bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell-to-cell heterogeneity drives host-virus coexistence in a bloom-forming alga
Authors: Joffe Nir , Kuhlisch Constanze , Schleyer Guy , Ahlers Nadia Samira , Shemi Adva , Vardi Assaf 
Published: October 2023

AbstractAlgal blooms drive global biogeochemical cycles of key nutrients in the oceans and serve as hotspots for biological interactions. The massive spring blooms of the cosmopolitan coccolithophoreEmiliania huxleyi (E. huxleyi)are often infected by the lyticEmiliania huxleyispecific virus (EhV) which is a major mortality agent triggering bloom demise. Nonetheless, the multi-annual “boom and bust” pattern ofE. huxleyisuggests that mechanisms of coexistence are essential for these host-virus dynamics. To investigate host-virus coexistence, we developed a new model system from anE. huxleyiculture which recovered from viral infection. The recovered population coexists with the virus, as host cells continue to grow in parallel to viral production. By applying a single-molecule fluorescencein situhybridization (smFISH) approach to quantify the fraction of infected cells and assessing infection-specific lipid biomarkers, we identified a small subpopulation (5-7% of cells) that was infected and produced new virions, whereas the majority of the host population could resist infection. To further assess population heterogeneity, we generated monoclonal strain collections using single-cell sorting and subsequently phenotyped their susceptibility to EhV infection. This unraveled a substantial cell-to-cell heterogeneity across a continuum of susceptibility to resistance, suggesting that infection outcomes may vary depending on the individual cell. These results add a new dimension to our understanding of the complexity of host-virus interactions that are commonly assessed in bulk and described by binary definitions of resistance or susceptibility. We propose that phenotypic heterogeneity drivesE. huxleyi-EhV coexistence and may potentially provide the coexisting strain an ecological advantage by killing competing susceptible strains.
CRISPR Screening in Tandem with Targeted mtDNA Damage Reveals WRNIP1 Essentiality
Authors: Sack Tanja , Dhavarasa Piriththiv , Szames Daniel , O’Brien Siobhan , Angers Stephane , Kelley Shana O. 
Published: October 2023

AbstractA major impediment to the characterization of mtDNA repair mechanisms, in comparison to nuclear DNA repair mechanisms, is the difficulty of specifically addressing mitochondrial damage. Using a mitochondria-penetrating peptide, we can deliver DNA-damaging agents directly to mitochondria, bypassing the nuclear compartment. Here, we describe the use of a mtDNA-damaging agent in tandem with CRISPR/Cas9 screening for the genome-wide discovery of factors essential for mtDNA damage response. Using mitochondria-targeted doxorubicin (mtDox) we generate mtDNA double-strand breaks (mtDSBs) specifically in this organelle. Combined with an untargeted Dox screen, we identify genes with significantly greater essentiality during mitochondrial versus nuclear DNA damage. We characterize the essentially of our top hit - WRNIP1 - observed here for the first time to respond to mtDNA damage. We further investigate the mitochondrial role of WRNIP1 in innate immune signaling and nuclear genome maintenance, outlining a model that experimentally supports mitochondrial turnover in response to mtDSBs.
MFSD7c functions as a transporter of choline at the blood-brain barrier
Authors: Nguyen Xuan T.A. , Le Thanh Nha Uyen , Ha Hoa Thi Thuy , Nguyen Toan Q. , Artati Anna , Leong Nancy C.P. , Nguyen Dat T. , Lim Pei Yen , Susanto Adelia Vicanatalita , Qianhui Huang , Ling Fam , Ngah Leong Lo , Bonne Isabelle , Lee Angela , Gooch Catherine , Luque Jorge Luis Granadillo De , Yu Dejie , Hua Huang , Soong Tuck Wah , Chang Matthew Wook , Wenk Markus R. , Adamski Jerzy , Cazenave-Gassiot Amaury , Nguyen Long N. 
Published: October 2023

AbstractMutations of MFSD7c (also known asFlvcr2), which is an orphan transporter, are linked to Fowler syndrome1, 2. Here, we useMfsd7cknockout mice and cell-based assays to reveal that MFSD7c is a choline transporter at the blood-brain barrier (BBB). We performed comprehensive metabolomics and detected differential changes of metabolites in the brains and livers ofMfsd7cknockout (Mfsd7c−/−) embryos. Particularly, we found that choline-related metabolites were altered in the brains but not in the livers ofMfsd7c−/−embryos. Thus, we hypothesized that MFSD7c regulates the levels of choline in the brain. Indeed, expression of humanMFSD7cin cells significantly increased choline uptake. Interestingly, we showed that choline uptake byMFSD7cis greatly increased by choline-metabolizing enzymes, leading us to demonstrate that MFSD7c is a facilitative transporter of choline. Furthermore, single-cell patch-clamp showed that the import of choline by MFSD7c is electrogenic. Choline transport function of MFSD7c is conserved in vertebrates, but not in yeasts. We show that human MFSD7c is a functional ortholog of HNM1, the yeast choline importer. Employing our transport assays, we showed that several missense mutations of humanMFSD7cfrom Fowler patients had abolished or reduced choline transport activity. Mice lackingMfsd7cin the CNS endothelial cells suppressed the import of exogenous choline from blood but unexpectedly had increased choline levels in the brain. Stable-isotope tracing study revealed that MFSD7c is required for exporting choline derived from lysophosphatidylcholine (LPC) in the brain. Collectively, our work identifies MFSD7c as a choline transporter at the BBB. This study suggests that defective export of choline in the brain may be a cause of Fowler syndrome.
Virological characteristics correlating with SARS-CoV-2 spike protein fusogenicity
Authors: Begum MST Monira , Ichihara Kimiko , Takahashi Otowa , Nasser Hesham , Jonathan Michael , Tokunaga Kenzo , Yoshida Isao , Nagashima Mami , Sadamasu Kenji , Yoshimura Kazuhisa ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium, Sato Kei , Ikeda Terumasa 
Published: October 2023

AbstractThe severe acute respiratory syndrome coronavirus (SARS-CoV-2) spike (S) protein is essential in mediating membrane fusion of the virus with the target cells. Several reports demonstrated that SARS-CoV-2 S protein fusogenicity is reportedly closely associated with the intrinsic pathogenicity of the virus determined using hamster models. However, the association between S protein fusogenicity and other virological parameters remains elusive. In this study, we investigated the virological parameters of eleven previous variants of concern (VOCs) and variants of interest (VOIs) correlating with S protein fusogenicity. S protein fusogenicity was found to be strongly correlated with S1/S2 cleavage efficiency and plaque size formed by clinical isolates. However, S protein fusogenicity was less associated with pseudoviral infectivity, pseudovirus entry efficiency, and viral replication kinetics. Taken together, our results suggest that S1/S2 cleavage efficiency and plaque size could be potential indicators to predict the intrinsic pathogenicity of newly emerged SARS-CoV-2 variants.
Engineering ofSalmonellaphages into novel antimicrobial Tailocins
Authors: Woudstra Cedric , Sørensen Anders Nørgaard , Brøndsted Lone 
Published: October 2023

AbstractDue to the extensive use of antibiotics, the increase of infections caused by antibiotic resistant bacteria are now a global health concern. Phages have proven useful for treating bacterial infections and represent a promising alternative or complement to antibiotic treatment. Yet, other alternative exists, such as bacteria-produced non-replicative protein complexes that can kill their targeted bacteria by puncturing their membrane (Tailocins). To expand the repertoire of Tailocins available, we suggest a new approach transforming phages into Tailocins. Here we genetically engineered the virulentAckermannviridaephage S117, as well as temperate phages Fels-1, -2 and Gifsy-1 and -2 targeting the food pathogenSalmonella, by deleting theportal vertexormajor capsidgene using CRISPR-Cas9. We report the production of Tailocin particles from engineered virulent and temperate phages able to kill their native host. Our work represents a steppingstone to tape into the huge diversity of phages and transform them into versatile puncturing new antimicrobials.
Developmental conversion of thymocyte-attracting cells into self-antigen-displaying cells in embryonic thymus medulla epithelium
Authors: Ohigashi Izumi , White Andrea J. , Yang Mei-Ting , Fujimori Sayumi , Tanaka Yu , Jacques Alison , Kiyonari Hiroshi , Matsushita Yosuke , Turan Sevilay , Kelly Michael C. , Anderson Graham , Takahama Yousuke 
Published: October 2023

AbstractThymus medulla epithelium establishes immune self-tolerance and comprises diverse cellular subsets. Functionally relevant medullary thymic epithelial cells (mTECs) include a self-antigen-displaying subset that exhibits genome-wide promiscuous gene expression promoted by the nuclear protein Aire and that resembles a mosaic of extrathymic cells including mucosal tuft cells. An additional mTEC subset produces the chemokine CCL21, thereby attracting positively selected thymocytes from the cortex to the medulla. Both self-antigen-displaying and thymocyte-attracting mTEC subsets are essential for self-tolerance. Here we identify a developmental pathway by which mTECs gain their diversity in functionally distinct subsets. We show that CCL21-expressing mTECs arise early during thymus ontogeny. Fate-mapping analysis reveals that self-antigen-displaying mTECs, including Aire-expressing mTECs and thymic tuft cells, are derived from CCL21-expressing cells. The differentiation capability of CCL21-expressing embryonic mTECs is verified in reaggregate thymus experiments. These results indicate that CCL21-expressing embryonic mTECs carry a developmental potential to give rise to self-antigen-displaying mTECs, revealing that the sequential conversion of thymocyte-attracting subset into self-antigen-displaying subset serves to assemble functional diversity in the thymus medulla epithelium.
Targeting the Hippo pathway in cancers via ubiquitination dependent TEAD degradation
Authors: Pham Trang H. , Pahuja Kanika Bajaj , Hagenbeek Thijs J. , Zbieg Jason , Noland Cameron L. , Pham Victoria C. , Yao Xiaosai , Rose Christopher M. , Browder Kristen C. , Lee Ho-June , Yu Mamie , Liang-Chu May , Martin Scott , Verschueren Erik , Li Jason , Kubala Marta H. , Fong Rina , Lorenzo Maria , Beroza Paul , Hsu Peter , Paul Sayantanee , Villemure Elisia , Lee Wendy , Cheung Tommy K. , Clausen Saundra , Lacap Jennifer , Liang Yuxin , Cheng Jason , Schmidt Steve , Modrusan Zora , Cohen Michael , Crawford James , Jasper Heinrich , Ashworth Alan , Lill Jennie R. , Malek Shiva , Rudolph Joachim , Wertz Ingrid E. , Chang Matthew T. , Ye Xin , Dey Anwesha 
Published: October 2023

ABSTRACTThe Hippo pathway is among the most frequently altered key signaling pathways in cancer. TEAD1-4 are essential transcription factors and key downstream effectors in the Hippo pathway in human cells. Here, we identified RNF146 as a ubiquitin ligase (E3) of TEADs, which negatively regulates their stability in cells through proteasome-mediated degradation. We show that RNF146-mediated TEAD ubiquitination is dependent on the TEAD PARylation state. We further validated the genetic interaction between RNF146 and the Hippo pathway in cancer cell lines and the model organismDrosophila melanogaster.Despite the RNF146 and proteasome-mediated degradation mechanisms, TEADs are stable proteins with a long half-life in cells. We demonstrate that degradation of TEADs can be greatly enhanced pharmacologically with heterobifunctional chemical inducers of protein degradation (CIDEs). These TEAD-CIDEs can effectively suppress activation of YAP/TAZ target genes in a dose-dependent manner and exhibit significant anti-proliferative effects in YAP/TAZ-dependent tumor cells, thus phenocopying the effect of genetic ablation of TEAD protein. Collectively, this study demonstrates that the ubiquitin-proteasome system plays an important role in regulating TEAD functions and provides a proof-of-concept demonstration that pharmacologically induced TEAD ubiquitination could be leveraged to target YAP/TAZ-driven cancers.
Programming dynamic division of labor using horizontal gene transfer
Authors: Hamrick Grayson S. , Maddamsetti Rohan , Son Hye-In , Wilson Maggie L. , Davis Harris M. , You Lingchong 
Published: October 2023

AbstractThe metabolic engineering of microbes has broad applications, including in biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multi-step pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is division of labor (DOL), in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted inter-strain population dynamics. Through modeling, we show that dynamic division of labor (DDOL) mediated by horizontal gene transfer (HGT) can overcome these limitations and enable the robust maintenance of burdensome, multi-step pathways. We also use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.
Backbone extension acyl rearrangements enable cellular synthesis of proteins with internal β2-peptide linkages
Authors: Roe Leah T. , Schissel Carly K. , Dover Taylor L. , Shah Bhavana , Hamlish Noah X. , Zheng Shuai , Dilworth Diondra A. , Wong Nicole , Zhang Zhongqi , Chatterjee Abhishek , Francis Matthew B. , Miller Scott J. , Schepartz Alanna 
Published: October 2023

AbstractProteins and polypeptides containing extended backbone monomers embody highly desirable structures and functions, but they cannot yet be biosynthesized in cells. There are two challenges at work. First is the ribosome, whose ability to promote rapid bond-forming reactions to and from anything other than an α-amino acid or α-hydroxy acid is unknown. The second challenge is the absence of orthogonal enzymes that acylate tRNA with extended backbone monomers. Here we describe a general approach to the programmed cellular synthesis of proteins containing extended backbone monomers that circumvents both of these challenges. Rather than relying on direct and uncharacterized reactions of non-α-amino acid monomers within the ribosomal PTC, we develop a proximity-guided intramolecular rearrangement that effectively edits the protein backbone post-translationally. The method relies on the ability of PylRS-like aminoacyl-tRNA synthetase enzymes to accept diverse α-hydroxy acid monomers, including those whose side chains contain masked nucleophiles. Introduction of such an α-hydroxy acid monomer into a protein translatedin vivo, followed by nucleophile unmasking, sets up a thermodynamically favored and quantitative intramolecular Backbone Extension Acyl Rearrangement (BEAR) reaction that edits the protein backbone to install an extended backbone monomer. In the examples described here, the intramolecular rearrangement converts an α-peptide backbone directly into a β-backbone. As far as we know, this report represents the first example in which a much-desired expanded backbone β-amino acid linkage has been introduced site-selectively into a protein in a cell.
A dual-pathway architecture enables chronic stress to disrupt agency and promote habit formation
Authors: Giovanniello Jacqueline R. , Paredes Natalie , Wiener Anna , Ramírez-Armenta Kathia , Oragwam Chukwuebuka , Uwadia Hanniel O. , Yu Abigail L. , Lim Kayla , Pimenta Jenna S. , Vilchez Gabriela E. , Nnamdi Gift , Wang Alicia , Sehgal Megha , Reis Fernando MCV , Sias Ana C. , Silva Alcino J. , Adhikari Avishek , Malvaez Melissa , Wassum Kate M. 
Published: October 2023

ABSTRACTChronic stress can change how we learn and, thus, how we make decisions. Here we investigated the neuronal circuit mechanisms that enable this. Using a multifaceted systems neuroscience approach in male and female mice, we reveal a dual pathway, amygdala-striatal neuronal circuit architecture by which a recent history of chronic stress disrupts the action-outcome learning underlying adaptive agency and promotes the formation of inflexible habits. We found that the basolateral amygdala projection to the dorsomedial striatum is activated by rewarding events to support the action-outcome learning needed for flexible, goal-directed decision making. Chronic stress attenuates this to disrupt action-outcome learning and, therefore, agency. Conversely, the central amygdala projection to the dorsomedial striatum mediates habit formation. Following stress this pathway is progressively recruited to learning to promote the premature formation of inflexible habits. Thus, stress exerts opposing effects on two amygdala-striatal pathways to disrupt agency and promote habit. These data provide neuronal circuit insights into how chronic stress shapes learning and decision making, and help understand how stress can lead to the disrupted decision making and pathological habits that characterize substance use disorders and mental health conditions.
A DRP-like pseudoenzyme coordinates with MICOS to promote cristae architecture
Authors: Kumar Abhishek , Gok Mehmet Oguz , Nguyen Kailey N. , Reese Michael L. , Wideman Jeremy G. , Muñoz-Gómez Sergio A. , Friedman Jonathan R. 
Published: October 2023

AbstractMitochondrial cristae architecture is crucial for optimal respiratory function of the organelle. Cristae shape is maintained in part by the mitochondrial inner membrane-localized MICOS complex. While MICOS is required for normal cristae morphology, the precise mechanistic role of each of the seven human MICOS subunits, and how the complex coordinates with other cristae shaping factors, has not been fully determined. Here, we examine the MICOS complex inSchizosaccharomyces pombe, a minimal model whose genome only encodes for four core subunits. Using an unbiased proteomics approach, we identify a poorly characterized inner mitochondrial membrane protein that interacts with MICOS and is required to maintain cristae morphology, which we name Mmc1. We demonstrate that Mmc1 works in concert with MICOS complexes to promote normal mitochondrial morphology and respiratory function. Bioinformatic analyses reveal that Mmc1 is a distant relative of the Dynamin-Related Protein (DRP) family of GTPases, which are well established to shape and remodel membranes. We find that, like DRPs, Mmc1 self-associates and forms high molecular weight assemblies. Interestingly, however, Mmc1 is a pseudoenzyme that lacks key residues required for GTP binding and hydrolysis, suggesting it does not dynamically remodel membranes. These data are consistent with a model in which Mmc1 stabilizes cristae architecture by acting as a scaffold to support cristae ultrastructure on the matrix side of the inner membrane. Our study reveals a new class of proteins that evolved early in fungal phylogeny and is required for the maintenance of cristae architecture. This highlights the possibility that functionally analogous proteins work with MICOS to establish cristae morphology in metazoans.
Uterine secretome initiates growth of gynecologic tissues in ectopic locations
Authors: Sunde Jan , Wasickanin Morgan , Katz Tiffany A , Bidadi Sanam , O’Neil Derek , Burney Richard O , Pennington Kathleen A 
Published: October 2023

AbstractEndosalpingiosis (ES) and endometriosis (EM) refer to the growth of tubal and endometrial epithelium respectively, outside of their site of origin. We hypothesize that uterine secretome factors drive ectopic growth. To test this, we developed a mouse model of ES and EM using tdTomato (tdT) transgenic fluorescent mice as donors. To block implantation factors, progesterone knockout (PKO) tdT mice were created. Post-ovulatory endometrium was induced hormonally in donor tdT and wild-type (WT) female mice. tdT oviductal cells and WT endometrium were harvested for intraperitoneal injection into synchronized recipient WT mice. Ectopic lesions were identified using fluorescence in-vivo imaging and then harvested for histological evaluation. Fluorescent lesions were present after oviduct implantation with and without WT endometrium. Implantation was increased (p<0.05) when tdt oviductal tissue was implanted with endometrium compared to oviductal tissue alone. Implantation was reduced (p<0.0005) in animals implanted with minced tdT oviductal tissue with PKO tdT endometrium compared to WT endometrium. In conclusion, endometrial derived implantation factors are necessary to initiate ectopic tissue growth. We have developed an animal model of ectopic growth of gynecologic tissues in a WT mouse which will potentially allow for development of new prevention and treatment modalities.
Direct and indirect effects of fire on parasites in an African savanna
Authors: Donaldson Jason E. , Holdo Ricardo M. , Anderson T. Michael , Morrison Thomas A. , Hopcraft J. Grant C. , McIntyre Jennifer , Devaney Eileen , Hempson Gareth , Senso Basil , Trentinus Aidan , Ezenwa Vanessa O. 
Published: October 2023

Abstract

Fires in grassy ecosystems consume vegetation and initiate high‐quality regrowth, which results in pyric herbivory when mammalian grazers concentrate feeding in recent burns. For environmentally transmitted parasites with transmission mechanisms linked to vegetation structure, fire should exert direct effects on parasites, as well as indirect effects resulting from subsequent enhanced herbivory, which can affect parasite input and exposure to environmental conditions.

We combined an experimental manipulation with observational data in the Serengeti National Park to investigate the direct and indirect effects of fire on parasites. We assessed the direct effects of fire by measuring changes in parasitic nematode larvae in the grass layer before and after fire on paired experimental burned and control plots. To investigate indirect effects linked to pyric herbivory, we sampled herbivore dung, grass biomass, ground temperature and larval densities every month for 5 months following fire in seven pairs of burned and unburned monitoring plots. Finally, to assess if fire‐driven changes to larval densities affected host infection burdens, we collected faecal samples from a key host, Grant's gazelle (Nanger granti), each month for 5 months to estimate within‐host parasite burdens.

Fire killed all larvae and increased grazer dung inputs by 40% for 2 months following fire. Dung inputs after fire led to larval parasite recolonization of burned patches, but intense herbivory kept grass short and larval densities were associated with changes in ground temperature linked to grass biomass and ambient temperature. Grant's gazelles had lower parasite burdens when sampled in areas with higher compared to lower burned area fraction.

Fire and pyric herbivory change the densities of larval parasites in the environment and divide the landscape into burned and unburned regions with distinct infection risks for local herbivores.

The indirect effects quantified here represent a novel finding with major implications for all grazing systems impacted by fire.