bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Kalirin Missense Mutation Enhances Dendritic RhoA Signaling and Leads to Regression of Cortical Dendritic Arbors Across Development
Authors: Grubisha MJ , Sun T , Erickson SL , Eisenman L , Chou S , Helmer CD , Trudgen MT , Ding Y , Homanics GE , Penzes P , Wills ZP , Sweet RA 
Published: March 2021

ABSTRACTNormally, dendritic size is established prior to adolescence then remains relatively constant into adulthood due to a homeostatic balance between growth and retraction pathways. However, schizophrenia is characterized by accelerated reductions of cerebral cortex gray matter volume and onset of clinical symptoms during adolescence, with reductions in layer 3 pyramidal neuron dendritic length, complexity, and spine density identified in multiple cortical regions postmortem. Nogo receptor 1 (NGR1) activation of the GTPase RhoA is a major pathway restricting dendritic growth in the cerebral cortex. We show that the NGR1 pathway is stimulated by OMGp and requires the Rho guanine nucleotide exchange factor, Kalirin-9 (KAL9). Using a genetically encoded RhoA sensor, we demonstrate that a naturally occurring missense mutation inKalrn, KAL-PT, that was identified in a schizophrenia cohort, confers enhanced RhoA activitation in neuronal dendrites compared to wildtype KAL. In mice containing this missense mutation at the endogenous locus there is an adolescent-onset reduction in dendritic length and complexity of layer 3 pyramidal neurons in the primary auditory cortex. Tissue density of dendritic spines was also reduced. Early adult mice with these structural deficts exhibited impaired detection of short gap durations. These findings provide a neuropsychiatric model of disease capturing how a mild genetic vulnerability may interact with normal developmental processes such that pathology only emerges around adolescence. This interplay between genetic susceptibility and normal adolescent development, both of which possess inherent individual variability, may contribute to heterogeneity seen in phenotypes in human neuropsychiatric disease.SIGNIFICANCE STATEMENTDendrites are long branching processes on neurons that contain small processes called spines that are the site of connections with other neurons, establishing cortical circuitry. Dendrites have long been considered stable structures, with rapid growth prior to adolescence followed by maintenance of size into adulthood. However, schizophrenia is characterized by accelerated reductions of cortical gray matter volume and onset of clinical symptoms during adolescence, with reductions in dendritic length present when examined after death. We show that dendrites retain the capacity for regression, and that a mild genetic vulnerability in a regression pathway leads to onset of structural impairments in previously formed dendrites across adolescence. This suggests that targeting specific regression pathways could potentially lead to new therapeutics for schizophrenia.
Catalase Activity is Critical forProteus mirabilisBiofilm Development, EPS Composition, and Dissemination During Catheter-Associated Urinary Tract Infection
Authors: White Ashley N. , Learman Brian S. , Brauer Aimee L. , Armbruster Chelsie E. 
Published: March 2021

AbstractProteus mirabilisis a leading uropathogen of catheter-associated urinary tract infections (CAUTIs), which are among the most common healthcare-associated infections worldwide. A key factor that contributes toP. mirabilispathogenesis and persistence during CAUTI is the formation of catheter biofilms, which provide increased resistance to antibiotic treatment and host defense mechanisms. Another factor that is important for bacterial persistence during CAUTI is the ability to resist reactive oxygen species (ROS), such as through the action of the catalase enzyme. Potent catalase activity is one of the defining biochemical characteristics ofP. mirabilis,and its single catalase gene (katA) was recently identified as a candidate fitness factor for UTI, CAUTI, and bacteremia. Here we show that disruption ofkatAresults in increased ROS levels, increased sensitivity to peroxide, and decreased biofilm biomass. The biomass defect was due to a decrease in extracellular polymeric substances (EPS) production by the ΔkatAmutant, and specifically due to reduced carbohydrate content. Importantly, the biofilm defect resulted in decreased antibiotic resistancein vitroand a colonization defect during experimental CAUTI. The ΔkatAmutant also exhibited decreased fitness in a bacteremia model, supporting a dual role for catalase inP. mirabilisbiofilm development and immune evasion.
Glycosaminoglycan content of a mineralized collagen scaffold promotes mesenchymal stem cell secretion of factors to modulate angiogenesis and monocyte differentiation
Authors: Dewey Marley J. , Kolliopoulos Vasiliki , Ngo Mai T. , Harley Brendan A.C. 
Published: March 2021

ABSTRACTEffective design of biomaterials to aid regenerative repair of craniomaxillofacial (CMF) bone defects requires approaches that modulate the complex interplay between exogenously added progenitor cells and cells in the wound microenvironment, such as osteoblasts, osteoclasts, endothelial cells, and immune cells. We are exploring the role of the glycosaminoglycan (GAG) content in a class of mineralized collagen scaffolds recently shown to promote osteogenesis and healing of craniofacial bone defects. We previously showed that incorporating chondroitin-6-sulfate or heparin improved mineral deposition by seeded human mesenchymal stem cells (hMSCs). Here, we examine the effect of varying scaffold GAG content on hMSC behavior, and their ability to modulate osteoclastogenesis, vasculogenesis, and the immune response. We report the role of hMSC-conditioned media produced in scaffolds containing chondroitin-6-sulfate (CS6), chondroitin-4-sulfate (CS4), or heparin (Heparin) GAGs on endothelial tube formation and monocyte differentiation. Notably, endogenous production by hMSCs within Heparin scaffolds most significantly inhibits osteoclastogenesis via secreted osteoprotegerin (OPG), while the secretome generated by CS6 scaffolds reduced pro-inflammatory immune response and increased endothelial tube formation. All conditioned media down-regulated many pro- and anti-inflammatory cytokines, such as IL6, IL-1β, and CCL18 and CCL17 respectively. Together, these findings demonstrate that modifying mineralized collagen scaffold GAG content can both directly (hMSC activity) and indirectly (production of secreted factors) influence overall osteogenic potential and mineral biosynthesis as well as angiogenic potential and monocyte differentiation towards osteoclastic and macrophage lineages. Scaffold GAG content is therefore a powerful stimulus to modulate reciprocal signaling between multiple cell populations within the bone healing microenvironment.
Serotonin and dopamine modulate aging in response to food perception and availability
Authors: Miller Hillary A. , Huang Shijiao , Schaller Megan L. , Dean Elizabeth S. , Tuckowski Angela M. , Munneke Allyson S. , Beydoun Safa , Pletcher Scott D. , Leiser Scott F. 
Published: March 2021

AbstractAn organism’s ability to perceive and respond to changes in its environment is crucial for its health and survival. Here we reveal how the most well-studied longevity intervention, dietary restriction (DR), acts in-part through a cell non-autonomous signaling pathway that is inhibited by the perception of attractive smells. Using an intestinal reporter for a key gene induced by DR but suppressed by attractive smells, we identify three compounds that block food perception inC. elegans, thereby increasing longevity as DR mimetics. These compounds clearly implicate serotonin and dopamine in limiting lifespan in response to food perception. We further identify an enteric neuron in this pathway that signals through the serotonin receptor 5-HT1A/ser-4 and dopamine receptor DRD2/dop-3. Aspects of this pathway are conserved in D. melanogaster and mammalian cells. Thus, blocking food perception through antagonism of serotonin or dopamine receptors is a plausible approach to mimic the benefits of dietary restriction.
The architecture of Cidec-mediated interfaces between lipid droplets
Authors: Ganeva Iva , Lim Koini , Boulanger Jerome , Hoffmann Patrick C. , Savage David B. , Kukulski Wanda 
Published: March 2021

AbstractLipid droplets (LDs) are intracellular organelles responsible for storing surplus energy as neutral lipids. Their size and number vary enormously (1). In white adipocytes, they reach up to 100µm in size, occupying >90% of the cell. Cidec, which is strictly required for the formation of such large LDs, is concentrated at interfaces between adjacent LDs and facilitates the directional flux of neutral lipids from the smaller to the larger LD (2-7). However, the mechanism of lipid transfer is unclear, in part because the architecture of interfaces between LDs has remained elusive. Here we visualised interfaces between LDs by electron cryo-tomography (cryo-ET) and analysed the kinetics of lipid transfer by quantitative live fluorescence microscopy (FM). We show that transfer occurs through closely apposed intact monolayers, is slowed down by increasing the distance between the monolayers and follows exponential kinetics suggesting a pressure-driven mechanism. We thus propose that unique architectural features of LD-LD interfaces are mechanistic determinants of neutral lipid transfer.
Protein-primed RNA synthesis in SARS-CoVs and structural basis for inhibition by AT-527
Authors: Shannon Ashleigh , Fattorini Véronique , Sama Bhawna , Selisko Barbara , Feracci Mikael , Falcou Camille , Gauffre Pierre , Kazzi Priscila El , Decroly Etienne , Rabah Nadia , Alvarez Karine , Eydoux Cécilia , Guillemot Jean-Claude , Debart Françoise , Vasseur Jean-Jacques , Noel Mathieu , Moussa Adel , Good Steven , Lin Kai , Sommadossi Jean-Pierre , Zhu Yingxiao , Yan Xiaodong , Shi Hui , Ferron François , Canard Bruno 
Published: March 2021

SummaryHow viruses from theCoronaviridaefamily initiate viral RNA synthesis is unknown. Here we show that the SARS-CoV-1 and −2NidovirusRdRp-AssociatedNucleotidyltransferase (NiRAN) domain on nsp12 uridylates the viral cofactor nsp8, forming a UMP-Nsp8 covalent intermediate that subsequently primes RNA synthesis from a poly(A) template; a protein-priming mechanism reminiscent ofPicornaviridaeenzymes. In parallel, the RdRp active site of nsp12 synthesizes a pppGpU primer, which primes (-)ssRNA synthesis at the precise genome-poly(A) junction. The guanosine analogue 5’-triphosphate AT-9010 (prodrug: AT-527) tightly binds to the NiRAN and inhibits both nsp8-labeling and the initiation of RNA synthesis. A 2.98 Å resolution Cryo-EM structure of the SARS-CoV-2 nsp12-nsp7-(nsp8)2/RNA/NTP quaternary complex shows AT-9010 simultaneously binds to both NiRAN and RdRp active site of nsp12, blocking their respective activities. AT-527 is currently in phase II clinical trials, and is a potent inhibitor of SARS-CoV-1 and −2, representing a promising drug for COVID-19 treatment.
The fern CYPome: Fern-specific cytochrome P450 family involved in convergent evolution of chemical defense
Authors: Thodberg Sara , Hansen Cecilie Cetti , Takos Adam M. , Pičmanová Martina , Møller Birger Lindberg , Nelson David R. , Neilson Elizabeth H. Jakobsen 
Published: March 2021

AbstractPlant natural products encompass an enormous chemical diversity bearing witness to great molecular innovation that occured throughout land plant evolution. Cytochrome P450 monooxygenases (CYPs) catalyze a wide variety of monooxygenation reactions essential to the metabolic repertoire of plants natural products. Ferns constitute the second largest group of vascular plants and hold a significant phylogenetic position in land evolution, lying sister to seed plants. To date, CYP diversity has not been described for this taxon and pathway discovery in ferns in general is scarce, despite possessing a rich diversity of natural products. We analysed over 8000 available fern CYPs, classifing and characterizing the landscape of this super-enzyme group. Fern CYPs are dominated by fern-specific families (∼60%), with the largest family – CYP981 – constituting approximately 15% of all predicted fern CYPs in the dataset. The abundancy and dynamics of the CYP981 family suggest a position equivalent to the CYP71 family present in seed plants, with potential roles in natural product biosynthesis. Ferns are the evolutionary oldest group to biosynthesize cyanogenic glycosides; amino acid-derived defense compounds. We show that CYP981F5 from the highly cyanogenic fernPhlebodium aureumcatalyzes the conversion of phenylacetonitrile to mandelonitrile, an intermediate step in cyanogenic glycoside biosynthesis. The fern CYPome provides an important platform to further understand evolution of metabolite biosynthesis throughout the plant kingdom, and in ferns specifically.
Membrane insertion mechanism of the caveolae coat protein Cavin1
Authors: Liu Kang-cheng , Pace Hudson , Larsson Elin , Hossain Shakhawath , Kabedev Aleksei , Shukla Ankita , Jerschabek Vanessa , Mohan Jagan , Bergström Christel A. S. , Bally Marta , Schwieger Christian , Hubert Madlen , Lundmark Richard 
Published: March 2021

AbstractCaveolae are small plasma membrane invaginations, important for control of membrane tension, signaling cascades and lipid sorting. The caveolae coat protein Cavin1 is essential for shaping such high curvature membrane structures. Yet, a mechanistic understanding of how Cavin1 assembles at the membrane interface is lacking. Here, we used model membranes combined with biophysical dissection and computational modelling to show that Cavin1 inserts into membranes. We establish that initial PI(4,5)P2-dependent membrane adsorption of the trimeric helical region 1 (HR1) of Cavin1 mediates the subsequent partial separation and membrane insertion of the individual helices. Insertion kinetics of the HR1 is further enhanced by the presence of flanking negatively charged disordered regions, which was found important for the co-assembly of Cavin1 with Caveolin1 in living cells. We propose that this intricate mechanism potentiates membrane curvature generation and facilitates dynamic rounds of assembly and disassembly of Cavin1 at the membrane.Significance statementCaveolae are cholesterol enriched membrane invaginations coupled to severe muscle and lipid disorders. Their formation is dependent on assembly of the protein Cavin1 at the lipid membrane interface driving membrane curvature. In this work, we dissect the mechanism for how Cavin1 binds and inserts into membranes using a combination of biochemical and biophysical characterization as well as computational modelling. The proposed model for membrane assembly potentiates dynamic switching between shielded and exposed hydrophobic helices used for membrane insertion and clarifies how Cavin1 can drive membrane curvature and the formation of caveolae.
Single cell transcriptome analysis of decidua macrophages in normal and recurrent spontaneous abortion patients
Authors: Zheng Qingliang , Xu XiangHong , Yang Fenglian , Gan Haili , Zhao Yongbo , Wan Xiaoping , Jin Liping 
Published: March 2021

ABSTRACTDue to the heterogeneity and different polarization state of decidual macrophages (dMΦ), they play an important role during the pregnancy, but their definition and exact function remain elusive. We isolated CD14+CD45+dMΦ from the normal or RSA decidua by flow cytometry, followed by single cell RNA sequencing (scRNA-seq). In total, 23,062 single-cell transcriptomes of macrophage were profiled (12,470 Normal and 10,592 RSA), which were divided into 13 major clusters via T-distributed stochastic neighbor embedding (t-SNE) visualization. We observed that there is higher percentage composition of M1 cells (70.6%) in the normal decidua, and higher percentage composition of M2 cells (68.3%) in the RSA decidua. We identified new markers (M1: S100A8, S100A9, M2: SELENOP, FOLR2, RNASE1) and secreted cytokines (M1: IL1β, TNFSF13B and MMP9; M2: CCL3, CCL4) of the dMΦ. We found that cluster 10 as the specific cluster of dMΦ highly expressing BAG3 in normal group and cluster 7 specific highly expressing CXCL9/10/11 chemokine. After pseudo-time trajectory analysis, we found that the dMΦ formed a continuous “V-shaped” trajectory, with M1 and M2 type cells mainly occupying the two heads. We found that NFκB1, MYC and TCF12 acted as the key transcription factors of dMΦ. Our study redefined the polarization state and physiological characteristic of dMΦ in early normal and RSA pregnancy, which suggests a novel view and therapeutic target for spontaneous abortion prevention.
Insight into Lipopolysaccharide Translocation by Cryo-EM structures of a LptDE Transporter in Complex with Pro-Macrobodies
Authors: Botte Mathieu , Ni Dongchun , Schenck Stephan , Zimmermann Iwan , Chami Mohamed , Bocquet Nicolas , Egloff Pascal , Bucher Denis , Trabuco Matilde , Cheng Robert K.Y. , Brunner Janine D. , Seeger Markus A. , Stahlberg Henning , Hennig Michael 
Published: March 2021

AbstractLipopolysaccharides (LPS) are major constituents of the extracellular leaflet in the bacterial outer membrane and form an effective physical barrier for environmental threats and for antibiotics in Gram-negative bacteria1. The last step of LPS insertion via the Lpt pathway is mediated by the LptD/E protein complex2. Despite detailed insights from X-ray crystallography into the architecture of LptDE transporter complexes3–5, no structure of a laterally open LptD transporter has been described, a transient state that occurs during LPS release6. To facilitate the acquisition of hitherto unknown conformations we subjected LptDE ofN. gonorrhoeaeto cryo-EM analyses. In complex with newly designed rigid chaperones derived from nanobodies (Pro-Macrobodies, PMbs) we obtained a map of a partially opened LptDE transporter at 3.4 Å resolution and in addition we captured a laterally fully opened LptDE complex from a subset of particles. Our work offers new insights into the mechanism of LPS insertion, provides a structural framework for the development of antibiotics targeting LptD and describes a novel, highly rigid and widely applicable chaperone scaffold to enable structural biology of challenging protein targets.
Distinct domains of Me31B interact with different eIF4E isoforms in the male germ line ofDrosophila melanogaster
Authors: Layana Carla , Vilardo Emiliano Salvador , Corujo Gonzalo , Hernández Greco , Rivera-Pomar Rolando 
Published: March 2021

ABSTRACTEukaryotic translation initiation factor 4E (eIF4E) is a key factor involved in different aspects of mRNA metabolism.Drosophila melanogastergenome encodes eight eIF4E isoforms, and the canonical isoform eIF4E-1 is a ubiquitous protein that plays a key role in mRNA translation. eIF4E-3 is specifically expressed in testis and controls translation during spermatogenesis. In eukaryotic cells, translational control and mRNA decay is highly regulated in different cytoplasmic ribonucleoprotein foci, which include the processing bodies (PBs). In this study, we show thatDrosophilaeIF4E-1 and eIF4E-3 occur in PBs where might play a role in mRNA storage and translational repression. We also demonstrate that the DEAD-box RNA helicase Me31B, a component of PBs, physically interacts with eIF4E-1 and eIF4E-3 both in the yeast two-hybrid system and FRET inDrosophilaS2 cells.Moreover, truncated and point mutated Me31B proteins indicate that the binding sites of Me31B for eIF4E-1 and eIF4E-3 are located in different domains. Residues Y401-L407 (at the carboxy-terminal) are essential for interaction with eIF4E-1, whereas residues F63-L70 (at the amino-terminal) are critical for interaction with eIF4E-3. Thus, Me31B represents a novel type of eIF4E-interacting protein. Our observations suggest that Me31B might recognize different eIF4E isoforms in different tissues, which could be the key to silencing specific messengers. They provide further evidence that alternative forms of eIF4E and their interactions with various partners add complexity to the control of gene expression in eukaryotes.
Rapid thermophilization of understorey plant communities in a 9 year‐long temperate forest experiment
Authors: Govaert Sanne , Vangansbeke Pieter , Blondeel Haben , Steppe Kathy , Verheyen Kris , De Frenne Pieter 
Published: March 2021

Abstract

The vast majority of plant biodiversity associated with temperate forests is harboured by the understorey layer. This layer also plays crucial roles in ecosystem functions such as tree regeneration, nutrient cycling and carbon dynamics. Research using space‐for‐time substitutions and resurveys of vegetation plots has shown that climate warming, changes in forest management and resource availability are key determinants of forest understorey biodiversity change and functioning. However, long‐term experiments are needed to better unravel their complex interactive effects.

Here we study the influence of nearly a decade of experimental warming, light addition using fluorescent tubes (as a proxy for management‐driven changes in forest‐floor light levels) and nitrogen input on understorey plant communities of temperate broadleaved forest.

Plant communities shifted towards a higher dominance of warm‐adapted species, a process referred to as thermophilization. We detected a marked community shift in all treatments including the control plots, reflecting ongoing ambient environmental changes. This reordering over time was greater than the shift induced by the treatments. Thermophilization was, however, greatest when temperature and/or light availability were enhanced. Communities were also taller in response to warming and increased light availability.

Synthesis. Our experiment provides important insights into 9 years of vegetation changes in a temperate forest and how canopy density and forest management can be adapted to limit thermophilization of forest understorey biodiversity under climate change. [Correction added on 27 April 2021, after first online publication: The Synthesis section in the abstract has been updated to reflect the original text supplied.]
Can it be all more simple? Manufacturing aflatoxin biocontrol products using dry spores of atoxigenic isolates of Aspergillus flavus as active ingredients
Authors: Ortega‐Beltran Alejandro , Kaptoge Lawrence , Senghor Amadou L. , Aikore Morounranti O. S. , Jarju Patrick , Momanyi Henry , Konlambigue Matieyedou , Falade Titilayo D. O. , Bandyopadhyay Ranajit 
Published: March 2021

SummaryAflatoxin contamination of staple crops, commonly occurring in warm areas, negatively impacts human and animal health, and hampers trade and economic development. The fungus Aspergillus flavus is the major aflatoxin producer. However, not all A. flavus genotypes produce aflatoxins. Effective aflatoxin control is achieved using biocontrol products containing spores of atoxigenic A. flavus. In Africa, various biocontrol products under the tradename Aflasafe are available. Private and public sector licensees manufacture Aflasafe using spores freshly produced in laboratories adjacent to their factories. BAMTAARE, the licensee in Senegal, had difficulties to obtain laboratory equipment during its first year of production. To overcome this, a process was developed in Ibadan, Nigeria, for producing high‐quality dry spores. Viability and stability of the dry spores were tested and conformed to set standards. In 2019, BAMTAARE manufactured Aflasafe SN01 using dry spores produced in Ibadan and sent via courier and 19 000 ha of groundnut and maize in Senegal and The Gambia were treated. Biocontrol manufactured with dry spores was as effective as biocontrol manufactured with freshly produced spores. Treated crops contained safe and significantly (P < 0.05) less aflatoxin than untreated crops. The dry spore innovation will make biocontrol manufacturing cost‐efficient in several African countries.