bluuebunny/crossref_metadata_2025 huggingface dataset:
Natural mutations of humanXDHpromote the nitrite (NO2-)-reductase capacity of xanthine oxidoreductase: a novel mechanism to promote redox health?
Authors: Massimo G. , Khambata R. S. , Chapman T. , Birchall K. , Shabbir A. , Dyson Nicki , Rathod K. , Borghi C. , Ahluwalia A.
Published: March 2023

Several rare genetic variations of humanXDHhave been shown to alter xanthine oxidoreductase (XOR) activity leading to impaired purine catabolism. However, XOR is a multi-functional enzyme that depending upon the environmental conditions also expresses oxidase activity leading to both O·-and H O and nitrite (·NO-) reductase activity leading to NO. Since these products express important, and often diametrically opposite, biological activity consideration of the impact of XOR mutations in the context of each aspect of the biochemical activity of the enzyme is needed to determine the potential full impact of these variants. Herein, we show that known naturally occurringhXDHmutations do not have a uniform impact upon the biochemical activity of the enzyme in terms of uric acid (UA), reactive oxygen species (ROS) and nitric oxide (·NO) formation. We show that the His1221Arg mutant, in the presence of xanthine, increases UA, O2·-and NO generation compared to the WT, whilst the Ile703Val increases UA and ·NO formation, but not O2·-. We speculate that this change in the balance of activity of the enzyme is likely to endow those carrying these mutations with a harmful or protective influence over health that may explain the current equipoise underlying the perceived importance ofXDHmutations. We also suggest that targeting enzyme activity to enhance the NO2--reductase profile in those carrying such mutations may provide novel therapeutic options, particularly in cardiovascular disease.

Highlights

Mutations of xanthine oxidoreductase modulate both its expression and activity

The His1221Arg natural mutation increases xanthine oxidoreductase activity

Raised xanthine oxidoreductase activity coupled with increased availability of nitrite substrate leads to increased NO provision
Mathematical models disentangle the role of IL-10 feedbacks in human monocytes upon proinflammatory activation
Authors: Nikaein Niloofar , Tuerxun Kedeye , Cedersund Gunnar , Eklund Daniel , Kruse Robert , Särndahl Eva , Nånberg Eewa , Thonig Antje , Repsilber Dirk , Persson Alexander , Nyman Elin
Published: March 2023

Inflammation is one of the vital mechanisms through which the immune system responds to harmful stimuli. During inflammation, pro and anti-inflammatory cytokines interplay to orchestrate fine-tuned, dynamic immune responses. The cytokine interplay governs switches in the inflammatory response and dictates the propagation of inflammation. Molecular pathways underlying the interplay are complex, and time-resolved monitoring of mediators and cytokines is necessary as a basis to study them in detail. Our understanding can be advanced byin silicomodels which enable to analyze the system of interactions and their dynamical interplay in detail. We, therefore, used a mathematical modeling approach to study the interplay between prominent pro and anti-inflammatory cytokines with a focus on Tumor Necrosis Factor (TNF) and Interleukin 10 (IL-10) in lipopolysaccharide (LPS)-primed primary human monocytes. Relevant time-resolved data were generated by experimentally adding or blocking IL-10 at different time points. The model was successfully trained and could predict independent validation data and was further used to performin silicoexperiments to disentangle the role of IL-10 feedbacks in acute inflammation. We used the insight to obtain a reduced predictive model including only the necessary IL-10-mediated feedbacks. Finally, the validated reduced model was used to predict early IL-10 – TNF switches in the inflammatory response. Overall, we gained detailed insights into fine-tuning of inflammatory responses in human monocytes and present a model for further use in studying the complex and dynamic process of cytokine-regulated acute inflammation.
Di-berberine conjugates as chemical probes ofPseudomonas aeruginosaMexXY-OprM efflux function and inhibition
Authors: Kavanaugh Logan G. , Mahoney Andrew R. , Dey Debayan , Wuest William M. , Conn Graeme L.
Published: March 2023

The Resistance-Nodulation-Division (RND) efflux pump superfamily is pervasive among Gram-negative pathogens and contributes extensively to clinical antibiotic resistance. The opportunistic pathogenPseudomonas aeruginosacontains 12 RND-type efflux systems, with four contributing to resistance including MexXY-OprM which is uniquely able to export aminoglycosides. At the site of initial substrate recognition, small molecule probes of the inner membrane transporter (e.g., MexY) have potential as important functional tools to understand substrate selectivity and a foundation for developing adjuvant efflux pump inhibitors (EPIs). Here, we optimized the scaffold of berberine, a known but weak MexY EPI, using anin-silicohigh-throughput screen to identify di-berberine conjugates with enhanced synergistic action with aminoglycosides. Further, docking and molecular dynamics simulations of di-berberine conjugates reveal unique contact residues and thus sensitivities of MexY from distinctP. aeruginosastrains. This work thereby reveals di-berberine conjugates to be useful probes of MexY transporter function and potential leads for EPI development.
split-intein Gal4 provides intersectional genetic labeling that is fully repressible by Gal80
Authors: Ewen-Campen Ben , Luan Haojiang , Xu Jun , Singh Rohit , Joshi Neha , Thakkar Tanuj , Berger Bonnie , White Benjamin H. , Perrimon Norbert
Published: March 2023

The split-Gal4 system allows for intersectional genetic labeling of highly specific cell-types and tissues inDrosophila. However, the existing split-Gal4 system, unlike the standard Gal4 system, cannot be repressed by Gal80, and therefore cannot be controlled temporally. This lack of temporal control precludes split-Gal4 experiments in which a genetic manipulation must be restricted to specific timepoints. Here, we describe a new split-Gal4 system based on a self-excising split-intein, which drives transgene expression as strongly as the current split-Gal4 system and Gal4 reagents, yet which is fully repressible by Gal80. We demonstrate the potent inducibility of “split-intein Gal4”in vivousing both fluorescent reporters and via reversible tumor induction in the gut. Further, we show that our split-intein Gal4 can be extended to the drug-inducible GeneSwitch system, providing an independent method for intersectional labeling with inducible control. We also show that the split-intein Gal4 system can be used to generate highly cell-type specific genetic drivers based onin silicopredictions generated by single cell RNAseq (scRNAseq) datasets, and we describe a new algorithm (“Two Against Background” or TAB) to predict cluster-specific gene pairs across multiple tissue-specific scRNA datasets. We provide a plasmid toolkit to efficiently create split-intein Gal4 drivers based on either CRISPR knock-ins to target genes or using enhancer fragments. Altogether, the split-intein Gal4 system allows for the creation of highly specific intersectional genetic drivers that are inducible/repressible.

Significance statement

The split-Gal4 system allowsDrosophilaresearchers to drive transgene expression with extraordinary cell type specificity. However, the existing split-Gal4 system cannot be controlled temporally, and therefore cannot be applied to many important areas of research. Here, we present a new split-Gal4 system based on a self-excising split-intein, which is fully controllable by Gal80, as well as a related drug-inducible split GeneSwitch system. This approach can both leverage and inform single-cell RNAseq datasets, and we introduce an algorithm to identify pairs of genes that precisely and narrowly mark a desired cell cluster. Our split-intein Gal4 system will be of value to theDrosophilaresearch community, and allow for the creation of highly specific genetic drivers that are also inducible/repressible.
Microbiomes of blood feeding triatomines in the context of their predatory relatives and the environment
Authors: Tarabai Hassan , Floriano Anna Maria , Zima Jan , Filová Natalia , Brown Joel J. , Roachell Walter , Smith Robert L. , Beatty Norman L. , Vogel Kevin J. , Nováková Eva
Published: March 2023

Abstract

The importance of gut microbiomes has become generally recognized in vector biology. This study addresses microbiome signatures in North AmericanTriatomaspecies of public health significance (vectors ofTrypanosoma cruzi) linked to their blood feeding strategy and the natural habitat. To place theTriatomaassociated microbiomes within a complex evolutionary and ecological context, we sampled sympatricTriatomapopulations, related predatory reduviids, unrelated ticks, and environmental material from vertebrate nests where these arthropods reside. Along with fiveTriatomaspecies, we have characterized microbiomes of five reduviids (Stenolemoides arizonensis,Ploiaria hirticornis,Zelus longipes, and twoReduviusspecies), a single soft tick species,Ornithodoros turicata,and environmental microbiomes from selected sites in Arizona, Texas, Florida and Georgia. The microbiomes of predatory reduviids lack a shared core microbiota. Like in triatomines, microbiome dissimilarities among species corelate with dominance of a single bacterial taxa. These includeRickettsia,Lactobacillus, CandidatusMidichloria, andZymobacter, which are often accompanied by known symbiotic genera, i.e.,Wolbachia,CandidatusLariskella,Asaia,Gilliamella, andBurkholderia.We have further identified compositional convergence of analyzed microbiomes in respect to the host phylogenetic distance in both blood feeding and predatory reduviids. While microbiomes of two reduviid species from Emesinae family reflect their close relationship, the microbiomes of allTriatomaspecies repeatedly form a distinct monophyletic cluster highlighting their phylosymbiosis. Furthermore, based on environmental microbiome profiles and blood meal analysis, we propose three epidemiologically relevant and mutually interrelated bacterial sources forTriatomamicrobiomes, i.e., host abiotic environment, host skin microbiome, and pathogens circulating in host blood.

Importance

This study places microbiomes of blood feeding North AmericanTriatomavectors (Reduviidae) into a broader evolutionary and ecological context provided by related predatory assassin bugs (Reduviidae), another unrelated vector species (soft tickOrnithodor turicata), and the environment these arthropods cohabit. For both vectors, microbiome analyses suggest three interrelated sources of bacteria, i.e., microbiome of vertebrate nests as their natural habitat, vertebrate skin microbiome, and pathobiome circulating in vertebrate blood. Despite an apparent influx of environment-associated bacteria into the arthropod microbiomes,Triatomamicrobiomes retain their specificity, forming a distinct cluster that significantly differ from both predatory relatives and ecologically comparable ticks. Similarly, within the related predatory Reduviidae, we found the host phylogenetic distance to underlie microbiome similarities.
Efficient Visual Heuristics in the Perception of Physical Object Properties
Authors: Paulun Vivian C. , Bayer Florian S. , Tenenbaum Joshua B. , Fleming Roland W.
Published: March 2023

Vision is more than object recognition: In order to interact with the physical world, we estimate object properties such as mass, fragility, or elasticity by sight. The computational basis of this ability is poorly understood. Here, we propose a model based on the statistical appearance of objects, i.e., how they typically move, flow, or fold. We test this idea using a particularly challenging example: estimating the elasticity of bouncing objects. Their complex movements depend on many factors, e.g., elasticity, initial speed, and direction, and thus every object can produce an infinite number of different trajectories. By simulating and analyzing the trajectories of 100k bouncing cubes, we identified and evaluated 23 motion features that could individually or in combination be used to estimate elasticity. Experimentally teasing apart these competing but highly correlated hypotheses, we found that humans represent bouncing objects in terms of several different motion features but rely on just a single one when asked to estimate elasticity. Which feature this is, is determined by the stimulus itself: Humans rely on the duration of motion if the complete trajectory is visible, but on the maximal bounce height if the motion duration is artificially cut short. Our results suggest that observers take into account the computational costs when asked to judge elasticity and thus rely on a robust and efficient heuristic. Our study provides evidence for how such a heuristic can be derived—in an unsupervised manner—from observing the natural variations in many exemplars.

Significance Statement

How do we perceive the physical properties of objects? Our findings suggest that when tasked with reporting the elasticity of bouncing cubes, observers rely on simple heuristics. Although there are many potential visual cues, surprisingly, humans tend to switch between just a handful of them depending on the characteristics of the stimulus. The heuristics predict not only the broad successes of human elasticity perception but also the striking pattern of errors observers make when we decouple the cues from ground truth. Using a big data approach, we show how the brain could derive such heuristics by observation alone. The findings are likely an example of ‘computational rationality’, in which the brain trades off task demands and relative computational costs.
Activity of estrogen receptor beta expressing neurons in the medial amygdala regulates preference towards receptive females in male mice
Authors: Takenawa Satoshi , Nagasawa Yutaro , Go Kim , Chérasse Yoan , Mizuno Seiya , Sano Kazuhiro , Ogawa Sonoko
Published: March 2023

The processing of information regarding the sex and reproductive state of conspecific individuals is critical for successful reproduction and survival in males. Generally, male mice exhibit a preference towards sexually receptive (RF) over non-receptive females (XF) or gonadally intact males (IM). Previous studies suggested the involvement of estrogen receptor beta (ERβ) expressed in the medial amygdala (MeA) in male preference towards RF. To further delineate the role played by ERβ in the MeA in the neuronal network regulating male preference, we developed a new ERβ-iCre mouse line using the CRISPR-Cas9 system. Fiber-photometry Ca2+imaging revealed that ERβ expressing neurons in the postero-dorsal part of the MeA (MeApd-ERβ+neurons) were more active during social investigation towards RF compared to copresented XF or IM mice in a preference test. Chemogenetic inhibition of MeApd-ERβ+neuronal activity abolished a preference to RF in “RF vs. XF”, but not “RF vs. IM”, tests. Analysis with cre-dependent retrograde tracing viral vectors identified the principal part of the bed nucleus of stria terminalis (BNSTp) as a primary projection site of MeApd-ERβ+neurons. Fiber-photometry recording in the BNSTp during a preference test revealed that chemogenetic inhibition of MeApd-ERβ+neurons abolished differential neuronal activity of BNSTp cells as well as a preference to RF against XF but not against IM mice. Collectively, these findings demonstrate for the first time that MeApd-ERβ+neuronal activity is required for expression of receptivity-based preference (i.e., RF vs XF) but not sex-based preference (i.e., RF vs IM) in male mice.

Significance Statement

In this study, by introducing a new Cre mice line for ERβ+cells, we described the function of MeApd-ERβ+neurons and characteristics of their neuronal activity during preference tests. Using fiber photometry and DREADD techniques we have found MeApd-ERβ+neurons have a specific role in receptivity-based (receptive female vs. non-receptive female) preference but not in sexbased (receptive female vs. intact male) preference in male mice. We have also described this specific role of MeApd-ERβ+neurons is achieved by regulating the neuronal activity of downstream BNSTp neurons during receptivity-based, but not sex-based, preference tests. Our findings contribute to a better understating of the function of estrogen receptor expressing neurons in the neuronal network for the male-typical reproductive behaviors.
Production of 130 diterpenoids by combinatorial biosynthesis in yeast
Authors: Bathe Ulschan , Schmidt Jürgen , Frolov Andrej , Soboleva Alena , Frank Oliver , Dawid Corinna , Tissier Alain
Published: March 2023

Diterpenoids form a diverse group of natural products, many of which are or could become pharmaceuticals or industrial chemicals. However, low concentration, presence in complex mixtures and challenging synthesis often limit their exploitation. The modular character of diterpene biosynthesis and the substrate flexibility of the enzymes involved make combinatorial biosynthesis a promising approach. Here, we report on the assembly in yeast of 130 diterpenoids by pairwise combinations of ten diterpene synthases producing (+)-copalyl diphosphate-derived backbones and four cytochrome P450 enzymes (CYPs); 80 of these diterpenoids have not yet been reported. The CYPs accepted the majority of substrates they were given but remained regioselective. Our results bode well for the systematic exploration of diterpenoid chemical space using combinatorial assembly in yeast.
Predicting future conservation areas while avoiding competition in two alpine urodele amphibians severely threatened by climate change
Authors: Dubos Nicolas , Havard Antoine , Crottini Angelica , Seglie Daniele , Andreone Franco
Published: March 2023

Climate change will cause important declines in species distributions, especially when living at high altitudes. The Critically EndangeredSalamandra lanzaifrom SW Alps may be severely exposed to future climate change effects and its suitable climate may shrink or shift. Another Alpine salamander (S. atra) is present in the region, which in case of spatial overlap may represent a competitor forS. lanzai. It is urgent to estimate the effect of future climate change on these species and identify priority areas for conservation while accounting for competition between both species. With a Species Distribution Modelling (SDM) approach, we projected the current and future climate suitability of both salamander species. We accounted for uncertainty related to the methods (model replicates) and climate projections (data source, global circulation model and scenario) to provide a consensus map for practitioners. This map also takes into account potential competition withS. atraby penalizing the suitability scores of S.lanzaiby the scores ofS. atra. We predict a severe effect of climate change on both species. Most of the current habitats are projected to become largely unsuitable by 2070, regardless of the climatology and scenario. We identified important spatial disagreements between projections based on different data sources, mostly due to precipitation projections and daily temperature variation. This highlights the need to account for multiple climatologies in mountainous environments. Both species’ habitats are highly fragmented, which is expected to prevent distributional shifts through natural dispersion. We suggest to explore the possibility of translocation for the most threatened populations and simultaneously develop captive breeding programs. Biotic interactions are rarely accounted for in SDMs, and we encourage the documentation of species with similar ecological requirements to improve the relevance of SDMs for future conservation planning.
The best of two worlds: Decoding and source-reconstructing M/EEG oscillatory activity with a unique model
Authors: Westner Britta U. , King Jean-Rémi
Published: March 2023

The application of decoding models to electrophysiological data has become standard practice in neuroscience. The use of such methods on sensor space data can, however, limit the interpretability of the results, since brain sources cannot be readily estimated from the decoding of sensor space responses. Here, we propose a new method that combines the common spatial patterns (CSP) algorithm with beamformer source reconstruction for the decoding of oscillatory activity. We compare this method to sensor and source space decoding and show that it performs equally well as source space decoding with respect to both decoding accuracy and source localization without the extensive computational cost. We confirm our simulation results on a real MEG data set. In conclusion, our proposed method performs as good as source space decoding, is highly interpretable in the spatial domain, and has low computational cost.
Wandering albatrosses exert high take-off effort only when both wind and waves are gentle
Authors: Uesaka Leo , Goto Yusuke , Naruoka Masaru , Weimerskirch Henri , Sato Katsufumi , Sakamoto Kentaro Q.
Published: March 2023

The relationship between the environment and marine animal small-scale behavior is not fully understood. This is largely due to the difficulty in obtaining environmental datasets with a high spatiotemporal precision. The problem is particularly pertinent in assessing the influence of environmental factors in rapid, high energy consuming behavior such as seabird take-off. To fill the gaps in the existing environmental datasets, we employed novel techniques using animal-borne sensors with motion records to estimate wind and ocean wave parameters and evaluated their influence on wandering albatross take-off patterns. Measurements revealed that wind speed and wave heights experienced by wandering albatrosses during take-off ranged from 0.7 ∼ 15.4 m/s and 1.6 ∼ 6.4 m, respectively. The four indices measured (flapping number, frequency, sea surface running speed, and duration) also varied with the environmental conditions (e.g., flapping number varied from 0 to over 20). Importantly, take-off was easier under higher wave conditions than under lower wave conditions at a constant wind speed, and take-off effort increased only when both wind and waves were gentle. Our data suggests that both ocean waves and winds play important roles for albatross take-off and advances our current understanding of albatross flight mechanisms.

Impact statement

Wind and ocean wave conditions experienced by albatrosses were estimated using an animal-borne recorder and revealed that take-off was easier under higher wave conditions.
Shifting the selectivity of pyrido[2,3-d]pyrimidin-7(8H)-one inhibitors towards the salt-inducible kinase (SIK) subfamily
Authors: Rak Marcel , Tesch Roberta , Berger Lena M. , Shevchenko Ekaterina , Raab Monika , Tjaden Amelie , Zhubi Rezart , Balourdas Dimitrios-Ilias , Joerger Andreas C. , Poso Antti , Krämer Andreas , Elson Lewis , Lučić Aleksandar , Kronenberger Thales , Hanke Thomas , Strebhardt Klaus , Sanhaji Mourad , Knapp Stefan
Published: March 2023

Salt-inducible kinases 1-3 (SIK1-3) are key regulators of the LKB1-AMPK pathway and play an important role in cellular homeostasis. Dysregulation of any of the three isoforms has been associated with tumorigenesis in liver, breast, and ovarian cancers. We have recently developed the dual pan-SIK/group I p21-activated kinase (PAK) chemical probe MRIA9. However, inhibition of p21-activated kinases has been associated with cardiotoxicityin vivo, which complicates the use of MRIA9 as a tool compound. Here, we present a structure-based approach involving the back-pocket and gatekeeper residues, for narrowing the selectivity of pyrido[2,3-d]pyrimidin-7(8H)-one-based inhibitors towards SIK kinases, eliminating PAK activity. Optimization was guided by high-resolution crystal structure analysis and computational methods, resulting in a pan-SIK inhibitor, MR22, which no longer exhibited activity on STE group kinases and displayed excellent selectivity in a representative kinase panel. MR22-dependent SIK inhibition led to centrosome dissociation and subsequent cell-cycle arrest in ovarian cancer cells, as observed with MRIA9, conclusively linking these phenotypic effects to SIK inhibition. Taken together, MR22 represents a valuable tool compound for studying SIK kinase function in cells.
Constitutive expression of the Type VI secretion system carries no measurable fitness cost inVibrio cholerae
Authors: Zhang Christopher , Ratcliff William C. , Hammer Brian K.
Published: March 2023

The Type VI Secretion System (T6SS) is a widespread and highly effective mechanism of microbial warfare; it confers the ability to efficiently kill susceptible cells within close proximity. Due to its large physical size, complexity, and ballistic basis for intoxication it has widely been assumed to incur significant growth costs in the absence of improved competitive outcomes. In this study, we precisely examine the fitness costs of constitutive T6SS firing in the bacteriumVibrio cholerae. We find that, contrary to expectations, constitutive use of T6SS has a negligible impact on growth, reducing growth fitness by 0.025 ± 0.5% (95% CI) relative to a T6SS-control. Mathematical modeling of microbial populations demonstrates that, due to clonal interference, constitutive expression of the T6SS will often be neutral, with little impact on evolutionary outcomes. Our findings underscore the importance of precisely measuring the fitness costs of microbial social behaviors, and help explain the prevalence of the T6SS across Gram negative bacteria.
Elastomeric Pillar Cages Modulate Actomyosin Contractility of Epithelial Microtissues by Substrate Stiffness and Topography
Authors: Esser Lisann , Springer Ronald , Dreissen Georg , Lövenich Lukas , Konrad Jens , Hampe Nico , Merkel Rudolf , Hoffmann Bernd , Noetzel Erik
Published: March 2023

Cell contractility regulates epithelial tissue geometry development and homeostasis. The underlying mechanobiological regulation circuits are poorly understood and experimentally challenging. We developed an elastomeric pillar cage (EPC) array to quantify cell contractility as a mechanoresponse of epithelial microtissues to substrate stiffness and topography. The spatially confined EPC geometry consisted of 24 circularly arranged slender pillars (1.2 MPa, height: 50 μm, diameter: 10 μm, distance: 5 μm). These high-aspect-ratio pillars were confined at both ends by planar substrates with different stiffness (0.15 – 1.2 MPa). Analytical modeling and finite elements simulation retrieved cell forces from pillar displacements. For evaluation, highly contractile myofibroblasts and cardiomyocytes were assessed to demonstrate that the EPC device can resolve static and dynamic cellular force modes. Human breast (MCF10A) and skin (HaCaT) cells grew as adherence junction-stabilized 3D microtissues within the EPC geometry. Planar substrate areas triggered the spread of monolayered clusters with substrate stiffness-dependent actin stress fiber (SF)-formation and substantial single-cell actomyosin contractility (150 - 200 nN). Within same continuous microtissues, the pillar-ring topography induced bilayered cell tube growth. Here, low effective pillar stiffness overwrote local substrate stiffness sensing and induced SF-lacking roundish cell shapes with extremely low cortical actin tension (11 - 15 nN). This work introduced a versatile biophysical tool to explore mechanobiological regulation circuits driving low- and high-tensional states in developing and homeostatic microtissues. EPC arrays facilitate simultaneously analyzing the impact of planar substrate stiffness and topography on microtissue contractility hence microtissue geometry and function.
The complexity of micro-and nanoplastic research in the genusDaphnia– A systematic review of study variability and meta-analysis of immobilization rates
Authors: Brehm Julian , Ritschar Sven , Laforsch Christian , Mair Magdalena M.
Published: March 2023

In recent years, the number of publications on nano-and microplastic particles (NMPs) effects on freshwater organisms has increased rapidly. Freshwater crustaceans of the genusDaphniaare widely used in ecotoxicological research as model organisms for assessing the impact of NMPs. However, the diversity of experimental designs in these studies makes conclusions about the general impact of NMPs onDaphniachallenging. To approach this, we systematically reviewed the literature on NMP effects onDaphniaand summarized the diversity of test organisms, experimental conditions, NMP properties and measured endpoints to identify gaps in our knowledge of NMP effects onDaphnia.We use a meta-analysis on mortality and immobilization rates extracted from the compiled literature to illustrate how NMP properties and study parameters can impact outcomes in toxicity bioassays. In addition, we investigate the extent to which the available data can be used to predict the toxicity of untested NMPs based on the extracted parameters. Based on our results, we argue that focusing on a more diverse set of NMP properties combined with a more detailed characterization of the particles in future studies will help to fill current research gaps, improve predictive models and allow the identification of NMP properties linked to toxicity.

Highlights

Systematic review of NMP effects on the model systemDaphnia

Organismic, experimental and NMP properties influence observed effects

In silicoidentification of traits likely linked to NMP toxicity (immobilization)

More detailed standardized characterization of NMP needed to improve predictions
High-Content Screening to Identify Inhibitors of Dengue Virus Replication
Authors: Hoffstadt Jillian G. , Wotring Jesse W. , Porter Sam , Halligan Benjamin , O’Meara Matthew J. , Tai Andrew W. , Sexton Jonathan Z.
Published: March 2023

Dengue Virus (DENV) causes dengue fever, a pandemic-potential disease with currently no FDA-approved antivirals. Additionally, the available vaccine for DENV can increase the risk of severe dengue fever for those who have never had a DENV infection due to antibody-dependent enhancements. Thus, there is an urgent need to identify dengue virus antivirals. Antivirals that target NS4B, the replication compartment forming protein of DENV and the flavivirus family, are a promising new drug class that minimize cytotoxic effects to host cells. Drug-repurposing and high-content screening were leveraged to efficiently identify antivirals likely to inhibit NS4B. Using high-content screening, we quantified the morphological patterns of NS4B and envelope (E) protein expression versus time and developed a viral pseudotime model that was able to predict the infection progression to enable drug screening. We then developed a single cell infection classifier for antiviral efficacy and performed high-throughput drug screening of 960 compounds. We identified four concentration-dependent inhibitors of DENV with nanomolar potencies including: Nexium, Pralatrexate, GW4064, and LY411575. LY411575, a gamma secretase inhibitor, exhibited an IC50of 72nM and reduced percent infection to levels indistinguishable from the mock infection control.
Inhibition of CD40-TRAF6 signaling protects against aneurysm development and progression
Authors: Ommer-Bläsius Miriam , Vajen Tanja , Elster Christin , Verheyen Sarah , Pfeiler Susanne , Quast Christine , Odendahl Julia , Lang Alexander , Kelm Malte , Lutgens Esther , Gerdes Norbert
Published: March 2023

Objective

Inflammation is a critical process during the progressive development and complication of abdominal aortic aneurysm. The co-stimulatory dyad CD40-CD40L is a major driver of inflammation and modulates immune responses. This study evaluates the potential of a small molecule inhibitor, which blocks the interaction between CD40 and tumor necrosis factor (TNF) receptor-associated factor (TRAF)-6, referred to as TRAF-STOP, in the early and later phase during AAA progression.

Methods and results

AAAs were induced in C57BL/6J mice by infrarenal aortic porcine pancreatic elastase infusion for 7, 14 or 28 days. Inhibition of CD40 signaling by TRAF-STOP resulted in less severe AAA formation and reduced the incidence of AAA development. TRAF-STOP treatment attenuated aortic structural remodeling, characterized by a reduced elastic fiber degradation, lowered expression of matrix metalloproteinase (MMP)-2 and MMP9, as well as preserved collagen type IV content in aneurysmal tissue. Furthermore, this is accompanied by the reduction of key pro-inflammatory genes such as TNFα.

Conclusion

Pharmacological inhibition of CD40-TRAF6 signaling protects from adverse aortic structural remodeling during the early phase of AAA progression representing a translational strategy to limit progression of human AAA disease.
Normal and cancer tissues are accurately characterised by intergenic transcription at RNA polymerase 2 binding sites
Authors: de Langen Pierre , Hammal Fayrouz , Guéret Elise , Spinelli Lionel , Ballester Benoit
Published: March 2023

Intergenic transcription in normal and cancerous tissue is pervasive and incompletely understood. To investigate this activity at a global level, we constructed an atlas of over 180,000 consensus RNA Polymerase II (RNAP2) bound intergenic regions from more than 900 RNAP2 ChIP-seq experiments across normal and cancer samples. Using unsupervised analysis, we identified 51 RNAP2 consensus clusters, many of which map to specific biotypes and identify tissue-specific regulatory signatures. We developed a meta-clustering methodology to integrate our RNAP2 atlas with active transcription across 28,797 RNA-seq samples from TCGA, GTEx and ENCODE, which revealed strong tissue- and disease-specific interconnections between RNAP2 occupancy and transcription. We demonstrate that intergenic transcription at RNAP2 bound regions are novel per-cancer and pan-cancer biomarkers showing genomic and clinically relevant characteristics including the ability to differentiate cancer subtypes and are associated with overall survival. Our results demonstrate the effectiveness of coherent data integration to uncover and characterise intergenic transcriptional activity in both normal and cancer tissues.
Population-level antagonism between FGF and BMP signaling steers mesoderm differentiation in embryonic stem cells
Authors: Gattiglio Marina , Protzek Michelle , Schröter Christian
Published: March 2023

The mesodermal precursor populations for different internal organ systems are specified during gastrulation by the combined activity of extracellular signaling systems such as BMP, Wnt, Nodal, and FGF. The BMP, Wnt and Nodal signaling requirements for the differentiation of specific mesoderm subtypes in mammals have been mapped in detail, but how FGF shapes mesodermal cell type diversity is not precisely known. It is also not clear how FGF signaling integrates with the activity of other signaling systems involved in mesoderm differentiation. Here, we address these questions by analyzing the effects of targeted signaling manipulations in differentiating stem cell populations with single cell resolution. We identify opposing functions of BMP and FGF, and map FGF-dependent and -independent mesodermal lineages. Stimulation with exogenous FGF boosts the expression of endogenous Fgfs while repressing Bmp ligands. This positive autoregulation of FGF signaling, coupled to the repression of BMP signaling, may contribute to the specification of reproducible and coherent cohorts of cells with the same identity via a community effect, both in the embryo and in synthetic embryo-like systems.
Age-related variability in network engagement during music listening
Authors: Faber S. , Belden A.G. , Loui P. , McIntosh A.R.
Published: March 2023

Listening to music is an enjoyable behaviour that engages multiple networks of brain regions. As such, the act of music listening may offer a way to interrogate network activity, and to examine the reconfigurations of brain networks that have been observed in healthy aging. The present study is an exploratory examination of brain network dynamics during music listening in healthy older and younger adults. Network measures were extracted and analyzed together with behavioural data using a combination of hidden Markov modelling and partial least squares. We found age- and preference-related differences in fMRI data collected during music listening in healthy younger and older adults. Both age groups showed higher occupancy (the proportion of time a network was active) in a temporal-mesolimbic network while listening to self-selected music. Activity in this network was strongly positively correlated with liking and familiarity ratings in younger adults, but less so in older adults. Additionally, older adults showed a higher degree of correlation between liking and familiarity ratings consistent with past behavioural work on age-related dedifferentiation. We conclude that, while older adults do show network and behaviour patterns consistent with dedifferentiation, activity in the temporal-mesolimbic network is relatively robust to dedifferentiation. These findings may help explain how music listening remains meaningful and rewarding in old age.
Cbp1-Cren7 chromatinization of CRISPR arrays favours transcription from leader-over cryptic promoters
Authors: Blombach Fabian , Sýkora Michal , Case Jo , Feng Xu , Baquero Diana P , Fouqueau Thomas , Phung Duy Khanh , Barker Declan , Krupovic Mart , She Qunxin , Werner Finn
Published: March 2023

CRISPR arrays form the physical memory of CRISPR adaptive immune systems by incorporating foreign DNA as spacers that are often AT-rich and derived from viruses. As promoter elements such as the TATA-box are AT-rich, CRISPR arrays are prone to harbouring cryptic promoters. Sulfolobales harbor extremely long CRISPR arrays spanning several kilobases, a feature that is accompanied by the CRISPR-specific transcription factor Cbp1. Aberrant Cbp1 expression modulates CRISPR array transcription, but the molecular mechanisms underlying this regulation are unknown. Here, we characterise the genome-wide Cbp1 binding at nucleotide resolution and characterise the binding motifs on distinct CRISPR arrays, as well as on unexpected non-canonical binding sites associated with transposasons. Cbp1 recruits Cren7 forming together ‘chimeric’ chromatin-like structures at CRISPR arrays. We dissect Cbp1 functionin vitroandin vivoand show that the third HTH domain is responsible for Cren7 recruitment, and that Cbp1-Cren7 chromatinization plays a dual role in the transcription of CRISPR arrays. It suppresses spurious transcription from cryptic promoters within CRISPR arrays but enhances CRISPR RNA transcription directed from their cognate promoters in their leader region. Our results show that Cbp1-Cren7 chromatinization drives the productive expression of long CRISPR arrays.
ZFP281 coordinates DNMT3 and TET1 for transcriptional and epigenetic control in pluripotent state transitions
Authors: Huang Xin , Balmer Sophie , Lyu Cong , Xiang Yunlong , Malik Vikas , Wang Hailin , Zhang Yu , Xie Wei , Hadjantonakis Anna-Katerina , Zhou Hongwei , Wang Jianlong
Published: March 2023

The progression from naive through formative to primedin vitropluripotent stem cell states recapitulates the development of the epiblastin vivoduring the peri-implantation period of mammalian development. Activation of thede novoDNA methyltransferases and reorganization of transcriptional and epigenetic landscapes are key events occurring during these pluripotent state transitions. However, the upstream regulators that coordinate these events are relatively underexplored. Here, usingZfp281knockout mouse and degron knock-in cell models, we uncover the direct transcriptional activation ofDnmt3a/3bby ZFP281 in pluripotent stem cells. Chromatin co-occupancy of ZFP281 and DNA hydroxylase TET1, dependent on the formation of R loops in ZFP281-targeted gene promoters, undergoes a “high-low-high” bimodal pattern regulating dynamic DNA methylation and gene expression during the naïve-formative-primed transitions. ZFP281 also safeguards DNA methylation in maintaining primed pluripotency. Our study demonstrates a previously unappreciated role for ZFP281 in coordinating DNMT3A/3B and TET1 functions to promote pluripotent state transitions.

In Brief

The naive, formative, and primed pluripotent states and their interconversions recapitulate pluripotency continuum during early development. Huang and colleagues investigated the transcriptional programs during successive pluripotent state transitions and revealed an essential role for ZFP281 in coordinating DNMT3A/3B and TET1 to establish the DNA methylation and gene expression programs during the transitions.

Highlights

ZFP281 activatesDnmt3a/3b in vitroin pluripotent stem cells andin vivoin epiblast.

ZFP281 and TET1 undergo bimodal chromatin occupancy in pluripotent state transitions.

Chromatin-binding of ZFP281 and TET1 depends on the formation of R-loops at promoters.

ZFP281 is necessary for the establishment and maintenance of primed pluripotency.
Production of extracellular polymeric substances in granular sludge under selection forAccumulibacterandCompetibacter
Authors: Guimarães Lorena B. , Gubser Nina R. , Lin Yuemei , Zlópasa Jure , Felz Simon , Tomás Martínez Sergio , Pronk Mario , Neu Thomas R. , Dueholm Morten K. D. , Albertsen Mads , da Costa Rejane H. R. , Nielsen Per Halkjær , van Loosdrecht Mark C. M. , Weissbrodt David G.
Published: March 2023

Granular sludge intensifies the removal of nutrients from wastewater. Granules structured by extracellular polymeric substances (EPS) can be recovered as biomaterial. Links between microbial selection and EPS formation during granulation need to get uncovered. We inoculated anaerobic-aerobic sequencing batch reactors with either flocs or granules to study the relationships between microbial selection, bioaggregation, exopolymer formation, and EPS composition. Selection for slow-growing organisms like the model polyphosphate- accumulating organism “Candidatus Accumulibacter” (max. 83% vs. amplicon sequencing read counts) and glycogen-accumulating organism “Ca. Competibacter” (max. 45%) sustained granulation. Gel-forming exopolymers were produced as high as above 40% of the volatile solids of the biomass by stepwise increase of the organic loading rate (0.3 to 2.0 g CODAcd-1LR-1). Confocal laser scanning microscopy, FT-IR spectroscopy, and HPAE-PAD chromatography revealed the complex and dynamic chemical compositions of the structural EPS in relation to microbial population shifts along reactor regimes. The analysis of 20 representative genomes of “Ca. Accumulibacter” and “Ca. Competibacter” recovered from public databases revealed their functional potential to produce EPS among other representative wastewater microorganisms. The more than 40 functional gene categories annotated highlight the complexity of EPS metabolic networks from monomers processing to assembly, export, and epimerizations. The combination of ecological engineering principles and systems microbiology will help unravel and direct the production of EPS from wastewater, valorizing residual granular sludge into beneficial biomaterials for the circular economy.

Highlights

Selection for slow-growing organisms like PAOs and GAOs fostered a robust granulation.

Structural EPS were produced above 40% of biomass volatile content under high loading.

Chemical composition of EPS evolved together with the microbial community composition.

Genomic insights highlighted the genetic potential of PAOs and GAOs for EPS formation.

Microbial communities are complex; further are their EPS compositions and metabolisms.

Graphical abstract
Arf1-PI4KIIIβ positive vesicles regulate phosphatidylinositol-3-phosphate signalling to facilitate the fission of lysosomal tubules
Authors: Boutry Maxime , DiGiovanni Laura F. , Demers Nicholas , Fountain Aaron , Mamand Sami , Botelho Roberto J. , Kim Peter K.
Published: March 2023

Formation and fission of tubules from lysosomal organelles, such as autolysosomes, endolysosomes or phagolysosomes, are required for lysosome reformation. However, the mechanisms governing these processes in the different forms of lysosomal organelles are poorly understood. For instance, the role of phosphatidylinositol-4-phosphate (PI(4)P) is unclear as it was shown to promote the formation of tubules from phagolysosomes but was proposed to inhibit tubule formation on autolysosomes because the loss of PI4KIIIβ causes extensive lysosomal tubulations. Using super-resolution live-cell imaging, we show that Arf1-PI4KIIIβ positive vesicles are recruited to tubule fission sites from autolysosomes, endolysosomes and phagolysosomes. Moreover, we show that PI(4)P is required to form autolysosomal tubules and that increased lysosomal tubulation caused by loss of PI4KIIIβ represents impaired tubule fission. At the site of fission, we propose that Arf1-PI4KIIIβ positive vesicles mediate a PI(3)P signal on lysosomes in a process requiring the lipid transfer protein SEC14L2. Our findings indicate that Arf1-PI4KIIIβ positive vesicles and their regulation of PI(3)P are critical components of the lysosomal tubule fission machinery.
Post-fibrillization nitration of alpha-synuclein abolishes its seeding activity and pathology formation in primary neurons andin vivo
Authors: Donzelli Sonia , OSullivan Sinead A. , Mahul-Mellier Anne-Laure , Ulusoy Ayse , Fusco Giuliana , Kumar Senthil T. , Chiki Anass , Burtscher Johannes , Boussouf Manel L.D. , Rostami Iman , Simone Alfonso De , Di Monte Donato A. , Lashuel Hilal A.
Published: March 2023

Increasing evidence points to post-translational modifications (PTMs) as key regulators of alpha-synuclein (α-Syn) function in health and disease. However, whether these PTMs occur before or after α-Syn pathology formation and their role in regulating α-Syn toxicity remain unclear. In this study, we demonstrate that post-fibrillization nitration of α-Syn fibrils induced their fragmentation, modified their surface and dynamic properties but not their structure, and nearly abolished their seeding activity in primary neurons andin vivo. Furthermore, we show that the dynamic and surface properties of the fibrils, rather than simply their length, are important determinants of α-Syn fibril seeding activity. Altogether, our work demonstrates that post-aggregation modifications of α-Syn may provide novel approaches to target a central process that contributes to pathology formation and disease progression. Finally, our results suggest that the pattern of PTMs on pathological aggregates, rather than simply their presence, could be a key determinant of their toxicity and neurodegeneration. This calls for reconsidering current approaches relying solely on quantifying and correlating the level of pathology to assess the efficacy of novel therapies, as not all α-Syn aggregates in the brain are pathogenic.
The impact of Fintech on inflation and unemployment: the case of Asia
Authors: Ben Romdhane Youssra , Kammoun Souhaila , Loukil Sahar
Published: March 2023

Purpose

This study attempts to explain the impact of Fintech on the Asian economies through two main indicators, inflation and unemployment over the period 2011-2014-2017.

Design/methodology/approach

This study uses panel data regression models to explain the relationship between Fintech, inflation as an indicator of currency circulation and unemployment since Fintech has disrupted the labor market.

Findings

Empirical results show a consistently strong and positive relationship between the development of financial technologies and the reduction of inflation and unemployment unless these technologies are actively used. Digital finance has become a new driver of economic development. Therefore, governors should not only improve their economies but also expand their information and communication technologies to develop their digital infrastructure, especially for businesses.

Originality/value

The present study contributes to the existing literature on the impact of disruptive digital innovation on the socioeconomic development of emerging countries. The empirical evidence highlights the importance of distinguishing between active and passive uses of Fintech in order to anticipate its economic impact.