bluuebunny/crossref_metadata_2025 huggingface dataset:
Recovery of 447 Eukaryotic bins reveals major challenges for Eukaryote genome reconstruction from metagenomes
Authors: Saraiva Joao Pedro , Bartholomäus Alexander , Toscan Rodolfo Brizola , Baldrian Petr , da Rocha Ulisses Nunes
Published: April 2022

An estimated 8.7 million eukaryotic species exist on our planet. However, recent tools for taxonomic classification of eukaryotes only dispose of 734 reference genomes. As most Eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although approaches to recover Prokaryotic genomes have become common in genome biology, few studies have tackled the recovery of Eukaryotic genomes from metagenomes. This study assessed the reconstruction of Eukaryotic genomes using 215 metagenomes from diverse environments using the EukRep pipeline. We obtained 447 eukaryotic bins from 15 classes (e.g., Saccharomycetes, Sordariomycetes, and Mamiellophyceae) and 16 orders (e.g., Mamiellales, Saccharomycetales, and Hypocreales). More than 73% of the obtained eukaryotic bins were recovered from samples whose biomes were classified as host-associated, aquatic and anthropogenic terrestrial. However, only 93 bins showed taxonomic classification to (9 unique) genera and 17 bins to (6 unique) species. A total of 193 bins contained completeness and contamination measures. Average completeness and contamination were 44.64% (σ=27.41%) and 3.97% (σ=6.53%), respectively. Micromonas commoda was the most frequent taxa found while Saccharomyces cerevisiae presented the highest completeness, possibly resulting from a more significant number of reference genomes. However, mapping eukaryotic bins to the chromosomes of the reference genomes suggests that completeness measures should consider both single-copy genes and chromosome coverage. Recovering eukaryotic genomes will benefit significantly from long-read sequencing, intron removal after assembly, and improved reference genomes databases.
Less is more - loss of EGFL7 improves memory by upregulation of VEGF-D
Authors: Vasić Verica , Barth Kathrin , Bicker Frank , Schumann Ulrike , Maurer Christine , Heinig Nora , Röhlecke Cora , Nimtschke Ute , Schumann Lana , Meinhardt Matthias , Mittmann Thomas , Radyushkin Konstantin , Baumgart Jan , Tenzer Stefan , Zipp Frauke , Tegeder Irmgard , Schmidt Mirko HH
Published: April 2022

Neural stem cells reside in a specialized neurogenic niche of the hippocampus termed the subgranular zone. Throughout life, they give rise to adult-born neurons in the dentate gyrus thereby contributing to learning and memory. Here, we report that neurons together with neural stem and precursor cells secrete the neurovascular protein epidermal growth factor-like protein 7 (EGFL7) to shape this niche. EGFL7 knock-out in vivo promoted adult neurogenesis generating neurons forming additional spines which permanently integrated into the neural circuit until old age. RNA-sequencing identified the cytokine VEGF-D as a major molecular driver of this process in vivo. In behavioral studies EGFL7 knock-out mice displayed stronger maintenance of memory suggesting longer-lasting spatial memory and improved memory consolidation in the hippocampus by modulation of pattern separation in young and aged mice. Taken together, EGFL7 is an upstream regulator of the VEGF-D in adult neurogenesis and a key regulator of learning and memory.
Statistical learning for sparser fine-mapped polygenic models: the prediction of LDL-cholesterol
Authors: Maj Carlo , Staerk Christian , Borisov Oleg , Klinkhammer Hannah , Yeung Ming Wai , Krawitz Peter , Mayr Andreas
Published: April 2022

Polygenic risk scores quantify the individual genetic predisposition regarding a particular trait. We propose and illustrate the application of existing statistical learning methods to derive sparser models for genome-wide data with a polygenic signal. Our approach is based on three consecutive steps. First, potentially informative loci are identified by a marginal screening approach. Then, fine-mapping is independently applied for blocks of variants in linkage disequilibrium, where informative variants are retrieved by using variable selection methods including boosting with probing and stochastic searches with the Adaptive Subspace method. Finally, joint prediction models with the selected variants are derived using statistical boosting. In contrast to alternative approaches relying on univariate summary statistics from genome-wide association studies, our three-step approach enables to select and fit multivariable regression models on large-scale genotype data. Based on UK Biobank data, we develop prediction models for LDL-cholesterol as a continuous trait. Additionally, we consider a recent scalable algorithm for the Lasso. Results show that statistical learning approaches based on fine-mapping of genetic signals result in a competitive prediction performance compared to classical polygenic risk approaches, while yielding sparser risk models that tend to be more robust regarding deviations from the target population.
Nicotine measurement on Cambridge Filter PADs: an interlaboratory comparison to evaluate exposure by different electronic devices and traditional cigarette
Authors: Zuccarello Pietro , Emma Rosalia , Caruso Massimo , Pulvirenti Roberta , Rust Sonja , Poulas Konstantinos , Zadjali Fahad , Boffo Silvia , Volarevic Vladislav , Lesmana Ronny , Abdulkhakov Sayar R , Mesiakaris Konstantinos , Tobi Mohammed Al , Giordano Antonio , Arsenijevic Aleksandar , Barliana Melisa I , Kitaeva Kristina V , Polosa Riccardo , Volti Giovanni Li , Ferrante Margherita
Published: April 2022

Inter-laboratory comparison is widely used to ensure quality control among laboratories. In in vitro toxicology studies for tobacco harm reduction (THR), exposure system performance and laboratory proficiency along with product smoke and aerosol stream are tested for variability to assess accuracy. Here we aim to test a novel inter-laboratory setup created in a new collaborative research group using identical and small footprint systems- in order to minimize variability factors and increase reproducibility.

Seven independent laboratories from different geographical areas tested the aerosol and smoke stream and exposure system performance (LM1 and LM4E) using Cambridge Filter Pad (CFP) trapping techniques. We tested 1R6F reference cigarettes, two electronic cigarettes (Vype e-Pen and Vype e-Stick Maxx), and two tobacco heating products (IQOS and Glo™) under the appropriate ISO and/or HCI regimes. Nicotine quantification was performed by GC-FID at the laboratory of the leading center. The performance of participant laboratories was assessed by z-score values obtained from results either in relation to the mean and standard deviation of total participants or in relation to the reference leading center. Z-Scores were satisfactory when |z| ≤ 2, questionable when 2 < |z| < 3 and, unsatisfactory when |z| ≥ 3. In the first evaluation, for all the tested devices, Z- scores values generated by dosimetry data ranged from -2 to +2. However, high intra-laboratory variability (RSD> 10%) was observed for almost all laboratories. In the second, data showed borderline and unsatisfactory exposure performances versus LAB-A. Particularly, Z-scores ≥ 3 were observed once for LAB-B (e-Stick exposure) and LAB-G (e-Pen exposure), twice for LAB-C (1R6F-ISO and e-Stick exposures) and LAB-E (e-Pen and e-Stick exposures), and three times for LAB-F (1R6F-HCI, e-Pen, and Glo exposures).

This study demonstrates that nicotine dosimetry is a fundamental method for quality assurance of smoke/vapor run exposure in the early stage of an interlaboratory study, allowing the identification and possibly the resolution of gaps. Extended practice sessions on exposure runs and several rounds of nicotine dosimetry testing should be planned to keep in check overall equipment and operator performance.
Genetically defined nucleus incertus neurons differ in connectivity and function
Authors: Spikol Emma D. , Cheng Ji , Macurak Michelle , Subedi Abhignya , Halpern Marnie E.
Published: April 2022

The nucleus incertus (NI), a conserved hindbrain structure implicated in the stress response, arousal, and memory, is a major site for production of the neuropeptide relaxin-3. On the basis ofgoosecoid homeobox 2(gsc2) expression, we identified a neuronal cluster that lies adjacent torelaxin 3a(rln3a) neurons in the zebrafish analogue of the NI. To delineate the characteristics of thegsc2andrln3aNI neurons, we used CRISPR/Cas9 targeted integration to drive gene expression specifically in each neuronal group, and found that they differ in their efferent and afferent connectivity, spontaneous activity, and functional properties.gsc2andrln3aNI neurons have widely divergent projection patterns and innervate distinct subregions of the midbrain interpeduncular nucleus (IPN). Whereasgsc2neurons are activated by electric shock,rln3aneurons exhibit spontaneous fluctuations in calcium signaling and regulate locomotor activity. Our findings define heterogeneous neurons in the NI and provide new tools to probe its diverse functions.
A macroecological perspective on genetic diversity in the human gut microbiome
Authors: Shoemaker William R.
Published: April 2022

While the human gut microbiome has been intensely studied, we have yet to obtain a sufficient understanding of the genetic diversity that it harbors. Research efforts have demonstrated that a considerable fraction of within-host genetic variation in the human gut is driven by the ecological dynamics of co-occurring strains belonging to the same species, suggesting that an ecological lens may provide insight into empirical patterns of genetic diversity. Indeed, an ecological model of self-limiting growth and environmental noise known as the Stochastic Logistic Model (SLM) was recently shown to successfully predict the temporal dynamics of strains within a single human host. However, its ability to predict patterns of genetic diversity across human hosts has yet to be tested. In this manuscript I determine whether the predictions of the SLM explain patterns of genetic diversity across unrelated human hosts for 22 common microbial species. Specifically, the stationary distribution of the SLM explains the distribution of allele frequencies across hosts and predicts the fraction of hosts harboring a given allele (i.e., prevalence) for a considerable fraction of sites. The accuracy of the SLM was correlated with independent estimates of strain structure, suggesting that patterns of genetic diversity in the gut microbiome follow statistically similar forms across human hosts due to the existence of strain-level ecology.
Assessing the importance of resistance, persistence and hyper-mutation for antibiotic treatment success with stochastic modelling
Authors: Witzany Christopher , Regoes Roland R. , Igler Claudia
Published: April 2022

Antimicrobial resistance poses a rising threat to global health, making it crucial to understand the routes of bacterial survival during antimicrobial treatments. Treatment failure can result from genetic or phenotypic mechanisms, which diminish the effect of antibiotics. By assembling empirical data, we find that, for example, Pseudomonas aeruginosa infections in cystic fibrosis patients frequently contain persisters, transiently non-growing and antibiotic-refractory subpopulations, and hyper-mutators, mutants with elevated mutation rates and thus higher probability of genetic resistance emergence. Resistance, persistence and hyper-mutation dynamics are difficult to disentangle experimentally. Hence, we use stochastic population modelling and deterministic fitness calculations of bacterial evolution under antibiotic treatment to investigate how genetic resistance and phenotypic mechanisms affect treatment success. We find that treatment failure is caused by resistant mutants at lower antibiotic concentrations (with high final bacterial numbers), but by persistence phenotypes at higher antibiotic concentrations (with low final bacterial numbers). Facilitation of resistance occurs through hyper-mutators during treatment, but through persistence only after treatment is discontinued, which allows for persisters to resume growth and evolve resistance in the absence of antibiotics. Our findings highlight the time- and concentration-dependence of different bacterial mechanisms to escape antibiotic killing, which should be considered when designing ‘resistance-proof’ antimicrobial treatments.
Quantitative MRI maps of human neocortex explored using cell type-specific gene expression analysis
Authors: Edwards Luke J. , McColgan Peter , Helbling Saskia , Zarkali Angeliki , Vaculčiaková Lenka , Pine Kerrin J. , Dick Fred , Weiskopf Nikolaus
Published: April 2022

Quantitative MRI (qMRI) allows extraction of reproducible and robust parameter maps. However, the connection to underlying biological substrates remains murky, especially in the complex, densely packed cortex. We investigated associations in human neocortex between qMRI parameters and neocortical cell types by comparing the spatial distribution of the qMRI parameters longitudinal relaxation rate (R1), effective transverse relaxation rate (R2∗), and magnetization transfer saturation (MTsat) to gene expression from the Allen Human Brain Atlas, then combining this with lists of genes enriched in specific cell types found in the human brain. As qMRI parameters are magnetic field strength-dependent, the analysis was performed on MRI data at 3T and 7T. All qMRI parameters significantly covaried with genes enriched in GABA- and glutamatergic neurons, i.e. they were associated with cytoarchitecture. The qMRI parameters also significantly covaried with the distribution of genes enriched in astrocytes (R2∗ at 3T, R1 at 7T), endothelial cells (R1 and MTsat at 3T), microglia (R1 and MTsat at 3T, R1 at 7T), and oligodendrocytes (R1 at 7T). These results advance the potential use of qMRI parameters as biomarkers for specific cell types.
Caenorhabditis elegansMES-3 is a highly divergent ortholog of the canonical PRC2 component SUZ12
Authors: Snel Berend , van den Heuvel Sander , Seidl Michael F.
Published: April 2022

Polycomb Repressive Complex 2 (PRC2) catalyzes the mono-, di, and trimethylation of histone protein H3 on lysine 27 (H3K27), which is strongly associated with transcriptionally silent chromatin. The functional core of PRC2 is highly conserved in animals and consists of four subunits. One of these, SUZ12, has not been identified in the genetic modelCaenorhabditis elegans, whereasC. elegansPRC2 contains the clade-specific MES-3 protein. Through unbiased sensitive sequence similarity searches complemented by high-quality structure predictions of monomers and multimers, we here demonstrate that MES-3 is a highly divergent ortholog of SUZ12. MES-3 shares protein folds and conserved residues of key domains with SUZ12 and is predicted to interact with core PRC2 members similar to SUZ12 in human PRC2. Thus, in agreement with previous genetic and biochemical studies, we provide evidence thatC. eleganscontains a diverged yet evolutionary conserved core PRC2, like other animals.
Probing Notch1-Dll4 Signaling in Regulating Osteogenic Differentiation of Human Mesenchymal Stem Cells using Single Cell Nanobiosensor
Authors: Zhao Yuwen , Yang Rui , Bousraou Zoe , Richardson Kiarra , Wang Shue
Published: April 2022

Human mesenchymal stem cells (hMSCs) have great potential in cell-based therapies for tissue engineering and regenerative medicine due to their self-renewal and multipotent properties. Recent studies indicate that Notch1-Dll4 signaling is an important pathway in regulating osteogenic differentiation of hMSCs. However, the fundamental mechanisms that govern osteogenic differentiation are poorly understood due to a lack of effective tools to detect gene expression at single cell level. Here, we established a double-stranded locked nucleic acid (LNA)/DNA (LNA/DNA) nanobiosensor for gene expression analysis in single hMSC in both 2D and 3D microenvironments. We first characterized this LNA/DNA nanobiosensor and demonstrated the Dll4 mRNA expression dynamics in hMSCs during osteogenic differentiation. By incorporating this nanobiosensor with live hMSCs imaging during osteogenic induction, we performed dynamic tracking of hMSCs differentiation and Dll4 mRNA gene expression profiles of individual hMSC during osteogenic induction. Our results showed the dynamic expression profile of Dll4 during osteogenesis, indicating the heterogeneity of hMSCs during this dynamic process. We further investigated the role of Notch1-Dll4 signaling in regulating hMSCs during osteogenic differentiation. Pharmacological perturbation is applied to disrupt Notch1-Dll4 signaling to investigate the molecular mechanisms that govern osteogenic differentiation. In addition, the effects of Notch1-Dll4 signaling on hMSCs spheroids differentiation were also investigated. Our results provide convincing evidence supporting that Notch1-Dll4 signaling is involved in regulating hMSCs osteogenic differentiation. Specifically, Notch1-Dll4 signaling is active during osteogenic differentiation. Our results also showed that Dll4 is a molecular signature of differentiated hMSCs during osteogenic induction. Notch inhibition mediated osteogenic differentiation with reduced Alkaline Phosphatase (ALP) activity. Lastly, we elucidated the role of Notch1-Dll4 signaling during osteogenic differentiation in a 3D spheroid model. Our results showed that Notch1-Dll4 signaling is required and activated during osteogenic differentiation in hMSCs spheroids. Inhibition of Notch1-Dll4 signaling mediated osteogenic differentiation and enhanced hMSCs proliferation, with increased spheroid sizes. Taken together, the capability of LNA/DNA nanobiosensor to probe gene expression dynamics during osteogenesis, combined with the engineered 2D/3D microenvironment, enables us to study in detail the role of Notch1-Dll4 signaling in regulating osteogenesis in 2D and 3D microenvironment. These findings will provide new insights to improve cell-based therapies and organ repair techniques.
Genome structures resolve the early diversification of teleost fishes
Authors: Parey Elise , Louis Alexandra , Montfort Jerome , Bouchez Olivier , Roques Céline , Iampietro Carole , Lluch Jerome , Castinel Adrien , Donnadieu Cécile , Desvignes Thomas , Bucao Christabel Floi , Jouanno Elodie , Wen Ming , Mejri Sahar , Dirks Ron , Jansen Hans , Henkel Christiaan , Chen Wei-Jen , Zahm Margot , Cabau Cédric , Klopp Christophe , Thompson Andrew W. , Robinson-Rechavi Marc , Braasch Ingo , Lecointre Guillaume , Bobe Julien , Postlethwait John H. , Berthelot Camille , Crollius Hugues Roest , Guiguen Yann
Published: April 2022

Accurate species phylogenies are a prerequisite for evolutionary research. Teleosts are by far the largest and the most diversified group of extant vertebrates, but relationships among the three oldest lineages of extant teleosts remain unresolved. Based on seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (bony-tongues) in a monophyletic group sister to all other teleosts, i.e., the Clupeocephala lineage. This finding resolves over 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.

One-Sentence Summary

Whole-genome analyses place Elopomorpha (tarpons, eels) and Osteoglossomorpha (bony-tongues) as sister groups at the deepest branching of crown teleosts.
mulEEG: A Multi-View Representation Learning on EEG Signals
Authors: Kumar Vamsi , Reddy Likith , Sharma Shivam Kumar , Dadi Kamalakar , Yarra Chiranjeevi , Raju Bapi , Rajendran Srijithesh
Published: April 2022

Modeling effective representations using multiple views that positively influence each other is challenging, and the existing methods perform poorly on Electroencephalogram (EEG) signals for sleepstaging tasks. In this paper, we propose a novel multi-view self-supervised method (mulEEG) for unsupervised EEG representation learning. Our method attempts to effectively utilize the complementary information available in multiple views to learn better representations. We introduce diverse loss that further encourages complementary information across multiple views. Our method with no access to labels, beats the supervised training while outperforming multi-view baseline methods on transfer learning experiments carried out on sleep-staging tasks. We posit that our method was able to learn better representations by using complementary multi-views. †
Parvalbumin basket cell myelination accumulates axonal mitochondria to internodes
Authors: Kole Koen , Voesenek Bas J. B. , Brinia Maria E. , Petersen Naomi , Kole Maarten H. P.
Published: April 2022

Parvalbumin-expressing (PV+) basket cells are fast-spiking interneurons that exert critical control over local neuronal circuit activity and oscillations. PV+interneuron axons are partially myelinated but the electrical and metabolic roles of myelin in axonal functions remain poorly understood. Here, we developed Cre-dependent AAV vectors for cell type-specific investigation of mitochondria with genetically encoded fluorescent probes. Single-cell reconstructions and mining of ultrastructural data revealed that mitochondria selectively cluster to myelinated segments of PV+basket cell axons. Cuprizone-induced demyelination abolished mitochondrial clustering in PV+axons but increased axonal mitochondrial densities in excitatory axons. The internodal clustering of mitochondria was preserved with genetic deletion of myelin basic protein, suggesting that noncompacted myelin is sufficient. Finally, two-photon imaging of action potential-evoked mitochondrial calcium (mt-Ca2+) responses showed that internodal mitochondria did not contribute in buffering activity-dependent Ca2+influx. These findings suggest that oligodendrocyte-PV+axon signaling assembles mitochondria to branch selectively fine-tune metabolic demands.
Lipidoid nanoparticles increase ATP uptake into hypoxic brain endothelial cells
Authors: Khare Purva , Conway James F. , Manickam Devika S
Published: April 2022

Lipidoid nanoparticles (LNPs) are clinically successful carriers for nucleic acid delivery to liver and muscle targets. Their ability to load and deliver small molecule drugs has not been reported yet. We propose that the delivery of adenosine triphosphate (ATP) to brain endothelial cells (BECs) lining the blood-brain barrier may increase cellular energetics of the injured BECs. We formulated and studied the physicochemical characteristics of ATP-loaded LNPs using the C12-200 ionizable cationic lipid and other helper lipids. Polyethylene glycol-dimyristoyl glycerol (PEG-DMG), one of the helper lipids, played a crucial role in maintaining colloidal stability of LNPs over time whereas the inclusion of both ATP and PEG-DMG maintained the colloidal stability of LNPs in the presence of serum proteins. ATP-LNPs formulated with PEG-DMG resulted in a 7.7- and 6.6-fold increased uptake of ATP into normoxic and hypoxic BECs, respectively. Altogether, our results demonstrate the potential of LNPs as a novel carrier for the delivery of small molecular mass actives to BECs—a CNS target.

Highlights

LNPs were formulated with ATP, a small molecule drug

PEG-DMG plays a critical role in maintaining particle stability over tim

ATP and PEG-DMG play a critical role in maintaining particle stability in 10% serum

ATP-LNPs were internalized by normoxic and hypoxic brain endothelial cells (BECs)

LNP delivery to BECs broadens its applicability to CNS targets

Graphical Abstract
Subtractive proteomics analysis to uncover the potent drug targets for distinctive drug design of Candida auris
Authors: Islam Bappy Md. Nazmul , Robin Tanjin Barketullah , Prome Anindita Ash , Laskar Fayeza Sadia , Roy Anindita , Akter Hafsa , Zinnah Kazi Md. Ali
Published: April 2022

Candida auris is a serious health concern of current world that possess serious global health threat and is emerging at a high rate. Available antifungal drugs are failing to combat this pathogen as they are growing resistance toward those drugs and some strains have already showed resistant to all three available antifungal drugs in the market. Finding alternative treatments is a must, therefore, to save lives from this foe. To make the way easier for developing new treatments, we have made some insilico analysis of this pathogen to identify suitable targets for designing drugs and also suggested some potential metabolites to test in vivo condition after some computational analysis. After the subtraction of duplicate, non-essential, human homologs, non-metabolic, human microbiome similar and druggable proteins we ended up with three proteins (XP_028890156.1, XP_028891672.1 and XP_028891858.1) from a total of 5441 C. auris proteins. Blocking those proteins will result in the destruction of the pathogen while the host will remain safe from unintentional blocking. Their subcellular locations and interaction with high number of proteins also indicate their suitability as drug target candidates. After analyzing in silico docking of 29 potential antifungal from plant origin with those three proteins we selected Caledonixanthone E, Viniferin, Glaucine, Jatrorrhizine as the most potent weapon to block those proteins as they showed higher binding affinity. Furthermore, they were predicted to be safe and also showed proper ADME properties (Figure 1).
Neuronal HLH-30/TFEB modulates muscle mitochondrial fragmentation to improve thermoresistance in C. elegans
Authors: Wong Shi Quan , Ryan Catherine J , Lapierre Louis R
Published: April 2022

Transcription factor EB (TFEB) is a conserved master transcriptional activator of autophagy and lysosomal genes that modulates organismal lifespan regulation and stress resistance. As neurons can coordinate organism-wide mechanisms, we investigated the role of neuronal TFEB in stress resistance and longevity. To this end, the C. elegans TFEB orthologue, hlh-30, was rescued panneuronally in hlh-30 loss of function mutants. While important in the long lifespan of daf-2 animals, neuronal hlh-30 was not sufficient to restore normal lifespan in short-lived hlh-30 mutants. However, neuronal HLH-30/TFEB rescue mediated robust improvements in the heat stress resistance of wild-type but not daf-2 animals. Notably, these mechanisms can be uncoupled, as neuronal HLH-30/TFEB regulates longevity and thermoresistance dependently and independently of DAF-16/FOXO respectively. Through transcriptomics profiling and functional analysis, we identified the uncharacterized gene W06A11.1 as a bona fide mediator of heat stress resistance via the induction of mitochondrial fragmentation in distal muscles. Neuron-to-muscle communication occurred through a modulation of neurotransmission. Taken together, this study uncovers a novel mechanism of heat stress protection mediated by neuronal HLH-30/TFEB.
Human Platelet Lysate as Alternative of Fetal Bovine Serum for Enhanced Human in vitro Bone Resorption and Remodeling
Authors: de Wildt Bregje W.M. , Ito Keita , Hofmann Sandra
Published: April 2022

To study human physiological and pathological bone remodeling while addressing the principle of replacement, reduction and refinement of animal experiments (3Rs), human in vitro bone remodeling models are being developed. Despite increasing safety-, scientific-, and ethical concerns, fetal bovine serum (FBS), a nutritional medium supplement, is still routinely used in these models. To comply with the 3Rs and to improve the reproducibility of such in vitro models, xenogeneic-free medium supplements should be investigated. Human platelet lysate (hPL) might be a good alternative as it has been shown to accelerate osteogenic differentiation of mesenchymal stromal cells (MSCs) and improve subsequent mineralization. However, for a human in vitro bone model, hPL should also be able to adequately support osteoclastic differentiation and subsequent bone resorption. In addition, optimizing co-culture medium conditions in mono-cultures might lead to unequal stimulation of co-cultured cells. Here, we compared supplementation with 10% FBS vs. 10%, 5%, and 2.5% hPL for osteoclast formation and resorption by human monocytes (MCs) in mono-culture and in co-culture with (osteogenically stimulated) human MSCs. Our results indicate that the supplementation of hPL can lead to a less donor-dependent and more homogeneous osteoclastic differentiation of MCs when compared to supplementation with 10% FBS. In co-cultures, osteoclastic differentiation and resorption in the 10% FBS group was almost completely inhibited by MSCs, while the supplementation with hPL still allowed for resorption, mostly at low concentrations. The addition of hPL to osteogenically stimulated MSC mono- and MC-MSC co-cultures resulted in osteogenic differentiation and bone-like matrix formation, mostly at high concentrations. Therefore, we conclude that hPL could support both osteoclastic differentiation of human MCs and osteogenic differentiation of human MSCs in mono- and in co-culture, and that this can be balanced by the hPL concentration. Thus, the use of hPL could limit the need for FBS, which is currently commonly accepted for in vitro bone remodeling models.
Dispersal and Plant Arrangement Condition the Timing and Magnitude of Coffee Rust Infection
Authors: Van Cauwelaert Emilio Mora , González Cecilia González , Boyer Denis , Forooshani Zachary Hajian , Vandermeer John , Benítez Mariana
Published: April 2022

One central issue in coffee-leaf rust (Hemileia vastatrix) epidemiology is to understand what determines the intensity and the timing of yearly infections in coffee plantations. However, most experimental and theoretical studies report infection as an average at the plot level, obscuring the role of potentially key factors like rust dispersal or the planting pattern. Here, we first review the rust epidemic patterns of different sites, which reveal large variability in the duration and magnitude of the different epidemiologic phases. We then present a spatially explicit and parametrised model, where the host population is subdivided into discrete patches linked through spore dispersal, modelled as simple diffusion. With this model, we study the role of the planting arrangement, the dispersal intensity and plant-level variables on the maximum average tree infection (MATI) and its timing. Our results suggest that the epidemic timeline can be divided into two phases: a time lag and a growth phaseper se. The model shows that the combination of the dispersal magnitude and plant aggregation modifies the MATI and the time to MATI, mainly by preventing some plants from reaching their maximum peak during the epidemic. It also affects the epidemic curves, which can have a stepped, or a rather smooth pattern in plots with otherwise similar conditions. The initial rust infection modulates the time lag before the epidemic and the infected leaf-fall rate drastically changes the MATI. These findings highlight the importance of explicitly considering the spatial aspects of coffee agroecosystems when measuring and managing rust infection, and help us to further understand the spatio-temporal dynamics of ecological systems in general.
The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats
Authors: Munro Daniel , Wang Tengfei , Chitre Apurva S , Polesskaya Oksana , Ehsan Nava , Gao Jianjun , Gusev Alexander , Solberg Woods Leah C , Saba Laura M , Chen Hao , Palmer Abraham A , Mohammadi Pejman
Published: April 2022

Heterogeneous Stock (HS) rats are a genetically diverse outbred rat population that is widely used for studying genetics of behavioral and physiological traits. Mapping Quantitative Trait Loci (QTL) associated with transcriptional changes would help to identify mechanisms underlying these traits. We generated genotype and transcriptome data for five brain regions from 88 HS rats. We identified 21,392 cis-QTLs associated with expression and splicing changes across all five brain regions and validated their effects using allele specific expression data. We identified 80 cases where eQTLs were colocalized with genome-wide association study (GWAS) results from nine physiological traits. Comparing our dataset to human data from the Genotype-Tissue Expression (GTEx) project, we found that the HS rat data yields twice as many significant eQTLs as a similarly sized human dataset. We also identified a modest but highly significant correlation between genetic regulatory variation among orthologous genes. Surprisingly, we found less genetic variation in gene regulation in HS rats relative to humans, though we still found eQTLs for the orthologs of many human genes for which eQTLs had not been found. These data are available from the RatGTEx data portal (RatGTEx.org) and will enable new discoveries of the genetic influences of complex traits.
Neuro-cognitive models of single-trial EEG measures describe latent effects of spatial attention during perceptual decision making
Authors: Ghaderi-Kangavari Amin , Rad Jamal Amani , Parand Kourosh , Nunez Michael D.
Published: April 2022

Visual perceptual decision-making involves multiple components including visual encoding, attention, accumulation of evidence, and motor execution. Recent research suggests that EEG oscillations can identify the time of encoding and the onset of evidence accumulation during perceptual decision-making. Although scientists show that spatial attention improves participant performance in decision making, little is know about how spatial attention influences the individual cognitive components that gives rise to that improvement in performance. We found evidence in this work that both visual encoding time (VET) before evidence accumulation and other non-decision time process after or during evidence accumulation are influenced by spatial top-down attention, but not evidence accumulation itself. Specifically we used an open-source data set in which participants were informed about the location of a target stimulus in the visual field on some trials during a face-car perceptual decision-making task. Fitting neural drift-diffusion models to response time, accuracy, and single-trial N200 latencies (~ 125 to 225 ms post-stimulus) of EEG allowed us to separate the processes of visual encoding and the decision process from other non-decision time processes such as motor execution. These models were fit in a single step in a hierarchical Bayesian framework. Model selection criteria and comparison to model simulations show that spatial attention manipulates both VET and other non-decision time process. We discuss why spatial attention may affect other non-evidence accumulation processes, such as motor execution time (MET), and why this may seem unexpected given the literature. We make recommendations for future work on this topic.
Production of adaptive movement patterns via an insect inspired Spiking Neural Network Central Pattern Generator
Authors: Steinbeck Fabian , Nowotny Thomas , Philippides Andy , Graham Paul
Published: April 2022

Navigation in ever-changing environments requires effective motor behaviours. Many insects have developed adaptive movement patterns which increase their success in achieving navigational goals. A conserved brain area in the insect brain, the Lateral Accessory Lobe, is involved in generating small scale search movements which increase the efficacy of sensory sampling. When the reliability of an essential navigational stimulus is low, searching movements are initiated whereas if the stimulus reliability is high, a targeted steering response is elicited. Thus the network mediates an adaptive switching between motor patterns. We developed Spiking Neural Network models to explore how an insect inspired architecture could generate adaptive movements in relation to changing sensory inputs. The models are able to generate a variety of adaptive movement patterns, the majority of which are of the zig-zagging kind, as seen in a variety of insects. Furthermore, these networks are robust to noise. Because a large spread of network parameters lead to the zig-zagging movement dynamics, we conclude that the investigated network architecture is inherently well suited to generating adaptive movement patterns.
Mathematical Modeling of Rhesus Cytomegalovirus (RhCMV) Placental Transmission in Seronegative Rhesus Macaques
Authors: Gong Yishu , Moström Matilda , Otero Claire , Valencia Sarah , Kaur Amitinder , Permar Sallie R. , Chan Cliburn
Published: April 2022

Approximately 1 in 200 infants is born with congenital cytomegalovirus (CMV), making it the most common congenital infection. About 1 in 5 congenitally-infected babies will suffer long-term sequelae, including sensorineural deafness, intellectual disability, and epilepsy. CMV infection is highly species-dependent, and the Rhesus CMV (RhCMV) infection of rhesus monkey fetuses is the only animal model that replicates essential features of congenital CMV infection in humans, including placental transmission, fetal disease, and fetal loss. To better understand the determinants and dynamics of congenital CMV transmission, we developed a mathematical model for placental transmission, comprising of maternal, placental, and fetal compartments using parameters from literature and experimental data from RhCMV seronegative rhesus macaques inoculated with RhCMV at 7.7-9.0 weeks of pregnancy. The model was then used to study the effect of the timing of inoculation, maternal immune suppression, and hyper-immune globulin infusion on the risk of placental transmission in the context of primary and reactivated chronic maternal CMV infection.

Author summary

Congenital cytomegalovirus (CMV) is the most common congenital infection in humans. Congenial CMV affects 1 in 200 infants, and can result in sensorineural deafness, intellectual disability, epilepsy, and death. The Rhesus CMV (RhCMV) model is the only animal model that replicates essential features of congenital CMV infection and fetal sequelae in humans and provides a critical experimental system to develop mechanistic insight. We propose a novel mathematical model for CMV transmission that integrates viral dynamics in the maternal, placental, and fetal compartments. We calibrate the model using data from RhCMV transmission experiments and show that the model can recapitulate experimental observations of primary versus reactivated chronic CMV infection in pregnancy, primary infection at different stages in pregnancy, and infection in the presence of varying degrees of immune suppression and hyper-immune globulin infusion. Our in-silico model provides a means to rapidly explore mechanistic hypotheses for the physical, viral, and immune determinants of CMV transmission to complement and support expensive and difficult experiments on non-human primates.
Genome-wide analysis reveals PhoP regulates pathogenicity in Riemerella anatipestifer
Authors: Zhang Yang , Wang Ying , Zhang Yanhao , Jia Xiangchao , Li Chenxi , Zhou Zutao , Hu Sishun , Li Zili
Published: April 2022

Duck infectious serositis, also known as the Riemerella anatipestifer disease infects domestic ducks, geese, turkeys, and wild birds. However, the regulatory mechanism of its pathogenicity remains unclear. The phoP/phoR two-component system was first reported in gram-negative bacteria in our previous research and was demonstrated to be involved in virulence and gene expression. Here, the DNA-affinity-purified sequencing (DAP-seq) was applied to further explore the regulation of phoP/phoR to pathogenicity in R. anatipestifer. A conserved motif was identified in the upstream of 583 candidate target genes which were directly regulated by phoP. To further confirm the genes which are regulated by phoP/phoR, phoR and phoP, the single-gene deletion strains were constructed. The results of transcriptome analysis using next-generation RNA sequencing showed 136 differential expression genes (DEGs) between ΔphoP and RA-YM, and 183 DEGs between ΔphoR and WT. The candidate target genes of PhoP were further identified by combining transcriptome analysis and DAP-seq. The results of DAP-seq and RNA-seq of ΔphoP in combination revealed that the main direct regulons of PhoP are located on the membrane and PhoP is involved in regulating aerotolerance. Using the in vivo duck model, the pathogenicity of ΔphoP or ΔphoR was significantly lower than that of the WT. Together, our findings provided a perception about the direct regulation of PhoP and suggested that phoP/phoR is essential for the pathogenicity of R. anatipestifer, and phoP/phoR is related to the aerotolerance of R. anatipestifer. The gene deletion strains are expected to be the candidate live vaccine strains of R. anatipestifer which can be used as ideal genetic engineering vector strains for the expression of foreign antigens.

Author summary

Riemerella anatipestifer is a severe pathogen in the poultry industry with high mortality in ducks and geese mainly due to acute septicemia and infectious polyserositis. A two-component system phoP/phoR was previously characterized in R. anatipestifer, and the phoP/phoR TCS was reported for the first time in Gram-negative bacteria. A deleted phoP/phoR in R. anatipestifer has been reported to almost lose its pathogenicity in ducklings. However, the mechanism of phoP/phoR regulating the virulence of R. anatipestifer had not been explored in detail. This study has utilized DAP-seq to explore the DNA-binding sites of PhoP as a response regulator in the global genome. Furthermore, the phoP and phoR were deleted separately and the transcriptomics of the corresponding gene-deleted strains was analyzed. A series of directly regulated genes of phoP/phoR TCS were determined in combination. The duckling model revealed both PhoP and PhoR as essential virulence-related factors of R. anatipestifer.
Myeloid hypoxia-inducible factor HIF1A provides cardio-protection during ischemia and reperfusion via induction of netrin-1
Authors: Heck-Swain Ka Lin , Li Jiwen , Ruan Wei , Yuan Xiaoyi , Wang Yanyu , Koeppen Michael , Eltzschig Holger K.
Published: April 2022

The transcription factor hypoxia-inducible factor HIF1A elicitics cardioprotection from ischemia and reperfusion injury. Here, we investigated tissue-specific pathways that are critical for HIF1A-elicited tissue protection. Initial studies showed that mice with induced global deletion of Hif1a (Hif1aloxP/loxP UbiquitinCre+) have exaggerated myocardial injury during in situ ischemia and reperfusion. Surprisingly, this phenotype was mirrored only in mice with myeloid-specific Hif1a deletion (Hif1aloxP/loxP LysM Cre+). In contrast, mice with myocardial specific (Hif1aloxP/loxP Myosin Cre+), or vascular Hif1a deletion (Hif1aloxP/loxP VEcadherin Cre+) experienced similar injury levels as controls. Subsequent studies using adoptive transfer of Hif1a-deficient polymorphonuclear neutrophils (PMNs) prior to myocardial injury demonstrated increased reperfusion injury. In contrast, adoptive transfer of PMNS treated ex-vivo with the HIF stabilizer dimethyloxalylglycine (DMOG) was associated with attenuated myocardial injury. Moreover, cardioprotection mediated by DMOG was abolished in Hif1aloxP/loxP LysM Cre+ mice, but not in Hif2aloxP/loxP LysM Cre+ mice. Finally, studies of PMN-dependent HIF1A target genes implicated the neuronal guidance molecule netrin-1 in mediating the cardioprotective effects of myeloid HIF1A. Taken together, the present studies identified a functional role for myeloid-expressed HIF1A in providing cardio-protection during ischemia and reperfusion injury, which - at least in part - is mediated by the induction of neuronal guidance molecule netrin-1 in neutrophils.
Natural and human-mediated drivers of microevolution in Neotropical palms: a historical genomics approach
Authors: Brousseau Louise , Santoni Sylvain , Weber Audrey , Odonne Guillaume
Published: April 2022

Microevolution in Amazonia has been far less documented than in temperate regions and still constitutes a major knowledge gap. Moreover, the actual influence of pre-Columbian societies through the Holocene remains unclear, although it could provide interesting insights on the relationship between natural and human-mediated evolutionary processes in driving microevolution.

Because they are widespread and traditionally managed since pre-Columbian times, Neotropical palms are choice models to investigate the drivers of microevolution in Amazonia. In this study, we carried out a preliminary exploration of the genomic diversity in two pairs of congeneric palm species in French Guiana (Astrocaryumspp. andOenocarpusspp.).

We built upon an original sampling design, taking into account both regional climate variations and local-scale pre-Columbian occupation, and designed a new target capture kit of 20,000 molecular probes scattered across exonic regions of more than 5,000 nuclear genes in Arecoïdeae (“ARECO5000+”). Hundreds of palm libraries were sequenced through Illumina sequencing, providing a unique – high-coverage – genomic dataset in these non-model species.

We explored patterns of genomic diversity and differentiation within and across populations, bringing state-of-the-art knowledge about the roles of climate adaptation and pre-Columbian domestication. By documenting original cases of “incipient” domestication, these pioneer results open new avenues toward a better understanding of microevolution in Amazonia and of the impact of pre-Columbian societies on present-day biodiversity patterns.
Targeting RNA:Protein Interactions with an Integrative Approach Leads to the Identification of Potent YB-1 Inhibitors
Authors: El Hage Krystel , Babault Nicolas , Maciejak Olek , Desforges Bénédicte , Craveur Pierrick , Steiner Emilie , Rengifo-Gonzalez Juan Carlos , Henrie Hélène , Clément Marie-Jeanne , Joshi Vandana , Bouhss Ahmed , Wang Liya , Bauvais Cyril , Pastré David
Published: April 2022

RNA-binding proteins are promising targets for developing new molecules of therapeutic interest. Nevertheless, targeting RNA:Protein interfaces is hampered by the lack of methods able to detect these interactions in cells while being amenable to High Content Screening. Here, we adapt the microtubule bench assay to score small molecules targeting interactions of endogenous mRNA with a specific protein in cells and demonstrate its robustness by targeting YB-1 (YBX-1 gene), a mRNA-binding protein involved in cancer progression and resistance to chemotherapy. The implementation of an integrative approach led to the identification of 22 hits validated by NMR and MD simulations of which 11 were found to significantly interfere with the binding of mRNA to YB-1 in cells at low micromolar concentrations. One of our leads is P1, an FDA-approved PARP-1 inhibitor. This work shows the potential of our integrative approach and paves the way for the development of RNA:Protein Interaction inhibitors.