bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding the Structural Basis of Epha1 and Epha2 Homo‐Dimerization, Membrane Proximal Domain Interactions and its Implications for Cancer
Authors: Buck Matthias , Sahoo Amita 
Published: May 2022

EphA1 and EphA2 are receptor tyrosine kinases which play a critical role in cellular growth, differentiation and cell motility. In line with the mRNA expression in multiple tissues and organs, the overexpression of these receptors has been reported in several different cancer types, and even in cancer‐derived cell lines. This makes them key therapeutic targets for treatment of several cancers. In Eph receptors, ligand binding regulates the monomer‐dimer equilibrium through stabilization of the dimeric state by inducing a conformational change in the extracellular region (ECR). Thus, dimerization is a key regulatory step in the activity and signaling process of these receptors. However, the involvement of the transmembrane (TM), the immediate two extracellular FibronectinIII domains (FN1&2) and the juxtamembrane (JM) region in the dimerization process is not clearly defined [1]. Moreover, it is clear that the FN domains and the JM region also functions in synergy with the TM domain for signal transduction. The JM domain has several basic residues (K/R) that are closely positioned to the membrane surface, while the surface of the EphA2 2nd FN domain has also been reported to interact with the lipid bilayer. Therefore, studying the structural mechanisms of EphA1 and EphA2 dimerization and membrane interactions will help us better understand the activity and signaling of these receptors in different cancer types. Importantly, working with membrane proteins is extremely challenging. However, the recent developments in molecular dynamics simulation have provided a powerful tool to study membrane proteins and their interactions. Here, we modeled the relevant domains of the EphA1 and EphA2 receptors and studied their structural mechanism of activation by using the coarse‐grain (CG) molecular dynamics simulations using the recently published Martini3 potential function [2]. We show that the Fibronectin domains, TM and JM domains all differ in their interactions and in their interactions with the membrane between EphA1 and A2. Furthermore, the FN domains constrain the TM region of EphA2 to be non‐dimeric in many of the simulations, whereas FN domain dimerization and membrane orientation is more compatible with TM helix dimers in EphA1. The underlying differences in the primary sequence which are likely responsible for these observations as well as future directions of the project are discussed.References:[1] Sahoo AR, Buck M. Structural and Functional Insights into the Transmembrane Domain Association of Eph Receptors. Int J Mol Sci. 2021 Aug 10;22(16):8593.[2] Sahoo, AR, Souza, PCT, Meng, Z, Buck M. Predicting Transmembrane (TM) Domain Dimer Structures using Martini 3. BioRxiv doi: https://doi.org/10.1101/2021.09.10.459840.
Intestinal Dmt1 is Required for Iron Loading in Mice Modeling β‐Thalassemia Intermedia
Authors: Yu Yang , Yang Chunhua , Shine Jacob S. , Lee Jennifer K. , Ebea Pearl , Zhu Sean , Merlin Didier , Collins James F. 
Published: May 2022

β‐thalassemia intermedia (βTI) is characterized by chronic anemia, ineffective erythropoiesis, and excessive intestinal iron absorption leading to systemic iron overload. Divalent metal‐ion transporter 1 (DMT1), the main intestinal iron transporter, may mediate excessive iron absorption in Th3/+ mice, which model βTI.ObjectiveTo determine if intestinal DMT1 is required for iron‐loading in beta‐thalassemia, and if so, to utilize a ginger nanoparticle‐derived lipid vector (GDLVs) siRNA delivery system to normalize iron absorption in Th3/+ mice.HypothesisDMT1 mediates excessive iron absorption in βTI mice and decreasing DMT1 expression by GDLVs‐siRNA will prevent iron accumulation in these mice.MethodsTh3/+ mice were crossed with mice lacking intestinal DMT1 generating double KOs. Also, weanling mice were gavaged daily for 16 days with GDLVs carrying functional DMT1 siRNA, and iron absorption and iron loading were assessed.ResultsLiver, spleen, kidney, heart, and duodenum non‐heme iron levels were decreased in Th3/+ mice lacking intestinal DMT1. Serum non‐heme iron content, serum ferritin levels, and transferrin saturation also decreased in Th3/+ mice lacking intestinal DMT1. Splenomegaly was alleviated in the double KO mice. Oral gavage of GDLVs carrying DMT1 siRNA blunted intestinal DMT1 expression and mitigated hepatic and splenic iron loading. Serum non‐heme iron levels, serum ferritin, and transferrin saturation also decreased in Th3/+ mice receiving GDLVs with DMT1 siRNA.ConclusionIntestinal DMT1 is required for iron‐loading in Th3/+ mice, and in vivo DMT1 knock down is an effective approach to blunt iron loading in mice modeling βTI.
The Regulation of Basal Autophagic Flux by an ATG13‐ATG101 Complex
Authors: Youngs Joshua C. , Poole Daniel , Kannangara Ashari , Lewis Riley J. , Andersen Joshua L. 
Published: May 2022

Autophagy is an essential cellular process by which cellular debris is collected and broken down in the lysosome. Cancer cells rely on autophagy for survival during chemotherapy treatment and periods of hypoxia within solid tumors. In this project, we investigate the ATG13‐ATG101 protein complex, a sub‐complex of the ULK1 initiatory complex whose regulatory role in autophagy is not completely understood. Our recent data demonstrate that an ULK1‐independent ATG13‐ATG101 complex is essential for the basal autophagic degradation of protein aggregates—a process known as aggrephagy. Furthermore, we found that the ULK1‐independent ATG13‐ATG101 complex traffics to condensates of poly‐ubiquitinated protein aggregates where it colocalizes with the autophagy regulator ATG9A.1 Our current data suggest that this ATG13‐ATG101 complex cooperates with ATG9A in the degradation of these protein aggregates. To further elucidate the function of the ATG13‐ATG101 complex, we have developed a protein‐fragment complementation assay using a novel split TurboID (BioID) system in which complementary halves of TurboID are fused to ATG13 and ATG101. Using this split BioID system, together with quantitative LC‐MS/MS and mutants of ATG13 that cannot bind ULK1, we are identifying interactors that are unique to the ULK1‐independent ATG13‐ATG101 complex. Based on previous data, we hypothesize that the ATG13‐ATG101 sub‐complex participates in ATG9A trafficking pathways and recruitment of autophagy regulators to protein aggregate condensates. Thus, our project characterizes the first proximity interactome for the ATG13‐ATG101 complex.1. Kannangara, A. R.; Poole, D. M.; McEwan, C. M.; Youngs, J. C.; Weerasekara, V. K.; Thornock, A. M.; Lazaro, M. T.; Balasooriya, E. R.; Oh, L. M.; Soderblom, E. J.; Lee, J. J.; Simmons, D. L.; Andersen, J. L., BioID reveals an ATG9A interaction with ATG13‐ATG101 in the degradation of p62/SQSTM1‐ubiquitin clusters. EMBO Rep2021, e51136.
Calcium Assimilation for Regenerative Purposes in Axolotls
Authors: Braagaard‐Sørensen Alexander , Lauridsen Henrik 
Published: May 2022

BackgroundThe Mexican axolotl (Ambystoma mexicanum (Shaw and Nodder, 1798)) is an urodele amphibian with intrinsic regenerative capacity in a range of organs and tissues e.g. heart, spinal cord and appendages.Urodeles represents one of few tetrapods that can recreate the embryonic/undifferentiated environment of cells to regenerate once differentiation has already occurred. When trauma occurs, the wound is sealed off by wound epithelium which stems from migrating epithelial cells. Dedifferentiated local cells are activated in the stump accumulate at the tip and form the blastema. The blastema cells proliferate and control the pattern formation so the limb reforms in the right way. This includes the position of cartilage cells, and it takes around 2‐3 months to have a fully differentiated limb. Most studies although only look at the first stages of the regenerated limb (until cartilage formation) whereas calcification may take even longer.The route of calcium uptake during limb regeneration in the axolotl is not known. However, there is anecdotal evidence for the observation that age matched axolotls develop mineralized limbs at different rates in different laboratories with varying water supply and food, suggesting an effect of the of ambient calcium level.Our hypothesis is that calcium uptake during limb regeneration is maintained by ambient available calcium dissolved in either the food or aquatic environment, and low levels of ambient calcium results in lack of mineralization in the regenerated appendage and/or results in transient/permanent osteopenia in the remaining skeleton.Materials and methodsAxolotls (n=24) is divided into four groups respectively: Control (n=6), calcium enriched food (n=6), Calcium free water and enriched food (n=6), High calcium water (0,61 g/l CaCl2) and food(n=6). Calcium enriched pellets was soaked in a saturated CaCl2 solution (850g/l) for 1h and dried for 24h at 21oC.To assess mineral density the animals was scanned by non‐invase microCT prior to amputation. It is planned to be done again 3 months post amputation, 4,5 months and before euthanization.Bone mineral content will subsequently be validated by ashing and some animals will sacrificed at different stages of mineralization for histological staining, but this has yet to be done.ResultsTo ascertain the amount of calcium uptake trough eating we found the calcium enriched pellets to have mean factor of 4.67 times more calcium in them than the normal pellets (Ca enriched mean: 56ppm and normal pellets mean: 12ppm).ConclusionWith the initial assessment of regeneration between the different groups. We expect to see a difference in mineralization.
Circulating Exosomal Proteins are linked to Neuropathogenesis in SIV‐infected Rhesus Macaque: A Proteomic Approach
Authors: Chandra Partha K. , Braun Stephen E. , Baddoo Melody C. , Kim Hogyoung , Castorena‐Gonzalez Jorge A. , Cikic Sinisa , Rutkai Ibolya , Guidry Jessie J. , Worthylake David K. , Flemington Erik K. , Abdel‐Mageed Asim B. , Busija David W. 
Published: May 2022

BackgroundCombined antiretroviral therapy suppresses HIV replication, but 30‐60% of patients suffer from HIV‐1 associated neurocognitive disorders (HAND). Studies are uncovering the role of extracellular vesicles (EVs), especially exosomes, in HIV CNS infection. Using proteomics, we investigated possible circulating exosomal protein links to neuropathogenesis in SIV‐infected rhesus macaque (RM).MethodsExosomes were isolated from sera of SIV‐infected (SIV‐Exo) and uninfected (CTL‐Exo) RM (N = 3/group) by QIAGEN exoEasy kit and characterized by the qNano‐IZON system. Proteomic analysis of the isolated exosomes was performed using liquid chromatography/mass spectrometry (LC‐MS/MS).ResultsqNano‐IZON analysis indicated that isolated EVs were predominantly exosomes (particle size < 150 nm). In the LC‐MS/MS study, 5,654 proteins were quantified, with 236 proteins (~ 4%) significantly differentially expressed (DE) between CTL‐Exo and SIV‐Exo. Two or more unique peptides were detected in 85% (4777/5654) of quantified proteins, and in 89% (211/236) of significant DE proteins, indicating the depth of analysis. We quantified most of the exosome‐associated proteins (tetraspanins, enzymes, lipid rafts, cytoskeletal, and endosome‐specific proteins) reported in previous studies. The heat‐maps and hierarchical clustering indicated that proteins involved in latent viral reactivation (heat shock transcription factor 1), inflammation (complement factor H, antioxidants, glycoproteins), unfolded protein response (UPR) (proteasome activators, cochaperones), neuropathology (amyloid beta [Aβ] precursor, chromogranin‐A and ‐B), and signaling (cytoskeleton regulators, cyclin‐H, mTOR complex 2, CD74) were expressed at significantly higher levels in SIV‐Exo than CTL‐Exo. However, proteins involved in mitochondrial (Mt) fission (Mt‐fission 1, ‐fission factor, and fission regulator 1), and ATP production (Mt Complex‐I, ‐IV, and ‐V), that play a critical role in the brain energy supply, were significantly decreased in SIV‐Exo. Moreover, exosomal‐proteins involved in autophagy‐mediated degradation (autophagy related 9A, ‐2B, lysosomal associated membrane protein 2), endosomal recycling (sorting nexin 4) and exocytosis (synaptogyrin), sprouting angiogenesis (jumonij domain‐containing 6), and cytoskeleton organization (calponin) were also expressed at significantly lower levels in SIV‐Exo than CTL‐Exo.ConclusionsOur novel findings suggest that circulating exosomal proteins are associated with viral reactivation, inflammation, UPR, mitochondrial dysfunction, defective autophagy, and Aβ and Tau pathology that may elucidate the etiology of HAND, and possibly provide novel therapeutic targets.
Effects of a Bonded Arginine Silicate Inositol combination (nooLVL®) on Cognitive function in esports Gamers
Authors: Emerson Katie , Perez Ojalvo Sara , Greenberg Danielle 
Published: May 2022

ObjectivesThe purpose of this open‐label study was to assess the ability of a bonded arginine silicate inositol combination (nooLVL) to affect reaction time and responses to cognitive tasks in esports gamers. nooLVL is a non‐stimulant complex of bonded arginine silicate with inositol. Previous studies have evaluated nooLVL in esports gamers showing improvements in accuracy, decision making, and reaction time during gaming. This study looks to further detect cognitive changes in esports gamers on an array of cognitive tests developed by Cambridge Brain Sciences.MethodsAssessments were evaluated on six Cambridge Brain Sciences (CBS) cognitive tasks: Feature Match, Double Trouble, Mental Rotations, Polygons, Odd One Out, and Spatial Planning. These tests measure visuospatial processing, deductive reasoning, intelligent behavior, concentration, and attention. The subjects were healthy adult males and females (age >18; n=9) with minimum previous gaming experience of 3‐5 hours of video games per week for at least 6 months. All study participants consumed 1600mg per day of nooLVL (600mg arginine, 105mg silicon, 385mg inositol and 60mg potassium) for seven days. They completed the CBS tests at baseline, on day 1 after a single dose of nooLVL, and again on day 7.ResultsMean changes within group at baseline to day 1, day 1 to day 7 and baseline to day 7 were analyzed with paired t‐tests. Significant differences were found in Double Trouble (baseline vs day 1 [p=0.0019], day 1 vs day 7 [p=0.0369] and baseline vs day 7 [p=0.0005]), Mental Rotations (baseline to day 1 [p=0.0506] and baseline to day 7 [p=0.0192]), and Spatial Planning (baseline to day 7 was observed [p=0.0266]). The Double Trouble assessment measures concentration, Mental Rotations examination measures the function of visual representation in the brain, and Spatial Planning assessment measures intelligent behavior through forethought and sequencing performance.Outcomes of the Feature Match, Polygons, and Odd One Out tests did not show significance.ConclusionsThese data show that nooLVL® a complex of bonded arginine silicate with inositol, when used in esport gamers, improves outcomes on certain functioning tests such as visual processing, concentration, and spatial learning as early as after a single dose and lasting up to seven days.
Arteria Lusoria and its relation to Dysphagia Lusoria. A systematic review
Authors: Syed Qareen H. , Valenzuela Juan J. , Orellana Mathias , Farfan Emilio , Gold Marjorie , Beas Antonia 
Published: May 2022

IntroductionAnatomically, the aberrant subclavian artery is the last branch of the aortic arch. On its way to the right upper limb it runs posterior to the esophagus. During this passage it can compress the esophagus, producing Lusoria Dysphagia.Materials and methodsDifferent databases were subjected to a systematized literature search, using the following criteria: articles published between 2000 and 2020, and articles that established a clinical correlation between an aberrant subclavian artery and Lusoria Dysphagia.ResultsAfter full text analysis of the articles that met the criteria, 48 articles were found in which three types of aberrant arteries were identified. These were associated with symptoms of Dysphagia Lusoria in the subjects of the analyzed studies. The most common type of variation in the origin of the aberrant artery was Type I, an aberrant right subclavian artery that arises as the last branch of the aortic arch, maintaining the origins of the other branches of this arch. The most common course was retroesophageal, which was most commonly associated with the symptoms of patients with Dysphagia Lusoria.ConclusionsThe knowledge of the variations and courses of these types of aberrant arteries and their clinical associations is relevant for specialist professionals who treat patients diagnosed with Dysphagia Lusoria.
The sciatic nerve and and its relation to the piriformis muscle syndrome regarding daily clinical practice. A review
Authors: Beas Antonia , Salas Catalina , Valenzuela Juan José , Orellana Mathias , Syed Qareen , Santana Andrés 
Published: May 2022

IntroductionThe sciatic nerve innervates most of the muscles of the lower limb, so any alteration in it'sits function or clinical presentation could directly affect the functioning of the lower limb. Therefore, the normal anatomy, anatomical variants and how these can influence clinical implications in the gluteal region are of importance in daily clinical practice.MethodsodologyA systematic review was carried out in the scientific literature to answer our research question. We searched in the databases MEDLINE, SCOPUS, WOS, Scielo, GOOGLE SCHOLAR and other scientific sources, using search terms in relation to our stated objectives and connected through Boolean terms.ResultsThe results of this study show that the variations of the sciatic nerve can be ample, which associated to the variability in the geographic regions of the studies, sex of the sample and incidence of the variation, will make it necessary to consider different multifactorial components for the anatomical analysis of sciatic nerve variations and for clinical considerations in patients with and without these anatomical variations.ConclusionWith the results of our review, we can infer that the sciatic nerve presents a variability of distribution patterns, which may be presented in the classical anatomical literature as a variability that is found differently in the population. In addition to inferring that the variation of the sciatic nerve can be little attributed to the symptoms of the piriformis muscle syndrome.
LncRNAs imported into mitochondria possess distinct features stratified by machine learning that promote interaction with the mitochondrial import protein PNPase
Authors: Taylor Andrew , Hathaway Quincy , Robart Aaron , Cook Chris , Kunovac Amina , Durr Andrya , Rizwan Saira , Cramer Evan , Starcovic Sarah , Hollander John 
Published: May 2022

Understanding the localization and regulatory activity of extra‐nuclear long non‐coding RNAs (lncRNAs) is especially critical in the context of the mitochondrion, which possesses a genome separate from the nucleus that dictates bioenergetic function and is influenced by a broad range of pathologies. Prior research including efforts from our own laboratory have identified Polynucleotide Phosphorylase (PNPase) to be critical for selective RNA passage through the mitochondrial membrane, including microRNAs and other ncRNAs. However, the dynamics of lncRNA binding with PNPase have not yet been determined. Understanding how lncRNAs interact with PNPase is a crucial initial step for predicting their ability to be imported into mitochondria and how the process can be manipulated to regulate mitochondrial genome expression.The objective of this study was to evaluate lncRNAs present in mitochondria and classify sequence‐based features that might permit interaction with PNPase. Sequencing performed on mitochondrial and cytoplasmic isolates from human and mouse cardiac tissue identified over 500 mitochondrially‐localized nuclear genome‐encoded lncRNAs. Crosslinked immunoprecipitation (CLIP) of mitochondrial isolates using antibodies for PNPase pulled down predominantly lncRNAs in both human and mouse. The most highly bound lncRNA sequences were run though supervised machine learning using 10‐fold cross validation through Support Vector Machines (SVM) and Classification and Regression Trees (CART) machine learning algorithms, which identified stratification of primary and secondary sequence features as compared to random RNA and low binding lncRNA sequences, with an accuracy of 82% for SVM and an area under curve value of 0.89 for CART. Primary sequence features such as dissimilarities from coding sequences, various k‐mer frequencies, and overall GC content correlated with increased lncRNA interaction with PNPase (p<0.001), as did secondary features such as minimum free energy and electron‐ion interaction pseudopotential (p<0.001). These features were integrated into an artificial RNA fragment sequence that was gel shifted with purified PNPase protein and showed higher binding affinity than a random RNA fragment of equal length.LncRNAs are a unique species of ncRNA with a diverse range of regulatory functions. Understanding the mechanism behind lncRNA import into the mitochondrion could lead to novel therapeutic interventions to preserve bioenergetic activity. This study indicates that PNPase has affinity for rankable primary sequence and secondary structural features within lncRNAs, and application of the most critical features can be used to improve interaction with PNPase and potentially import into mitochondria.