Pub Date : 2021-05-20DOI: 10.1101/2021.05.18.444721
Daniel Ariad, Stephanie M. Yan, A. Victor, F. Barnes, C. Zouves, M. Viotti, R. McCoy
Significance Whole-chromosome gains and losses (aneuploidies) are the leading cause of human pregnancy loss and congenital disorders. Recent work has demonstrated that in addition to harmful meiotic aneuploidies, mitotic aneuploidies (which lead to mosaic embryos harboring cells with different numbers of chromosomes) may also be common in preimplantation embryos but potentially compatible with healthy birth. Here we developed and tested a method for distinguishing these forms of aneuploidy using genetic testing data from 8,154 in vitro fertilization (IVF) embryos. We reclassified embryos based on signatures of meiotic and mitotic error, while also revealing lethal forms of chromosome abnormality that were previously hidden. Our method complements standard protocols for preimplantation genetic testing, while offering insight into the biology of early development. Extra or missing chromosomes—a phenomenon termed aneuploidy—frequently arise during human meiosis and embryonic mitosis and are the leading cause of pregnancy loss, including in the context of in vitro fertilization (IVF). While meiotic aneuploidies affect all cells and are deleterious, mitotic errors generate mosaicism, which may be compatible with healthy live birth. Large-scale abnormalities such as triploidy and haploidy also contribute to adverse pregnancy outcomes, but remain hidden from standard sequencing-based approaches to preimplantation genetic testing for aneuploidy (PGT-A). The ability to reliably distinguish meiotic and mitotic aneuploidies, as well as abnormalities in genome-wide ploidy, may thus prove valuable for enhancing IVF outcomes. Here, we describe a statistical method for distinguishing these forms of aneuploidy based on analysis of low-coverage whole-genome sequencing data, which is the current standard in the field. Our approach overcomes the sparse nature of the data by leveraging allele frequencies and linkage disequilibrium (LD) measured in a population reference panel. The method, which we term LD-informed PGT-A (LD-PGTA), retains high accuracy down to coverage as low as 0.05 × and at higher coverage can also distinguish between meiosis I and meiosis II errors based on signatures spanning the centromeres. LD-PGTA provides fundamental insight into the origins of human chromosome abnormalities, as well as a practical tool with the potential to improve genetic testing during IVF.
{"title":"Haplotype-aware inference of human chromosome abnormalities","authors":"Daniel Ariad, Stephanie M. Yan, A. Victor, F. Barnes, C. Zouves, M. Viotti, R. McCoy","doi":"10.1101/2021.05.18.444721","DOIUrl":"https://doi.org/10.1101/2021.05.18.444721","url":null,"abstract":"Significance Whole-chromosome gains and losses (aneuploidies) are the leading cause of human pregnancy loss and congenital disorders. Recent work has demonstrated that in addition to harmful meiotic aneuploidies, mitotic aneuploidies (which lead to mosaic embryos harboring cells with different numbers of chromosomes) may also be common in preimplantation embryos but potentially compatible with healthy birth. Here we developed and tested a method for distinguishing these forms of aneuploidy using genetic testing data from 8,154 in vitro fertilization (IVF) embryos. We reclassified embryos based on signatures of meiotic and mitotic error, while also revealing lethal forms of chromosome abnormality that were previously hidden. Our method complements standard protocols for preimplantation genetic testing, while offering insight into the biology of early development. Extra or missing chromosomes—a phenomenon termed aneuploidy—frequently arise during human meiosis and embryonic mitosis and are the leading cause of pregnancy loss, including in the context of in vitro fertilization (IVF). While meiotic aneuploidies affect all cells and are deleterious, mitotic errors generate mosaicism, which may be compatible with healthy live birth. Large-scale abnormalities such as triploidy and haploidy also contribute to adverse pregnancy outcomes, but remain hidden from standard sequencing-based approaches to preimplantation genetic testing for aneuploidy (PGT-A). The ability to reliably distinguish meiotic and mitotic aneuploidies, as well as abnormalities in genome-wide ploidy, may thus prove valuable for enhancing IVF outcomes. Here, we describe a statistical method for distinguishing these forms of aneuploidy based on analysis of low-coverage whole-genome sequencing data, which is the current standard in the field. Our approach overcomes the sparse nature of the data by leveraging allele frequencies and linkage disequilibrium (LD) measured in a population reference panel. The method, which we term LD-informed PGT-A (LD-PGTA), retains high accuracy down to coverage as low as 0.05 × and at higher coverage can also distinguish between meiosis I and meiosis II errors based on signatures spanning the centromeres. LD-PGTA provides fundamental insight into the origins of human chromosome abnormalities, as well as a practical tool with the potential to improve genetic testing during IVF.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"116 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79560514","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 : 2021-05-18DOI: 10.1101/2021.05.18.444668
Vijayendran Chandran, Mei-Ling Bermúdez, Mert Koka, Brindha Chandran, Dhanashri Pawale, Ramana V Vishnubhotla, Suresh Alankar, R. Maturi, B. Subramaniam, S. Sadhasivam
Significance Several studies on the impact of yoga and meditation on mental and physical health have demonstrated beneficial effects. However, the potential molecular mechanisms and critical genes involved in this beneficial outcome have yet to be comprehensively elucidated. This study identified and characterized the transcriptional program associated with advanced meditation practice, and we bioinformatically integrated various networks to identify meditation-specific core network. This core network links several immune signaling pathways, and we showed that this core transcriptional profile is dysfunctional in multiple sclerosis and severe COVID-19 infection. Very importantly, we demonstrated that the meditative practice enhanced immune function without activating inflammatory signals. Together, these results make meditation an effective behavioral intervention for treating various conditions associated with a weakened immune system. The positive impact of meditation on human well-being is well documented, yet its molecular mechanisms are incompletely understood. We applied a comprehensive systems biology approach starting with whole-blood gene expression profiling combined with multilevel bioinformatic analyses to characterize the coexpression, transcriptional, and protein–protein interaction networks to identify a meditation-specific core network after an advanced 8-d Inner Engineering retreat program. We found the response to oxidative stress, detoxification, and cell cycle regulation pathways were down-regulated after meditation. Strikingly, 220 genes directly associated with immune response, including 68 genes related to interferon signaling, were up-regulated, with no significant expression changes in the inflammatory genes. This robust meditation-specific immune response network is significantly dysregulated in multiple sclerosis and severe COVID-19 patients. The work provides a foundation for understanding the effect of meditation and suggests that meditation as a behavioral intervention can voluntarily and nonpharmacologically improve the immune response for treating various conditions associated with excessive or persistent inflammation with a dampened immune system profile.
{"title":"Large-scale genomic study reveals robust activation of the immune system following advanced Inner Engineering meditation retreat","authors":"Vijayendran Chandran, Mei-Ling Bermúdez, Mert Koka, Brindha Chandran, Dhanashri Pawale, Ramana V Vishnubhotla, Suresh Alankar, R. Maturi, B. Subramaniam, S. Sadhasivam","doi":"10.1101/2021.05.18.444668","DOIUrl":"https://doi.org/10.1101/2021.05.18.444668","url":null,"abstract":"Significance Several studies on the impact of yoga and meditation on mental and physical health have demonstrated beneficial effects. However, the potential molecular mechanisms and critical genes involved in this beneficial outcome have yet to be comprehensively elucidated. This study identified and characterized the transcriptional program associated with advanced meditation practice, and we bioinformatically integrated various networks to identify meditation-specific core network. This core network links several immune signaling pathways, and we showed that this core transcriptional profile is dysfunctional in multiple sclerosis and severe COVID-19 infection. Very importantly, we demonstrated that the meditative practice enhanced immune function without activating inflammatory signals. Together, these results make meditation an effective behavioral intervention for treating various conditions associated with a weakened immune system. The positive impact of meditation on human well-being is well documented, yet its molecular mechanisms are incompletely understood. We applied a comprehensive systems biology approach starting with whole-blood gene expression profiling combined with multilevel bioinformatic analyses to characterize the coexpression, transcriptional, and protein–protein interaction networks to identify a meditation-specific core network after an advanced 8-d Inner Engineering retreat program. We found the response to oxidative stress, detoxification, and cell cycle regulation pathways were down-regulated after meditation. Strikingly, 220 genes directly associated with immune response, including 68 genes related to interferon signaling, were up-regulated, with no significant expression changes in the inflammatory genes. This robust meditation-specific immune response network is significantly dysregulated in multiple sclerosis and severe COVID-19 patients. The work provides a foundation for understanding the effect of meditation and suggests that meditation as a behavioral intervention can voluntarily and nonpharmacologically improve the immune response for treating various conditions associated with excessive or persistent inflammation with a dampened immune system profile.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90200744","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 : 2021-05-17DOI: 10.1101/2021.05.17.444471
Ji Wang, H. Filippakis, Thomas R. Hougard, H. Du, Chenyang Ye, Heng-Jia Liu, Long Zhang, Khadijah Hindi, Shefali Bagwe, Julie Nijmeh, J. Asara, W. Shi, S. El-Chemaly, E. Henske, H. Lam
Significance The tumor suppressor syndrome tuberous sclerosis complex (TSC) affects 1:10,000 live births. We discovered that the inflammatory cytokine Interleukin-6 (IL-6) promotes the proliferation and migration of TSC2-deficient cells in part through the regulation of PSAT1 and de novo serine biosynthesis. Importantly, IL-6 neutralizing antibody treatments reduced renal cyst and cystadenoma formation in Tsc2+/− mice. This study highlights a therapeutically targetable vulnerability of TSC, which may have broad clinical application to mTORC1-activated tumors. Tuberous sclerosis complex (TSC) and lymphangioleiomyomatosis (LAM) are caused by aberrant mechanistic Target of Rapamycin Complex 1 (mTORC1) activation due to loss of either TSC1 or TSC2. Cytokine profiling of TSC2-deficient LAM patient–derived cells revealed striking up-regulation of Interleukin-6 (IL-6). LAM patient plasma contained increased circulating IL-6 compared with healthy controls, and TSC2-deficient cells showed up-regulation of IL-6 transcription and secretion compared to wild-type cells. IL-6 blockade repressed the proliferation and migration of TSC2-deficient cells and reduced oxygen consumption and extracellular acidification. U-13C glucose tracing revealed that IL-6 knockout reduced 3-phosphoserine and serine production in TSC2-deficient cells, implicating IL-6 in de novo serine metabolism. IL-6 knockout reduced expression of phosphoserine aminotransferase 1 (PSAT1), an essential enzyme in serine biosynthesis. Importantly, recombinant IL-6 treatment rescued PSAT1 expression in the TSC2-deficient, IL-6 knockout clones selectively and had no effect on wild-type cells. Treatment with anti–IL-6 (αIL-6) antibody similarly reduced cell proliferation and migration and reduced renal tumors in Tsc2+/− mice while reducing PSAT1 expression. These data reveal a mechanism through which IL-6 regulates serine biosynthesis, with potential relevance to the therapy of tumors with mTORC1 hyperactivity.
{"title":"Interleukin-6 mediates PSAT1 expression and serine metabolism in TSC2-deficient cells","authors":"Ji Wang, H. Filippakis, Thomas R. Hougard, H. Du, Chenyang Ye, Heng-Jia Liu, Long Zhang, Khadijah Hindi, Shefali Bagwe, Julie Nijmeh, J. Asara, W. Shi, S. El-Chemaly, E. Henske, H. Lam","doi":"10.1101/2021.05.17.444471","DOIUrl":"https://doi.org/10.1101/2021.05.17.444471","url":null,"abstract":"Significance The tumor suppressor syndrome tuberous sclerosis complex (TSC) affects 1:10,000 live births. We discovered that the inflammatory cytokine Interleukin-6 (IL-6) promotes the proliferation and migration of TSC2-deficient cells in part through the regulation of PSAT1 and de novo serine biosynthesis. Importantly, IL-6 neutralizing antibody treatments reduced renal cyst and cystadenoma formation in Tsc2+/− mice. This study highlights a therapeutically targetable vulnerability of TSC, which may have broad clinical application to mTORC1-activated tumors. Tuberous sclerosis complex (TSC) and lymphangioleiomyomatosis (LAM) are caused by aberrant mechanistic Target of Rapamycin Complex 1 (mTORC1) activation due to loss of either TSC1 or TSC2. Cytokine profiling of TSC2-deficient LAM patient–derived cells revealed striking up-regulation of Interleukin-6 (IL-6). LAM patient plasma contained increased circulating IL-6 compared with healthy controls, and TSC2-deficient cells showed up-regulation of IL-6 transcription and secretion compared to wild-type cells. IL-6 blockade repressed the proliferation and migration of TSC2-deficient cells and reduced oxygen consumption and extracellular acidification. U-13C glucose tracing revealed that IL-6 knockout reduced 3-phosphoserine and serine production in TSC2-deficient cells, implicating IL-6 in de novo serine metabolism. IL-6 knockout reduced expression of phosphoserine aminotransferase 1 (PSAT1), an essential enzyme in serine biosynthesis. Importantly, recombinant IL-6 treatment rescued PSAT1 expression in the TSC2-deficient, IL-6 knockout clones selectively and had no effect on wild-type cells. Treatment with anti–IL-6 (αIL-6) antibody similarly reduced cell proliferation and migration and reduced renal tumors in Tsc2+/− mice while reducing PSAT1 expression. These data reveal a mechanism through which IL-6 regulates serine biosynthesis, with potential relevance to the therapy of tumors with mTORC1 hyperactivity.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"182 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91551464","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 : 2021-05-17DOI: 10.1101/2021.05.14.444263
A. Aabedi, Benjamin Lipkin, J. Kaur, Sofia Kakaizada, Sheantel J. Reihl, Jacob S. Young, Anthony T. Lee, S. Krishna, E. Chang, D. Brang, Shawn L. Hervey Jumper
Significance As gliomas proliferate, they infiltrate healthy brain tissue. Often, patients with such tumors in the language areas of the brain develop aphasia. Understanding how gliomas interact with normal neural circuits is critical for developing neuroprostheses that restore speech. Recent evidence demonstrates that glioma cells interact synaptically with neurons and thus can modulate neural circuits. However, it is unclear the extent to which glioma-infiltrated cortex participates in cognitive processing. Using electrocorticography to record both glioma-infiltrated and normal-appearing cortex during speech, we found that glioma-infiltrated cortex is capable of coordinated neural responses but has reduced capacity for information encoding. Instead, glioma-infiltrated cortex recruits a broader network of cortical regions during speech, which may represent a compensatory mechanism with implications for future neuroprostheses. Recent developments in the biology of malignant gliomas have demonstrated that glioma cells interact with neurons through both paracrine signaling and electrochemical synapses. Glioma–neuron interactions consequently modulate the excitability of local neuronal circuits, and it is unclear the extent to which glioma-infiltrated cortex can meaningfully participate in neural computations. For example, gliomas may result in a local disorganization of activity that impedes the transient synchronization of neural oscillations. Alternatively, glioma-infiltrated cortex may retain the ability to engage in synchronized activity in a manner similar to normal-appearing cortex but exhibit other altered spatiotemporal patterns of activity with subsequent impact on cognitive processing. Here, we use subdural electrocorticography to sample both normal-appearing and glioma-infiltrated cortex during speech. We find that glioma-infiltrated cortex engages in synchronous activity during task performance in a manner similar to normal-appearing cortex but recruits a diffuse spatial network. On a temporal scale, we show that signals from glioma-infiltrated cortex have decreased entropy, which may affect its ability to encode information during nuanced tasks such as production of monosyllabic versus polysyllabic words. Furthermore, we show that temporal decoding strategies for distinguishing monosyllabic from polysyllabic words were feasible for signals arising from normal-appearing cortex but not from glioma-infiltrated cortex. These findings inform our understanding of cognitive processing in chronic disease states and have implications for neuromodulation and prosthetics in patients with malignant gliomas.
{"title":"Functional alterations in cortical processing of speech in glioma-infiltrated cortex","authors":"A. Aabedi, Benjamin Lipkin, J. Kaur, Sofia Kakaizada, Sheantel J. Reihl, Jacob S. Young, Anthony T. Lee, S. Krishna, E. Chang, D. Brang, Shawn L. Hervey Jumper","doi":"10.1101/2021.05.14.444263","DOIUrl":"https://doi.org/10.1101/2021.05.14.444263","url":null,"abstract":"Significance As gliomas proliferate, they infiltrate healthy brain tissue. Often, patients with such tumors in the language areas of the brain develop aphasia. Understanding how gliomas interact with normal neural circuits is critical for developing neuroprostheses that restore speech. Recent evidence demonstrates that glioma cells interact synaptically with neurons and thus can modulate neural circuits. However, it is unclear the extent to which glioma-infiltrated cortex participates in cognitive processing. Using electrocorticography to record both glioma-infiltrated and normal-appearing cortex during speech, we found that glioma-infiltrated cortex is capable of coordinated neural responses but has reduced capacity for information encoding. Instead, glioma-infiltrated cortex recruits a broader network of cortical regions during speech, which may represent a compensatory mechanism with implications for future neuroprostheses. Recent developments in the biology of malignant gliomas have demonstrated that glioma cells interact with neurons through both paracrine signaling and electrochemical synapses. Glioma–neuron interactions consequently modulate the excitability of local neuronal circuits, and it is unclear the extent to which glioma-infiltrated cortex can meaningfully participate in neural computations. For example, gliomas may result in a local disorganization of activity that impedes the transient synchronization of neural oscillations. Alternatively, glioma-infiltrated cortex may retain the ability to engage in synchronized activity in a manner similar to normal-appearing cortex but exhibit other altered spatiotemporal patterns of activity with subsequent impact on cognitive processing. Here, we use subdural electrocorticography to sample both normal-appearing and glioma-infiltrated cortex during speech. We find that glioma-infiltrated cortex engages in synchronous activity during task performance in a manner similar to normal-appearing cortex but recruits a diffuse spatial network. On a temporal scale, we show that signals from glioma-infiltrated cortex have decreased entropy, which may affect its ability to encode information during nuanced tasks such as production of monosyllabic versus polysyllabic words. Furthermore, we show that temporal decoding strategies for distinguishing monosyllabic from polysyllabic words were feasible for signals arising from normal-appearing cortex but not from glioma-infiltrated cortex. These findings inform our understanding of cognitive processing in chronic disease states and have implications for neuromodulation and prosthetics in patients with malignant gliomas.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88672877","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 : 2021-05-12DOI: 10.1101/2021.05.11.443692
Jiandong Chen, Leann To, Francois de Mets, Xing Luo, N. Majdalani, Chin-Hsien Tai, S. Gottesman
Significance The ability to promptly switch genes on and off allows bacteria to adapt rapidly to changing environments for better survival. Many small regulatory RNAs (sRNAs), including RyhB, a sRNA made in response to iron starvation, are important switches in bacteria. We discovered factors that can keep the sRNA switch off by using a facile genetic screen platform. These factors include an RNA sponge and an adaptor protein for a ribonuclease, providing distinct perspectives on controlling sRNA signaling in bacteria. As key players of gene regulation in many bacteria, small regulatory RNAs (sRNAs) associated with the RNA chaperone Hfq shape numerous phenotypic traits, including metabolism, stress response and adaptation, as well as virulence. sRNAs can alter target messenger RNA (mRNA) translation and stability via base pairing. sRNA synthesis is generally under tight transcriptional regulation, but other levels of regulation of sRNA signaling are less well understood. Here we used a fluorescence-based functional screen to identify regulators that can quench sRNA signaling of the iron-responsive sRNA RyhB in Escherichia coli. The identified regulators fell into two classes, general regulators (affecting signaling by many sRNAs) and RyhB-specific regulators; we focused on the specific ones here. General regulators include three Hfq-interacting sRNAs, CyaR, ChiX, and McaS, previously found to act through Hfq competition, RNase T, a 3′ to 5′ exonuclease not previously implicated in sRNA degradation, and YhbS, a putative GCN5-related N-acetyltransferase (GNAT). Two specific regulators were identified. AspX, a 3′end-derived small RNA, specifically represses RyhB signaling via an RNA sponging mechanism. YicC, a previously uncharacterized but widely conserved protein, triggers rapid RyhB degradation via collaboration with the exoribonuclease PNPase. These findings greatly expand our knowledge of regulation of bacterial sRNA signaling and suggest complex regulatory networks for controlling iron homeostasis in bacteria. The fluorescence-based genetic screen system described here is a powerful tool expected to accelerate the discovery of novel regulators of sRNA signaling in many bacteria.
{"title":"A fluorescence-based genetic screen reveals diverse mechanisms silencing small RNA signaling in E. coli","authors":"Jiandong Chen, Leann To, Francois de Mets, Xing Luo, N. Majdalani, Chin-Hsien Tai, S. Gottesman","doi":"10.1101/2021.05.11.443692","DOIUrl":"https://doi.org/10.1101/2021.05.11.443692","url":null,"abstract":"Significance The ability to promptly switch genes on and off allows bacteria to adapt rapidly to changing environments for better survival. Many small regulatory RNAs (sRNAs), including RyhB, a sRNA made in response to iron starvation, are important switches in bacteria. We discovered factors that can keep the sRNA switch off by using a facile genetic screen platform. These factors include an RNA sponge and an adaptor protein for a ribonuclease, providing distinct perspectives on controlling sRNA signaling in bacteria. As key players of gene regulation in many bacteria, small regulatory RNAs (sRNAs) associated with the RNA chaperone Hfq shape numerous phenotypic traits, including metabolism, stress response and adaptation, as well as virulence. sRNAs can alter target messenger RNA (mRNA) translation and stability via base pairing. sRNA synthesis is generally under tight transcriptional regulation, but other levels of regulation of sRNA signaling are less well understood. Here we used a fluorescence-based functional screen to identify regulators that can quench sRNA signaling of the iron-responsive sRNA RyhB in Escherichia coli. The identified regulators fell into two classes, general regulators (affecting signaling by many sRNAs) and RyhB-specific regulators; we focused on the specific ones here. General regulators include three Hfq-interacting sRNAs, CyaR, ChiX, and McaS, previously found to act through Hfq competition, RNase T, a 3′ to 5′ exonuclease not previously implicated in sRNA degradation, and YhbS, a putative GCN5-related N-acetyltransferase (GNAT). Two specific regulators were identified. AspX, a 3′end-derived small RNA, specifically represses RyhB signaling via an RNA sponging mechanism. YicC, a previously uncharacterized but widely conserved protein, triggers rapid RyhB degradation via collaboration with the exoribonuclease PNPase. These findings greatly expand our knowledge of regulation of bacterial sRNA signaling and suggest complex regulatory networks for controlling iron homeostasis in bacteria. The fluorescence-based genetic screen system described here is a powerful tool expected to accelerate the discovery of novel regulators of sRNA signaling in many bacteria.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"32 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79178863","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 : 2021-05-10DOI: 10.26434/CHEMRXIV.14556006.V1
Jaeyeon Hwang, B. Mercado, Scott J. Miller
Significance Chiral catalysts are generally used to control stereochemistry in organic reactions. Generally, they control enantioselectivity or diastereoselectivity. In recent years, applications have expanded to include control over site selectivity in reactions involving complex molecules. Even more rarely, they can control chemoselectivity along with stereochemistry. We report herein that a carefully chosen chiral catalyst can also be decisive for efficient macrocyclization reactions in cases where simple achiral catalysts or stereochemically mismatched catalysts fail. Notably, in these reactions, a chiral catalyst proves essential for control of a reaction in which no new static (i.e., not “dynamic”) stereogenic elements are introduced. While fundamentally intriguing, these observations could also influence strategies for efficient synthesis of macrocyclic compounds in a variety of settings. Macrocycles, formally defined as compounds that contain a ring with 12 or more atoms, continue to attract great interest due to their important applications in physical, pharmacological, and environmental sciences. In syntheses of macrocyclic compounds, promoting intramolecular over intermolecular reactions in the ring-closing step is often a key challenge. Furthermore, syntheses of macrocycles with stereogenic elements confer an additional challenge, while access to such macrocycles are of great interest. Herein, we report the remarkable effect peptide-based catalysts can have in promoting efficient macrocyclization reactions. We show that the chirality of the catalyst is essential for promoting favorable, matched transition-state relationships that favor macrocyclization of substrates with preexisting stereogenic elements; curiously, the chirality of the catalyst is essential for successful reactions, even though no new static (i.e., not “dynamic”) stereogenic elements are created. Control experiments involving either achiral variants of the catalyst or the enantiomeric form of the catalyst fail to deliver the macrocycles in significant quantity in head-to-head comparisons. The generality of the phenomenon, demonstrated here with a number of substrates, stimulates analogies to enzymatic catalysts that produce naturally occurring macrocycles, presumably through related, catalyst-defined peripheral interactions with their acyclic substrates.
{"title":"Chirality-matched catalyst-controlled macrocyclization reactions","authors":"Jaeyeon Hwang, B. Mercado, Scott J. Miller","doi":"10.26434/CHEMRXIV.14556006.V1","DOIUrl":"https://doi.org/10.26434/CHEMRXIV.14556006.V1","url":null,"abstract":"Significance Chiral catalysts are generally used to control stereochemistry in organic reactions. Generally, they control enantioselectivity or diastereoselectivity. In recent years, applications have expanded to include control over site selectivity in reactions involving complex molecules. Even more rarely, they can control chemoselectivity along with stereochemistry. We report herein that a carefully chosen chiral catalyst can also be decisive for efficient macrocyclization reactions in cases where simple achiral catalysts or stereochemically mismatched catalysts fail. Notably, in these reactions, a chiral catalyst proves essential for control of a reaction in which no new static (i.e., not “dynamic”) stereogenic elements are introduced. While fundamentally intriguing, these observations could also influence strategies for efficient synthesis of macrocyclic compounds in a variety of settings. Macrocycles, formally defined as compounds that contain a ring with 12 or more atoms, continue to attract great interest due to their important applications in physical, pharmacological, and environmental sciences. In syntheses of macrocyclic compounds, promoting intramolecular over intermolecular reactions in the ring-closing step is often a key challenge. Furthermore, syntheses of macrocycles with stereogenic elements confer an additional challenge, while access to such macrocycles are of great interest. Herein, we report the remarkable effect peptide-based catalysts can have in promoting efficient macrocyclization reactions. We show that the chirality of the catalyst is essential for promoting favorable, matched transition-state relationships that favor macrocyclization of substrates with preexisting stereogenic elements; curiously, the chirality of the catalyst is essential for successful reactions, even though no new static (i.e., not “dynamic”) stereogenic elements are created. Control experiments involving either achiral variants of the catalyst or the enantiomeric form of the catalyst fail to deliver the macrocycles in significant quantity in head-to-head comparisons. The generality of the phenomenon, demonstrated here with a number of substrates, stimulates analogies to enzymatic catalysts that produce naturally occurring macrocycles, presumably through related, catalyst-defined peripheral interactions with their acyclic substrates.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"44 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85544374","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 : 2021-05-03DOI: 10.1101/2021.05.02.442297
Logan Chariker, R. Shapley, M. Hawken, L. Young
Significance Motion perception is important for primates, and direction selectivity (DS), the ability to perceive the direction a target is moving, is an essential part of motion perception. Yet no satisfactory mechanistic explanation has been proposed for the origin of DS in the primate visual cortex up until now. In this paper, we hypothesize that DS is initiated in feed-forward LGN input as a result of the dynamic differences between the ON and OFF pathways. The mechanisms we propose are biology based, and our theory explains experimental data for all spatial and temporal frequencies in visual stimuli. Exploiting temporal biases in parallel pathways is relevant beyond visual neuroscience; similar ideas likely apply to other types of neural signal processing. This paper offers a theory for the origin of direction selectivity (DS) in the macaque primary visual cortex, V1. DS is essential for the perception of motion and control of pursuit eye movements. In the macaque visual pathway, neurons with DS first appear in V1, in the Simple cell population of the Magnocellular input layer 4Cα. The lateral geniculate nucleus (LGN) cells that project to these cortical neurons, however, are not direction selective. We hypothesize that DS is initiated in feed-forward LGN input, in the summed responses of LGN cells afferent to a cortical cell, and it is achieved through the interplay of 1) different visual response dynamics of ON and OFF LGN cells and 2) the wiring of ON and OFF LGN neurons to cortex. We identify specific temporal differences in the ON/OFF pathways that, together with item 2, produce distinct response time courses in separated subregions; analysis and simulations confirm the efficacy of the mechanisms proposed. To constrain the theory, we present data on Simple cells in layer 4Cα in response to drifting gratings. About half of the cells were found to have high DS, and the DS was broadband in spatial and temporal frequency (SF and TF). The proposed theory includes a complete analysis of how stimulus features such as SF and TF interact with ON/OFF dynamics and LGN-to-cortex wiring to determine the preferred direction and magnitude of DS.
{"title":"A theory of direction selectivity for macaque primary visual cortex","authors":"Logan Chariker, R. Shapley, M. Hawken, L. Young","doi":"10.1101/2021.05.02.442297","DOIUrl":"https://doi.org/10.1101/2021.05.02.442297","url":null,"abstract":"Significance Motion perception is important for primates, and direction selectivity (DS), the ability to perceive the direction a target is moving, is an essential part of motion perception. Yet no satisfactory mechanistic explanation has been proposed for the origin of DS in the primate visual cortex up until now. In this paper, we hypothesize that DS is initiated in feed-forward LGN input as a result of the dynamic differences between the ON and OFF pathways. The mechanisms we propose are biology based, and our theory explains experimental data for all spatial and temporal frequencies in visual stimuli. Exploiting temporal biases in parallel pathways is relevant beyond visual neuroscience; similar ideas likely apply to other types of neural signal processing. This paper offers a theory for the origin of direction selectivity (DS) in the macaque primary visual cortex, V1. DS is essential for the perception of motion and control of pursuit eye movements. In the macaque visual pathway, neurons with DS first appear in V1, in the Simple cell population of the Magnocellular input layer 4Cα. The lateral geniculate nucleus (LGN) cells that project to these cortical neurons, however, are not direction selective. We hypothesize that DS is initiated in feed-forward LGN input, in the summed responses of LGN cells afferent to a cortical cell, and it is achieved through the interplay of 1) different visual response dynamics of ON and OFF LGN cells and 2) the wiring of ON and OFF LGN neurons to cortex. We identify specific temporal differences in the ON/OFF pathways that, together with item 2, produce distinct response time courses in separated subregions; analysis and simulations confirm the efficacy of the mechanisms proposed. To constrain the theory, we present data on Simple cells in layer 4Cα in response to drifting gratings. About half of the cells were found to have high DS, and the DS was broadband in spatial and temporal frequency (SF and TF). The proposed theory includes a complete analysis of how stimulus features such as SF and TF interact with ON/OFF dynamics and LGN-to-cortex wiring to determine the preferred direction and magnitude of DS.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82975810","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 : 2021-04-26DOI: 10.1130/abs/2020am-357068
Gwen S. Antell, Isabel S. Fenton, P. Valdes, E. Saupe
Significance We examined the degree to which temperature tolerances changed on 8,000-y timescales across 700,000 y of glacial–interglacial climate change. We coupled a new fossil occurrence database of planktonic foraminifera, an abundant type of zooplankton, with Atmosphere–Ocean Global Circulation Model reconstructions of past climates. Our suite of analyses demonstrated that foraminiferal species have not shifted their temperature tolerances in response to glacial cycles; species occupied the same temperature conditions regardless of the magnitude of global temperature change. The limited tendency of planktonic foraminifera to change their tolerances suggests that ongoing global change could hasten local or global extinctions of plankton and other widely dispersing marine species. Abiotic niche lability reduces extinction risk by allowing species to adapt to changing environmental conditions in situ. In contrast, species with static niches must keep pace with the velocity of climate change as they track suitable habitat. The rate and frequency of niche lability have been studied on human timescales (months to decades) and geological timescales (millions of years), but lability on intermediate timescales (millennia) remains largely uninvestigated. Here, we quantified abiotic niche lability at 8-ka resolution across the last 700 ka of glacial–interglacial climate fluctuations, using the exceptionally well-known fossil record of planktonic foraminifera coupled with Atmosphere–Ocean Global Climate Model reconstructions of paleoclimate. We tracked foraminiferal niches through time along the univariate axis of mean annual temperature, measured both at the sea surface and at species’ depth habitats. Species’ temperature preferences were uncoupled from the global temperature regime, undermining a hypothesis of local adaptation to changing environmental conditions. Furthermore, intraspecific niches were equally similar through time, regardless of climate change magnitude on short timescales (8 ka) and across contrasts of glacial and interglacial extremes. Evolutionary trait models fitted to time series of occupied temperature values supported widespread niche stasis above randomly wandering or directional change. Ecotype explained little variation in species-level differences in niche lability after accounting for evolutionary relatedness. Together, these results suggest that warming and ocean acidification over the next hundreds to thousands of years could redistribute and reduce populations of foraminifera and other calcifying plankton, which are primary components of marine food webs and biogeochemical cycles.
{"title":"Thermal niches of planktonic foraminifera are static throughout glacial–interglacial climate change","authors":"Gwen S. Antell, Isabel S. Fenton, P. Valdes, E. Saupe","doi":"10.1130/abs/2020am-357068","DOIUrl":"https://doi.org/10.1130/abs/2020am-357068","url":null,"abstract":"Significance We examined the degree to which temperature tolerances changed on 8,000-y timescales across 700,000 y of glacial–interglacial climate change. We coupled a new fossil occurrence database of planktonic foraminifera, an abundant type of zooplankton, with Atmosphere–Ocean Global Circulation Model reconstructions of past climates. Our suite of analyses demonstrated that foraminiferal species have not shifted their temperature tolerances in response to glacial cycles; species occupied the same temperature conditions regardless of the magnitude of global temperature change. The limited tendency of planktonic foraminifera to change their tolerances suggests that ongoing global change could hasten local or global extinctions of plankton and other widely dispersing marine species. Abiotic niche lability reduces extinction risk by allowing species to adapt to changing environmental conditions in situ. In contrast, species with static niches must keep pace with the velocity of climate change as they track suitable habitat. The rate and frequency of niche lability have been studied on human timescales (months to decades) and geological timescales (millions of years), but lability on intermediate timescales (millennia) remains largely uninvestigated. Here, we quantified abiotic niche lability at 8-ka resolution across the last 700 ka of glacial–interglacial climate fluctuations, using the exceptionally well-known fossil record of planktonic foraminifera coupled with Atmosphere–Ocean Global Climate Model reconstructions of paleoclimate. We tracked foraminiferal niches through time along the univariate axis of mean annual temperature, measured both at the sea surface and at species’ depth habitats. Species’ temperature preferences were uncoupled from the global temperature regime, undermining a hypothesis of local adaptation to changing environmental conditions. Furthermore, intraspecific niches were equally similar through time, regardless of climate change magnitude on short timescales (8 ka) and across contrasts of glacial and interglacial extremes. Evolutionary trait models fitted to time series of occupied temperature values supported widespread niche stasis above randomly wandering or directional change. Ecotype explained little variation in species-level differences in niche lability after accounting for evolutionary relatedness. Together, these results suggest that warming and ocean acidification over the next hundreds to thousands of years could redistribute and reduce populations of foraminifera and other calcifying plankton, which are primary components of marine food webs and biogeochemical cycles.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"93 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83212107","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 : 2021-04-24DOI: 10.1101/2021.04.24.441237
Anna Katharina Schlusche, S. Vay, N. Kleinenkuhnen, S. Sandke, R. Campos-Martin, Marta Florio, W. Huttner, A. Tresch, J. Roeper, M. A. Rueger, I. Jakovcevski, M. Stockebrand, D. Isbrandt
Significance Impaired cell cycle regulation of neural stem and progenitor cells can affect cortical development and cause microcephaly. During cell cycle progression, the cellular membrane potential changes through ion channel activity and tends to be more depolarized in proliferating cells. Hyperpolarization-activated cyclic nucleotide-gated cation (HCN) channels, which mediate a depolarizing current in neurons and cardiac cells, are linked to neurodevelopmental diseases and also contribute to the control of cell cycle progression and proliferation of neuronal precursor cells. In this study, HCN channel deficiency during embryonic brain development resulted in marked microcephaly of mice with impaired HCN channel function in dorsal forebrain progenitors. The findings suggest that HCN channel subunits are part of a general mechanism influencing cortical development in mammals. The development of the cerebral cortex relies on the controlled division of neural stem and progenitor cells. The requirement for precise spatiotemporal control of proliferation and cell fate places a high demand on the cell division machinery, and defective cell division can cause microcephaly and other brain malformations. Cell-extrinsic and -intrinsic factors govern the capacity of cortical progenitors to produce large numbers of neurons and glia within a short developmental time window. In particular, ion channels shape the intrinsic biophysical properties of precursor cells and neurons and control their membrane potential throughout the cell cycle. We found that hyperpolarization-activated cyclic nucleotide-gated cation (HCN) channel subunits are expressed in mouse, rat, and human neural progenitors. Loss of HCN channel function in rat neural stem cells impaired their proliferation by affecting the cell-cycle progression, causing G1 accumulation and dysregulation of genes associated with human microcephaly. Transgene-mediated, dominant-negative loss of HCN channel function in the embryonic mouse telencephalon resulted in pronounced microcephaly. Together, our findings suggest a role for HCN channel subunits as a part of a general mechanism influencing cortical development in mammals.
{"title":"Developmental HCN channelopathy results in decreased neural progenitor proliferation and microcephaly in mice","authors":"Anna Katharina Schlusche, S. Vay, N. Kleinenkuhnen, S. Sandke, R. Campos-Martin, Marta Florio, W. Huttner, A. Tresch, J. Roeper, M. A. Rueger, I. Jakovcevski, M. Stockebrand, D. Isbrandt","doi":"10.1101/2021.04.24.441237","DOIUrl":"https://doi.org/10.1101/2021.04.24.441237","url":null,"abstract":"Significance Impaired cell cycle regulation of neural stem and progenitor cells can affect cortical development and cause microcephaly. During cell cycle progression, the cellular membrane potential changes through ion channel activity and tends to be more depolarized in proliferating cells. Hyperpolarization-activated cyclic nucleotide-gated cation (HCN) channels, which mediate a depolarizing current in neurons and cardiac cells, are linked to neurodevelopmental diseases and also contribute to the control of cell cycle progression and proliferation of neuronal precursor cells. In this study, HCN channel deficiency during embryonic brain development resulted in marked microcephaly of mice with impaired HCN channel function in dorsal forebrain progenitors. The findings suggest that HCN channel subunits are part of a general mechanism influencing cortical development in mammals. The development of the cerebral cortex relies on the controlled division of neural stem and progenitor cells. The requirement for precise spatiotemporal control of proliferation and cell fate places a high demand on the cell division machinery, and defective cell division can cause microcephaly and other brain malformations. Cell-extrinsic and -intrinsic factors govern the capacity of cortical progenitors to produce large numbers of neurons and glia within a short developmental time window. In particular, ion channels shape the intrinsic biophysical properties of precursor cells and neurons and control their membrane potential throughout the cell cycle. We found that hyperpolarization-activated cyclic nucleotide-gated cation (HCN) channel subunits are expressed in mouse, rat, and human neural progenitors. Loss of HCN channel function in rat neural stem cells impaired their proliferation by affecting the cell-cycle progression, causing G1 accumulation and dysregulation of genes associated with human microcephaly. Transgene-mediated, dominant-negative loss of HCN channel function in the embryonic mouse telencephalon resulted in pronounced microcephaly. Together, our findings suggest a role for HCN channel subunits as a part of a general mechanism influencing cortical development in mammals.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83222844","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 : 2021-04-23DOI: 10.1101/2021.04.23.441023
Pablo J. Lituma, E. Woo, B. O’Hara, P. Castillo, N. Sibinga, Sayan Nandi
Significance Abnormal microglia–neuron interaction is increasingly implicated in neurodevelopmental and neuropsychiatric conditions, such as autism spectrum disorders and schizophrenia, as well as in neurodegenerative disorders, such as Alzheimer’s disease. This study demonstrates that the deletion of the microglia-specific protein Iba1, which has long been utilized as a selective microglial marker but whose role has remained unidentified, results in microglial structural and functional impairments that significantly impact synaptic development and behavior. These findings not only highlight the importance of microglia in brain function but may also suggest that modifying the microglial function could provide a therapeutic strategy for the treatment of neurodevelopmental, neuropsychiatric, and neurodegenerative disorders. Growing evidence indicates that microglia impact brain function by regulating synaptic pruning and formation as well as synaptic transmission and plasticity. Iba1 (ionized Ca+2-binding adapter protein 1), encoded by the Allograft inflammatory factor 1 (Aif1) gene, is an actin-interacting protein in microglia. Although Iba1 has long been used as a cellular marker for microglia, its functional role remains unknown. Here, we used global, Iba1-deficient (Aif1−/−) mice to characterize microglial activity, synaptic function, and behavior. Microglial imaging in acute hippocampal slices and fixed tissues from juvenile mice revealed that Aif1−/− microglia display reductions in ATP-induced motility and ramification, respectively. Biochemical assays further demonstrated that Aif1−/− brain tissues exhibit an altered expression of microglial-enriched proteins associated with synaptic pruning. Consistent with these changes, juvenile Aif1−/− mice displayed deficits in the excitatory synapse number and synaptic drive assessed by neuronal labeling and whole-cell patch-clamp recording in acute hippocampal slices. Unexpectedly, microglial synaptic engulfment capacity was diminished in juvenile Aif1−/− mice. During early postnatal development, when synapse formation is a predominant event in the hippocampus, the excitatory synapse number was still reduced in Aif1−/− mice. Together, these findings support an overall role of Iba1 in excitatory synaptic growth in juvenile mice. Lastly, postnatal synaptic deficits persisted in adulthood and correlated with significant behavioral changes in adult Aif1−/− mice, which exhibited impairments in object recognition memory and social interaction. These results suggest that Iba1 critically contributes to microglial activity underlying essential neuroglia developmental processes that may deeply influence behavior.
{"title":"Altered synaptic connectivity and brain function in mice lacking microglial adapter protein Iba1","authors":"Pablo J. Lituma, E. Woo, B. O’Hara, P. Castillo, N. Sibinga, Sayan Nandi","doi":"10.1101/2021.04.23.441023","DOIUrl":"https://doi.org/10.1101/2021.04.23.441023","url":null,"abstract":"Significance Abnormal microglia–neuron interaction is increasingly implicated in neurodevelopmental and neuropsychiatric conditions, such as autism spectrum disorders and schizophrenia, as well as in neurodegenerative disorders, such as Alzheimer’s disease. This study demonstrates that the deletion of the microglia-specific protein Iba1, which has long been utilized as a selective microglial marker but whose role has remained unidentified, results in microglial structural and functional impairments that significantly impact synaptic development and behavior. These findings not only highlight the importance of microglia in brain function but may also suggest that modifying the microglial function could provide a therapeutic strategy for the treatment of neurodevelopmental, neuropsychiatric, and neurodegenerative disorders. Growing evidence indicates that microglia impact brain function by regulating synaptic pruning and formation as well as synaptic transmission and plasticity. Iba1 (ionized Ca+2-binding adapter protein 1), encoded by the Allograft inflammatory factor 1 (Aif1) gene, is an actin-interacting protein in microglia. Although Iba1 has long been used as a cellular marker for microglia, its functional role remains unknown. Here, we used global, Iba1-deficient (Aif1−/−) mice to characterize microglial activity, synaptic function, and behavior. Microglial imaging in acute hippocampal slices and fixed tissues from juvenile mice revealed that Aif1−/− microglia display reductions in ATP-induced motility and ramification, respectively. Biochemical assays further demonstrated that Aif1−/− brain tissues exhibit an altered expression of microglial-enriched proteins associated with synaptic pruning. Consistent with these changes, juvenile Aif1−/− mice displayed deficits in the excitatory synapse number and synaptic drive assessed by neuronal labeling and whole-cell patch-clamp recording in acute hippocampal slices. Unexpectedly, microglial synaptic engulfment capacity was diminished in juvenile Aif1−/− mice. During early postnatal development, when synapse formation is a predominant event in the hippocampus, the excitatory synapse number was still reduced in Aif1−/− mice. Together, these findings support an overall role of Iba1 in excitatory synaptic growth in juvenile mice. Lastly, postnatal synaptic deficits persisted in adulthood and correlated with significant behavioral changes in adult Aif1−/− mice, which exhibited impairments in object recognition memory and social interaction. These results suggest that Iba1 critically contributes to microglial activity underlying essential neuroglia developmental processes that may deeply influence behavior.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81660040","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}