bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vimentin supports directional cell migration by controlling focal adhesions
Authors: Venu Arun P. , Modi Mayank , Aryal Ujjwal , Tcarenkova Elena , Jiu Yaming , Jacquemet Guillaume , Minin Alexander , Cheng Fang , Eriksson John E. 
Published: October 2022

AbstractFibroblastic migration is of key importance in wound healing. While the intermediate filament (IF) protein vimentin is required for normal wound healing, we examined whether vimentin-mediated regulation of fibroblast migration could be involved. In wound healing assays triggering cell polarization and directed migration, we observed that vimentin-deficient mouse and rat embryonic fibroblasts lost their directional persistence. We show that vimentin maintains directionality by guiding focal adhesions (FAs) in fibroblasts. Detailed analysis showed that vimentin stabilizes FAs and regulates their disassembly rate. The destabilization of Vim-/- FAs was reflected by smaller FAs. Live cell and super-resolution imaging demonstrate that vimentin interacts dynamically with the key molecules of FAs and, importantly, with FAK, which is crucial for the maturation of FAs. These results demonstrate that vimentin IFs control the maturation, stability, dynamics, arrangement, and overall orientation of FAs, with a net effect on FA coordination during migration.
Knock-sideways by inducible ER retrieval enables a novel approach for studyingPlasmodiumsecreted proteins
Authors: Fierro Manuel A , Hussain Tahir , Campin Liam J , Beck Josh R 
Published: October 2022

AbstractMalaria parasites uniquely depend on protein secretion for their obligate intracellular lifestyle but approaches for dissectingPlasmodiumsecreted protein functions are limited. We report knockER, a novel DiCre-mediated knock-sideways approach to sequester secreted proteins in the ER by inducible fusion with a KDEL ER-retrieval sequence. We show conditional ER sequestration of diverse proteins is not generally toxic, enabling loss-of-function studies. We employed knockER in multiplePlasmodiumspecies to interrogate the trafficking, topology and function of an assortment of proteins that traverse the secretory pathway to diverse compartments including the apicoplast (ClpB1), rhoptries (RON6), dense granules and parasitophorous vacuole (EXP2, PTEX150, HSP101). Taking advantage of the unique ability to redistribute secreted proteins from their terminal destination to the ER, we reveal vacuolar levels of the PTEX translocon component HSP101 but not PTEX150 are maintained in excess of what is required to sustain effector protein export into the erythrocyte. Intriguingly, vacuole depletion of HSP101 hypersensitized parasites to a destabilization tag that inhibits HSP101-PTEX complex formation but not to translational knockdown of the entire HSP101 pool, illustrating how redistribution of a target protein by knockER can be used to query function in a compartment-specific manner. Collectively, our results establish knockER as a novel tool for dissecting secreted protein function with sub-compartmental resolution that should be widely amenable to genetically tractable eukaryotes.SignificanceProtein trafficking and secretion through the endomembrane system is a defining feature of eukaryotes. The secretory pathway is central to the unique biology and pathology of the obligate intracellular malaria parasite, however tools for studying secreted protein function are limited. Knock-sideways is a powerful mutagenesis strategy that conditionally sequesters a protein away from its site of function but is generally not applicable to secreted proteins. We developed a simple approach to conditionally sequesterPlasmodiumsecreted proteins in the ER by inducible C-terminal fusion with a KDEL ER-retrieval sequence that can be used for trafficking, topology and loss-of-function studies. The knockER strategy is broadly applicable to functional dissection of proteins that traverse the eukaryotic secretory pathway.
Development in context: interferon response networks regulate human fetal thymic epithelial cell differentiation
Authors: Mohammed Abdulvasey , Solomon Benjamin D. , Slepicka Priscila F. , Hubka Kelsea M. , Nguyen Hanh Dan , Wang Wenqing , Arreola Martin , Chavez Michael G. , Yeh Christine Y. , Kim Doo Kyung , Winn Virginia , Gifford Casey A. , Kedlian Veronika , Park Jong-Eun , Hollander Georg A. , Sebastiano Vittorio , Khatri Purvesh , Teichmann Sarah A. , Gentles Andrew J. , Weinacht Katja G. 
Published: October 2022

ABSTRACTThe thymus instructs T cell immunity and central tolerance, yet its therapeutic potential remains untapped. The quest to regenerate thymic function for clinical application is lagging while the signals that drive thymic epithelial cell differentiation remain incompletely understood. Here, we elucidate pathways instructing commitment and specialization of the human thymic epithelial stroma through complementary single cell transcriptomic approaches. First, we identify gene regulatory networks that define fetal thymic epithelium in the thus far unexplored context of other anterior foregut-derived organs; then, we characterize lineage trajectories within the thymic epithelial compartment across embryonic, fetal, and early postnatal stages. Activation of interferon response gene regulatory networks distinguished epithelial cells of the thymus from those of all other anterior foregut-derived organs. Interferon signals were processed differentially within thymic cortical and medullary lineages, reflected in distinctNFκBandIRFsignatures, respectively. Our study reveals novel, translatable insights into the developmental programs underlying thymic epithelial cell differentiation that may advance the field of regenerative cell therapies.SUMMARYSingle cell transcriptomics of anterior foregut-derived organs identifies pathways governing thymic epithelial commitment and specialization.
Pharmacologic Inhibition of DYRK1A Results in MYC Hyperactivation and ERK Hyperphosphorylation rendering KMT2A-R ALL Cells Sensitive to BCL2 Inhibition
Authors: Hurtz Christian , Ayyadevara V. S. S. Abhinav , Wertheim Gerald , Chukinas John A , Loftus Joseph P , Lee Sung June , Kumar Anil , Bhansali Rahul S , Swaminathan Srividya , Geng Huimin , Milne Thomas , Hua Xianxin , Bernt Kathrin M , Besson Thierry , Shi Junwei , Crispino John D. , Carroll Martin , Tasian Sarah K 
Published: October 2022

AbstractKMT2A-rearranged (KMT2A-R) B cell acute lymphoblastic leukemia (ALL) is a high-risk disease in children and adults that is often chemotherapy resistant. To identify non-cytotoxic approaches to therapy, we performed a domain-specific kinome-wide CRISPR screen in KMT2A-R cell lines and patient derived xenograft samples (PDX) and identified dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) as a potential target. Pharmacologic inhibition of the KMT2A-fusion transcriptional co-regulator Menin released the KMT2A-fusion complex from the DYRK1A promoter thereby lowering DYRK1A expression levels confirming DYRK1A as a direct target of the KMT2A fusion oncogene. Direct pharmacologic inhibition of DYRK1A decreased cell proliferation of KMT2A-R ALL, thereby confirming the requirement of DYRK1A in this ALL subtype. To further understand the biologic function of DYRK1A in KMT2A-R ALL, we leveraged pharmacologic DYRK1A inhibitors in KMT2A-R PDX and cell line models. DYRK1A inhibition consistently led to upregulation of MYC protein levels, and hyperphosphorylation of ERK, which we confirmed via in vivo treatment experiments. Furthermore, DYRK1A inhibition decreased ALL burden in mice. Our results further demonstrate that DYRK1A inhibition induces the proapoptotic factor BIM, but ERK hyperphosphorylation is the driving event that induces cell cycle arrest. In contrast, combined treatment of KMT2A-R ALL cells in vitro and in vivo with DYRK1A inhibitors and the BCL2 inhibitor, venetoclax, synergistically decreases cell survival and reduced the leukemic burden in mice. Taken together these results demonstrate a unique function of DYRK1A specially in KMT2A-R ALL. Synergistic inhibition of DRYK1A and BCL2 may provide a low-toxic approach to treat this high risk ALL subtype.
EEG-based speaker-listener neural coupling reflects speech-selective attentional mechanisms beyond the speech stimulus
Authors: Li Jiawei , Hong Bo , Nolte Guido , Engel Andreas K. , Zhang Dan 
Published: October 2022

AbstractWhen we pay attention to someone, do we focus only on the sound they make, the word they use, or do we form a mental space shared with the speaker we want to pay attention to? Some would argue that the human language is no other than a simple signal, but others claim that human beings understand each other not only by relying on the words that have been said but also formed a shared ground in the specific conversation. This debate was raised early, but the conclusion remains vague. Our study aimed to investigate how attention modulates the neural coupling between the speaker and the listener in a cocktail party paradigm. The temporal response function (TRF) method was employed to reveal how the listener was coupled to the speaker at the neural level. The results showed that the neural coupling between the listener and the attended speaker peaked 5 seconds before speech onset at the delta band over the left frontal region, and was correlated with speech comprehension performance. In contrast, the attentional processing of speech acoustics and semantics occurred primarily at a later stage after speech onset and was not significantly correlated with comprehension performance. These findings suggest that our human brain might have adopted a predictive mechanism to achieve speaker-listener neural coupling for successful speech comprehension.Three key pointsListener’s EEG signals coupled to the speaker’s 5 s before the speech onset, which revealed a “beyond the stimulus” attentional modulation.Speaker-listener attentional coupling is correlated to the listener’s comprehension performance, but the speech-listener’s coupling didn’t.The implementation of temporal response function methods and the neural language methods yielded novel perspectives to the analysis of the inter-brain studies.
Auxin production in the green alga Chlamydomonas involves an extracellular L-amino acid oxidase and supports algal-bacterial mutualism with methylobacteria
Authors: Calatrava Victoria , Hom Erik F. Y. , Llamas Angel , Fernández Emilio , Galván Aurora 
Published: October 2022

AbstractInteractions between algae and bacteria are widespread in aquatic and terrestrial ecosystems and play fundamental roles in nutrient cycling and biomass production. However, the chemical basis for many of these interactions is poorly characterized and understood. Recent studies have shown that the plant auxin indole acetic acid (IAA) can mediate chemical crosstalk between algae and bacteria, resembling its role in plant-bacterial associations. While algae have been shown to produce IAA, molecular pathways for IAA synthesis in algae have remained elusive. Here, we report a mechanism for IAA production from L-tryptophan mediated by the extracellular enzyme L-amino acid oxidase (LAO1) in the model alga Chlamydomonas reinhardtii. Under inorganic nitrogen limitation but in the presence of L-tryptophan and other amino acids, high levels of IAA are generated in an LAO1-dependent manner. Thus, LAO1 plays a dual role in scavenging nitrogen from L-amino acids and in producing the phytohormone IAA, which subsequently inhibits algal cell multiplication and chlorophyll degradation. We show that these inhibitory effects can be relieved in the presence of Methylobacterium spp., well-known plant growth-promoting bacteria (PGPB), whose growth is mutualistically enhanced by the presence of the alga. These findings reveal a complex interplay of microbial auxin production and degradation by algal-bacterial consortia under nitrogen limitation and draws attention to potential ecophysiological roles of terrestrial microalgae and PGPB in association with land plants.
Volatile metabolites in lavage fluid are correlated to Valley fever disease severity in murine model lung infections
Authors: Keppler Emily A. Higgins , Van Dyke Marley C. Caballero , Mead Heather L. , Lake Douglas F. , Magee D. Mitchell , Barker Bridget M. , Bean Heather D. 
Published: October 2022

ABSTRACTCoccidioides immitis and Coccidioides posadasii are soil-dwelling fungi of arid regions in North and South America that are responsible for Valley fever (coccidioidomycosis). Forty percent of patients with Valley fever exhibit symptoms ranging from mild, self-limiting respiratory infections, to severe, life-threatening pneumonia that requires treatment. Misdiagnosis as bacterial pneumonia commonly occurs in symptomatic Valley fever cases, resulting in inappropriate treatment with antibiotics, increased medical costs, and delay in diagnosis. In this study, we explored the feasibility of developing breath-based diagnostics for Valley fever using a murine lung infection model. To investigate potential volatile biomarkers of Valley fever that arise from host-pathogen interactions, we infected C57BL/6J mice with C. immitis RS and C. posadasii Silveira via intranasal inoculation. We measured fungal dissemination and collected bronchoalveolar lavage fluid (BALF) for cytokine profiling and for untargeted volatile metabolomics via solid phase microextraction (SPME) and two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOFMS). We identified 36 volatile organic compounds (VOCs) that were significantly correlated to cytokine abundances and clustered mice by disease severity. These 36 VOCs were also able to separate mice with a moderate to high disease severity by infection strain. The data presented here show that Coccidioides and/or the host produce volatile metabolites that may yield biomarkers for a Valley fever breath test that can detect Coccidioidal infection and provide clinically relevant information on disease severity.IMPORTANCECoccidioidomycosis, or Valley fever, is a fungal disease endemic to the North and South American arid regions. Forty percent of individuals infected with Valley fever will exhibit symptoms consistent with community-acquired pneumonia. However, misdiagnosis frequently occurs in these cases, resulting in inappropriate treatment with antibiotics, increased medical costs, and delay in receiving an accurate diagnosis. Herein, we used a murine lung infection model as a step towards developing a breath-based diagnostic for Valley fever. We infected C57BL/6J mice with C. immitis RS and C. posadasii Silveira and collected bronchoalveolar lavage fluid for untargeted volatile metabolomics. We observed that volatile metabolites in the bronchoalveolar lavage fluid of Cocci-inoculated mice were significantly correlated to disease severity, as measured by immune response. The data presented here show that Coccidioides and/or the host produce volatile metabolites that may yield biomarkers for a Valley fever breath test.
Proteomic analysis of flagella fromChlamydomonasmutants lacking the central pair apparatus reveals loss of radial spoke head proteins
Authors: Wemmer Kimberly A. , Azimzadeh Juliette , Marshall Wallace F. 
Published: October 2022

AbstractThe flagellar axoneme is a complex protein-based machine capable of generating motile forces by coordinating the action of thousands of dynein motors. A key element of the axoneme is the central pair apparatus, consisting of a pair of microtubules surrounded by additional structures. In an effort to better understand the organization of the central pair, we used 2D DIGE to identify proteins that are depleted from flagella isolated from two differentChlamydomonas reinhardtiimutants,pf15andpf18, that lack the central pair. The set of proteins contained almost no components of the central apparatus. We find that three proteins of the radial spoke head RSP1, RSP9, and RSP10, as well as a number of other protein components associated with the outer doublets, are depleted from flagella of mutants lacking the central apparatus. Two of the other proteins depleted frompf15andpf18flagella, the microtubule inner proteins (MIPs) FAP21 and FAP161, are missing from the genome ofThalassiosira, an organism that lacks a central pair and radial spokes, and RNAi of FAP21 in planaria shows that it has a role in ciliary motility. Based on the depletion of radial spoke head proteins, as well as MIPs and other axonemal components, from flagella lacking the central pair apparatus, we hypothesize that the central apparatus may play a role in scaffolding the assembly or retention of radial spokes and other axonemal structures.
Estrogen receptor beta in the central amygdala regulates the deleterious behavioral and neuronal consequences of repeated social stress in female rats
Authors: Smiley Cora E. , Pate Brittany S. , Bouknight Samantha J. , Francis Megan J. , Nowicki Alexandria V. , Harrington Evelynn N. , Wood Susan K. 
Published: October 2022

AbstractWhile over 95% of the population has reported experiencing extreme stress or trauma, females of reproductive age develop stress-induced neuropsychiatric disorders at twice the rate of males. This suggests that estrogen may facilitate neural processes that increase stress susceptibility and underlie the heightened rates of these disorders, like depression and anxiety, that result from stress exposure in females. However, there is contradicting evidence in the literature regarding estrogen’s role in stress-related behavioral outcomes. Estrogen signaling through estrogen receptor beta (ERβ) has been traditionally thought of as anxiolytic, but recent studies suggest estrogen exhibits distinct effects in the context of stress. Furthermore, ERβ is found abundantly in many stress-sensitive brain loci, including the central amygdala (CeA), in which transcription of the vital stress hormone, corticotropin releasing factor (CRF), can be regulated by an estrogen response element. Therefore, these experiments sought to identify the role of CeA ERβ activity during stress on behavioral outcomes in naturally cycling, adult, female Sprague-Dawley rats. Rats were exposed to an ethological model of vicarious social stress, witness stress (WS), in which they experienced the sensory and psychological aspects of an aggressive social defeat encounter between two males. Following stress, rats exhibited stress-induced anxiety-like behaviors in the marble burying task, and, finally, brain analysis revealed increased ERβ and CRF specifically within the CeA following exposure to stress cues. Subsequent experiments were designed to target this receptor in the CeA using microinjections of the ERβ antagonist, PHTPP, prior to each stress session. Sucrose preference, acoustic startle, and marble burying tasks determined that blocking ERβ in the CeA during WS prevented the development of depressive-,anxiety-like, and hypervigilant behaviors. Additionally, brain analysis revealed a long-term decrease of intra-CeA CRF expression in PHTPP-treated WS rats compared to vehicle. These experiments indicate that ERβ signaling in the CeA, through its effects on CRF, contribute to the development of negative valence behaviors that result from exposure to repeated social stress in female rats.
AKIR-1 Regulates Proteasome Localization and Function inCaenorhabditis elegans
Authors: Pispa Johanna , Mikkonen Elisa , Arpalahti Leena , Jin Congyu , Martínez-Fernández Carmen , Cerón Julián , Holmberg Carina I. 
Published: October 2022

AbstractRegulated protein clearance is vital for cells to maintain protein homeostasis and the conditions essential for survival. The primary machinery for intracellular protein degradation is the ubiquitin– proteasome system (UPS), by which ubiquitin-tagged proteins are degraded by the proteasome. Proteasomes are present both in the cytoplasm and the nucleus, but the mechanisms coordinating proteasome activity and its subcellular localization in a multicellular organism are still unclear. Here, we identified the nuclear protein-encoding geneakir-1as a proteasome regulator in a genome-wideCaenorhabditis elegans(C. elegans) RNAi screen. We show that the depletion ofakir-1causes accumulation of endogenous polyubiquitinated proteins in the nuclei of intestinal cells, concomitant with slowerin vivoproteasomal degradation in this subcellular compartment. Remarkably, the loss ofakir-1does not induce an accumulation of polyubiquitinated proteins in oocyte nuclei, thoughakir-1is essential for the nuclear localization of proteasomes in both cell types. We further show that the importin family memberima-3genetically interacts withakir-1, and affects subcellular distribution of polyubiquitinated proteins in intestinal cells. We show for the first time that conserved AKIR-1 is important for the nuclear transport of proteasomes in a multicellular organism, suggesting a role for AKIR-1 in the maintenance of proteostasis.
Intranasal delivery of NS1-deleted influenza virus vectored COVID-19 vaccine restrains the SARS-CoV-2 inflammatory response
Authors: Zhang Liang , Jiang Yao , He Jinhang , Chen Junyu , Qi Ruoyao , Yuan Lunzhi , Shao Tiange , Chen Congjie , Chen Yaode , Wang Xijing , Lei Xing , Gao Qingxiang , Zhuang Chunlan , Zhou Ming , Ma Jian , Liu Wei , Yang Man , Fu Rao , Wu Yangtao , Chen Feng , Xiong Hualong , Nie Meifeng , Chen Yiyi , Wu Kun , Fang Mujing , Wang Yingbin , Zheng Zizheng , Huang Shoujie , Ge Shengxiang , Cheng Shih Chin , Zhu Huachen , Cheng Tong , Yuan Quan , Wu Ting , Zhang Jun , Chen Yixin , Zhang Tianying , Qi Hai , Guan Yi , Xia Ningshao 
Published: October 2022

AbstractThe emergence of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) variants and “anatomical escape” characteristics threaten the effectiveness of current coronavirus disease (COVID-19) vaccines. There is an urgent need to understand the immunological mechanism of broad-spectrum respiratory tract protection to guide broader vaccines development. In this study, we investigated immune responses induced by an NS1-deleted influenza virus vectored intranasal COVID-19 vaccine (dNS1-RBD) which provides broad-spectrum protection against SARS-CoV-2 variants. Intranasal delivery of dNS1-RBD induced innate immunity, trained immunity and tissue-resident memory T cells covering the upper and lower respiratory tract. It restrained the inflammatory response by suppressing early phase viral load post SARS-CoV-2 challenge and attenuating pro-inflammatory cytokine (IL-6, IL-1B, and IFN-γ) levels, thereby reducing excess immune-induced tissue injury compared with the control group. By inducing local cellular immunity and trained immunity, intranasal delivery of NS1-deleted influenza virus vectored vaccine represents a broad-spectrum COVID-19 vaccine strategy to reduce disease burden.
Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity
Authors: Jurdzinski Krzysztof T , Mehrshad Maliheh , Delgado Luis Fernando , Deng Ziling , Bertilsson Stefan , Andersson Anders F 
Published: October 2022

AbstractThe crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as are molecular adaptations facilitating cross-biome transitions. Here, we conduct large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,276 MAGs). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. Distinct brackish basins co-hosted numerous species despite differences in salinity and geographic distance, the latter having stronger intra-species population structuring effects. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed towards the brackish biome. Transitions were accompanied by changes in isoelectric point distribution and amino acid composition of inferred proteomes, as well as convergent gains or losses of specific gene functions. Therefore, adaptive challenges entailing proteome reorganization and specific changes in gene content result in species-level separation between aquatic biomes.