bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of fetal liver stroma in spectral cytometry using the parameter autofluorescence
Authors: Peixoto Marcia Mesquita , Soares-da-Silva Francisca , Schmutz Sandrine , Mailhe Marie-Pierre , Novault Sophie , Cumano Ana , Ait-Mansour Cedric 
Published: October 2021

AbstractThe fetal liver is the main hematopoietic organ during embryonic development. The fetal liver is also the unique anatomical site where hematopoietic stem cells expand before colonizing the bone marrow, where they ensure life-long blood cell production and become mostly resting. The identification of the different cell types that comprise the hematopoietic stroma in the fetal liver is essential to understand the signals required for the expansion and differentiation of the hematopoietic stem cells. We used a panel of monoclonal antibodies to identify fetal liver stromal cells in a 5-laser equipped spectral flow cytometry analyzer. The “Autofluorescence Finder” of SONY ID7000 software identified two distinct autofluorescence emission spectra. Using autofluorescence as a fluorescence parameter we could assign the two autofluorescent signals to three distinct cell types and identified surface markers that characterize these populations. We found that one autofluorescent population corresponds to hepatoblasts and cholangiocytes whereas the other expresses mesenchymal transcripts and was identified as stellate cells. Importantly, after birth, autofluorescence becomes the unique identifying property of hepatoblasts because mature cholangiocytes are no longer autofluorescent.These results show that autofluorescence used as a parameter in spectral flow cytometry is a useful tool to identify new cell subsets that are difficult to analyze in conventional flow cytometry.
A novel approach to develop wheat chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in doubled haploid introgression lines
Authors: Grewal Surbhi , Coombes Benedict , Joynson Ryan , Hall Anthony , Fellers John , Yang Cai-yun , Scholefield Duncan , Ashling Stephen , Isaac Peter , King Ian P. , King Julie 
Published: October 2021

ABSTRACTMany wild relative species are being used in pre-breeding programmes to increase the genetic diversity of wheat. Genotyping tools such as single nucleotide polymorphism (SNP)-based arrays and molecular markers have been widely used to characterise wheat-wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP-based KASP markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome- and PCR-amplicon-based sequencing of the wild species. But chromosome-specific KASPs assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum and development of a SNP discovery pipeline that generated ∼38,000 SNPs in single-copy wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as functional. Together with assays validated in previous studies, 498 well distributed chromosome-specific markers were used to recharacterize previously genotyped wheat-Am. muticum doubled haploid (DH) introgression lines. The chromosome specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines.Key MessageA novel methodology to generate chromosome-specific SNPs between wheat and its wild relative Amblyopyrum muticum and their use in the development of KASP markers to genotype wheat-Am. muticum introgression lines.
Modeling spatial, developmental, physiological, and topological constraints on human brain connectivity
Authors: Oldham S. , Fulcher B. D. , Aquino K. , Arnatkevičiūtė A. , Paquola C. , Shishegar R. , Fornito A. 
Published: October 2021

AbstractThe complex connectivity of nervous systems is thought to have been shaped by competitive selection pressures to minimize wiring costs and support adaptive function. Accordingly, recent modeling work indicates that stochastic processes, shaped by putative trade-offs between the cost and value of each connection, can successfully reproduce many topological properties of macroscale human connectomes measured with diffusion magnetic resonance imaging. Here, we derive a new formalism with the aim to more accurately capture the competing pressures of wiring cost minimization and topological complexity. We further show that model performance can be improved by accounting for developmental changes in brain geometry and associated wiring costs, and by using inter-regional transcriptional or microstructural similarity rather than topological wiring-rules. However, all models struggled to capture topologies spatial embedding. Our findings highlight an important role for genetics in shaping macroscale brain connectivity and indicate that stochastic models offer an incomplete account of connectome organization.
Transmembrane Signaling Regulates the Remodeling of the Actin Cytoskeleton: Roles of PKC and Adducin
Authors: Shieh Bih-Hwa , Sun Wesley , Ferng Darwin 
Published: October 2021

AbstractWe tested the hypothesis that Pkc53E regulates adducin to orchestrate the remodeling of the membrane skeleton following the transmembrane GPCR-Gq signaling. Adducin is a known substrate of PKC and is critical for the assembly of the membrane skeleton by cross-linking actin filaments with the spectrin network. In Drosophila photoreceptors, loss of function in pkc53E leads to retinal degeneration while Pkc53E-RNAi negatively impacts the actin cytoskeleton of the visual organelle rhabdomeres. Unexpectedly, Pkc53E-RNAi enhances the degeneration caused by the loss of PLCβ4 (norpAP24). We show that when PLCβ4 is absent Plc21C may be activated instead for activating Pkc53E. We investigate whether Pkc53E phosphorylates adducin in vivo and observed that levels of phosphorylated adducin at the conserved PKC site were greatly reduced in a null allele of pkc53E. We show Pkc53E-RNAi did not modify adducin-RNAi, which exerts a more severe effect on the actin cytoskeleton. Moreover, overexpression of the mCherry-tagged adducin that appears to act in a dominant-negative manner interferes with the spectrin interaction leading to the apical expansion of rhabdomeres similar to that of β-spectrin-RNAi. We performed epistasis analysis and show that double mutants of the tagged adducin and Pkc53E-RNAi display the expansion phenotype at the eclosion, but progress to severe degeneration in adult photoreceptors. Together, most of our findings support that adducin is likely regulated by Pkc53E in Drosophila photoreceptors.
In vivo production of pederin by labrenzin pathway expansion
Authors: Kačar Dina , Schleissner Carmen , Cañedo Librada M. , Rodríguez Pilar , de la Calle Fernando , Cuevas Carmen , Galán Beatriz , García José Luis 
Published: October 2021

SummaryPederin is a potent polyketide toxin that causes severe skin lesions in humans after contact with insects of genus Paederus. Due to its potent anticancer activities, pederin family compounds have raised the interest of pharmaceutical industry. Despite extensive studies on the cluster of biosynthetic genes responsible for the production of pederin, it has not yet been possible to isolate and cultivate its bacterial endosymbiont producer. However, the marine bacterium Labrenzia sp. PHM005 was recently reported to produce labrenzin, the closest pederin analog. By cloning a synthetic pedO gene encoding one of the three O-methyltraferase of the pederin cluster into Labrenzia sp. PHM005 we have been able to produce pederin for the first time by fermentation in the new recombinant strain.
Analysis of centrosomal area actin reorganization and centrosome polarization upon lymphocyte activation at the immunological synapse
Authors: Fernández-Hermira Sara , Sanz-Fernández Irene , Botas Marta , Calvo Víctor , Izquierdo Manuel 
Published: October 2021

ABSTRACTT cell receptor (TCR) and B cell receptor (BCR) stimulation of T and B lymphocytes, by antigen presented on an antigen-presenting cell (APC) induces the formation of the immunological synapse (IS). IS formation is associated with an initial increase in cortical filamentous actin (F-actin) at the IS, followed by a decrease in F-actin density at the central region of the IS, which contains the secretory domain. This is followed by the convergence of secretion vesicles towards the centrosome, and the polarization of the centrosome to the IS. These reversible, cortical actin cytoskeleton reorganization processes occur during lytic granule secretion in cytotoxic T lymphocytes (CTL) and natural killer (NK) cells, proteolytic granules secretion in B lymphocytes and during cytokine-containing vesicle secretion in T-helper (Th) lymphocytes. In addition, several findings obtained in T and B lymphocytes forming IS show that actin cytoskeleton reorganization also occurs at the centrosomal area. F-actin reduction at the centrosomal area appears to be associated with centrosome polarization. In this chapter we deal with the analysis of centrosomal area F-actin reorganization, as well as the centrosome polarization analysis towards the IS.
PTPN14, a modifier of HHT, protects SMAD4 from ubiquitination and turnover to potentiate BMP9 signaling in endothelial cells
Authors: Mamai Ons , Beleford Daniah T. , Taylor Mark , Basu Sugandha , Cen Xinjian , Trilok Suprita , Zhang Jiamin , Balmain Allan , Akhurst Rosemary J. 
Published: October 2021

ABSTRACTHereditary Hemorrhagic Telangiectasia (HHT) results from germline loss-of-function mutations of ENG, ACVRL1, or SMAD4, encoding TGFβ/BMP signaling components. Telangiectasias occur in most patients, and pulmonary, visceral, or cerebral arteriovenous malformations (AVMs) in 20-50% of these. How HHT mutations cause these clinical manifestations and why some patients suffer more serious sequelae than others is unknown. PTPN14 is a genetic modifier of pulmonary AVM incidence, and here we show by gene expression network analysis of a large panel of genetically diverse mouse lung RNA samples, that Ptpn14 is ontologically associated with markers of angiogenesis, vascular remodeling, and BMP/TGFβ and Rho kinase signaling. We demonstrate physical interaction between protein tyrosine phosphatase non-receptor, type 14 (PTPN14) and SMAD4 in nucleus and cytoplasm of primary human endothelial cells. PTPN14 suppresses ubiquitination and turnover of SMAD4 to augment tonic SMAD-mediated transcriptional readouts. This is the first report that PTPN14 binds and stabilizes SMAD4, a key component of the HHT signaling pathway. Through this mechanism, and its inhibition of YAP/TAZ signaling, PTPN14 levels may protect against development of AVMs in HHT. We discuss potential druggable targets for HHT within the ENG-ALK1-SMAD4-PTPN14 network.One Sentence SummaryPTPN14 binds and stabilizes SMAD4 to potentiate BMP9 signaling in endothelial cells and components of the PTPN14 network may be drug targets for HHT.
TheDaphniacarapace and the origin of novel structures
Authors: Bruce Heather S. , Patel Nipam H. 
Published: October 2021

SummaryUnderstanding how novel structures arise is a central question in evolution. Novel structures are often defined as structures that are not derived from (homologous to) any structure in the ancestor1. The carapace of the water fleaDaphnia magnais a bivalved “cape” of exoskeleton that has been proposed to be one of many novel arthropod structures that arose through repeated co-option of genes that also pattern insect wings2–4. To determine whether theDaphniacarapace is a novel structure, we compare the expression ofpannier, araucan, andvestigialbetweenDaphnia, Parhyale, andTribolium. Our results suggest that theDaphniacarapace did not arise by co-option, but instead derives from an exite (lateral lobe) that emerges from an ancestral proximal leg segment that was incorporated into theDaphniabody wall. TheDaphniacarapace therefore appears to be homologous to theParhyaletergal plate and the insect wing5. Remarkably, thevestigial-positive region that gives rise to theDaphniacarapace appears to be present inParhyale6andTriboliumas a small, inconspicuous protrusion. Similarly, thevestigial-positive regions that form thoracic tergal plates inParhyaleappear to be present inDaphnia, even thoughDaphniadoes not form thoracic tergal plates. Thus, rather than a novel structure resulting from gene co-option, theDaphniacarapace appears to have arisen from a shared, ancestral tissue (morphogenetic field) that persists in a cryptic state in other arthropod lineages. Cryptic persistence of unrecognized serial homologs may thus be a general solution for the origin of novel structures.
Moderate prenatal alcohol exposure modifies sex-specific CRFR1 activity in the central amygdala and anxiety-like behavior in adolescent offspring
Authors: Rouzer Siara Kate , Diaz Marvin R. 
Published: October 2021

AbstractAnxiety disorders are highly prevalent among individuals with a history of prenatal alcohol exposure (PAE), and adolescent rodents demonstrate anxiety-like behavior following moderate PAE on Gestational Day (G) 12. A likely systemic target of PAE is the stress peptide corticotrophin-releasing factor (CRF), as activation of CRF receptor 1 (CRFR1) in the medial nucleus of the central amygdala (CeM) is known to increase anxiety-like behavior in adults. To determine if CRF-CRFR1 interactions underly PAE-induced anxiety, functional changes in CRF system activity were investigated in adolescent male and female Sprague Dawley rats following G12 PAE. Compared to air-exposed controls, PAE increased basal spontaneous (s) inhibitory post-synaptic current (IPSC) frequency in the CeM of males, but not females. Furthermore, PAE blunted CRFR1-regulated miniature (m) IPSCs in a sex- and dose-specific manner, and only PAE males demonstrated tonic CRFR1 activity in the CeM. It was further determined that G12 PAE decreased CRFR1 mRNA in the CeM of males while increasing regional expression in females. Finally, infusion of a CRFR1 agonist into the CeM of adolescents produced a blunted expression of CRFR1-induced anxiety-like behavior exclusively in PAE males, mirroring the blunted physiology demonstrated by PAE males. Cumulatively, these data suggest that CRFR1 function within the CeM is age- and sex-specific, and PAE not only increases the expression of anxiety-like behavior, but may reduce the efficacy of treatment for PAE-induced anxiety through CRFR1-associated mechanisms. Therefore, future research will be necessary to develop targeted treatment of anxiety disorders in individuals with a history of PAE.
Evaluation of calcium-sensitive adenylyl cyclase AC1 and AC8 mRNA expression in the anterior cingulate cortex of mice with neuropathic pain
Authors: Shiers Stephanie , Elahi Hajira , Hennen Stephanie , Price Theodore J 
Published: October 2021

AbstractThe anterior cingulate cortex (ACC) is a critical region of the brain for the emotional and affective components of pain in rodents and humans. Hyperactivity in this region has been observed in neuropathic pain states in both patients and animal models and ablation of this region from cingulotomy, or inhibition with genetics or pharmacology can diminish pain and anxiety. Two adenylyl cyclases (AC), AC1 and AC8 play an important role in regulating nociception and anxiety-like behaviors through an action in the ACC, as genetic and pharmacological targeting of these enzymes reduces mechanical hypersensitivity and anxietylike behavior, respectively. However, the distribution of these ACs in the ACC has not been studied in the context of neuropathic pain. To address this gap in knowledge, we conducted RNAscope in situ hybridization to assess AC1 and AC8 mRNA distribution in mice with spared nerve injury (SNI). Given the key role of AC1 in nociception in neuropathic, inflammatory and visceral pain animal models, we hypothesized that AC1 would be upregulated in the ACC of mice following nerve injury. This hypothesis was also founded on data showing increased AC1 expression in the ACC of mice with zymosan-induced visceral inflammation. We found that AC1 and AC8 are widely expressed in many regions of the mouse brain including the hippocampus, ACC, medial prefrontal cortex and midbrain regions, but AC1 is more highly expressed. Contrary to our hypothesis, SNI causes an increase in AC8 mRNA expression in NMDAR-2B (Nr2b) positive neurons in the contralateral ACC but does not affect AC1 mRNA expression. Our findings show that changes in Adcy1 mRNA expression in the ACC are insufficient to explain the important role of this AC in mechanical hypersensitivity in mice following nerve injury and suggest a potential unappreciated role of AC8 in regulation of ACC synaptic changes after nerve injury.
Subcortical Segmentation of the Fetal Brain in 3D Ultrasound using Deep Learning
Authors: Hesse Linde S. , Aliasi Moska , Moser Felipe ,   the INTERGROWTH-21st Consortium, Haak Monique C. , Xie Weidi , Jenkinson Mark , Namburete Ana I.L. 
Published: October 2021

AbstractThe quantification of subcortical volume development from 3D fetal ultrasound can provide important diagnostic information during pregnancy monitoring. However, manual segmentation of subcortical structures in ultra-sound volumes is time-consuming and challenging due to low soft tissue contrast, speckle and shadowing artifacts. For this reason, we developed a convolutional neural network (CNN) for the automated segmentation of the choroid plexus (CP), lateral posterior ventricle horns (LPVH), cavum septum pellucidum et vergae (CSPV), and cerebellum (CB) from 3D ultrasound. As ground-truth labels are scarce and expensive to obtain, we applied few-shot learning, in which only a small number of manual annotations (n = 9) are used to train a CNN. We compared training a CNN with only a few individually annotated volumes versus many weakly labelled volumes obtained from atlas-based segmentations. This showed that segmentation performance close to intra-observer variability can be obtained with only a handful of manual annotations. Finally, the trained models were applied to a large number (n = 278) of ultrasound image volumes of a diverse, healthy population, obtaining novel US-specific growth curves of the respective structures during the second trimester of gestation.
The proSAAS chaperone provides neuroprotection and attenuates transsynaptic α–synuclein spread in rodent models of Parkinson’s disease
Authors: Lindberg Iris , Shu Zhan , Lam Hoa , Helwig Michael , Yucer Nur , Laperle Alexander , Svendsen Clive , Di Monte Donato A. , Maidment Nigel T. 
Published: October 2021

ABSTRACTParkinson’s disease is a devastating motor disorder involving the aberrant aggregation of the synaptic protein synuclein (aSyn) and degeneration of the nigrostriatal dopaminergic tract. We previously showed that proSAAS, a small secreted chaperone protein widely expressed in neurons within the brain, is able to block aSyn-induced dopaminergic cytotoxicity in primary nigral neuron cultures. We show here that coinjection of proSAAS-encoding lentivirus profoundly reduced the motor asymmetry caused by unilateral nigral AAV-mediated human aSyn overexpression. This positive functional outcome was accompanied by significant amelioration of the human aSyn-induced loss of both nigral tyrosine hydroxylase-positive cells and striatal tyrosine hydroxylase-positive terminals, demonstrating clear proSAAS-mediated protection of the nigro-striatal tract. ProSAAS overexpression also reduced the content of human aSyn protein in both the nigra and striatum and reduced the loss of tyrosine hydroxylase protein in both regions. Since proSAAS is a secreted protein, we tested the possibility that proSAAS is able to block the transsynaptic spread of aSyn from the periphery to the central nervous system, increasingly recognized as a potentially significant pathological mechanism. The number of human aSyn-positive neurites in the pons and caudal midbrain of mice following administration of human aSyn-encoding AAV into the vagus nerve was considerably reduced in mice coinjected with proSAAS-encoding AAV, supporting proSAAS-mediated blockade of transsynaptic aSyn transmission. We suggest that proSAAS may represent a promising target for therapeutic development in Parkinson’s disease.SignificanceThis paper describes two independent avenues of research that both provide support for the in vivo neuroprotective function of this small chaperone protein. In the first approach, we show that proSAAS overexpression provides remarkably effective protection against dopaminergic neurotoxicity in a rat model of Parkinson’s disease. This conclusion is supported both by three independent assays of motor function as well as by quantitative analysis of surviving dopaminergic neurons in brain areas involved in the control of motor function. In the second line of research, we show that in mice, the spread of human synuclein across synapses can be blunted by proSAAS overexpression.
Single-cell and nucleus RNA-seq in a mouse model of AD reveal activation of distinct glial subpopulations in the presence of plaques and tangles
Authors: Balderrama-Gutierrez Gabriela , Liang Heidi , Rezaie Narges , Carvalho Klebea , Forner Stefania , Matheos Dina , Rebboah Elisabeth , Green Kim N. , Tenner Andrea J. , LaFerla Frank , Mortazavi Ali 
Published: October 2021

ABSTRACTMultiple mouse models have been generated that strive to recapitulate human Alzheimer’s disease (AD) pathological features to investigate disease mechanisms and potential treatments. The 3xTg-AD mouse presents the two major hallmarks of AD, which are plaques and tangles that increase during aging. While behavioral changes and the accumulation of plaques and tangles have been well described in the 3xTg-AD mice, the subpopulations of neurons and glial cells present throughout disease progression have not been characterized. Here, we used single-cell RNA-seq to investigate changes in subpopulations of microglia, and single-nucleus RNA-seq to explore subpopulations of neurons, astrocytes, and oligodendrocytes in the hippocampus and cortex of aging 3xTg-AD as well as 5xFAD mice for comparison. We recovered a common path of age-associated astrocyte activation between the 3xTg-AD and the 5xFAD models and found that 3xTg-AD-derived astrocytes seem to be less activated. We identified multiple subtypes of microglia, including a subpopulation with a distinct transcription factor expression profile that showed an early increase inCsf1expression before the switch to disease associated microglia (DAM). We used bulk RNA-seq in the hippocampus of 3xTg-AD mice across their lifespan to identify distinct modules of genes whose expression increases with aging and worsening pathology. Finally, scATAC-seq revealed multiple subpopulations of cells with accessible chromatin in regions around genes associated with glial activation. Overall, differences between the main glial groups point to a slower activation process in the 3xTg-AD model when compared to the 5xFAD. Our study contributes to the identification of progressive transcriptional changes of glial cells in a mouse model that has plaques and tangles, thus providing information to aid in targeted AD therapeutics that could translate into positive clinical outcomes.