bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biophysical and functional characterization of K+-Cl-co-transporters fromDrosophila melanogasterandHydra vulgaris
Authors: Fudo Satoshi , Verkhovskaya Marina , Scala Coralie Di , Rivera Claudio , Kajander Tommi 
Published: May 2022

AbstractThe cation-chloride co-transporter (CCC) superfamily includes ion symporters, which co-transport monovalent cations and Cl-. CCCs have crucial roles in shaping signalling and neuronal connectivity in the vertebrate brain. K+-Cl-co-transporters (KCCs) are a subfamily of CCCs and carry out the symport of K+and Cl−ions across the plasma membrane. The KCC proteins are involved in various physiological processes, such as cell volume regulation, transepithelial ion transport, synapse formation and signal transmission, and blood pressure regulation.Among KCCs, KCC2 has gained attention because of its unique and crucial functions in the central nervous system neuronal network. Loss of activity of this transporter has been associated with several neurological disorders including schizophrenia, epilepsy, and chronic pain.On the other hand, only a limited number of studies of KCCs have been published for invertebrates. Among invertebrate proteins, theDrosophila melanogasterKCC (DmKCC) has been studied most and suggested critical for neuronal transmission. Also CnidarianHydra vulgarishas been shown to have a functional KCC (HvKCC). Comparative analyses of these transporters with vertebrate ones and understanding functional and biophysical aspects of them as a model system can help understand the KCC mechanism of ion transport and its regulation and evolution broadly.In this study, we choseDmKCC andHvKCC as model systems and purifiedDmKCC andHvKCC from Sf9 insect cells and characterized their biophysical properties with differential scanning fluorimetry and light scattering techniques. We tested their functionality using a fluorescence assay and developed a method to measure recombinant KCC ion transport activity with flame photometry.
Selective auditory attention modulates cortical responses to sound location change for speech in quiet and in babble
Authors: Ozmeral Erol J. , Palandrani Katherine N. 
Published: May 2022

AbstractListeners use the spatial location or change in spatial location of coherent acoustic cues to aid in auditory object formation. From stimulus-evoked onset responses in normal-hearing listeners using electroencephalography (EEG), we have previously shown measurable tuning to stimuli changing location in quiet, revealing a potential window into cortical object formation. These earlier studies used non-fluctuating, spectrally narrow stimuli, so it was still unknown whether previous observations would translate to speech stimuli and whether responses would be preserved for stimuli in the presence of background maskers. To examine the effects that selective auditory attention and interferers have on object formation, we measured cortical responses to speech changing location in the free field with and without background babble (+6 dB SNR) during both passive and active conditions. Active conditions required listeners to respond to the onset of the speech stream when it occurred at a new location, explicitly indicating yes or no to whether the stimulus occurred at a block-specific location either 30 degrees to the left or right of midline. In the aggregate, results show similar evoked responses to speech stimuli changing location in quiet compared to babble background. However, the effect of the two background environments diverges when considering the magnitude and direction of the location change, in which there was a clear influence of change vector in quiet but not in babble. Therefore, consistent with challenges associated with cocktail party listening, directed spatial attention can be shunted in the presence of stimulus noise and likely leads to poorer use of spatial cues in auditory streaming.
Aspects of the glycome of endochondral ossification
Authors: McClure Sheena F , McClure John 
Published: May 2022

ABSTRACTComparatively little is known about the glycome (the set of glycans and glycoconjugates made by the cell, tissue or organism) of bone and cartilage. The glycome has a high-density coding capacity and is important in post-translational modification. Lectin histochemistry provides insights into the glycome and we applied this technique to an ectopic ossification site in human bronchial cartilages.Our results show that cartilage matrix at the site of erosion by chondroclasts has a limited but definite glycoprofile. In contrast, bone matrix does not express many lectin ligands. Chondroclasts have an extensive glycoprofile similar to that of, but not identical to, osteoclasts. N and O glycans are both expressed in the zone of presumptive mineralization and are relevant to that process. Bone trabecular lining cells communicate with osteocytes via intracanalicular processes and some lectin ligands were expressed by these three components.Mast cells and angiogenesis were prominent. Since cartilage normally resists vascular penetration by the secretion of antiangiogenesis factors it is postulated that the hypertrophic chondrocytes in the mineralization zone produce proteases which inhibit antiangiogenesis and facilitate angiogenesis by mast cells.
Small-molecule inhibitors targeting prokaryotic ClpQ protease in Plasmodium display anti-malarial efficacies against blood and liver stages
Authors: Jain Shaifali , Asad Mohd , Caldelari Reto , Datta Gaurav , Singh Shweta , Rathore Sumit , Stanway Rebecca R. , Heussler Volker T. , Mohmmed Asif 
Published: May 2022

AbstractThe ATP-dependent ClpQY system is a prokaryotic proteasome-like machinery in the mitochondrion of malaria parasite, Plasmodium. This protease system is identified as a validated target for malaria intervention. Here we have identified drug-like small chemical compounds, pyrimidotriazine derivatives, as specific inhibitors of P. falciparum ClpQ (PfClpQ) having effective parasiticidal efficacies on asexual and liver stages. Screening of the ‘Malaria Box’ compound library, using a robust in vitro activity assay, identified a hit compound targeting the PfClpQ protease with IC50 at ~750nM. Further, Structure-Activity Relationship (SAR) analysis, using a small library of derivatives of the hit compound, identified three potential lead compounds, ICGEB-L1, ICGEB-L2 and ICGEB-L3, which inhibited enzyme activity with IC50 in 100-200nM ranges. The three lead compounds effectively inhibited in vitro asexual stage parasite growth in similar concentration ranges with ~100-fold selectivity over mammalian cell line; in addition, these compounds effectively inhibited in vitro growth and maturation of hepatocytic stage parasites with EC50 in low nano-molar ranges. These compounds were found to effectively block the development of trophozoite stages to schizont stage, concurrently arresting development and segregation of parasite mitochondria, in asexual as well as hepatocytic stages of the parasite. These morphological and developmental effects of the drugs on parasites mimic the data from genetic ablation of PfClpQ. Importantly, all three compounds showed significant in vivo anti-parasitic efficacies on blood stages of P. berghei mouse malaria model. Overall these results suggest that these PfClpQ targeting compounds are promising candidates to develop new anti-malarials.
An Updated Gene Regulatory Network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851
Authors: da Silva Chagas Márcia , Filho Fernando Medeiros , dos Santos Marcelo Trindade , de Menezes Marcio Argollo , Carvalho-Assef Ana Paula D’Alincourt , da Silva Fabricio Alves Barbosa 
Published: May 2022

BACKGROUNDHealthcare-associated infections due to multidrug-resistant (MDR) bacteria such as Pseudomonas aeruginosa are significant public health issues worldwide. A system biology approach can help understand bacterial behavior and provide novel ways to identify potential therapeutic targets and the development of new drugs. Gene regulatory networks (GRN) are an example of interaction representation in silico between regulatory genes and their targets.OBJECTIVESIn this work, we update the reconstruction of the MDR P. aeruginosa CCBH4851 GRN, and analyze and discuss its structural properties.METHODSWe based this study on the gene orthology inference methodology using the reciprocal best hit method. The P. aeruginosa CCBH4851 genome and GRN, published in 2019, and the P. aeruginosa PAO1 GRN, published in 2020, were used for this update reconstruction process.FINDINGSOur result is a GRN with a larger number of regulatory genes, target genes, and interactions compared to the previous networks, and its structural properties are consistent with the complexity of biological networks and the biological features of P. aeruginosa.MAIN CONCLUSIONSHere, we present the largest and most complete version of P. aeruginosa GRN published to this date, to the best of our knowledge.
HSF1 excludes CD8+ T cells from breast tumors via suppression of CCL5
Authors: Jacobs Curteisha , Shah Sakhi , Lu Wen-Cheng , Ray Haimanti , Wang John , Sandusky George , Nephew Kenneth P. , Lu Xin , Cao Sha , Carpenter Richard L. 
Published: May 2022

AbstractHeat shock factor 1 (HSF1) is a stress-responsive transcription factor that promotes cancer cell malignancy. A novel HSF1 Activity Signature (HAS) was found to be negatively associated with antitumor immune cells in breast tumors. Knockdown of HSF1 decreased tumor size and caused an influx of several antitumor immune cells, most notably CD8+ T cells. Depletion of CD8+ T cells prevented tumors from shrinking after knockdown of HSF1, suggesting HSF1 prevents CD8+ T cell influx to avoid immune-mediated tumor killing. HSF1 was also found to suppress expression of CCL5, a chemokine for CD8+ T cells, that significantly contributed to the attraction of CD8+ T cells upon the loss of HSF1. This study demonstrates a model whereby HSF1 suppresses CCL5 leading to reduced CD8+ T cells in breast tumors that prevented immune-mediated destruction. For the first time, these studies indicate HSF1 suppresses antitumor immune activity within tumors.
Ancient DNA from the extinct New Zealand grayling (Prototroctes oxyrhynchus) reveals evidence for Miocene marine dispersal
Authors: Scarsbrook Lachie , Mitchell Kieren J. , McGee Matthew D. , Closs Gerard P. , Rawlence Nicolas J. 
Published: May 2022

AbstractThe evolutionary history of Southern Hemisphere graylings (Retropinnidae) in Aotearoa New Zealand—including the number of colonisation events, the directionality and timing of dispersal, and their relationship to the Australian grayling—is poorly understood. The New Zealand grayling (Prototroctes oxyrhynchus) is the only known freshwater fish species to have gone extinct since human arrival in New Zealand. Despite its historical abundance, only 23 formalin-fixed specimens (both wet and dried) exist in museum collections globally, which were previously non-amenable to palaeogenetic analysis.Here, we used high-throughput DNA sequencing techniques, specifically designed for formalin-fixed specimens, to generate mitochondrial genomes ofP. oxyrhynchus, and analysed these within a temporal phylogenetic framework of retropinnid and osmerid taxa.We recovered strong evidence for a sister relationship between the New Zealand and Australian grayling (P. mareana), with the two having a common ancestor around 13.8 Mya (95% HPD: 6.1–23.2 Mya), after the height of Oligocene marine inundation in New Zealand.Our temporal phylogenetic analysis suggests a single marine dispersal event between New Zealand and Australia, though the direction of dispersal is equivocal, followed by divergence into genetically and morphologically distinguishable species through isolation by distance.This study provides further insights into the possible drivers of the extinction of the New Zealand grayling, and highlights how advancements in palaeogenetic techniques can be used to test evolutionary hypotheses in extinct (and living) fish, which have been comparatively neglected in the field of ancient DNA.
Replication stress tolerance and management differs between naïve and primed pluripotent cells
Authors: Kafer Georgia R. , O’Connor Aisling , Rogers Samuel , Osteil Pierre , Nelson Christopher B. , Pickett Hilda A. , Tam Patrick P.L. , Cesare Anthony J. 
Published: May 2022

SummaryReplication stress is an endemic threat to genome stability. For reasons unknown, replication stress response factors become essential during peri-implantation development. This coincides with a stem cell potency switch from the naïve to the primed state. Using genetically matched, chimera-derived mouse naïve embryonic (mESC) and primed epiblast stem cells (mEpiSC) we found that replication stress management differs between potency states. Primed mEpiSCs rely on Atr activity to prevent replication catastrophe, minimize genomic damage, avoid apoptosis, and re-enter the cell cycle. Conversely, under replications stress, mESCs readily activate Atm regardless of Atr activity, undergo replication catastrophe, and induce apoptosis. Primed pluripotent cells therefore engage Atr to counteract replication difficulties and maintain viability, whereas cells in the naïve state are more readily cleared under the same conditions. We anticipate these divergent strategies enable pluripotent cells of different potency states to meet associated proliferative or developmental demands during early development.
A potentialToxoplasma gondiilipoxygenase is necessary for virulence and associated with the host immune response
Authors: Ramírez-Flores Carlos J. , Tibabuzo Perdomo Andrés M. , Wilson Sarah K. , Cavazos Carolina Mendoza , Flores Billy Joel Erazo , Barnes Katie L. , Knoll Laura J. 
Published: May 2022

AbstractWhile the asexual cycle ofToxoplasma gondiican occur in any warm-blooded animal, the sexual cycle is restricted to the feline intestine. We previously determined that because cats lack delta-6-desaturase activity in their intestines, they build up excess linoleic acid, which signalsT. gondiito undergo sexual development. We hypothesized thatT. gondiioxygenates linoleic acid to signal sexual development, so we examined theT. gondiigenome for potential lipoxygenases (TgLOX) enzymes. We identified seven potential TgLOXs that were at least 100-fold more abundant in the cat intestinal versus the tissue culture tachyzoite stage. Parasites deleted in TgLOX1 (TgΔLOX1) had no significant growth differences in tissue culture fibroblast cells. Because the sexual development assay begins with brain cysts, we infected mice with TgΔLOX1 and were surprised to find that TgΔLOX1 had reduced virulence. The TgΔLOX1 parasitemia was reduced by 3 days postinfection and largely cleared by 7 days postinfection. At 3 days postinfection, the cytokines IFNγ, IL-6, MCP-1, and TNF-α were significantly reduced in TgΔLOX1-infected mice, which prompted us to examine TgΔLOX1 in IFNγKO mice. We found that IFNγKO mice infected with TgΔLOX1 succumbed to acute infection with the same kinetics as the parental and complemented strains, suggesting the role of TgLOX1 in mice was IFNγ dependent. In tissue culture fibroblasts, TgLOX1 was localized within the parasite, but in leukocytes from infected mice and activated macrophages, TgLOX1 was localized in vesicular structures in the host cytoplasm. These results suggest that TgLOX1 in these vesicular structures modifies the host immune response.ImportanceLipoxygenases are enzymes that catalyze the dioxygenation of polyunsaturated fatty acids such as linoleic and arachidonic acid. These modifications create signaling molecules that are best characterized for modulating the immune response. Deletion of the first lipoxygenase characterized forToxoplasma gondii(TgLOX1) generated a less virulent strain and infected mice showed a decreased immune response. This virulence defect was dependent on the mouse cytokine IFNγ. TgLOX1 changes location from inside the parasite in tissue culture conditions to vesicular structures within the host immune cells during mouse infection. These results suggest that TgLOX1 plays a role in the modification of the host immune response in mice.
Feasibility and evaluation of an emergency department-based GP streaming and treatment service
Authors: Aldus Clare , Pope Ian , Brainard Julii , Ruston Annmarie , Hughes Gareth , Everden Paul 
Published: May 2022

AbstractBACKGROUNDEmergency departments (EDs) are under ever-increasing pressure. The General Practitioner Streaming and Treatment (GPST) service implemented at a large ED in England UK aimed to identify and treat patients who attended an ED but who might effectively be managed in primary care to reduce pressure on ED services.METHODSPatients attending ED were met by a GP nurse practitioner who ‘streamed’ them to the GPST service or usual ED care. Routinely collected electronic records, satisfaction questionnaires and interviews were used to evaluate patient outcomes, staff experiences, service outcomes and impacts on usual ED services.RESULTSApproximately 96% of GPST patients were seen by a clinician within one hour and all within 87 minutes. Routinely collected ED datasets indicate statistically significant reductions in patients streamed to usual ED care who had to wait > 4 hours for disposition (p=<0.005). Of 769 patients with GPST consultation (approximately 10% of all walk-in patients) 421 (55%) needed no further intervention by ED. The speed at which GPST patients were managed exceeded patients’ expectations and was a major determinant of their satisfaction. No staff expressed dissatisfaction, but some suggested possible improvements in patient eligibility criteria and built environment design features.CONCLUSIONSConcurrent provision of GPST correlated with shorter waits for ED attenders to receive health care. Patient and staff experiences of GPST were positive. A robust assessment of safety and health economic outcomes would be useful to refine eligibility criteria and cost effectiveness.
Spondyloarthritis, acute anterior uveitis, and Crohn’s disease have both shared and distinct gut microbiota
Authors: Essex Morgan , Rios Rodriguez Valeria , Rademacher Judith , Proft Fabian , Löber Ulrike , Markó Lajos , Pleyer Uwe , Strowig Till , Marchand Jérémy , Kirwan Jennifer A. , Siegmund Britta , Forslund Sofia Kirke , Poddubnyy Denis 
Published: May 2022

AbstractObjectivesSpondyloarthritis (SpA) is a group of immune-mediated diseases highly concomitant with non-musculoskeletal inflammatory disorders, such as acute anterior uveitis (AAU) and Crohn’s disease (CD). The gut microbiome represents a promising avenue to elucidate shared and distinct underlying pathophysiology.MethodWe performed 16S rRNA sequencing on stool samples of 277 patients (72 CD, 103 AAU, and 102 SpA) included in the German Spondyloarthritis Inception Cohort (GESPIC) and 62 back pain controls without any inflammatory disorder. Discriminatory statistical methods were used to disentangle microbial disease signals from one another and a wide range of potential confounders. Patients were naïve to or had not received treatment with biological disease-modifying anti-rheumatic drugs for at least three months before enrollment, providing a better approximation of a true baseline disease signal.ResultsWe identified a shared, immune-mediated disease signal represented by low abundances of Lachnospiraceae taxa relative to controls, most notablyFusicatenibacter, which partially mediated higher serum CRP levels and was most abundant in controls receiving NSAID monotherapy. Patients with SpA drove an enrichment ofCollinsella, while HLA-B27+ individuals displayed enrichedFaecalibacterium. CD patients had higher abundances of aRuminococcustaxon, and previous csDMARD therapy was associated with increasedAkkermansia.ConclusionOur work supports the existence of a common gut dysbiosis in SpA and related inflammatory pathologies. We reveal shared and disease-specific microbial associations and potential mediators of disease activity. Validation studies are needed to clarify the role ofFusicatenibacterin gut-joint inflammation, and metagenomic resolution is needed to understand the relationship betweenFaecalibacteriumcommensals and HLA-B27.
Selective observation of semi-rigid non-core residues in dynamically complex mutant huntingtin protein fibrils
Authors: Matlahov Irina , Boatz Jennifer C. , van der Wel Patrick C. A. 
Published: May 2022

AbstractMany amyloid-forming proteins, which are normally intrinsically disordered, undergo a disorder-to-order transition to form fibrils with a rigid β-sheet core flanked by disordered domains. Solid-state NMR (ssNMR) and cryogenic electron microscopy (cryoEM) excel at resolving the rigid structures within amyloid cores but studying the dynamically disordered domains remains challenging. This challenge is exemplified by mutant huntingtin exon 1 (HttEx1), which self-assembles into pathogenic neuronal inclusions in Huntington disease (HD). The mutant protein’s expanded polyglutamine (polyQ) segment forms a fibril core that is rigid and sequestered from the solvent. Beyond the core, solvent-exposed surface residues mediate biological interactions and other properties of fibril polymorphs. Here we deploy magic angle spinning ssNMR experiments to probe for semi-rigid residues proximal to the fibril core and examine how solvent dynamics impact the fibrils’ segmental dynamics. Dynamic spectral editing (DYSE) 2D ssNMR based on a combination of cross-polarization (CP) ssNMR with selective dipolar dephasing reveals the weak signals of solvent-mobilized glutamine residues, while suppressing the normally strong background of rigid core signals. This type of ‘intermediate motion selection’ (IMS) experiment based on cross-polarization (CP) ssNMR, is complementary to INEPT- and CP-based measurements that highlight highly flexible or highly rigid protein segments, respectively. Integration of the IMS-DYSE element in standard CP-based ssNMR experiments permits the observation of semi-rigid residues in a variety of contexts, including in membrane proteins and protein complexes. We discuss the relevance of semi-rigid solvent-facing residues outside the fibril core to the latter’s detection with specific dyes and positron emission tomography tracers.HighlightsMutant huntingtin exon 1 fibrils feature a broad range of molecular dynamics.Molecular motion is coupled to water dynamics outside the fiber core.Dynamics-based spectral editing ssNMR reveals mobile non-core residues.Intermediate-motion selection via dipolar dephasing of rigid sites.Semi-mobile glutamines outside the fiber core observed and identified.
Mycorrhizas shape the evolution of plant adaptation to drought
Authors: Cosme Marco 
Published: May 2022

SummaryPlant adaptation to drought facilitates major ecological transitions, and is likely to play a vital role under looming climate change. Mycorrhizas can influence the physiological capacity of plants to tolerate drought. Here, I show how mycorrhizal strategy and drought adaptation shape one another throughout the course of plant evolution.To characterize the evolutions of both plant characters, I applied a phylogenetic comparative method using data of 1,638 extant species globally distributed.The detected correlated evolution unveiled gains and losses of drought tolerance occurring at faster rates in lineages with an ecto- or ericoid mycorrhizal strategy, which were on average about 15 and 300 times quicker than that in lineages with the arbuscular mycorrhizal and naked root (non-mycorrhiza or facultatively arbuscular mycorrhiza) strategy, respectively. Among mycorrhiza shifts, the arbuscular mycorrhiza losses in drought sensitive lineages were more frequent than any symbiont switching or other mutualism breakdown.My study suggests that mycorrhizas play a key facilitator role in the evolutionary process of plant adaptation to critical changes in water availability across global climates.