bluuebunny/crossref_metadata_2025 huggingface dataset:
A stargate mechanism ofMicroviridaegenome delivery unveiled by cryogenic electron tomography
Authors: Bardy Pavol , MacDonald Conor I.W. , Kirchberger Paul C. , Jenkins Huw T. , Botka Tibor , Byrom Lewis , Alim Nawshin T.B. , Traore Daouda A.K. , König Hannah C. , Nicholas Tristan R. , Chechik Maria , Hart Samuel J. , Turkenburg Johan P. , Blaza James N. , Beatty J. Thomas , Fogg Paul C.M. , Antson Alfred A.
Published: June 2024

Single-stranded DNA bacteriophages of theMicroviridaefamily are major components of the global virosphere. Microviruses are highly abundant in aquatic ecosystems and are prominent members of the mammalian gut microbiome, where their diversity has been linked to various chronic health disorders. Despite the clear importance of microviruses, little is known about the molecular mechanism of host infection. Here, we have characterized an exceptionally large microvirus, Ebor, and provide crucial insights into long-standing mechanistic questions. Cryogenic electron microscopy of Ebor revealed a capsid with trimeric protrusions that recognise lipopolysaccharides on the host surface. Cryogenic electron tomography of the host cell colonized with virus particles demonstrated that the virus initially attaches to the cell via five such protrusions, located at the corners of a single pentamer. This interaction triggers a stargate mechanism of capsid opening along the 5-fold symmetry axis, enabling delivery of the virus genome. Despite variations in specific virus-host interactions among differentMicroviridaefamily viruses, structural data indicate that the stargate mechanism of infection is universally employed by all members of the family. Startlingly, our data reveal a mechanistic link for the opening of relatively small capsids made out of a single jelly-roll fold with the structurally unrelated giant viruses.
Spatial resolution of transcriptomic plasticity states underpinning lethal morphologies in lung adenocarcinoma
Authors: Williams Hannah L , Poulain Nicolas , Powley Ian , Martinelli Silvia , Bielik Robert , Leslie Holly , Nixon Colin , Wilson Claire R , Sereno Marco , He Zhangyi , Officer-Jones Leah , Ballantyne Fiona , Pennie Rachel , Wood Colin S , Lewis David Y , Jamieson Nigel B , Le Quesne John
Published: June 2024

Adenocarcinoma of the lung (LUAD) is a common and highly lethal disease. Clinical grading of disease strongly predicts recurrence and survival after surgery and is determined by morphological assessment of histological growth patterns in resected tumours. The molecular basis of growth pattern is poorly understood at present, as are the mechanisms linking growth pattern to recurrence and death.

Interestingly, the two archetypal lethal morphologies, solid and micropapillary patterns, are characterised by their biphasic appearance. Both have an epithelial fraction which is in direct stromal contact, and a fraction which is not. This morphological variance seems likely to represent plasticity, and to be causally linked to mechanisms of virulence.

To investigate the gene expression changes related to growth pattern both intra- and intertumoral, we applied spatial transcriptomics (Nanostring GeoMx DSP) to tissue microarray specimens of primary resected human lung adenocarcinoma. Using a variety of region-of-interest (ROI) selection strategies, we sampled 160 pure epithelial ROIs across 7 distinct morphological features of LUAD from 51 patients. Analyses of gene expression reveal fundamental trajectories connecting growth patterns, and crucial modes of plasticity which underly high-risk morphologies. These modes suggest mechanisms for the origins of growth pattern and mechanisms of virulence.

Our work highlights dramatic divergence in gene expression programmes between highly lethal but morphologically diverse modes of tumour growth. Furthermore, it provides an explanation for how microscopically localised hypoxia in the primary tumour helps to establish and maintain survival strategies which ultimately determine morphology-specific mechanisms of tumour metastasis, suggesting new therapeutic vulnerabilities.
Depolarization induces calcium-dependent BMP4 release from mouse embryonic palate mesenchyme
Authors: Follmer Mikaela L , Isner Trevor , Ozekin Yunus H. , Levitt Claire , Bates Emily Anne
Published: June 2024

Ion channels are essential for proper morphogenesis of the craniofacial skeleton. However, the molecular mechanisms underlying this phenomenon are unknown. Loss of theKcnj2potassium channel disrupts Bone Morphogenetic Protein (BMP) signaling within the developing palate. BMP signaling is essential for the correct development of several skeletal structures, including the palate, though little is known about the mechanisms that govern BMP secretion. We introduce a tool to image the release of bone morphogenetic protein 4 (BMP4) from mammalian cells. Using this tool, we show that depolarization induces BMP4 release from mouse embryonic palate mesenchyme cells in a calcium-dependent manner. We show native transient changes in intracellular calcium occur in cranial neural crest cells, the cells from which embryonic palate mesenchyme derives. Waves of transient changes in intracellular calcium suggest that these cells are electrically coupled and may temporally coordinate BMP release. These transient changes in intracellular calcium persist in palate mesenchyme cells from embryonic day (E) 9.5 to 13.5 mice. Disruption ofKcnj2significantly decreases the amplitude of calcium transients and the ability of cells to secrete BMP. Together, these data suggest that temporal control of developmental cues is regulated by ion channels, depolarization, and changes in intracellular calcium for mammalian craniofacial morphogenesis.

We show that embryonic palate mesenchyme cells undergo transient changes in intracellular calcium. Depolarization of these cells induces BMP4 release suggesting that ion channels are a node in BMP4 signaling.
BCR, not TCR, repertoire diversity is associated with favorable COVID-19 prognosis
Authors: Paran Faith Jessica , Oyama Rieko , Khasawneh Abdullah , Ai Tomohiko , Ismanto Hendra Saputra , Sherif Aalaa Alrahman , Saputri Dianita Susilo , Ono Chikako , Saita Mizue , Takei Satomi , Horiuchi Yuki , Yagi Ken , Yoshiharu Matsuura DVM , Okazaki Yasushi , Takahashi Kazuhisa , Standley Daron M , Tabe Yoko , Naito Toshio
Published: June 2024

The SARS-CoV-2 pandemic has had a widespread and severe impact on society, yet there have also been instances of remarkable recovery, even in critically ill patients. In this study, we used single-cell RNA sequencing to analyze the immune responses in recovered and deceased COVID-19 patients during moderate and critical stages. The study included three unvaccinated patients from each outcome category. Although expanded T cell receptor (TCR) clones were predominantly SARS-CoV-2-specific, they represented only a small fraction of the total repertoire in all patients. In contrast, while deceased patients exhibited monoclonal B cell receptor (BCR) expansions without COVID-19 specificity, survivors demonstrated diverse and specific BCR clones. These findings suggest that neither TCR diversity nor BCR monoclonal expansions are sufficient for viral clearance and subsequent recovery. Differential gene expression analysis revealed that protein biosynthetic processes were enriched in survivors, but that potentially damaging mitochondrial ATP metabolism was activated in the deceased. This study underscores that BCR repertoire diversity, but not TCR diversity, correlates with favorable outcomes in COVID-19.
HIV-1 neutralizing antibodies in SHIV-infected macaques recapitulate structurally divergent modes of human V2 apex recognition with a single D gene
Authors: Roark Ryan S. , Habib Rumi , Gorman Jason , Li Hui , Connell Andrew Jesse , Bonsignori Mattia , Guo Yicheng , Hogarty Michael P. , Olia Adam S. , Sowers Kirsten , Zhang Baoshan , Bibollet-Ruche Frederic , Callaghan Sean , Carey John W. , Cerutti Gabriele , Harris Darcy R. , He Wanting , Lewis Emily , Liu Tracy , Mason Rosemarie D. , Park Younghoon , Rando Juliette M. , Singh Ajay , Wolff Jeremy , Lei Q. Paula , Louder Mark K. , Doria-Rose Nicole A. , Andrabi Raiees , Saunders Kevin O. , Seaman Michael S. , Haynes Barton F. , Kulp Daniel W. , Mascola John R. , Roederer Mario , Sheng Zizhang , Hahn Beatrice H. , Shaw George M. , Kwong Peter D. , Shapiro Lawrence
Published: June 2024

Broadly neutralizing antibodies targeting the V2 apex of the HIV-1 envelope trimer are among the most common specificities elicited in HIV-1-infected humans and simian-human immunodeficiency virus (SHIV)-infected macaques. To gain insight into the prevalent induction of these antibodies, we isolated and characterized 11 V2 apex-directed neutralizing antibody lineages from SHIV-infected rhesus macaques. Remarkably, all SHIV-induced V2 apex lineages were derived from reading frame two of the rhesus DH3-15*01 gene. Cryo-EM structures of envelope trimers in complex with antibodies from nine rhesus lineages revealed modes of recognition that mimicked three canonical human V2 apex-recognition modes. Notably, amino acids encoded by DH3-15*01 played divergent structural roles, inserting into a hole at the trimer apex, H-bonding to an exposed strand, or forming part of a loop scaffold. Overall, we identify a DH3-15*01-signature for rhesus V2 apex broadly neutralizing antibodies and show that highly selected genetic elements can play multiple roles in antigen recognition.

Highlights

Isolated 11 V2 apex-targeted HIV-neutralizing lineages from 10 SHIV-infected Indian-origin rhesus macaques

Cryo-EM structures of Fab-Env complexes for nine rhesus lineages reveal modes of recognition that mimic three modes of human V2 apex antibody recognition

All SHIV-elicited V2 apex lineages, including two others previously published, derive from the same DH3-15*01 gene utilizing reading frame two

The DH3-15*01 gene in reading frame two provides a necessary, but not sufficient, signature for V2 apex-directed broadly neutralizing antibodies

Structural roles played by DH3-15*01-encoded amino acids differed substantially in different lineages, even for those with the same recognition mode

Propose that the anionic, aromatic, and extended character of DH3-15*01 in reading frame two provides a selective advantage for V2 apex recognition compared to B cells derived from other D genes in the naïve rhesus repertoire

Demonstrate that highly selected genetic elements can play multiple roles in antigen recognition, providing a structural means to enhance recognition diversity
Deciphering the Binding of 5’ Stem Loop RNA to the La Domain of Human LARP6
Authors: Gordon Blaine H. , Blackford Nolan , Silvers Robert
Published: June 2024

La-related protein 6 regulates the highly organized biosynthesis of type I procollagen polypeptides and affects proper assembly of procollagen peptides into heterotrimers of type I procollagen. LARP6-mediated regulation of collagen biosynthesis is mediated through interaction with the 5’ stem loop motif found in type I and III collagen mRNA. Recent studies highlight the involvement of HsLARP6 in fibroproliferative diseases and its potential as a target for therapeutic intervention. The intrinsic instability of the La domain of HsLARP6 hampers studies probing the molecular basis of biologically- and disease-relevant structure-function relationship, particularly when high concentrations are required. This work provides detailed procedures to produce milligram amounts of RNase-free and functional La domain of HsLARP6. Furthermore, we investigated the effect of the construct length as well as RNA binding on protein stability. N- and C-terminal extensions greatly impact stability based on interactions with the core domain and modulation of the pI. When in complex with its cognate 5’SL RNA, the La domain shows unprecedented stability compared to the aggregation-prone unbound state. The protein-RNA complex remains stable for at least 50x longer than the unbound state, under identical conditions, likely due to a global change in conformational plasticity upon RNA binding. These results provide a foundation for further studies of the molecular recognition of 5’SL by HsLARP6 as well as a platform for refining potential antifibrotic therapeutics.
Cell deformations generated by dynamic cortical actin waves drivein vivoswimming migration
Authors: Andrieu Cyril , Lee Bren Hunyi , Franz Anna
Published: June 2024

Amoeboid cell migration drives many important developmental and disease-related processes including immune responses and cancer metastasis. Swimming cell migration is a subtype of amoeboid migration observed in cells in suspensionex vivo.However, the mechanism underlying swimming migrationin vivounder physiological conditions is unknown. UsingDrosophilafat body cells (FBCs) as a model, we show that FBCs actively swim to patrol the pupa. Their stop-and-go random walk is powered through the generation of oscillatory actomyosin waves, rather than persistent actin flows used by cells swimmingin vitro.These actomyosin waves exert peristaltic compressive forces as they move to the cell rear. This causes cell elongation towards the front to propel the cell forward. In addition, we demonstrate that, unlike in other types of amoeboid migration, all three RhoGTPases, RhoA, Cdc42 and Rac1, are required for FBC migration. They control actin wave formation by regulating actin polymerisation through the formin Dia. Furthermore, RhoA at the cell rear induces actomyosin contractions via Rho kinase and myosin II to generate cell deformations. Importantly, our work reveals that swimming migration is a novelin vivomigration mode for rapid and long-range cell dispersal, potentially also used by other cells such as immune cells and cancer cells when encountering an aqueous environment.
A generalized structured coalescent for purifying selection without recombination
Authors: Strütt Stefan , Excoffier Laurent , Peischl Stephan
Published: June 2024

Purifying selection is a critical factor in shaping genetic diversity. Current theoretical models only address scenarios of either very weak or strong selection, leaving a significant gap in our knowledge. The effects of purifying selection on patterns of genomic diversity remain poorly understood when selection against deleterious mutations is weak to moderate, particularly when recombination is limited or absent. In this study, we extend an existing approach, the fitness-class coalescent, to incorporate arbitrary levels of purifying selection. This model offers a comprehensive framework for exploring the influence of purifying selection in a wide range of demographic scenarios. Moreover, our research reveals potential sources of qualitative and quantitative biases in demographic inference, highlighting the significant risk of attributing genetic patterns to past demographic events rather than purifying selection. This work expands our understanding of the complex interplay between selection, drift, and population dynamics, and how purifying selection distorts demographic inference.
Intrastromal graft of anterior lens capsule. A substitute for Bowman layer graft transplantation for keratoconus
Authors: Rodríguez-Barrientos Carlos A. , Translateur-Grynspan Amir , Zavala-Arcos Judith , Valdez Jorge E. , Santaella Gisella , Barraquer-Coll Carmen
Published: June 2024

Purpose

The shortage of donor corneas limits Bowman layer transplantation for keratoconus. In this study, we evaluate the clinical outcome of anterior lens capsule xenograft transplantation in the corneal stroma of a rabbit model as substitute for Bowman layer graft that is used in stromal transplantation for advanced keratoconus.

Methods

Transplantation of an anterior lens capsule in the corneal stroma was performed in four New Zealand white rabbits through the creation of a stromal pocket. Corneal transparency, central corneal thickness, and topographic characteristics of corneas were evaluated at different time points: pre- (0) and post- (7, 14, 21, and 28) operative days. Additionally, at the end of the study histopathological findings were evaluated.

Results

In comparison to pre-operative day, transplantation of an anterior lens capsule preserved corneal transparency, central corneal thickness, and topographic characteristics remained constant throughout the study period. Histopathological analysis revealed the presence of the anterior lens capsule as a fully integrated lamellar graft without adverse effects in host stroma.

Conclusion

The anterior lens capsule may be useful as a graft for intrastromal corneal trasplantation. Similarly to Bowman layer, anterior lens capsule has mechanical characteristics that facilitate corneal transplantation. In post-transplanted corneas the preservation of transparency, as well as the effect on corneal thickness, and topographic characteristics support the possibility of using anterior lens capsule as a substitute for Bowman layer graft.
Phenotypic analysis of the edible fruits ofLardizabala biternata, an endemic and monotypic vine from the Chilean biodiversity hotspot in South America
Authors: Herrera Jaime , Fernández Leonardo D.
Published: June 2024

Introduction

Lardizabala biternatais a vine endemic to Chile, distributed between 32°S and 40°S. Its sweet edible fruits have historically been harvested by hand from the wild as there are no productive systems for this vine. Herein, we conducted the first phenotypic analysis ofL. biternatafruits, which includes qualitative and quantitative analyses of morphological and morphometric traits. This phenotypic analysis is the baseline for the development of production systems that could reduce anthropogenic pressure on wild populations and favour theex-situconservation of this vine.

Materials and methods

We collected 282 fruits from two geographically distant populations during four fruiting seasons. In all of them we recorded 14 morphological attributes, including total weight, length, width, height, diameter, volume, edible pulp content, seed number weight and individual seed weight. We investigated morphometric differences between populations and seasons by analysis of variance (ANOVAs), phenotypic correlations by regressions and associations between traits by principal component analysis (PCA).

Results

On overage, fruits weighed 20.8 g (3.0 – 44.6 g) and measured 54 mm in length (20.1 – 83.4 mm) and 23.7 mm in diameter. Edible pulp contributed around 44.4% of total fruit weight. Observed traits displayed significant variations between seasons and among traits (length vs width vs height). Fruit weight showed a high correlation with edible pulp weight, fruit length, seed weight, seed number, and others.

Discussion and conclusions

Our study represents the first phenotypic analysis of the fruits of this wild, endemic, and rare plant. We comprehensively describe the morphological and morphometric characteristics of its fruits. The characteristics ofL. biternatafruits show significant morphometric variation between populations and seasons. However, the edible pulp consistently remains the main component of the fresh fruit weight. Like other domesticated members of the Lardizabalaceae, the fruits of this wild plant have the potential for cultivation through the development of sustainable production systems. The information we provide serves as a baseline for the development of such systems through selection and genetic improvement of the plant.
Optimizing Fed-Batch Processes with Dynamic Control Flux Balance Analysis
Authors: Gotsmy Mathias , Giannari Dafni , Mahadevan Radhakrishnan , Zanghellini Jürgen
Published: June 2024

Fed-batch processes are prevalent in biotechnological industries, but design of experiments often results in sub-optimal conditions due to incomplete solution space characterization. We employ a single-level dynamic control (DC) algorithm for dynamic flux balance analysis (dFBA), enhancing efficiency by reducing Karush-Kuhn-Tucker (KKT) condition constraints and adapting the algorithm for predicting optimal process length. In a growth-decoupled plasmid DNA production case study, we predict the optimal feeding profile and switching time between growth and production phase. Comparing our algorithm to its predecessor shows a speed-up of at least a factor of four. When the process length is part of the objective function the speed-up becomes considerably larger.
Transcriptomic analysis ofPicea abiestissue culture reveals the impact of culture conditions and the presence of glucuronoxylan on extracellular lignin production
Authors: Sapouna Ioanna , Sivan Pramod , Vilaplana Francisco , Srivastava Vaibhav , McKee Lauren Sara
Published: June 2024

Tissue cultures are an important study model for woody plant tissue and can be used to study lignin biosynthesis. The greatest disadvantage of protocols based on extraction of lignin from wood biomass is the almost inevitable alteration of the native structure of lignin. Using a Norway spruce tissue culture with the ability to secrete monolignols into a liquid culture medium, fundamental aspects of lignin have been studied in the past, such as its structure, the enzyme activity related to its polymerization, and its interactions with a secondary cell wall hemicellulose. In this study, parameters that can induce monolignol production and secretion in the tissue culture are investigated via gene expression analysis. The impact of the composition of the solid growth medium, which was in some cases supplemented with xylan, was studied in depth through transcriptomic investigation. We find that the state (i.e. liquid or solid) and the xylan content of the medium can impact gene expression, although microscopic analysis suggests that cellular morphology is consistent. Extracellular lignin was collected from a formulation of liquid medium with the same composition as that used for cellular growth, which was previously presumed to be “non-inducing” of lignin biosynthesis. Chemical analysis of this lignin was performed using nuclear magnetic resonance spectroscopy and size exclusion chromatography, which revealed changes in its structure compared to the polymer produced in the previously developed “inducing” liquid medium. These experiments show that there is still much we do not understand about an oft-used tissue culture system, but show the way to a deeper understanding of the genetic control of lignin biosynthesis.
Differences in fMRI-based functional connectivity during abstinence or interventions between heroin-dependent individuals and healthy controls
Authors: Kurtin Danielle L. , Prabhu Anusha M. , Groen Alissa , Amer Matthew J. , Lingford-Hughes Anne , Paterson Louise M.
Published: June 2024

The substantial personal, societal, and economic impacts of opioid addiction drive research investigating how opioid addiction affects the brain, and whether therapies attenuate addiction-related metrics of brain function. One useful approach to characterise the effects of opioid addiction on the brain is functional connectivity (FC). FC assesses the pairwise relationship of brain region function over time. This work is a systematic narrative review of studies investigating the effect of abstinence or interventions on FC in people who are dependent on heroin (HD) and healthy controls (HC). We found that HD typically showed weaker FC between three functional networks: the Executive Control Network, Default Mode Network, and the Salience Network. Abstinence and Transcranial Magnetic Stimulation (TMS) both attenuated differences in FC between HD and HC, often by increasing FC in HD. We critically assessed the clinical relevance of these results and the impact of study methods on the robustness of study results. We concluded with practical suggestions to improve the translational potential of neuromodulatory interventions (e.g., noninvasive brain stimulation) targeting the neural correlates of opioid addiction.

Highlights

Functional connectivity (FC) informs how neural resources are organised.

FC is weaker in people with heroin dependence (HD) vs healthy controls (HC)

Weaker FC is observed among resting, reward, cognitive, and attentional networks.

Abstinence and brain stimulation strengthen FC and reduce craving/relapse in HD.

FC may be a biomarker for developing therapies for HD.
Contribution of the neuron-specific ATP1A3 to embryonic spinal circuit emergence
Authors: Dinvaut Sarah , Calvet Sophie , Comte Jean-Christophe , Gury Raphael , Pascual Olivier , André Maelys , Ferrigno Rosaria , Honnorat Jérôme , Moret Frédéric , Marcy Guillaume , Falk Julien , Castellani Valérie
Published: June 2024

The early neurodevelopmental contributions of ion pumps remain poorly characterized. Combining analysis of public human embryo single-cell transcriptomic datasets and an embryonic chicken model, we found a conserved differentiation sequence whereby spinal cord neurons switch on neuron-specific alpha3 subunit (ATP1A3) of Na+/K+ATPases. In the chicken model, ATP1A3 is distributed along axons and growth cones. Its knockdown alters axon pathfinding of dorsal interneurons (DIN) that wire spinocerebellar circuits. In mirror of reported electric field (EF)-driven cell migration, we found that DIN axons align in EFs, which was abolished by Na+/K+ATPase inhibitor Ouabain and ATP1A3 knockdown. We recorded an embryonic trans-neural-epithelial potential generating EF whose pharmacological and surgical manipulation mimicked ATP1A3 knock-down-induced altered DIN axon pathfinding. Using DINs transplantation paradigm, we found that ATP1A3 is required cell-autonomously for EF-mediated long-range guidance. Finally, dominant-negative ATP1A3 mutation causing an early ATP1A3 childhood disease disrupts this fundamental developmental process, revealing unexpected pathogenic mechanisms.
Ferroptosis regulates hemolysis in stored murine and human red blood cells
Authors: D’Alessandro Angelo , Keele Gregory R. , Hay Ariel , Nemkov Travis , Earley Eric J. , Stephenson Daniel , Vincent Matthew , Deng Xutao , Stone Mars , Dzieciatkowska Monika , Hansen Kirk C. , Kleinman Steve , Spitalnik Steven L , Roubinian Nareg H. , Norris Philip J , Busch Michael P. , Page Grier P , Stockwell Brent R. , Churchill Gary A. , Zimring James C
Published: June 2024

Red blood cell (RBC) metabolism regulates hemolysis during aging in vivo and in the blood bank. Here, we leveraged a diversity outbred mouse population to map the genetic drivers of fresh/stored RBC metabolism and extravascular hemolysis upon storage and transfusion in 350 mice. We identify the ferrireductase Steap3 as a critical regulator of a ferroptosis-like process of lipid peroxidation. Steap3 polymorphisms were associated with RBC iron content, in vitro hemolysis, and in vivo extravascular hemolysis both in mice and 13,091 blood donors from the Recipient Epidemiology and Donor evaluation Study. Using metabolite Quantitative Trait Loci analyses, we identified a network of gene products (FADS1/2, EPHX2 and LPCAT3) - enriched in donors of African descent - associated with oxylipin metabolism in stored human RBCs and related to Steap3 or its transcriptional regulator, the tumor protein TP53. Genetic variants were associated with lower in vivo hemolysis in thousands of single-unit transfusion recipients.

Highlights

Steap3 regulates lipid peroxidation and extravascular hemolysis in 350 diversity outbred mice

Steap3 SNPs are linked to RBC iron, hemolysis, vesiculation in 13,091 blood donors

mQTL analyses of oxylipins identified ferroptosis-related gene products FADS1/2, EPHX2, LPCAT3

Ferroptosis markers are linked to hemoglobin increments in transfusion recipients

Graphical abstract
Chromogranin A (CgA) Deficiency Attenuates Tauopathy by Altering Epinephrine–Alpha-Adrenergic Receptor Signaling
Authors: Jati Suborno , Munoz-Mayorga Daniel , Shahabi Shandy , Tang Kechun , Tao Yuren , Dickson Dennis W. , Litvan Irene , Ghosh Gourisankar , Mahata Sushil K. , Chen Xu
Published: June 2024

Our previous studies have indicated that insulin resistance, hyperglycemia, and hypertension in aged wild-type (WT) mice can be reversed in mice lacking chromogranin-A (CgA-KO mice). These health conditions are associated with a higher risk of Alzheimer’s disease (AD). CgA, a neuroendocrine secretory protein has been detected in protein aggregates in the brains of AD patients. Here, we determined the role of CgA in tauopathies, including AD (secondary tauopathy) and corticobasal degeneration (CBD, primary tauopathy). We found elevated levels of CgA in both AD and CBD brains, which were positively correlated with increased phosphorylated tau in the frontal cortex. Furthermore, CgA ablation in a human P301S tau (hTau) transgenic mice (CgA-KO/hTau) exhibited reduced tau aggregation, resistance to tau spreading, and an extended lifespan, coupled with improved cognitive function. Transcriptomic analysis of mice cortices highlighted altered levels of alpha-adrenergic receptors (Adra) in hTau mice compared to WT mice, akin to AD patients. Since CgA regulates the release of the Adra ligands epinephrine (EPI) and norepinephrine (NE), we determined their levels and found elevated EPI levels in the cortices of hTau mice, AD and CBD patients. CgA-KO/hTau mice exhibited reversal of EPI levels in the cortex and the expression of several affected genes, including Adra1 and 2, nearly returning them to WT levels. Treatment of hippocampal slice cultures with EPI or an Adra1 agonist intensified, while an Adra1 antagonist inhibited, tau hyperphosphorylation and aggregation. These findings reveal a critical role of CgA in regulation of tau pathogenesis via the EPI-Adra signaling axis.
Organ-Specific Microbiomes ofBiomphalariaSnails
Authors: Carruthers Lauren V. , Nordmeyer Stephanie C. , Anderson Timothy JC. , Chevalier Frédéric D. , Le Clec’h Winka
Published: June 2024

Background

The microbiome is increasingly recognized to shape many aspects of its host biology and is a key determinant of health and disease. The microbiome may influence transmission of pathogens by their vectors, such as mosquitoes or aquatic snails. We previously sequenced the V4 region of the bacterial 16S rRNA gene from the hemolymph (blood) ofBiomphalariaspp. snails, vectors of the human blood fluke schistosome. We showed that snail hemolymph harbored an abundant and diverse microbiome. This microbiome is distinct from the water environment and can discriminate snail species and populations. As hemolymph bathes snail organs, we then investigated the heterogeneity of the microbiome in these organs.

Results

We dissected ten snails for each of two different species (B. alexandrinaandB. glabrata) and collected their hemolymph and organs (ovotestis, hepatopancreas, gut, and stomach). We also ground in liquid nitrogen four whole snails of each species. We sampled the water in which the snails were living (environmental controls). Sequencing the 16S rRNA gene revealed organ-specific microbiomes. These microbiomes harbored a lower diversity than the hemolymph microbiome, and the whole-snail microbiome. The organ microbiomes tend to cluster by physiological function. In addition, we showed that the whole-snail microbiome is more similar to hemolymph microbiome.

Conclusions

These results are critical for future work on snail microbiomes and show the necessity of sampling individual organ microbiomes to provide a complete description of snail microbiomes.
A massively parallelin vivoassay of TdT mutants yields variants with altered nucleotide insertion biases
Authors: Carlson Courtney K. , Loveless Theresa B. , Milisavljevic Marija , Kelly Patrick I. , Mills Jeremy H. , Tyo Keith E. J. , Liu Chang C.
Published: June 2024

Terminal deoxynucleotidyl transferase (TdT) is a unique DNA polymerase capable of template-independent extension of DNA with random nucleotides. TdT’sde novoDNA synthesis ability has found utility in DNA recording, DNA data storage, oligonucleotide synthesis, and nucleic acid labeling, but TdT’s intrinsic nucleotide biases limit its versatility in such applications. Here, we describe a multiplexed assay for profiling and engineering the bias and overall activity of TdT variants in high throughput. In our assay, a library of TdTs is encoded next to a CRISPR-Cas9 target site in HEK293T cells. Upon transfection of Cas9 and sgRNA, the target site is cut, allowing TdT to intercept the double strand break and add nucleotides. Each resulting insertion is sequenced alongside the identity of the TdT variant that generated it. Using this assay, 25,623 unique TdT variants, constructed by site-saturation mutagenesis at strategic positions, were profiled. This resulted in the isolation of several altered-bias TdTs that expanded the capabilities of our TdT-based DNA recording system, Cell History Recording by Ordered Insertion (CHYRON), by increasing the information density of recording through an unbiased TdT and achieving dual-channel recording of two distinct inducers (hypoxia and Wnt) through two differently biased TdTs. Select TdT variants were also testedin vitro, revealing concordance between each variant’sin vitrobias and thein vivobias determined from the multiplexed high throughput assay. Overall, our work, and the multiplex assay it features, should support the continued development of TdT-based DNA recorders,in vitroapplications of TdT, and further study of the biology of TdT.
The first interneuron of the mouse visual system is tailored to the natural environment through morphology and electrical coupling
Authors: Spinelli Matteo , Acevedo H. Alejandra , Block Christoph T. , Lindenthal Lucia , Schuhmann Fabian , Greschner Martin , Janssen-Bienhold Ulrike , Dedek Karin , Puller Christian
Published: June 2024

The topographic complexity of the mouse retina has long been underestimated, as obvious specializations, like a fovea or visual streak, are absent. However, anatomical and functional gradients exist. It was recently shown that receptive fields of retinal ganglion cells change their shape along the dorso-ventral retinal axis. These variations likely reflect the non-uniform statistics of the visual environment which vary dramatically from ground to sky. Horizontal cells are the first visual interneurons and dictate the synaptic signaling between photoreceptors and bipolar cells by lateral interactions, thereby shaping the receptive fields of down-stream neurons. Thus, we asked whether regional specializations are present at this earliest stage of synaptic circuitry, i.e. at the level of horizontal cells. We analyzed horizontal cell density distributions, morphological properties, localization of gap junction proteins, and the spatial extent of horizontal cell electrical coupling across complete retinas. All of these horizontal cell key features were asymmetrically organized along the dorso-ventral axis. Dorsal horizontal cells were less densely distributed, had larger dendritic trees, and electrical coupling was more extensive than in their ventral counterparts. The steepest change along this gradient occurred at the opsin transition zone of photoreceptors, i.e. the mouse visual horizon. Therefore, our results show that the cellular and synaptic organization of the mouse visual system are adapted to the visual environment at the earliest possible level, and that horizontal cells are well suited to form the cellular substrate for the global gradient previously described for the receptive field structures of retinal ganglion cells.
Synaptic alterations in pyramidal cells following genetic manipulation of neuronal excitability in monkey prefrontal cortex
Authors: Gonzalez Burgos Guillermo , Miyamae Takeaki , Nishihata Yosuke , Krimer Olga L , Wade Kirsten , Fish Kenneth N , Arion Dominique , Cai Zhao-Lin , Xue Mingshan , Stauffer William R , Lewis David A
Published: June 2024

In schizophrenia, layer 3 pyramidal neurons (L3PNs) in the dorsolateral prefrontal cortex (DLPFC) are thought to receive fewer excitatory synaptic inputs and to have lower expression levels of activity-dependent genes and of genes involved in mitochondrial energy production. In concert, these findings from previous studies suggest that DLPFC L3PNs are hypoactive in schizophrenia, disrupting the patterns of activity that are crucial for working memory, which is impaired in the illness. However, whether lower PN activity produces alterations in inhibitory and/or excitatory synaptic strength has not been tested in the primate DLPFC. Here, we decreased PN excitability in rhesus monkey DLPFCin vivousing adeno-associated viral vectors (AAVs) to produce Cre recombinase-mediated overexpression of Kir2.1 channels, a genetic silencing tool that efficiently decreases neuronal excitability. In acute slices prepared from DLPFC 7-12 weeks post-AAV microinjections, Kir2.1-overexpressing PNs had a significantly reduced excitability largely attributable to highly specific effects of the AAV-encoded Kir2.1 channels. Moreover, recordings of synaptic currents showed that Kir2.1-overexpressing DLPFC PNs had reduced strength of excitatory synapses whereas inhibitory synaptic inputs were not affected. The decrease in excitatory synaptic strength was not associated with changes in dendritic spine number, suggesting that excitatory synapse quantity was unaltered in Kir2.1-overexpressing DLPFC PNs. These findings suggest that, in schizophrenia, the excitatory synapses on hypoactive L3PNs are weaker and thus might represent a substrate for novel therapeutic interventions.

Significance Statement

In schizophrenia, dorsolateral prefrontal cortex (DLPFC) pyramidal neurons (PNs) have both transcriptional and structural alterations that suggest they are hypoactive. PN hypoactivity is thought to produce synaptic alterations in schizophrenia, however the effects of lower neuronal activity on synaptic function in primate DLPFC have not been examined. Here, we used, for the first time in primate neocortex, adeno-associated viral vectors (AAVs) to reduce PN excitability with Kir2.1 channel overexpression and tested if this manipulation altered the strength of synaptic inputs onto the Kir2.1-overexpressing PNs. Recordings in DLPFC slices showed that Kir2.1 overexpression depressed excitatory (but not inhibitory), synaptic currents, suggesting that, in schizophrenia, the hypoactivity of PNs might be exacerbated by reduced strength of the excitatory synapses they receive.
Leveraging single cell multiomic analyses to identify factors that drive human chondrocyte cell fate
Authors: Venkatasubramanian Divya , Senevirathne Gayani , Capellini Terence D. , Craft April M.
Published: June 2024

Cartilage plays a crucial role in skeletal development and function, and abnormal development contributes to genetic and age-related skeletal disease. To better understand how human cartilage developsin vivo, we jointly profiled the transcriptome and open chromatin regions in individual nuclei recovered from distal femurs at 2 fetal timepoints. We used these multiomic data to identify transcription factors expressed in distinct chondrocyte subtypes, link accessible regulatory elements with gene expression, and predict transcription factor-based regulatory networks that are important for growth plate or epiphyseal chondrocyte differentiation. We developed a human pluripotent stem cell platform for interrogating the function of predicted transcription factors during chondrocyte differentiation and used it to testNFATC2. We expect new regulatory networks we uncovered using multiomic data to be important for promoting cartilage health and treating disease, and our platform to be a useful tool for studying cartilage developmentin vitro.

Statement of Significance

The identity and integrity of the articular cartilage lining our joints are crucial to pain-free activities of daily living. Here we identified a gene regulatory landscape of human chondrogenesis at single cell resolution, which is expected to open new avenues of research aimed at mitigating cartilage diseases that affect hundreds of millions of individuals world-wide.
Patch and matrix striatonigral neurons differentially regulate locomotion
Authors: Dong Jie , Wang Lupeng , Sullivan Breanna T. , Sun Lixin , Chang Lisa , Martinez Smith Victor M. , Ding Jinhui , Le Weidong , Gerfen Charles R. , Cai Huaibin
Published: June 2024

Striatonigral neurons, known to promote locomotion, reside in both the patch and matrix compartments of the dorsal striatum. However, their compartment-specific contributions to locomotion remain largely unexplored. Using molecular identifierKremen1andCalb1, we showed in mouse models that patch and matrix striatonigral neurons exert opposite influences on locomotion. Matrix striatonigral neurons reduced their activity before the cessation of self-paced locomotion, while patch striatonigral neuronal activity increased, suggesting an inhibitory function. Indeed, optogenetic activation of patch striatonigral neurons suppressed ongoing locomotion with reduced striatal dopamine release, contrasting with the locomotion-promoting effect of matrix striatonigral neurons, which showed an initial increase in dopamine release. Furthermore, genetic deletion of the GABA-B receptor in Aldehyde dehydrogenase 1A1-positive (ALDH1A1+) nigrostriatal dopaminergic neurons completely abolished the locomotion-suppressing effect of patch striatonigral neurons. Our findings unravel a compartment-specific mechanism governing locomotion in the dorsal striatum, where patch striatonigral neurons suppress locomotion by inhibiting ALDH1A1+nigrostriatal dopaminergic neurons.
Beyond histones: the elusive substrates of chromatin regulators
Authors: Mannervik Mattias
Published: June 2024

Gene transcription is intimately linked to chromatin state and histone modifications. However, the enzymes mediating these post-translational modifications have many additional, nonhistone substrates, making it difficult to ascribe the most relevant modification. In this issue ofGenes & Development, Crain and colleagues (doi:10.1101/gad.351698.124) have combined a powerful histone replacement system with mutational analysis of a chromatin regulator and a chromatin reader inDrosophila melanogaster. Importantly, they discovered that genes controlled by the histone 4 lysine 20 (H4K20) methyltransferase Set8 and the protein recognizing H4K20 monomethylation, L(3)mbt, differ substantially from those affected by mutation of H4K20 itself. This demonstrates that H4K20 is not the key substrate for Set8 but that methylation of other, unidentified proteins mediates its effects on transcription.
Electromagnetic properties of vector doubly charmed tetraquark states
Authors: Özdem U. , Azizi K.
Published: June 2024

We conduct a systematic study of the electromagnetic properties of multiquark systems with undetermined internal structures. Motivated by the recent observation of the Tcc+ state, we apply the light-cone version of the QCD sum rule method to extract the magnetic dipole moments of several possible doubly charmed vector tetraquark states. When analyzing the magnetic dipole moment of these states, they are modeled to have the diquark-antidiquark configurations. The magnetic dipole moments for the members are extracted as μTccu¯d¯=1.17−0.32+0.44μN, μTccu¯s¯=1.35−0.37+0.50μN, μTccd¯s¯=−2.69−0.75+1.02μN, μTccu¯u¯=1.33−0.40+0.56μN, μTccd¯d¯=1.41−0.43+0.57μN, and μTccs¯s¯=1.44−0.41+0.53μN. Comparing the results obtained for the magnetic dipole moments of the Tccu¯d¯ state with the Tccu¯s¯ state, the U symmetry is seen to be broken at about 15%, while, for the Tccd¯d¯ and Tccs¯s¯ states, this symmetry is minimally broken. The obtained results may be useful to determine the true nature of these new interesting states.

Published by the American Physical Society
2024
Low-energy Compton scattering in materials
Authors: Essig Rouven , Hochberg Yonit , Shoji Yutaro , Singal Aman , Suczewski Gregory
Published: June 2024

Low-energy Compton scattering is an important background for sub-GeV dark matter direct-detection and other experiments. Current Compton scattering calculations typically rely on assumptions that are not valid in the low-energy region of interest, beneath ∼50  eV. Here we relate the low-energy Compton scattering differential cross section to the dielectric response of the material. Our new approach can be used for a wide range of materials and includes all-electron, band-structure, and collective effects, which can be particularly relevant at low energies. We demonstrate the strength of our approach in several solid-state systems, in particular, Si, Ge, GaAs, and SiC, which are relevant for current and proposed experiments searching for dark matter, neutrinos, and millicharged particles.

Published by the American Physical Society
2024
Interpolating bremsstrahlung function in ABJM model
Authors: Castiglioni Luigi , Penati Silvia , Tenser Marcia , Trancanelli Diego
Published: June 2024

In ABJM theory, enriched RG flows between circular 1/6 BPS bosonic and 1/2 BPS fermionic Wilson loops have been introduced in L. Castiglioni [L. Castiglioni, S. Penati, M. Tenser, and D. Trancanelli, Interpolating Wilson loops and enriched RG flows, .]. These flows are triggered by deformations corresponding to parametric 1/6 BPS fermionic loops. In this paper, we revisit the study of these operators, but instead of circular contours, we consider an interpolating cusped line and a latitude and study their RG flow in perturbation theory. This allows for the definition of a bremsstrahlung function away from fixed points. We generalize to this case the known cusp/latitude correspondence that relates the bremsstrahlung function to a latitude Wilson loop. We find that away from the conformal fixed points the ordinary identity is broken by the conformal anomaly in a controlled way. From a defect perspective, the breaking of the correspondence can be traced back to the appearance of an anomalous dimension for fermionic operators localized on the defect. As a by-product, we provide a brand new result for the two-loop cusp anomalous dimension of the 1/6 BPS fermionic and the 1/6 BPS bosonic Wilson lines.

Published by the American Physical Society
2024
Capped black hole in five dimensions
Authors: Suzuki Ryotaku , Tomizawa Shinya
Published: June 2024

We present the first non-BPS (Bogomol’nyi-Prasad-Sommerfield) exact solution of an asymptotically flat, stationary spherical black hole having domain of outer communication with nontrivial topology in five-dimensional minimal supergravity. It describes a charged rotating black hole capped by a disk-shaped bubble. The existence of the “capped black hole” shows the nonuniqueness of spherical black holes.

Published by the American Physical Society
2024
Standard form of master equations for general non-Markovian jump processes: The Laplace-space embedding framework and asymptotic solution
Authors: Kanazawa Kiyoshi , Sornette Didier
Published: June 2024

We present a standard form of master equations (MEs) for general one-dimensional non-Markovian (history-dependent) jump processes, complemented by an asymptotic solution derived from an expanded system-size approach. The ME is obtained by developing a general Markovian embedding using a suitable set of auxiliary field variables. This Markovian embedding uses a Laplace-convolution operation applied to the velocity trajectory. We introduce an asymptotic method tailored for this ME standard, generalizing the system-size expansion for these jump processes. Under specific stability conditions tied to a single noise source, upon coarse graining, the generalized Langevin equation (GLE) emerges as a universal approximate model for point processes in the weak-coupling limit. This methodology offers a unified analytical tool set for general non-Markovian processes, reinforcing the universal applicability of the GLE founded in microdynamics and the principles of statistical physics.

Published by the American Physical Society
2024