bluuebunny/crossref_metadata_2025 huggingface dataset:
Room-Temperature Aerosol Dehydration of Green Fluorescent Protein
Authors: Pan Zehao , Wang Junshi , Stone Howard A. , Mezhericher Maksim
Published: September 2024

Rapid Room-Temperature Aerosol Dehydration (RTAD) is a novel, scalable drying technology for powderization and thermal stabilization of pharmaceutical drug products. Compared to conventional spray drying, RTAD utilizes sub-20µm droplets that evaporate rapidly at room temperature, thereby reducing drying-induced stresses for thermally sensitive biologics. In this study, we employed Green Fluorescent Protein (GFP) as a model biological molecule to optimize the RTAD system design and process parameters. We investigated the effects of droplet size, multiphase flow patterns in the drying chamber, and usage of polysorbate 20 as a model surfactant on GFP fluorescence after drying and powder reconstitution. The experiments demonstrated that the presence of polysorbate 20 in the formulation significantly influenced GFP fluorescence intensity, especially for smaller droplets. The numerical studies using Computational Fluid Dynamics simulations revealed that the intensity of GFP fluorescence in the produced dry powders was dependent on the patterns of multiphase flow in the drying chamber. Non-axisymmetric flows and closed circulating streamlines near the drying gas inlet negatively impacted the GFP fluorescence intensity. Through iterative optimization of chamber design, process parameters, and feedstock formulation, we achieved the recovery (compared to the initial samples) of GFP fluorescence intensity exceeding 96% in the obtained dry powders. This work establishes GFP as a sensitive model biologic and its fluorescence intensity as a powerful tool for rapidly assessing bioactivity following dehydration. The insights gained from this study have broad implications for the design and scale-up of room-temperature drying technologies, which can potentially transform the production of dry powder biopharmaceuticals.
Integration of metabolomic and transcriptomic analyses reveals novel regulatory functions of the ChREBP transcription factor in energy metabolism
Authors: An Jie , Astapova Inna , Zhang Guofang , Cangelosi Andrew L. , Ilkayeva Olga , Marchuk Hannah , Muehlbauer Michael J. , George Tabitha , Brozinick Joseph , Herman Mark A. , Newgard Christopher B.
Published: September 2024

Carbohydrate Response Element-Binding Protein (ChREBP) is a transcription factor that activates key genes involved in glucose, fructose, and lipid metabolism in response to carbohydrate feeding, but its other potential roles in metabolic homeostasis have not been as well studied. We used liver-selective GalNAc-siRNA technology to suppress expression of ChREBP in rats fed a high fat/high sucrose diet and characterized hepatic and systemic responses by integrating transcriptomic and metabolomic analyses. GalNAc-siChREBP-treated rats had lower levels of multiple short-chain acyl CoA metabolites compared to rats treated with GalNAc-siCtrl containing a non-targeting siRNA sequence. These changes were related to a sharp decrease in free CoA levels in GalNAc-siChREBP treated-rats, accompanied by lower expression of transcripts encoding enzymes and transporters involved in CoA biosynthesis. These activities of ChREBP likely contribute to its complex effects on hepatic lipid and energy metabolism. While core enzymes of fatty acid (FA) oxidation are induced by ChREBP knockdown, accumulation of liver acylcarnitines and circulating ketones indicate diversion of acetyl CoA to ketone production rather than complete oxidation in the TCA cycle. Despite strong suppression of pyruvate kinase and activation of pyruvate dehydrogenase, pyruvate levels were maintained, likely via increased expression of pyruvate transporters, and decreased expression of lactate dehydrogenase and alanine transaminase. GalNAc-siChREBP treatment increased hepatic citrate and isocitrate levels while decreasing levels of distal TCA cycle intermediates. The drop in free CoA levels, needed for the 2-ketoglutarate dehydrogenase reaction, as well as a decrease in transcripts encoding the anaplerotic enzymes pyruvate carboxylase, glutamate dehydrogenase, and aspartate transaminase likely contributed to these effects. GalNAc-siChREBP treatment caused striking increases in PRPP and ZMP/AICAR levels, and decreases in GMP, IMP, AMP, NaNM, NAD(P), and NAD(P)H levels, accompanied by reduced expression of enzymes that catalyze late steps in purine and NAD synthesis. ChREBP suppression also increased expression of a set of plasma membrane amino acid transporters, possibly as an attempt to replenish TCA cycle intermediates. In sum, combining transcriptomic and metabolomic analyses has revealed regulatory functions of ChREBP that go well beyond its canonical roles in control of carbohydrate and lipid metabolism to now include mitochondrial metabolism and cellular energy balance.
Microbial strategies of environmental adaptation revealed by trait-environmental relationships
Authors: Ren Minglei , Hu Ang , Zhao Zhonghua , Yao Xiaolong , Kimirei Ismael Aaron , Zhang Lu , Wang Jianjun
Published: September 2024

Microbial trait variation along environment gradients is crucial to understanding their ecological adaptation mechanisms. With the increasing availability of microbial genomes, making full use of the genome-based traits to decipher their adaptation strategies becomes promising and urgent. Here, we examined microbial communities in water and sediments of 20 East African lakes with pH values ranging from 7.2 to 10.1 through taxonomic-profiling and genome-centric metagenomics. We identified functional traits important for microbial adaptation to the stresses of alkalinity and salinity based on the significant trait-environment relationships (TERs), including those involved in cytoplasmic pH homeostasis, compatible solute accumulation, cell envelope modification and energy requisition. By integrating these significant-TER traits, we further developed an environmental adaptation index to quantify the species-level adaptive capacity for environmental stresses, such as high pH environments. The adaptation index of pH showed consistently significant positive relationships with species pH optima across regional and global genomic datasets from freshwater, marine and soda lake ecosystems. The generality of the index for quantifying environmental adaptation was demonstrated by showing significant relationships with the species niche optima for the gradients of soil temperature and seawater salinity. These results highlight the importance of trait-environment relationships in facilitating the inference of microbial genomic-based adaptation mechanisms, and expand our understanding of ecological adaptative strategies along environmental gradients.
Distinct duration and diet dependent lipid profiles and renal complications in GCK-MODY
Authors: Huang Yadi , Fan Yuxin , Liu Yang , Liu Xuan , Li Wei , Yang Ying , Zhang Ziyue , Ma Shifeng , Ji Shuhui , Chen Shanshan , Shu Hua , Feng Wenli , Wang Kunling , He Qing , Qi Wenjun , Fan Yu , Li Xin , Liu Ming
Published: September 2024

Heterozygous inactivating mutations in the glucokinase (GCK) gene cause one of the most common types of maturity-onset diabetes of the young type 2 (MODY2), also named GCK-MODY. Studies suggest that, unlike other types of diabetes, patients with GCK-MODY do not have increased risk of diabetic complications and therefore do not typically require antihyperglycemic therapy. However, long-term outcomes of GCK-MODY on lipid profiles and chronic complications under different dietary scenarios remain unclear. Herein, using a knock-in mouse model expressing a novel MODY causing mutation GCK-Q26L (GCKMut), we examined age- and diet-related lipid profiles and diabetic complications. We found that, although GCKMutmice exhibited mild elevated blood glucose, the lipid profiles, body fat composition, and diabetic kidney disease (DKD) were initially improved in high-fat-diet (HFD) fed mice at the age of 28 weeks, supporting potential beneficial effects of GCKMuton lipid metabolism and kidney health. Unexpectedly however, those protective effects diminished by 40 weeks, and became more severe dyslipidemia and kidney injury associated with renal fibrosis and inflammation at 60-week-old mice fed with normal diet (ND) or HFD. Those findings revealed distinct duration- and diet-dependent effects of inactivating GCK mutation on lipid profiles and DKD, highlighting previously unrealized long-term chronic complications in GCK-MODY.
ExonViz: A website and Python package to visualize transcripts and genetic variants
Authors: van den Berg Redmar R. , Lauffer Marlen C. , Laros Jeroen F.J.
Published: September 2024

ExonViz is an application and website that creates biologically accurate transcript figures, including features such as coding regions, genetic variants and exon reading frames. Transcript definitions are automatically retrieved from Ensembl and RefSeq. We illustrate the full functionality of ExonViz by generating a figure for all ClinVar variants reported inCYLD.

Alvailability and Implementation

ExonViz is available online viaDutch Center for RNA Therapeuticsand can be installed locally viaPyPI.

Contact

Redmar R. van den Berg

Supplementary information

Extensive documentation on ExonViz is available onRead the Docs.
Involvement of 5’ and 3’ UTRs on SARS-CoV-2 Genome Packaging
Authors: Zhang Zhang , Yang Kun , Shao Fangze , Shen Wenlong , Li Ping , Zhang Yue , Xu Junjie , Yu Guoying , Zhang Jun , Zhao Zhihu , Zhang Yan
Published: September 2024

The SARS-CoV-2 virus, responsible for the COVID-19 pandemic, packages its large single-stranded RNA genome through a precise yet enigmatic mechanism. A packaging signal (PS) within its genome was proposed to facilitate the assembly of new viral particles. Here in this study, we report the role of the 5’ and 3’ untranslated regions (UTRs) in PS-mediated genome packaging. Utilizing proximity ligation data, we demonstrate direct interactions between the UTRs and the PS9 element, a key packaging signal within the SARS-CoV-2 genome. Multiple evidence confirmed that the presence of UTRs enhance the packaging efficiency of infectious virus-like particles (iVLPs) and recruits more nucleocapsid (N) protein, suggesting a critical role in genome compaction and packaging. These insights into the regulatory mechanisms of SARS-CoV-2 genome packaging provide novel targets for antiviral therapeutics and contribute to the broader understanding of coronavirus assembly.
Integrating collecting systems in kidney organoids through fusion of distal nephron to ureteric bud
Authors: Shi Min , Crouse Brittney , Sundaram Nambirajan , Shakked Naomi Pode , Ester Lioba , Zhang Weitao , Janakiram Vinothini , Kopan Raphael , Helmrath Michael A. , Bonventre Joseph V. , McCracken Kyle W.
Published: September 2024

The kidney maintains homeostasis through an array of parallel nephrons, which all originate in development as isolated epithelial structures that later fuse through their distal poles to a system of collecting ducts (CD). This connection is required to generate functional nephrons by providing a pathway for excretion of metabolic waste and byproducts. Currently, methods for differentiating human pluripotent stem cells into kidney organoids generate nephrons that lack CDs and instead terminate as blind-ended tubules. Here we describe a developmentally inspired system that addresses this deficiency through assembly of induced nephrogenic mesenchyme with ureteric bud (UB) tissues, the embryonic building blocks of the kidney’s collecting system. The UB progenitors grow and develop into a network of CDs within the organoid, and importantly, they functionally integrate with the nephrons through recapitulating fusion between the distal tubule and CD to create a continuous epithelial lumen. We further showed that proximal-distal nephron specification, fusion frequency, and maturation of the CD can be augmented through temporal manipulation of developmental signaling pathways. This work provides a platform for interrogating the principles and mechanisms underlying nephron-UB fusion and a framework for engineering unobstructed nephrons with patterned collecting systems, an important step toward the de novo generation of functional kidney tissue.
Efficient production of functional proaerolysin fromE.coli
Authors: Pham Quynh Thi-Huong , Tagawa Ayako , Iwata Narumi , Miyanari Yusuke
Published: September 2024

Proaerolysin is a bacterial toxin produced byAeromonas hydrophilathat specifically binds to GPI-anchored proteins on the plasma membrane, creating transmembrane pores that lead to cell death within a few hours. Leveraging this unique property, proaerolysin is widely used in diagnostic tests for paroxysmal nocturnal hemoglobinuria (PNH), a disease caused by somatic mutations in thePIGAgene, which is involved in the biosynthesis of GPI anchors. Additionally, proaerolysin serves as a counter-selection agent in genetic manipulations. Although bacterial expression and purification of proaerolysin have been previously reported, yields were low due to the absence of internal disulfide bonds, which are crucial for protein stability. Here, we demonstrate that using the ShuffleE. colistrain, which facilitates the formation of disulfide bonds in the cytoplasm, significantly improves the solubility and proper folding of proaerolysin. We achieved a high yield of proaerolysin, approximately 3 mg from a 50 ml bacterial culture, with a purity of over 99%. The functionality of recombinant proaerolysin was confirmed by testing in mouse embryonic stem cells (mESCs), demonstrating that this high-yield production method offers a reliable and cost-effective source of functional proaerolysin for a wide range of biotechnological applications.
Qualitative EEG abnormalities signal a shift towards inhibition-dominated brain networks. Results from the EU-AIMS LEAP studies
Authors: Juarez-Martinez Erika L. , Avramiea Arthur-Ervin , Garcés Pilar , Hipp Joerg F. , Poil Simon-Shlomo , Diachenko Marina , Mansvelder Huibert D. , Jones Emily , Mason Luke , Murphy Declan , Loth Eva , Oakley Bethany , Charman Tony , Banaschewski Tobias , Oranje Bob , Buitelaar Jan , Bruining Hilgo , Linkenkaer-Hansen Klaus
Published: September 2024

Qualitative EEG abnormalities are common in Autism Spectrum Disorder (ASD) and hypothesized to reflect disrupted excitation/inhibition balance. To test this, we recently introduced a functional measure of network-level E/I ratio (fE/I). Here, we applied fE/I and other quantitative EEG measures to alpha oscillations from source-reconstructed data in the EU-AIMS compilation of 267 EEG recordings from children-adolescents and adults with ASD and 209 controls. We analyzed these quantitative measures alongside evaluating for qualitative EEG abnormalities ranging from slowing of activity to epileptiform patterns aiming to replicate the findings from the SPACE-BAMBI study (Bruining et al., 2020). EEG abnormalities were only identified in a few adults and could not be statistically assessed. ASD children-adolescents with EEG abnormalities exhibited lower relative alpha power and lower fE/I compared to children-adolescents without abnormalities; however, the EEG-abnormality scoring did not stratify the behavioral heterogeneity of ASD using clinical measures. Surprisingly, several controls presented with qualitative EEG abnormalities and showed a strikingly similar anatomical distribution of lower fE/I to the one observed in the ASD group, suggesting a shift towards inhibition-dominated network dynamics, in regions associated with altered sensory processing. The robustness of this association between EEG abnormalities and reduced fE/I was further supported by re-analysis of the SPACE-BAMBI study in source space. Stratification by the presence of EEG abnormalities and their associated effects on network activity may help understand neurodevelopmental physiological heterogeneity and the difficulties in implementing E/I targeting treatments in unselected cohorts.
Designing and bioengineering of CDRs with higher affinity against receptor-binding domain (RBD) of SARS-CoV-2 Omicron variant
Authors: Singh Vishakha , Choudhary Shweta , Bhutkar Mandar , Nehul Sanketkumar , Ali Sabika , Singla Jitin , Kumar Pravindra , Tomar Shailly
Published: September 2024

The emergence of the SARS-CoV-2 Omicron variant highlights the need for innovative strategies to address evolving viral threats. This study bioengineered three nanobodies H11-H4, C5, and H3 originally targeting the Wuhan RBD, to bind more effectively to the Omicron RBD. A structure-basedin silicoaffinity maturation pipeline was developed to enhance their binding affinities. The pipeline consists of three key steps: high-throughputin silicomutagenesis of complementarity-determining regions (CDRs), protein-protein docking for screening, and molecular dynamics (MD) simulations for assessment of the complex stability. A total of 741, 551, and 684 mutations were introduced in H11-H4, C5, and H3 nanobodies, respectively. Protein-protein docking and MD simulations shortlisted high-affinity mutants for H11-H4(6), C5(5), and H3(6). Further, recombinant production of H11-H4 mutants and Omicron RBD enabled experimental validation through Isothermal Titration Calorimetry (ITC). The H11-H4 mutants R27E, S57D, S107K, D108W, and A110I exhibited improved binding affinities with dissociation constant (KD) values ranging from ∼8.8 to ∼27 µM, compared to the H11-H4 nanobody KDof ∼32 µM, representing a three-fold enhancement. This study demonstrates the potential of the developedin silicoaffinity maturation pipeline as a rapid, cost-effective method for repurposing nanobodies, aiding the development of robust prophylactic strategies against evolving SARS-CoV-2 variants and other pathogens.

Graphical Abstract
Low maternal plasma apelin in the second trimester is associated with adverse pregnancy outcome in severe, early-onset fetal growth restriction
Authors: Braun N. , Bethell K. , Chaloner L. , Maksym K. , Spencer R.N. , Maguire J.J. , Davenport A.P. ,   EVERREST consortium, David A.L. , Vaughan O.R.
Published: September 2024

Context

Fetal growth restriction increases adverse pregnancy outcomes such as preterm birth and intrauterine fetal death. Apelin is a secreted peptide expressed in placental syncytiotrophoblast and downregulated in fetal growth restriction.

Objectives

We tested the hypothesis that adverse pregnancy outcome is associated with low maternal plasma apelin at diagnosis of early-onset fetal growth restriction.

Methods

Plasma samples and fetomaternal blood flow Doppler velocimetry measurements were obtained from pregnant women (n=59) at diagnosis of early-onset fetal growth restriction in the second trimester. Plasma apelin was determined by ELISA and pregnancy outcome was recorded. Placental gene expression was analysed after birth by qRT-PCR, compared to term placentas from women with late-onset fetal growth restriction or with appropriate-for-gestational age infants.

Results

At diagnosis of early-onset fetal growth restriction, plasma apelin concentration was significantly lower in women who delivered extremely preterm (<28 weeks gestation) or had an intrauterine fetal death, compared to women who had a livebirth≥28 weeks (P<0.05). Plasma apelin correlated directly with uterine artery volume flow rate and inversely with pulsatility index. Placental gene expression of apelin, but not the apelin receptor or elabela, was lower in women with early-onset fetal growth restriction delivering preterm than in appropriate-for-gestational-age, term control women.

Conclusion

Low maternal circulating apelin during the second trimester is associated with impaired uteroplacental perfusion and subsequent adverse pregnancy outcome in severe, early-onset fetal growth restriction. Placental apelin deficiency may contribute mechanistically to the pathogenesis of early-onset fetal growth restriction.
Chromatin remodeler BRG1 recruits huntingtin to repair DNA double-strand breaks in neurons
Authors: Pradhan Subrata , Bush Keegan , Zhang Nan , Pandita Raj K. , Tsai Chi-Lin , Smith Charlene , Pandlebury Devon F. , Gaikwad Sagar , Leonard Francis , Nie Linghui , Tao Annie , Russell William , Yuan Subo , Choudhary Sanjeev , Ramos Kenneth S. , Elferink Cornelis , Wairkar Yogesh P. , Tainer John A. , Thompson Leslie M. , Pandita Tej K. , Sarkar Partha S.
Published: September 2024

Persistent DNA double-strand breaks (DSBs) are enigmatically implicated in neurodegenerative diseases including Huntington’s disease (HD), the inherited late-onset disorder caused by CAG repeat elongations in Huntingtin (HTT). Here we combine biochemistry, computation and molecular cell biology to unveil a mechanism whereby HTT coordinates a Transcription-Coupled Non-Homologous End-Joining (TC-NHEJ) complex. HTT joins TC-NHEJ proteins PNKP, Ku70/80, and XRCC4 with chromatin remodeler Brahma-related Gene 1 (BRG1) to resolve transcription-associated DSBs in brain. HTT recruitment to DSBs in transcriptionally active gene- rich regions is BRG1-dependent while efficient TC-NHEJ protein recruitment is HTT-dependent. Notably, mHTT compromises TC-NHEJ interactions and repair activity, promoting DSB accumulation in HD tissues. Importantly, HTT or PNKP overexpression restores TC-NHEJ in aDrosophilaHD model dramatically improving genome integrity, motor defects, and lifespan. Collective results uncover HTT stimulation of DSB repair by organizing a TC-NHEJ complex that is impaired by mHTT thereby implicating dysregulation of transcription-coupled DSB repair in mHTT pathophysiology.

Highlights

•

BRG1 recruits HTT and NHEJ components to transcriptionally active DSBs.

•

HTT joins BRG1 and PNKP to efficiently repair transcription related DSBs in brain.

•

Mutant HTT impairs the functional integrity of TC-NHEJ complex for DSB repair.

•

HTT expression improves DSB repair, genome integrity and phenotypes in HD flies.
Mpox mRNA-1769 Vaccine Inhibits Orthopoxvirus Replication at Intranasal, Intrarectal, and Cutaneous Sites of Inoculation
Authors: Cotter Catherine A. , Ignacio Maxinne A. , Americo Jeffrey L. , Earl Patricia L. , Mucker Eric M. , Hooper Jay W. , Frey Tiffany R. , Carfi Andrea , Freyn Alec W. , Moss Bernard
Published: September 2024

The increasing incidence of mpox in Africa and the recent global outbreak with evidence of sexual transmission have stimulated interest in new vaccines and therapeutics. Our previous study demonstrated that mice immunized twice with a quadrivalent lipid nanoparticle vaccine comprising four monkeypox virus mRNAs raised neutralizing antibodies and antigen-specific T cells and were protected against a lethal intranasal challenge with vaccinia virus. Here we extended these findings by using live animal imaging to demonstrate that the mRNA vaccine greatly reduced virus replication and spread from an intranasal site of inoculation and prevented detectable replication at intrarectal and cutaneous inoculation sites. Moreover, considerable protection was achieved with a single vaccination and a booster vaccination enhanced protection for at least 4 months. Protection was related to the amount of mRNA inoculated, which correlated with neutralizing antibody levels. The role of antibody in protection was demonstrated by passive transfer of immune serum pre- or post-challenge to immunocompetent and immunodeficient mice lacking mature B and T cells and therefore unable to mount an adaptive response. These findings provide insights into the mechanism and extent of mRNA vaccine induced protection of orthopoxviruses and support clinical testing.
Organ-specific Sympathetic Innervation Defines Visceral Functions
Authors: Wang Tongtong , Teng Bochuan , Yao Dickson R. , Gao Wei , Oka Yuki
Published: September 2024

The autonomic nervous system orchestrates the brain and body functions through the sympathetic and parasympathetic pathways. However, our understanding of the autonomic system, especially the sympathetic system, at the cellular and molecular levels is severely limited. Here, we show unique topological representations of individual visceral organs in the major abdominal sympathetic ganglion complex. Using multi-modal transcriptomic analyses, we identified distinct sympathetic populations that are both molecularly and spatially separable in the celiac-superior mesenteric ganglia (CG-SMG). Notably, individual CG-SMG populations exhibit selective and mutually exclusive axonal projections to visceral organs, targeting either the gastrointestinal (GI) tract or secretory areas including the pancreas and bile tract. This combinatorial innervation pattern suggests functional segregation between different CG-SMG populations. Indeed, our neural perturbation experiments demonstrated that one class of neurons selectively regulates GI food transit. Another class of neurons controls digestion and glucagon secretion independent of gut motility. These results reveal the molecularly diverse sympathetic system and suggest modular regulations of visceral organ functions through distinct sympathetic populations.
Ecophysiological behaviour of majorFusariumspecies in response to combinations of temperature and water activity constraints
Authors: Garcia Marie-Anne , Mahmoud Rémi , Bancal Marie-Odile , Bancal Pierre , Bernillon Stéphane , Pinson-Gadais Laetitia , Richard-Forget Florence , Foulongne-Oriol Marie
Published: September 2024

FusariumHead Blight (FHB) is a devastating fungal disease affecting cereals, caused byFusariumspecies that can produce harmful mycotoxins.Fusariumspecies share the same ecological niche, and their population dynamic and associated mycotoxin patterns are driven by the environment. The aim of the present study was to investigate ecophysiological characteristics of the majorFusariumspecies causing FHB under abiotic factors. Growth and mycotoxin production of different strains ofFusarium avenaceum, Fusarium graminearum,Fusarium langsethiae, Fusarium poaeandFusarium tricinctumwere characterized under a combined effect of temperature (ϴ = 15, 20, 25 and 30°C) and water activity (aw= 0.99, 0.98, 0.97, 0.96, 0.95 and 0.94). Using innovative statistical analyses, we demonstrated that thoseFusariumspecies greatly differ in their responses to the studied environmental constraints. Our findings indicated that ϴ, aw, and their interaction were the major factors with a significant impact on the species behaviour. The intraspecific variation was demonstrated as less pronounced than the interspecific one. Understanding the ecophysiological requirements ofFusariumspecies is crucial in the context of climate change that is predicted to worsen disease outbreaks. Our data constitute a valuable knowledge base for improving the reliability and robustness of FHB prediction models and anticipating the associated mycotoxin risk.

IMPORTANCE

Fusariumspecies pose a significant threat to major cereal crops, including wheat. These fungi not only reduce yield but also produce mycotoxins harmful to animals and humans. The prevalence of eachFusariumspecies is influenced by environmental conditions and shifts in pathogen populations, leading to changes in mycotoxin patterns have already been observed in relation to climate changes. This study revealed distinct ecophysiological behaviours, including mycelium growth and mycotoxin production, among the five majorFusariumspecies when exposed to varying temperature and water activity conditions. Our findings provide a valuable foundation for a more comprehensive understanding of the challenge of mycotoxin contamination and for the development of more effective mitigation strategies in the near future.
Extremely distinct microbial communities in closely related leafhopper subfamilies: Typhlocybinae and Eurymelinae (Cicadellidae, Hemiptera)
Authors: Kobiałka Michał , Świerczewski Dariusz , Walczak Marcin , Urbańczyk Weronika
Published: September 2024

Abstract

Among the Hemiptera insects, a widespread way of feeding is sucking sap from host plants. Due to diet poor in nutrients, these insects enter into obligate symbiosis with their microorganisms. However, within the Cicadellidae family, there is a relatively large group of mesophyll feeders – Typhlocybinae that is considered to be devoid of symbiotic companions. In this work, we examine the composition of microorganisms in this subfamily and compare the results with their close relatives – the Eurymelinae subfamily. To study the microbiome, we used high-throughput next-generation sequencing (NGS, Illumina) and advanced microscopic techniques such as transmission electron microscopy (TEM) and fluorescencein situhybridization (FISH) in a confocal microscope. The Typhlocybinae insects have very poor microbial communities in their bodies, these are mainly facultative microorganisms, such as alphaproteobacteria of the genusWolbachiaorRickettsia. We detected also the presence of bacteria that can be considered as facultative symbionts e.g.Spiroplasma, Acidocella, Arsenophonus, Sodalis, Lariskella, Serratia, CardiniumandAsaia.On the other hand, the Eurymelinae group is characterized by a large diversity of the microbial communities, similar to those described in other Cicadomorpha. We find obligate co-symbionts involved in the synthesis of essential amino acids such asSulcia,betaproteobacteria related to genusNasuiaor gammaproteobacteriaSodalis. In other representatives, we observed symbiotic yeast-like fungi from the family Ophiocordycipitaceae and within some genera we discoveredArsenophonusbacteria inhabiting the interior ofSulciabacteria. Additionally, we investigated the transovarial transmission of obligate symbionts, which occurs via infection of the ovaries of females.

Importance

The Typhlocybinae and Eurymelinae leafhoppers differ significantly in their symbiotic communities. This is undoubtedly due to their different diets, as Typhlocybinae insects feed on parenchyma, richer in nutrients, while Eurymelinae, like most representatives of Auchenorrhyncha, consume sap from the phloem fibers of plants. Our work presents comprehensive studies of 42 species belonging to two above-mentioned, so far poorly known Cicadomorpha subfamilies. Phylogenetic studies we conducted confirm that the insects from the groups studied have a common ancestor. Since obligate symbionts, having a reduced genome, may affect the reduction of their host’s adaptation to changing environmental conditions, e.g. temperature, and facultative microbiomes may influence the increase in such adaptation and expansion of host niche space. Therefore, Typhlocybinae species may show greater resistance to future climate change than representatives of the Eurymelinae. The research that considers the role of ecological niches in microbiome composition is essential in the era of climate change.
Novel insights into Emx2 and Dmrta2 cooperation during cortex development and evidence for Dmrta2 function in choroid plexus
Authors: Anirudhan Jithu , Shen Xueyi , Szemes Tünde , Dieu Marc , Azouz Abdulkader , Conrard Louise , Doumont Gilles , Sitte Maren , Achouri Younes , Kricha Sadia , Salinas-Riester Gabriela , Renard Patricia , Bellefroid Eric J.
Published: September 2024

Early dorsal telencephalon development is coordinated by an interplay of transcription factors that exhibit a graded expression pattern in neural progenitors. How they function together to orchestrate cortical development remains largely unknown. TheEmx2andDmrta2genes encode TFs that are expressed in a similar caudomedialhigh/ rostrolaterallowgradient in the ventricular zone of the developing dorsal telencephalon with, in the medial pallium,Dmrta2but notEmx2expressed in the developing choroid plexus. Their constitutive loss has been shown to impart similar cortical abnormalities, and their combined deletion exacerbates the phenotypes, suggesting possible cooperation during cortex development. In this study, we utilized molecular and genetic approaches to dissect how Emx2 functions with Dmrta2 during cortical development. Our results show that while they regulate a similar set of genes, their common direct targets are limited but include key regulators of cortical development. Identification of the interaction partners of Emx2 suggests that it coordinates with the LIM-domain binding protein Ldb1 to execute the activation and repression of some of its downstream targets. Finally, whileEmx2is known to suppress choroid plexus development, we also provide evidence thatDmrta2is in contrast required for choroid plexus since in its absence in medial telencephalic progenitors, mice develop hydrocephalous postnatally, a phenotype that appears to be due to a compromised cytoarchitecture. Together, these data indicate that Emx2 and Dmrta2 have similar but also distinct functions in telencephalon development and provide the first insights into Emx2 mechanism of action.

SIGNIFICANCE STATEMENT

Emx2andDmrta2encode transcription factors that generate similar phenotypes upon their loss in the developing cortex suggesting possible cooperation. Here we explored how Emx2 functions with Dmrta2 during cortical development. Results obtained indicate that Emx2 directly regulates with Dmrta2 only a few genes, some coding for key cortical determinants and that Emx2 utilizes the Ldb1 cofactor for the regulation of some of its targets. Results also suggest that, unlike Emx2 which suppresses choroid plexus development, Dmrta2 is required for choroid plexus as its loss in medial telencephalic progenitors leads to hydrocephalus. Together, our results reveal that Emx2 and Dmrta2 have similar but also distinct functions during telencephalon development and provide novel insights into the mechanism of action of Emx2.
Hippocampal γCaMKII dopaminylation promotes synaptic-to-nuclear signaling and memory formation
Authors: Stewart Andrew F. , Fulton Sasha L. , Durand-de Cuttoli Romain , Thompson Robert E. , Chen Peng-Jen , Brindley Elizabeth , Cetin Bulent , Farrelly Lorna A. , Futamura Rita , Claypool Sarah , Bastle Ryan M. , Di Salvo Giuseppina , Peralta Christopher , Molina Henrik , Baljinnyam Erdene , Marro Samuele G. , Russo Scott J. , DeVita Robert J. , Muir Tom W. , Maze Ian
Published: September 2024

Protein monoaminylation is a class of posttranslational modification (PTM) that contributes to transcription, physiology and behavior. While recent analyses have focused on histones as critical substrates of monoaminylation, the broader repertoire of monoaminylated proteins in brain remains unclear. Here, we report the development/implementation of a chemical probe for the bioorthogonal labeling, enrichment and proteomics-based detection of dopaminylated proteins in brain. We identified 1,557 dopaminylated proteins – many synaptic – including γCaMKII, which mediates Ca2+-dependent cellular signaling and hippocampal-dependent memory. We found that γCaMKII dopaminylation is largely synaptic and mediates synaptic-to-nuclear signaling, neuronal gene expression and intrinsic excitability, and contextual memory. These results indicate a critical role for synaptic dopaminylation in adaptive brain plasticity, and may suggest roles for these phenomena in pathologies associated with altered monoaminergic signaling.
Spatial Development of Brain Networks During The First Six Postnatal Months
Authors: Seraji Masoud , Shultz Sarah , Li Qiang , Fu Zening , Calhoun Vince D , Iraji Armin
Published: September 2024

The initial months of life constitute a crucial period for human development. A comprehensive understanding of this early phase is essential for unraveling the origins of neurodevelopmental disorders and promoting infant brain health. This study uniquely focuses on the spatial development of intrinsic brain connectivity networks during infancy, which has been less explored compared to functional connectivity. We utilized independent component analysis on resting-state fMRI data from 74 infants to assess how the spatial organization of infant brain networks evolves between birth and six months.

Our findings reveal significant changes in spatial characteristics, including an a notable rise in the network-averaged spatial similarity across age, reflecting how closely each participant-specific spatial map aligns with the group-level map for each network. We also observed a marked reduction in the network engagement range by age, representing the extent of voxel intensity range fluctuation within each network. This suggests a continuing process of consolidation, where voxel contributions to the network become more uniform, as indicated by the narrowing of intensity values. The network strength, calculated as the average of all the voxel intensities in the network, indicating the degree of involvement to the specific functional network, increased across age in several networks, such as frontal-mPFC, primary, and secondary visual networks. The network size, along with the network center of mass, illustrating spatial distribution alterations of brain networks by age, varied across different networks. For instance, both metrics increased across age in the secondary visual network but decreased in the temporal network. Additionally, we examined the networks in relation to their linear versus non-linear developmental trajectories across all spatial characteristics, providing a deeper understanding of how these patterns evolve during early infancy. These findings contribute to early brain development understanding and offer insights into potential markers of consolidation and spatial reorganization in large-scale brain networks during infancy.
TBC1D24 regulates mitochondria and endoplasmic reticulum-mitochondria contact sites
Authors: Benhammouda Sara , Rousseau Justine , Campeau Philippe M. , Germain Marc
Published: September 2024

The RabGAP protein TBC1D24 is mutated in several neurological disorders including DOORS syndrome (Deafness, Onycho-Osteodystrophy, Mental Retardation, Seizures). Although TBC1D24 comprises two highly conserved domains — the Tre2/Bub2/Cdc16 (TBC) domain and the TLDc domain — both of which seem to play critical roles in cellular functions, its exact physiological function within the cell remains poorly understood. Here, we show that TBC1D24 affects mitochondrial structure and activity. Specifically, both primary fibroblasts from patients with TBC1D24 mutations and cells in which TBC1D24 has been knocked down exhibit fragmented mitochondria, decreased ATP production, and reduced mitochondrial membrane potential. Importantly, loss or mutation of TBC1D24 also alters sites of contact between the endoplasmic reticulum (ER) and mitochondria (ERMCS). These sites are vital for mitochondrial fusion and fission processes, which regulate mitochondrial dynamics and, consequently, mitochondrial activity. Altogether, our results uncover a new role for TBC1D24 in the regulation of mitochondrial functions and ERMCS which likely contribute to the neurological dysfunction present in affected patients.
Sox9prevents retinal degeneration and is required for limbal stem cell differentiation in the adult mouse eye
Authors: Hurtado Alicia , López-Soriano Víctor , Lao Miguel , Celis-Barroso M. Ángeles , Lazúen Pilar , Chacón de Castro Alejandro , Ramírez-Casas Yolanda , Alaminos Miguel , Collinson J. Martin , Burgos Miguel , Jiménez Rafael , Carmona F. David , Barrionuevo Francisco J.
Published: September 2024

Sox9is a transcription factor with multiple roles during development and in adult organ homeostasis. In the adult eye,Sox9expression persists in several cell types, including the retinal pigmented epithelium cells and the Müller glial cells, as well as in the limbal and corneal basal epithelia. To uncover the role ofSox9in these cell types, we induced the deletion of the gene in adult mice. We found that, afterSox9ablation, mutant mice undergo a severe process of retinal degeneration characterized by the loss of Müller glial cells and complete depletion of the photoreceptors layer. Moreover, by combining single-cell RNA sequencing andSox9lineage tracing, we found thatSox9is expressed in a basal limbal stem cell population with the ability to form two types of long-lived cell clones involved in stem cell maintenance and homeostasis. Mosaic analysis ofSox9positive and negative cells confirmed that the gene is essential for limbal stem cell differentiation. Our results show thatSox9is required for the maintenance of retinal integrity and for limbal stem cell differentiation in the adult mouse eye.
Social Isolation Intensifiesadgrl3.1-Related Externalizing and Internalizing Behaviors in Zebrafish
Authors: Fontana Barbara D. , Alnassar Nancy , Norton William H.J. , Parker Matthew O.
Published: September 2024

Externalizing disorders (EDs) are characterized by outward-directed behaviors such as aggression and hyperactivity. They are influenced by gene-environment interactions, yet our understanding of the genetic predispositions and environmental contexts that give rise to them is incomplete. Additionally, people with EDs often exhibit comorbid internalizing symptoms, which can complicate the clinical presentation and treatment strategies. Following on from our previous studies, we examined genes x environment interaction as a risk factor for EDs by looking at internalizing and externalizing behaviors after social isolation. Specifically, we subjectedadgrl3.1knockout zebrafish — characterized by hyperactivity and impulsivity — to a 2-week social isolation protocol. We subsequently assessed the impact on anxiety-like behavior, abnormal repetitive behaviors, working memory, and social interactions. Genotype-specific additive effects emerged, with socially isolatedadgrl3.1knockout fish exhibiting intensified comorbid phenotypes, including increased anxiety, abnormal repetitive behaviors, reduced working memory, and altered shoaling, when compared to WT fish. The findings demonstrate that genetic predispositions interact with environmental stressors, such as social isolation, to exacerbate both externalizing and internalizing symptoms. This underlines the necessity for comprehensive diagnostic and intervention strategies.
Dynamic metal coordination controls chemoselectivity in radical halogenases
Authors: Kissman Elijah N. , Kipouros Ioannis , Slater Jeffrey W. , Stone Elizabeth A. , Yang Avery Y. , Braun Augustin , Ensberg Alder R. , Whitten Andrew M. , Chatterjee Kuntal , Bogacz Isabel , Yano Junko , Bollinger J. Martin , Chang Michelle C.Y.
Published: September 2024

The activation of inert C(sp3)-H bonds by non-heme Fe enzymes plays a key role in metabolism, epigenetics, and signaling, while providing a powerful biocatalytic platform for the chemical synthesis of molecules with increasedsp3complexity. In this context, FeII/α-ketoglutarate-dependent radical halogenases represent a broadly interesting system, as they are uniquely capable of carrying out transfer of a diverse array of bound anions following C-H activation. Here, we provide the first experimental evidence that bifurcation of H-atom abstraction and radical rebound is driven both by the ability of a dynamic metal coordination sphere to reorganize as well as by a second-sphere hydrogen-bond network where only two residues (Asn224 and Ile151) are necessary and sufficient. The identification of this minimal motif provides a paradigm for understanding the evolution of catalytic plasticity in these enzymes and yields new insight into the design principles by which to expand their reaction scope.
Viral fragments in the urine proteome: New clues to the cause of fever
Authors: Yang Minhui , Zhao Chenyang , Gao Youhe
Published: September 2024

[Background]

Fever of unknown origin refers to a medical condition where the cause of the fever is not yet clear. This condition is common in various potential diseases and usually requires detailed examination and testing to determine the specific cause. No one has ever looked for the cause of fever in urine proteomics, and this study provides clues and diagnostic evidence for patients with fever of unknown origin through urine proteomics analysis.

[Methods]

We attempted virus-wide database searching for the first time in urine samples, using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to analyze urine proteins from febrile patients. Virus protein fragments were identified and retrieved.

[Results]

In urine samples, we detected specific peptide segments from various viruses including monkeypox virus, saliva virus A, human herpesvirus 8 type P, Middle East respiratory syndrome-related coronavirus, rotavirus A, foot-and-mouth disease virus (strain NZ2), human herpesvirus 2 (strain HG52), human adenovirus E serotype 4, influenza A virus, human coronavirus NL63, influenza B virus (strain W3), Nipah virus, and hepatitis C virus genotype 2k (isolate VAT96), among others. Several viruses showed significantly higher detection levels in febrile patients compared to controls, with saliva virus A showing an increase by over 4200-fold, and multiple virus proteins increased by more than 20-fold. It is noteworthy that the overall protein retrieval error rate was less than 1%, and the individual protein retrieval error rate for each sample was less than 5%, ensuring highly reliable protein retrieval results with a probability of error across all proteins of only 1.2×e-17.

[Conclusion]

Reliable virus protein fragments can be retrieved from urine proteomics, providing clues for febrile patient investigation and potentially applicable to the exploration of any unknown diseases. By adopting our method, there is no need to know in advance what specific viruses are contained in the sample, as long as the information of these viruses has been stored in the virus database, comprehensive and extensive virus retrieval can be achieved. This method significantly expands the coverage of virus detection and improves the flexibility and efficiency of detection.
A Method for Visual Psychophysics based on the Navigational Behaviour of Desert Ants (Melophorus bagoti)
Authors: Deeti Sudhakar , Lionetti Vito , Cheng Ken
Published: September 2024

The Australian desert antMelophorus bagotiis known to navigate in their complex visual environment relying on path integration and landmark learning. We investigated the navigational behaviour of desert ants in response to visual stimulus changes along their route to a food source. Ants were trained to self-navigate a track between their nest and a feeder, with visual stimuli introduced near the feeder. After three days of training, we altered the visual scene by changing colours and observed the ants’ reactions. The results showed that ants in the test conditions, when visual changes were introduced, displayed more meandering paths, increased scanning behaviour, and slower speeds compared to control conditions. The sinuosity of their paths increased, and their orientation became less efficient. Additionally, changes in colour led to significant alterations in path characteristics, including a higher frequency of head oscillations and deviations from straight-line paths. These findings suggest that disruption to visual cues used for navigation causes noticeable changes in their movement patterns. A subset of these changes, easy to measure and calculate, can provide a signature to indicate that ants have detected a change in the visual stimuli. This proof-of-concept study thus highlights a method for studying visual psychophysics in ants in their natural habitat.