bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tumor protein D54 binds intracellular nanovesicles via an amphipathic lipid packing sensor (ALPS) motif
Authors: Reynaud Antoine , Magdeleine Maud , Patel Amanda , Gay Anne Sophie , Debayle Delphine , Abelanet Sophie , Antonny Bruno 
Published: December 2021

AbstractTumor Protein D54 (TPD54) is an abundant cytosolic protein that belongs to the TPD52 family, a family of four proteins (TPD52, 53, 54 and 55) that are overexpressed in several cancer cells. Even though the functions of these proteins remain elusive, recent investigations indicate that TPD54 binds to very small cytosolic vesicles with a diameter of ca. 30 nm, half the size of classical transport vesicles (e.g. COPI and COPII). Here, we investigated the mechanism of intracellular nanovesicle capture by TPD54. Bioinformatical analysis suggests that TPD54 contains a small coiled-coil followed by several amphipathic helices, which could fold upon binding to lipid membranes. One of these helices has the physicochemical features of an Amphipathic Lipid Packing Sensor (ALPS) motif, which, in other proteins, enables membrane binding in a curvature-dependent manner. Limited proteolysis, CD spectroscopy, tryptophan fluorescence and cysteine mutagenesis coupled to covalent binding of a membrane sensitive probe show that binding of TPD54 to small liposomes is accompanied by large structural changes in the amphipathic helix region. TPD54 binding to artificial liposomes is very sensitive to liposome size and to lipid unsaturation but is poorly dependent on lipid charge. Cellular investigations confirmed the key role of the ALPS motif in vesicle targeting. Surprisingly, the vesicles selected by TPD54 poorly overlap with those captured by the golgin GMAP-210, a long vesicle tether at the Golgi apparatus, which displays a dimeric coiled-coil architecture and an N-terminal ALPS motif. We propose that TPD54 recognizes nanovesicles through a combination of ALPS-dependent and -independent mechanisms.
Magnetic particle imaging of magnetotactic bacteria as living contrast agents is improved by altering magnetosome structures
Authors: Makela Ashley V. , Schott Melissa A. , Madsen Cody , Greeson Emily , Contag Christopher H. 
Published: December 2021

ABSTRACTIron nanoparticles used as imaging contrast agents can help differentiate between normal and diseased tissue, or track cell movement and localize pathologies. Magnetic particle imaging (MPI) is an imaging modality that uses the magnetic properties of iron nanoparticles to provide specific, quantitative and sensitive imaging data. MPI signals depend on the size, structure and composition of the nanoparticles; MPI-tailored nanoparticles have been developed by modifying these properties. Magnetotactic bacteria produce magnetosomes which mimic synthetic nanoparticles, and thus comprise a living contrast agent in which nanoparticle formation can be modified by mutating genes. Specifically, genes that encode proteins critical to magnetosome formation and regulation, such as mamJ which helps with filament turnover. Deletion of mamJ in Magnetospirillum gryphiswaldense, MSR-1 led to clustered magnetosomes instead of the typical linear chains. Here we examined the effects of this magnetosome structure and revealed improved MPI signal and resolution from clustered magnetosomes compared to linear chains. Bioluminescent MSR-1 with the mamJ deletion were injected intravenously into tumor-bearing and healthy mice and imaged using both in vivo bioluminescence imaging (BLI) and MPI. BLI revealed the location and viability of bacteria which was used to validate localization of MPI signals. BLI identified the viability of MSR-1 for 24 hours and MPI detected iron in the liver and in multiple tumors. Development of living contrast agents offers new opportunities for imaging and therapy by using multimodality imaging to track the location and viability of the therapy and the resulting biological effects.
Death-associated protein kinase 3 (DAPK3) contributes to intestinal epithelial wound healing and the resolution of experimental colitis in mice
Authors: Chen Huey-Miin , Carlson David A. , Haystead Timothy A.J. , MacDonald Justin A. 
Published: December 2021

ABSTRACTVarious signaling molecules affecting epithelial restitution and wound healing are dysregulated in ulcerative colitis. Recent evidence demonstrates the necessity of Hippo-YAP/TAZ signaling, interceded by cytoskeletal remodeling, for intestinal regeneration. Death-associated protein kinase 3 (DAPK3) is a regulator of actin cytoskeleton reorganization that controls proliferation and apoptosis. Pharmacological inhibition of DAPK3 in Caco-2 human intestinal epithelial cells (IECs) with the HS38 compound augmented cell proliferation and enhanced wound closure. This phenotype corresponded with the increased colocalization of Yes-associated protein (YAP) with F-actin, which is indicative of YAP activation. The administration of HS38 impeded the resolution of intestinal injury and attenuated epithelial-specific proliferation after acute colitis induced by dextran-sodium-sulphate (DSS) in mice. During recovery from DSS-induced colitis, IEC proliferation was repressed, and mice exhibited increased disease severity when HS38 was applied to inhibit DAPK3. Moreover, HS38 treatment increased YAP nuclear localization in IECs, an indicator of signal activation. In summary, this study established DAPK3 as a key factor in intestinal epithelial regeneration and colitis progression by way of YAP signaling. Nevertheless, the role that DAPK3 play in different cell types will need further investigation to decipher the full consequence of DAPK3 inhibition on epithelial homeostasis.
Converting antimicrobial into targeting peptides reveals key features governing protein import into mitochondria and chloroplasts
Authors: Caspari Oliver D , Garrido Clotilde , Law Chris O , Choquet Yves , Wollman Francis-André , Lafontaine Ingrid 
Published: December 2021

SummaryWe asked what peptide features govern targeting to the mitochondria versus the chloroplast using antimicrobial peptides as a starting point. This approach was inspired by the endosymbiotic hypothesis that organelle-targeting peptides derive from antimicrobial amphipathic peptides delivered by the host cell, to which organelle progenitors became resistant. To explore the molecular changes required to convert antimicrobial into targeting peptides, we expressed a set of 13 antimicrobial peptides inChlamydomonas reinhardtii. Peptides were systematically modified to test distinctive features of mitochondrial and chloroplast targeting peptides, and we assessed their targeting potential by following the intracellular localization and maturation of a Venus fluorescent reporter used as cargo protein. Mitochondrial targeting can be achieved by some unmodified antimicrobial peptide sequences. Targeting to both organelles is improved by replacing Lysines with Arginines. Chloroplast targeting is enabled by the presence of flanking unstructured sequences, additional constraints consistent with chloroplast endosymbiosis having occurred in a cell that already contained mitochondria. If indeed targeting peptides evolved from antimicrobial peptides, required modifications imply a temporal evolutionary scenario with an early exchange of cationic residues, and a late acquisition of chloroplast specific motifs.
Host-Adapted Strains of Spodoptera frugiperda Hold and Share a Core Microbial Community Across the Western Hemisphere
Authors: Oliveira Nathalia C. , Rodrigues Pedro A.P. , Cônsoli Fernando L. 
Published: December 2021

AbstractThe fall armyworm Spodoptera frugiperda is an important polyphagous agricultural pest in the Western Hemisphere and currently invasive to countries of the Eastern Hemisphere. This species has two host-adapted strains named “rice” and “corn” strains. Our goal was to identify the occurrence of core members in the gut bacterial community of Fall armyworm larvae from distinct geographical distribution and/or host strain. We used next-generation sequencing to identify the microbial communities of S. frugiperda from corn fields in Brazil, Colombia, Mexico, Panama, Paraguay, and Peru, and rice fields from Panama. The larval gut microbiota of S. frugiperda larvae did not differ between the host strains neither was it affected by the geographical distribution of the populations investigated. Our findings provide additional support for Enterococcus and Pseudomonas as core members of the bacterial community associated with the larval gut of S. frugiperda, regardless of the site of collection or strain, suggesting that these bacteria may maintain true symbiotic relationships with the fall armyworm. Further investigations are required for a deeper understanding of the nature of this relationship.
Subfamily-specific differential contribution of individual monomers and the tether sequence to mouse L1 promoter activity
Authors: Kong Lingqi , Saha Karabi , Hu Yuchi , Tschetter Jada N. , Habben Chase E. , Whitmore Leanne S. , Yao Changfeng , Ge Xijin , Ye Ping , Newkirk Simon J. , An Wenfeng 
Published: December 2021

AbstractBackgroundThe internal promoter in L1 5’UTR is critical for autonomous L1 transcription and initiating retrotransposition. Unlike the human genome, which features one contemporarily active subfamily, four subfamilies (A_I, Gf_I and Tf_I/II) have been amplifying in the mouse genome in the last one million years. Moreover, mouse L1 5’UTRs are organized into tandem repeats called monomers, which are separated from ORF1 by a tether domain. In this study, we aim to compare promoter activities across young mouse L1 subfamilies and investigate the contribution of individual monomers and the tether sequence.ResultsWe observed an inverse relationship between subfamily age and the average number of monomers among evolutionarily young mouse L1 subfamilies. The youngest subgroup (A_I and Tf_I/II) on average carry 3-4 monomers in the 5’UTR. Using a single-vector dual-luciferase reporter assay, we compared promoter activities across six L1 subfamilies (A_I/II, Gf_I and Tf_I/II/III) and established their antisense promoter activities in a mouse embryonic fibroblast cell line. Using consensus promoter sequences for three subfamilies (A_I, Gf_I and Tf_I), we dissected the differential roles of individual monomers and the tether domain in L1 promoter activity. We validated that, across multiple subfamilies, the second monomer consistently enhances the overall promoter activity. For individual promoter components, monomer 2 is consistently more active than the corresponding monomer 1 and/or the tether for each subfamily. Importantly, we revealed intricate interactions between monomer 2, monomer 1 and tether domains in a subfamily-specific manner. Furthermore, using three-monomer 5’UTRs, we established a complex nonlinear relationship between the length of the outmost monomer and the overall promoter activity.ConclusionsThe laboratory mouse is an important mammalian model system for human diseases as well as L1 biology. Our study extends previous findings and represents an important step toward a better understanding of the molecular mechanism controlling mouse L1 transcription as well as L1’s impact on development and disease.
Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-β selection pre-T cells
Authors: Ratiu Jeremy J , Barclay William , Wang Qun , Mehta Naren , Harnois Melissa J , DiPalma Devon , Wellford Sebastian , Roy Sumedha , Contreras Alejandra V , Wiest David , Zhuang Yuan 
Published: December 2021

AbstractProduction of a diverse peripheral T cell compartment requires massive expansion of the bone marrow progenitors that seed the thymus. There are two main phases of expansion during T cell development, following T lineage commitment at the DN2 stage and following successful rearrangement and selection for functional TCRβ chains in DN3 thymocytes, which promotes development of DN4 cells to the DP stage. Signals driving expansion of DN2 thymocytes are well studied, however, factors regulating the proliferation and survival of DN4 cells remain poorly understood. Here, we uncover an unexpected link between the transcription factor Zfp335 and control of cGAS/STING-dependent cell death in post-β-selection DN4 thymocytes. Zfp335 controls survival by sustaining expression of Ankle2, which suppresses cGAS/STING-dependent cell death. Together, this study identifies Zfp335 as a key transcription factor controlling the survival of proliferating post-β-selection thymocytes and demonstrates a key role for the cGAS/STING pathway driving apoptosis of developing T cells.
Ecophysiological genomics identifies a pleiotropic locus mediating drought tolerance in sorghum
Authors: Maina Fanna , Harou Abdou , Hamidou Falalou , Morris Geoffrey P. 
Published: December 2021

ABSTRACTDrought is a key constraint on plant productivity and threat to food security. Sorghum (Sorghum bicolorL. Moench), a global staple food and forage crop, is among the most drought-adapted cereal crops, but its adaptation is not yet well understood. This study aims to better understand the genetic basis of preflowering drought in sorghum and identify loci underlying variation in water use and yield components under drought. A panel of 219 diverse sorghum from West Africa was phenotyped for yield components and water use in an outdoor large-tube lysimeter system under well-watered (WW) versus a preflowering drought water-stressed (WS) treatment. The experimental system was validated based on characteristic drought response in international drought tolerance check genotypes and genome-wide association studies (GWAS) that mapped the major height locus atQHT7.1andDw3. GWAS further identified marker trait associations (MTAs) for drought-related traits (plant height, flowering time, forage biomass, grain weight, water use) that each explained 7–70% of phenotypic variance. Most MTAs for drought-related traits correspond to loci not previously reported, but some MTA for forage biomass and grain weight under WS co-localized with staygreen post-flowering drought tolerance loci (Stg3aandStg4). A globally common allele at S7_50055849 is associated with several yield components under drought, suggesting that it tags a major pleiotropic variant controlling assimilate partitioning to grain versus vegetative biomass. The GWAS findings revealed oligogenic variants for drought tolerance in sorghum landraces which could be used as trait predictive markers for improved drought adaptation.
Plug and play: Is “directed endosymbiosis” of chloroplasts possible?
Authors: Shapiro Karin Olszewski 
Published: December 2021

AbstractThe origin of mammalian mitochondria and plant chloroplasts is thought to be endosymbiosis. Millennia ago, a bacterium related to typhus-causing bacteria may have been consumed by a proto-eukaryote and over time evolved into an organelle inside eukaryotic cells, known as a mitochondrion. The plant chloroplast is believed to have evolved in a similar fashion from cyanobacteria. This project attempted to use “directed endosymbiosis” (my term) to investigate if chloroplasts can be taken up by a land animal and continue to function. It has been shown previously that mouse fibroblasts could incorporate isolated chloroplasts when co-cultured. Photosynthetic bacteria containing chloroplasts have been successfully injected into zebrafish embryos, mammalian cells, and ischemic rodent hearts. The photosynthetic alga Chlamydomonas reinhardtii (C. reinhardtii) has also been injected into zebrafish embryos. However, to the best of my knowledge, injection of isolated chloroplasts into a land animal embryo has not been attempted before.In four pilot experiments, solutions of chloroplasts in PBS were microinjected into Drosophila melanogaster (D. melanogaster) embryos to determine if the embryos would tolerate the foreign protein. Interestingly, results indicated that a portion of the D. melanogaster embryos appeared to tolerate the injections and survive to adulthood. To determine if chloroplasts had indeed been transferred, larvae were placed under fluorescent microscopy. Chlorophyll (serving as the reporter) was found to be present in several larvae and to decline in amount over time. To investigate if the chloroplasts still functioned, a radiotracer food intake assay was performed. It was hypothesized that if the chloroplasts were generating ATP (and possibly glucose), the larvae might need less food. Results indicated a decrease in intake, however this might have occurred for other reasons.
Single cell profiling of Hofbauer cells and fetal brain microglia reveals shared programs and functions
Authors: Ceasrine Alexis M , Batorsky Rebecca , Shook Lydia L. , Kislal Sezen , Bordt Evan A. , Devlin Benjamin A. , Perlis Roy H. , Slonim Donna K. , Bilbo Staci D. , Edlow Andrea G. 
Published: December 2021

SummaryMaternal immune activation is associated with adverse offspring neurodevelopmental outcomes, many of which are mediated by in utero microglial programming. Microglia remain inaccessible at birth and throughout development, thus identification of noninvasive biomarkers that can reflect fetal brain microglial programming may permit screening and intervention during critical developmental windows. Here we used lineage tracing to demonstrate the shared ontogeny between fetal brain macrophages (microglia) and fetal placental macrophages (Hofbauer cells). Single-cell RNA sequencing of murine fetal brain and placental macrophages demonstrated shared transcriptional programs. Comparison with human datasets demonstrated that placental resident macrophage signatures are highly conserved between mice and humans. Single-cell RNA-seq identified sex differences in fetal microglial and Hofbauer cell programs, and robust differences between placenta-associated maternal macrophage/monocyte (PAMM) populations in the context of a male versus a female fetus. We propose that Hofbauer cells, which are easily accessible at birth, provide novel insights into fetal brain microglial programs, potentially facilitating the early identification of offspring most vulnerable to neurodevelopmental disorders.
A genome-wide CRISPR screen identifies the glycosylation enzyme DPM1 as a modifier of DPAGT1 deficiency and ER stress
Authors: Dalton Hans M. , Viswanatha Raghuvir , Brathwaite Ricky , Zuno Jae Sophia , Mohr Stephanie E. , Perrimon Norbert , Chow Clement Y. 
Published: December 2021

AbstractPartial loss-of-function mutations in glycosylation pathways underlie a set of rare diseases called Congenital Disorders of Glycosylation (CDGs). In particular, DPAGT1-CDG is caused by mutations in the gene encoding the first step in N-glycosylation, DPAGT1, and this disorder currently lacks effective therapies. To identify potential therapeutic targets for DPAGT1-CDG, we performed CRISPR knockout screens in Drosophila cells for genes associated with better survival and glycoprotein levels under DPAGT1 inhibition. We identified hundreds of candidate genes that may be of therapeutic benefit. Intriguingly, inhibition of the mannosyltransferase Dpm1, or its downstream glycosylation pathways, could rescue two in vivo models of DPAGT1 inhibition and ER stress, even though impairment of these pathways alone usually cause CDGs. While both in vivo models ostensibly cause ER stress (through DPAGT1 inhibition or a misfolded protein), we found a novel difference in fructose metabolism that may indicate glycolysis as a modulator of DPAGT1-CDG. Our results provide new therapeutic targets for DPAGT1-CDG, include the unique finding of Dpm1-related pathways rescuing DPAGT1 inhibition, and reveal a novel interaction between fructose metabolism and ER stress.
Microglia Mediate Early Corticostriatal Synapse Loss and Cognitive Dysfunction in Huntington’s Disease Through Complement-Dependent Mechanisms
Authors: Wilton D.K. , Mastro K. , Heller M.D. , Gergits F.W. , Willing C R. , Frouin A. , Daggett A. , Gu X. , Kim A.Y. , Faull R. , Jayadev S. , Yednock T , Yang X.W. , Stevens B. 
Published: December 2021

AbstractHuntington’s disease (HD) is a devastating monogenic neurodegenerative disease characterized by early, selective pathology in the basal ganglia despite the ubiquitous expression of mutant huntingtin. The molecular mechanisms underlying this region-specific neuronal degeneration and how these relate to the development of early cognitive phenotypes are poorly understood. Here, we show that there is selective loss of synaptic connections between the cortex and striatum in postmortem tissue from HD patients that is associated with the increased activation and localization of complement proteins, innate immune molecules, to markers of these synaptic elements. We also find that levels of these secreted innate immune molecules are elevated in the CSF of premanifest HD patients and correlate with established measures of disease burden.In preclinical genetic models of HD we show that complement proteins mediate the selective elimination of corticostriatal synapses at an early stage in disease pathogenesis marking them for removal by microglia, the brain’s resident macrophage population. This process requires mutant huntingtin to be expressed in both cortical and striatal neurons and inhibition of this complement-dependent elimination mechanism through administration of a therapeutically relevant C1q function blocking antibody or genetic ablation of a complement receptor on microglia, prevented synapse loss, increased excitatory input to the striatum and rescued the early development of visual discrimination learning and cognitive flexibility deficits in these models. Together, our findings implicate microglia and the complement cascade in the selective, early degeneration of corticostriatal synapses and the development of cognitive deficits in presymptomatic HD, and also provide new preclinical data to support complement as a therapeutic target for early intervention.
Glutamine deficiency in solid tumors confers resistance to ribosomal RNA synthesis inhibitors
Authors: Pan Melvin , Zorbas Christiane , Sugaya Maki , Ishiguro Kensuke , Kato Miki , Nishida Miyuki , Zhang Hai-Feng , Candeias Marco M , Okamoto Akimitsu , Ishikawa Takamasa , Soga Tomoyoshi , Aburatani Hiroyuki , Sakai Juro , Matsumura Yoshihiro , Suzuki Tsutomu , Proud Christopher G. , Lafontaine Denis L. J. , Osawa Tsuyoshi 
Published: December 2021

SummaryRibosome biogenesis involves the processing of precursor ribosomal RNAs (pre-rRNAs) and sequential assembly with ribosomal proteins. Here we report that nutrient deprivation severely impairs pre-rRNA processing and leads to the accumulation of unprocessed rRNAs. Upon nutrient restoration, the accumulated pre-rRNAs are processed into mature rRNAs that are utilized for ribosome biogenesis. Failure to accumulate pre-rRNAs under nutrient deprivation leads to perturbed ribosome assembly during nutrient restoration and subsequent apoptosis via uL5/uL18-mediated activation of p53. Restoration of glutamine alone activates p53 by triggering uL5/uL18 translation. Induction of uL5/uL18 protein synthesis by glutamine was dependent on the translation factor eukaryotic elongation factor 2 (eEF2), which was in turn dependent on Raf/MEK/ERK signalling. Depriving cells of glutamine prevents the activation of p53 by rRNA synthesis inhibitors. Our data reveals a mechanism that cancer cells can exploit to suppress p53-mediated apoptosis during fluctuations in environmental nutrient availability.