bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure and mechanism of the tripartite ATP-independent periplasmic (TRAP) transporter
Authors: Davies James S. , Currie Michael J. , North Rachel A. , Wright Joshua D. , Scalise Mariafrancesca , Copping Jack M. , Remus Daniela M. , Gulati Ashutosh , Morado Dustin R. , Jamieson Sam A. , Abeysekera Gayan S. , Ramaswamy Subramanian , Friemann Rosmarie , Wakatsuki Soichi , Allison Jane R. , Indiveri Cesare , Drew David , Mace Peter D. , Dobson Renwick C.J. 
Published: February 2022

AbstractIn bacteria and archaea, tripartite ATP-independent periplasmic (TRAP) transporters uptake essential carboxylate- and sulfonate-containing nutrients into the cytoplasm. Unlike other secondary active transporters, TRAP transporters cannot receive their substrates directly, but do so indirectly via a secreted soluble substrate-binding protein. How a sodium-driven secondary active transporter is strictly coupled to a passenger-carrying substrate-binding domain is poorly understood. Here, we report the cryo-EM structure of the sialic acid TRAP transporter SiaQM from Photobacterium profundum at 2.97 Å resolution. SiaM has 12-TMs that come together to form a “transport” domain and a “scaffold” domain, with the transport domain consisting of helical hairpins as seen in the sodium-coupled elevator transporter VcINDY. Interestingly, the SiaQ protein forms intimate contacts with SiaM to extend the size of the scaffold domain, indicating TRAP transporters may operate as monomers, rather than the typically observed oligomers. We have identified the Na+ and sialic acid binding sites in SiaM and confirmed a strict dependence on the substrate-binding protein SiaP for uptake. We have determined the SiaP crystal structure that, together with co-evolution driven docking studies, provides a molecular basis for how sialic acid is delivered to the SiaQM transporter complex. We conclude that TRAP proteins are conceptually a marriage between an ABC importer and a secondary active transporter, which we describe herein as an ‘elevator-with-an-operator’ mechanism.
Syncollin secreted by activated human neutrophils targets bacteria
Authors: Waters Rosie A. , Robinson James , Edwardson J. Michael 
Published: February 2022

AbstractSyncollin is a 16-kDa protein that was originally isolated from the pancreatic zymogen granule. Syncollin is also found in human neutrophils and is secreted from promyelocytic HL-60 cells upon stimulation. Recently, we reported that syncollin is able to bind to bacterial peptidoglycan, to damage the bacterial envelope and to restrict bacterial growth. Here, we show that syncollin is secreted from activated primary human neutrophils, and interacts with extracellular neutrophil traps (NETs) in a similar manner to the well-characterized granular protein myeloperoxidase. In addition, secreted syncollin is able to coat the surface of E. coli in co-cultures of neutrophils and bacteria. On the basis of our findings, we suggest that syncollin plays a role in host defence in the blood.
Daam1 negatively regulates USP10 activity
Authors: Phillips Andrew T. , Boumil Edward F. , Venkatesan Arunkumar , Castro Nileyma , Bernstein Audrey M. 
Published: February 2022

AbstractThe differentiation of fibroblasts into pathological myofibroblasts during wound healing is in part characterized by increased cell surface expression of αv-integrins. Our previous studies found that the deubiquitinase (DUB) USP10 removes ubiquitin from αv-integrins, leading to cell surface integrin accumulation, subsequent TGFβ1 activation, and myofibroblast differentiation. In this study, a yeast-two hybrid screen elucidated a novel binding partner for USP10, the formin, Daam1. The USP10/Daam1 interaction was also supported by proximity ligation assay (PLA) activity. Treatment with TGFβ1 significantly increased USP10 and Daam1 protein expression, PLA signal, and co-localization to actin stress fibers. Furthermore, Daam1 siRNA knockdown significantly reduced a) co-precipitation of USP10 and Daam1 on purified actin stress fibers, and b) β1- and β5-integrin ubiquitination resulting in increased αv-, β1-, and β5-integrin total protein levels, αv integrin recycling to the cell surface, and extracellular fibronectin (FN) organization. Together, our data suggest that Daam1 negatively regulates USP10’s DUB activity and subsequently maintains integrin protein homeostasis.
Single extracellular vesicle analysis in human amniotic fluid shows evidence of phenotype alterations in preeclampsia
Authors: Gebara Natalia , Scheel Julia , Skovronova Renata , Grange Cristina , Marozio Luca , Gupta Shailendra , Giorgione Veronica , Caicci Federico , Benedetto Chiara , Khalil Asma , Bussolati Benedetta 
Published: February 2022

AbstractAmniotic fluid surrounding the developing fetus is a complex biological fluid rich in metabolically active bio-factors. The presence of extracellular vesicles (EVs) in amniotic fluid has been mainly related to fetal urine. We here characterized EVs from term amniotic fluid in terms of surface marker expression using different orthogonal techniques. EVs appeared to be a heterogeneous population expressing markers of renal, placental, epithelial and stem cells. Moreover, we compared amniotic fluid EVs from normal pregnancies with those of preeclampsia, a hypertensive disorder affecting up to 8% of pregnancies worldwide. An increase of CD105 (endoglin) expressing EVs was observed in preeclamptic amniotic fluid by bead-based cytofluorimetric analysis, and further confirmed using a chip-based analysis. HLA-G, a typical placental marker, was not co-expressed by the majority of CD105+EVs, suggesting their origin from amniotic fluid cells. At a functional level, preeclampsia-derived EVs, but not normal pregnancy EVs, showed an antiangiogenic effect, possibly due to the decoy effect of endoglin. In addition, several miRNAs were differentially expressed in preeclampsia-derived EVs and directly related to the modulation of angiogenesis and trophoblast function. Our results provide a characterization of term amniotic fluid-EVs, supporting their origin from fetal and placental cells. In preeclampsia, the observed antiangiogenic characteristics of amniotic fluid-EVs may reflect the hypoxic and antiangiogenic microenvironment and could possibly impact on the developing fetus or on the surrounding fetal membranes.
Biosynthesis of aurodox, a Type III secretion system inhibitor from Streptomyces goldiniensis
Authors: McHugh Rebecca E , Munnoch John T , Braes Robyn E , McKean Iain J. W. , Giard Josephine M , Taladriz-Sender Andrea , Peschke Frederik , Burley Glenn A , Roe Andrew J , Hoskisson Paul A 
Published: February 2022

AbstractThe global increase in antimicrobial-resistant infections means that there is a need to develop new antimicrobial molecules and strategies to combat the issue. Aurodox is a linear polyketide natural product that is produced by Streptomyces goldiniensis, yet little is known about aurodox biosynthesis or the nature of the biosynthetic gene cluster (BGC) that encodes its production. To gain a deeper understanding of aurodox biosynthesis by S. goldiniensis, the whole genome of the organism was sequenced, revealing the presence of an 87 kb hybrid Polyketide Synthase/Non-Ribosomal Peptide Synthetase (PKS/NRPS) BGC. The aurodox BGC shares significant homology with the kirromycin BGC from S. collinus Tϋ 365; however, the genetic organisation of the BGC differs significantly. The candidate aurodox gene cluster was cloned and expressed in a heterologous host to demonstrate that it was responsible for aurodox biosynthesis and disruption of the primary PKS gene (aurAI) abolished aurodox production. These data support a model whereby the initial core biosynthetic reactions involved in aurodox biosynthesis follow that of kirromycin. Cloning aurM* from S. goldiniensis and expressing this in the kirromycin producer S. collinus Tϋ 365 enabled methylation of the pyridone group, suggesting this is the last step in biosynthesis. This methylation step is also sufficient to confer the unique Type III Secretion System inhibitory properties to aurodox.ImportanceEnterohaemorrhagic Escherichia coli (EHEC) is a significant global pathogen for which traditional antibiotic treatment is not recommended. Aurodox inhibits the ability of EHEC to establish infection in the host gut through the specific targeting of the Type III Secretion System, whilst circumventing the induction of toxin production associated with traditional antibiotics. These properties suggest aurodox could be a promising anti-virulence compound for EHEC, which merits further investigation. Here, we have characterised the aurodox biosynthetic gene cluster from Streptomyces goldiniensis and have established the key enzymatic steps of aurodox biosynthesis that give rise to the unique anti-virulence activity. These data provide the basis for future chemical and genetic approaches to produce aurodox derivatives with increased efficacy and the potential to engineer novel elfamycins.
The Transcription Factor Bach2 Negatively Regulates Natural Killer Cell Maturation and Function
Authors: Li Shasha , Bern Michael D. , Miao Benpeng , Inoue Takeshi , Piersma Sytse J. , Colonna Marco , Kurosaki Tomohiro , Yokoyama Wayne M. 
Published: February 2022

AbstractBTB domain And CNC Homolog 2 (Bach2) is a transcription repressor that actively participates in T and B lymphocyte development, but it is unknown if Bach2 is also involved in the development of innate immune cells, such as natural killer (NK) cells. Here, we followed the expression of Bach2 during NK cell development, finding that it peaked in CD27+CD11b+cells and decreased upon further maturation. Bach2 expression positively correlated with that of the transcription factor TCF1 and negatively correlated with genes encoding NK effector molecules as well as genes involved in the cell cycle. Bach2-deficient mice showed increased numbers of terminally differentiated NK cells with increased production of granzymes and cytokines. NK cell-mediated control of tumor metastasis was also augmented in the absence of Bach2. Therefore, Bach2 is a key checkpoint protein regulating NK terminal maturation.
Single-cell transcriptomic and proteomic analysis of Parkinson’s disease Brains
Authors: Zhu Biqing , Park Jae-Min , Coffey Sarah , Hsu I-Uen , Lam TuKiet T. , Gopal Pallavi P. , Ginsberg Stephen D. , Wang Jiawei , Su Chang , Zhao Hongyu , Hafler David A. , Chandra Sreeganga S. , Zhang Le 
Published: February 2022

AbstractParkinson’s disease (PD) is a prevalent neurodegenerative disorder where recent evidence suggests pathogenesis may be mediated by inflammatory processes. The molecular architecture of the disease remains to be fully elucidated. We performed single-nucleus transcriptomics and unbiased proteomics using postmortem tissue obtained from the prefrontal cortex of 12 individuals with late-stage PD and age-matched controls. We analyzed ∼80,000 nuclei and identified eight major cell types, including brain-resident T cells, each with distinct transcriptional changes in line with the known genetics of PD. By analyzing Lewy body pathology in the same postmortem tissue, we found that α-synuclein pathology is inversely correlated with chaperone expression in excitatory neurons. Examining cell-cell interactions, we found a selective abatement of neuron-astrocyte interactions and enhanced neuroinflammation. Proteomic analyses of the same brains identified synaptic proteins in prefrontal cortex that were preferentially downregulated in PD. Strikingly, comparing this dataset to a regionally similar published analysis for Alzheimer’s disease (AD), we found no common differentially expressed genes in neurons, but identified many shared differentially expressed genes in glial cells, suggesting that disease etiology in PD and AD are likely distinct. These data are presented as a resource for interrogating the molecular and cellular basis of PD and other neurodegenerative diseases.One Sentence SummaryWe provide an extensive single cell analysis profiling nearly 80,000 brain nuclei from prefrontal cortex of late-stage Parkinson’s disease brains, demonstrate that α-synuclein pathology is inversely correlated with chaperone expression in excitatory neurons, found a selective abatement of neuron-astrocyte interactions with enhanced neuroinflammation, and augmented the study with proteomic analysis and cross-comparisons with Alzheimer’s disease datasets, providing valuable insights into the pathways of neurodegeneration and a deep definition of the underlying molecular pathology for Parkinson’s disease.
Constitutively active STAT5b feminizes mouse liver gene expression
Authors: Lau-Corona Dana , Ma Hong , Vergato Cameron , Sarmento-Cabral Andre , del Rio-Moreno Mercedes , Kineman Rhonda D , Waxman David J 
Published: February 2022

AbstractSTAT5 is an essential transcriptional regulator of the sex-biased actions of growth hormone (GH) in the liver. Delivery of constitutively active STAT5 (STAT5CA) to male mouse liver using an engineered adeno-associated virus with high tropism for the liver is shown to induce widespread feminization of the liver, with extensive induction of female-biased genes and repression of male-biased genes, largely mimicking results obtained when male mice are given GH as a continuous infusion. Many of the gene expression changes observed were associated with STAT5 binding to liver chromatin, supporting the proposed direct role of persistently active STAT5 in continuous GH-induced liver feminization. The feminizing effects of STAT5CA were dose-dependent; moreover, at higher levels, overexpression of STAT5CA resulted in some histopathology not seen in continuous GH-infused male liver, including hepatocyte hyperplasia and distorted liver architecture. These findings establish that the persistent activation of STAT5 by GH that characterizes female liver is by itself sufficient to account for the female-biased expression of a majority of female-biased genes. Moreover, histological changes seen when STAT5CA is overexpressed highlight the importance of carefully evaluating such effects before considering such STAT5 derivatives for therapeutic use in treating liver disease.
Insulin/IGF Signaling Regulates Presynaptic Glutamate Release in Aversive Olfactory Learning
Authors: Cheng Du , Lee James , Brown Maximillian , Ebert Margaret S. , Tomioka Masahiro , Iino Yuichi , Bargmann Cornelia I 
Published: February 2022

SUMMARYInformation flow through neural circuits is continuously modified by context-dependent learning. In the nematode Caenorhabditis elegans, pairing specific odors with food deprivation results in aversion to the odor. Here we identify cell-specific mechanisms of insulin/IGF receptor signaling that integrate sensory information with food context during aversive olfactory learning. Using a conditional allele of the insulin/IGF receptor DAF-2, we show that aversive learning to butanone, an odor sensed only by the AWCON olfactory neuron, requires DAF-2 in AWCON. Learning requires an axonally-localized DAF-2c isoform and the insulin receptor substrate (IRS) protein IST-1, but is partly independent of the FoxO transcription factor DAF-16. Upon food deprivation, the unconditioned stimulus for learning, DAF-2 expression increases post-transcriptionally through an insulin- and ist-1-dependent process. Aversive learning suppresses odor-regulated glutamate release from AWCON in wild-type animals but not in ist-1 mutants, suggesting that localized insulin signaling drives presynaptic depression to generate an aversive memory.
The calcium channel Orai1 is required for osteoblast development: studies in a chimeric mouse with variable in vivo Runx-cre deletion of Orai-1
Authors: Robinson Lisa J , Soboloff Jonathan , Tourkova Irina L , Larrouture Quitterie C , Papachristou Dionysios J , Gross Scott , Hooper Robert , Samakai Elsie , Worley Paul F , Tuckermann Jan , Witt Michelle R , Blair Harry C 
Published: February 2022

AbstractThe calcium-selective ion channel Orai1 has a complex role in bone homeostasis, with defects in both bone production and resorption detected in Orai1 germline knock-out mice. To determine whether Orai1 has a direct, cell-intrinsic role in osteoblast differentiation and function, we bred Orai1 flox/flox (Orai1f/f) mice with Runx2-cre mice to eliminate its expression in osteoprogenitor cells. Interestingly, Orai1 was expressed in a mosaic pattern in Orai1f/f-Runx2-cre bone. Specifically, antibody labeling for Orai1 in vertebral sections was uniform in wild type animals, but patchy regions in Orai1f/f-Runx2-cre bone revealed Orai1 loss while in other areas expression persisted. Nevertheless, by micro-CT, bones from Orai1f/f-Runx2-cre mice showed reduced bone mass overall, with impaired bone formation identified by dynamic histomorphometry. Cortical surfaces of Orai1f/f-Runx2-cre vertebrae however exhibited patchy defects. In cell culture, Orai1-negative osteoblasts showed profound reductions in store-operated Ca2+ entry, exhibited decreased alkaline phosphatase activity, and had markedly impaired substrate mineralization. We conclude that defective bone formation observed in the absence of Orai1 reflects an intrinsic role for Orai1 in differentiating osteoblasts.
Mineralized coleoid cranial cartilage from the Late Triassic Polzberg Konservat-Lagerstätte (Austria)
Authors: Lukeneder Petra , Lukeneder Alexander 
Published: February 2022

AbstractAlthough hyaline cartilage is widely distributed in various invertebrate groups such as sabellid polychaetes, molluscs (cephalopods, gastropods) and a chelicerate arthropod group (horseshoe crabs), the enigmatic relationship and distribution of cartilage in taxonomic groups remains to be explained. It can be interpreted as a convergent trait in animal evolution and thus does not seem to be a vertebrate invention. Due to the poor fossil record of cartilaginous structures, occurrences of mineralized fossil cartilages are important for evolutionary biology and paleontology. Although the biochemical composition of recent cephalopod cartilage differs from vertebrate cartilage, histologically the cartilages of these animal groups resemble one another remarkably. In this study we present fossil material from the late Triassic Polzberg Konservat-Lagerstätte near Lunz am See (Lower Austria, Northern Calcareous Alps). A rich Carnian fauna is preserved here, whereby a morphogroup (often associated with coleoid remains) of black, amorphous appearing fossils still remained undetermined. These multi-elemental, mirroring fossils show remarkable similarities to recent cephalopod cartilage. We examined the conspicuous micro- and ultrastructure of these enigmatic fossils by thin-sectioning and Scanning Electron Microscopy (SEM). The geochemical composition analyzed by Microprobe and Energy Dispersive X-ray Spectroscopy (SEM-EDX) revealed carbonisation as the taphonomic pathway for this fossil group. 3D preservation of this otherwise degradable soft tissue can be explained by the mineralization processes that may take place in particular environments. Fifty-nine specimens from the Polzberg locality and five specimens from Cave del Predil (formerly Raibl, Julian Alps, Italy) underwent extensive studies. The detected grooves are interpreted to be muscular attachment areas, and the preserved branched system of canaliculi is comparable to a channel system that is also present in recent coleoid cartilage. The new findings on these long-known enigmatic structures strongly point to the preservation of cranial cartilage belonging to the belemnoid Phragmoteuthis bisinuata.
Omicron-specific mRNA vaccination alone and as a heterologous booster against SARS-CoV-2
Authors: Fang Zhenhao , Peng Lei , Filler Renata , Suzuki Kazushi , McNamara Andrew , Lin Qianqian , Renauer Paul A. , Yang Luojia , Menasche Bridget , Sanchez Angie , Ren Ping , Xiong Qiancheng , Strine Madison , Clark Paul , Lin Chenxiang , Ko Albert I. , Grubaugh Nathan D. , Wilen Craig B. , Chen Sidi 
Published: February 2022

AbstractThe Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has high transmissibility and recently swept the globe. Due to the extensive number of mutations, this variant has high level of immune evasion, which drastically reduced the efficacy of existing antibodies and vaccines. Thus, it is important to test an Omicron-specific vaccine, evaluate its immune response against Omicron and other variants, and compare its immunogenicity as boosters with existing vaccine designed against the reference wildtype virus (WT). Here, we generated an Omicron-specific lipid nanoparticle (LNP) mRNA vaccine candidate, and tested its activity in animals, both alone and as a heterologous booster to existing WT mRNA vaccine. Our Omicron-specific LNP-mRNA vaccine elicited strong and specific antibody response in vaccination-naïve mice. Mice that received two-dose WT LNP-mRNA, the one mimicking the commonly used Pfizer/Moderna mRNA vaccine, showed a >40-fold reduction in neutralization potency against Omicron variant than that against WT two weeks post second dose, which further reduced to background level >3 months post second dose. As a booster shot for two-dose WT mRNA vaccinated mice, a single dose of either a homologous booster with WT LNP-mRNA or a heterologous booster with Omicron LNP-mRNA restored the waning antibody response against Omicron, with over 40-fold increase at two weeks post injection as compared to right before booster. Interestingly, the heterologous Omicron LNP-mRNA booster elicited neutralizing titers 10-20 fold higher than the homologous WT booster against the Omicron variant, with comparable titers against the Delta variant. All three types of vaccination, including Omicron mRNA alone, WT mRNA homologous booster, and Omicron heterologous booster, elicited broad binding antibody responses against SARS-CoV-2 WA-1, Beta, and Delta variants, as well as other Betacoronavirus species such as SARS-CoV, but not Middle East respiratory syndrome coronavirus (MERS-CoV). These data provided direct proof-of-concept assessments of an Omicron-specific mRNA vaccination in vivo, both alone and as a heterologous booster to the existing widely-used WT mRNA vaccine form.