bluuebunny/crossref_metadata_2025 huggingface dataset:
The Aedes aegypti peritrophic matrix controls arbovirus vector competence through HPx1, a heme–induced peroxidase
Authors: Talyuli Octavio A. C. , Oliveira Jose Henrique M. , Bottino-Rojas Vanessa , Silveira Gilbert O. , Alvarenga Patricia H. , Kantor Asher M. , Paiva-Silva Gabriela O. , Barillas-Mury Carolina , Oliveira Pedro L.
Published: June 2022

Aedes aegypti mosquitoes are the main vectors of arboviruses. The peritrophic matrix (PM) is an extracellular layer that surrounds the blood bolus and acts as an immune barrier that prevents direct contact of bacteria with midgut epithelial cells during blood digestion. Here, we describe a heme-dependent peroxidase, hereafter referred to as heme peroxidase 1 (HPx1). HPx1 promotes PM assembly and antioxidant ability, modulating vector competence. Mechanistically, the heme presence in a blood meal induces HPx1 transcriptional activation mediated by the E75 transcription factor. HPx1 knockdown increases midgut reactive oxygen species (ROS) production by the DUOX NADPH oxidase. Elevated ROS levels reduce microbiota growth while enhancing epithelial mitosis, a response to tissue damage. However, simultaneous HPx1 and DUOX silencing was not able to rescue bacterial population growth, as explained by increased expression of antimicrobial peptides (AMPs), which occurred only after double knockdown. This result revealed hierarchical activation of ROS and AMPs to control microbiota. HPx1 knockdown produced a 100-fold decrease in Zika and Dengue 2 midgut infection, demonstrating the essential role of the mosquito PM in the modulation of arbovirus vector competence. Our data show that the PM connects blood digestion to midgut immunological sensing of the microbiota and viral infections.
PPP2R1A Regulates Migration Persistence through the WAVE Shell Complex
Authors: Wang Yanan , Chiappetta Giovanni , Guérois Raphaël , Romero Stéphane , Krause Matthias , Dessalles Claire , Babataheri Avin , Barakat Abdul I. , Vinh Joelle , Polesskaya Anna , Gautreau Alexis M.
Published: June 2022

The RAC1-WAVE-Arp2/3 signaling pathway generates branched actin networks that power lamellipodium protrusion of migrating cells. Feedback is thought to control protrusion lifetime and migration persistence, but its molecular circuitry remains elusive. Using proteomics, we identified PPP2R1A among proteins differentially associated with the WAVE complex subunit ABI1 when RAC1 was activated and downstream generation of branched actin was blocked. PPP2R1A was found to associate at the lamellipodial edge with a novel form of WAVE complex, the WAVE Shell Complex (WSC), that contains NHSL1 instead of the Arp2/3 activating subunit WAVE as in the canonical WAVE Regulatory Complex (WRC). PPP2R1A was required for persistence in random and directed migration assays and for RAC1-dependent actin polymerization in cell extracts. PPP2R1A requirement was abolished by NHSL1 depletion. PPP2R1A mutations found in tumors impaired WSC binding and migration regulation, suggesting that this novel function of PPP2R1A is critical for its tumor suppressor activity.
The extracellular RNA pool within Zea mays apoplast: composition and differential expression during Ustilago maydis infection
Authors: Mukherjee Dibya , Singh Nagendra Pratap , Roy Anisha , Mondal Rituparna , Acharya Udita , Chattopadhyay Debasis , Ghosh Anupama
Published: June 2022

The existence of an extracellular pool of RNA (exRNA) has been documented in both animal and plant cells in a number of instances. These exRNA species play important role in host response against different environmental stimuli. The mechanism of their function however remains largely unknown. In this study we report the composition of the exRNA pool within the leaf apoplast of Z. mays under normal growth condition. We could detect RNA transcripts originating from both the genic as well as the intergenic regions of the nuclear, mitochondrial and chloroplast genomes of maize in our exRNA sequencing data. Our data showed increased abundance of about 75% of the exRNA transcripts during infection with a basidiomycete smut fungi, Ustilago maydis. Functional classification of the differentially abundant exRNA transcripts within U. maydis SG200 WT infected maize apoplast with respect to uninfected apoplast revealed significant enrichment of the exRNA transcripts corresponding to the ribosome biogenesis pathway. Data related to the effect of two extracellular T2 type ribonucleases, Nuc1 and Nuc2 from U. maydis on the composition of exRNA pool of maize is also presented.
Robust deep learning based protein sequence design using ProteinMPNN
Authors: Dauparas J. , Anishchenko I. , Bennett N. , Bai H. , Ragotte R. J. , Milles L. F. , Wicky B. I. M. , Courbet A. , de Haas R. J. , Bethel N. , Leung P. J. Y. , Huddy T. F. , Pellock S. , Tischer D. , Chan F. , Koepnick B. , Nguyen H. , Kang A. , Sankaran B. , Bera A. K. , King N. P. , Baker D.
Published: June 2022

While deep learning has revolutionized protein structure prediction, almost all experimentally characterized de novo protein designs have been generated using physically based approaches such as Rosetta. Here we describe a deep learning based protein sequence design method, ProteinMPNN, with outstanding performance in both in silico and experimental tests. The amino acid sequence at different positions can be coupled between single or multiple chains, enabling application to a wide range of current protein design challenges. On native protein backbones, ProteinMPNN has a sequence recovery of 52.4%, compared to 32.9% for Rosetta. Incorporation of noise during training improves sequence recovery on protein structure models, and produces sequences which more robustly encode their structures as assessed using structure prediction algorithms. We demonstrate the broad utility and high accuracy of ProteinMPNN using X-ray crystallography, cryoEM and functional studies by rescuing previously failed designs, made using Rosetta or AlphaFold, of protein monomers, cyclic homo-oligomers, tetrahedral nanoparticles, and target binding proteins.

One-sentence summary

A deep learning based protein sequence design method is described that is widely applicable to current design challenges and shows outstanding performance in both in silico and experimental tests.
Selection on plastic adherence leads to hyper-multicellular strains and incidental virulence in the budding yeast
Authors: Ekdahl Luke I. , Salcedo Juliana A. , Dungan Matthew M. , Mason Despina V. , Myagmarsuren Dulguun , Murphy Helen A.
Published: June 2022

Many disease-causing microbes are not obligate pathogens; rather, they are environmental microbes taking advantage of an ecological opportunity. The existence of microbes that are not normally pathogenic, yet are well-suited to host exploitation, is an evolutionary paradox. One hypothesis posits that selection in the environment may favor traits that incidentally lead to pathogenicity and virulence, or serve as pre-adaptations for survival in a host. An example of such a trait is surface adherence. To experimentally test the idea of “accidental virulence”, replicate populations of the yeast, Saccharomyces cerevisiae, which can be an opportunistic pathogen, were evolved to attach to a plastic bead for hundreds of generations. Along with plastic adherence, two multicellular phenotypes— biofilm formation and flor formation— increased; another phenotype, pseudohyphal growth, responded to the nutrient limitation. Thus, experimental selection led to the evolution of highly-adherent, hyper-multicellular strains. Wax moth larvae injected with evolved hyper-multicellular strains were significantly more likely to die than those injected with evolved non-multicellular strains. Hence, selection on plastic adherence incidentally led to the evolution of enhanced multicellularity and increased virulence. Our results support the idea that selection in the environment for a trait unrelated to virulence can inadvertently generate opportunistic, “accidental” pathogens.
Wetting and complex remodeling of membranes by biomolecular condensates
Authors: Mangiarotti Agustín , Chen Nannan , Zhao Ziliang , Lipowsky Reinhard , Dimova Rumiana
Published: June 2022

Cells compartmentalize their components in liquid-like condensates, which can be reconstitutedin vitro. Although these condensates interact with membrane-bound organelles, the potential of membrane remodeling and the underlying mechanisms are not well understood. Here, we demonstrate that interactions between protein condensates (including hollow ones) and membranes can lead to remarkable morphological transformations and describe these with theory. Modulation of solution salinity or membrane composition drives the condensate-membrane system through two wetting transitions, from dewetting, through a broad regime of partial wetting, to complete wetting. A new phenomenon, namely fingering or ruffling of the condensate-membrane interface is observed when sufficient membrane area is available, producing intricately curved structures. The observed morphologies are governed by the interplay of adhesion, membrane elasticity, and interfacial tension. Our results highlight the relevance of wetting in cell biology, and pave the way for the design of synthetic membrane-droplet based biomaterials and compartments with tunable properties.
Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss
Authors: Larouche Jacqueline A. , Wallace Emily C. , Spence Bonnie D. , Johnson Scott A. , Kulkarni Mangesh , Buras Eric , Brown Bryan N. , Badylak Stephen F. , Aguilar Carlos A.
Published: June 2022

Volumetric muscle loss (VML) is an acute trauma that results in persistent inflammation, supplantation of muscle tissue with fibrotic scarring, and decreased muscle function. The cell types, nature of cellular communication and tissue locations that drive the aberrant VML response have remained elusive. Herein, we used spatial transcriptomics integrated with single-cell RNA sequencing on mouse and canine models administered VML. We observed VML engenders a unique spatial pro-fibrotic pattern driven by crosstalk between macrophages and fibro-adipogenic progenitors that was conserved between murine and canine models albeit with varying kinetics. This program was observed to restrict muscle stem cell mediated repair and targeting this circuit in a murine model resulted in increased regeneration and reductions in inflammation and fibrosis. Collectively, these results enhance our understanding of the immune cell-progenitor cell-stem cell crosstalk that drives regenerative dysfunction and provides further insight into possible avenues for fibrotic therapy exploration.
NOS2 and COX2 Blockade Limits TNBC Disease Progression and Alters CD8+T Cell Spatial Orientation and Density
Authors: Somasundaram Veena , Ridnour Lisa A , Cheng Robert YS , Walke Abigail J , Kedei Noemi , Bhattacharyya Dibyangana D , Wink Adelaide L , Edmondson Elijah F , Butcher Donna , Warner Andrew , Dorsey Tiffany H , Scheiblin David A , Heinz William , Bryant Richard J. , Kinders Robert , Lipkowitz Stanley , Wong Stephen TC , Pore Milind , Hewitt Stephen M. , McVicar Daniel W , Anderson Stephen K , Chang Jenny , Glynn Sharon A , Ambs Stefan , Lockett Stephen J. , Wink David A
Published: June 2022

Anti-tumor immune polarization is a key predictor of clinical outcomes to cancer therapy. An emerging concept influencing clinical outcome involves the spatial location of CD8+T cells, within the tumor. Our earlier work demonstrated immunosuppressive effects of NOS2/ COX2 tumor expression. Here, we show that NOS2/COX2 levels influence the polarization and spatial location of lymphoid cells including CD8+T cells. Importantly, elevated tumor NOS2/COX2 correlated with exclusion of CD8+T cells from the tumor epithelium. In contrast, tumors expressing low NOS2/COX2 had increased CD8+T cell penetration into the tumor epithelium. Consistent with a causative relationship between these observations, pharmacological inhibition of COX2 with indomethacin dramatically reduced tumor growth of the 4T1 model of TNBC in bothWTandNos2-/-mice. This regimen led to complete tumor regression in ∼20% of tumor-bearingNos2-/-mice, and these animals were resistant to tumor rechallenge. Th1 cytokines were elevated in the blood of treated mice and intratumoral CD4+and CD8+T cells were higher in mice that received indomethacin when compared to control untreated mice. Multiplex immunofluorescence imaging confirmed our phenotyping results and demonstrated that targeted Nos2/Cox2 blockade improved CD8+T cell penetration into the 4T1 tumor core. These findings are consistent with our observations in low NOS2/COX2 expressing breast tumors` proving that COX2 activity is responsible for limiting the spatial distribution of effector T cells in TNBC. Together these results suggest that clinically available NSAID’s may provide a cost-effective, novel immunotherapeutic approach for treatment of aggressive tumors including triple negative breast cancer.
Protein nanobarcodes enable single-step multiplexed fluorescence imaging
Authors: de Jong-Bolm Daniëlle , Sadeghi Mohsen , Bao Guobin , Klaehn Gabriele , Hoff Merle , Mittelmeier Lucas , Basmanav F. Buket , Opazo Felipe , Noé Frank , Rizzoli Silvio O.
Published: June 2022

Multiplexed cellular imaging typically relies on the sequential application of detection probes, such as antibodies or DNA barcodes, which is complex and time-consuming. To address this, we developed here protein nanobarcodes, composed of combinations of epitopes recognized by specific sets of nanobodies. The nanobarcodes are read in a single imaging step, relying on nanobodies conjugated to distinct fluorophores, which enables a precise analysis of large numbers of protein combinations.
The “Proxitome” of Arabidopsis Processing Bodies Reveals a Condensate-Membrane Interface Instructing Actin-Driven Directional Growth
Authors: Liu Chen , Mentzelopoulou Andriani , Muhammad Amna , Volkov Andriy , Weijers Dolf , Gutierrez-Beltran Emilio , Moschou Panagiotis N.
Published: June 2022

Cellular condensates can comprise membrane-less ribonucleoprotein assemblies with liquid-like properties. These cellular condensates influence various biological outcomes, but their liquidity hampers their isolation and characterization. Here, we investigated the composition of the condensates known as processing bodies (PBs) in the model plant Arabidopsis through a proximity-biotinylation pipeline. Using in situ protein–protein interaction approaches, genetics and high-resolution imaging, we show that PBs comprise networks that interface with membranes. Surprisingly, the conserved component of PBs, DECAPPING PROTEIN 1 (DCP1), can interface with unique plasma membrane subdomains that include cell edges and vertices. We characterized these plasma membrane interfaces and discovered a developmental module that can control cell shape. This module is modulated by the liquid-like properties of DCP1 and the actin-nucleating SCAR–WAVE complex, whereby the DCP1-SCAR–WAVE interaction confines actin nucleation. This study reveals an unexpected repertoire for a conserved condensate at unique membrane-condensate interfaces.
Male sex hormone and reduced plakoglobin jointly impair atrial conduction and cardiac sodium currents
Authors: Sommerfeld Laura C. , Holmes Andrew P. , Yu Ting Y. , O’Shea Christopher , Kavanagh Deirdre M. , Pike Jeremy M. , Wright Thomas , Syeda Fahima , Aljehani Areej , Kew Tania , Cardoso Victor R. , Kabir S. Nashitha , Hepburn Claire , Menon Priyanka M. , Broadway-Stringer Sophie , O’Reilly Molly , Witten Anika , Fortmueller Lisa , Lutz Susanne , Kulle Alexandra , Gkoutos Georgios V. , Pavlovic Davor , Arlt Wiebke , Lavery Gareth G. , Steeds Richard , Gehmlich Katja , Stoll Monika , Kirchhof Paulus , Fabritz Larissa
Published: June 2022

Androgenic anabolic steroids (AAS) are commonly abused by young men. Male sex associates with earlier manifestation of common and rare cardiac conditions including atrial fibrillation and arrhythmogenic right ventricular cardiomyopathy (ARVC). Clinical data suggest an atrial involvement in ARVC. The disease is caused by desmosomal gene defects such as reduced plakoglobin expression. Analysis of clinical records from 146 ARVC patients identified male preponderance and increased prevalence of atrial arrhythmias in patients with definite ARVC. Definite patients displayed ECG changes suggesting atrial remodelling. To study mechanisms of atrial remodelling due to desmosomal vulnerability and AAS, young adult male mice, heterozygously deficient for plakoglobin (Plako+/-) and wildtype (WT) littermates, were chronically exposed to 5α-dihydrotestosterone (DHT) or placebo. DHT increased atrial expression of pro-hypertrophic, fibrotic and inflammatory transcripts. DHT caused atrial conduction slowing, decreased peak sodium current density, reduced action potential amplitude and lowered the peak depolarisation rate in Plako+/- but not WT atria. Super-resolution microscopy revealed a reduction in Nav1.5 clustering in Plako+/- atrial cardiomyocytes following DHT exposure. These data reveal that AAS combined with plakoglobin deficiency cause pathological atrial electrical remodelling in young male hearts. AAS abuse may increase the risk of atrial myopathy in males with desmosomal gene variants.
Systemic Calcitonin Gene-Related Peptide (CGRP) modifies auditory and vestibular end organ electrical potentials, and increases sensory hypersensitivities
Authors: Rahman Shafaqat M. , Faucher Stefanie , Jonnala Raajan , Holt Joseph C. , Lee Choongheon , Luebke Anne E.
Published: June 2022

Migraine is a severe and chronic neurological disorder that affects ∼18% of people worldwide, the majority being female (3:1). It is characterized by recurrent, debilitating headaches and heightened sensory sensitivities. People with migraine may develop vestibular migraine (VM), characterized by a heightened motion sensitivity and preponderance for spontaneous vertigo attacks and balance problems such as postural instability. Calcitonin gene-related peptide (CGRP) is implicated in migraine and is believed to act on brain meninges or in subcortical central nervous system (CNS) structures, and CGRP-based antagonists have shown efficacy for migraine treatment. CGRP also signals at efferent synapses of the cochlea and vestibular end organs, but it is unclear if exogenous CGRP can modulate inner ear function at the end organ level and cause heightened behavioral responses consistent with VM. We tested if intraperitoneally (IP) delivered CGRP to wildtype mice can modulate end organ potentials to sound [via auditory brainstem responses (ABRs)] and jerk stimuli [via vestibular sensory evoked potentials (VsEPs)]. We also assessed behavioral measures of phonophobia [acoustic startle reflex (ASR)] and static imbalance [postural sway-center of pressure (CoP)] after IP CGRP, and observed female mice exhibited heightened sensitivities to IP CGRP in all assays. Male mice showed similar auditory sensitivity and end organ effects to CGRP, but systemic CGRP did not modify male postural sway as it did in females. In conclusion, we show that intraperitoneally delivered CGRP affects ABRs and VsEPs, and elicits behaviors suggestive of auditory hypersensitivity and postural instability in mice related to the phonophobia and postural instability seen in VM patients.

Significance Statement

Calcitonin Gene-Related Peptide (CGRP) has been implicated in migraine, and CGRP-based therapeutics have shown efficacy in the treatment of migraine headaches. CGRP is also present in efferent synapses of the inner ear, so we questioned if increases in systemic CGRP can act directly on inner ear end organs and modify corresponding behavioral responses. In this study, we determined systemic CGRP changes cochlear and vestibular end organ potentials and produces migraine behaviors similar to phonophobia and postural control deficits. Peripheral changes in auditory and vestibular compound action potentials following systemic CGRP administration suggest CGRP can act directly on the inner ear, which provides one site of action for CGRP’s involvement in hypersensitivity to sound and movement in migraine.
Network preservation analysis reveals dysregulated metabolic pathways in human vascular smooth muscle cell phenotypic switching
Authors: Perry R. Noah , Albarracin Diana , Aherrahrou Redouane , Civelek Mete
Published: June 2022

Vascular smooth muscle cells (VSMCs) are key players involved in atherosclerosis, the underlying cause of coronary artery disease (CAD). They can play either beneficial or detrimental roles in lesion pathogenesis, depending on the nature of their phenotypic changes. An in-depth characterization of their gene regulatory networks can help better understand how their dysfunction may impact disease progression. We conducted a gene expression network preservation analysis in aortic SMCs isolated from 151 multi-ethnic heart transplant donors cultured under quiescent or proliferative conditions. We identified 86 groups of co-expressed genes (modules) across the two conditions and focused on the 18 modules that are least preserved between the phenotypic conditions. Three of these modules were significantly enriched for genes belonging to proliferation, migration, cell adhesion, and cell differentiation pathways, characteristic of phenotypically modulated proliferative VSMCs. The majority of the modules, however, were enriched for metabolic pathways consisting of both nitrogen-related and glycolysis-related processes. Therefore, we explored correlations between nitrogen metabolism-related genes and CAD-associated genes and found significant correlations, suggesting the involvement of the nitrogen metabolism pathway in CAD pathogenesis. for six genes in the nitrogen metabolism pathway. We also created gene regulatory networks enriched for genes in glycolysis and predicted key regulatory genes driving glycolysis dysregulation. Our work suggests that dysregulation of VSMC metabolism participates in phenotypic transitioning, which may contribute to disease progression and suggests that AMT and MPI may play an important role in regulating nitrogen and glycolysis related metabolism in SMCs.
Population genomics of an emergent tri-species hybrid zone
Authors: Natola Libby , Seneviratne Sampath S. , Irwin Darren
Published: June 2022

Isolating barriers that drive speciation are commonly studied in the context of two-species hybrid zones. There is however evidence that more complex introgressive relationships are common in nature. Here, we use field observations and genomic analysis, including the sequencing and assembly of a novel reference genome, to study an emergent hybrid zone involving two colliding hybrid zones of three woodpecker species: Red-breasted, Red-naped, and Yellow-bellied Sapsuckers (Sphyrapicus ruber, S. nuchalis, and S. varius). Surveys of the area surrounding Prince George, British Columbia, Canada, show that all three species are sympatric, and Genotyping-by-Sequencing identifies hybrids from each species pair and birds with ancestry from all three species. Observations of mate pair phenotypes and genotypes provide evidence for assortative mating, though there is some heterospecific pairing. Hybridization is more extensive in this tri-species hybrid zone than in two di-species hybrid zones. However, there is no evidence of a hybrid swarm and admixture is constrained to contact zones, so we classify this region as a tension zone and invoke selection against hybrids as a likely mechanism maintaining species boundaries. Analysis of sapsucker age classes does not show disadvantages in hybrid survival to adulthood, so we speculate the selection upholding the tension zone may involve hybrid fecundity. Gene flow among all sapsuckers in di-species hybrid zones suggests introgression likely occurred before the formation of this tri-species hybrid zone, and might result from bridge hybridization, vagrancies, or other three-species interactions.
Cyclin B3 implements timely vertebrate oocyte arrest for fertilization
Authors: Bouftas Nora , Schneider Lena , Halder Marc , Demmig Rebecca , Baack Martina , Cladière Damien , Walter Melanie , Abdallah Hiba Al , Kleinhempel Camilla , Müller Janina , Passarelli Francesca , Wehrle Patrick , Heim Andreas , Wassmann Katja , Mayer Thomas U.
Published: June 2022

To ensure successful offspring ploidy, vertebrate oocytes must halt the cell cycle in meiosis II until sperm entry. Emi2 is essential to keep oocytes arrested until fertilization. Yet, how this arrest is implemented exclusively in meiosis II and not prematurely in meiosis I remained enigmatic. Using mouse and frog oocytes, we show here that cyclin B3, an understudied B- type cyclin, is essential to keep Emi2 levels low in meiosis I. Direct phosphorylation of Emi2 at an evolutionarily highly conserved site by Cdk1/cyclin B3 targets Emi2 for degradation. In contrast, Cdk1/cyclin B1 is inefficient in Emi2 phosphorylation providing a molecular explanation for the requirement of different B-type cyclins for oocyte maturation. Cyclin B3 degradation at exit from meiosis I enables Emi2 accumulation and thus, timely arrest in meiosis II. Our findings illuminate the evolutionarily conserved mechanisms controlling oocyte arrest for fertilization at the correct cell cycle stage, essential for embryo viability.
Saturated cell lysing is critical for high sensitivity microbiome analysis
Authors: Wang Ying , Zhao Cuiping , Lam Yan Y. , Zhao Liping , Wu Guojun
Published: June 2022

Introductory paragraph

For robust DNA-based gut microbiome analysis, all cells in the stool samples need to be lysed. However, no standards have been developed to evaluate a DNA extraction protocol’s capability of lysing all cells and its sensitivity on detecting microbial structural differences among samples. In this study, we incrementally increased the intensity of mechanical lysis and integrated lysozyme pretreatment to Protocol Q (PQ), which was recommended as the best from 21 protocols1. A new protocol (LPQ) was optimized when DNA yield, Gram-positive bacteria ratio, and beta diversity all reached to a plateau with no further significant changes, indicating the achievement of saturated lysing. LPQ detected significant differences among three groups of fiber-treated human stool samples and identified 64 responsive ASVs, while a commercial kit failed to detect any significant treatment effects and PQ only detected 17 responsive ASVs. Therefore, saturated lysing as defined in this study should be adopted for evaluating microbiome DNA extraction protocols.
Summer dynamics of microbial diversity on a mountain glacier
Authors: Hotaling Scott , Price Taylor L. , Hamilton Trinity L.
Published: June 2022

Under climate change, glaciers are rapidly receding worldwide. A melting cryosphere will dramatically alter global sea levels, carbon cycling, and water resource availability. Glaciers also host rich biotic communities that are dominated by microbial diversity and this biodiversity can impact surface albedo, thereby driving a feedback loop between biodiversity and cryosphere melt. However, the microbial diversity of glacier ecosystems remains largely unknown outside of major ice sheets, particularly from a temporal perspective. Here, we characterized temporal dynamics of bacteria, eukaryotes, and algae on the Paradise Glacier, Mount Rainier, USA, over the summer melt season. During our study, the glacier surface steadily darkened as seasonal snow melted and darkening agents accumulated until new snow fell in late September. From a community-wide perspective, the bacterial community remained generally constant and eukaryotes exhibited a clear temporal progression of community change while fungal diversity was intermediate. Individual taxonomic groups, however, exhibited considerable stochasticity. We found little support for our a priori prediction that autotroph abundance would peak before heterotrophs. Notably, two different trends in snow algae emerged—an abundant early-and late-season OTU with a different mid-summer OTU that peaked in August. Overall, our results highlight the need for temporal sampling to clarify microbial diversity on glaciers and that caution should be exercised when interpreting results from single or few timepoints.
A novel Wnt pathway orients Par complex-dependent cell polarity
Authors: Yoshiura Shigeki , Matsuzaki Fumio
Published: June 2022

The Par-complex is a highly conserved cell polarization machinery, playing critical roles in tissue development and homeostasis. However, how extracellular signals globally orient Par-dependent cell polarity in tissues remains poorly understood. We show here that four of seven Drosophila Wnts redundantly serve as directional cues for the Par-dependent cell polarity of neural stem cells, neuroblasts, through a novel pathway. Wnt2/5/6/D proteins, expressed in ectodermal cells, act via frizzled receptors on underlying neuroblasts to localize armadillo/β-catenin to neuroblast cytocortex facing the Wnt signal source. The localized armadillo recruits the Par complex and Pins complex to the neuroblast apical side, through the association of arm with Par3 and Inscuteable. Wnts consequently orient the cell polarity and asymmetric divisions of neuroblasts perpendicular to the epithelium, allowing nerve tissue to grow inward along the central-peripheral axis in Drosophila embryos. This novel non-canonical Wnt signaling pathway may regulate Par-dependent polarity in various biological contexts.
hnRNP R is a regulator of stress granule formation
Authors: Ji Changhe
Published: June 2022

hnRNP R (Heterogeneous nuclear ribonucleoproteins R) is one member of RNA-binding proteins (RBPs) in hnRNP family, it plays important role in nucleic acid metabolism including alternative splicing, mRNA stabilization, transcriptional and translational regulation, and mRNA transport. Mostly hnRNP R is localized in nuclear and extensively binds with RNA and chromatin, but still some part of it exports to cytosol. We found that long and short isoform hnRNP R can located in stress granules, depletion hnRNP R can facilitate the stress granule formation and accelerate mRNA in the stress granules. Meanwhile we found that depletion hnRNP R can alter the stress granule phenotype and impair stress granule resolving. Additionally, we also found that depletion hnRNP R also induce TDP43 granules formation. Furthermore, depletion hnRNP R can impair TDP43 binding with ribosome. Altogether, hnRNP R plays important role in the stress granule formation.
Efficient reconciliation of genomic datasets of high similarity
Authors: Shibuya Yoshihiro , Belazzougui Djamal , Kucherov Gregory
Published: June 2022

Abstract

We apply Invertible Bloom Lookup Tables (IBLTs) to the comparison of k-mer sets originated from large DNA sequence datasets. We show that for similar datasets, IBLTs provide a more space-efficient and, at the same time, more accurate method for estimating Jaccard similarity of underlying k-mer sets, compared to MinHash which is a go-to sketching technique for efficient pairwise similarity estimation. This is achieved by combining IBLTs with k-mer sampling based on syncmers, which constitute a context-independent alternative to minimizers and provide an unbiased estimator of Jaccard similarity. A key property of our method is that involved data structures require space proportional to the difference of k-mer sets and are independent of the size of sets themselves. As another application, we show how our ideas can be applied in order to efficiently compute (an approximation of) k-mers that differ between two datasets, still using space only proportional to their number. We experimentally illustrate our results on both simulated and real data (SARS-CoV-2 and Streptococcus Pneumoniae genomes).

Available at: https://github.com/yhhshb/km-peeler.git
Rapid evolution of the fine-scale recombination landscape in wild house mouse (Mus musculus) populations
Authors: Wooldridge Lydia K. , Dumont Beth L.
Published: June 2022

Meiotic recombination is an important evolutionary force and essential meiotic process. In many species, recombination events concentrate into “hotspots” defined by the site-specific binding of PRMD9. Rapid evolution of PRDM9’s zinc finger DNA-binding array leads to remarkably abrupt shifts in the genomic distribution of hotspots between species, but the question of how Prdm9 allelic variation shapes the landscape of recombination between populations remains less well understood. Wild house mice (Mus musculus) harbor exceptional Prdm9 diversity, with >100 alleles identified to date, and pose a particularly powerful system for addressing this open question. We employed a coalescent-based approach to construct fine-scale, sex-averaged recombination maps from contemporary patterns of linkage disequilibrium in nine geographically isolated wild house mouse populations, including multiple populations from each of three subspecies. Comparing maps between wild mouse populations and subspecies reveals several themes. First, we report weak fine- and broad-scale recombination map conservation across subspecies and populations, with genetic divergence offering no clear prediction for recombination map divergence. Second, most hotspots are unique to one population, an outcome consistent with minimal sharing of Prdm9 alleles between surveyed populations. Finally, by contrasting aggregate hotspot activity on the X versus autosomes, we uncover evidence for population-specific differences in the degree and direction of sex-dimorphism for recombination. Overall, our findings illuminate the variability of both the broad- and fine-scale recombination landscape in Mus musculus and underscore the functional impact of Prdm9 allelic variation in wild mouse populations.
Species existence and coexistence under nutrient enrichment in the Park Grass
Authors: Yao Qi , Feng Yanhao
Published: June 2022

Numerous studies have shown that nutrient enrichment causes the loss of plant diversity in different grasslands across the globe. Thus far, three main hypotheses (niche dimension, competitive asymmetry, and soil acidification) have been proposed to account for this general phenomenon, but our knowledge of the underlying mechanisms remains rather vague. To reveal the cryptic mechanisms, we analyzed the famous long-term Park Grass Experiment (1856-) under modern coexistence theory by fitting Lotka-Volterra competition models with time-series data from the different treatments (15 different combinations of nutrient addition fully crossed with four levels of soil pH) to quantitatively test the three competing hypotheses. Supportive of the competitive asymmetry and soil acidification hypotheses, both nutrient addition and soil acidification overall decreased intrinsic population growth rates (r) and intensified competitive differences or asymmetries dramatically, which mostly favored grasses over forbs and legumes (and also forbs over legumes). These changes in r and competitive differences or asymmetries are generally consistent with the abundance changes of different functional groups following the various treatments. Moreover, the altered r (determining species existence) and competitive differences (affecting species coexistence) effectively explained the diversity loss and recovery (after nitrogen addition was withheld). However, while nutrient addition significantly decreased per-capita intra- and inter-specific competition (which indicates that belowground competition becomes less intense when soil nutrients are more abundant), it did not decrease niche differences as predicted, poorly supporting the niche dimension hypothesis. These findings advance our understanding of fundamental mechanisms driving the response of plant communities to nutrient deposition in nature.

Significance Statement

An unresolved fundamental scientific mystery with the crucial applied value in ecology is what causes the general loss of biodiversity following nutrient enrichment in the Anthropocene. In this study, we combined the recent advance in coexistence theory with the longest-running fertilization experiment existing in the world to wrestle with this conundrum. Our major results, which highlight the critical role of both existence and coexistence, could help settle the debate between the three popular hypotheses and also, for the first time, provide quantitative explanations for the general findings in numerous nutrient-addition experiments. Our study shows the importance of applying modern coexistence theory to more quantitatively explain, predict and cope with the responses of ecological communities to global change factors in nature.
A machine learning based method for the identification of functionally important genes
Authors: Das Gourab , Ghosh Indira
Published: June 2022

Deciphering complex mechanisms underlying communicable and non-communicable diseases require comprehensive analysis of genetic factors and interactions between them. Experimental identification of genes related to pathogen’s virulence and human diseases is effective but laborious, time consuming and costly. Consequently, many genetic factors associated with pathogenesis or disease still remain to be unknown. In present work, a normalized point wise mutual information (nPMI) driven computational method has been developed to identify the association between biological entities (genes) and physiological responses utilizing published literatures in PubMed. Association prediction models are then developed using machine learning approach for four different datasets including virulent genes from two bacterial species (E. coli and S. enterica) and stress responsive genes from two plant species (A. thaliana and O. sativa). This approach provides a generic platform for identifying association of genes in diverse biological systems (host and pathogen) and provide up-to-date estimate of association measures of the genes with stress, virulence. In future, the causal relation between them may be of research importance.
Multi-channel recordings reveal age-related differences in the sleep of juvenile and adult zebra finches
Authors: Yeganegi Hamed , Ondracek Janie M.
Published: June 2022

Despite their phylogenetic differences and distinct pallial structures, mammals and birds show similar electroencephalography (EEG) traces during sleep, consisting of distinct rapid eye movement (REM) sleep and slow wave sleep (SWS) stages. Studies in human and a limited number of other mammalian species shows that this organization of sleep into interleaving stages undergoes radical changes during lifetime. Do these age-dependent variations in sleep patterns also occur in the avian brain? Does vocal learning have an effect on sleep patterns in birds? To answer this question, we recorded multi-channel sleep EEG from juveniles and adult zebra finches for several nights. Whereas adults spent more time in SWS and REM sleep, juveniles spent more time in intermediate sleep (IS). The amount of IS sleep was significantly larger in male juveniles engaged in vocal learning compared to female juveniles, which suggest that IS sleep could be important for learning. In addition, we observed that the functional connectivity increased rapidly during maturation of young juveniles, and was stable or declined at older ages. Synchronous activity during sleep was larger for recording sites in the left hemisphere for both juveniles and adults, and generally intra-hemispheric synchrony was larger than inter-hemispheric synchrony during sleep. A graph theory analysis revealed that in adults, highly correlated EEG activity tends to be distributed across fewer networks that are spread across a wider area of the brain, whereas in juveniles, highly correlated EEG activity is distributed across more numerous, albeit smaller, networks in the brain. Overall, our results reveal significant changes in the neural signatures of sleep during maturation in an avian brain.
Early adversity changes the economic conditions of structural brain network organisation
Authors: Carozza Sofia , Holmes Joni , Vértes Petra E. , Bullmore Ed , Arefin Tanzil M. , Pugliese Alexa , Zhang Jiangyang , Kaffman Arie , Akarca Danyal , Astle Duncan E.
Published: June 2022

Early adversity can change educational, cognitive, and mental health outcomes. However, the neural processes through which early adversity exerts these effects remain largely unknown. We used generative network modelling of the mouse connectome to test whether unpredictable postnatal stress shifts the constraints that govern the formation of the structural connectome. A model that trades off the wiring cost of long-distance connections with topological homophily (i.e. links between regions with shared neighbours) generated simulations that replicate the organisation of the rodent connectome. The imposition of early life adversity significantly shifted the best-performing parameter combinations toward zero, heightening the stochastic nature of the generative process. Put simply, unpredictable postnatal stress changes the economic constraints that shape network formation, introducing greater randomness into the structural development of the brain. While this change may constrain the development of cognitive abilities, it could also reflect an adaptive mechanism. In other words, neural development could harness heightened stochasticity to make networks more robust to perturbation, thereby facilitating effective responses to future threats and challenges.

Significance statement

Children who experience adversity early in life – such as chronic poverty or abuse – show numerous neural differences that are linked to poorer cognition and mental health later in life. To effectively mitigate the burden of adversity, it is critical to identify how these differences arise. In this paper, we use computational modelling to test whether growing up in an impoverished and unpredictable environment changes the development of structural connections in the mouse brain. We found that early adversity appears to introduce more stochasticity in the formation of neural architecture. Our findings point to a potential mechanism for how early adversity could change the course of child development.
Efficient stabilization of imprecise statistical inference through conditional belief updating
Authors: Drevet Julie , Drugowitsch Jan , Wyart Valentin
Published: June 2022

Statistical inference is the optimal process for forming and maintaining accurate beliefs about uncertain environments. However, human inference comes with costs due to its associated biases and limited precision. Indeed, biased or imprecise inference can trigger variable beliefs and unwarranted changes in behavior. Here, by studying decisions in a sequential categorization task based on noisy visual stimuli, we obtained converging evidence that humans reduce the variability of their beliefs by updating them only when the reliability of incoming sensory information is judged as sufficiently strong. Instead of integrating the evidence provided by all stimuli, participants actively discarded as much as a third of stimuli. This conditional belief updating strategy shows good test-retest reliability, correlates with perceptual confidence, and explains human behavior better than previously described strategies. This seemingly suboptimal strategy not only reduces the costs of imprecise computations, but counter-intuitively increases the accuracy of resulting decisions.
Lysine 27 of histone H3.3 is a fine modulator of developmental gene expression and stands as an epigenetic checkpoint for lignin biosynthesis in Arabidopsis
Authors: Fal Kateryna , Tomkova Denisa , Le Masson Marie , Faigenboim Adi , Pano Emeline , Ishkhneli Nickolay , Moyal Netta-Lee , Villette Claire , Chabouté Marie-Edith , Berr Alexandre , Williams Leor Eshed , Carles Cristel C.
Published: June 2022

Chromatin is a dynamic platform within which gene expression is controlled by epigenetic modifications, notably targeting amino acid residues of histone H3. Among them is Lysine 27 of H3 (H3K27), which trimethylation by the Polycomb Repressive Complex 2 (PRC2) is instrumental in regulating spatio-temporal patterns of key developmental genes. H3K27 is also subjected to acetylation, found at sites of active transcription. Most information on the function of histone residues and their associated modifications in plants was obtained from studies of loss-of-function mutants for the complexes that modify them.

In order to decrypt the genuine function of H3K27, we expressed a non-modifiable variant of H3 at residue K27 (H3.3K27A) in Arabidopsis, and developed a multi-scale approach combining in-depth phenotypical and cytological analyses, with transcriptomics and metabolomics.

We uncovered that the H3.3K27A variant causes severe developmental defects, part of them reminiscent of PRC2 mutants, part of them new. They include early flowering, increased callus formation, and short stems with thicker xylem cell layer. This latest phenotype correlates with mis-regulation of phenylpropanoid biosynthesis.

Overall, our results reveal novel roles of H3K27 in plant cell fates and metabolic pathways, and highlight an epigenetic control point for elongation and lignin composition of the stem.
Immune gene variation associated with chromosome-scale differences among individual zebrafish genomes
Authors: McConnell Sean C. , Hernandez Kyle M. , Andrade Jorge , de Jong Jill L.O.
Published: June 2022

Immune genes have evolved to maintain exceptional diversity, offering robust defense against pathogens. We performed genomic sequencing and assembly to examine immune gene variation among three zebrafish individuals. We identified remarkably high levels of sequence divergence as well as presence/absence variation among these zebrafish genomes, particularly when compared with the level of variation in human genomes. Gene pathway analysis identified zebrafish immune genes as significantly enriched among genes with evidence of positive selection. A large subset of genes was absent from analysis of coding sequences due to apparent lack of reads, prompting us to examine genes overlapping zero coverage regions (ZCRs), defined as 2kb stretches without mapped reads. Zebrafish immune genes were also identified as highly enriched within ZCRs, including over 60% of zebrafish major histocompatibility complex (MHC) genes and NOD-like receptor (NLR) genes, mediators of direct and indirect pathogen recognition. This variation was most highly concentrated throughout one arm of zebrafish chromosome 4 carrying a large cluster of NLR genes, associated with large-scale structural variation covering more than half of a vertebrate chromosome. While previous studies have shown marked variation in NLR genes between vertebrate species, our study highlights extensive variation between individuals of the same species. Our genomic assemblies also provide sequences for alternative haplotypes and distinct complements of immune genes among individual zebrafish, including the MHC Class II locus. Taken together, these findings provide evidence of immune gene variation on a scale previously unknown in other vertebrate species and raise questions about potential impact on immune function.