Pub Date : 2023-11-14DOI: 10.1101/2023.11.13.566921
Bruce Futcher
Previously, Segev and Gerst found that mutants in any of the four ribosomal protein genes rpl1b, rpl2b, rps11a, or rps26b had a petite phenotype, i.e., the mutants were deficient in respiration. Strikingly, mutants of their paralogs rpl1a, rpl2a, rps11b, and rps26a were grande, i.e., competent for respiration. It is remarkable that these paralogs should have opposite phenotypes, because three of the paralog pairs (Rpl1a/Rpl1b, Rpl2a/Rpl2b, Rps11a/Rps11b) are 100% identical to each other in amino acid sequence, while Rps26a and Rps26b differ in 2 amino acids out of 119. However, while attempting to use this paralog specific petite phenotype in an unrelated experiment, I found that the rpl1b, rpl2b, rps11a, and rps26b deletion mutants are competent for respiration, contrary to Segev and Gerst.
{"title":"The yeast ribosomal protein Rpl1b is not required for respiration","authors":"Bruce Futcher","doi":"10.1101/2023.11.13.566921","DOIUrl":"https://doi.org/10.1101/2023.11.13.566921","url":null,"abstract":"Previously, Segev and Gerst found that mutants in any of the four ribosomal protein genes rpl1b, rpl2b, rps11a, or rps26b had a petite phenotype, i.e., the mutants were deficient in respiration. Strikingly, mutants of their paralogs rpl1a, rpl2a, rps11b, and rps26a were grande, i.e., competent for respiration. It is remarkable that these paralogs should have opposite phenotypes, because three of the paralog pairs (Rpl1a/Rpl1b, Rpl2a/Rpl2b, Rps11a/Rps11b) are 100% identical to each other in amino acid sequence, while Rps26a and Rps26b differ in 2 amino acids out of 119. However, while attempting to use this paralog specific petite phenotype in an unrelated experiment, I found that the rpl1b, rpl2b, rps11a, and rps26b deletion mutants are competent for respiration, contrary to Segev and Gerst.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"35 8","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1101/2023.11.14.567058
Mariana Romeiro Motta, Francois Nedelec, Elke Woelken, Helen Saville, Claire Jacquerie, Martine Pastuglia, Sara Christina Stolze, Eveline Van De Slijke, Poyu Chen, Lev Boettger, Katia Belcram, Hirofumi Nakagami, Geert De Jaeger, David Bouchez, Arp Schnittger
To ensure an even segregation of chromosomes during somatic cell division, eukaryotes rely on specific microtubule structures called mitotic spindles. There are, however, striking differences in overall spindle organization among eukaryotic super groups, and in particular little is known about how spindle architecture is determined in plants. As a foundation for our work, we have measured prime characteristics of Arabidopsis mitotic spindles and built a three-dimensional dynamic model of the Arabidopsis mitotic spindle using Cytosim. Next, we identified the cell-cycle regulator CYCLIN-DEPENDENT KINASE B1 (CDKB1) together with its cyclin partner CYCB3;1 as key regulators of spindle shape and organization in Arabidopsis. Loss of CDKB1 function resulted in a high number of astral microtubules that are normally absent from plant spindles, as opposed to animal ones. We identified an augmin complex member, ENDOSPERM DEFECTIVE1 (EDE1), as a substrate of the CDKB1;1-CYCB3;1 complex. A non-phosphorylatable mutant of EDE1 displayed spindles with extended pole-to-pole distance, resembling the phenotypes of cycb3;1 and cdkb1 mutants. Moreover, we found that the mutated EDE1 version associated less efficiently with spindle microtubules. Consistently, reducing the level of augmin in Cytosim simulations largely recapitulated the spindle phenotypes observed in cycb3;1 and cdkb1 mutants. Our results emphasize the importance of cell cycle-dependent phospho-control of the mitotic spindle in plant cells. They also support the validity of our computational model as a framework for the exploration of mechanisms controlling the organization of the spindle in plants and in other species.
{"title":"The cell cycle controls spindle architecture in Arabidopsis by modulating the augmin pathway","authors":"Mariana Romeiro Motta, Francois Nedelec, Elke Woelken, Helen Saville, Claire Jacquerie, Martine Pastuglia, Sara Christina Stolze, Eveline Van De Slijke, Poyu Chen, Lev Boettger, Katia Belcram, Hirofumi Nakagami, Geert De Jaeger, David Bouchez, Arp Schnittger","doi":"10.1101/2023.11.14.567058","DOIUrl":"https://doi.org/10.1101/2023.11.14.567058","url":null,"abstract":"To ensure an even segregation of chromosomes during somatic cell division, eukaryotes rely on specific microtubule structures called mitotic spindles. There are, however, striking differences in overall spindle organization among eukaryotic super groups, and in particular little is known about how spindle architecture is determined in plants. As a foundation for our work, we have measured prime characteristics of Arabidopsis mitotic spindles and built a three-dimensional dynamic model of the Arabidopsis mitotic spindle using Cytosim. Next, we identified the cell-cycle regulator CYCLIN-DEPENDENT KINASE B1 (CDKB1) together with its cyclin partner CYCB3;1 as key regulators of spindle shape and organization in Arabidopsis. Loss of CDKB1 function resulted in a high number of astral microtubules that are normally absent from plant spindles, as opposed to animal ones. We identified an augmin complex member, ENDOSPERM DEFECTIVE1 (EDE1), as a substrate of the CDKB1;1-CYCB3;1 complex. A non-phosphorylatable mutant of EDE1 displayed spindles with extended pole-to-pole distance, resembling the phenotypes of cycb3;1 and cdkb1 mutants. Moreover, we found that the mutated EDE1 version associated less efficiently with spindle microtubules. Consistently, reducing the level of augmin in Cytosim simulations largely recapitulated the spindle phenotypes observed in cycb3;1 and cdkb1 mutants. Our results emphasize the importance of cell cycle-dependent phospho-control of the mitotic spindle in plant cells. They also support the validity of our computational model as a framework for the exploration of mechanisms controlling the organization of the spindle in plants and in other species.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"36 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mexican native maize (Zea mays ssp. mays) is adapted to a wide range of climatic and edaphic conditions. Here, we focus specifically on the potential role of root anatomical variation in this adaptation. In light of the investment required to characterize root anatomy, we present a machine learning approach using environmental descriptors to project trait variation from a relatively small training panel onto a larger panel of genotyped and georeferenced Mexican maize accessions. The resulting models defined potential biologically relevant clines across a complex environment and were used subsequently in genotype-environment association. We found evidence of systematic variation in maize root anatomy across Mexico, notably a prevalence of trait combinations favoring a reduction in axial conductance in cooler, drier highland areas. We discuss our results in the context of previously described water-banking strategies and present candidate genes that are associated with both root anatomical and environmental variation. Our strategy is a refinement of standard environmental genome wide association analysis that is applicable whenever a training set of georeferenced phenotypic data is available.
{"title":"Evidence that variation in root anatomy contributes to local adaptation in Mexican native maize","authors":"Chloee McLaughlin, Meng Li, Melanie Perryman, Adrien Heymans, Hannah Schneider, Jesse Lasky, Ruairidh Sawers","doi":"10.1101/2023.11.14.567017","DOIUrl":"https://doi.org/10.1101/2023.11.14.567017","url":null,"abstract":"Mexican native maize (Zea mays ssp. mays) is adapted to a wide range of climatic and edaphic conditions. Here, we focus specifically on the potential role of root anatomical variation in this adaptation. In light of the investment required to characterize root anatomy, we present a machine learning approach using environmental descriptors to project trait variation from a relatively small training panel onto a larger panel of genotyped and georeferenced Mexican maize accessions. The resulting models defined potential biologically relevant clines across a complex environment and were used subsequently in genotype-environment association. We found evidence of systematic variation in maize root anatomy across Mexico, notably a prevalence of trait combinations favoring a reduction in axial conductance in cooler, drier highland areas. We discuss our results in the context of previously described water-banking strategies and present candidate genes that are associated with both root anatomical and environmental variation. Our strategy is a refinement of standard environmental genome wide association analysis that is applicable whenever a training set of georeferenced phenotypic data is available.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"38 11","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134993129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Transcribed cis-regulatory elements (tCREs), such as promoters and enhancers, are fundamental to modulate gene expression and define cell identity. The detailed mapping of tCREs at single-cell resolution is essential for understanding the regulatory mechanisms that govern cellular functions. Prior tCRE catalogs, limited by bulk analysis, have often overlooked cellular heterogeneity. We have constructed a tCRE atlas using single-cell 5-RNA-seq, capturing over 340,000 single-cells from 23 human tissues and annotating more than 175,000 tCREs, substantially enhancing the scope and granularity of existing cis-regulatory element annotations in the human genome. This atlas unveils patterns of gene regulation, revealing connections between broadly expressed promoters and cell type-specific distal tCREs. Assessing trait heritability at single-cell resolution with a novel tCRE module-based approach, we uncovered the nuanced trait-gene regulatory relationships across a continuum of cell populations, offering insights beyond traditional gene-level and bulk-sample analyses. Our study bridges the gap between gene regulation and trait heritability, underscoring the potential of single-cell analysis to elucidate the genetic foundations of complex traits. These insights set the stage for future research to investigate the impact of genetic variations on diseases at the individual level, advancing the understanding of cellular and molecular basis of trait heritability.
{"title":"A single-cell atlas of transcribed cis-regulatory elements in the human genome","authors":"Jonathan Moody, Tsukasa Kouno, Miki Kojima, Ikuko Koya, Julio Leon, Akari Suzuki, Akira Hasegawa, Taishin Akiyama, Nobuko Akiyama, Masayuki Amagai, Jen-Chien Chang, Ayano Fukushima-Nomura, Mika Handa, Kazunori Hino, Mizuki Hino, Tomoko Hirata, Yuuki Imai, Kazunori Inoue, Hiroshi Kawasaki, Toshihiro Kimura, Tomofumi Kinoshita, Ken-ichiro Kubo, Yasuto Kunii, Fernando Lopez-Redondo, Ri-ichiroh Manabe, Tomohiro Miyai, Satoru Morimoto, Atsuko Nagaoka, Jun Nakajima, Shohei Noma, Yasushi Okazaki, Kokoro Ozaki, Noritaka Saeki, Hiroshi Sakai, Kuniaki Seyama, Youtaro Shibayama, Tomohisa Sujino, Michihira Tagami, Hayato Takahashi, Masaki Takao, Masaru Takeshita, Tsuyoshi Takiuchi, Chikashi Terao, Chi Wai Yip, Satoshi Yoshinaga, Hideyuki Okano, Kazuhiko Yamamoto, Takeya Kasukawa, Yoshinari Ando, Piero Carninci, Jay W. Shin, Chung-Chau Hon","doi":"10.1101/2023.11.13.566791","DOIUrl":"https://doi.org/10.1101/2023.11.13.566791","url":null,"abstract":"Transcribed cis-regulatory elements (tCREs), such as promoters and enhancers, are fundamental to modulate gene expression and define cell identity. The detailed mapping of tCREs at single-cell resolution is essential for understanding the regulatory mechanisms that govern cellular functions. Prior tCRE catalogs, limited by bulk analysis, have often overlooked cellular heterogeneity. We have constructed a tCRE atlas using single-cell 5-RNA-seq, capturing over 340,000 single-cells from 23 human tissues and annotating more than 175,000 tCREs, substantially enhancing the scope and granularity of existing cis-regulatory element annotations in the human genome. This atlas unveils patterns of gene regulation, revealing connections between broadly expressed promoters and cell type-specific distal tCREs. Assessing trait heritability at single-cell resolution with a novel tCRE module-based approach, we uncovered the nuanced trait-gene regulatory relationships across a continuum of cell populations, offering insights beyond traditional gene-level and bulk-sample analyses. Our study bridges the gap between gene regulation and trait heritability, underscoring the potential of single-cell analysis to elucidate the genetic foundations of complex traits. These insights set the stage for future research to investigate the impact of genetic variations on diseases at the individual level, advancing the understanding of cellular and molecular basis of trait heritability.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"39 18","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134953775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1101/2023.11.14.566895
Kimberly R Madhwani, Shanzeh Sayied, Carlson H Ogata, Caley A Hogan, Jenna M Lentini, Moushami Mallik, Jennifer L Dumouchel, Erik Storkebaum, Dragony Fu, Kate M. O'Connor-Giles
Post-transcriptional modification of RNA regulates gene expression at multiple levels. ALKBH8 is a tRNA modifying enzyme that methylates wobble uridines in specific tRNAs to modulate translation. Through methylation of tRNA-selenocysteine, ALKBH8 promotes selenoprotein synthesis and regulates redox homeostasis. Pathogenic variants in ALKBH8 have been linked to intellectual disability disorders in the human population, but the role of ALKBH8 in the nervous system is unknown. Through in vivo studies in Drosophila, we show that ALKBH8 controls oxidative stress in the brain to restrain synaptic growth and support learning and memory. ALKBH8 null animals lack wobble uridine methylation and exhibit a global reduction in protein synthesis, including a specific decrease in selenoprotein levels. Loss of ALKBH8 or independent disruption of selenoprotein synthesis results in ectopic synapse formation. Genetic expression of antioxidant enzymes fully suppresses synaptic overgrowth in ALKBH8 null animals, confirming oxidative stress as the underlying cause of dysregulation. ALKBH8 animals also exhibit associative learning and memory impairments that are reversed by pharmacological antioxidant treatment. Together, these findings demonstrate the critical role of tRNA modification in redox homeostasis in the nervous system and reveal antioxidants as a potential therapy for ALKBH8-associated intellectual disability.
{"title":"tRNA modification enzyme-dependent redox homeostasis regulates synapse formation and memory","authors":"Kimberly R Madhwani, Shanzeh Sayied, Carlson H Ogata, Caley A Hogan, Jenna M Lentini, Moushami Mallik, Jennifer L Dumouchel, Erik Storkebaum, Dragony Fu, Kate M. O'Connor-Giles","doi":"10.1101/2023.11.14.566895","DOIUrl":"https://doi.org/10.1101/2023.11.14.566895","url":null,"abstract":"Post-transcriptional modification of RNA regulates gene expression at multiple levels. ALKBH8 is a tRNA modifying enzyme that methylates wobble uridines in specific tRNAs to modulate translation. Through methylation of tRNA-selenocysteine, ALKBH8 promotes selenoprotein synthesis and regulates redox homeostasis. Pathogenic variants in ALKBH8 have been linked to intellectual disability disorders in the human population, but the role of ALKBH8 in the nervous system is unknown. Through in vivo studies in Drosophila, we show that ALKBH8 controls oxidative stress in the brain to restrain synaptic growth and support learning and memory. ALKBH8 null animals lack wobble uridine methylation and exhibit a global reduction in protein synthesis, including a specific decrease in selenoprotein levels. Loss of ALKBH8 or independent disruption of selenoprotein synthesis results in ectopic synapse formation. Genetic expression of antioxidant enzymes fully suppresses synaptic overgrowth in ALKBH8 null animals, confirming oxidative stress as the underlying cause of dysregulation. ALKBH8 animals also exhibit associative learning and memory impairments that are reversed by pharmacological antioxidant treatment. Together, these findings demonstrate the critical role of tRNA modification in redox homeostasis in the nervous system and reveal antioxidants as a potential therapy for ALKBH8-associated intellectual disability.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"29 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134954554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1101/2023.11.14.567006
Michael Haffner, Oliver Mantovani, Philipp Spaet, Boris Macek, Martin Hagemann, Karl Forchhammer, Khaled A. Selim
In nature, the photoautotrophic lifestyle of cyanobacteria has to cope with the successive diurnal changes in light supply. Light supply throughout the day enables photosynthesis and glycogen biosynthesis, while night phases require the switch to a heterotrophic-like lifestyle relying on glycogen catabolism. We previously highlighted a unique function of the carbon control protein, SbtB, and its effector molecule c-di-AMP, for the nighttime survival of cyanobacteria through the regulation of glycogen anabolism. However, the extent to which c-di-AMP and SbtB impact the cellular metabolism for day-night survivability remained elusive. To gain better understanding of cellular processes regulated by SbtB or c-di-AMP, we compared the metabolomic and proteomic landscapes of ΔsbtB and the c-di-AMP-free (ΔdacA) mutants of the model strain Synechocystis sp. PCC 6803. While our results indicate that the cellular role of SbtB is restricted to carbon/glycogen metabolism, the diurnal lethality of ΔdacA seems to be a sum of dysregulation of multiple metabolic processes. These processes include photosynthesis and redox regulation, which lead to elevated levels of intracellular ROS and glutathione. Further, we show an impact of c-di-AMP on central carbon as well as on nitrogen metabolism. Effects on nitrogen metabolism are linked to reduced levels of the global nitrogen transcription regulator NtcA and highlighted by an imbalance of the glutamine to glutamate ratio as well as reduced metabolite levels of the arginine pathway. We further identified the HCO3- uptake systems, BicA and BCT1 as novel SbtB targets, in agreement with its broader role in regulating carbon homeostasis.
{"title":"Diurnal rhythm causes metabolic crises in the cyanobacterial mutants of c-di-AMP signalling cascade","authors":"Michael Haffner, Oliver Mantovani, Philipp Spaet, Boris Macek, Martin Hagemann, Karl Forchhammer, Khaled A. Selim","doi":"10.1101/2023.11.14.567006","DOIUrl":"https://doi.org/10.1101/2023.11.14.567006","url":null,"abstract":"In nature, the photoautotrophic lifestyle of cyanobacteria has to cope with the successive diurnal changes in light supply. Light supply throughout the day enables photosynthesis and glycogen biosynthesis, while night phases require the switch to a heterotrophic-like lifestyle relying on glycogen catabolism. We previously highlighted a unique function of the carbon control protein, SbtB, and its effector molecule c-di-AMP, for the nighttime survival of cyanobacteria through the regulation of glycogen anabolism. However, the extent to which c-di-AMP and SbtB impact the cellular metabolism for day-night survivability remained elusive. To gain better understanding of cellular processes regulated by SbtB or c-di-AMP, we compared the metabolomic and proteomic landscapes of ΔsbtB and the c-di-AMP-free (ΔdacA) mutants of the model strain Synechocystis sp. PCC 6803. While our results indicate that the cellular role of SbtB is restricted to carbon/glycogen metabolism, the diurnal lethality of ΔdacA seems to be a sum of dysregulation of multiple metabolic processes. These processes include photosynthesis and redox regulation, which lead to elevated levels of intracellular ROS and glutathione. Further, we show an impact of c-di-AMP on central carbon as well as on nitrogen metabolism. Effects on nitrogen metabolism are linked to reduced levels of the global nitrogen transcription regulator NtcA and highlighted by an imbalance of the glutamine to glutamate ratio as well as reduced metabolite levels of the arginine pathway. We further identified the HCO3- uptake systems, BicA and BCT1 as novel SbtB targets, in agreement with its broader role in regulating carbon homeostasis.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"49 15","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1101/2023.11.13.566827
Chi-Huey Wong
ABSTRACT: Recent development of SARS-CoV-2 spike mRNA vaccines to control the pandemic is a breakthrough in the field of vaccine development. mRNA vaccines are generally formulated with lipid nanoparticles (LNPs) which are composed of several lipids with specific ratios; however, they generally lack selective delivery. To develop a simpler method selective delivery of mRNA, we reported here the synthesis of biodegradable copolymers decorated with guanidine and zwitterionic groups and an aryl-trimannoside ligand as polymeric nanoparticles (PNPs) for encapsulation and selective delivery of an mRNA to dendritic cells (DCs). A representative DC-targeted SARS-CoV-2 spike mRNA-PNP vaccine was shown to elicit a stronger protective immune response in mice as compared to the mRNA-LNP and mRNA-PNP vaccines without the selective delivery design. It is anticipated that this technology will be generally applicable to development of DC-targeted mRNA vaccines with enhanced immune response.
{"title":"Synthesis of Dendritic Cell-Targeted Polymeric Nanoparticles for Selective Delivery of mRNA Vaccines to Elicit Enhanced Immune Responses","authors":"Chi-Huey Wong","doi":"10.1101/2023.11.13.566827","DOIUrl":"https://doi.org/10.1101/2023.11.13.566827","url":null,"abstract":"ABSTRACT: Recent development of SARS-CoV-2 spike mRNA vaccines to control the pandemic is a breakthrough in the field of vaccine development. mRNA vaccines are generally formulated with lipid nanoparticles (LNPs) which are composed of several lipids with specific ratios; however, they generally lack selective delivery. To develop a simpler method selective delivery of mRNA, we reported here the synthesis of biodegradable copolymers decorated with guanidine and zwitterionic groups and an aryl-trimannoside ligand as polymeric nanoparticles (PNPs) for encapsulation and selective delivery of an mRNA to dendritic cells (DCs). A representative DC-targeted SARS-CoV-2 spike mRNA-PNP vaccine was shown to elicit a stronger protective immune response in mice as compared to the mRNA-LNP and mRNA-PNP vaccines without the selective delivery design. It is anticipated that this technology will be generally applicable to development of DC-targeted mRNA vaccines with enhanced immune response.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"46 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1101/2023.11.13.566806
Nandan Haloi, Emelia Karlsson, Rebecca J. Howard, Erik Lindahl
Ligand-gated ion channels propagate electrochemical signals in the nervous system by opening ion-selective pores in response to neurotransmitter release. A diverse set of allosteric modulators including neurosteroids, anesthetics, and lipids modulate their function in myriad ways, suggesting a complex conformational landscape. However, structures of ligand-bound ion-channel complexes can be difficult to capture by experimental techniques like cryogenic electron microscopy, particularly when binding is dynamic or transient. Here, we used computational methods to identify a possible bound state of a modulatory stimulant derivative (4-bromoamphetamine) in a cryptic vestibular pocket of a mammalian serotonin-3A receptor. Starting from an experimental activated structure containing a closed pocket, we first applied a molecular dynamics (MD) simulations-based goal-oriented adaptive sampling method to identify possible open-pocket conformations. To find plausible ligand-binding poses, we performed ensemble docking of the newly identified modulator, and reweighted docking scores by the Boltzmann energy function derived from Markov state model analysis of our trajectories. We then performed replicates of unbiased MD simulations of representative complexes in two forcefields to estimate ligand stability, and screened the most stable complexes for accessibility to the aqueous environment. For one relatively stable and accessible site, mutations predicted to disrupt ligand binding were validated by electrophysiology recordings in Xenopus laevis oocytes, and provided a mechanistic rationale for allosteric stabilization of an activated state. Given the pharmaceutical relevance of serotonin-3 receptors in emesis, pain, psychiatric and gastrointestinal diseases, characterizing relatively unexplored modulatory sites in these proteins could open valuable avenues to understanding conformational cycling and designing state-dependent drugs.
{"title":"Discovering cryptic pocket opening and ligand binding in a vestibular site of the 5-HT3A receptor","authors":"Nandan Haloi, Emelia Karlsson, Rebecca J. Howard, Erik Lindahl","doi":"10.1101/2023.11.13.566806","DOIUrl":"https://doi.org/10.1101/2023.11.13.566806","url":null,"abstract":"Ligand-gated ion channels propagate electrochemical signals in the nervous system by opening ion-selective pores in response to neurotransmitter release. A diverse set of allosteric modulators including neurosteroids, anesthetics, and lipids modulate their function in myriad ways, suggesting a complex conformational landscape. However, structures of ligand-bound ion-channel complexes can be difficult to capture by experimental techniques like cryogenic electron microscopy, particularly when binding is dynamic or transient. Here, we used computational methods to identify a possible bound state of a modulatory stimulant derivative (4-bromoamphetamine) in a cryptic vestibular pocket of a mammalian serotonin-3A receptor. Starting from an experimental activated structure containing a closed pocket, we first applied a molecular dynamics (MD) simulations-based goal-oriented adaptive sampling method to identify possible open-pocket conformations. To find plausible ligand-binding poses, we performed ensemble docking of the newly identified modulator, and reweighted docking scores by the Boltzmann energy function derived from Markov state model analysis of our trajectories. We then performed replicates of unbiased MD simulations of representative complexes in two forcefields to estimate ligand stability, and screened the most stable complexes for accessibility to the aqueous environment. For one relatively stable and accessible site, mutations predicted to disrupt ligand binding were validated by electrophysiology recordings in Xenopus laevis oocytes, and provided a mechanistic rationale for allosteric stabilization of an activated state. Given the pharmaceutical relevance of serotonin-3 receptors in emesis, pain, psychiatric and gastrointestinal diseases, characterizing relatively unexplored modulatory sites in these proteins could open valuable avenues to understanding conformational cycling and designing state-dependent drugs.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"36 19","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1101/2023.11.10.566613
Hannah M Starnes, Thomas W Jackson, Kylie D Rock, Scott M Belcher
Per- and polyfluoroalkyl substances (PFAS) are a class of over 8,000 chemicals that are persistent, bioaccumulative, and toxic to humans, livestock, and wildlife. Serum protein binding affinity is instrumental in understanding PFAS toxicity, yet experimental binding data is limited to only a few PFAS congeners. Previously, we demonstrated the usefulness of a high-throughput, in vitro differential scanning fluorimetry assay for determination of relative binding affinities of human serum albumin for 24 PFAS congeners from 6 chemical classes. In the current study, we used this differential scanning fluorimetry assay to comparatively examine differences in human, bovine, porcine, and rat serum albumin binding of 8 structurally informative PFAS congeners from 5 chemical classes. With the exception of the fluorotelomer alcohol 1H,1H,2H,2H-perfluorooctanol (6:2 FTOH), each PFAS congener bound by human serum albumin was also bound by bovine, porcine, and rat serum albumin. The critical role of the charged functional headgroup in albumin binding was supported by the inability of serum albumin of each species tested to bind 6:2 FTOH. Significant interspecies differences in serum albumin binding affinities were identified for each of the bound PFAS congeners. Relative to human albumin, perfluoroalkyl carboxylic and sulfonic acids were bound with greater affinity by porcine and rat serum albumin, and perfluoroalkyl ether congeners bound with lower affinity to porcine and bovine serum albumin. These comparative affinity data for PFAS binding by serum albumin from human, experimental model and livestock species reduce critical interspecies uncertainty and improve accuracy of predictive toxicity assessments for PFAS.
{"title":"Quantitative Cross-Species Comparison of Serum Albumin Binding of Per- and Polyfluoroalkyl Substances from Five Structural Classes","authors":"Hannah M Starnes, Thomas W Jackson, Kylie D Rock, Scott M Belcher","doi":"10.1101/2023.11.10.566613","DOIUrl":"https://doi.org/10.1101/2023.11.10.566613","url":null,"abstract":"Per- and polyfluoroalkyl substances (PFAS) are a class of over 8,000 chemicals that are persistent, bioaccumulative, and toxic to humans, livestock, and wildlife. Serum protein binding affinity is instrumental in understanding PFAS toxicity, yet experimental binding data is limited to only a few PFAS congeners. Previously, we demonstrated the usefulness of a high-throughput, in vitro differential scanning fluorimetry assay for determination of relative binding affinities of human serum albumin for 24 PFAS congeners from 6 chemical classes. In the current study, we used this differential scanning fluorimetry assay to comparatively examine differences in human, bovine, porcine, and rat serum albumin binding of 8 structurally informative PFAS congeners from 5 chemical classes. With the exception of the fluorotelomer alcohol 1H,1H,2H,2H-perfluorooctanol (6:2 FTOH), each PFAS congener bound by human serum albumin was also bound by bovine, porcine, and rat serum albumin. The critical role of the charged functional headgroup in albumin binding was supported by the inability of serum albumin of each species tested to bind 6:2 FTOH. Significant interspecies differences in serum albumin binding affinities were identified for each of the bound PFAS congeners. Relative to human albumin, perfluoroalkyl carboxylic and sulfonic acids were bound with greater affinity by porcine and rat serum albumin, and perfluoroalkyl ether congeners bound with lower affinity to porcine and bovine serum albumin. These comparative affinity data for PFAS binding by serum albumin from human, experimental model and livestock species reduce critical interspecies uncertainty and improve accuracy of predictive toxicity assessments for PFAS.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"44 21","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Implementing integrated pest management programs to limit agricultural pest damage requires an understanding of the interactions between the environmental variability and population demographic processes. However, identifying key environmental drivers of spatiotemporal pest population dynamics remains challenging as numerous candidate factors can operate at a range of scales, from the field (e.g. agricultural practices) to the regional scale (e.g. weather variability). In such a context, data-driven approaches applied to pre-existing data may allow identifying patterns, correlations, and trends that may not be apparent through more restricted hypothesis-driven studies. The resulting insights can lead to the generation of novel hypotheses and inform future experimental work focusing on a limited and relevant set of environmental predictors. In this study, we developed an ecoinformatics approach to unravel the multi-scale environmental conditions that lead to the early re-infestation of mango orchards by a major pest in Senegal, the oriental fruit fly Bactrocera dorsalis (BD). We gathered abundance data from a three-year monitoring conducted in 69 mango orchards as well as environmental data (i.e. orchard management, landscape structure and weather variability) across a range of spatial scales. We then developed a flexible analysis pipeline centred on a recent machine learning algorithm (GPBoost), which allows the combination of gradient boosting and mixed-effects models or Gaussian processes, to hierarchize the effects of multi-scale environmental variables on the timing of annual BD population growth in orchards. We found that physical factors (temperature, humidity), and to some extent landscape features, were the main drivers of the spatio-temporal variability of the onset of population growth in orchards. These results suggest that favourable microclimate conditions could provide refuges for small BD populations that could survive, with little or no reproduction, during the mango off-season and, then, recolonize neighbouring orchards at the beginning of the next mango season. Confirmation of such a hypothesis could help to prioritize surveillance and preventive control actions in refuge areas.
{"title":"Hierarchizing multi-scale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchards","authors":"Cecile Caumette, Paterne Diatta, Sylvain Piry, Marie-Pierre Chapuis, Emile Faye, Fabio Sigrist, Olivier Martin, Julien Papaix, Thierry Brevault, Karine Berthier","doi":"10.1101/2023.11.10.566583","DOIUrl":"https://doi.org/10.1101/2023.11.10.566583","url":null,"abstract":"Implementing integrated pest management programs to limit agricultural pest damage requires an understanding of the interactions between the environmental variability and population demographic processes. However, identifying key environmental drivers of spatiotemporal pest population dynamics remains challenging as numerous candidate factors can operate at a range of scales, from the field (e.g. agricultural practices) to the regional scale (e.g. weather variability). In such a context, data-driven approaches applied to pre-existing data may allow identifying patterns, correlations, and trends that may not be apparent through more restricted hypothesis-driven studies. The resulting insights can lead to the generation of novel hypotheses and inform future experimental work focusing on a limited and relevant set of environmental predictors. In this study, we developed an ecoinformatics approach to unravel the multi-scale environmental conditions that lead to the early re-infestation of mango orchards by a major pest in Senegal, the oriental fruit fly Bactrocera dorsalis (BD). We gathered abundance data from a three-year monitoring conducted in 69 mango orchards as well as environmental data (i.e. orchard management, landscape structure and weather variability) across a range of spatial scales. We then developed a flexible analysis pipeline centred on a recent machine learning algorithm (GPBoost), which allows the combination of gradient boosting and mixed-effects models or Gaussian processes, to hierarchize the effects of multi-scale environmental variables on the timing of annual BD population growth in orchards. We found that physical factors (temperature, humidity), and to some extent landscape features, were the main drivers of the spatio-temporal variability of the onset of population growth in orchards. These results suggest that favourable microclimate conditions could provide refuges for small BD populations that could survive, with little or no reproduction, during the mango off-season and, then, recolonize neighbouring orchards at the beginning of the next mango season. Confirmation of such a hypothesis could help to prioritize surveillance and preventive control actions in refuge areas.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"44 13","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：