, the measure of motivation was the vigor with which rats executed a two-lever response chain, in a standard operant-conditioning chamber, to earn rewarding electrical stimulation of the lateral hypothalamus. In a second experiment, we introduced a modification that entails self-administered priming stimulation and alternating blocks of primed and unprimed trials. Reliable, consistent priming effects of substantial magnitude were obtained in the modified paradigm, which is closely analogous to the runway paradigm. In a third experiment, the modified paradigm served to assess the dependence of the priming effect on dopamine D2-like receptors. The priming effect proved resilient to the effect of eticlopride, a selective D2-like receptor antagonist. These results are discussed within the framework of a new model of brain reward circuitry in which non-dopaminergic medial forebrain bundle fibers and dopamine axons provide parallel inputs to the final common paths for reward and incentive motivation.
Vutiglabridin improves neurodegeneration in MPTP-induced Parkinson’s disease mice by targeting mitochondrial paraoxonase-2
Authors: Kang Sora , Choi Leo S. , Im Suyeol , Kim Ji Hwan , Lee Keun Woo , Kim Dong Hwan , Park Jung Hee , Park Min-Ho , Lee Jaemin , Park Sun Kyung , Kim Kwang Pyo , Lee Hyeong Min , Jeon Hyun Ju , Park Hyung Soon , Yoo Sang-Ku , Pak Youngmi Kim
Published: October 2022

Parkinson’s disease (PD), characterized by degeneration of dopaminergic neurons, share pathogenic features with obesity, including mitochondrial dysfunction and oxidative stress. Paraoxonase 2 (PON2) is an inner mitochondrial membrane protein that is highly expressed in dopaminergic neurons and is involved in the regulation of mitochondrial oxidative stress. However, no drug targeting PON2 has ever been developed for the treatment of PD. Here, we show that vutiglabridin, a clinical phase 2-stage drug for the treatment of obesity, has therapeutic effects in PD models, targeting mitochondrial PON2. Vutiglabridin penetrates into the brain, binds to PON2, and restores 1-methyl-4-phenylpyridinium (MPP+)-induced mitochondrial dysfunction in SH-SY5Y neuroblastoma cells. Knockdown of PON2 by lentiviral shRNA infection abolished the effects of vutiglabridin on mitochondria. In mice, vutiglabridin significantly alleviated motor impairments and damage to dopaminergic neurons in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD model, and these effects were also abolished in PON2-knockdown mice, suggesting that vutiglabridin is neuroprotective via PON2. Extensive in vitro and in vivo assessment of potential neurotoxicity showed vutiglabridin to be safe. Overall, these findings provide support for the clinical development of vutiglabridin as a novel PON2 modulator for the treatment of PD.

One Sentence Summary

Targeting paraoxonase-2 by a clinical-stage compound vutiglabridin provides neuroprotective effects in preclinical models of Parkinson’s disease.
Hydrogen Cyanamide Causes Reversible G2/M Cell Cycle Arrest Accompanied by Oxidation of the Nucleus and Cytosol inArabidopsis thalianaRoot Apical Meristem Cells
Authors: Velappan Yazhini , De Simone Ambra , Signorelli Santiago , Considine John A , Foyer Christine H , Considine Michael J
Published: October 2022

Hydrogen cyanamide (HC) is known to stimulate the production of reactive oxygen species (ROS) and also alter growth through modification of the cell cycle. However, the mechanisms by which HC alters cell proliferation and redox homeostasis are largely unknown. This study used roGFP2 expressing Arabidopsis seedlings to measure the oxidation states of the nuclei and cytosol in response to HC treatment. The Cytrap dual cell cycle phase marker system and flow cytometry were used to study associated changes in cell proliferation. HC (1.5mM) reversibly inhibited root growth during a 24h treatment. Higher concentrations were not reversible. HC did not synchronize the cell cycle. In contrast to hydroxyurea, HC caused a gradual accumulation of cells in the G2/M phase and decline of G1/S phase cells 16 to 24h post-treatment. This was accompanied by increased oxidation of both the nuclei and cytosol. Taken together, HC impairs proliferation of embryonic root meristem cells in a reversible manner through restriction of G2/M transition accompanied by increased oxidative poise.
Neutral genetic structuring of pathogen populations during rapid adaptation
Authors: Saubin Méline , Stoeckel Solenn , Tellier Aurélien , Halkett Fabien
Published: October 2022

Pathogen species are experiencing strong joint demographic and selective events, especially when they adapt to a new host, for example through overcoming plant resistance. Stochasticity in the founding event and the associated demographic variations hinder our understanding of the expected evolutionary trajectories and the genetic structure emerging at both neutral and selected loci. What would be the typical genetic signatures of such a rapid adaptation event is not elucidated. Here, we build a demogenetic model to monitor pathogen population dynamics and genetic evolution on two host compartments (susceptible and resistant). We design our model to fit two plant pathogen life cycles, ‘with’ and ‘without’ host alternation. Our aim is to draw a typology of eco-evolutionary dynamics. Using time-series clustering, we identify three main scenarios: 1) small variations in the pathogen population size and small changes in genetic structure, 2) a strong founder event on the resistant host that in turn leads to the emergence of genetic structure on the susceptible host, and 3) evolutionary rescue that results in a strong founder event on the resistant host, preceded by a bottleneck on the susceptible host. We pinpoint differences between life cycles with notably more evolutionary rescue ‘with’ host alternation. Beyond the selective event itself, the demographic trajectory imposes specific changes in the genetic structure of the pathogen population. Most of these genetic changes are transient, with a signature of resistance overcoming that vanishes within a few years only. Considering time-series is therefore of utmost importance to accurately decipher pathogen evolution.
AtFZL is required for correct starch granule morphology in Arabidopsis chloroplasts
Authors: Esch Lara , Ngai Qi Yang , Barclay J. Elaine , Seung David
Published: October 2022

The control of starch granule number and morphology in plastids is poorly understood. Here, we demonstrate thatAtFZL, a protein involved in thylakoid membrane organisation, is required for correct starch granule morphology in Arabidopsis. Leaves of mutants lackingAtFZL had the same starch content as wild-type leaves, but their starch granules were smaller and had a distinct, uneven surface morphology. Most chloroplasts in the mutant were larger than those of the wild type.

However, the difference in chloroplast size could not explain the difference in granule size and shape in theAtfzlmutants, since other mutants with larger chloroplasts than the wild type (arcmutants) had granules that were similar in size and shape to wild-type granules. As reported previously, theAtfzlmutant had aberrant thylakoid organisation. We found that this phenomenon was particularly pronounced in regions surrounding starch granules. The location of the thylakoid-bound granule initiation protein MFP1 was unaffected in theAtfzlmutant. We propose thatAtFZL affects starch granule size and shape by influencing thylakoid organisation at the periphery of starch granules. Our results are consistent with an important role for thylakoid architecture in determining granule morphology.
T-RHEX-RNAseq – A tagmentation-based, rRNA blocked, random hexamer primed RNAseq method for generating stranded RNAseq libraries directly from very low numbers of lysed cells
Authors: Gustafsson Charlotte , Hauenstein Julia , Frengen Nicolai , Krstic Aleksandra , Luc Sidinh , Månsson Robert
Published: October 2022

Background

RNA sequencing has become the mainstay for studies of gene expression. Still, analysis of rare cells with random hexamer priming – to allow analysis of a broader range of transcripts – remains challenging.

Results

We here describe a tagmentation-based, rRNA blocked, random hexamer primed RNAseq approach (T-RHEX-RNAseq) for generating stranded RNAseq libraries from very low numbers of FACS sorted cells without RNA purification steps.

Conclusion

T-RHEX-RNAseq provides an easy-to-use, time efficient and automation compatible method for generating stranded RNAseq libraries from rare cells.
Small molecule modulatesα-Synuclein conformation and its oligomerization via Entropy Expansion
Authors: Menon Sneha , Mondal Jagannath
Published: October 2022

Aberrant misfolding and progressive aggregation of the intrinsically disordered protein (IDP),α-synuclein, are associated with the etiology of several neurodegenerative diseases. However, the structurally heterogeneous ensemble of this IDP and lack of a well-defined binding pocket make it difficult to probe the druggability ofα-synuclein. Here, by building a comprehensive statistical model of the fuzzy ensemble of a millisecond-long atomistic simulation trajectory of monomericα-synuclein interacting with the small-molecule drug fasudil, we identify exhaustive sets of metastable binding-competent states ofα-synuclein. The model reveals that the interaction with the drug primes this IDP to explore both more compact and more extended conformational sub-ensemble than those in neat water, thereby broadening its structural repertoire in presence of small-molecule via anentropy expansionmechanism. Subsequent simulation of the dimerisation process shows that similar motif of entropic-expansion mechanism helps fasudil to retard the self-aggregation propensity ofα-synuclein via trapping it into multiple distinct states of diverse compaction featuring aggregation-resistant long-range interactions. Furthermore, small-molecule binding interactions in dimerisation-competent relatively extended states have a screening effect that hinders the formation of stable dimer contacts. Together, the investigation demonstrates the ability of small-molecules to have an ensemble-modulatory effect on IDPs that can be effectively utilised in therapeutic strategies probing aggregation-related diseases.
Biosynthesis of the Multifunctional Isopropylstilbene inPhotorhabdus laumondiiInvolves Cross-Talk between Specialized and Primary Metabolism
Authors: Kavakli Siyar , Grammbitter Gina L. C. , Bode Helge B.
Published: October 2022

Isopropylstilbene (IPS) derived from the entomopathogenic bacteriumPhotorhabdusrepresents the only known stilbene which is not produced by a plant stilbene synthase but a bacterial PKS II synthase. While the exclusive cyclization reaction, responsible for the formation of the characteristic iso-branched side-chain of the molecule, was studied in the past, some parts of the biosynthetic route remained elusive. In this study, we revealed the role of StlB that is able to produce CoA-derivatives and demonstrated the elongation of cinnamoyl-CoA with enzymes from the bacterial fatty acid biosynthesis pathway. Thus, we deciphered cross-talk between the enzymes from primary and specialized metabolism. These insights led, for the first time, to the production of IPS in a heterologous host.
Categorising update mechanisms for graph-structured metapopulations
Authors: Yagoobi Sedigheh , Sharma Nikhil , Traulsen Arne
Published: October 2022

The structure of a population strongly influences its evolutionary dynamics. In various settings ranging from biology to social systems, individuals tend to interact more often with those present in their proximity and rarely with those far away. A common approach to model the structure of a population is Evolutionary Graph Theory. In this framework, each graph node is occupied by a reproducing individual. The links connect these individuals to their neighbours. The offspring can be placed on neighbouring nodes, replacing the neighbours – or the progeny of its neighbours can replace a node during the course of ongoing evolutionary dynamics. Extending this theory by replacing single individuals with subpopulations at nodes yields a graph-structured metapopulation. The dynamics between the different local subpopulations is set by an update mechanism. There are many such update mechanisms. Here, we classify update mechanisms for structured metapopulations, which allows to find commonalities between past work and illustrate directions for further research and current gaps of investigation.
Carboxylic acids that drive mosquito attraction to humans activate Ionotropic Receptors
Authors: Ray Garrett , Huff Robert M. , Castillo John S. , Bellantuono Anthony J. , DeGennaro Matthew , Pitts R. Jason
Published: October 2022

Female mosquitoes are attracted to sources of blood by responding to odor plumes that are emitted by their preferred hosts. Acidic volatile compounds, including carboxylic acids, represent particularly salient odors driving this attraction. Importantly, carboxylic acids are major constituents of human sweat and volatiles generated by skin microbes. As such, they are likely to impact human host preference, which is a dominant factor in disease transmission cycles. A more complete understanding of mosquito host attraction will necessitate the elucidation of molecular mechanisms of volatile odor detection that function in peripheral sensory neurons. Recent studies have shown that members of the variant ionotropic glutamate receptor gene family are necessary for physiological and behavioral responses to acidic volatiles inAedes. In this study, we have identified a subfamily of variant ionotropic receptors that share sequence homology across several important vector species and are likely to be activated by carboxylic acids. Moreover, we demonstrate that selected members of this subfamily are activated by short chain carboxylic acids in a heterologous cell expression system. Our results are consistent with the hypothesis that members of this receptor class underlie acidic volatile sensitivity in vector mosquitoes and provide a frame of reference for future development of novel mosquito attractant and repellent technologies.
PMI estimation through metabolomics and potassium analysis on animal vitreous humour
Authors: Locci Emanuela , Stocchero Matteo , Gottardo Rossella , Chighine Alberto , De-Giorgio Fabio , Ferino Giulio , Nioi Matteo , Demontis Roberto , Tagliaro Franco , d’Aloja Ernesto
Published: October 2022

Introduction

The estimation of post-mortem interval remains a major challenge in forensic science. Most of the proposed approaches lack the reliability required to meet the rigorous forensic standards.

Objectives

We applied1H NMR metabolomics to estimate PMI on ovine vitreous humour comparing the results with the actual scientific gold standard, namely vitreous potassium concentrations.

Methods

Vitreous humour samples were collected in a time frame ranging from 6 to 86 hours after death. Experiments were performed by using1H NMR metabolomics and Ion Capillary Analysis. Data were submitted to multivariate statistical data analysis.

Results

A multivariate calibration model was built to estimate PMI based on 47 vitreous humour samples. The model was validated with an independent test set of 24 samples, obtaining a prediction error on the entire range of 6.9 h for PMI<24h, 7.4 h for PMI between 24 and 48h, and 10.3 h for PMI>48 h. Time-related modifications of the1H NMR vitreous metabolomic profile could predict PMI better than potassium up to 48 hours after death, while a combination of the two is better than the single approach for higher PMIs estimation.

Conclusion

The present study, although in a proof-of-concept animal model, shows that vitreous metabolomics can be a powerful tool to predict PMI providing a more accurate estimation compared to the widely studied approach based on vitreous potassium concentrations.
RECIFS: a centralized geo-environmental database for coral reef research and conservation
Authors: Selmoni Oliver , Lecellier Gaël , Berteaux-Lecellier Véronique , Joost Stéphane
Published: October 2022

Host to intricated networks of marine species, coral reefs are among the most biologically diverse ecosystems on Earth. Over the past decades, major degradations of coral reefs have been observed worldwide, which is largely attributed to the effects of climate change and local stressors related to human activities. Now more than ever, characterizing how the environment shapes the dynamics of the reef ecosystem is key to (1) uncovering the environmental drivers of reef degradation, and (2) enforcing efficient conservation strategies in response. To achieve these objectives, it is pivotal that environmental data characterizing such ecosystem dynamics, which occur across specific spatial and temporal scales, are easily accessible to coral reef researchers and conservation stakeholders alike.

Here we present the Reef Environment Centralized Information System (RECIFS), an online repository of datasets describing reef environments worldwide over the past few decades.

The data served through RECIFS originate from remote sensed datasets available in the public domain, and characterize various facets of the reef environment, including water chemistry and physics (e.g. temperature, pH, chlorophyll concentration), as well as anthropogenic local pressures (e.g. boat detection, distance from agricultural or urban areas). The datasets from RECIFS can be accessed at different spatial and temporal resolutions and are delivered through an intuitive web-application featuring an interactive map requiring no prior knowledge working with remote sensing or geographic information systems. The RECIFS web-application is available in complete open access athttps://recifs.epfl.ch.

We describe two case studies showing possible implementations of RECIFS to 1) characterize coral diversity in the Caribbean and 2) investigate local adaptation of a reef fish population in Northwest Australia.
TORC1 is an essential regulator of nutrient-dependent differentiation inLeishmania
Authors: Myburgh Elmarie , Geoghegan Vincent , Alves-Ferreira Eliza V.C. , Nievas Y. Romina , Grewal Jaspreet S. , Brown Elaine , McLuskey Karen , Mottram Jeremy C.
Published: October 2022

Leishmaniaparasites undergo differentiation between various proliferating and non-dividing forms to adapt to changing host environments. The mechanisms that link environmental cues with the parasite’s developmental changes remain elusive. Here, we report thatLeishmaniaTORC1 is a key environmental sensor for parasite differentiation in the sand fly-stage promastigotes and for replication of mammalian-stage amastigotes. We show thatLeishmaniaRPTOR1, interacts with TOR1 and LST8. We investigate TORC1 function by conditional deletion ofRPTOR1, where under nutrient rich conditions RPTOR1 depletion results in decreased protein synthesis and growth, G1 cell cycle arrest and premature differentiation from proliferative promastigotes to non-dividing mammalian-infective metacyclic forms. These parasites cannot develop into proliferative amastigotes in the mammalian host, or respond to nutrients to differentiate to proliferative retroleptomonads, which are required for their blood-meal induced amplification in sand flies and enhanced mammalian infectivity. RPTOR1-dependent TORC1 functionality represents a critical mechanism for driving parasite growth and proliferation.
Simulation of Gilbert Theory for Self-Association in Sedimentation Velocity Experiments: A Guide to Evaluate Best Fitting Models
Authors: Bishop GR , Correia JJ
Published: October 2022

There is a long tradition in the Biophysics community of using simulations as a means to understand macromolecular behavior in various physicochemical methods. This allows a rigorous means to interpret observations in terms of fundamental principles, including chemical equilibrium, reaction kinetics, transport processes and thermodynamics. Here we simulate data for the Gilbert Theory for self-association, a fundamental analytical ultracentrifuge (AUC) technique to understand the shape of sedimentation velocity reaction boundaries that involve reversible monomer-Nmer interactions. Simulating monomer-dimer through monomer-hexamer systems as a function of concentration about the equilibrium constant allows a visual means to differentiate reaction stoichiometry by determining end points and inflexion positions. Including intermediates (eg A1-A2-A3-A4-A5-A6) in the simulations reveals the smoothing of the reaction boundary and the removal of sharp inflexions between monomers and polymers. The addition of cooperativity restores sharp boundaries or peaks to the observation and allows more discrimination in the selection of possible fitting models. Thermodynamic nonideality adds additional features when applied across wide ranges of concentration that might be appropriate for high concentration therapeutic monoclonal antibody (mAb) solutions. This presentation serves as a tutorial for using modern AUC analysis software like SEDANAL for selecting potential fitting models.