bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mmp14 is required for matrisome homeostasis and circadian rhythm in fibroblasts
Authors: Chloé Yeung Ching-Yan , Garva Richa , Pickard Adam , Lu Yinhui , Mallikarjun Venkatesh , Swift Joe , Taylor Susan H. , Rai Jyoti , Eyre David R. , Chaturvedi Mayank , Itoh Yoshifumi , Meng Qing-Jun , Mauch Cornelia , Zigrino Paola , Kadler Karl E. 
Published: April 2022

ABSTRACTThe circadian clock in tendon regulates the daily rhythmic synthesis of collagen-I and the appearance and disappearance of small-diameter collagen fibrils in the extracellular matrix. How the fibrils are assembled and removed is not fully understood. Here, we first showed that the collagenase, membrane type I-matrix metalloproteinase (MT1-MMP, encoded byMmp14), is regulated by the circadian clock in postnatal mouse tendon. Next, we generated tamoxifen-inducedCol1a2-Cre-ERT2::Mmp14KO mice (Mmp14conditional knockout (CKO)). The CKO mice developed hind limb dorsiflexion and thickened tendons, which accumulated narrow-diameter collagen fibrils causing ultrastructural disorganization. Mass spectrometry of control tendons identified 1195 proteins of which 212 showed time-dependent abundance. InMmp14CKO mice 19 proteins had reversed temporal abundance and 176 proteins lost time dependency. Among these, the collagen crosslinking enzymes lysyl oxidase-like 1 (LOXL1) and lysyl hydroxylase 1 (LH1; encoded byPlod2) were elevated and had lost time-dependent regulation. High-pressure chromatography confirmed elevated levels of hydroxylysine aldehyde (pyridinoline) crosslinking of collagen in CKO tendons. As a result, collagen-I was refractory to extraction. We also showed that CRISPR-Cas9 deletion ofMmp14from cultured fibroblasts resulted in loss of circadian clock rhythmicity of period 2 (PER2), and recombinant MT1-MMP was highly effective at cleaving soluble collagen-I but less effective at cleaving collagen pre-assembled into fibrils. In conclusion, our study shows that circadian clock-regulatedMmp14controls the rhythmic synthesis of small diameter collagen fibrils, regulates collagen crosslinking, and its absence disrupts the circadian clock and matrisome in tendon fibroblasts.
Reduced mitochondria provide an essential function for the cytosolic methionine cycle
Authors: Zítek Justyna , Füssy Zoltán , Treitli Sebastian C. , Peña-Diaz Priscila , Vaitová Zuzana , Zavadska Daryna , Harant Karel , Hampl Vladimír 
Published: April 2022

SummaryIt has been long hypothesised that mitochondrial reduction is intrinsically related to the remodelling of Fe-S clusters assembly. Yet as our knowledge of divergent free-living protists broadens, so does the spectrum of variability within the range of mitochondrial-related organelles (MROs) fundamental functions. We resolved to high precision the MRO proteome of Paratrimastix pyriformis using Localisation of Organelle Proteins by Isotope Tagging (LOPIT) and demonstrate its role in the synthesis of folate derivates bearing one-carbon (1C) units, its link to the glycine cleavage system (GCS) and their only conceivable role as suppliers for the cytosolic methionine cycle, involved in recycling of S-adenosine methionine. This observation provides congruity to the presence of GCS in MROs of free-living anaerobes and its absence in endobionts, which typically lose the methionine cycle and, in the case of oxymonads, also mitochondria.
Oncogenic mutations in the DNA-binding domain of FOXO1 disrupt folding: quantitative insights from experiments and molecular simulations
Authors: Novack Dylan , Qian Lei , Acker Gwyneth , Voelz Vincent A. , Baxter Richard H. G. 
Published: April 2022

AbstractFOXO1, a member of the family of winged-helix motif Forkhead box (FOX) transcription factors, is the most abundantly expressed FOXO member in mature B-cells. Sequencing of diffuse large B-cell lymphoma (DLBCL) tumors and cell lines identified specific mutations in the forkhead domain linked to loss of function. Differential scanning calorimetry and thermal shift assays were used to characterize how eight of these mutations affect the stability of the FOX domain. Mutations L183P and L183R were found to be particularly destabilizing. Electrophoresis mobility shift assays show these same mutations also disrupt FOXO1 binding to their canonical DNA sequences, suggesting the loss of function is due to destabilization of the folded structure. Computational modeling of the effects of mutations on FOXO1 folding was performed using alchemical FEP, and a Markov model of the entire folding reaction was constructed from massively parallel molecular simulations, which predicts folding pathways involving the late folding of helix α3. Although FEP is able to qualitatively predict the destabilization from L183 mutations, we find that a simple hydrophobic transfer model, combined with estimates of unfolded-state solvent accessible surface areas from molecular simulation, is able to more accurately predict changes in folding free energies due to mutations. These results suggest that atomic detail provided from simulation is important for accurate prediction of mutational effects on folding stability. Corresponding disease-associated mutations in other FOX family members support further experimental and computational studies of the folding mechanism of FOX domains.
Surface curvature and basal hydraulic stress induce spatial bias in cell extrusion
Authors: Huang Cheng-Kuang , Yong Xianbin , She David T. , Lim Chwee Teck 
Published: April 2022

ABSTRACTEpithelial cell extrusion is employed in maintaining a healthy epithelium. It remains unclear how environmental conditions specific to various epithelial tissues, such as geometry and fluid osmolarity, affect cell extrusions. We found that, over curved surfaces, epithelial monolayers exhibited higher extrusion rates in concave regions than convex ones. This difference, and overall extrusions, decreased when osmotically induced basal hydraulic stress was reduced by increasing media osmolarity or by culturing monolayers on hydrogels. Mechanistically, basal fluid accumulation antagonized cell-substrate adhesions and the subsequent FAK-Akt survival pathway, leading to apoptotic cell death. Convex surfaces induced cellular forces that acted against osmosis, thereby promoting adhesions and lowering apoptosis. This effect was reversed in concave regions, and together, resulted in a curvature induced spatial bias in cell extrusions.
Reduced cutaneous CD200:CD200R1 signalling in psoriasis enhances neutrophil recruitment to skin
Authors: Linley Holly , Jaigirdar Shafqat , Mohamed Karishma , Griffiths Christopher EM , Saunders Amy 
Published: April 2022

AbstractThe skin immune system is tightly regulated to prevent inappropriate inflammation in response to harmless environmental substances. This regulation is actively maintained by mechanisms including cytokines and cell surface receptors and its loss results in inflammatory disease. In the case of psoriasis, inappropriate immune activation leads to IL-17-driven chronic inflammation, but molecular mechanisms underlying this loss of regulation are not well understood.We reveal that immunoglobulin superfamily member CD200, and signalling via its receptor, CD200R1 are reduced in non-lesional psoriasis skin. To examine the consequences of this, CD200R1 was blocked in a mouse model of psoriasis demonstrating that the receptor limits psoriasis-like inflammation. Specifically, CD200R1 blockade enhances acanthosis, CCL20 production and neutrophil recruitment but surprisingly, macrophage function and IL-17 production were not affected, and neutrophil reactive oxygen species production was reduced.Collectively, our data show that CD200R1 affects neutrophil function and limits inflammatory responses in healthy skin by restricting neutrophil recruitment. However, the CD200 pathway is reduced in psoriasis, resulting in a loss of immune control, and increased neutrophil recruitment in mouse models. In conclusion, we highlight a pathway that might be targeted to dampen inflammation in patients with psoriasis.
Artificial selection methods from evolutionary computing show promise for directed evolution of microbes
Authors: Lalejini Alexander , Dolson Emily , Vostinar Anya E. , Zaman Luis 
Published: April 2022

AbstractDirected microbial evolution harnesses evolutionary processes in the laboratory to construct microorganisms with enhanced or novel functional traits. Attempting to direct evolutionary processes for applied goals is fundamental to evolutionary computation, which harnesses the principles of Darwinian evolution as a general purpose search engine for solutions to challenging computational problems. Despite their overlapping approaches, artificial selection methods from evolutionary computing are not commonly applied to living systems in the laboratory. In this work, we ask if parent selection algorithms—procedures for choosing promising progenitors—from evolutionary computation might be useful for directing the evolution of microbial populations when selecting for multiple functional traits. To do so, we introduce an agent-based model of directed microbial evolution, which we used to evaluate how well three selection algorithms from evolutionary computing (tournament selection, lexicase selection, and non-dominated elite selection) performed relative to methods commonly used in the laboratory (elite and top-10% selection). We found that multi-objective selection techniques from evolutionary computing (lexicase and non-dominated elite) generally outperformed the commonly used directed evolution approaches when selecting for multiple traits of interest. Our results motivate ongoing work transferring these multi-objective selection procedures into the laboratory. Additionally, our findings suggest that more sophisticated artificial selection methods from evolutionary computation should also be evaluated for use in directed microbial evolution.
Pleiotrophin signals through ALK receptor to enhance growth of neurons in the presence of inhibitory CSPGs
Authors: Gupta Somnath J , Churchward Matthew A , Todd Kathryn G , Winship Ian R 
Published: April 2022

AbstractChondroitin sulfate proteoglycans (CSPGs), one of the major extracellular matrix components of the glial scar that surrounds central nervous system (CNS) injuries, are known to inhibit the regeneration of neurons. This study investigated whether pleiotrophin (PTN), a growth factor upregulated during early CNS development, can overcome the inhibition mediated by CSPGs and promote the neurite outgrowth of neurons in vitro. The data showed that a CSPG matrix inhibited the outgrowth of neurites in primary cortical neuron cultures compared to a control matrix. PTN elicited a dose dependent increase in the neurite outgrowth even in the presence of the growth inhibitory CSPG matrix, with optimal growth at 15 ng mL-1 of PTN (114.8% of neuronal outgrowth relative to laminin control). The growth promoting effect of PTN was blocked by inhibition of the receptor anaplastic lymphoma kinase (ALK) by alectinib in a dose dependent manner. Neurite outgrowth in the presence of this CSPG matrix was induced by activation of the protein kinase B (AKT) pathway, a key downstream mediator of ALK activation. This study identified PTN as a dose-dependent regulator of neurite outgrowth in primary cortical neurons cultured in the presence of a CSPG matrix, and identified ALK activation as a key driver of PTN-induced growth.Summary statementFunction in the central nervous system (CNS) is attributed to the complex interactions of neurons and glia. These cells are anchored in extracellular matrix (ECM) which constitutes about 10% - 20% of brain volume. Cells in the brain produce different components of the ECM in brain including chondroitin sulfate proteoglycans (CSPGs). After a nervous system injury, glial cells produce excess CSPGs that restrict the regeneration of neurons, thus limiting functional recovery. This study examines the role of the endogenous growth factor pleiotrophin (PTN) in driving the growth of neurons even in the presence of inhibitory CSPGs, and anaplastic lymphoma kinase (ALK) receptor as a key mediator by which PTN potentiates growth.
Modulation of C5a-C5aR1 signaling alters the dynamics of AD progression
Authors: Carvalho Klebea , Schartz Nicole D. , Balderrama-Gutierrez Gabriela , Liang Heidi Y. , Chu Shu-Hui , Selvan Purnika , Gomez-Arboledas Angela , Petrisko Tiffany J. , Fonseca Maria I. , Mortazavi Ali , Tenner Andrea J. 
Published: April 2022

AbstractBackgroundThe complement system is part of the innate immune system that clears pathogens and cellular debris. In the healthy brain, complement influences neurodevelopment and neurogenesis, synaptic pruning, clearance of neuronal blebs, recruitment of phagocytes, and protects from pathogens. However, excessive downstream complement activation that leads to generation of C5a, and C5a engagement with its receptor C5aR1, instigates a feed-forward loop of inflammation, injury, and neuronal death, making C5aR1 a potential therapeutic target for neuroinflammatory disorders. C5aR1 ablation in the Arctic (Arc) model of Alzheimer’s disease protects against cognitive decline and neuronal injury without altering amyloid plaque accumulation.MethodsTo elucidate the effects of C5a-C5aR1 signaling on AD pathology, we crossed Arc mice with a C5a overexpressing mouse (ArcC5a+) and tested hippocampal memory. RNA-seq was performed on hippocampus and cortex from Arc, ArcC5aR1KO, and ArcC5a+ mice at 2.7-10 months and age-matched controls to assess mechanisms involved in each system. Immunohistochemistry was used to probe for protein markers of microglia and astrocytes activation states.ResultsArcC5a+ mice had accelerated cognitive decline compared to Arc. Deletion of C5ar1 delayed or prevented the expression of some, but not all, AD-associated genes in the hippocampus and a subset of pan-reactive and A1 reactive astrocyte genes, indicating a separation between genes induced by amyloid plaques alone and those influenced by C5a-C5aR1 signaling.. Biological processes associated with AD and AD mouse models, including inflammatory signaling, microglial cell activation, and astrocyte migration, were delayed in the ArcC5aR1KO hippocampus. Interestingly, C5a overexpression also delayed the increase of some AD-, complement-, and astrocyte-associated genes, suggesting the possible involvement of neuroprotective C5aR2. However, these pathways were enhanced in older ArcC5a+ mice compared to Arc. Immunohistochemistry confirmed that C5a-C5aR1 modulation in Arc mice delayed the increase in CD11c-positive microglia, while not affecting other pan-reactive microglial or astrocyte markers.ConclusionC5a-C5aR1 signaling in AD largely exerts its effects by enhancing microglial activation pathways that accelerate disease progression. While C5a may have neuroprotective effects via C5aR2, engagement of C5a with C5aR1 is detrimental in AD models. These data support specific pharmacological inhibition of C5aR1 as a potential therapeutic strategy to treat AD.
Xport-A functions as a chaperone by stabilizing the first 5 transmembrane domains of Rhodopsin-1
Authors: Gaspar Catarina J , Martins Joana C , Melo Manuel N , Cordeiro Tiago N , Adrain Colin , Domingos Pedro M 
Published: April 2022

SummaryRhodopsin-1 (Rh1), the main photo-sensitive protein ofDrosophila, is a seven transmembrane domain protein, which is inserted co-translationally in the endoplasmic reticulum (ER) membrane. Maturation of Rh1 occurs in the ER, where various chaperones interact with Rh1 to aid in its folding and subsequent transport in the secretory pathway. Xport-A has been shown to be a chaperone/ transport factor for Rh1, but the exact molecular mechanism for Xport-A activity upon Rh1 is not known. Here, based on computational predictions, we propose a model where Xport-A functions as a chaperone in the biosynthesis of Rh1 by stabilizing the first 5 transmembrane domains of Rh1, but not the full length Rh1 protein.
IMC10 and LMF1 mediate membrane contact between the mitochondrion and the inner membrane complex in Toxoplasma gondii
Authors: Souza Rodolpho Ornitz Oliveira , Jacobs Kylie N. , Arrizabalaga Gustavo 
Published: April 2022

ABSTRACTThe single mitochondrion of Toxoplasma gondii is highly dynamic, being predominantly in a peripherally distributed lasso-shape in intracellular parasites and collapsed in extracellular ones. The peripheral positioning of the mitochondrion is associated with apparent contacts between the mitochondrion membrane and the parasite pellicle. The outer mitochondrial membrane-associated protein LMF1 is critical for the correct positioning of the mitochondrion, and in its absence, intracellular parasites fail to form the lasso-shaped mitochondrion. To identify other proteins that participate in tethering the parasite’s mitochondrion to the pellicle, we performed a yeast two-hybrid screen for LMF1 interactors. We identified 70 putative interactors, six of which are known to localize to the apical end of the parasite, two to the mitochondrial membrane, and three localize to the inner membrane complex (IMC), a component of the parasite pellicle. Using reciprocal immunoprecipitation and proximity ligation assays, we confirmed the interaction of LMF1 with the pellicle protein IMC10, with a hypothetical protein known to be part of the conoid, and with an ATPase-Guanylyl Cyclase. Conditional knockdown of IMC10 does not affect parasite viability but severely affects mitochondrial morphology in intracellular parasites and mitochondrial distribution to the daughter cells during division. In effect, IMC10 knockdown phenocopies disruption of LMF1, suggesting that these two proteins define a novel membrane tether between Toxoplasma’s mitochondrion and the inner membrane complex.IMPORTANCEToxoplasma gondii is an opportunistic parasite that can cause life-threatening disease in immunocompromised patients and those infected congenitally. As current therapies against this parasite can be poorly tolerated and are not effective against the latent stage of the parasite, there is an urgent need to identify new drug targets. The single mitochondrion of this parasite is a validated drug target, but little is known about the machinery that controls its division and structure, information that would be critical for a thorough exploration of the mitochondrion as a drug target. We have identified parasite-specific proteins that are essential to maintain the normal structure of the mitochondrion. We have discovered a complex of two proteins that tether the mitochondrion to the periphery of the parasite. Loss of this connection results in changes in mitochondrial morphology and cell division defects. Our results provide important insight into the molecular mechanisms regulating Toxoplasma mitochondrial morphology.
Appia: simpler chromatography analysis and visualization
Authors: Posert Richard , Baconguis Isabelle 
Published: April 2022

AbstractChromatography is an essential family of assays for molecular biology and chemistry. Typically, only a qualitative assessment of peak height, position, and shape are sufficient to proceed. However, there are more advanced forms of chromatography that require integration of peak width, baseline subtraction, and precise peak position calling. To handle these precise workflows, instrument manufacturer software is complicated and arcane; this makes simpler day-to-day analyses inefficient. Additionally, each manufacturer reports the data in their own proprietary format, requiring that analysis is performed at instrument computers and making data sharing between labs difficult. Here we present Appia, a free, open-source chromatography processing and visualization package focused on making analysis, collaboration, and publication quick and easy.
Activation of the integrative and conjugative element Tn916causes growth arrest and death of host bacteria
Authors: Bean Emily L. , McLellan Lisa K. , Grossman Alan D. 
Published: April 2022

ABSTRACTIntegrative and conjugative elements (ICEs) serve as major drivers of bacterial evolution. These elements often confer some benefit to a host cell, including antibiotic resistance, metabolic capabilities, or pathogenic determinants. ICEs can also have negative impacts on their host cells. Here, we investigated the effects of the ICE (conjugative transposon) Tn916on host cells. Because Tn916is active in a relatively small subpopulation of host cells, we developed a fluorescent reporter system for monitoring activation of Tn916in single cells. We found that when active inBacillus subtilisand its natural hostEnterococcus faecalis, Tn916inhibited cell division and most cells died. We also observed these phenotypes on the population level inB. subtilisutilizing a modified version of Tn916that can be activated in the majority of cells. We identified two genes (orf17andorf16) in Tn916that were sufficient to cause host growth defects and identified a single gene,yqaR, that is found in a defective phage (skin) in theB. subtilischromosome that is required for this phenotype. However, these three genes are only partially responsible for the growth defect caused by Tn916, indicating that Tn916possesses multiple mechanisms to affect growth and viability of host cells. These results highlight the complex relationships that conjugative elements have with their host cells and the interplay between mobile genetic elements.
The behavioral signature of stepwise learning strategy and its neural correlate in the basal forebrain
Authors: Manzur Hachi E. , Vlasov Ksenia , Jhong You-Jhe , Chen Hung-Yen , Lin Shih-Chieh 
Published: April 2022

SummaryStudies of associative learning have commonly focused on how rewarding outcomes are predicted by either sensory stimuli or animals’ actions. However, in many learning scenarios, reward delivery requires the occurrence of both sensory stimuli and animals’ actions in a specific order, in the form of behavioral sequences. How such behavioral sequences are learned is much less understood. Here we provide behavioral and neurophysiological evidence to show that behavioral sequences are learned using a stepwise strategy. In rats learning a new association, learning started from the behavioral event closest to the reward and sequentially incorporated earlier events. This led to the sequential refinement of reward-seeking behaviors, which was characterized by the stepwise elimination of ineffective and non-rewarded behavioral sequences. At the neuronal level, this stepwise learning process was mirrored by the sequential emergence of basal forebrain neuronal responses toward each event, which quantitatively conveyed a reward prediction error signal and promoted reward-seeking behaviors. Together, these behavioral and neural signatures revealed how behavioral sequences were learned in discrete steps and when each learning step took place.