bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feeder-Free Generation of Endocardial and Cardiac Valve Cells from Human Pluripotent Stem Cells
Authors: Liu Clifford Z. , Prasad Aditi , Jadhav Bharati , Sharp Andrew J. , Gelb Bruce D. 
Published: March 2023

SummaryValvular heart disease presents a significant health burden, yet advancements in valve biology and novel therapeutics have been hindered by the lack of accessibility to human valve cells. In this study, we have developed a scalable and feeder-free method to differentiate human induced pluripotent stem cells (iPSCs) into endocardial cells. Importantly, we show that these endocardial cells are transcriptionally and phenotypically distinct from vascular endothelial cells and can be directed to undergo endothelial-to-mesenchymal transition (EndMT) to generate cardiac valve cell populations. Following this, we identified two distinct populations—one population undergoes EndMT to become valvular interstitial cells (VICs), while the other population reinforces their endothelial identity to become valvular endothelial cells (VECs). Lastly, we confirmed the identities of our iPSC-derived cell populations and identified putative markers through transcriptomic analyses. By increasing the accessibility to these cell populations, we aim to accelerate discoveries for cardiac valve biology and disease.
Proteomic-based stratification of intermediate-risk prostate cancer patients
Authors: Zhong Qing , Rui Sun , Aref Adel T. , Noor Zainab , Anees Asim , Zhu Yi , Lucas Natasha , Poulos Rebecca C. , Lyu Mengge , Zhu Tiansheng , Wang Bo , Chen Guo-Bo , Wang Yingrui , Ding Xuan , Rutishauser Dorothea , Rupp Niels J. , Rueschoff Jan H. , Poyet Cédric , Hermanns Thomas , Fankhauser Christian , Martínez María Rodríguez , Shao Wenguang , Buljan Marija , Neumann Janis Frederick , Beyer Andreas , Hains Peter G. , Reddel Roger R. , Robinson Phillip J. , Aebersold Ruedi , Guo Tiannan , Wild Peter J. 
Published: March 2023

ABSTRACTGleason grading is an important prognostic indicator for prostate adenocarcinoma and is crucial for patient treatment decisions. However, intermediate-risk patients diagnosed in Gleason Grade Groups (GG) 2 and GG3 can harbour either aggressive or non-aggressive disease, resulting in under- or over-treatment of a significant number of patients. Here, we performed proteomic, differential expression, machine learning, and survival analyses for 1,348 matched tumour and benign sample runs from 278 patients. Three proteins (F5, TMEM126B and EARS2) were identified as candidate biomarkers in patients with biochemical recurrence. Multivariate Cox regression yielded 18 proteins, from which a risk score was constructed to dichotomise prostate cancer patients into low- and high-risk groups. This 18-protein signature is prognostic for the risk of biochemical recurrence and completely independent of the intermediate GG. Our results suggest that markers generated by computational proteomic profiling have the potential for clinical applications including integration into prostate cancer management.
Seven naturally variant loci serve as genetic modifiers ofLamc2jebinduced non-Herlitz Junctional Epidermolysis Bullosa in mice
Authors: Sproule Thomas J. , Philip Vivek M. , Chaudhry Nabig A. , Roopenian Derry C. , Sundberg John P. 
Published: March 2023

AbstractEpidermolysis Bullosa (EB) is a group of rare genetic disorders that compromise the structural integrity of the skin such that blisters and subsequent erosions occur after minor trauma. While primary genetic risk of all subforms of EB adhere to Mendelian patterns of inheritance, their clinical presentations and severities can vary greatly, implying genetic modifiers. TheLamc2jebmouse model of non-Herlitz junctional EB (JEB-nH) demonstrated that genetic modifiers can contribute substantially to the phenotypic variability of JEB and likely other forms of EB. The innocuous changes in an ‘EB related gene’,Col17a1, have shown it to be a dominant modifier ofLamc2jeb. This work identifies six additional Quantitative Trait Loci (QTL) that modify disease inLamc2jeb/jebmice. Three QTL include other known ‘EB related genes’, with the strongest modifier effect mapping to a region including the epidermal hemi-desmosomal structural gene dystonin (Dst-e/Bpag1-e). Three other QTL map to intervals devoid of known EB-associated genes. Of these, one contains the nuclear receptor coactivatorPpargc1aas its primary candidate and the others contain related genesPpargandIgf1, suggesting modifier pathways. These results, demonstrating the potent disease modifying effects of normally innocuous genetic variants, greatly expand the landscape of genetic modifiers of EB and therapeutic approaches that may be applied.
Arabidopsis thalianaBBX14 is a target of GLK1 and involved in high-light acclimation, photomorphogenesis and GUN-type retrograde signaling
Authors: Atanasov Vasil , Schumacher Julia , Muiño Jose M , Larasati Catharina , Wang Liangsheng , Kaufmann Kerstin , Leister Dario , Kleine Tatjana 
Published: March 2023

SUMMARYDevelopment of photosynthetically competent seedlings requires both light and retrograde biogenic signaling pathways. The transcription factor GLK1 functions at the interface between these pathways, and receives input from the biogenic-signaling integrator GUN1. BBX14 was previously identified, together with GLK1, in a core module that mediates the response to high light levels and biogenic signaling. To gain insight into the function of BBX14, we generatedBBX14overexpressors and CRISPR/Cas-mediatedbbx14mutant plants, conducted high-light, RT-qPCR and ChIP-Seq experiments, measured photosynthetic parameters, chlorophyll contents and growth rates, and analyzed alterations in transcriptomics. We found that, although overexpression of BBX14 is deleterious under normal growth conditions, BBX14 is needed to acclimate plants to high light stress.BBX14is a direct target of GLK1, and RNA-Seq analysis suggests that BBX14 is involved in the circadian clock. Knockout ofBBX14results in a long-hypocotyl phenotype that depends on a retrograde signal, andBBX14expression during biogenic signaling requires GUN1. Finally, we clarify the role of BBX14 in GUN-type biogenic signaling. We conclude that BBX14 is an integrator of photomorphogenetic and biogenic signals, and suggest that BBX14 is a nuclear target of retrograde signals downstream of the GUN1/GLK1 module.
Sensing volatiles throughout the body: Geographic and tissue-specific olfactory receptor expression in the fig waspCeratosolen fusciceps
Authors: Krishnan Sushma , Karpe Snehal Dilip , Kumar Hithesh , Nongbri Lucy B , Ramanathan Sowdhamini , Grosse-Wilde Ewald , Hansson Bill S. , Borges Renee M. 
Published: March 2023

AbstractAn essential adaptive strategy in insects is the evolution of olfactory receptors (ORs) to recognize important volatile environmental chemical cues. Our model species,Ceratosolen fusciceps,a specialist wasp pollinator ofFicus racemosa, likely possesses an OR repertoire that allows it to distinguish fig-specific volatiles in highly variable environments. Using a newly assembled genome-guided transcriptome, we annotated 63 ORs in the species and reconstructed the phylogeny ofCeratosolenORs in conjunction with other hymenopteran species. Expression analysis showed that though ORs were mainly expressed in the antennae, 20 percent were also expressed in non-antennal tissues such as the head, thorax, abdomen, legs, wings, and ovipositor. Specific upregulated expression was observed in OR30C in the head and OR60C in the wings. We identified OR expression from all major body parts ofC. fusciceps, suggesting novel roles of ORs throughout the body. Further examination of OR expression ofC. fuscicepsin widely separated geographical locations, i.e., south (urban) and northeast (rural) India, revealed distinct OR expression levels in different locations. This discrepancy likely parallels the observed variation in fig volatiles between these regions and provides new insights into the evolution of insect ORs and their expression across geographical locations and tissues.
The global distribution of paired eddy covariance towers
Authors: Stoy Paul C. , Chu Housen , Dahl Emma , Cala Daniela S. , Shveytser Victoria , Wiesner Susanne , Desai Ankur R. , Novick Kimberly A. 
Published: March 2023

AbstractThe eddy covariance technique has revolutionized our understanding of ecosystem-atmosphere interactions. Eddy covariance studies often use a “paired” tower design in which observations from nearby towers are used to understand how different vegetation, soils, hydrology, or experimental treatment shape ecosystem function and surface-atmosphere exchange. Paired towers have never been formally defined and their global distribution has not been quantified. We compiled eddy covariance tower information to find towers that could be considered paired. Of 1233 global eddy covariance towers, 692 (56%) were identified as paired by our criteria. Paired towers had cooler mean annual temperature (mean = 9.9 °C) than the entire eddy covariance network (10.5 °C) but warmer than the terrestrial surface (8.9 °C) from WorldClim 2.1, on average. The paired and entire tower networks had greater average soil nitrogen (0.57-0.58 g/kg) and more silt (36.0-36.4%) than terrestrial ecosystems (0.38 g/kg and 30.5%), suggesting that eddy covariance towers sample richer soils than the terrestrial surface as a whole. Paired towers existed in a climatic space that was more different from the global climate distribution sampled by the entire eddy covariance network, as revealed by an analysis of the Kullback-Leibler divergence, but the edaphic space sampled by the entire network and paired towers was similar. The lack of paired towers with available data across much of Africa, northern, central, southern, and western Asia, and Latin America with few towers in savannas, shrublands, and evergreen broadleaf forests point to key regions, ecosystems, and ecosystem transitions in need of additional research. Few if any paired towers study the flux of ozone and other atmospherically active trace gases at the present. By studying what paired towers measure – and what they do not – we can make infrastructural investments to further enhance the value of FLUXNET as it moves toward its fourth decade.
Acis-regulatory element regulatesERAP2expression through autoimmune disease risk SNPs
Authors: Venema Wouter J. , Hiddingh Sanne , van Loosdregt Jorg , Bowes John , Balliu Brunilda , de Boer Joke H. , Norel Jeanette Ossewaarde-van , Thompson Susan. D. , Langefeld Carl D. , van der Veken Lars T. , Sofiadis Konstantinos , Krijger Peter H.L. , de Laat Wouter , Kuiper Jonas J.W. 
Published: March 2023

AbstractSingle nucleotide polymorphisms (SNP) near theERAP2gene are associated with autoimmune conditions such asCrohn’s disease, andbirdshot chorioretinopathy, as well as protection against lethal infections, including theBlack Death. Due to high linkage disequilibrium (LD), a great number of trait-associated SNPs are correlated withERAP2expression, however their functional mechanisms remain unidentified. We used genome editing and functional genomics to identify causal variants that remain obscured by LD. We demonstrate by reciprocal allelic replacement thatERAP2expression is directly controlled by the genotype of splice region SNP rs2248374. However, we demonstrate that autoimmune disease-risk SNPs located near the downstreamLNPEPgene promoter are independently associated withERAP2expression. Allele-specific conformation capture assays revealed long-range chromatin contacts between theLNPEPpromoter region and theERAP2promoter and showed that interactions were stronger in patients carrying the alleles that increase susceptibility to autoimmune diseases. Replacing the disease-associated SNPs in theLNPEPpromoter by reference sequences loweredERAP2expression. These findings show that clustered GWAS signals associated with diverse autoimmune conditions and lethal infections act in concert to control ERAP2 expression and that disease-associated variants can convert a gene promoter region into a potent enhancer of a distal gene.
Amyloid fibril proteomics of AD brains reveals modifiers of aggregation and toxicity
Authors: Upadhyay Arun , Chhangani Deepak , Rao Nalini R. , Kofler Julia , Vassar Robert , Rincon-Limas Diego E. , Savas Jeffrey N. 
Published: March 2023

ABSTRACTBackgroundThe accumulation of amyloid beta (Aβ) peptides in fibrils is prerequisite for Alzheimer’s disease (AD). Our understanding of the proteins that promote Aβ fibril formation and mediate neurotoxicity has been limited due to technical challenges in isolating pure amyloid fibrils from brain extracts.MethodsTo investigate how amyloid fibrils form and cause neurotoxicity in AD brain, we developed a robust biochemical strategy. We benchmarked the success of our purifications using electron microscopy, amyloid dyes, and a large panel of Aβ immunoassays. Tandem mass-spectrometry based proteomic analysis workflows provided quantitative measures of the amyloid fibril proteome. These methods allowed us to compare amyloid fibril composition from human AD brains, three amyloid mouse models, transgenic Aβ42 flies, and Aβ42 seeded cultured neurons.ResultsAmyloid fibrils are primarily composed by Aβ42 and unexpectedly harbor Aβ38 but generally lack Aβ40 peptides. Multidimensional quantitative proteomics allowed us to redefine the fibril proteome by identifying 17 new amyloid-associated proteins. Notably, we confirmed 126 previously reported plaque-associated proteins. We validated a panel of these proteins as bona fide amyloid-interacting proteins using antibodies and orthogonal proteomic analysis. One metal-binding chaperone metallothionein-3 is tightly associated with amyloid fibrils and modulates fibril formationin vitro.Lastly, we used a transgenic Aβ42 fly model to test if knock down or over-expression of fibril-interacting gene homologues modifies neurotoxicity. Eight RNAi lines suppressed and 11 enhanced Aβ42 toxicity.ConclusionsThese discoveries and subsequent confirmation indicate that fibril-associated proteins play a key role in amyloid formation and AD pathology.
PREMISE: A database of 20Macaca FascicularisPET/MRI brain imaging available for research
Authors: Chalet Lucie , Debatisse Justine , Wateau Oceane , Boutelier Timothe , Wiart Marlène , Costes Nicolas , Merida Ines , Redouté Jérôme , Langlois Jean-Baptiste , Lancelot Sophie , Léon Christelle , Cho Tae-Hee , Mechtouff Laura , Eker Omer Faruk , Nighoghossian Norbert , Canet-Soulas Emmanuelle , Becker Guillaume 
Published: March 2023

AbstractNon-human primate (NHP) studies are unique in translational research, especially in neurosciences and neuroimaging approaches are a preferred method for scaling cross-species comparative neurosciences. In this regard, neuroimaging database development and sharing are encouraged to increase the number of subjects available to the community while limiting the number of animals used in research. We present here a simultaneous PET/MR dataset of 20 Macaca Fascicularis structured according to the Brain Imaging Data Structure (BIDS) standards. This database contains multiple MRI sequences (anatomical, diffusion and perfusion imaging notably), as well as PET perfusion and inflammation using respectively [15O]H2O and [11C]PK11195 radiotracers. We describe the pipeline method to assemble baseline data from various cohorts and qualitatively assessed all the data using signal-to-noise and contrast-to-noise ratios as well as the median of intensity. The database is stored and available through the PRIME-DE consortium repository.
Addition of adjuvant to DTaP modulates vaccine-induced immunological responses but is insufficient to improve protection in CD-1 mice
Authors: Weaver Kelly L. , Pyles Gage M. , Dublin Spencer R. , Huckaby Annalisa B. , Miller Sarah J. , Paz Gutierrez Maria De La , Sen-Kilic Emel , Witt William T. , Boehm Dylan T. , Damron F. Heath , Barbier Mariette 
Published: March 2023

3.1AbstractPertussis is a vaccine-preventable respiratory disease caused by the Gram-negative bacteriumBordetella pertussis. While vaccination rates remain high in developed countries, incidence of pertussis has increased following the transition from wP vaccines to aP vaccines. The reemergence of pertussis is attributed, in part, to waning immunity induced by aP vaccination. Therefore, the objective of this work was to determine if addition of adjuvant to DTaP can modulate the immune response and improve protection compared to DTaP alone. In this study we immunized outbred, female CD-1 mice with 1/320ththe human dose of vehicle control, DTaP, and DTaP supplemented with adjuvant. Markers of early vaccine-induced memory were measured using a chemokine assay or by flow cytometry. Protection was assessed by measuring serological responses and quantifying bacterial burden in the respiratory tract at day 3 post-challenge. From this work we identified a partially protective aP vaccine dose to use for vaccination and challenge studies. We observed that MPLA and SWE promote robust anti-B. pertussisantibody responses and stimulate significant increases in early markers of vaccine-induced memory such as CXCL13, FDCs, and TFHcells. Quil-A induced Th1 responses compared to DTaP alone, but none of the adjuvants improved protection against challenge withB. pertussis. Overall, the data suggests that addition of adjuvant modulates the protective immune responses induced by aPs. Further studies are needed to evaluate the B cell compartment and longevity of protection.
Jedi-1/MEGF12-mediated phagocytosis controls the pro-neurogenic properties of microglia in the ventricular-subventricular zone
Authors: Morrison Vivianne E. , Houpert Matthew G. , Trapani Jonathan B. , Brockman Asa A. , Kingsley Philip J. , Katdare Ketaki A. , Layden Hillary M. , Nguena-Jones Gabriela , Trevisan Alexandra J. , Maguire-Zeiss Kathleen A. , Marnett Lawrence J. , Bixa Gregory J. , Ihrie Rebecca A. , Carter Bruce D. 
Published: March 2023

AbstractMicroglia are the primary phagocytes in the central nervous system and are responsible for clearing dead cells generated during development or disease. The phagocytic process shapes the phenotype of the microglia, which affects the local environment. A unique population of microglia reside in the ventricular-subventricular zone (V-SVZ) of neonatal mice, but how they influence this neurogenic niche is not well-understood. Here, we demonstrate that phagocytosis creates a pro-neurogenic microglial phenotype in the V-SVZ and that these microglia phagocytose apoptotic cells via the engulfment receptor Jedi-1. Deletion of Jedi-1 decreases apoptotic cell clearance, triggering the development of a neuroinflammatory phenotype, reminiscent of neurodegenerative and-age-associated microglia, that reduces neural precursor proliferation via elevated interleukin (IL)-1β signaling; inhibition of IL-1 receptor rescues precursor proliferation in vivo. Together, these results reveal a critical role for Jedi-1 in connecting microglial phagocytic activity to a phenotype that promotes neurogenesis in the developing V-SVZ.Graphical Abstract. Jedi-1-dependent phagocytosis supports neurogenesis via suppression of microglial inflammatory pathway activationTop: Wild-type Proliferative-zone-Associated Microglia (PAMs) (cyan) use the engulfment receptor Jedi-1 (‘Jedi’) to engulf apoptotic cells (yellow) in the neurogenic ventricular-subventricular zone (V-SVZ) of the early postnatal brain. Jedi activation supports neural precursor cell (NPC) proliferation and the generation of new neurons.Bottom: Deletion of Jedi reduces microglial phagocytosis and transforms PAMs into Disease-associated Inflammatory Microglia (DIMs) characterized by the upregulation of canonical inflammatory genes and core DIM markers iden ified in the aging and neurodegenerative brain (Nlrp3, NLR family pyrin domain-containing 3; Tnf, tumor necrosis factor; Ccl4, C-C chemokine ligand 4 (also called macrophage inflammatory protein 1β); Ccr5, C-C chemokine receptor type 5). Increased interleukin-1β (IL-1β) synthesis, release, and signaling in the Jedi-null V-SVZ reduces NPC proliferation and newborn neuron number.HighlightsThe engulfment receptor Jedi-1 is expressed by microglia in the neonatal ventricular-subventricular zone (V-SVZ) neurogenic niche.Jedi-1knockout microglia have decreased engulfment ability, resulting in accumulation of dead cells in the V-SVZ.Loss ofJedi-1leads to a neuroinflammatory phenotype in microglia that is characteristic of neurodegenerative and age-associated microglia.Microglial-specific loss ofJedi-1 reduces neurogenesis, which is rescuedin vivoby inhibition of interleukin-1β signaling.
State-dependent effectiveness of cathodal transcranial direct current stimulation on cortical excitability
Authors: Vergallito Alessandra , Varoli Erica , Pisoni Alberto , Mattavelli Giulia , Del Mauro Lilia , Feroldi Sarah , Vallar Giuseppe , Romero Lauro Leonor J. 
Published: March 2023

AbstractThe extensive use of transcranial direct current stimulation (tDCS) in experimental and clinical settings does not correspond to an in-depth understanding of its underlying neurophysiological mechanisms. In previous studies, we employed an integrated system of Transcranial Magnetic Stimulation and Electroencephalography (TMS-EEG) to track the effect of tDCS on cortical excitability. At rest, anodal tDCS (a-tDCS) over the right Posterior Parietal Cortex (rPPC) elicits a widespread increase in cortical excitability. In contrast, cathodal tDCS (c-tDCS) fails to modulate cortical excitability, being indistinguishable from sham stimulation.Here we investigated whether an endogenous task-induced activation during stimulation might change this pattern, improving c-tDCS effectiveness in modulating cortical excitability.In Study 1, we tested whether performance in a Visuospatial Working Memory Task (VWMT) and a modified Posner Cueing Task (mPCT), involving rPPC, could be modulated by c-tDCS. Thirty-eight participants were involved in a two-session experiment receiving either c-tDCS or sham during tasks execution. In Study 2, we recruited sixteen novel participants who performed the same paradigm but underwent TMS-EEG recordings pre- and 10 minutes post-sham and c-tDCS.Behavioral results showed that c-tDCS significantly modulated mPCT performance compared to sham. At a neurophysiological level, c-tDCS significantly reduced cortical excitability in a frontoparietal network involved in task execution. Taken together, our results provide evidence of the state dependence of c-tDCS in modulating cortical excitability effectively. The conceptual and applicative implications are discussed.
Cell type-specific intracellular protein delivery with inactivated botulinum toxin
Authors: Roh Heegwang , Dorner Brigitte G. , Ting Alice Y. 
Published: March 2023

AbstractThe ability to deliver proteins and peptides across the plasma membrane into the cytosol of living mammalian cells would be highly impactful for both basic science and medicine. Natural cell-penetrating protein toxins have shown promise as protein delivery platforms but existing approaches are limited by immunogenicity, lack of cell type specificity, or their multicomponent nature. Here we explore inactivated botulinum toxin (BoNT) as a protein delivery platform. Using split luciferase reconstitution in the cytosol as a readout for endosomal escape and cytosolic delivery, we showed that BoNT chimeras with nanobodies replacing their natural receptor binding domain could be selectively targeted to cells expressing nanobody-matched surface markers. We used chimeric BoNTs to deliver a range of cargo from 1.3-55 kD, and demonstrated selective delivery of orthogonal cargoes to distinct cell populations within a heterogenous mixture. These explorations suggest that BoNT can be a versatile platform for targeted protein and peptide delivery into mammalian cells.