bluuebunny/crossref_metadata_2025 huggingface dataset:
The Impact of T-cell Aging on Alloimmunity and Inflammaging
Authors: Iske Jasper , Dedeilia Aikaterini , Xiao Yao , Martin Friederike , Emmert Maximilian Y. , Sage Pete T. , Abdi Reza , Zhou Hao , Tullius Stefan G.
Published: June 2023

Aging affects immunity broadly through changes caused by immunosenescence, clinically resulting in augmented susceptibility to infections, autoimmunity, and cancer. The most striking alterations associated with immunosenescence have been observed in the T-cell compartment with a significant shift toward a terminally differentiated memory phenotype taking on features of innate immune cells. At the same time, cellular senescence impairs T-cell activation, proliferation, and effector functions, compromising the effectiveness of immunity. In clinical transplantation, T-cell immunosenescence has been the main driver of less frequent acute rejections in older transplant recipients. This patient population, at the same time, suffers more frequently from the side effects of immunosuppressive therapy including higher rates of infections, malignancies, and chronic allograft failure. T-cell senescence has also been identified as an instigator of age-specific organ dysfunction through a process that has been coined “inflammaging,” accelerating organ injury and potentially contributing to the limited lifetime of organ transplants. Here, we provide a summary of the latest evidence on molecular characteristics of T-cell senescence affecting alloimmunity and organ quality while dissecting the consequences of unspecific organ injury and immunosuppression on T-cell senescence. Rather than conceptualizing immunosenescence as a broad and general “weaker” alloimmune response, it appears critical to understand both mechanisms and clinical effects in detail as a basis to refine treatment.
Production of antigenically stable enterovirus A71 virus-like particles in Pichia pastoris as a vaccine candidate
Authors: Kingston Natalie J. , Snowden Joseph S. , Martyna Agnieszka , Shegdar Mona , Grehan Keith , Tedcastle Alison , Pegg Elaine , Fox Helen , Macadam Andrew J. , Martin Javier , Hogle James M. , Rowlands David J. , Stonehouse Nicola J.
Published: June 2023

Enterovirus A71 (EVA71) causes widespread disease in young children with occasional fatal consequences. In common with other picornaviruses, both empty capsids (ECs) and infectious virions are produced during the viral lifecycle. While initially antigenically indistinguishable from virions, ECs readily convert to an expanded conformation at moderate temperatures. In the closely related poliovirus, these conformational changes result in loss of antigenic sites required to elicit protective immune responses. Whether this is true for EVA71 remains to be determined and is the subject of this investigation.

We previously reported the selection of a thermally resistant EVA71 genogroup B2 population using successive rounds of heating and passage. The mutations found in the structural protein-coding region of the selected population conferred increased thermal stability to both virions and naturally produced ECs. Here, we introduced these mutations into a recombinant expression system to produce stabilized virus-like particles (VLPs) in Pichia pastoris.

The stabilized VLPs retain the native virion-like antigenic conformation as determined by reactivity with a specific antibody. Structural studies suggest multiple potential mechanisms of antigenic stabilization, however, unlike poliovirus, both native and expanded EVA71 particles elicited antibodies able to directly neutralize virus in vitro. Therefore, anti-EVA71 neutralizing antibodies are elicited by sites which are not canonically associated with the native conformation, but whether antigenic sites specific to the native conformation provide additional protective responses in vivo remains unclear. VLPs are likely to provide cheaper and safer alternatives for vaccine production and these data show that VLP vaccines are comparable with inactivated virus vaccines at inducing neutralising antibodies.
Social Determinants of Health and Fatal Crashes Involving US Geriatric and Non-Geriatric Road Users
Authors: Adeyemi Oluwaseun , DiMaggio Charles , Grudzen Corita , Konda Sanjit , Rogers Erin , Goldfeld Keith , Blecker Saul , Chodosh Joshua
Published: June 2023

Introduction

Social determinants of health (SDoH), defined as nonmedical factors that impact health outcomes, have been associated with fatal crash occurrences. Road users who live in communities with negative SDoH may be at increased risk of crash-related mortality, and the risks may be further heightened among geriatric road users and in rural areas. We evaluated the relationship between the county-level measure of SDoH and county-level fatal crash counts among geriatric and non-geriatric road users living in rural, suburban, and urban areas.

Methods

For this ecological study, we pooled data from Fatality Analysis Reporting System (2018 to 2020) and the U.S. Census Bureau (2019 data) and limited our analyses to the 3,108 contiguous US counties. The outcome measures were county-level fatal crash counts involving (1) geriatric (65 years and older) road users (2) non-geriatric road users, and (2) the general population. The predictor variable was the Multidimensional Deprivation Index (MDI), a score that measures the five domains of SDoH - economic quality, healthcare access, education, community, and neighborhood quality. We defined the MDI as a three-level categorical variable: at or below the national average, within two-fold of the national average, and higher than two-fold of the national average. We controlled for county-level demographics and crash characteristics. We performed a Bayesian spatial Poisson regression analysis using Integrated Nested Laplace Approximations and reported the crash fatality rate ratios (plus 95% Credible Intervals (CrI)).

Results

The median (Q1, Q3) standardized mortality rate ratios among geriatric and non-geriatric road users were 1.3 (0.6, 2.5) and 1.6 (0.9, 2.7), respectively. A total of 283 (9.1%) and 806 (15.9%) counties were classified as very highly deprived and highly deprived, respectively. Clusters of counties with high deprivation rates were identified in the Southern states. Counties classified as very highly deprived and highly deprived had 40% (95% CrI: 1.24 – 1.57) and 25% (95% CrI: 1.17 – 1.34) increased geriatric fatality crash rate ratios and this pattern of association persisted in suburban and urban areas. Also, counties classified as very highly deprived and highly deprived had 42% (95% CI: 1.27 – 1.58) and 32% (95% CI: 1.23 – 1.38) increased fatality crash rate ratios among all road users and this pattern persisted in suburban and urban areas. Counties with more than four-fold increased fatality rate ratios were located commonly in Texas, Oklahoma, Nevada, and Utah.

Conclusion

Despite older adults being less frequent road users, county-level deprivation measures of the SDoH are equally associated with geriatric and non-geriatric crash-related fatal rate ratios. Policies that improve county-level SDoH may reduce the county-level fatal rate ratios equally among geriatric and non-geriatric road users.
Crop modeling suggests limited transpiration would increase yield of sorghum across drought-prone regions of the United States
Authors: Raymundo Rubí , Mclean Greg , Sexton-Bowser Sarah , Morris Geoffrey
Published: June 2023

Breeding sorghum for drought adaptation is pivotal to secure crop production in drought-prone regions. Limited transpiration (LT) restricts water demand at high vapor pressure deficit, saving water for use in critical periods later in the growing season. Here we evaluated the hypothesis that LT would increase sorghum grain yield in the United States. We used a process-based crop model, APSIM, which simulates interactions of genotype, environment, and management (G × E × M). In this study, the G component includes the LT trait (GT) and maturity group (GM), the E component entails water deficit patterns, and the M component represents different planting dates. Simulations were conducted over 33 years (1986-2018) for representative locations across the US sorghum belt (Kansas, Texas, and Colorado) for three planting dates and maturity groups. The interaction of GTx E indicated a higher impact of LT sorghum on grain for LD, MD, and ED (8%), than on WW environments (4%). Thus significant impacts of LT can be achieved in western regions of the sorghum belt. Otherwise, the lack of interaction of GT× GM× M suggested that an LT sorghum would increase yield by around 8% across maturity groups and planting dates. Although the interaction GM× M revealed that specific combinations are better suited across geographical regions. Overall, the findings suggest that breeding for LT would increase sorghum yield in the drought-prone areas of the US without tradeoffs.
Dysregulated Pulmonary Inflammatory Responses Exacerbate the Outcome of Secondary Aspergillosis Following Influenza
Authors: Lee Chrono K. , Oliveira Lorena V. N. , Akalin Ali , Specht Charles A. , Lourenco Diana , Gomez Christina L. , Ramirez-Ortiz Zaida G. , Wang Jennifer P. , Levitz Stuart M.
Published: June 2023

Inhalation of airborne conidia of the ubiquitous fungusAspergillus fumigatuscommonly occurs but invasive aspergillosis is rare except in profoundly immunocompromised persons. Severe influenza predisposes patients to invasive pulmonary aspergillosis by mechanisms that are poorly defined. Using a post-influenza aspergillosis model, we found that superinfected mice had 100% mortality when challenged withA. fumigatusconidia on days 2 and 5 (early stages) of influenza A virus infection but 100% survival when challenged on days 8 and 14 (late stages). Influenza-infected mice superinfected withA. fumigatushad increased levels of the pro-inflammatory cytokines and chemokines IL-6, TNFα, IFNβ, IL-12p70, IL-1α, IL-1β, CXCL1, G-CSF, MIP-1α, MIP-1β, RANTES and MCP-1. Surprisingly, on histopathological analysis, superinfected mice did not have greater lung inflammation compared with mice infected with influenza alone. Mice infected with influenza had dampened neutrophil recruitment to the lungs following subsequent challenge withA. fumigatus, but only if the fungal challenge was executed during the early stages of influenza infection. However, influenza infection did not have a major effect on neutrophil phagocytosis and killing ofA. fumigatusconidia. Moreover, minimal germination of conidia was seen on histopathology even in the superinfected mice. Taken together, our data suggest that the high mortality rate seen in mice during the early stages of influenza-associated pulmonary aspergillosis is multifactorial, with a greater contribution from dysregulated inflammation than microbial growth.

Importance

Severe influenza is a risk factor for fatal invasive pulmonary aspergillosis; however, the mechanistic basis for the lethality is unclear. Utilizing an influenza-associated pulmonary aspergillosis (IAPA) model, we found that mice infected with influenza A virus followed byA. fumigatushad 100% mortality when superinfected during the early stages of influenza but survived at later stages. While superinfected mice had dysregulated pulmonary inflammatory responses compared to controls, they had neither increased inflammation nor extensive fungal growth. Although influenza-infected mice had dampened neutrophil recruitment to the lungs following subsequent challenge withA. fumigatus, influenza did not affect the ability of neutrophils to clear the fungi. Our data suggest that the lethality seen in our model IAPA is multifactorial with dysregulated inflammation being a greater contributor than uncontrollable microbial growth. If confirmed in humans, our findings provide a rationale for clinical studies of adjuvant anti-inflammatory agents in the treatment of IAPA.
OrthoPhyl – Streamlining large scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales
Authors: Middlebrook Earl , Katani Robab , Fair Jeanne M
Published: June 2023

There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI′s GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification, but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (>1200 tested here) by identifying a diversity spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use-cases: E. coli/Shigella, Brucella/Ochrobactrum, and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.
NeuroMabSeq: high volume acquisition, processing, and curation of hybridoma sequences and their use in generating recombinant monoclonal antibodies and scFvs for neuroscience research
Authors: Mitchell Keith G. , Gong Belvin , Hunter Samuel S. , Burkart-Waco Diana , Gavira-O’Neill Clara E. , Templeton Kayla M. , Goethel Madeline E. , Bzymek Malgorzata , MacNiven Leah M. , Murray Karl D. , Settles Matthew L. , Froenicke Lutz , Trimmer James S.
Published: June 2023

The Neuroscience Monoclonal Antibody Sequencing Initiative (NeuroMabSeq) is a concerted effort to determine and make publicly available hybridoma-derived sequences of monoclonal antibodies (mAbs) valuable to neuroscience research. Over 30 years of research and development efforts including those at the UC Davis/NIH NeuroMab Facility have resulted in the generation of a large collection of mouse mAbs validated for neuroscience research. To enhance dissemination and increase the utility of this valuable resource, we applied a high-throughput DNA sequencing approach to determine immunoglobulin heavy and light chain variable domain sequences from source hybridoma cells. The resultant set of sequences was made publicly available as searchable DNA sequence database (neuromabseq.ucdavis.edu) for sharing, analysis and use in downstream applications. We enhanced the utility, transparency, and reproducibility of the existing mAb collection by using these sequences to develop recombinant mAbs. This enabled their subsequent engineering into alternate forms with distinct utility, including alternate modes of detection in multiplexed labeling, and as miniaturized single chain variable fragments or scFvs. The NeuroMabSeq website and database and the corresponding recombinant antibody collection together serve as a public DNA sequence repository of mouse mAb heavy and light chain variable domain sequences and as an open resource for enhancing dissemination and utility of this valuable collection of validated mAbs.
Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy
Authors: Larivière Delphine , Abueg Linelle , Brajuka Nadolina , Gallardo-Alba Cristóbal , Grüning Bjorn , Ko Byung June , Ostrovsky Alex , Palmada-Flores Marc , Pickett Brandon D. , Rabbani Keon , Balacco Jennifer R. , Chaisson Mark , Cheng Haoyu , Collins Joanna , Denisova Alexandra , Fedrigo Olivier , Gallo Guido Roberto , Giani Alice Maria , Gooder Grenville MacDonald , Jain Nivesh , Johnson Cassidy , Kim Heebal , Lee Chul , Marques-Bonet Tomas , O’Toole Brian , Rhie Arang , Secomandi Simona , Sozzoni Marcella , Tilley Tatiana , Uliano-Silva Marcela , van den Beek Marius , Waterhouse Robert M. , Phillippy Adam M. , Jarvis Erich D. , Schatz Michael C. , Nekrutenko Anton , Formenti Giulio
Published: June 2023

Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last ∼500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).
Epigenetic changes and serotype-specific interferon-responses of lung epithelial cells in late post-influenza pneumococcal pneumonia
Authors: Boehme Julia D , Jeron Andreas , Schultz Kristin , Melcher Lars , Schott Katharina , Gelmez Elif , Kröger Andrea , Stegemann-Koniszewski Sabine , Bruder Dunja
Published: June 2023

Pneumococcal infection following influenza A virus (IAV) pneumonia is a synergistic complication with high mortality. IAV modulates host antibacterial responses and invasiveness of pneumococcal serotypes and is an important pathogenic factor2. Yet, serotype-specifc immediate-early responses of the IAV-perturbed alveolar epithelium have not been adressed. We analyzed gene transcription in alveolar type II epithelial cells (AECII) from mice infected with IAV and/or one of threeS. pneumoniae(S.pn.) serotypes of varying invasiveness (4 > 7F > 19F). IAV, 14 days post infection, rendered the lung susceptible to invasiveS.pn.infection with serotype 4 and the mildly invasive 7F but not 19F. Only 7F secondary infection induced exacerbated cytokine/chemokine responses. IAV/7F infection induced superior protein expression of type I and II interferons, exceeding that in IAV/serotype 4 infection. Inference of a scale-free-like ARACNE gene co-expression network revealed interferon-response network modules. Network-mapping unfoldedS.pn.serotype-specific transcriptional network responses/usage. SecondaryS.pn.infection abrogated the IAV-induced pneumocyte proliferative configuration and IAV infection rendered the transcriptional response to 7F comparable to that of serotype 4. This related to network genes correlating with the expression of two master regulators of interferon responses:Irf7andStat1. Epigenetic ATAC-seq analysis of AECII in resolved IAV infection identified enhanced expression of ARACNE network genesHist1h2bf,Igtp,Mki67,Rasl10b,H2-Q6andH2-Q7to be associated with increased chromatin accessability at promoter regions. We show that AECII retain a sustained IAV-associated transcriptional configuration with epigenetic involvement that serotype-specifically affects proliferation and intensifies the AECII transcriptional response, mainly to interferons, inS.pn.infection.
Profiling ofZea maysL. proteome at early stages of compatible interactions withMeloidogyne arenariaindicates changes in signaling, oxidative stress responses, and S-adenosylmethionine biosynthesis
Authors: Arnika Przybylska , Barbara Wrzesińska-Krupa , Aleksandra Obrępalska-Stęplowska
Published: June 2023

Root-knot nematodes (RKNs) are distributed worldwide group of plant parasitic nematodes, with a very wide host range, including mono- and dicotyledonous hosts.Meloidogyne arenariais, next toM. hapla, M. incognita, andM. javanica, one of the most economically important species from this genus. RKNs during parasitism hijack host metabolism to establish giant cells and to break down plant defense mechanisms. To date, studies on the interaction of RKN with maize (Zea maysL.) have been underrepresented, and a description of the early response to attack by these nematodes, vital to understanding the process, is scarce in the literature. We hypothesize that in the early stage of maize response toM. arenariainfection, significant changes in the accumulation level of proteins mainly related to plant defense response, plant cell wall modifications, and phytohormone biosynthesis can be observed.

In this study, a mass spectrometry approach and a label-free quantification technique were used to assess the qualitative and quantitative composition of proteins changes in the proteome of maize roots afterM. arenariainfection. We used a susceptible maize variety and carried out analyses of plant proteome at two time points: 24 hours after nematode inoculation and 3 days after inoculation. Statistical analyses of significant differences between protein intensities were performed for the datasets obtained from healthy andM. arenaria-infected plants, and differentially expressed proteins (DEPs), with both lower and higher abundance were determined. DEPs were mapped, classified to the gene ontology (GO) terms into functional categories, and assigned to appropriate Kyoto Encyclopedia of Genes and Genomes (KEGG) processes and pathways.

As a result, a total of 3,743 proteins were identified with 124 DEPs at 24 hpi and 66 at 3 dpi, and significant changes in the accumulation of proteins associated with processes such as cell wall modifications, reaction to stress, as well as processes and pathways related to phenylpropanoid biosynthesis and metabolism, signal transduction and to S-adenosylmethionine biosynthesis.
Non-coding mutations at enhancer clusters contribute to pancreatic ductal adenocarcinoma
Authors: Patel Minal B. , Maniati Eleni , Atanur Santosh S. , Pal Debosree , Rio-Machin Ana , Heward James , Kocher Hemant M. , Fitzgibbon Jude , Pradeepa Madapura M. , Wang Jun
Published: June 2023

Non-coding mutations (NCMs) that perturb the function ofcis-regulatory elements (CRE, enhancers) contribute to cancer. Due to the vast search space, mutation abundance and indirect activity of non-coding sequences, it is challenging to identify which somatic NCMs are contributing to tumour development and progression. Here, we focus our investigation on the somatic NCMs that are enriched at enhancers from 659 pancreatic ductal adenocarcinoma (PDAC) tumours. We identifycis-regulatory NCMs within PDAC-specific enhancers derived from high and low-grade PDAC cell lines and patient derived organoids using two independent computational approaches. Five such CREs enriched for PDAC associated NCMs are also frequently mutated in other common solid tumours. Functional validation using STARR-seq reporter assays enables the prioritisation of 43 NCMs (7.3%) from a pool of 587 NCMs with 6,082 oligos, that significantly alter reporter enhancer activity compared to wild-type sequences. CRISPRi perturbation of an enhancer cluster harbouring NCMs over long non-coding RNA geneMIR100HG, which hosts a microRNA cluster (mir100-let7a-2-125b-1), leads to the downregulation of MIR100HG accompanied by a significant reduction in the TGF-β pathway (known to induceMIR100HG) and other PDAC critical pathways, including KRAS, p53, MTOR and TNF α signalling. Collectively, we have reported herecis-regulatory NCMs in PDAC proximal to many cancer-relevant genes, and our integrated approach paves way to explore CRE-associated NCMs in other human cancer genomes.
The long non-coding RNALINDArestrains cellular collapse following DNA damage inArabidopsis thaliana
Authors: Herbst Josephine , Nagy Solveig Henriette , Vercauteren Ilse , De Veylder Lieven , Kunze Reinhard
Published: June 2023

The genomic integrity of every organism is endangered by various intrinsic and extrinsic stresses. To maintain the genomic integrity, a sophisticated DNA damage response (DDR) network is activated rapidly after DNA damage. Notably, the fundamental DDR mechanisms are conserved in eukaryotes. However, knowledge about many regulatory aspects of the plant DDR is still limited. Important, yet little understood, regulatory factors of the DDR are the long non-coding RNAs (lncRNAs). In humans, 13 lncRNAs functioning in DDR have been characterized to date, whereas no such lncRNAs have been characterized in plants yet. By meta-analysis, we identified thelong intergenicnon-coding RNA induced by DNAdamage(LINDA) that responds strongly to various DNA double-strand break-inducing treatments, but not to replication stress induced by mitomycin C. After DNA damage,LINDAis rapidly induced in an ATM- and SOG1-dependent manner. Intriguingly, the transcriptional response ofLINDAto DNA damage is similar to that of its flanking hypothetical protein-encoding gene. Phylogenetic analysis of putative Brassicales and MalvalesLINDAhomologs indicates thatLINDAlncRNAs originate from duplication of a flanking small protein-encoding gene followed by pseudogenization. We demonstrate thatLINDAis not only needed for the regulation of this flanking gene, but also for fine-tuning of the DDR after the occurrence of DNA double-strand breaks. Moreover, Δlindamutant root stem cells are unable to recover from DNA damage, most likely due to hyper-induced cell death.

SIGNIFICANT STATEMENT

We unraveled the functional relevance of the first lncRNA within the DNA damage response network ofArabidopsis thaliana.This lncRNA, termedLINDA, is an important part of the DNA damage response network, as it is needed for accurate regulation of cell death and cell cycle progression.
A Glance into the Destiny of Transcriptomic Activity, Embodied by the HOX Genes, in Neonatal and Aging Dermal Cells
Authors: Ko Doyeong , Kim Minji , Nho Youn-Hwa , Lee Dong-Geol , Kang Seunghyun , Han Kyudong , Mun Seyoung , Kim Misun
Published: June 2023

Skin is an organ having a crucial role in the protection of muscle, bone, and internal organs and undergoing continuous self-renewal and aged. The growing interest in the prevention of skin aging and rejuvenation has sparked a surge of industrial and research studies focusing on the biological and transcriptional changes that occur during skin development and aging. In this study, we aimed to identify transcriptional differences between two main types of human skin cells: the HDFs and the HEK isolated from 30 neonatal and 30 adults (old) skin. Through differentially expressed gene (DEG) profiling using DEseq2, 604 up-, and 769 down-regulated genes were identified in the old group. The functional classification analysis using Metascape Gene Ontology and Reactome pathway was performed. We report the systematic transcriptomic changes in key biological markers involved in skin formation and maintenance and a unique difference inHOXgene families which are important for developing embryonic formation and regulating numerous biological processes. Among the 39 humanHOXgenes, 10 genes (HOXA10,11,13,HOXB13,HOXC11, andHOXD9-13) were significantly down-regulated, and 25 genesHOXA2-7,HOXB1-9,HOXC4-6and8-9, andHOXD1,3,4and8) were up-regulated, especially in the old HDFs. We have successfully established a correlation betweenHOXgenes and the process of skin aging, thereby proposingHOXgenes as a novel marker for assessing skin aging. Our findings provide compelling evidence supporting the involvement ofHOXgenes in this biological phenomenon such as skin aging.
Expanding the Evo-Devo Toolkit: Generation of 3D mammary tissue from diverse mammals
Authors: Kim Hahyung Y. , Sinha Ishani , Sears Karen E. , Kuperwasser Charlotte , Rauner Gat
Published: June 2023

The divergent events during mammary gland development between species and across evolution are not well studied mainly due to the lack of tractable model systems. In theory, advancements in the field of organoid technology now make it possible to study developmental processes adapted throughout species evolutions to accommodate advantageous phenotypes. However, its application to the mammary gland remains limited to rodents and humans.

In the current study, we successfully created next-generation 3D mammary gland organoids from eight eutherian mammals and the first 3D organoid of a marsupial mammary gland (the gray short-tailed opossum), representing a more ancient version of the mammary gland. Using mammary organoids, we identified a role for ROCK protein in regulating branching morphogenesis, a role that manifests differently in human and opossum mammary organoids. This finding demonstrates the utility of 3D organoid model for understanding the evolution and adaptations of signaling pathways.

Overall, the establishment of mammary organoids as animal model surrogates is a significant advancement in the field of mammary gland biology and evolution and paves the way for future studies utilizing this model. This achievement highlights the potential of organoid models to expand our understanding of mammary gland biology and evolution and their utility in studying milk production and breast cancer research.
Maltodextrin administration ameliorates brain pathology in a mouse model of mitochondrial disease
Authors: Domínguez-Martínez Adán , Molina-Menor Esther , Blanco-Ramos Marcos , Urpi Andrea , Peretó Juli , Porcar Manuel , Quintana Albert
Published: June 2023

Mitochondrial dysfunction lead to a wide group of progressive and fatal pathologies known as mitochondrial diseases (MD). One of the most common pediatric representation of MD is Leigh Syndrome, affecting 1/40.000 births. LS is characterized by neurodegeneration in specific brain areas, such as brainstem and basal ganglia, and by respiratory and motor alterations. However, the results obtained from clinical trials based on antioxidant therapies are controversial. Thus, the development novel antioxidant strategy is required to improve the efficacy of current palliative treatments. In this regard, Ndufs4KO mouse model is a suitable model to test new drugs in the field of MD and LS. Therefore, we set to assess the therapeutic potential of oral administration ofMicrococcus luteus, a high-antioxidant content microorganism. Incidentally, we identified that whileM. luteusadministration did not possess any beneficial actions, the cryopreservant maltodextrin (MDX), included in the preparation, ameliorated the phenotype of Ndufs4KO mice. Our results show that MDX treatment at a concentration of 30 g/L increased lifespan and reduced microglial reaction compared to vehicle-treated Ndufs4KO mice. However, no improvement in locomotion nor respiratory function was observed in MDX-treated mice compared to vehicle-treated Ndufs4KO mice. Metataxonomic characterization of intestinal microbiome identified differential profiles in Ndufs4KO mice at the genus level. Furthermore, MDX treatment increased the variability of the abundance ofAkkermansia sp. Thus, this work paves the way for further studies to confirm the therapeutic potential of MDX in mitochondrial disease.
Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses
Authors: Micheva Kristina D. , Gong Belvin , Collman Forrest , Weinberg Richard J. , Smith Stephen J. , Trimmer James S. , Murray Karl D.
Published: June 2023

Antibody-based imaging techniques rely on reagents whose performance may be application-specific. Because commercial antibodies are validated for only a few purposes, users interested in other applications may have to perform extensive in-house antibody testing. Here we present a novel application-specific proxy screening step to efficiently identify candidate antibodies for array tomography (AT), a serial section volume microscopy technique for high-dimensional quantitative analysis of the cellular proteome. To identify antibodies suitable for AT-based analysis of synapses in mammalian brain, we introduce a heterologous cell-based assay that simulates characteristic features of AT, such as chemical fixation and resin embedding that are likely to influence antibody binding. The assay was included into an initial screening strategy to generate monoclonal antibodies that can be used for AT. This approach simplifies the screening of candidate antibodies and has high predictive value for identifying antibodies suitable for AT analyses. In addition, we have created a comprehensive database of AT-validated antibodies with a neuroscience focus and show that these antibodies have a high likelihood of success for postembedding applications in general, including immunogold electron microscopy. The generation of a large and growing toolbox of AT-compatible antibodies will further enhance the value of this imaging technique.

Significance Statement

Array tomography (AT) is a powerful volume microscopy technique for high-dimensional analysis of complex protein populations in cells and organelles, including synapses. AT involves the use of ultrathin serial sections embedded in resin and subjected to multiple rounds of immunofluorescence antibody (Ab) labeling and imaging. AT relies on antibody-based detection of proteins but because commercial antibodies are typically validated for other applications they often fail for AT. To identify antibodies with high probability of success in AT we developed a novel screening strategy and used this to create a comprehensive database of AT-validated antibodies for neuroscience.
Metabolomic approaches highlight two mechanisms of accelerated grain filling in Mediterranean oat (Avena sativaL.) cultivars during drought
Authors: Girija Aiswarya , Canales Francisco J , Haddadi Bahareh Sadat , Dye Rachel , Corke Fiona , Han Jiwan , Brook Jason , Williams Kevin , Beckmann Manfred , Prats Elena , Doonan John H , Mur Luis A J
Published: June 2023

Grain filling in cereals is complex process that determines the final grain yield and quality. Abiotic stresses can have major impact on grain filling. Oats (Avena sativaL.) is sensitive to drought which adversely affect yield and productivity. In this study, we characterised the grain filling responses of two Mediterranean oat cultivars Flega and Patones under severe drought. Grains from the top (older) and bottom (younger) spikelets of primary panicle were larger in size in response to drought, particularly in Patones, suggesting accelerated grain development. The metabolomes of source (sheath, flag leaf) and sink (developing grains) tissues were profiled to describe source-sink partitioning. In Patones, the developing grains showed increased sugars and amino acids which indicate accelerated grain filling. These were associated with elevated α-linolenic acid levels in source tissues but decreased in developing grains under drought. There was also a significant decrease in C18 fatty acids (FA) and jasmonates (JA) derivatives in the developing grains which suggested a role for JA signalling in Patones with drought. Flega showed a different response, with accelerated flowering and enhanced energy metabolism in both source and sink organs. The accumulation of ophthalmic acid in grains of Flega and lower levels of reduced glutathione in source tissues suggested greater oxidative stress than Patones under drought may be driving the grain filling phenotype. This study suggests that oats cultivars can use α-linolenic acid-linked signalling or oxidative events influences accelerated grain filling with drought. These could be important traits in developing oat cultivars that maintain yield in drought-prone environments.

Highlight

The impact on drought in one tolerant and one susceptible oat cultivar was assessed at the grain filling stage. The drought tolerant cultivar, Patones, showed accelerated grain development which could be a strategy to escape drought. Metabolite mapping of flag leaves, sheath and grains of Flega suggested that alpha linolenic acid could be regulating the altered sink-source relationships. The drought susceptible cultivar, Metabolomics shifts in Flega suggested that oxidative stress accelerated flowering.
Yellow fever disease severity and endothelial dysfunction are associated with elevated serum levels of viral NS1 protein and syndecan-1
Authors: Sousa Francielle T. G. de , Warnes Colin M. , Manuli Erika R. , Ng Arash , Zanella Luiz G. F. A. B. D’Elia , Ho Yeh-Li , Bhat Samhita , Romano Camila M. , Beatty P. Robert , Biering Scott B. , Kallas Esper G. , Sabino Ester C. , Harris Eva
Published: June 2023

Yellow fever virus (YFV) infections can cause severe disease manifestations, including hepatic injury, endothelial damage, coagulopathy, hemorrhage, systemic organ failure, and shock, and are associated with high mortality in humans. While nonstructural protein 1 (NS1) of the related dengue virus is implicated in contributing to vascular leak, little is known about the role of YFV NS1 in severe YF and mechanisms of vascular dysfunction in YFV infections. Here, using serum samples from qRT-PCR-confirmed YF patients with severe (n=39) or non-severe (n=18) disease in a well-defined hospital cohort in Brazil, plus samples from healthy uninfected controls (n=11), we investigated factors associated with disease severity. We developed a quantitative YFV NS1 capture ELISA and found significantly increased levels of NS1, as well as syndecan-1, a marker of vascular leak, in serum from severe YF as compared to non-severe YF or control groups. We also showed that hyperpermeability of endothelial cell monolayers treated with serum from severe YF patients was significantly higher compared to non-severe YF and control groups as measured by transendothelial electrical resistance (TEER). Further, we demonstrated that YFV NS1 induces shedding of syndecan-1 from the surface of human endothelial cells. Notably, YFV NS1 serum levels significantly correlated with syndecan-1 serum levels and TEER values. Syndecan-1 levels also significantly correlated with clinical laboratory parameters of disease severity, viral load, hospitalization, and death. In summary, this study points to a role for secreted NS1 in YF disease severity and provides evidence for endothelial dysfunction as a mechanism of YF pathogenesis in humans.

Significance

Yellow fever virus (YFV) infections cause a major global disease burden, and as such it is critical to identify clinical correlates of disease severity. Using clinical samples from our hospital cohort in Brazil, we show that YF disease severity is associated with increased serum levels of the viral nonstructural protein 1 (NS1) and soluble syndecan-1, a marker of vascular leak. This study extends the role of YFV NS1 in triggering endothelial dysfunction to human YF patients, previously demonstratedin vitroand in mouse models. Further, we developed a YFV NS1-capture ELISA that serves as a proof-of-concept for low-cost NS1-based diagnosis/prognosis tools for YF. Together, our data shows that YFV NS1 and endothelial dysfunction are important components of YF pathogenesis.
Developmental molecular controls over arealization of descending cortical motor pathways
Authors: Abe Philipp , Lavalley Adrien , Morassut Ilaria , Klingler Esther , Santinha Antonio J. , Platt Randall J. , Jabaudon Denis
Published: June 2023

Layer 5 extratelencephalic (ET) neurons are a main class of neocortical projection neurons that predominate in the motor cortex and send their axon to the pons and spinal cord, and collaterals to the thalamus and multiple deep subcerebral structures1–3. Precise connectivity of ET neurons is critical for fine motor control; they are central to loss of function upon spinal cord injury and specifically degenerate in select neurodegenerative disorders4, 5. ET neurons consist of several types of cells with distinct laminar and areal locations, molecular identities, connectivities, and functions6, 7. Within layer 5 of the cortex, two cardinal subtypes of ET neurons have been identified: “ETlower” neurons, which express Slco2a1 and project to distal targets including the spinal cord, “ETupper“ neurons, which express Nprs1 or Hpgd and project more proximally to the pons and thalamus6. Despite their critical function, how these neuronal subtypes emerge during development and acquire their area-specific distributions remains unaddressed. Here, using combinations of anatomical labeling, MAPseq mapping8, and single-nucleus transcriptomics across developing cortical areas, we reveal that these two subtypes of ET neurons are present at birth along opposite antero-posterior cortical gradients. We first characterize area-specific developmental axonal dynamics of ETlowerand ETupperneurons and find that the latter can emerge by pruning of subsets of ETlowerneurons. We next identify area- and ET neuron type-specific developmental transcriptional programs to identify key target genesin vivo. Finally, we reprogram ET neuron area-specific connectivity from motor to visual by postnatalin vivocombinatorial knockout of three key type-specific transcription factors. Together, these findings delineate the functional transcriptional programs controlling ET neuron diversity across cortical areas and provide a molecular blueprint to investigate and direct the developmental emergence of corticospinal motor control.
gARID-associated chromatin remodeling events are essential for gametocyte development inPlasmodium
Authors: Nishi Tsubasa , Kaneko Izumi , Iwanaga Shiroh , Yuda Masao
Published: June 2023

Gametocyte development of thePlasmodiumparasite is a key step for transmission of the parasite from their vertebrate hosts to mosquitoes. Male and female gametocytes are produced from a subpopulation of asexual blood-stage parasites, but the mechanisms that regulate the differentiation of sexual stages are still under investigation. In this study, we investigated the role of gARID, a putative subunit of a chromatin remodeling complex, in transcriptional regulation during the gametocyte development ofP. berghei. gARID expression starts in early gametocytes before the manifestation of male and female-specific features, and disruption of its gene results in the complete loss of male gametocytes and the production of abnormal female gametocytes. ChIP-seq analysis of gARID showed that it forms a complex with gSNF2, a core subunit of the SWI/SNF chromatin remodeling complex, associating with the malecis-regulatory element. Moreover, ChIP-seq of gARID ingsnf2-knockout parasites revealed an association of gARID with anothercis-regulatory element, which is indicated to play a role in both male and female development. Our results showed that gARID functions in two chromatin remodeling events and that remodeling of chromatin states is essential for both male and female gametocyte development.
C-terminal amides mark proteins for degradation via SCF/FBXO31
Authors: Muhar Matthias , Farnung Jakob , Hofmann Raphael , Cernakova Martina , Sidiropoulos Nikolaos D. , Bode Jeffrey W. , Corn Jacob E.
Published: June 2023

During normal cellular homeostasis unfolded and mis-localized proteins are recognized and removed, preventing the build-up of toxic byproducts1. When protein homeostasis is perturbed during aging, neurodegeneration or cellular stress, proteins can accumulate several forms of chemical damage through reactive metabolites2, 3. Such modifications have been proposed to trigger the selective removal of chemically marked proteins3–6;however, discovering modifications sufficient to induce protein degradation has remained challenging. Using a semi-synthetic chemical biology approach coupled to cellular assays, we found that C-terminal amide-bearing proteins (CTAPs) are rapidly cleared from human cells. A CRISPR screen identified the SCF/FBXO31 ubiquitin ligase as a reader of C-terminal amides, which ubiquitylates CTAPs for subsequent proteasomal degradation. A conserved binding pocket enables FBXO31 to bind almost any C-terminal peptide bearing an amide while retaining exquisite selectivity over non-modified clients. This mechanism facilitates binding and turnover of endogenous CTAPs that are formed following oxidative stress. A dominant human mutation found in neurodevelopmental disorders switches CTAP recognition, such that non-amidated neosubstrates are now degraded and FBXO31 becomes markedly toxic. We propose that CTAPs may represent the vanguard of a largely unexplored class of modified amino acid degrons that could provide a general strategy for selective yet broad surveillance of chemically damaged proteins.
Complete zooplankton size spectra re-constructed from « in situ » imaging and Multinet data in the global ocean
Authors: Soviadan Yawouvi Dodji , Dugenne Mathilde , Drago Laetitia , Biard Tristan , Trudnowska Emilia , Lombard Fabien , Romagnan Jean-Baptiste , Jamet Jean-Louis , Kiko Rainer , Gorsky Gabriel , Stemmann Lars
Published: June 2023

Plankton size spectra are important indicators of the ecosystem state, as they illustrate the quantity of organisms available for higher marine food web and reflect multiple size-dependent processes. Yet, such measurements are typically biased by the available sampling methods, either disrupting fragile organisms or lacking good resolution (in size and/or time and space). In this study, we combined two of the most common approaches to measure zooplankton Normalized Biomass/Biovolume Size Spectra (NBSS) to calculate a complete zooplankton distribution for organisms larger than 1 mm. The reconstructed NBSS slopes appeared steeper and closer to those measured by the UVP5 (+7.6%) and flatter than those of the Multinet (- 20%) particularly in tropics and temperate latitudes. The overall gain in polar biomass was relatively small for reconstructed biomass compared to bulk estimates from Multinet (+0.24 mgC/m3 or +4.25%) and high from the UVP5 (+2.0 mgC/m3 or +53%). In contrast, in the tropical and temperate ecosystems, the gain in biomass was small for UVP5 (+0.67 mgC/m3 or +30.44% and +0.74 mgC/m3 or +19.59% respectively) and high for Multinet (+1.66 mgC/m3 or +136% and +3.4 mgC/m3 or +309% respectively). Given these differences, we suggest here to combinein situimaging sensors and net data in any comprehensive study exploring key living players in the ocean ecosystem and their contributions to the biological pump.