bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding Shape Factors That Influence The Tibial Tunnel Length in Anterior Cruciate Ligament Repair
Authors: Congdon Kimberly , O'Mary Kevin , Jergensen Jason 
Published: June 2021

Anterior cruciate ligament repairs are performed over 100,000 times annually in the US. A common surgical method is a bone‐patellar tendon‐bone graft, which requires the placement of a tibial tunnel through the proximal tibia. Mismatches between the length of the tibial tunnel and the length of the graft have been reported to occur 26% of the time or more, and require procedural modifications during surgery. Most methods for placing the tibial tunnel rely on consideration of patient height and/or angle of placement. Little is known about the variables that affect mismatches. Better understanding how the shape of the proximal tibia impacts the length of the tibial tunnel will allow for improved surgical technique and could lower the number of mismatches, and perhaps even graft failures. We examined 33 right proximal tibiae from donor cadavers (15 females, 18 males) via three‐dimensional scans that allowed us to take 6 linear measurements to describe the dimensions of the proximal tibia. We also used the directions for a popular tibial tunnel guide to simulate a tibial tunnel length on all individuals. Our analysis found the length of the tibial tunnel is influenced by multiple shape components that vary by sex. Specifically, male tibial measurements were always significantly larger than female measurements (p<0.05), there were a greater number of significant correlations among measurements in the male tibia than the female tibia, and the length of the tibial tunnel is more closely correlated to anterior‐posterior measurements in females in contrast to males, where it is more closely correlated to mediolateral measurements. These findings suggest there are sex‐based differences in the shape of the proximal tibia that may confound tibial tunnel placement. The development of surgical techniques should incorporate knowledge of shape‐based variables, and future research should continue to explore sex‐specific foundations of variable outcomes in clinical treatments.Support or Funding InformationThis project was funded by the Basic Sciences Department, College of Osteopathic Medicine, Touro University NevadaThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Anatomical Variations of the Axillary Artery of Human Cadavers
Authors: Mathis Monica , Marshall Jonathan , Hammer Leah , Chambers Paige , Rosario Martin G. 
Published: June 2021

Anatomical variation is demarcated as the standard discrepancy in the structure and morphology of body arrangements, for instance, arteries and nerves. Numerous variations are benign and can be attributed to changes in the embryologic development. The axillary artery (AA) is an extension of the subclavian artery. Typically, the AA extends from the first rib (outer border) to the teres major muscle (lower border). The pectoralis major divide the AA into three parts, for identification purposes, above (first part), underneath (second part) and below the muscle (third part). From the second part the lateral thoracic artery branches, supplying the pectoralis and serratus anterior muscles. The thoracodorsal artery branches out of the third part of the AA to supply the latissimus dorsi and subscapularis muscles.PURPOSEReport anatomical variations in the axillary arteries explicitly on the second and third division.METHODSThe AA's were dissected by students of the Physical Therapy program at Texas Woman's University Dallas under the supervision of the Anatomist of the same program. The primary technique used was blunt dissection for the identification of the AAs. Out of Ten human anatomical specimens, Three exhibited variations of the AA.RESULTSFirst variations we identified was lateral thoracic artery branched out of the third division of the AA and not the second. Furthermore, from the third division we identified that out of the subscapular artery we had branches for latissimus dorsi (two branches), subscapularis (Thoracodorsal artery) and the Serratus Anterior (two branches) muscles (Lateral thoracic).CONCLUSIONSIt appears that the axillary artery had several deviations from its standard structures. Clinically this variation might not cause any impairment. However, the knowledge of this different arrangements can help prevent unwanted difficulties throughout several interventions.
The H3K36 histone methyltransferase SETD2 as a target of leukemogenic chemicals: molecular and cellular studies.
Authors: BERTHELET Jérémy , DUVAL Romain , BUI Linh‐Chi , MATHIEU Cécile , PETIT Emile , DUPRET Jean‐Marie , GUIDEZ Fabien , CHOMIENNE Christine , RODRIGUES‐LIMA Fernando 
Published: June 2021

SETD2 is a key histone modifying enzyme that is responsible for the trimethylation of lysine 36 of histone H3 (H3K36me3) in mammals. During transcriptional elongation in normal cells, H3K36me3 marks the zone on exons for accurate gene transcription and plays an important role in the regulation of alternative splicing. In addition, SETD2‐mediated H3K36me3 is required for DNA repair and recruitment of other epigenetic enzymes. Several studies have shown that loss of function mutations in SETD2 are involved in cancer development. In particular, SETD2 inactivating mutations have been shown to be critical drivers in leukemia development.Benzene (BZ) is a chemical of great industrial interest. BZ is also known to be a major hazardous air pollutant originating from anthropogenic (road transport, tobacco smoke, etc) and natural sources (forest fires). BZ is classified as a class I human carcinogen. Environmental and occupational exposure to BZ lead to bone marrow malignancies such as leukemia. The leukemogenic effects of BZ relies on its metabolization in lungs and bone marrow cells into reactive metabolites, in particular benzoquinone (BQ). However, most of the key molecular and cellular mechanisms underlying its hematotoxicity are not fully understood.Here we provide evidence that SETD2 is a target of BQ, the prime hematotoxic metabolite of BZ. Using a specific HPLC based SETD2 assay, we found that the methyltransferase activity of SETD2 is readily inhibited by BQ in vitro and in cellulo in an irreversible manner (kinact=300 M−1.s−1). This inhibition is due to the covalent modification (arylation) of cysteine residues present in Zn2+ finger motifs (AWS and post‐SET domains) by BQ with concomitant release of Zn2+. Accordingly, exposure of cells (K562 or HEK293T) to BQ leads to global loss of H3K36me3.The H3K36 histone methyltransferase SETD2 is increasingly recognized as a tumor suppressor gene, which can facilitate the initiation and maintenance of leukemia. Our data suggest that BQ, the major hematoxic metabolite of benzene, can impair the functions of SETD2 which may contribute to benzene‐dependent leukemogenesis.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Analysis of CoREST Complex‐Chromatin Interactions with Chemical Tools
Authors: Wu Mingxuan , Hayward Dawn , Kalin Jay H. , Song Yun , Schwabe John , Cole Philip A. 
Published: June 2021

Chromatin remodeling and histone modifications play essential roles in the regulation of gene activation or silencing in physiologic and disease processes. Among the histone modifying enzymes, histone deacetylases (HDACs) and lysine specific demethylase 1 (LSD1) have been shown to be critical in transcriptional regulation and are considered drug targets in cancer and other diseases. The CoREST complex contains HDAC1 (or HDAC2) and LSD1 but the interplay between subunits of this complex and their interactions with nucleosomes is poorly understood. We have employed engineered sortase to generated histone H3 containing post‐translational modifications (PTMs) that ligates H3 N‐tail depsipeptides and globular histone H3 with excellent conversions and all native sequence. These semisynthetic histone H3s possessing various combinations of H3K4‐dimethyl and N‐tail Lys acetylation marks were incorporated into reconstituted mononucleosomes and investigated as substrates with the purified core CoREST complex. These experiments revealed an interdependence of particular PTMs in CoREST processing and regioselective CoREST deacetylation. In addition, we prepared nucleosomes containing N‐propargyl and hydroxamic acid Lys analogs as probes of CoREST interaction. These unnatural warheads enhanced the stability of CoREST complex‐nucleosome complexes which should facilitate biophyiscal characterization.Support or Funding InformationNIHThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Overlap Extension Polymerase Chain to Create a New Expression Vector and the Protein Binding Affinity Analysis using MST of Eph Receptors
Authors: Bowman Deanna , Muller‐Greven Jeannine , Smith Adam , Buck Matthias 
Published: June 2021

Erythropoietin‐producing human hepatocellular (Eph) receptors are a subfamily of protein tyrosine kinases (RTKs) that possess a sterile alpha motif (SAM) domain. These receptors are important for cell‐cell communication, proliferation, cell growth, and migratory responses. They are also over‐expressed in cancer cells and tumor vessels. Eph receptors are thought to be involved in tumor progression and metastatic spread. The behavior is dependent on the density of the receptor and the presence of ephrin ligand in opposing cells. Oligomerization of the EphA2 receptor plays a key role in its function. Dimerization and oligomerization are part of the activation of RTKs and the response to ligand stimulation. Restricting the cluster size of active EphA2 affects the signaling output, and preformed, ligand independent dimers are one possible source of aberrant signaling. One way to study the EphA2 receptors is to produce the intracellular domain (ICD) in E.coli. However the protein expression is very low and thioredoxin (Trx) is needed as a fusion tag to improve the level of soluble protein. For clustering and dimerization study as well as binding study of the ICD domain to the plasma membrane, the large Trx tag of 110 amino‐acids may block the binding hindering the results and should be removed. A highly sequence‐specific cysteine protease from Tobacco Etch Virus (TEV) was used to cleave the fusion protein by inserting the TEV protease recognition site between the Trx tag and EphA2ICD. Genetic engineering using overlap extension polymerase chain was used to create this new expression vector fusing the Trx tag at the N‐terminus of EphA2 with the insertion of a TEV protease recognition site in between. The EphA2 fusion gene was then cloned into the pET28a expression vector. The new construct was then transformed into E. coli strain BL21 and the recombinant EphA2 was expressed as a soluble and active protein. The protein was purified using the Nickel‐NTA affinity resin. After protein purification, cleavage conditions of the Trx tag using TEV protease were optimized and EphA2ICD cleaved and uncleaved was tested for its ability to bind liposomes using Microscale thermophoresis (MST). The MST shows a higher binding affinity of the cleaved protein to the liposomes compared to the uncleaved protein indicating some obstructive effect of the Trx tag. This new expression construct can be used to analyze the role of Eph receptors a more accurate way. Further investigation of the structural determinants of oligomerization through the manipulation of the receptor sequence will lead to a better understanding of the role that EphA2 plays in metastasis and tumorigenesis.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Probing the role of the interface on activity and regulation of gMDH
Authors: Garcia Nina Marie , Schwabe Michael , Graham Sasha , Bell Ellis 
Published: June 2021

Interfaces between subunits often play important roles in communicating activation or inhibition critical for an organism's survival. The molecular mechanism of such interactions has not yet been fully understood. Glyoxysomal malate dehydrogenase (gMDH) is a homodimeric enzyme whose interface is thought to participate in the regulation both by citrate and by substrate inhibition as well as a proposed reciprocating subunit mechanism of the overall catalytic cycle. The interface contains a variety of electrostatic (some favorable, some repulsive) and non‐polar interactions. To understand the mechanism of subunit interactions we have probed the role of individual sidechains at the interface by site directed mutagenesis to determine the effects on stability, activity, and regulation. L269 and S266 appear to form a relay system that connects the active site to the interface. We have constructed, expressed, and purified two mutants, L269A and S266A. Biochemical and biophysical techniques were used to evaluate the structure and stability of the mutants. Size exclusion chromatography and chemical cross‐linking experiments demonstrate that L269A and S266A maintain a dimeric quaternary structure. Comparison of CD spectra of the mutants to the native showed similar secondary structure and, via thermal melts at 222nm, TM values. To study, the role of these residues in gMDH activity, initial rate kinetic studies were performed and showed that S266A and L269A have a lower affinity for OAA while, unlike the native enzyme, the L269A mutant is not saturated by NADH over experimentally accessible ranges. This, coupled with the decreased activity of both mutants, suggests that the residues play a key role in the binding of NADH and regulation of gMDH by OAA. This was further supported by fluorescence based thermal shift (FTS) studies that demonstrated how NADH binding is greatly decreased in L269A. Thus, the results suggest that subunit interactions mediated at least in part by S266 and L269 are part of a relay system between active sites in the homo‐dimer that regulates activity and inhibition of gMDH.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Identification of Microprotein‐Protein Interactions via APEX Tagging
Authors: Chu Qian , Rathore Annie , Diedrich Jolene K. , Donaldson Cynthia J. , Yates John R. , Saghatelian Alan 
Published: June 2021

Microproteins are peptides and small proteins encoded by small open reading frames (smORFs). Genomics and proteomics technologies have led to the recent discovery of hundreds to thousands of new microproteins. Emerging evidence demonstrates that these microproteins have fundamental roles in various biological processes including metabolism, apoptosis, and development, highlighting the value of characterizing these molecules. The identification of microprotein‐protein interactions (MPIs) has proven to be a successful approach to the functional characterization of these genes; however, traditional immunoprecipitation methods result in the enrichment of non‐specific interactions for microproteins. To address this issue, we tested and applied an in situ proximity tagging method that relies on an engineered ascorbate peroxidase (APEX) to elucidate MPIs. The results demonstrated that APEX tagging is superior to traditional immunoprecipitation methods for microproteins. Furthermore, the application of APEX‐tagging to two uncharacterized microproteins, C11orf98‐MP and MIEF‐MP revealed that they interact with nucleolar proteins nucleophosmin and nucleolin (C11orf98‐MP) and acyl carrier protein in mitochondria (MIEF‐MP) respectively, demonstrating the ability of this approach to identify novel hypothesis‐generating MPIs.Support or Funding InformationQ.C. is a postdoctoral fellow funded by the George E. Hewitt Foundation for medical research. This study was supported by the NIH with an NCI Cancer Center Support Grant P30 (CA014195 MASS core, A.S.) and R01 (GM102491, A.S.), the Leona M. and Harry B. Helmsley Charitable Trust grant (#2012‐PG‐MED002, A.S.), and Dr. Frederick Paulsen Chair/Ferring Pharmaceuticals (A.S.). Imaging work in this study was supported by the Waitt Advanced Biophotonics Core Facility of the Salk Institute with funding from NIH‐NCI CCSG: P30 014195, NINDS Neuroscience Core Grant: NS072031 and the Waitt Foundation. We also want to thank the Cancer Center Support Grant P30 CA014195 for purchasing and providing access to the MGC collection.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
New assays reveal opposing effects of 17b‐estradiol in the presence and absence of ovaries on the cardiac network of calmodulin‐binding proteins
Authors: Patton John Harrison , Kaster Kyle Nicholas , Gebert‐Oberle Briana , Clayton Sarah , Giles Jennifer , Tran Quang‐Kim 
Published: June 2021

Reduced estrogen concentrations following menopause are associated with increases in the incidence of cardiovascular disease. Calmodulin (CaM) is required for the activities of numerous cardiac proteins yet is not sufficiently expressed for its binding targets. We have begun to examine the effects of 17b‐estradiol (E2) on the cardiac network of CaM‐binding proteins. Female rats received sham surgery or ovariectomy, followed by treatment with vehicle or E2 for 2 weeks. E2 treatment in sham animals increases the interaction between endogenous CaM and the cardiac α adrenergic receptor type 1A. Surprisingly, ovariectomy substantially increases this interaction, while E2 replacement now reduces it. To examine the effects of these treatments on the population of cardiac CaM‐binding sites that are unsaturated by endogenous CaM, lysate from left ventricle was subjected to saturating Ca2+ concentration and processed through a CaM sepharose column. Flow through contained CaM‐binding sites saturated by endogenous CaM, while sepharose‐bound fraction represented endogenously unsaturated CaM‐binding sites. The fractions eluted from the CaM sepharose were subsequently used in competitive binding assays using purified CaM and a CaM biosensor. E2 treatment in sham animals increases the number of unsaturated CaM‐binding sites. Ovariectomy further increases this number, while E2 treatment now reduces it. The data indicate that E2 treatment exerts opposing effects in the presence and absence of ovaries on specific endogenous CaM‐target associations and the number of endogenously unsaturable Ca2+‐dependent CaM‐binding sites in the heart. These results suggest that estrogen replacement may have unpredictable functional outcomes.Support or Funding InformationSupported by NIH Grant HL112184 to Quang‐Kim Tran and Grants from the Iowa Osteopathic and Educational Research Funds to Sarah Clayton and Quang‐Kim Tran.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Spatial Compartmentalization of Akt/mTOR Signaling: What Happens in the Nucleus
Authors: Zhou Xin , Zhong Yanghao , Zhang Jiao , Shyy John Y. ‐J. , Zhang Jin 
Published: June 2021

The Akt/mTOR pathway is a central player in regulating distinct and diverse cellular processes, such as cell growth, survival, and metabolism. We hypothesize that spatial compartmentalization is a critical mechanism for achieving signaling specificity of Akt/mTOR signaling. To examine this spatial regulation of Akt/mTOR signaling within subcellular compartments, we developed a series of genetically encoded fluorescent protein‐based molecular tools, including Akt activity reporter (AktAR2) and mTORC1 activity reporter (TORCAR), to directly visualize the kinase activities dynamics of Akt and mTORC1 in single living cell. We found that cellular mTORC1 activity is intricately regulated in a signal‐ and location‐specific manner. Surprisingly, both growth factor and amino acid surrogate induce mTORC1 activity in the nucleus, in contrast to the current thinking that mTORC1 is not active in nucleus. To further dissect the regulatory mechanisms of nuclear mTORC1 activity, we developed Akt‐STOPS (Akt Substrate‐based Tandem Occupancy Peptide Sponge), which allows perturbation of Akt signaling at distinct subcellular compartments. Expression of Akt‐STOPS in the nucleus suppressed the growth factor stimulated nuclear Akt activity without significant inhibition of Akt activity in the cytosol. Strikingly, expression of Akt‐STOPS in the nucleus largely diminished the growth factor‐induced nuclear mTORC1 activity, and down‐regulated the transcription by mTORC1‐dependent RNA pol III, suggesting that growth factor induced nuclear mTORC1 activity is dependent on nuclear Akt activity. These results have led to a new model of regulation of mTORC1 in nucleus. Taken together, we developed new molecular tools to interrogate the spatial control of Akt/mTOR signaling and uncovered new insights into the spatial compartmentalization of Akt/mTOR signaling.Support or Funding InformationThis work was supported by NIH grants R35 CA197622 and R01 GM111665.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Bacteriological Evaluation of Essential‐Oil Based Products from a Local Small Business
Authors: Santos Anael A. , Butler Russ , Gillen Craig , Santos Amanda B. , Santos Fernanda B.O. 
Published: June 2021

All‐natural, essential‐oil based products are becoming a significant segment of local small business. In fact, an increasing number of consumers are choosing organic plant‐based alternatives over the cosmetics currently available. Independently of the source of ingredients, cosmetics should be tested before becoming available for purchase. It has been recognized that microorganisms can grow and reproduce in cosmetic products, and may cause spoilage or chemical changes in these products, which can result in injury to the user. Standards for the analyses of food and cosmetics have been established by the Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM). The present study followed these analytical guidelines to ensure the quality and safety of All‐Natural products (defined as such by the business owner) from a local small business. The tested products included a lotion, a diaper balm, and a bug spray. Two bottles of each product from different batches were randomly chosen and used for testing. Each bottle of each product was tested separately using the Aerobic Plate Count (APC) method and the total coliform analysis according to the BAM. After incubation in the appropriate agar plates, no colonies were found. Therefore, all plate readings from all products were below detectable limits of these methods. These results indicate that the products meet the FDA's requirements for distribution to, and safe use of, the consumer.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.