bioRxiv : the preprint server for biology最新文献

{"title":"WITHDRAWN: Progranulin inhibits phospholipase sPLA2-IIA to control neuroinflammation.","authors":"Huan Du, Cha Yang, Alissa L Nana, William W Seeley, Marcus Smolka, Fenghua Hu","doi":"10.1101/2023.04.06.535844","DOIUrl":"10.1101/2023.04.06.535844","url":null,"abstract":"<p><p>The authors have withdrawn this manuscript because more work is needed to fully define the role of sPLA2-IIA. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/5c/76/nihpp-2023.04.06.535844v1.PMC10104136.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9828553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Constructed languages are processed by the same brain mechanisms as natural languages.","authors":"Saima Malik-Moraleda, Maya Taliaferro, Steve Shannon, Niharika Jhingan, Sara Swords, David J Peterson, Paul Frommer, Marc Okrand, Jessie Sams, Ramsey Cardwell, Cassie Freeman, Evelina Fedorenko","doi":"10.1101/2023.07.28.550667","DOIUrl":"10.1101/2023.07.28.550667","url":null,"abstract":"<p><p>What constitutes a language? Natural languages share features with other domains: from math, to music, to gesture. However, the brain mechanisms that process linguistic input are highly specialized, showing little response to diverse non-linguistic tasks. Here, we examine constructed languages (conlangs) to ask whether they draw on the same neural mechanisms as natural languages, or whether they instead pattern with domains like math and programming languages. Using individual-subject fMRI analyses, we show that understanding conlangs recruits the same brain areas as natural language comprehension. This result holds for Esperanto (n=19 speakers) and four fictional conlangs (Klingon (n=10), Na'vi (n=9), High Valyrian (n=3), and Dothraki (n=3)). These findings suggest that conlangs and natural languages share critical features that allow them to draw on the same representations and computations, implemented in the left-lateralized network of brain areas. The features of conlangs that differentiate them from natural languages-including recent creation by a single individual, often for an esoteric purpose, the small number of speakers, and the fact that these languages are typically learned in adulthood-appear to not be consequential for the reliance on the same cognitive and neural mechanisms. We argue that the critical shared feature of conlangs and natural languages is that they are symbolic systems capable of expressing an open-ended range of meanings about our outer and inner worlds.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/22/c8/nihpp-2023.07.28.550667v1.PMC10402139.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9978388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Viral genomic features predict <i>Orthopoxvirus</i> reservoir hosts.","authors":"Katie K Tseng, Heather Koehler, Daniel J Becker, Rory Gibb, Colin J Carlson, Maria Del Pilar Fernandez, Stephanie N Seifert","doi":"10.1101/2023.10.26.564211","DOIUrl":"10.1101/2023.10.26.564211","url":null,"abstract":"<p><p>Orthopoxviruses (OPVs), including the causative agents of smallpox and mpox have led to devastating outbreaks in human populations worldwide. However, the discontinuation of smallpox vaccination, which also provides cross-protection against related OPVs, has diminished global immunity to OPVs more broadly. We apply machine learning models incorporating both host ecological and viral genomic features to predict likely reservoirs of OPVs. We demonstrate that incorporating viral genomic features in addition to host ecological traits enhanced the accuracy of potential OPV host predictions, highlighting the importance of host-virus molecular interactions in predicting potential host species. We identify hotspots for geographic regions rich with potential OPV hosts in parts of southeast Asia, equatorial Africa, and the Amazon, revealing high overlap between regions predicted to have a high number of potential OPV host species and those with the lowest smallpox vaccination coverage, indicating a heightened risk for the emergence or establishment of zoonotic OPVs. Our findings can be used to target wildlife surveillance, particularly related to concerns about mpox establishment beyond its historical range.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10634857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92158004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new pipeline SPICE identifies novel JUN-IKZF1 composite elements.","authors":"Peng Li, Sree H Pulugulla, Sonali Das, Jangsuk Oh, Rosanne Spolski, Jian-Xin Lin, Warren J Leonard","doi":"10.1101/2023.05.31.543110","DOIUrl":"10.1101/2023.05.31.543110","url":null,"abstract":"<p><p>Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. Using SPICE, we successfully identified known composite elements, such as AP1-IRF composite elements (AICEs) and STAT5 tetramers, and also uncovered several novel binding partners, including JUN-IKZF1 composite elements. One such novel interaction was identified at CNS9, an upstream conserved noncoding region in the human <i>IL10</i> gene, which harbors a non-canonical IKZF1 binding site. We confirmed cooperative binding of JUN and IKZF1 and showed that the activity of an <i>IL10</i> -luciferase reporter construct in primary B and T cells depended on both this site and the AP1 binding site within this composite element. Overall, our findings reveal an unappreciated global association of IKZF1 and AP1 and establish SPICE as a valuable new pipeline for predicting novel transcription binding complexes.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11703198/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73906740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The <i>MUC19</i> gene in Denisovans, Neanderthals, and Modern Humans: An Evolutionary History of Recurrent Introgression and Natural Selection.","authors":"Fernando A Villanea, David Peede, Eli J Kaufman, Valeria Añorve-Garibay, Elizabeth T Chevy, Viridiana Villa-Islas, Kelsey E Witt, Roberta Zeloni, Davide Marnetto, Priya Moorjani, Flora Jay, Paul N Valdmanis, María C Ávila-Arcos, Emilia Huerta-Sánchez","doi":"10.1101/2023.09.25.559202","DOIUrl":"10.1101/2023.09.25.559202","url":null,"abstract":"<p><p>We study the gene MUC19, for which modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions. We find the diagnostic variants for the Denisovan-like MUC19 haplotype at high frequencies in admixed Latin American individuals among global populations, and at highest frequency in 23 ancient Indigenous American individuals, all predating population admixture with Europeans and Africans. We find that the Denisovan-like MUC19 haplotype carries a higher copy number of a 30 base-pair variable number tandem repeat, and that copy numbers of this repeat are exceedingly high in American populations and are under positive selection. This study provides the first example of positive selection acting on archaic alleles at coding sites and VNTRs. Finally, we find that some Neanderthals carry the Denisovan-like MUC19 haplotype, and that it was likely introgressed into human populations through Neanderthal introgression rather than Denisovan introgression.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10557577/pdf/nihpp-2023.09.25.559202v1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41163561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of exportin 1/XPO1 nuclear export pathway inhibition on coronavirus replication.","authors":"Masmudur M Rahman, Bereket Estifanos, Honor L Glenn, Ami D Gutierrez-Jensen, Karen Kibler, Yize Li, Bertram Jacobs, Grant McFadden, Brenda G Hogue","doi":"10.1101/2023.02.09.527884","DOIUrl":"10.1101/2023.02.09.527884","url":null,"abstract":"<p><p>Nucleocytoplasmic transport of proteins using XPO1 (exportin 1) plays a vital role in cell proliferation and survival. Many viruses also exploit this pathway to promote infection and replication. Thus, inhibiting the XPO1-mediated nuclear export pathway with selective inhibitors has a diverse effect on virus replication by regulating antiviral, proviral, and anti-inflammatory pathways. The XPO1 inhibitor, Selinexor, is an FDA-approved anticancer drug predicted to have antiviral or proviral functions against viruses. Here, we observed that pretreatment of cultured cell lines from human or mouse origin with nuclear export inhibitor Selinexor significantly enhanced protein expression and replication of Mouse Hepatitis Virus (MHV), a mouse coronavirus. Knockdown of cellular XPO1 protein expression also significantly enhanced the replication of MHV in human cells. However, for SARS-CoV-2, selinexor treatment had diverse effects on virus replication in different cell lines. These results indicate that XPO1-mediated nuclear export pathway inhibition might affect coronavirus replication depending on cell types and virus origin.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9948980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9332566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Logic-Based Modeling of Inflammatory Macrophage Crosstalk with Glomerular Endothelial Cells in Diabetic Kidney Disease.","authors":"Krutika Patidar, Ashlee N Ford Versypt","doi":"10.1101/2023.04.04.535594","DOIUrl":"10.1101/2023.04.04.535594","url":null,"abstract":"<p><p>Diabetic kidney disease is a complication in one out of three patients with diabetes. Aberrant glucose metabolism in diabetes leads to structural and functional damage in glomerular tissue and a systemic inflammatory immune response. Complex cellular signaling is at the core of metabolic and functional derangement. Unfortunately, the mechanism underlying the role of inflammation in glomerular endothelial cell dysfunction during diabetic kidney disease is not fully understood. Mathematical models in systems biology allow the integration of experimental evidence and cellular signaling networks to understand mechanisms involved in disease progression. This study developed a logic-based ordinary differential equations model to study inflammatory crosstalk between macrophages and glomerular endothelial cells during diabetic kidney disease progression using a protein signaling network stimulated with glucose and lipopolysaccharide. This modeling approach reduced the biological parameters needed to study signaling networks. The model was fitted to and validated against available biochemical data from textit{in vitro} experiments. The model identified mechanisms for dysregulated signaling in macrophages and glomerular endothelial cells during diabetic kidney disease. In addition, the influence of signaling interactions on glomerular endothelial cell morphology through selective knockdown and downregulation was investigated. Simulation results showed that partial knockdown of VEGF receptor 1, PLC-γ, adherens junction proteins, and calcium partially recovered the intercellular gap width between glomerular endothelial cells. These findings contribute to understanding signaling and molecular perturbations that affect the glomerular endothelial cells in the early stage of diabetic kidney disease.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10104015/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9310822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cancer immunotherapy response persists after lymph node resection.","authors":"Hengbo Zhou, Lutz Menzel, James W Baish, Meghan J O'Melia, Laurel B Darragh, Emma Specht, Derek N Effiom, Juliane Czapla, Pin-Ji Lei, Johanna J Rajotte, Lingshan Liu, Mohammad R Nikmaneshi, Mohammad S Razavi, Matthew G Vander Heiden, Jessalyn M Ubellacker, Lance L Munn, Sana D Karam, Genevieve M Boland, Sonia Cohen, Timothy P Padera","doi":"10.1101/2023.09.19.558262","DOIUrl":"10.1101/2023.09.19.558262","url":null,"abstract":"<p><p>Lymphatic transport facilitates the presentation of cancer antigens in tumor-draining lymph nodes (tdLNs), leading to T cell activation and the generation of systemic antitumor immune surveillance. Surgical removal of LNs to control cancer progression is routine in clinical practice. However, whether removing tdLNs impairs immune checkpoint blockade (ICB) is still controversial. Our analysis demonstrates that melanoma patients remain responsive to PD-1 checkpoint blockade after LN dissection. We were able to recapitulate the persistent response to ICB after complete LN resection in murine melanoma and mammary carcinoma models. Mechanistically, soluble antigen and antigen-carrying migratory dendritic cells are diverted to non-directly tumor draining LNs (non-tdLNs) after tdLN dissection. Consistently, robust ICB responses in patients with head and neck cancer after primary tumor and tdLN resection correlated with the presence of reactive LNs in distant areas. These findings indicate that non-tdLNs sufficiently compensate for the removal of direct tdLNs and sustain the response to ICB.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10541098/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41179676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Monocytes use protrusive forces to generate migration paths in viscoelastic collagen-based extracellular matrices.","authors":"Kolade Adebowale, Cole James Allan, Byunghang Ha, Aashrith Saraswathibhatla, Junqin Zhu, Dhiraj Indana, Medeea Popescu, Sally Demirdjian, Hunter Antonio Martinez, Alex Esclamado, Jin Yang, Michael C Bassik, Christian Franck, Paul Bollyky, Ovijit Chaudhuri","doi":"10.1101/2023.06.09.544394","DOIUrl":"10.1101/2023.06.09.544394","url":null,"abstract":"<p><p>Circulating monocytes are recruited to the tumor microenvironment, where they can differentiate into macrophages that mediate tumor progression. To reach the tumor microenvironment, monocytes must first extravasate and migrate through the type-1 collagen rich stromal matrix. The viscoelastic stromal matrix around tumors not only stiffens relative to normal stromal matrix, but often exhibits enhanced viscous characteristics, as indicated by a higher loss tangent or faster stress relaxation rate. Here, we studied how changes in matrix stiffness and viscoelasticity, impact the three-dimensional migration of monocytes through stromal-like matrices. Interpenetrating networks of type-1 collagen and alginate, which enable independent tunability of stiffness and stress relaxation over physiologically relevant ranges, were used as confining matrices for three-dimensional culture of monocytes. Increased stiffness and faster stress relaxation independently enhanced the 3D migration of monocytes. Migrating monocytes have an ellipsoidal or rounded wedge-like morphology, reminiscent of amoeboid migration, with accumulation of actin at the trailing edge. Matrix adhesions and Rho-mediated contractility were dispensable for monocyte migration in 3D, but migration did require actin polymerization and myosin contractility. Mechanistic studies indicate that actin polymerization at the leading edge generates protrusive forces that open a path for the monocytes to migrate through in the confining viscoelastic matrices. Taken together, our findings implicate matrix stiffness and stress relaxation as key mediators of monocyte migration and reveal how monocytes use pushing forces at the leading edge mediated by actin polymerization to generate migration paths in confining viscoelastic matrices.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10274922/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10018448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cell membranes sustain phospholipid imbalance via cholesterol asymmetry.","authors":"Milka Doktorova, Jessica L Symons, Xiaoxuan Zhang, Hong-Yin Wang, Jan Schlegel, Joseph H Lorent, Frederick A Heberle, Erdinc Sezgin, Edward Lyman, Kandice R Levental, Ilya Levental","doi":"10.1101/2023.07.30.551157","DOIUrl":"10.1101/2023.07.30.551157","url":null,"abstract":"<p><p>Membranes are molecular interfaces that compartmentalize cells to control the flow of nutrients and information. These functions are facilitated by diverse collections of lipids, nearly all of which are distributed asymmetrically between the two bilayer leaflets. Most models of biomembrane structure and function often include the implicit assumption that these leaflets have similar abundances of phospholipids. Here, we show that this assumption is generally invalid and investigate the consequences of lipid abundance imbalances in mammalian plasma membranes (PM). Using quantitative lipidomics, we discovered that cytoplasmic leaflets of human erythrocyte membranes have >50% overabundance of phospholipids compared to exoplasmic leaflets. This imbalance is enabled by an asymmetric interleaflet distribution of cholesterol, which regulates cellular cholesterol homeostasis. These features produce unique functional characteristics, including low PM permeability and resting tension in the cytoplasmic leaflet that regulates protein localization. These largely overlooked aspects of membrane asymmetry represent an evolution of classic paradigms of biomembrane structure and physiology.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":"288 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83138435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}