bluuebunny/crossref_metadata_2025 huggingface dataset:
Vγ9Vδ2 T cells recognize butyrophilin 2A1 and 3A1 heteromers
Authors: Fulford Thomas S. , Soliman Caroline , Castle Rebecca G. , Rigau Marc , Ruan Zheng , Dolezal Olan , Seneviratna Rebecca , Brown Hamish G. , Hanssen Eric , Hammet Andrew , Li Shihan , Redmond Samuel J. , Chung Amy , Gorman Michael A. , Parker Michael W. , Patel Onisha , Peat Thomas S. , Newman Janet , Behren Andreas , Gherardin Nicholas A. , Godfrey Dale I. , Uldrich Adam P.
Published: September 2023

Butyrophilin (BTN) molecules are emerging as key regulators of T cell immunity, however, how they trigger cell-mediated responses is poorly understood. Here, the crystal structure of a gamma-delta T cell receptor (γδTCR) in complex with BTN member 2A1 (BTN2A1) revealed that BTN2A1 engages the side of the γδTCR, leaving the apical TCR surface bioavailable. We reveal that BTN3A1 is a second γδTCR ligand, that co-engages γδTCR via binding to this accessible apical surface. BTN2A1 and BTN3A1 also directly interact with each other in cis, and structural analysis revealed formation of W-shaped heteromeric multimers. This BTN2A1–BTN3A1 interaction involved the same epitopes that BTN2A1 and BTN3A1 each use to engage γδTCR; indeed, either forced separation or locking together of BTN2A1 and BTN3A1 resulted in enhanced or abrogated γδTCR interaction, respectively. Our findings reveal a new paradigm in immune activation, whereby γδTCRs recognize dual epitopes on BTN2A1 and BTN3A1 complexes.
Enhancement of Protein Stability by Quenching Millisecond Conformational Dynamics
Authors: Hou Xue-Ni , Zhao Chang , Song Bin , Ruan Mei-Xia , Dong Xu , Gong Zhou , Weng Yu-Xiang , Zheng Jie , Tang Chun
Published: September 2023

Protein folding may involve folding intermediates. Ubiquitin (Ub) is a 76-residue small protein essential in post-translational modification and cell signaling. Ub is also a model system of protein folding. Previous studies have indicated the involvement of a folding intermediate, as Ub C-terminal residues, including strand β5, only dock correctly at a later stage. The natively folded Ub undergoes conformational dynamics over a vast range of timescales. At the millisecond timescale, Ub transiently digresses to a C-terminally retracted state, which is extremely rare and has only been recently identified at an elevated temperature. Herein through a conjoint use of NMR, MS, and MD simulations, we have established a link between Ub millisecond dynamics and protein stability. Among the alanine mutations that have been systematically introduced to the hydrophobic residues in β5, L67A and L69A elevate the population of the retracted state and enhance conformational interconversion, which facilitates the undocking of β5 and the exposure of protein hydrophobic core. Conversely, L71A and L73A mutations decrease the population of the retracted state and quench millisecond dynamics, which causes a significant enhancement of protein stability. As such, the transition state of Ub millisecond dynamics is the much sought-after folding intermediate, whereas C-terminal mutations alleviate the dependence on this intermediate and reduce the unfolding to an all-or-none process. Though having a negative impact on protein stability, Ub millisecond dynamics likely facilitate proper protein turnover and allow the fulfillment of its biological function.
Effects of pharmacological interventions on short- and long-term mortality in patients with takotsubo syndrome: a report from the SWEDEHEART registry
Authors: Petursson P , Oštarijaš E , Redfors B , Råmunddal T , Angerås O , Völz S , Rawshani A , Hambraeus K , Koul S , Alfredsson J , Hagström H , Loghman H , Hofmann R , Fröbert O , Jernberg T , James S , Erlinge D , Omerovic E
Published: September 2023

Aim

Takotsubo cardiomyopathy (TS) is a heart condition mimicking acute myocardial infarction. TS is characterized by a sudden weakening of the heart muscle, usually triggered by physical or emotional stress. In this study, we aimed to investigate the effect of pharmacological interventions on short– and long-term mortality in patients with TS.

Methods

We analyzed data from the SWEDEHEART (The Swedish Web-system for Enhancement and Development of Evidence-based care in Heart disease Evaluated According to Recommended Therapies) registry, which included 1,724 patients with TS among 228,263 unique individuals who underwent coronary angiography between 2009 and 2016. The majority of patients were female (77.0%), and the average age was 66 ± 14 years.

Results

Nearly half of the TS patients (49.4%) presented with non-ST-elevation acute coronary syndrome and a quarter (25.9%) presented as ST-elevation myocardial infarction. Most patients had non-obstructive coronary artery disease on angiography, while 11.7% had a single-vessel disease and 9.2% had multivessel disease. All patients received at least one pharmacological intervention, most used being beta-blockers or antiplatelet agents. All-cause mortality rates were 3.9% after 30-days and and 16.7% at long-term follow-up (median 877 days). Intravenous use of inotropes, diuretics, and orally administered digoxin were associated with increased mortality in TS, while ACE-I and statins were associated with decreased long-term mortality. Unfractionated and low-molecular-weight heparin (UH/LMWH) were associated with reduced 30-day mortality. However, medications such as ARBs, oral anticoagulants, P2Y12 antagonists, aspirin, and beta-blockers did not statistically correlate with mortality.

Conclusion

Our findings suggest that some medications commonly used to treat TS are associated with higher mortality while others with lower mortality. These results could inform clinical decision-making and improve patient outcomes in TS. Further research is warranted to validate these findings and to identify optimal pharmacological interventions for patients with TS.
Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Ciénegas Basin, Mexico
Authors: Cisneros-Martínez Alejandro Miguel , Rodriguez-Cruz Ulises E. , Alcaraz Luis D. , Becerra Arturo , Eguiarte Luis E. , Souza Valeria
Published: September 2023

The sheer diversity of unculturable viruses has prompted the need to describe new viruses through culture-independent techniques. The associated host is one important phenotypic feature that can be inferred from metagenomic viral contigs -- thanks to the development of various bioinformatic tools. Here we compare the performance of recently developed tools for virus-host prediction on a dataset of 1,046 virus-host pairs and then apply the best-performing tools on a metagenomic dataset derived from a highly diverse transiently hypersaline site known as Archaean Domes within the Cuatro Ciénegas Basin, Coahuila, Mexico. We also introduce a virus-host prediction tool called CrisprCustomDB, which uses specific criteria to solve controversial host assignments with custom spacers databases. Host-dependent alignment-based methods showed an average precision of 83% and a sensitivity from 13.7% to 17.7%, whereas host-dependent alignment-free methods achieved an average precision of 75.7% and a sensitivity of 57.5%. RaFAH, a virus-dependent alignment-based tool, had the best performance overall (F1_score = 95.7%). However, when applied to the highly diverse metagenomic dataset, the host-dependent alignment-based (e.g., CrisprCustomDB) and alignment-free (e.g., PHP) methods showed the greatest agreement with each other, even though they are fundamentally different methods. This is because instead of depending on known hosts or viruses-with-known-host databases, they can directly relate metagenomic viral contigs and metagenome-assembled genomes from the same dataset. Such methods also showed the greatest consistency between the source environment and the predicted host taxonomy, habitat, lifestyle, or metabolism, revealing that Archaean Domes viruses likely infect halophilic Archaea as well as a variety of Bacteria which may be halophilic, halotolerant, alkaliphilic, thermophilic, oligotrophic, sulfate-reducing or marine-related. Consequently, using a combination of methods and qualitative validations relating to the source environment and the predicted host biology will increase the number of correct predictions, mainly when dealing with novel viruses.
PTMNavigator: Interactive Visualization of Differentially Regulated Post-Translational Modifications in Cellular Signaling Pathways
Authors: Müller Julian , Bayer Florian P. , Wilhelm Mathias , Schuh Maximilian G. , Kuster Bernhard , The Matthew
Published: September 2023

Post-translational modifications (PTMs) play pivotal roles in regulating cellular signaling, fine-tuning protein function, and orchestrating complex biological processes. Despite their importance, the lack of comprehensive tools for studying PTMs from a pathway-centric perspective has limited our ability to understand how PTMs modulate cellular pathways on a molecular level. Here, we present PTMNavigator, a tool integrated into the ProteomicsDB platform, which offers an interactive interface for researchers to overlay experimental PTM data with pathway diagrams. PTMNavigator provides ∼3000 canonical pathways from manually curated databases and further enables users to modify and create custom diagrams, tailored to their data. Additionally, PTMNavigator automatically runs multiple kinase and pathway enrichment algorithms whose results are directly integrated into the visualization. This offers a comprehensive view of the intricate relationship between PTMs and signaling pathways. To demonstrate the utility of PTMNavigator, we applied it to two phosphoproteomics perturbation datasets. First, PTMNavigator enhanced pathway enrichment analysis by showing how the regulated peptides and proteins are distributed in the pathways with high enrichment scores. Second, it visualized how drug treatments result in a discernable flow of PTM-driven signaling within pathways. Third, PTMNavigator aided in proposing extensions to an existing pathway by suggesting putative new links between both PTMs and pathway components. By enhancing our understanding of cellular signaling dynamics and facilitating the discovery of novel PTM-pathway interactions, PTMNavigator advances our knowledge of PTM biology and its implications in health and disease.
Gut microbes contribute to variation in foraging intensity in the honey bee,Apis mellifera
Authors: Vernier Cassondra L. , Nguyen Thi Lan Anh , Gernat Tim , Ahmed Amy Cash , Chen Zhenqing , Robinson Gene E.
Published: September 2023

Gut microbiomes are increasingly recognized for mediating diverse biological aspects of their hosts, including complex behavioral phenotypes. While many studies have reported that experimental disruptions to the gut microbiome result in atypical host behavior, studies that address how gut microbes contribute to adaptive behavioral trait variation are rare. Eusocial insects represent a powerful model to test this, due to their simple microbiomes and complex division of labor characterized by colony-level variation in behavioral phenotypes. While previous studies report correlational differences in gut microbiome associated with division of labor, here, we provide evidence that gut microbes play a causal role in defining differences in foraging behavior between honey bees. Gut microbial community structure consistently differed between hive-based nurse bees and bees that leave the hive to forage for floral resources. These differences were associated with variation in the abundance of individual microbes, includingBifidobacterium asteroides, Bombilactobacillus mellis,andLactobacillus melliventris. Manipulations of colony demography and individual foraging experience suggested that differences in microbiome composition were associated with task experience. Moreover, single microbe inoculations withB. asteroides,B. mellis,andL. melliventriscaused changes in foraging intensity. These results demonstrate that gut microbes contribute to division of labor in a social insect, and support a role of gut microbes in modulating host behavioral phenotypic variation.
Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53
Authors: Lee Jonathan D. , Menasche Bridget L. , Mavrikaki Maria , Uyemura Madison M. , Hong Su Min , Kozlova Nina , Wei Jin , Alfajaro Mia M. , Filler Renata B. , Müller Arne , Saxena Tanvi , Posey Ryan R. , Cheung Priscilla , Muranen Taru , Heng Yujing J. , Paulo Joao A. , Wilen Craig B. , Slack Frank J.
Published: September 2023

COVID-19 remains a significant public health threat due to the ability of SARS-CoV-2 variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and MERS-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here we used our recently developed integrative DNA And Protein Tagging (iDAPT) methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. SARS-CoV-2 infection induces TP53 stabilization on chromatin, which contributes to its host cytopathic effect. We mapped this TP53 stabilization to the SARS-CoV-2 spike and its propensity to form syncytia, a consequence of cell-cell fusion. Differences in SARS-CoV-2 spike variant-induced syncytia formation modify chromatin accessibility, cellular senescence, and inflammatory cytokine release via TP53. Our findings suggest that differences in syncytia formation alter senescence-associated inflammation, which varies among SARS-CoV-2 variants.
SOD1is a synthetic lethal target inPPM1D-mutant leukemia cells
Authors: Zhang Linda , Hsu Joanne I. , Braekeleer Etienne D. , Chen Chun-Wei , Patel Tajhal D. , Martell Alejandra G. , Guzman Anna G. , Wohlan Katharina , Waldvogel Sarah M. , Urya Hidetaka , Tovy Ayala , Callen Elsa , Murdaugh Rebecca , Richard Rosemary , Jansen Sandra , Vissers Lisenka , de Vries Bert B.A. , Nussenzweig Andre , Huang Shixia , Coarfa Cristian , Anastas Jamie N. , Takahashi Koichi , Vassiliou George , Goodell Margaret A.
Published: September 2023

The DNA damage response is critical for maintaining genome integrity and is commonly disrupted in the development of cancer. PPM1D (protein phosphatase, Mg2+/Mn2+ dependent 1D) is a master negative regulator of the response; gain-of-function mutations and amplifications ofPPM1Dare found across several human cancers making it a relevant pharmacologic target. Here, we used CRISPR/Cas9 screening to identify synthetic-lethal dependencies ofPPM1D,uncovering superoxide dismutase-1 (SOD1) as a potential target for PPM1D-mutant cells. We revealed a dysregulated redox landscape characterized by elevated levels of reactive oxygen species and a compromised response to oxidative stress inPPM1D-mutant cells. Altogether, our results demonstrate the protective role of SOD1 against oxidative stress inPPM1D-mutant leukemia cells and highlight a new potential therapeutic strategy againstPPM1D-mutant cancers.
Cryo-EM structures of Tau filaments from the brains of mice transgenic for human mutant P301S Tau
Authors: Schweighauser Manuel , Murzin Alexey G. , Macdonald Jennifer , Lavenir Isabelle L. , Crowther R. Anthony , Scheres Sjors H.W. , Goedert Michel
Published: September 2023

Mice transgenic for human mutant P301S tau are widely used as models for human tauopathies. They develop neurodegeneration and abundant filamentous inclusions made of human mutant four-repeat tau. Here we used electron cryo-microscopy (cryo-EM) to determine the structures of tau filaments from the brains of Tg2541 and PS19 mice. Both lines express human P301S tau (0N4R for Tg2541 and 1N4R for PS19) on mixed genetic backgrounds and downstream of different promoters (murineThy1for Tg2541 and murinePrnpfor PS19). The structures of tau filaments from Tg2541 and PS19 mice differ from each other and those of tau filaments from human brains. However, they share a substructure at the junction of repeats 2 and 3, which comprises residues I297-V312 of tau and includes the P301S mutation. The filament core from the brainstem of Tg2541 mice consists of residues K274-H329 of tau and two disconnected protein densities. Two non-proteinaceous densities are also in evidence. The filament core from the cerebral cortex of line PS19 extends from residues G271-P364 of tau. One strong non-proteinaceous density is also present. Unlike the tau filaments from human brains, the sequences following repeat 4 are missing from the cores of tau filaments from the brains of Tg2541 and PS19 mice.
A Two-Step Activation Mechanism Enables Mast Cells to Differentiate their Response between Extracellular and Invasive Enterobacterial Infection
Authors: von Beek Christopher , Fahlgren Anna , Geiser Petra , Di Martino Maria Letizia , Lindahl Otto , Prensa Grisna I. , Mendez-Enriquez Erika , Eriksson Jens , Hallgren Jenny , Fällman Maria , Pejler Gunnar , Sellin Mikael E.
Published: September 2023

Mast cells (MCs) localize to mucosal tissues and contribute to innate immune defenses against infection. How MCs sense, differentiate between, and respond to bacterial pathogens remains a topic of ongoing debate. Using the prototype enteropathogenSalmonellaTyphimurium (S.Tm) and other closely related enterobacteria, we here demonstrate that MCs can regulate their cytokine secretion response to distinguish between extracellular and invasive bacterial infection. Tissue-invasiveS.Tm and MCs colocalize in theSalmonella-infected mouse gut. Toll-like Receptor 4 (TLR4) sensing of extracellularS.Tm, or pure LPS, causes a slow and modest induction of MC cytokine transcripts and proteins, including IL-6, IL-13, and TNF. By contrast, type-III-secretion-system-1 (TTSS-1)-dependentS.Tm invasion of both mouse and human MCs triggers rapid and potent inflammatory gene expression and >100-fold elevated cytokine secretion. TheS.Tm TTSS-1 effectors SopB, SopE, and SopE2 here elicit a second activation signal, including Akt phosphorylation downstream of effector translocation, which combines with TLR activation to promote the full-blown MC response. Supernatants fromS.Tm-infected MCs boost macrophage survival and maturation from bone-marrow progenitors. Taken together, this study shows that MCs can differentiate between extracellular and host-cell invasive enterobacteria via a two-step activation mechanism and tune their inflammatory output accordingly.
In-situ Single-Molecule Investigations of the Impacts of Biochemical Perturbations on Conformational Intermediates of Monomeric α-Synuclein
Authors: Huang Wenmao , Le Shimin , Yao Mingxi , Shi Yi , Yan Jie
Published: September 2023

α-Synuclein aggregation is a common trait in synucleinopathies, including Parkinson’s disease. Being an unstructured protein, α-synuclein exists in several distinct conformational intermediates, contributing to both its function and pathogenesis. However, the regulation of these monomer conformations by biochemical factors and potential drugs has remained elusive. In this study, we devised an in-situ single-molecule manipulation approach to pinpoint kinetically stable conformational intermediates of monomeric α-synuclein and explore the effects of various biochemical factors and drugs. We uncovered a partially folded conformation located in the non-amyloid-β component (NAC) region of monomeric α-synuclein, which is regulated by preNAC region. This conformational intermediate is sensitive to biochemical perturbations and small-molecule drugs that influencing α-synuclein’s aggregation tendency. Our findings reveal that this partially folded intermediate may play a role in α-synuclein aggregation, offering fresh perspectives for potential treatments aimed at the initial stage of higher-order α-synuclein aggregation. The single-molecule approach developed here can be broadly applied to the study of disease-related intrinsically disordered proteins.
Transcriptome-wide meta-analysis of codon usage inEscherichia coli
Authors: Sutradhar Anima , Pointon Jonathan , Lennon Christopher , Stracquadanio Giovanni
Published: September 2023

The preference for synonymous codons, termed codon usage bias (CUB), is a fundamental feature of coding sequences, with distinct preferences being observed across species, genomes and genes. Accurately quantifying codon usage frequencies is useful for a range of applications, from guiding mRNA vaccine design, to elucidating protein folding and uncovering co-evolutionary relationships. However, current methods are either based on a single genome assembly, lack functional stratification, or are extremely outdated. To address this, we adopted a data-driven approach and developed Codon Usage Bias estimation from RNA-sequencing data (CUBSEQ), a fully automatic meta-analysis pipeline to estimate CUB at the trascriptome-level and for gene panels. Here, we used CUBSEQ to perform, to our knowledge, the largest and most comprehensive CUB analysis of the transcriptome and highly expressed genes inEscherichia coli, using RNA sequencing data from 6,763 samples across 72 strains. By capturing sequence variants of these genes through variant calls, we constructed a per-sample representation of theE. colitranscriptome revealing a rich mutational landscape. We then identified a set of 81 highly expressed genes with consistent expression patterns across strains, sample library size and experimental conditions, and found significant differences in CUB compared to transcriptome-wide genes and alternative codon usage tables. Finally, we found codons with a high relative frequency were often associated with a larger repertoire of isoaccepting tRNAs and not necessarily high tRNA abundance.
The Alzheimer’s disease risk gene CD2AP functions in dendritic spines by remodelling F-actin
Authors: Mirfakhar Farzaneh S. , Castanheira Jorge , Domingues Raquel , Ramalho José S. , Almeida Cláudia Guimas
Published: September 2023

CD2AP was identified as a genetic risk factor for late-onset Alzheimer’s disease (LOAD). However, how CD2AP contributes to LOAD synaptic dysfunction underlying AD memory deficits is unclear. We have shown that CD2AP loss-of-function increases β-amyloid (Aβ) endocytic production, but whether it contributes to synapse dysfunction is unknown. Because CD2AP is an actin-binding protein, it may also function in F-actin-rich dendritic spines, the excitatory postsynaptic compartment. Here, we demonstrate that CD2AP colocalises with F-actin in dendritic spines. Cell-autonomous depletion of CD2AP specifically reduces spine density and volume, with a functional decrease in synapse formation and neuronal network activity. Post-synaptic reexpression of CD2AP but not blocking Aβ-production is sufficient to rescue spine density. CD2AP overexpression increases spine density, volume, and synapse formation, while a rare LOAD CD2AP mutation induces aberrant F-actin spine-like protrusions without synapses. CD2AP controls postsynaptic actin turnover, with the LOAD mutation in CD2AP decreasing F-actin dynamicity. Our data support that CD2AP risk variants could contribute to LOAD synapse dysfunction by disrupting spine formation and growth by deregulating actin dynamics.

Graphical abstract
Multifractal signatures in ossification reveal a disordered-to-ordered transition in mineral patterns
Authors: Bahadorian Mohammadreza , Lattner Johanna , Tabler Jacqueline M. , Modes Carl D.
Published: September 2023

Developing biological systems can exhibit both dynamic pattern formation and cross-scale interactions. Multiscale relationships are critical in the establishment of these patterns but remain poorly understood. Classification of mineral pattern in bone is a quintessential example. One approach to quantifying these patterns relies upon statistical self-similarity and, in particular, monofractal analysis. However, simple monofractal characterisations fail to capture the complexity of multiscale interactions in developing biological systems. Here we show that multifractal techniques, effectively capture the complex patterns of self-similarity in a dimensionally reduced, usable way. Further, we show that a simple generative model of ossification in the mouse skull, coupled with multifractal methods indicates a primary role of collagen density in pattern establishment and predicts the existence of a sharp boundary in pattern complexity.
Gene expression analysis suggests immunosuppressive roles of endolysosomes in glioblastoma
Authors: Sun Michael A , Yao Haipei , Yang Qing , Pirozzi Christopher J. , Chandramohan Vidyalakshmi , Ashley David M. , He Yiping
Published: September 2023

Targeting endolysosomes is a strategy extensively pursued for treating cancers, including glioblastomas (GBMs), mainly on the basis that the intact function of these subcellular organelles is key to tumor cell autophagy and survival. Here, by gene expression analyses and cell type abundance estimation in GBMs, we showed that genes associated with the endolysosomal machinery are more prominently featured in non-tumor cells in GBMs than in tumor cells, and that tumor-associated macrophages represent the primary immune cell type that contributes to this trend. Further analyses found an enrichment of endolysosomal pathway genes in immunosuppressive (pro-tumorigenic) macrophages, such as M2-like macrophages or those associated with worse prognosis in glioma patients, but not in those linked to inflammation (anti-tumorigenic). Specifically, genes critical to the hydrolysis function of endolysosomes, including progranulin and cathepsins, were among the most positively correlated with immunosuppressive macrophages, and elevated expression of these genes is associated with worse patient survival in GBMs. Together, these results implicate the hydrolysis function of endolysosomes in shaping the immunosuppressive microenvironment of GBM. We propose that targeting endolysosomes, in addition to its detrimental effects on tumor cells, can be leveraged for modulating immunosuppression to render GBMs more amendable to immunotherapies.
The Dynamics of the Female Microbiome: Unveiling Abrupt Changes of Microbial Domains across Body Sites from Preconception to Perinatal Phase
Authors: Neumann Charlotte J , Pausan Manuela-Raluca , Haid Victoria , Weiss Eva-Christine , Kolovetsiou-Kreiner Vassiliki , Amtmann Bettina , Winkler Petra , Mahnert Alexander , Jantscher-Krenn Evelyn , Moissl-Eichinger Christine
Published: September 2023

The microbial ecosystem of women undergoes enormous changes during pregnancy and the perinatal period. Little is known about the extent of changes in the maternal microbiome beyond the vaginal cavity and its recovery after birth. In this study, we followed pregnant women (mpre,n= 30) into the postpartum period (1 month postpartum, mpost,n= 30). We profiled their oral, urinary, and vaginal microbiome, archaeome, mycobiome and urinary metabolome and compared them with nonpregnant women (np,n= 29).

Overall, pregnancy status (np, mpre, mpost) had a smaller effect on the microbiomes than body site, but massive transitions were observed for the oral and urogenital (vaginal and urinary) microbiomes. While the oral microbiome fluctuates during pregnancy but stabilizes rapidly within the first month postpartum, the urogenital microbiome is characterized by a major remodeling caused by a massive loss ofLactobacillusand thus a shift from vaginal community state type (CST) I (40% of women) to CST IV (85% of women). The urinary metabolome rapidly reached an np-like composition after delivery, apart from lactose and oxaloacetic acid, which were elevated during active lactation. Fungal and archaeal profiles were indicative of pregnancy status.Methanobacteriumsignatures were found exclusively in np women, andMethanobrevibactershowed opposite behavior in oral cavity (increased) and vagina (decreased) during pregnancy.

Our findings suggest that the massive remodeling of the maternal microbiome and metabolome needs more attention and that potential interventions could be envisioned to optimize recovery and avoid long-term effects on maternal health and subsequent pregnancies.
Homeostasis of cytoplasmic crowding by cell wall fluidization and ribosomal counterions
Authors: Mukherjee Avik , Huang Yanqing , Oh Seungeun , Sanchez Carlos , Chang Yu-Fang , Liu Xili , Bradshaw Gary Andrew , Benites Nina Catherine , Paulsson Johan , Kirschner Marc W. , Sung Yongjin , Elgeti Jens , Basan Markus
Published: September 2023

In bacteria, algae, fungi, and plant cells, the wall must expand in concert with cytoplasmic biomass production, otherwise cells would experience toxic molecular crowding1,2or lyse. But how cells achieve expansion of this complex biomaterial in coordination with biosynthesis of macromolecules in the cytoplasm remains unexplained3, although recent works have revealed that these processes are indeed coupled4,5. Here, we report a striking increase of turgor pressure with growth rate inE. coli, suggesting that the speed of cell wall expansion is controlled via turgor. Remarkably, despite this increase in turgor pressure, cellular biomass density remains constant across a wide range of growth rates. By contrast, perturbations of turgor pressure that deviate from this scaling directly alter biomass density. A mathematical model based on cell wall fluidization by cell wall endopeptidases not only explains these apparently confounding observations but makes surprising quantitative predictions that we validated experimentally. The picture that emerges is that turgor pressure is directly controlled via counterions of ribosomal RNA. Elegantly, the coupling between rRNA and turgor pressure simultaneously coordinates cell wall expansion across a wide range of growth rates and exerts homeostatic feedback control on biomass density. This mechanism may regulate cell wall biosynthesis from microbes to plants and has important implications for the mechanism of action of antibiotics6.
SMAD4 promotes somatic-germline contact during murine oocyte growth
Authors: Granados-Aparici Sofia , Yang Qin , Clarke Hugh
Published: September 2023

Development of the mammalian oocyte requires physical contact with the surrounding granulosa cells of the follicle, which provide it with essential nutrients and regulatory signals. This contact is achieved through specialized filopodia, termed transzonal projections (TZPs), that extend from the granulosa cells to the oocyte surface. Transforming growth factor (TGFβ) family ligands produced by the oocyte increase the number of TZPs, but how they do so is unknown. Using an inducible Cre recombinase strategy together with expression of green fluorescent protein to verify Cre activity in individual granulosa cells, we examined the effect of depleting the canonical TGFβ mediator, SMAD4. We observed a 20-50% decrease in the total number of TZPs in SMAD4-depleted granulosa cell-oocyte complexes, and a 50% decrease in the number of newly generated TZPs when the granulosa cells were reaggregated with granulosa cell-free wild-type oocytes. Three-dimensional image analysis revealed that TZPs of SMAD4-depleted cells were also longer than controls and more frequently oriented towards the oocyte. Strikingly, the transmembrane proteins, N-cadherin and Notch2, were reduced by 50% in these cells. SMAD4 may thus modulate a network of cell adhesion proteins that stabilize the attachment of TZPs to the oocyte, thereby amplifying signalling between the two cell types.

Impact statement

Genetic deletion of SMAD4 in the granulosa cells of growing ovarian follicles reduces the number of transzonal projections that contact the oocyte, implicating TGFβ-family signaling in maintaining soma-germ line communication.
What is the best method for estimating ancestral states from discrete characters?
Authors: Keating Joseph N
Published: September 2023

Ancestral state estimation is a formal phylogenetic method for inferring the nature of ancestors and performing tests of character evolution. As such, it is among the most important tools available to evolutionary biologists. However, there are a profusion of methods available, the accuracy of which remains unclear. Here I use a simulation approach to test between parsimony and likelihood methods for estimating ancestral states from discrete binary characters. I simulate 500 characters using 15 different Markov generating models, a range of tree sizes (8-256 tips) and three topologies representing end members of tree symmetry and branch length heterogeneity. Simulated tip states were subjected to ancestral state estimation under the Equal Rates (ER) and All-Rates-Different (ARD) models, as well as under parsimony assuming accelerated transformations (ACCTRAN). The results demonstrate that both parsimony and likelihood approaches obtain high accuracy applied to trees with more tips. Parsimony performs poorly when trees contain long branches, whereas the ER model performs well across simulations and is reasonably robust to model violation. The ER model frequently outperforms the ARD model, even when data are simulated using unequal rates. Furthermore, the ER model exhibits less transition rate error when compared to ER models. These results suggest that ARD models may be overparameterized when character data is limited. Surprisingly, the difference in likelihood-based information criteria between models was found to be a poor predictor of difference in model error; better fitting models are not necessarily more accurate. However, there is a strong correlation between model uncertainty and model error; likelihood models with more certain ancestral state estimates are typically more accurate. Using empirical morphological datasets, I demonstrate that applying different methods often results in substantively different ancestral state estimates. The results of the simulation study highlight the importance of incorporating fossils in ancestral state estimation. Fossils increase the total number of tips, break long branches and are closer to internal nodes, thereby lowering average branch length and overall branch length heterogeneity of trees. These factors will all contribute to increasing the accuracy of ancestral state estimates, irrespective of the method used.
Optimization of RNAi efficiency in PVD neuron ofC. elegans
Authors: Singh Pallavi , Selvarasu Kavinila , Ghosh-Roy Anindya
Published: September 2023

PVD neuron ofC. eleganshas become an attractive model for the study of dendrite development and regeneration due to the elaborate and stereotype dendrite morphology in this neuron. The molecular basis for dendrite maintenance and regeneration is poorly understood. RNA interference (RNAi) by feedingE. coliexpressing dsRNA has been the basis of several genome wide screens performed usingC. elegans. However, the feeding method often fails when it comes to nervous system. Using an optimal induction condition for the dsRNA expression inE coli, we fed the worm strains with HT115 bacteria expressing dsRNA against genes likemec-3, hpo-30,andtiam-1, whose loss of function are known to show dendrite morphology defects in PVD neuron. We found that RNAi of these genes in the strains such asnre-1(-) lin-15b(-), lin-15b(-)andsid-1(-); lin-15b(-); Punc-119::sid-1[+]resulted in significant reduction of dendrite branching. However, the phenotypes were significantly modest compared to the respective loss of function mutants. To obtain stronger phenotype for PVD specific genes, we have made a strain, which strongly expressessid-1undermec-3promoter specific for PVD. WhenPmec-3::sid-1is expressed in eithernre-1(-);lin-15b(-)orlin-15b(-)background, the higher order branching phenotype after RNAi ofmec-3, hpo-30,andtiam-1was significantly enhanced as compared tonre-1(-);lin-15b(-)andlin-15b(-)background alone. Next we tested thenre-1(-) lin-15b(-),Pmec-3-sid-1[+]strain for the knockdown of genes playing role in dendrite regeneration process. We found that whenaff-1andced-10genes were knocked down in thenre-1(-) lin-15b(-),Pmec-3-sid-1[+]background, the dendrite regeneration was significantly reduced and the extent of reduction was comparable to that of the mutants ofaff-1andced-10. Essentially, our strain expressingsid-1in PVD neuron optimizes the condition for RNAi for high throughput screening for PVD development, maintenance and regeneration.
Sequential early-life viral infections modulate the microbiota and adaptive immune responses to systemic and mucosal vaccination
Authors: Li Yuhao , Molleston Jerome M. , Kim Andrew H. , Ingle Harshad , Aggarwal Somya , Nolan Lila S. , Hassan Ahmed O. , Foster Lynne , Diamond Michael S. , Baldridge Megan T.
Published: September 2023

Increasing evidence points to the microbial exposome as a critical factor in maturing and shaping the host immune system, thereby influencing responses to immune challenges such as infections or vaccines. To investigate the effect of early-life viral exposures on immune development and vaccine responses, we inoculated mice with six distinct viral pathogens in sequence beginning in the neonatal period, and then evaluated their immune signatures before and after intramuscular or intranasal vaccination against SARS-CoV-2. Sequential viral infection drove profound changes in all aspects of the immune system, including increasing circulating leukocytes, altering innate and adaptive immune cell lineages in tissues, and markedly influencing serum cytokine and total antibody levels. Beyond these immune responses changes, these exposures also modulated the composition of the endogenous intestinal microbiota. Although sequentially-infected mice exhibited increased systemic immune activation and T cell responses after intramuscular and intranasal SARS-CoV-2 immunization, we observed decreased vaccine-induced antibody responses in these animals. These results suggest that early-life viral exposures are sufficient to diminish antibody responses to vaccination in mice, and highlight their potential importance of considering prior microbial exposures when investigating vaccine responses.
Global conservation prioritization approach provides credible results at a regional scale
Authors: Roswell Michael , Espíndola Anahí
Published: September 2023

Aim

Conservationists and managers must direct resources and enact measures to protect species, despite uncertainty about their present status. One approach to covering the data gap is borrowing information from data-rich species or populations to guide decisions about data-poor ones, via machine learning. Recent efforts demonstrated proof-of-concept at the global scale, leaving unclear whether similar approaches are feasible at the local and regional scales at which conservation actions most typically occur. To address this gap, we tested a global-scale predictive approach at a regional scale, using two groups of taxa.

Location

State of Maryland, USA.

Taxa

Vascular land plants and lepidopterans.

Methods

Using publicly available occurrence and biogeographic data, we trained random forest classifiers to predict the State-level conservation status of species in each of the two focal taxa. We assessed model performance with cross-validation, and explored trends in the predictions.

Results

Our models had strong discriminatory ability, accurately predicting status for species with existing status assessments. They predict that the northwestern part of Maryland, USA, which overlaps the Appalachian Mountains, harbors a higher concentration of unassessed, but likely threatened plants and lepidopterans. Our predictions track known biogeographic patterns, and unassessed species predicted as most likely threatened in Maryland were often recognized as also needing conservation in nearby jurisdictions, providing external validation to our results.

Main Conclusions

We demonstrate that a modelling approach developed for global analysis can be downscaled and credible when applied at a regional scale that is smaller than typical species ranges. We identified select unassessed plant and lepidopteran species, and the western, montane region of Maryland as priority targets for additional monitoring, assessment, and conservation. By rapidly aggregating disparate data and integrating information across taxa, models like those we used can complement traditional assessment tools and assist in prioritization for formal assessments, as well as protection.
Consideration of a Liquid mutation-accumulation Experiment to Measure Mutation Rates by Successive Serial Dilution
Authors: Baehr Stephan , Ho Wei-Chin , Perez Sam , Cenzano Alyssa , Hancock Katelyn , Patrick Lea , Brown Adalyn , Miller Sam , Lynch Michael
Published: September 2023

The mutation-accumulation (MA) experiment is a fixture of evolutionary biology, though it is laborious to perform. MA experiments typically take between months and years to acquire sufficient mutations to measure DNA mutation rates and mutation spectra. MA experiments for many organisms rely on colony formation on agar plates and repetitive streaking, an environment which at first glance appears somewhat contrived, a poor imitation of real environmental living conditions. We propose that a fully liquid-phase mutation-accumulation experiment may at times more accurately reflect the environment of an organism. We note also that whereas automation of streaking plates is a daunting prospect, automation of liquid handling and serial dilution is already commonplace. In principle, this type of MA experiment can be automated so as to reduce the human capital requirements of measuring mutation rates. We demonstrate that a liquid MA recapitulates the mutation rate estimated for MMR-E. coliin liquid LB culture vs. plate LB culture. We detect a modified mutation spectrum with a transition skew of 4:1 of A:T→G:C vs G:C→A:T mutations, highlighting the potential role of tautomerization as a DNA mutation mechanism. We also find that using a plate reader to measure OD600 as a proxy for cell growth to be incapable of measuring carrying capacity for MA lines burdened with many mutations.
Time-lapse mesoscopy ofCandida albicansandStaphylococcus aureusdual-species biofilms reveals a structural role for the hyphae ofC. albicansin biofilm formation
Authors: Baxter Katherine J. , Sargison Fiona A. , Fitzgerald J. Ross , McConnell Gail , Hoskisson Paul A.
Published: September 2023

Polymicrobial infection withCandida albicansandStaphylococcus aureusmay result in a concomitant increase in virulence and resistance to antimicrobial drugs. This enhanced pathogenicity phenotype is mediated by numerous factors including metabolic processes and direct interaction ofS. aureuswithC. albicanshyphae. The overall structure of biofilms is known to contribute to their recalcitrance to treatment, however the dynamics of direct interaction between species and how it contributes to pathogenicity is poorly understood. To address this, a novel time-lapse mesoscopic optical imaging method was developed to enable the formation ofC. albicans/S. aureuswhole dual-species biofilms to be followed. It was found that yeast-form or hyphal-formC. albicansin the biofilm founder-population profoundly affects the structure of the biofilm as it matures. Different sub-populations ofC. albicansandS. aureusarise within each biofilm as a result of the differentC. albicansmorphotypes, resulting in distinct sub-regions. These data reveal thatC. albicanscell morphology is pivotal in the development of global biofilm architecture and the emergence of colony macrostructures and may temporally influence synergy in infection.
Space wandering in the rodent default mode network
Authors: Nghiem Trang-Anh Estelle , Lee Byeongwook , Chao Tzu-Hao Harry , Branigan Nicholas K. , Mistry Percy K. , Shih Yen-Yu Ian , Menon Vinod
Published: September 2023

The default mode network (DMN) is a large-scale brain network known to be suppressed during a wide range of cognitive tasks. However, our comprehension of its role in naturalistic and unconstrained behaviors has remained elusive because most research on the DMN has been conducted within the restrictive confines of MRI scanners. Here we use multisite GCaMP fiber photometry with simultaneous videography to probe DMN function in awake, freely exploring rats. We examined neural dynamics in three core DMN nodes— the retrosplenial cortex, cingulate cortex, and prelimbic cortex— as well as the anterior insula node of the salience network, and their association with the rats’ spatial exploration behaviors. We found that DMN nodes displayed a hierarchical functional organization during spatial exploration, characterized by stronger coupling with each other than with the anterior insula. Crucially, these DMN nodes encoded the kinematics of spatial exploration, including linear and angular velocity. Additionally, we identified latent brain states that encoded distinct patterns of time-varying exploration behaviors and discovered that higher linear velocity was associated with enhanced DMN activity, heightened synchronization among DMN nodes, and increased anticorrelation between the DMN and anterior insula. Our findings highlight the involvement of the DMN in collectively and dynamically encoding spatial exploration in a real-world setting. Our findings challenge the notion that the DMN is primarily a “ task-negative” network disengaged from the external world. By illuminating the DMN’s role in naturalistic behaviors, our study underscores the importance of investigating brain network function in ecologically valid contexts.

Significance statement

Our research advances understanding of the default mode network (DMN), a brain network implicated in numerous neuropsychiatric and neurological disorders. In contrast to previous research examining immobilized subjects, we took the novel approach of investigating DMN function during naturalistic behaviors in freely moving rodents. Using a combination of multisite fiber photometry, video tracking, and computational modeling, we discovered a prominent role for the DMN in naturalistic real-world spatial exploration. Our findings challenge conventional views that the DMN is disengaged from interactions with the external world and underscore the importance of probing brain function in ecologically relevant settings. This work enriches our understanding of brain function and has important implications for pre-clinical investigations of disorders involving DMN dysfunction.
Characterization of low copy number human angiotensin-converting enzyme 2 (hACE2)-transgenic mice as an improved model of SARS-CoV-2 infection
Authors: Bradshaw Christine M. , Georgieva Teodora , Tankersley Trevor N. , Taylor-Doyle Tama , Johnson Larry , Uhrlaub Jennifer L. , Besselsen David , Nikolich Janko Ž.
Published: September 2023

Coronaviridae are significant human pathogens, as evidenced by several outbreaks of severe respiratory infections in the past 20 years and culminating with the COVID-19 pandemic. Mouse models of COVID-19 have included transgenic expression of the main SARS coronavirus entry receptor on human cells, human angiotensin-converting enzyme 2 (hACE2). However, the original hACE2-Tg mouse strain overexpresses many copies of the transgene, leading to neuropathology not representative of human infection. Aiming to improve physiological relevance, we generated two new lines of hACE2-Tg mice using the original transgene construct expressing hACE2 under the control of the keratin 18 promoter (K18-hACE2).

We show that relative to the original strain, which expressed 8 copies of the transgene (8-hACE2-Tg), lines 1 and 2 expressed 1 and 2 copies of the transgene (1-hACE-2-Tg and 2-hACE-2-Tg, respectively). Upon intranasal (i.n.) infection with 103plaque-forming units (pfu) SARS-CoV-2 WA-1/US, 8-hACE2-Tg mice succumbed to infection by d. 7. 2-hACE2-Tg mice exhibited 31% survival, with less viral replication in the lung and brain when compared to 8-hACE2-Tg mice. Furthermore, SARS-CoV-2 infection in 1-hACE2-Tg mice exhibited no mortality and had no detectable virus in the brain, although they did show clear virus replication in the lung. All three mouse strains analyzed showed SARS-CoV-2-related weight loss that tracked with the mortality rates. 1-hACE2-Tg mice mounted detectable primary and memory T effector cell and antibody responses. We conclude that these strains, particularly 1-hACE2-Tg mice, provide improved models to study hACE2-mediated viral infections.