bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional heterogeneity of muscle satellite cells in both somite‐derived and branchiomeric muscles
Authors: Ono Yusuke , Boldrin Luisa , Knopp Paul , Morgan Jennifer E. , Zammit Peter S. 
Published: June 2021

Muscle satellite cells are responsible for postnatal muscle growth and regeneration. Most skeletal muscles of the trunk and limb are derived from somites, but head muscles originate from cranial mesoderm. Here we first investigated the range of functional properties of satellite cells and then determined whether they were different in cells with separate embryonic origins, before examining how satellite cells respond to aging. Cultured satellite cells from head muscles proliferated more and differentiated later than those from limb muscles. Although some gene expression profiles in head‐derived satellite cells were different from limbs, head cells were able to regenerate limb muscles when transplanted. Surprisingly, clonal analysis showed that functional properties differed markedly between satellite cells: ranging from cells that proliferated extensively and gave rise to both differentiated and self‐renewed progeny, to other clones that divided only a few times before then differentiating completely. This heterogeneous distribution in satellite cell properties was preserved in both limb and head muscles from old mice. In conclusion, satellite cells exist as a functionally heterogeneous population, with many occupants of the satellite cell niche exhibiting stem cell characteristics in both somite‐derived and branchiomeric muscles. This study is supported by The Muscular Dystrophy Campaign.Grant Funding Source: Muscular Dystrophy Campaign. Medical Research Council. Wellcome Trust
Evaluation of computer visualizations developed for anatomy education
Authors: Nguyen Ngan , Nelson Andrew , Wilson Timothy D. 
Published: June 2021

IntroductionThe use of computer visualizations in anatomy courses is expanding, but there is little evidence available suggesting that these visuals enhance learning of spatial anatomical information.PurposeTo evaluate computer visualizations of the superior mediastinum developed with different display modes and interactive control features.MethodsParticipants will be students from the University of Western Ontario. General information about the participants, including their gender, program of study, and past experiences with spatial tasks will be collected in a baseline questionnaire. A mental rotation task that has been standardized for university students will be used to determine participants' spatial ability. Next, participants will be randomly allocated to one of three visual groups: stereoscopic 3D, 3D, or 2D. Participants in each visual group will be subdivided into one of two interactive groups: active control or no control. Each participant will complete an identical standardized electronic learning module pertaining to anatomy of the superior mediastinum. The module will have clearly defined learning objectives and will differ only by the visualization and manipulation capabilities of the model. Learning will be assessed by a post‐knowledge test consisting of 50 multiple‐choice questions – half spatially related and half non‐spatially related. The spatial questions are assumed to require manipulation of mental representations, while the non‐spatial questions involve the recognition and identification of anatomical structures.SignificanceThe results will help establish guiding principles that will facilitate the design and implementation of effective and efficient computer visualizations that can be adapted to the individual learner's level of spatial ability.Grant Funding Source: n/a
Promoting Student Scholarship: A Web‐Based Peer‐Reviewed Educational Resource
Authors: Pearson William G. , Zumwalt Ann , Hoagland Todd 
Published: June 2021

BackgroundFourth year medical students enrolled in the Teaching in Anatomy elective serve as prosectors in the BUSM gross anatomy course. Their clinical experience combined with the opportunity to revisit anatomy creates fresh insight into the clinical relevance of anatomy. Writing a case study for educational purposes allows them to engage in the scholarly process, synthesize their clinical experience with anatomical knowledge, and share this understanding with first year medical students.MethodsDuring the elective students developed a case study in an area of interest to be published as a web‐based clinical anatomy educational module. They presented and reviewed their cases in groups of four to six. Powerpoint™ files are converted into Quicktime™ and posted via Apple iWeb™ to anatomycases.com. First year students are encouraged to use the site for optional study material.ResultsIn the past two years fourth year students have generated 34 case‐based teaching modules on various topics. In fall semester 2009, 47% of first year students accessed the website as an optional exercise. 73% of first year students accessed the website when promised a bonus question would be derived from this optional study material.DiscussionStudents are a remarkable resource for developing educational materials if anatomy educators are available to facilitate the scholarly process. Students in turn find that doing scholarly work is more enjoyable than initially perceived and have rated this as a useful exercise (mean=4.3 out of 5). Future plans include developing a global educational component to this project to elevate social consciousness about global health needs.Grant Funding Source: none
The development of a web‐based module on Gestational Diabetes Mellitus for patients and healthcare professionals
Authors: Clancy Alicia , Johnson Marjorie , Watson Andrew , Paul Terri , Mottola Michelle 
Published: June 2021

Gestational Diabetes Mellitus (GDM), the most common endocrine disorder during pregnancy, poses short‐term and long‐ term risks for mother and baby. However, intense management of GDM has been shown to reduce negative maternal and fetal outcomes. Such management requires that both healthcare providers and patients are capable of making informed decisions in the control of GDM. Reports from local diabetes clinics and medical professionals suggest healthcare providers’ knowledge of GDM is unsatisfactory. The objective of this project was to create an interactive web‐based module to educate medical students and to provide an effective resource for healthcare providers. The case‐based, self‐study tool was designed using Adobe Dreamweaver Creative Suite 3 and Articulate Studio 09. The modular content draws from the current Clinical Practice Guidelines established by the Canadian Diabetes Association, and will be available to medical students, practicing physicians, and women with GDM. Formative feedback from a questionnaire of the module is anticipated for the spring. We expect the GDM module will educate healthcare providers and patients on the prevalence and risk factors, as well as, the importance of early screening, treatment and prevention of GDM. This empowerment tool should encourage educated decision making, facilitate the management of GDM, and curtail known risks associated with poorly managed GDM.Grant Funding Source: Internal
A functional role for CHD8 in transcriptional regulation through the modulation of chromatin structure
Authors: Bochar Daniel A , Menon Tushar , Yates Joel A 
Published: June 2021

ATP‐dependent chromatin remodeling by the CHD family of proteins plays an important role in the regulation of gene transcription. The CHD family can be subdivided into three subfamilies: CHD1‐2, CHD3‐5, and CHD6‐9. Despite being linked to several human diseases, very little functional data exists for the CHD6‐9 family as compared to the other two subfamilies.In order to understand the function of CHD8, we have isolated a CHD8 containing protein complex which includes WDR5, Ash2L, and RbBP5. These proteins are required components of the MLL/Set1 histone methyltransferase complex. We demonstrate that CHD8 localizes to the promoters of MLL regulated genes upon gene activation. During activation of these target genes, depletion of CHD8 enhances gene expression and causes a decrease in both histone H3 lysine 4 trimethylation and histone H3 lysine 27 trimethylation. Furthermore, depletion of CHD8 results in a loss of WDR5/Ash2L/RbBP5 subcomplex localization at target promoters. These studies suggest that CHD8 alters eukaryotic gene expression by modulating the methylation status of histones at target promoters through the recruitment of chromatin modifying enzymes.This work was supported in part by an American Cancer Society Research Scholar Grant (RSG‐07‐189‐01) to D.A.B
A liver mitochondrial outer membrane (MOM) fatty acid transfer complex
Authors: Lee Kwangwon , Kerner Janos , Hoppel Charles L. 
Published: June 2021

Carnitine palmitoyltransferase‐I (CPT‐I) catalyzes the regulated step in overall mitochondrial fatty acid oxidation. Here we present both a Blue‐Native PAGE (BNE) and an immunological approach to isolate and characterize the MOM CPT‐I and its interacting partners. When solubilized MOM was subjected to BNE, a series of high molecular weight bands greater than the monomeric CPT‐I (88 kDa) were identified. The proteins in these bands were characterized by in‐gel digestion and sequence analysis by LC‐MS/MS (Center for Proteomics and Bioinformatics). An immunocapture system was designed using an antibody mixture of five CPT‐I specific peptide‐derived IgGs. Immunocaptured proteins were subjected to LC‐MS/MS. Using this method, not only the expected CPT‐I, but also LCAS (long‐chain acyl‐CoA synthase), and VDAC (voltage‐dependent anion channel) isoforms were captured and identified. These accompanying proteins also were identified with BNE. Therefore, we conclude that the MOM contains a complex for fatty acid transfer that consists of LCAS, VDAC and CPT‐I.Supported by the NIH grant DK‐066107.
Adipose‐specific deletion of SCD1 does not protect mice from obesity
Authors: Flowers Matthew , Strable Maggie , Ade Lacmbouh , Zhao Minghui , Ntambi James 
Published: June 2021

A critical regulator of lipogenesis is stearoyl‐CoA desaturase 1 (SCD1), which catalyzes the synthesis of monounsaturated fatty acids (MUFA) from saturated fatty acids. To explore the role of SCD1 in the adipose tissue, we used the Cre‐lox system to delete SCD1 from white and brown adipose tissue (AKO) using the aP2‐Cre recombinase transgene. We also generated mice with simultaneous deletion of SCD1 from both adipose and liver (LAKO) or from liver alone (LKO) using the albumin‐Cre transgene. Mice were subjected to high‐fat diet‐induced obesity (DIO; Research Diets 12492) or genetically‐induced obesity using the leptin‐resistant yellow agouti (Ay/a) allele and compared to control mice not expressing Cre recombinase (LOX). Food intakes and changes in body weights were similar amongst the LOX, AKO, LKO and LAKO mice in both models of obesity. Additionally, fat pad mass (epididymal and subcutaneous) was unaffected by adipose and/or liver deletion of SCD1. Immunoblot analysis confirmed deletion of SCD1 and fatty acid composition analysis by gas chromatography revealed reduced MUFA content in the targeted tissues. In light of our previous observations that mice with a whole‐body or skin‐specific deletion of SCD1 are resistant to obesity, the current study suggest that SCD1 deletion from adipose and/or liver is insufficient to elicit protection from obesity.Research supported by funding from NIH‐NIDDK and AHA.
GIT1 Act As GAP For Arf6 Downstream Integrin Outside‐In Signaling During Platelet Aggregation
Authors: Huang Yunjie , Sidney Whiteheart 
Published: June 2021

Our previous work showed that ADP‐ribosylation factor (Arf) 6 is critical for platelet function. Arf6‐GTP is relatively high in resting platelet but quickly converts to Arf6‐GDP during platelet activation in response to primary agonists (thrombin, collagen, etc.). An additional control of Arf6 nucleotide state is hypothesized since blocking integrin‐mediated signaling with RGDS peptides leads to a partial recovery of Arf6‐GTP; this phenotype is also observed in β3 integrin knock‐out mice. This recovery of Arf6‐GTP could be through contact‐mediated signaling via an Eph kinase/ephrin mechanism or via an integrin‐based.The G protein‐coupled receptor kinase interacting protein (GIT) 1 is present in platelet and upon platelet activation, GIT1 is tyrosine‐phosphorylated, a process that is blocked by RGDS peptide treatment. Since GIT1 has an N‐terminal Arf GTPase‐activating domain, we hypothesize that GIT1 acts as a GTPase‐activating protein (GAP) for Arf6 and is downstream of cell‐cell contact‐mediated signaling. Western blotting analysis demonstrates that GIT1 is present in the insoluble cytoskeletal pellet after thrombin activation of platelets. Inhibiting Arf6‐GTP loss affects this redistribution. Further study is required to determine if GIT1 Arf6‐GAP activity is regulated by phosphorylation or whether Arf6‐GTP targets GIT1 to the cytoskeleton.Supported by NIH grants HL56652 and HL091893.
Computational prediction and experimental validation of 5 DNA‐binding residues of human flap endonuclease 1 (hFEN1)
Authors: Kanjanapangka Julie , Finger Lawrence David , Shen Binghui 
Published: June 2021

Human FEN1 is a structure‐specific DNA nuclease involved in removing 5′ RNA primers of Okazaki fragments and in long‐patch base excision repair. Defects in FEN1 lead to increased genomic instability. Identification of DNA‐binding residues will further elucidate the molecular mechanisms behind genome instability initiation and facilitate cancer therapy linked to hFEN1 mutations. No crystal structure data is available of hFEN1 actively bound to DNA; however, a structure of an hFEN1 homolog, T4 phage RNase H in its active form (pdb 2ihn), is available as well as hFEN1 complexed with PCNA in the inactive form (pdb 1ul1). The 2ihn pdb structure shows 31 DNA‐interacting residues. Computational structural alignment of the two X‐ray crystal structures has revealed 5 residues within the 31 subset of RNase H that have a seemingly structurally conserved equivalent in hFEN1; these are K74, L29, V30, F53, and H174. These conserved equivalents in hFEN1 may therefore interact with DNA. To validate our predictions, we use HPLC to measure specific activity levels of hFEN1 mutant proteins versus the wildtype using fluorescein‐labeled DNA substrate. We found that the specific activities of the mutants are impaired relative to the wildtype. We will measure DNA binding activity of hFEN1 mutants using gel shift with biotin‐labeled DNA substrate to validate if the results we observe are due to defects in DNA substrate binding.This work is funded by NIH R01CA076734: Fen1 in genome stability and cancer.
The effects of diet cycling on longevity
Authors: List Edward Owen , Wright‐Piekarski Jacob , Berryman Darlene E , Kopchick John J 
Published: June 2021

IntroductionIt has been suggested that diet cycling is unhealthy to the point that remaining obese is preferable to a fluctuating body weight.ObjectiveTo investigate the effects of diet cycling on longevity.MethodsMale C57BL/6J mice were placed in one of three dietary regimes: a high fat (HF) diet, a low fat (LF) diet or a continuous diet cycle (4 weeks HF, 4 weeks LF). The diets were maintained for the entire lifespan of the mice. Body weight, food consumption, body composition, glucose tolerance and longevity were determined.ResultsAs expected, body weight, body fat, food consumption and glucose tolerance were significantly elevated in the HF mice compared to LF controls. Diet cycling resulted in increases and decreases in the same parameters and the changes were concomitant with the HF and LF cycles. The HF and diet cycled mice consumed 61% and 20% more kcal/mouse/day than LF controls, respectively. At the time this abstract was written, 10% of the HF fed mice, 50% of the LF fed mice and 40% of the diet cycled mice remained alive, and the average lifespan of the HF, LF and diet cycled mice was 1.46, 2.38 and 2.15 years, respectively. Thus, the average lifespan of the HF fed mice was decreased by 38.7% compared to LF controls, while the diet cycled mice only exhibited a 9.7% decrease.ConclusionsSince diet cycled mice lived longer than non‐diet cycled mice on a HF diet, diet cycling was healthier with respect to lifespan than not “dieting” at all.This work was supported in part by the State of Ohio's Eminent Scholar Program that includes a gift from Milton and Lawrence Goll, by the AMVETS, by the Diabetes Research Initiative at Ohio University, and by NIH grants DK075436, AG019899, AG031736.
Biochemical‐structural‐phenotypic correlation of adenylosuccinate lyase deficiency based on analysis of mutant enzyme complexes
Authors: Zikanova Marie , Skopova Vaclava , Hnizda Ales , Krijt Jakub , Kmoch Stanislav 
Published: June 2021

Adenylosuccinate lyase (ADSL) deficiency is disorder of purine metabolism affecting mainly central nervous system. Three forms differing in severity of symptoms and correlating negatively with ratios of accumulating SAdo/SAICAr in body fluids were established. This diversity is not clear and may result from a genotype specific and thus structural related nonparallel loss of activity towards one of the substrates.To test this we selected 16 patients with individual disease causing genotypes and cloned, expressed, purified and characterized individual mutant proteins and co‐expressed genotype specific mutant proteins. We also located mutations in the structural model of ADSL.We found that phenotypic severity (eg. SAdo/SAICAr ratio) generally does not result from disproportional enzyme activities of mutant protein complexes but it correlates rather with their residual enzymatic activities and structural stability. We conclude that SAdo/SAICAr ratio value is probably not predictive of phenotype severity but rather it corresponds to degree of patient's development and brain maturation.This work was supported by CR grants CSF 301070600 and MSM 20620806.
Understanding molecular mechanisms in mitochondria underlying LRRK2‐related Parkinson's disease
Authors: LIU Huifang , Ho Wing Lok , Ho Wing Man , Zhou Zhong jun , Ho Shu Leong 
Published: June 2021

Parkinson's disease (PD) is a common neurodegenerative movement disorder. Mutation of LRRK2 is pathogenic in PD. So far, more than 20 mutations of LRRK2 have been reported in Parkinson patients of different races. Some of the mutations were shown to be able to increase. We aim to elucidate the importance of LRRK2 in the pathogenesis of PD by studying the effects of this protein on vulnerability of neuronal cell death under oxidative stress.Materials and MethodsWe have developed stable HEK293 cells overexpressing wild‐type and mutated (R1441G, G2019S) LRRK2. The effects of LRRK2 over‐expression on various mitochondrial parameters were determined, e.g. cell viability, mitochondrial complexes (I–IV) activity and membrane potential, ATP/ADP ratio, and mitochondrial fragmentation after challenged with H2O2 to induce oxidative stress. We generated R1441G LRRK2 knockin (KI) mice. We are characterizing the LRRK2 R1441G KI mice and wildtype mice by immunohistochemistry of tyrosine hydroxylase (TH) to identify TH+ neurons after challenged with MPTP injection (IP) for 2 weeks to induce nigrostriatal degeneration.ResultsOur preliminary data showed that the intracellular expression pattern of mutant LRRK2 (G2019S) in HEK293 was different from the wild‐type under oxidative stress by H2O2. Mutant LRRK2 was translocated towards mitochondria after treatment with H2O2. LDH release and ATP/ADP ratio proved more serious trend of apoptosis in mutant LRRK2 cell lines. Mitochondrial complexes I activity and mitochondrial fragmentation level were also changed between wild type and single mutation proteins (R1441G and G2019S) in HEK293.The results of this study have important implication on understanding the mitochondrial dysfunction in the pathogenesis of PD.
Systems biology approaches to characterize exposures to infectious agents
Authors: Hammamieh Rasha , Jett Marti 
Published: June 2021

There is an urgent need to assess exposure and infection of individuals by biological threat agents (BTA) well in advance of onset of illness or at various stages post‐exposure.The rapid development of genomics, proteomics and high‐throughput computing approaches to study diseases is now allowing us to apply an integrative systems biology work frame for biomarker development.Our research focuses on defining the molecular events/network systems involved in the host‐pathogen interactions to identify biomarkers and therapeutic targets for pathogenic agents.We apply systems approaches to provide a more complete understanding of the host‐pathogen interactions and pathways and networks regulated in both the host and pathogen during the course of infection and illness from various infectious diseases. Various types of ‐omics data are obtained to determine the kinetics of infection for exposures of human immune cells. These data are integrated with immunological, clinical and physiopathological data obtained from the animal models. Models are developed using the high‐throughput data to gain an overview of the host‐pathogen factors leading to the progression of the disease.
Quantitative phosphoproteomics of depolarization‐dependent protein phosphorylation in nerve terminals
Authors: Larsen Martin R. , Palmisano Giuseppe , Engholm‐Keller Kasper , Kulej Katarzyna , Xue Jung , Graham Mark , Robinson Phillip J. 
Published: June 2021

Depolarization‐dependent calcium influx activates a number of kinases and phosphatases which result in altered phosphorylation of key proteins in, exocytosis, endocytosis etc. Only a small number of phosphosites in these proteins have been identified to date.Here we have used iTRAQ labeling directly on TiO2 resin combined with the SIMAC strategy (Thingholm TE et al., MCP 2007), Hydrophilic interaction chromatography and high accuracy mass spectrometry to quantitatively assess phosphorylation sites in synaptosomes treated with KCL and low and high levels of 4‐aminopyridine (4AP).Using the new quantitative phosphoproteomics strategy we have successfully identified more than 1500 phosphorylated proteins from highly pure synaptosomes. In these 1500 phosphoproteins we have identified and quantified more than 2500 phosphosites. More than 30 % of all the phosphosites change upon depolarization using either KCL or 4AP. In addition, we have identified 72 kinases and 19 phosphatases in synaptosomes whereof many of those are specifically regulated upon stimulation. Overall we show changes in the phosphorylation status of proteins participating in e.g., transportation of SVs, exocytosis and endocytosis.
Identifying protease cleavage sites by label‐free mass spectrometry
Authors: Sun Qing , Gupta Nitin , Cieplak Piotr , Zhu Wenhong , Ratnikov Boris , Pevzner Pavel A , Smith Jeffrey W 
Published: June 2021

Methodsa method for identifying the cleavage sites for proteases in complex proteomes is described. The method makes use of a computer program called MS‐Cleave. The utility of the approach is demonstrated by determining of the cleavage sites in a set of recombinant Escherichia coli proteins generated by two matrix metalloproteinases (MMPs), MMP‐9 and MMP25. MS‐Cleave analyzes LC‐MS/MS data of standard samples with no additional chemical labels, processes them through a stringent peptide identification procedure, filters out tryptic cleavages and terminal trimming products. Each cleavage site is given a score based on the cleavage efficiency.ResultsTwenty‐two E. coli proteins were subjected to proteolysis by either MMP‐9 or MMP‐25. The cleaved samples were combined and analyzed by LC‐MS/MS. The cleavage sites are validated by comparison with the known substrate specificity of the two proteases which were defined with a substrate phage display library.ConclusionMS‐Cleave analysis is a reliable and convenient approach for the identification of protease cleavage sites without the use of additional chemical tags. The method is applicable for any standard proteomics facility.This work was supported by NIH 5U54RR020843‐05 grant to JWS, NIH 5R01RR016522‐05 and 1‐P41‐RR024851‐01 grants and Howard Hughes Medical Institute Professor Award to PP.