bluuebunny/crossref_metadata_2025 huggingface dataset:
Antibody-dependent DENV infection induces distinct transcriptomic responses in infected and bystander human macrophages
Authors: Hardy Céline S. C. , Wegman Adam D. , Waldran Mitchell J. , Waickman Adam T.
Published: July 2024

Dengue virus (DENV) is a mosquito-borne flavivirus which coexists as four genetically and immunologically distinct serotypes (DENV1-4). In secondary heterologous DENV infection, pre-existing immunity is believed to contribute to severe disease through antibody dependent enhancement (ADE). Although the elevated pathology observed in ADE conditions has been described, the cell intrinsic mechanisms governing this process remain unclear. Using scRNAseq, we investigated the transcriptomic profiles of human monocyte-derived macrophages infected by DENV via ADE compared to conventional infection conditions. Unsupervised analysis of scRNAseq data enabled the identification and differentiation of infected and bystander/uninfected cells in a heterogeneous cell culture. Differential gene expression and Ingenuity Pathway analyses revealed a number of significantly up- and down-regulated genes and gene networks between cells infected by ADE compared to conventional infection. Specifically, these pathways indicated mechanisms such as suppressed interferon signaling and inflammatory chemokine transcription in cells infected via ADE. Further analysis revealed that transcriptomic changes were independent of viral RNA within infected cells, suggesting that the observed changes are reflective of cell-intrinsic responses and not simply a function of per-cell viral burden. Bystander cells in ADE conditions also demonstrated distinct profiles, indicating an immunologically activated phenotype enriched for the expression of gene networks involved with protein translation, cytokine production, and antigen presentation. Together, these findings support the concept that DENV infection via ADE induces a qualitatively different transcriptomic response in infected and bystander cells, contributing to our understanding of ADE as a mechanistic driver of disease and pathogenesis.

IMPORTANCE

Dengue virus (DENV) is a mosquito-borne human pathogen with a significant and growing global health burden. Although correlates of severe dengue disease are poorly understood, pre-existing immunity to DENV has been associated with severe disease risk and known to contribute to an alternative route of viral entry termed antibody-dependent enhancement (ADE). Using single cell RNA sequencing, we identified distinct transcriptomic processes involved in antibody-mediated DENV entry compared to conventional receptor mediated entry. These data provide meaningful insight into the discrete processes contributing to DENV pathogenesis in ADE conditions.
T3SS translocon induces pyroptosis by direct interaction with NLRC4/NAIP inflammasome
Authors: Zhao Yan , Zhu Hanshuo , Li Jinqian , Xu Hang , Sun Li
Published: July 2024

Type III secretion system (T3SS) is a virulence apparatus existing in many bacterial pathogens. Structurally, T3SS consists of the base, needle, tip, and translocon. The NLRC4 inflammasome is the major receptor for T3SS needle and basal rod proteins. Whether other T3SS components are recognized by NLRC4 is unclear. In this study, usingEdwardsiella tardaas a model intracellular pathogen, we examined T3SS−inflammasome interaction and its effect on cell death.E. tardainduced pyroptosis in a manner that required the bacterial translocon and the host inflammasome proteins of NLRC4, NLRP3, ASC, and caspase 1/4. The translocon protein EseB triggered NLRC4/NAIP-mediated pyroptosis by binding NAIP via its C-terminal region, particularly the terminal 6 residues (T6R). EseB homologs exist widely in T3SS-positive bacteria and share high identities in T6R. LikeE. tardaEseB, all of the representatives of the EseB homologs exhibited T6R-dependent NLRC4 activation ability. Together these results revealed the function and molecular mechanism of EseB to induce host cell pyroptosis and suggested a highly conserved inflammasome-activation mechanism of T3SS translocon in bacterial pathogens.
Emergence of sympatric host-specific lineages of the fungal plant pathogenZymoseptoria passeriniiin natural ecosystems
Authors: Rojas-Barrera Idalia C. , Flores-Núñez Victor M. , Haueisen Janine , Alizadeh Alireza , Salimi Fatemeh , Stukenbrock Eva H.
Published: July 2024

The barley disease Septoria Speckled Leaf Blotch, caused by the fungal pathogenZymoseptoria passerinii,had its last outbreak in North America in the early 2000s. Although rare in agricultural settings, field sampling of wild grasses in the Middle East revealed the disease persistence in wild barley.

Identification ofZ. passeriniiin distinct wild barley species led us to investigate signatures of host specialization using genomics to address the mode of emergence by host tracking or host range expansion. Furthermore, we applied virulence assays and confocal laser microscopy to evaluate if the disease development differs between wild and domesticated barley.

Wild- and domesticated-host infecting populations have diverged, and phylogenetic relationships support the emergence of sympatric host-specific lineages. Cross-virulence assays showed thatZymoseptoriapasserinii from domesticated hosts infect domesticated barley and its wild ancestor,Hordeum spontaneum. However, wild isolates from Iran did not infect domesticated barley. Wild and domesticated pathosystems have similar disease timing and progression, suggesting its persistence in natural ecosystems might be tied to environmental conditions.

The study supports that a wide range of hosts can foster the emergence of host-specific lineages in sympatry and provide novel insights into the evolution of understudied fungal pathogens on wild crop relatives.
High fat diet induces differential age- and gender-dependent changes in neuronal function linked to redox stress
Authors: de Lange Megan , Yarosh Vladyslava , Farell Kevin , Oates Caitlin , Patil Renee , Hawthorn Isabel , Jung Mok-Min , Wenje Sophie , Steinert Joern R
Published: July 2024

The prevalence of neurodegenerative diseases, such as Alzheimer’s disease and Parkinson’s disease, is steadily increasing, posing significant challenges to global healthcare systems. Emerging evidence suggests that dietary habits, particularly consumption of high-fat diets specify which fats, may play a pivotal role in the development and progression of neurodegenerative disorders. Moreover, several studies have shed light on the intricate communication between the gut and the brain, known as the gut-brain axis and its involvement in neurodegenerative processes.

This study aims to assess the effects of a high-fat dietary intake on various aspects of neuronal function during aging and following gender separation to help understand the potential contributions of diet to neuronal function.

To investigate the effects of a high-fat diet,Drosophila melanogasterwas used and exposed to standard normal food diet (NF) and high-fat diet (HF). Adults were grouped at 10 and 45 days of age in male and female flies reared under the same conditions. Multiple assays were conducted, showing differential gender- and HF diet-induced oxidative stress levels as determined by malondialdehyde (MDA) measurements, enhanced caspase-3 expression and reduced climbing activity. Adult lifespan under both dietary conditions was unchanged but odour-associated learning ability was reduced in larvae reared in a HF diet.

This is the first study to characterise effects of diet on neuronal phenotypes in an age- and gender-specific manner in aDrosophilamodel. Our findings suggest a HF diet induces differential forms of neuronal dysfunction with age and sex-specific outcomes, characterised by enhanced oxidative stress and cell death which impacts on neuronal and behavioural functions.
Single-cell transcriptomics reveal differences between chorionic and basal plate cytotrophoblasts and trophoblast stem cells
Authors: Morey Robert , Soncin Francesca , Kallol Sampada , Sah Nirvay , Manalo Zoe , Bui Tony , Slamecka Jaroslav , Cheung Virginia Chu , Pizzo Don , Requena Daniela F. , Chang Ching-Wen , Farah Omar , Kittle Ryan , Meads Morgan , Horii Mariko , Fisch Kathleen , Parast Mana M.
Published: July 2024

Cytotrophoblast (CTB) of the early gestation human placenta are bipotent progenitor epithelial cells, which can differentiate into invasive extravillous trophoblast (EVT) and multinucleated syncytiotrophoblast (STB). Trophoblast stem cells (TSC), derived from early first trimester placentae, have also been shown to be bipotential. In this study, we set out to probe the transcriptional diversity of first trimester CTB and compare TSC to various subgroups of CTB. We performed single-cell RNA sequencing on six normal placentae, four from early (6-8 weeks) and two from late (12-14 weeks) first trimester, of which two of the early first trimester cases were separated into basal (maternal) and chorionic (fetal) fractions prior to sequencing. We also sequenced three TSC lines, derived from 6-8 week placentae, to evaluate similarities and differences between primary CTB and TSC. CTB clusters displayed notable distinctions based on gestational age, with early first trimester placentae showing enrichment for specific CTB subtypes, further influenced by origin from the basal or chorionic plate. Differential expression analysis of CTB from basal versus chorionic plate highlighted pathways associated with proliferation, unfolded protein response, and oxidative phosphorylation. We identified trophoblast states representing initial progenitor CTB, precursor STB, precursor and mature EVT, and multiple CTB subtypes. CTB progenitors were enriched in early first trimester placentae, with basal plate cells biased toward EVT, and chorionic plate cells toward STB, precursors. Clustering and trajectory inference analysis indicated that TSC were most like EVT precursor cells, with only a small percentage of TSC on the pre-STB differentiation trajectory. This was confirmed by flow cytometric analysis of 6 different TSC lines, which showed uniform expression of proximal column markers ITGA2 and ITGA5. Additionally, we found that ITGA5+ CTB could be plated in 2D, forming only EVT upon spontaneous differentiation, but failed to form self-renewing organoids; conversely, ITGA5-CTB could not be plated in 2D, but readily formed organoids. Our findings suggest that distinct CTB states exist in different regions of the placenta as early as six weeks gestation and that current TSC lines most closely resemble ITGA5+ CTB, biased toward the EVT lineage.
FLASH Bragg-peak irradiation with a therapeutic carbon ion beam: first in vivo results
Authors: Tinganelli Walter , Sokol Olga , Puspitasari Anggraeini , Helm Alexander , Simoniello Palma , Schuy Christoph , Lerchl Sylvie , Eckert Denise , Oppermann Julius , Rehm Anna , Janssen Stefan , Engel Denise , Moeller Ralf , Romano Rossana , Fournier Claudia , Durante Marco , Weber Uli
Published: July 2024

Background and purpose

In recent years, ultra-high dose rate (UHDR) irradiation has emerged as a promising innovative approach to cancer treatment. Characteristic feature of this regimen, commonly referred to as FLASH effect, demonstrated primarily for electrons, photons or protons, is the improved normal tissue sparing, while the tumor control is similar to the one of the conventional dose-rate (CDR) treatments. The FLASH mechanism is, however, unknown. One major question is whether this effect is maintained when using densely ionizing (high-LET) heavy nuclei.

Materials and Methods

Here we report the effects of 20 Gy UHDR heavy ion irradiation in clinically relevant conditions, i.e., at high-LET in the spread-out Bragg peak (SOBP) of a12C beam using an osteosarcoma mouse model.

Results

We show that UHDR irradiation was less toxic in the normal tissue compared to CDR while maintaining tumor control. The immune activation was also comparable in UHDR and CDR groups. We observed that the gut microbiome was altered in mice injected with the tumor compared to healthy animals, but both UHDR and CDR exposures steered the metagenome toward a balanced state.

Conclusions

The results show that the FLASH effect is safe and effective in heavy ion therapy and provide an important benchmark for the current mechanistic FLASH models.

Highlights

- FLASH irradiation with SOBP carbon ions spares normal tissue in mouse

- Tumor control, immune response, and gut microbioma changes are induced at the same extent both at conventional and ultra-high dose rate

- FLASH carbon ion irradiation is a safe and effective alternative to conventional radiotherapy.
Card9 and MyD88 differentially regulate Th17 immunity to the commensal yeastMalasseziain the murine skin
Authors: Tuor Meret , Stappers Mark H.T. , Ruchti Fiorella , Desgardin Alice , Sparber Florian , Orr Selinda J. , Gow Neil A.R. , LeibundGut-Landmann Salomé
Published: July 2024

The fungal community of the skin microbiome is dominated by a single genus,Malassezia. Besides its symbiotic lifestyle at the host interface, this commensal yeast has also been associated with diverse inflammatory skin diseases in humans and pet animals. Stable colonization is maintained by antifungal type 17 immunity. The mechanisms driving Th17 responses toMalasseziaremain, however, unclear. Here, we show that the C-type lectin receptors Mincle, Dectin-1, and Dectin-2 recognize conserved patterns in the cell wall ofMalasseziaand induce dendritic cell activationin vitro, while only Dectin-2 is required for Th17 activation during experimental skin colonizationin vivo.In contrast, Toll-like receptor recognition was redundant in this context. Instead, inflammatory IL-1 family cytokines signaling via MyD88 were also implicated in Th17 activation in a T cell-intrinsic manner. Taken together, we characterized the pathways contributing to protective immunity against the most abundant member of the skin mycobiome. This knowledge contributes to the understanding of barrier immunity and its regulation by commensals and is relevant considering how aberrant immune responses are associated with severe skin pathologies.
Species wide inventory ofArabidopsis thalianaorganellar variation reveals ample phenotypic variation for photosynthetic performance
Authors: Theeuwen Tom P.J.M. , Wijfjes Raúl Y. , Dorussen Delfi , Lawson Aaron W. , Lind Jorrit , Jin Kaining , Boekeloo Janhenk , Tijink Dillian , Hall David , Hanhart Corrie , Becker Frank F.M. , van Eeuwijk Fred A. , Kramer David M. , Wijnker Erik , Harbinson Jeremy , Koornneef Maarten , Aarts Mark G.M.
Published: July 2024

Efforts to improve photosynthetic performance are increasingly employing natural genetic variation. However, genetic variation in the organellar genomes (plasmotypes) is often disregarded due to the difficulty of studying the plasmotypes and the lack of evidence that this is a worthwhile investment. Here, we systematically phenotyped plasmotype diversity usingArabidopsis thalianaas a model species. A reanalysis of whole genome resequencing data of 1,531 representative accessions shows that the genetic diversity amongst the mitochondrial genomes is eight times lower than amongst the chloroplast genomes. Plasmotype diversity of the accessions divides the species into two major phylogenetic clusters, within which highly divergent subclusters are distinguished. We combined plasmotypes from 60A. thalianaaccessions with the nuclear genomes (nucleotypes) of fourA. thalianaaccessions to create a panel of 232 novel cytonuclear genotypes (cybrids). The cybrid plants were grown in a range of different light and temperature conditions and phenotyped using high-throughput phenotyping platforms. Analysis of the phenotypes showed that several plasmotypes alone or in interaction with the nucleotypes have significant effects on photosynthesis, and that the effects are highly dependent on the environment. Moreover, we introduce Plasmotype Association Studies (PAS) as a novel method to reveal plasmotypic effects. WithinA. thaliana,several organellar variants can influence photosynthetic phenotypes, which emphasizes the valuable role this variation has on improving photosynthetic performance. The increasing feasibility of producing cybrids in various species calls for further research into how these phenotypes may support breeding goals in crop species.

Significance statement

Photosynthesis is one of the few crop traits that has been largely unaddressed which can contribute to increasing crop yield potential. Exploiting genetic variation within organellar genomes presents a promising, yet untapped resource to improve photosynthesis. However, the extent of organellar variation and its impact on photosynthesis within a species remains largely unknown. UsingArabidopsis thalianaas a model species, we revealed highly divergent clusters of organellar variation. We constructed 232 novel combinations of species representative organellar and nuclear genomes, referred to as cybrids. High-throughput phenotyping of these cybrids revealed that organellar variants can substantially impact photosynthesis in different environments. These findings indicate that organellar genomes may be a valuable resource for improving photosynthesis in crops.
How the window of visibility varies around polar angle
Authors: Kwak Yuna , Lu Zhong-Lin , Carrasco Marisa
Published: July 2024

Contrast sensitivity, the amount of contrast required to detect or discriminate an object, depends on spatial frequency (SF): The Contrast Sensitivity Function (CSF) peaks at intermediate SFs and drops at lower and higher SFs and is the basis of computational models of visual object recognition. The CSF varies from foveal to peripheral vision, but only a couple studies have assessed changes around polar angle of the visual field. Sensitivity is generally better along the horizontal than the vertical meridian, and better at the lower vertical than the upper vertical meridian, yielding polar angle asymmetries. Here, we investigate CSF attributes at polar angle locations at both group and individual levels, using Hierarchical Bayesian Modeling. This method enables precise estimation of CSF parameters by decomposing the variability of the dataset into multiple levels and analyzing covariance across observers. At the group level, peak contrast sensitivity and corresponding spatial frequency with the highest sensitivity are higher at the horizontal than vertical meridian, and at the lower than upper vertical meridian. At an individual level, CSF attributes (e.g., maximum sensitivity, the most preferred SF) across locations are highly correlated, indicating that although the CSFs differ across locations, the CSF at one location is predictive of the CSF at another location. Within each location, the CSF attributes co-vary, indicating that CSFs across individuals vary in a consistent manner (e.g., as maximum sensitivity increases, so does the SF at which sensitivity peaks), but more so at the horizontal than the vertical meridian locations. These results show similarities and uncover some critical polar angle differences across locations and individuals, suggesting that the CSF should not be generalized across iso-eccentric locations around the visual field. Our window of visibility varies with polar angle: It is enhanced and more consistent at the horizontal meridian.
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes
Authors: Kobel Carl M. , Aho Velma T. E. , Øyås Ove , Nørskov-Lauritsen Niels , Woodcroft Ben J. , Pope Phillip B.
Published: July 2024

Here, we present CompareM2, a genomes-to-report pipeline for comparative analysis of bacterial and archaeal genomes derived from isolates and metagenomic assemblies. CompareM2 is easy to install and operate, and integrates community-adopted tools to perform genome quality control and annotation, taxonomic and functional predictions, as well as comparative analyses of core- and pan-genome partitions and phylogenetic relations. The central results generated via the CompareM2 workflow are emphasized in a portable dynamic report document. CompareM2 is free software and welcomes modifications and pull requests from the community on its Git repository athttps://github.com/cmkobel/comparem2.
Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo
Authors: Kucinski Jack , Tallan Alexi , Taslim Cenny , Wang Meng , Cannon Matthew V. , Silvius Katherine M. , Stanton Benjamin Z. , Kendall Genevieve C.
Published: July 2024

Fusion-positive rhabdomyosarcoma is an aggressive pediatric cancer molecularly characterized by arrested myogenesis. The defining genetic driver, PAX3::FOXO1, functions as a chimeric gain-of-function transcription factor. An incomplete understanding of PAX3::FOXO1’s in vivo epigenetic mechanisms has hindered therapeutic development. Here, we establish a PAX3::FOXO1 zebrafish injection model and semi-automated ChIP-seq normalization strategy to evaluate how PAX3::FOXO1 initially interfaces with chromatin in a developmental context. We investigated PAX3::FOXO1’s recognition of chromatin and subsequent transcriptional consequences. We find that PAX3::FOXO1 interacts with inaccessible chromatin through partial/homeobox motif recognition consistent with pioneering activity. However, PAX3::FOXO1-genome binding through a composite paired-box/homeobox motif alters chromatin accessibility and redistributes H3K27ac to activate neural transcriptional programs. We uncover neural signatures that are highly representative of clinical rhabdomyosarcoma gene expression programs that are enriched following chemotherapy. Overall, we identify partial/homeobox motif recognition as a new mode for PAX3::FOXO1 pioneer function and identify neural signatures as a potentially critical PAX3::FOXO1 tumor initiation event.
Consistent and scalable monitoring of birds and habitats along a coffee production intensity gradient
Authors: Somveille Marius , Grainger-Hull Joe , Ferguson Nicole , Sethi Sarab S. , González-García Fernando , Chassagnon Valentine , Oktem Cansu , Disney Mathias , Bautista Gustavo López , Vandermeer John , Perfecto Ivette
Published: July 2024

Land use change associated with agricultural intensification is a leading driver of biodiversity loss in the tropics. To evaluate the habitat-biodiversity relationship in production systems of tropical agricultural commodities, which is critical for certifying and examining the success of biodiversity-friendly agricultural practices, birds are commonly used as indicators. However, consistently and reliably monitoring how bird communities are affected by land use change throughout the annual cycle in a way that can be scalable is challenging using traditional survey methods. In this study, we examined whether the automated analysis of audio data collected by passive acoustic monitoring, together with the analysis of remote sensing data, can be used to efficiently monitor avian biodiversity along the gradient of habitat degradation associated with the intensification of coffee production. Coffee is an important crop produced in tropical forested regions, whose production is expanding and intensifying, and coffee production systems form a gradient of ecological complexity ranging from forest-like shaded polyculture to dense sun-exposed monoculture. We used LiDAR technology to survey the habitat, in combination with autonomous recording units and a vocalisation classification algorithm to assess bird community composition in a coffee landscape comprising a shade-grown coffee farm, a sun coffee farm, and a forest remnant, located in southern Mexico. We found that combining LiDAR with the automated analysis of continuously collected bioacoustics data can capture the expected functional signatures of avian communities as a function of habitat quality in the coffee landscape. Thus, we show that this approach can be a robust way to monitor how biodiversity responds to land use intensification in the tropics. A major advantage of this approach is that it has the potential to be deployed cost-effectively at large scales to help design and certify biodiversity-friendly productive landscapes.
Waves of transcription drive erythroid differentiation and launch the NRF2-activated antioxidant program
Authors: Karppi Ingrid , Pessa Jenny C. , Rabenius Adelina , Himanen Samu V. , Prajapati Bina , Jonsson Emilia Barkman , Vartiainen Maria K. , Sistonen Lea , Vihervaara Anniina
Published: July 2024

Transcriptional reprogramming drives differentiation and coordinates cellular responses. While mRNA expression in distinct cell types has been extensively analyzed, the mechanisms that control RNA synthesis upon lineage specifications remain unclear. Here, we induce erythroid differentiation in human cells, track transcription and its regulation at nucleotide-resolution, and identify molecular mechanisms that orchestrate gene and enhancer activity during erythroid specification. We uncover waves of transcription and reveal that a brief differentiation signal launches sustained and propagating changes in RNA synthesis and mRNA expression over cell divisions. NRF2, a strongtrans-activator upon oxidative stress, drives erythroid differentiation without a detectable increase in reactive oxygen species. In erythroid precursors, NRF2 induces architecturally primed, differentiation-linked enhancers, and genes encoding globin and antioxidant proteins. Projecting signal-induced transcription to DNA accessibility and mRNA expression in single human bone marrow cells, reveals ordered activation of myeloid (GABPA) and erythroid (GATA1, TAL1 and HEMGN) factors in lineage-specification, followed by NRF2-triggered antioxidant response in the late erythroid cells. This study establishes molecular mechanisms that prime, execute, and temporally coordinate RNA synthesis during erythroid differentiation. Furthermore, we show that master regulators of differentiation and stress co-orchestrate erythropoiesis and produce the antioxidant machinery before erythroid cells mature to oxygen transporting enucleated erythrocytes.
Elevational constraints on flight efficiency shape global gradients in avian wing morphology
Authors: Yang Jingyi , Yang Chenyue , Lin Hung-wei , Lees Alexander Charles , Tobias Joseph A
Published: July 2024

Wings with elongated shape or larger surface area are associated with increased flight efficiency and dispersal ability in a wide range of animals from insects to birds. Inter- and intraspecific variation in these attributes of wing shape is determined by a range of factors - including foraging ecology, migration and climatic seasonality - all of which may drive latitudinal gradients in wing morphology. A separate hypothesis predicts that wing shape should also follow an elevational gradient because air density and oxygen supply decline with altitude, altering the aerodynamics of flight, and driving the evolution of more efficient wings in high-elevation species to compensate for reduced lift. However, previous analyses have found only mixed support for the 'thin-air' hypothesis, and we currently lack a global synthesis of elevational gradients in wing design for any taxonomic group. In this study, we use phylogenetic comparative models to explore elevational effects on wing morphology in 9986 bird species, while accounting for multiple climatic and ecological attributes, including latitude, temperature seasonality, body mass, aerial lifestyle and migration. We found that relative wing elongation (hand-wing index) and wing area increase with elevation, particularly in the upper montane zone (>4 km above sea level). These results confirm a pervasive elevational gradient in avian wing morphology, highlighting the role of aerodynamic constraints as key mechanisms shaping global patterns of trait evolution in flying animals.
Upregulation of TNFR2 Precedes TOX Expression by Exhausted T cells and Restricts Antitumor and Antiviral Immunity
Authors: Hoyt-Miggelbrink Alexandra , Waibl Polania Jessica , Wachsmuth Luke , Lorrey Selena , Mohan Aditya , Hardigan Andrew , Blandford Emily , Lerner Emily , Wilkinson Daniel , Hotchkiss Kelly M. , Cook Sarah , Hemmers Saskia , Patel Anoop , Ayasoufi Katayoun , Fecci Peter
Published: July 2024

Exhaustion represents a collection of programmed T cell differentiation states and an important mode of T cell dysfunction. T cell progression from progenitor to terminal exhaustion is associated with upregulation of the transcription factor TOX and expression of TIM3. Our understanding of factors regulating TOX expression and the transition from progenitor to terminal exhaustion, however, remains incomplete. We reveal here that T cell upregulation of tumor necrosis factor receptor type II (TNFR2) coincides with the gain of phenotypic markers and functions reflective of terminal exhaustion. Meanwhile, knocking out TNFR2 affords a novel population of T cells that express TIM3 but possess diminished TOX levels and functional characteristics of both progenitor and terminally exhausted cells. TIM3+TNFR2 KO T cells exhibit reduced exhaustion transcriptional programs and enhanced AP1 pathway signatures. Finally, TNFR2 KO mice demonstrate improved T cell-dependent control of tumor and chronic lymphocytic choriomeningitis (cLCMV) infection, while pharmacologic antagonism of TNFR2 licenses responses to checkpoint blockade in multiple subcutaneous and intracranial tumor models.
Redundancy protects processing speed in healthy individuals with accelerated brain aging
Authors: Stanford William , Mucha Peter J , Dayan Eran
Published: July 2024

Recent advancements in computational learning techniques have enabled the estimation of brain age (BA) from neuroimaging data. The difference between chronological age (CA) and BA, known as the BA gap, can potentially serve as a biomarker of brain health. Studies, however, have documented low correlations between BA gap and cognition in healthy aging. This suggests that protective mechanisms in the brain may help counter the effect of accelerated brain aging. Here, we investigated whether redundancy in brain networks may protect cognitive function in individuals with accelerated brain aging. First, we employed deep learning to estimate individual brain ages from structural magnetic resonance imaging (MRI). Next, we associated CA, BA, and BA gap, with cognitive measures and network topology derived from diffusion MRI and tractography. We found that CA and BA were both similarly related to cognitive measures and network topology, while BA gap did not show strong relationships in either domain. Despite observing no strong relationships between brain-age gap (BA gap) and demographic variables, cognitive measures, or topological features in healthy aging, individuals with accelerated aging (BA gap+) exhibited lower average degree and redundancy within the dorsal attention network compared to those with delayed aging (BA gap-). Furthermore, redundancy in the dorsal attention network was positively associated with processing speed in BA gap+ individuals. These results indicate a potential neuroprotective role of redundancy in structural brain networks for mitigating the impact of accelerated brain atrophy on cognitive performance in healthy aging.
Complex Reticulation in Backbone Subfamily Relationships in Leguminosae
Authors: Stai Jacob , Cardinal-McTeague Warren , Bruneau Anne , Cannon Steven
Published: July 2024

Contradictory lines of evidence have made it difficult to resolve the phylogenetic history of the legume diversification era; this is true for the backbone topology, and for the number and timing of whole genome duplications (WGDs). By analyzing the transcriptomic data for 473 gene families in 76 species covering all six accepted legume subfamilies, we assessed the phylogenetic relationships of the legume backbone and uncovered evidence of independent whole genome duplications in each of the six legume subfamilies. Three subfamilies — Cercidoideae, Dialioideae, and Caesalpinioideae — bear evidence of an allopolyploid duplication pattern suggestive of ancient hybridization. In Cercidoideae and Dialioideae, the hybridization appears to be within-subfamily, with the generaCercisandPoeppigiaapparently unduplicated descendants of one of the parental lineages; in Caesalpinioideae, the hybridization appears to involve a member of the Papilionoideae lineage, and some other lineage, potentially extinct. Three independent lines of evidence, consisting of a concatenated superalignment, concordance factor analysis of the set of gene family alignments and topologies, and direct inference of reticulation events via maximum pseudo-likelihood implemented by PhyloNet, converged on a single backbone hypothesis and the above hypotheses of reticulate evolution.

Significance Statement

In a hybridization event, genes that have already been evolving separately for potentially millions of years become sister chromosomes, yet remain related to one another not at the moment of hybridization, but at the speciation node of the hybrid’s parents. Methodologies based on counts of bursts of duplicated genes, can therefore be fundamentally vulnerable to incorrect and contradictory conclusions about the number and timing of WGD events, unless interpreted carefully and in combination with data from gene trees discordant with the consensus backbone. Our assessment of the legume backbone in that light, resolves previous contradictory findings by concluding that three legume subfamilies are allopolyploid relative to the ur-legume.
Somy evolution in the honey bee infecting trypanosomatid parasite,Lotmaria passim
Authors: Markowitz Lindsey M. , Nearman Anthony , Zhao Zexuan , Boncristiani Dawn , Butenko Anzhelika , de Pablos Luis Miguel , Marin Arturo , Xu Guang , Machado Carlos A. , Schwarz Ryan S. , Palmer-Young Evan C. , Evans Jay D.
Published: July 2024

Lotmaria passimis a ubiquitous trypanosomatid parasite of honey bees nestled within the medically important subfamily Leishmaniinae. Although this parasite is associated with honey bee colony losses, the original draft genome—which was completed before its differentiation from the closely relatedCrithidia mellificae—has remained the reference for this species despite lacking improvements from newer methodologies. Here we report the updated sequencing, assembly, and annotation of the BRL type strain (ATCC PRA-422) ofLotmaria passim. The nuclear genome assembly has been resolved into 31 complete chromosomes and is paired with an assembled kinetoplast genome consisting of a maxicircle and 30 minicircle sequences. The assembly spans 33.7 Mb and contains very little repetitive content, from which our annotation of both the nuclear assembly and kinetoplast predicted 10,288 protein-coding genes. Analyses of the assembly revealed evidence of a recent chromosomal duplication event within chromosomes 5 and 6 and provides evidence for a high level of aneuploidy in this species, mirroring the genomic flexibility employed by other trypanosomatids as a means of adaptation to different environments. This high-quality reference can therefore provide insights into adaptations of trypanosomatids to the thermally regulated, acidic, and phytochemically rich honey bee hindgut niche, which offers parallels to the challenges faced by other Leishmaniinae during the challenges they undergo within insect vectors, during infection of mammals, and exposure to antiparasitic drugs throughout their multi-host life cycles. This reference will also facilitate investigations of strain-specific genomic polymorphisms, their role in pathogenicity, and the development of treatments for pollinator infection.
The Rbfox1/LASR complex controls alternative pre-mRNA splicing by recognition of multi-part RNA regulatory modules
Authors: Peyda Parham , Lin Chia-Ho , Onwuzurike Kelechi , Black Douglas L.
Published: July 2024

The Rbfox proteins regulate alternative pre-mRNA splicing by binding to the RNA element GCAUG. In the nucleus, most of Rbfox is bound to LASR, a complex of RNA-binding proteins that recognize additional RNA motifs. However, it remains unclear how the different subunits of the Rbfox/LASR complex act together to bind RNA and regulate splicing. We used a nuclease-protection assay to map the transcriptome-wide footprints of Rbfox1/LASR on nascent cellular RNA. In addition to GCAUG, Rbfox1/LASR binds RNA containing motifs for LASR subunits hnRNPs M, H/F, C, and Matrin3. These elements are often arranged in tandem, forming multi-part modules of RNA motifs. To distinguish contact sites of Rbfox1 from the LASR subunits, we analyzed a mutant Rbfox1(F125A) that has lost RNA binding but remains associated with LASR. Rbfox1(F125A)/LASR complexes no longer interact with GCAUG but retain binding to RNA elements for LASR. Splicing analyses reveal that in addition to activating exons through adjacent GCAUG elements, Rbfox can also stimulate exons near binding sites for LASR subunits. Mini-gene experiments demonstrate that these diverse elements produce a combined regulatory effect on a target exon. These findings illuminate how a complex of RNA-binding proteins can decode combinatorial splicing regulatory signals by recognizing groups of tandem RNA elements.
Dietary Branched Chain Amino Acids Modify Post-Infarct Cardiac Remodeling and Function in the Murine Heart
Authors: Nguyen Daniel C. , Wells Collin K. , Taylor Madison S. , Martinez-Ondaro Yania , Brittian Kenneth R. , Brainard Robert E. , Moore Joseph B. , Hill Bradford G.
Published: July 2024

Introduction

Branch-chain amino acids (BCAA) are markedly elevated in the heart following myocardial infarction (MI) in both humans and animal models. Nevertheless, it remains unclear whether dietary BCAA levels influence post-MI remodeling. We hypothesize that lowering dietary BCAA levels prevents adverse cardiac remodeling after MI.

Methods and Results

To assess whether altering dietary BCAA levels would impact circulating BCAA concentrations, mice were fed a low (1/3×), normal (1×), or high (2×) BCAA diet over a 7-day period. We found that mice fed the low BCAA diet had >2-fold lower circulating BCAA concentrations when compared with normal and high BCAA diet feeding strategies; notably, the high BCAA diet did not further increase BCAA levels over the normal chow diet. To investigate the impact of dietary BCAAs on cardiac remodeling and function after MI, male and female mice were fed either the low or high BCAA diet for 2 wk prior to MI and for 4 wk after MI. Although body weights or heart masses were not different in female mice fed the custom diets, male mice fed the high BCAA diet had significantly higher body and heart masses than those on the low BCAA diet. Echocardiographic assessments revealed that the low BCAA diet preserved stroke volume and cardiac output for the duration of the study, while the high BCAA diet led to progressive decreases in cardiac function. Although no discernible differences in cardiac fibrosis, scar collagen topography, or cardiomyocyte cross-sectional area were found between the dietary groups, male mice fed the high BCAA diet showed longer cardiomyocytes and higher capillary density compared with the low BCAA group.

Conclusions

Provision of a diet low in BCAAs to mice mitigates eccentric cardiomyocyte remodeling and loss of cardiac function after MI, with dietary effects more prominent in males.
Moderate-term dimethyl fumarate treatment reduces pathology of dystrophic skeletal and cardiac muscle in a mouse model
Authors: Kourakis Stephanie , Timpani Cara A. , Bagaric Ryan M. , Qi Bo , Ali Benazir A. , Boyer Rebecca , Spiesberger Guinevere , Kandhari Nitika , Peterson Amanda L. , Debrincat Didier , Yates Thomas J. , Yan Xu , Kuang Jujiao , de Haan Judy B. , Stupka Nicole , Nijagal Brunda , Deveson-Lucas Deanna , Fischer Dirk , Rybalka Emma
Published: July 2024

In Duchenne muscular dystrophy (DMD), corticosteroids significantly slow disease progression and have been used as a standard of care tool for more than 30 years. However, corticosteroids also impart side effects severe enough to preclude use in some patients. There remains an unmet need for new therapeutics that target the flow-on pathogenic mechanisms of DMD with a more favourable side-effect profile. We have previously demonstrated that short-term treatment with dual-purpose anti-inflammatory, anti-oxidative dimethyl fumarate (DMF), a drug with indication and established safety data in Multiple Sclerosis, more selectively modulates Duchenne (mdx) immunology than the frequently used corticosteroid, prednisone (PRED). Here, we assess the effect of moderate-term DMF treatment over 5 weeks in the typically mildmdxmouse model that we aggravated using exercise. We show that like PRED, DMF maintains anti-inflammatory action but with additional anti-fibrotic and anti-lipogenic effects on muscle with moderate-term use. This study supports our previous work highlighting DMF as a possible repurposing candidate for DMD, especially for patients who cannot tolerate chronic corticosteroid treatment.
Thermodynamics of unicellular life: Entropy production rate as function of the balanced growth rate
Authors: Droste Maarten J. , Remeijer Maaike , Planqué Robert , Bruggeman Frank J.
Published: July 2024

Abstract

In isothermal chemical reaction networks, reaction rates depend solely on the reactant concentrations setting their thermodynamic driving force. Living cells can, in addition, alter reaction rates in their enzyme-catalysed networks by changing enzyme concentrations. This gives them control over their metabolic activities, as function of conditions. Thermodynamics dictates that the steady-state entropy production rate (EPR) of an isothermal chemical reaction network rises with its reaction rates. Here we ask whether microbial cells that change their metabolism as function of growth rate can break this relation by shifting to a metabolism with a lower thermodynamic driving force at faster growth.

We address this problem by focussing on balanced microbial growth in chemostats. Since the driving force can then be determined and the growth rate can be set, chemostats allow for the calculation of the (specific) EPR.

First we prove that the EPR of a steady-state chemical reaction network rises with its driving force. Next, we study an example metabolic network with enzyme-catalysed reactions to illustrate that maximisation of specific flux can indeed lead to selection of a pathway with a lower driving force.

Following this idea, we investigate microbes that change their metabolic network responsible for catabolism from an energetically-efficient mode to a less efficient mode as function of their growth rate. This happens for instance during a shift from complete degradation of glucose at slow growth to partial degradation at fast growth. If partial degradation liberates less free energy, fast growth can occur at a reduced driving force and possibly a reduced EPR. We analyse these metabolic shifts using three models for chemostat cultivation of the yeastSaccharomyces cerevisiaethat are calibrated with experimental data. We also derive a criterion to predict when EPR drops after a metabolic switch that generalises to other organisms. Both analyses gave however inconclusive results, as current experimental evidence proved insufficient. We indicate which experiments are required to get a better understanding of the behaviour of the EPR during metabolic shifts in unicellular organisms.
Placental-brain axis in females detected within broadly impacted metabolic gene networks protects against prenatal PCB exposure
Authors: Chau Kelly , Neier Kari , Valenzuela Anthony E. , Schmidt Rebecca J. , Durbin-Johnson Blythe , Lein Pamela J. , Korf Ian , LaSalle Janine M.
Published: July 2024

Background

Neurodevelopmental disorders have a strong male bias that is poorly understood. Placenta is a rich source of molecular information about environmental interactions with genetics (including biological sex), that affect the developing brain. We investigated placental-brain transcriptional responses in an established mouse model of prenatal exposure to a human-relevant mixture of polychlorinated biphenyls (PCBs).

Results

To understand sex, tissue, and dosage effects in embryonic (E18) brain and placenta by RNAseq, we used weighted gene correlation network analysis (WGCNA) to create correlated gene networks that could be compared across sex or tissue. WGCNA revealed that expression within most correlated gene networks was significantly and strongly associated with PCB exposures, but frequently in opposite directions between male-female and placenta-brain comparisons. In both WGCNA and differentially expressed gene analyses, male brain showed more PCB-induced transcriptional changes than male placenta, but the reverse pattern was seen in females. Furthermore, non-monotonic dose responses to PCBs were observed in most gene networks but were most prominent in male brain. The transcriptomic effects of low dose PCB exposure were significantly reversed by dietary folic acid supplementation across both sexes, but these effects were strongest in female placenta. PCB-dysregulated and folic acid-reversed gene networks were commonly enriched in functions in metabolic pathways involved in energy usage and translation, with female-specific protective effects enriched in PPAR, thermogenesis, glycerolipids, and O-glycan biosynthesis, as opposed to toxicant responses in male brain.

Conclusions

The female protective effect in prenatal PCB exposures appears to be mediated by dose-dependent sex differences in transcriptional modulation of metabolism in placenta.

Graphical Abstract
Functionally constrained human proteins are less prone to mutational instability caused by single amino acid substitutions
Authors: Andrews T. Daniel , Lehmann Nicole , May Maryam , Goodall Llewelyn , Cho Eun , Chuah Aaron
Published: July 2024

It is well understood that missense mutations that disrupt protein structural stability are a common pathogenic mechanism in human genetic disease. At a proteome-wide scale, we have quantitated potential disruption of protein stability due to amino acid substitution and show that the most functionally constrained proteins are typically less susceptible to large mutational changes in stability. Mechanistically, this relates to greater intrinsic disorder among constrained proteins, but also to increased B-factors in the ordered regions of constrained proteins. This phenomenon means that constrained proteins exhibit smaller stability effects due missense mutations, and partly explains why overtransmission of pathogenic missense variation is less prevalent in genetic disorders characterised with protein truncating variation. From analysis of the predicted protein stability effects of missense genetic variation across all human proteins, we show that the most functionally constrained proteins are depleted of both destabilising (ΔΔG > 0.5 kcal/mol) and overly-stabilising (ΔΔG < -0.5 kcal/mol) amino acid variation in disease-free populations. Despite this, amino acid substitutions with large stability effects in functionally constrained proteins are still highly prevalent among pathogenic human genetic variation. Importantly, we observe that there are approximately five times more missense variants with large stability effects than there are unambiguous loss-of-function mutations. Missense variants with disruption of stability effects recapitulate the per-gene patterns of functional constraint observed with protein truncating loss-of-function variation, yet their relative abundance abrogates difficulties encountered when estimating functional constraint for the shortest human genes.