bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational flexibility of GRASP protein and its constituent PDZ subdomains reveals structural basis of its promiscuous interactome
Authors: Mendes Luis Felipe S. , Batista Mariana R. B. , Judge Peter J. , Watts Anthony , Redfield Christina , Costa-Filho Antonio J. 
Published: June 2019

AbstractThe Golgi complex is a central component of the secretory pathway, responsible for several critical cellular functions in eukaryotes. The complex is organized by the Golgi matrix, which includes the Golgi Reassembly and Stacking Proteins (GRASPs), which participate in cisternae stacking and lateral linkage in vertebrates. GRASPs also have critical roles in other processes, with an unusual ability to interact with several different protein binding partners. The conserved N-terminus of the GRASP family includes two PDZ domains. Previous crystallographic studies of orthologues suggest that PDZ1 and PDZ2 have similar conformations and secondary structure content, however PDZ1 alone mediates nearly all the interactions between GRASPs and their binding partners. In this work, NMR, Synchrotron-Radiation Circular Dichroism and Molecular Dynamics were used to examine the structure, flexibility and stability of the two constituent PDZ domains. GRASP PDZs are structured in an unusual β3α1β4β5α2β6β1β2 secondary structural arrangement and NMR data indicates that the PDZ1 binding pocket is formed by a stable β2-strand and a more flexible and unstable α2-helix, suggesting an explanation for the higher PDZ1 promiscuity. The conformational free energy profiles of the two PDZ domains were calculated using Molecular Dynamics simulations. The data suggest that, after binding, the protein partner significantly reduces the conformational space that GRASPs can access by stabilizing one particular conformation, in a partner-dependent fashion. The structural flexibility of PDZ1, modulated by PDZ2, and the coupled, coordinated movement between the two PDZs enable GRASPs to interact with multiple partners, allowing them to function as promiscuous, multitasking proteins.Significance StatementGolgi Reassembly and Stacking Proteins (GRASPs) play pivotal roles in the maintenance of Golgi structure as well as in unconventional protein secretion. Their broad network of interactions is mainly sustained by the two-PDZ domains located in the N-terminal portion of the protein. The asymmetry of the PDZ domains in terms of number and diversity of interacting partners has been long recognized, but the molecular determinants of that asymmetry remains largely unknown. The biophysical data presented here provide a firm basis for understanding why PDZ1 behaves differently to PDZ2 in solution, despite their similar 3D structures. Furthermore, we propose that PDZ2 assist ligand binding to PDZ1, by means of conformational stabilization.
Sperm quality parameters are increased and asymmetric in house mouse hybrids
Authors: Martincová Iva , Ďureje Ľudovít , Baird Stuart J. E. , Piálek Jaroslav 
Published: June 2019

AbstractSpermatogenesis is a tuned cascade of processes producing sperm; impairment of any phase of this process can affect fitness of males. The level of impairment can be pronounced in hybrids between genetically divergent populations. To explore the effect of hybridization on sperm quality we produced F1 hybrids from 29 wild derived strains of two house mouse subspecies,M. m. musculusandM. m. domesticus, which diverged 0.5 MY ago. The measured sperm quality traits did not significantly differ between intrasubspecific crosses. Effects of intersubspecific hybridization were dependent on sperm trait and cross direction. The proportion of sperm head abnormalities was increased in F1 intersubspecific hybrids. The frequency of dissociated sperm heads was increased in theM. m. musculus×M. m. domesticus(♀×♂) F1 but decreased inM. m. domesticus×M. m. musculus(♀×♂) F1 hybrids, with the difference in medians being more than 180%. We deduce that the dissociated sperm heads trait is associated with the X chromosome and modulated by interaction with the Y chromosome; nevertheless, the high proportion of unexplained variance (55.46 %) suggests the presence of polymorphic autosomal interactions. The reported differences in sperm quality between cross types may be highly relevant to male fitness in zones of secondary contact between the two subspecies. The cross direction asymmetry in frequency of dissociated sperm heads should favour theM. m. musculusY chromosome. This is consistent with the spread of theM. m. musculusY chromosome in nature across the hybrid zone between these two subspecies.
Uncyclized xanthommatin is a key ommochrome intermediate in invertebrate coloration
Authors: Figon Florent , Munsch Thibaut , Croix Cécile , Viaud-Massuard Marie-Claude , Lanoue Arnaud , Casas Jérôme 
Published: June 2019

AbstractOmmochromes are widespread pigments that mediate multiple functions in invertebrates. The two main families of ommochromes are ommatins and ommins, which both originate from the kynurenine pathway but differ in their backbone, thereby in their coloration and function. Despite its broad significance, how the structural diversity of ommochromes arisesin vivohas remained an open question since their first description. In this study, we combined organic synthesis, analytical chemistry and organelle purification to address this issue. From a set of synthesized ommatins, we derived a fragmentation pattern that helped elucidating the structure of new ommochromes. We identified uncyclized xanthommatin as the elusive biological intermediate that links the kynurenine pathway to the ommatin pathway within ommochromasomes, the ommochrome-producing organelles. Due to its unique structure, we propose that uncyclized xanthommatin functions as a key branching metabolite in the biosynthesis and structural diversification of ommatins and ommins, from insects to cephalopods.
Molecular and cellular determinants of motor asymmetry in zebrafish
Authors: Horstick Eric J. , Bayleyen Yared , Burgess Harold A. 
Published: June 2019

AbstractAsymmetries in motor behavior, such as human hand preference, are observed throughout bilateria. However, neural substrates and developmental signaling pathways that impose underlying functional lateralization on a broadly symmetric nervous system are unknown. Here we report that in the absence of over-riding visual information, zebrafish larvae show intrinsic lateralized motor behavior that is mediated by a cluster of 60 posterior tuberculum (PT) neurons in the forebrain. PT neurons impose motor bias via a projection through the epithalamic commissure to the habenula. Acquisition of left/right identity is disrupted by heterozygous mutations inmosaic eyesandmindbomb, genes that regulate Notch signaling. These results define the neuronal substrate for motor asymmetry in a vertebrate and support the idea that developmental pathways that establish visceral asymmetries also govern acquisition of left/right identity.
The P387 Thrombospondin-4 Variant Promotes Accumulation of Macrophages in Atherosclerotic Lesions
Authors: Muppala Santoshi , Rahman Mohammed Tanjimur , Krukovets Irene , Verbovetskiy Dmitriy , Pluskota Elzbieta , Fleischman Aaron , Vince D. Geoffrey , Plow Edward F. , Stenina-Adognravi Olga 
Published: June 2019

AbstractAimsThrombopspondin-4 (TSP4) is a pro-angiogenic protein that has been implicated in tissue remodeling and local vascular inflammation. TSP4 and, in particular, its SNP variant, P387 TSP4, have been associated with cardiovascular disease.Macrophages are central to initiation and resolution of inflammation and development of atherosclerotic lesions, but the effects of the P387 TSP4 on macrophages remain essentially unknown. We examined the effects of the P387 TSP4 variant on macrophages in cell culture andin vivoin a murine model of atherosclerosis. Further, the levels and distributions of the twoTSP4 variants were assessed in human atherosclerotic arteries.Methods and ResultsInApoE−/−/P387-TSP4 knock-in mice, atherosclerotic lesions accumulated more macrophages than lesions bearing A387 TSP4. The levels of inflammatory markers were increased in lesions ofApoE−/−/P387-TSP4 knock-in mice compared toApoE−/−mice. Lesions in human arteries from individuals carrying the P387 variant had higher levels of TSP4 and higher macrophage accumulation. P387 TSP4 was more active in supporting adhesion of cultured human and mouse macrophages in experiments using recombinant TSP4 variants and in cells derived from P387-TSP4 knock-in mice.ConclusionsTSP4 supports the adhesion of macrophages and their accumulation in atherosclerotic lesions. P387 TSP4 is more active in supporting these pro-inflammatory events in the vascular wall, which may contribute to the increased association of P387 TSP4 with cardiovascular disease.AbbreviationsBSA, bovine serum albumin; DMSO, dimethyl sulfoxide; ECM, extracellular matrix;Thbs4−/−, thrombospondin-4 gene knock-out; WT, wild type; P387-TSP4 KI, P387TSP4knock-in mice; OCT, Optimum Cutting Temperature; vWF, von Willebrand factor; α-SMA, alpha-smooth muscle actin; Egr2, Early Growth Response 2; PBS, Phosphate Buffer saline; DMEM, Dulbecco’s Modified Eagle Medium.
Kinetic mechanism of human mitochondrial RNase P
Authors: Liu Xin , Wu Nancy , Shanmuganathan Aranganathan , Klemm Bradley P. , Howard Michael J. , Lim Wan Hsin , Koutmos Markos , Fierke Carol A. 
Published: June 2019

ABSTRACTA first step in processing mitochondrial precursor tRNA (pre-tRNA) is cleavage of the 5’ leader catalyzed by ribonuclease P (RNase P). Human mitochondrial RNase P (mtRNase P) is composed of three protein subunits: mitochondrial RNase P protein (MRPP) 1, 2 and 3. Even though MRPP3 is the metallonuclease subunit responsible for catalysis, cleavage is observed only in the presence of the MRPP1/2 subcomplex. To understand the functional role of MRPP1/2, we reconstituted human mitochondrial RNase P in vitro and performed kinetic and thermodynamic analyses. MRPP1/2 significantly enhances both the catalytic activity and the apparent substrate affinity of mtRNase P. Additionally, pull-down and binding data demonstrate synergy between binding pre-tRNA and formation of a catalytically active MRPP1/2/3 complex. These data suggest that conformational changes in the MRPP1/2-pre-tRNA complex lead to protein-protein or protein-RNA interactions that increase both MRPP3 recognition and cleavage efficiency. This work presents the first kinetic model for human mtRNase P, providing a fundamental framework for the function of MRPP1/2 for recognition and processing of pre-tRNA.
Disrupting ß-catenin dependent Wnt signaling activates an invasive gene program predictive of colon cancer progression
Authors: Chen George T. , Tifrea Delia F. , Murad Rabi , Lyou Yung , Mortazavi Ali , Edwards Robert A. , Waterman Marian L. 
Published: June 2019

AbstractThe recent classification of colon cancer into molecular subtypes revealed that patients with the poorest prognosis harbor tumors with the lowest levels of Wnt signaling. This is contrary to the long-standing understanding that overactive Wnt signaling promotes tumor progression from early initiation stages through to the later stages including invasion and metastasis. Here, we lower the levels of Wnt signaling in colon cancer via interference with two different steps in the pathway that lie upstream or downstream of the effector protein ß-catenin. We find that these Wnt-reduced cancer cells exhibit a more aggressive disease phenotype, including increased mobility in vitro and localized invasion in an orthotopic mouse model. RNA sequencing reveals that interference with Wnt signaling leads to an upregulation of gene programs that favor cell migration and invasion. We identify a set of upregulated genes common among the Wnt perturbations and find that elevated expression of these genes is strongly predictive of poor patient outcomes in early-invasive colon cancer. These genes may have clinical applications as patient biomarkers or new drug targets to be used in concert with existing therapies.One Sentence SummaryLow Wnt Signaling Leads to Invasive Tumor Phenotypes in Colorectal Cancer.
Levodopa Responsiveness Subtypes of Freezing of Gait: Results Using a Levodopa Challenge
Authors: McKay J. Lucas , Goldstein Felicia C. , Sommerfeld Barbara , Bernhard Douglas , Perez Parra Sahyli , Factor Stewart A. 
Published: June 2019

AbstractObjectiveTo demonstrate that levodopa-unresponsive freezing of gait (ONOFF-FOG), which is a disabling untreatable feature of Parkinson’s disease (PD), is distinct from responsive/OFF only FOG (OFF-FOG) and potentially has a distinct pathophysiology.MethodsFifty-five PD patients completed levodopa challenges after >12 hours OFF with supratherapeutic doses to classify them as NOFOG, OFF-FOG or ONOFF-FOG. Serum levodopa levels ensured threshold levels were met. An “ON” response was defined as ≥20% improvement in MDS-UPDRS-III score. Main outcome measure was MDS-UPDRS-III based on clinical exam, timed-up-and-go tests and 360° turns.Results45 patients exhibited an “ON” response to the challenge. Levodopa-equivalent-dose was 142±56% of patients’ typical morning doses. Patients could be classified as: 19 ONOFF-FOG, 11 OFF-FOG, 15 NOFOG. The ONOFF-FOG group exhibited significantly higher NFOG-Q, MDS-UPDRS-II/III scores compared to the OFF-FOG group. MDS-UPDRS-III total varied significantly across medication response states (P<0.01) and groups (P=0.03). Among MDS-UPDRS-III subdomains, significant effects of group (highest in ONOFF-FOG group) were identified for measures of lower extremities and gait. Linear mixed models revealed a highly significant association between serum levodopa level and MDS-UPDRS-III score that did not vary across the groups. There was a highly significant group interaction effect on the association between serum levodopa level with MDS-UPDRS-III item 11 “Freezing of Gait” (P<0.001).ConclusionsONOFF-FOG is a distinct subtype of FOG in PD, as opposed to OFF-FOG. This is an important step in demonstrating that FOG is not a single entity and, in turn, could lead to better understanding of pathophysiology and development of effective therapies.
Evolving neoantigen profiles in colorectal cancers with DNA repair defects
Authors: Rospo Giuseppe , Lorenzato Annalisa , Amirouchene-Angelozzi Nabil , Magrì Alessandro , Cancelliere Carlotta , Corti Giorgio , Negrino Carola , Amodio Vito , Montone Monica , Bartolini Alice , Barault Ludovic , Novara Luca , Isella Claudio , Medico Enzo , Bertotti Andrea , Trusolino Livio , Germano Giovanni , Nicolantonio Federica Di , Bardelli Alberto 
Published: June 2019

AbstractBackgroundNeoantigens that arise as a consequence of tumour-specific mutations can be recognized by T lymphocytes leading to effective immune surveillance. In colorectal cancer (CRC) and other tumour types, a high number of neoantigens is associated with patient response to immune therapies. The molecular processes governing the generation of neoantigens and their turnover in cancer cells are poorly understood. We exploited CRC as a model system to understand how alterations in DNA repair pathways modulate neoantigen profiles over time.MethodsWe performed Whole Exome Sequencing (WES) and RNA sequencing (RNAseq) in CRC cell lines,in vitroandvivo, and in CRC patient-derived xenografts (PDXs) to track longitudinally genomic profiles, clonal evolution, mutational signatures and predicted neoantigens.ResultsThe majority of CRC models showed remarkably stable mutational and neoantigen profiles, however those carrying defects in DNA repair genes continuously diversified. Rapidly evolving and evolutionary stable CRCs displayed characteristic genomic signatures, and transcriptional profiles. Downregulation of molecules implicated in antigen presentation occurred selectively in highly mutated and rapidly-evolving CRC.ConclusionsThese results indicate that CRC carrying alterations in DNA repair pathways display dynamic neoantigen patterns that fluctuate over time. We define CRC subsets characterized by slow and fast evolvability and link this phenotype to downregulation of antigen-presenting cellular mechanisms. Longitudinal monitoring of the neoantigen landscape could be relevant in the context of precision medicine.
Children with Cerebral Palsy Return to Baseline Community Arm Movement after Constraint Induced Movement Therapy
Authors: Goodwin Brianna M. , Sabelhaus Emily K. , Pan Ying-Chun , Bjornson Kristie F. , Pham Kelly L. D. , Walker William O. , Steele Katherine M. 
Published: June 2019

AbstractImportanceConstraint Induced Movement Therapy (CIMT) is a common treatment for children with unilateral cerebral palsy (CP). While clinic-based assessments have demonstrated improvements in arm function after CIMT, quantifying if these changes are translated and sustained outside of a clinic setting remains unclear.ObjectiveAccelerometers were used to quantify arm movement for children with CP one week before, during, and 4+ weeks after CIMT and compared to typically-developing (TD) peers.DesignObservational during CIMTSettingClinical assessments and treatment occurred in a tertiary hospital and accelerometry data were collected in the communityParticipants7 children with CP (5m/2f, 7.4 ± 1.2 yrs) and 7 TD peers (2m/5f, 7.0 ± 2.3 yrs)Intervention30-hour CIMT protocolOutcomes and MeasuresThe use ratio, magnitude ratio, and bilateral magnitude were calculated from the accelerometry data. Clinical measures were evaluated before and after CIMT and surveys were used to assess the feasibility of using accelerometers.ResultsBefore CIMT, children with CP used their paretic arm less than their TD peers. During therapy, their frequency and magnitude of paretic arm use increased in the clinic and in daily life. After therapy, although clinical scores improved, children reverted to baseline accelerometry values. Additionally, children and parents in both cohorts had positive perceptions of wearing accelerometers.Conclusions and RelevanceThe lack of sustained improved accelerometry metrics following CIMT suggest therapy gains did not translate to increased movement outside the clinic. Additional therapy may be needed to help the transfer of skills to the community setting.What this Article AddsThis study compares the movement of children with CP undergoing CIMT in the community setting with their typically developing peers. Additional interventions may be needed in combination with or following CIMT to sustain the benefits of the therapy outside of the clinic.
PROTEINATOR: Web-UI exploring repurposing hypotheses of PROTEIN InhibiTORs based on protein interactions
Authors: Tangadu Santhosh , Shankara Susmitha , Varanasi Bhaskaram V. , Athri Prashanth 
Published: June 2019

AbstractPROTEINATOR is the first version of a staggered, multi-paradigm and extensible drug repurposing platform, focusing on a novel data analytic and integration strategy to find repurposing candidates that have potential to modulate targets through protein-protein interactions. The UI was created as an explorer to find ‘indirect’ drugs for a protein of interest. PROTEINATOR is developed as a web application that lets researchers search for alternate drugs for a protein of interest, based on the protein’s direct interaction with a another druggable protein. This unique tool provides researchers exploring specific implicated protein(s) (in the context of drug development), alternate, plausible routes to modulation by listing proteins that interact with the protein of interest that have reported inhibitors. It is a search engine to identify indirect drugs through connecting various databases, thus avoiding multiple steps and avoiding any manual errors. Using a representative set of databases, 112083 number of ‘indirect’ drug interactions are discovered that are potential modulators of proteins, detailed annotations of which are provided in the UI. PROTEINATOR is freely available athttp://www.proteinator.in.
The discriminant pattern of pleural fluid inflammatory mediators between tuberculosis and other causes of exudative pleural effusion
Authors: Lisboa Vinícius da Cunha , da Silva Corrêa Raquel , Ribeiro-Alves Marcelo , Lopes Isabelle Ramos , Mafort Thiago Thomaz , Gomes dos Santos Ana Paula , Amadeu Thaís Porto , Rufino Alves Rogério Lopes , Rodrigues Luciana Silva 
Published: June 2019

ABSTRACTPleural tuberculosis (PlTB), a form of extrapulmonary TB, remains as a challenge in the diagnosis among many causes of pleural effusion. We recently reported that the combinatorial analysis of interferon-gamma (IFN-γ), IFN-γ-inducible protein 10 (IP-10), and adenosine deaminase (ADA) from the pleural microenvironment was useful to distinguish pleural effusion caused by TB (microbiologically or not confirmed cases) among other etiologies. In this prospective cohort study, a set of inflammatory mediators was quantified in blood and pleural fluid (PF) from exudative pleural effusion cases, including PlTB (n = 22) and non-PlTB (NTB; n= 17) patients. The levels of IL-2, IL-4, IL-6, IL-10, IL-17A, IFN-γ, TNF, IP-10, TGF-β1, and ADA were measured and a principal component analysis was applied in order to identify the mediators who contributed most for the variance in data. IFN-γ, IP-10, TNF, TGF-β, and ADA quantified in PF showed significantly higher concentrations in PlTB patients when compared to NTB ones. When blood and PF were compared, we have identified significantly higher concentrations of IL-6 and IL-10 in PF, in both groups. TGF-β, solely, showed significantly increased levels in PF and blood from PlTB when both clinical specimens were compared to NTB patients. Principal components analysis from PF revealed that the ADA, IP-10, TGF-β, and IFN-γ contributed most for the discriminatory capacity between TPlB and NTB. Our findings showed that important inflammatory mediators in PF may discriminate TB cases from other causes of exudative effusion, the main diseases considered in the differential diagnosis of PlTB.
Deep Learning-Enabled Point-of-Care Sensing Using Multiplexed Paper-Based Sensors
Authors: Ballard Zachary , Joung Hyou-Arm , Goncharov Artem , Liang Jesse , Nugroho Karina , Di Carlo Dino , Garner Omai B. , Ozcan Aydogan 
Published: June 2019

ABSTRACTWe present a deep learning-based framework to design and quantify point-of-care sensors. As its proof-of-concept and use-case, we demonstrated a low-cost and rapid paper-based vertical flow assay (VFA) for high sensitivity C-Reactive Protein (hsCRP) testing, a common medical test used for quantifying the degree of inflammation in patients at risk of cardio-vascular disease (CVD). A machine learning-based sensor design framework was developed for two key tasks: (1) to determine an optimal configuration of immunoreaction spots and conditions, spatially-multiplexed on a paper-based sensing membrane, and (2) to accurately infer the target analyte concentration based on the signals of the optimal VFA configuration. Using a custom-designed mobile-phone based VFA reader, a clinical study was performed with 85 human serum samples to characterize the quantification accuracy around the clinically defined cutoffs for CVD risk stratification. Results from blindly-tested VFAs indicate a competitive coefficient of variation of 11.2% with a linearity of R2 = 0.95; in addition to the success in the high-sensitivity CRP range (i.e., 0-10 mg/L), our results further demonstrate a mitigation of the hook-effect at higher CRP concentrations due to the incorporation of antigen capture spots within the multiplexed sensing membrane of the VFA. This paper-based computational VFA that is powered by deep learning could expand access to CVD health screening, and the presented machine learning-enabled sensing framework can be broadly used to design cost-effective and mobile sensors for various point-of-care diagnostics applications.