bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of insertion forces on the surface wear of dental implants (922.14)
Authors: Adapalli Arvind , Sridhar Sathyanarayanan , Thomas Anie , Valderrama Pilar , Wilson Thomas , Rodrigues Danieli 
Published: June 2021

The main goal of this study was to understand the effects of insertion forces on the wear properties of dental implants. It is hypothesized in this study that titanium dental implants may be subjected to wear during implantation, which can result in particle generation and accumulation in the surrounding tissues. Metal particle accumulation may contribute to adverse tissue reaction and diseases like peri‐implantitis. To quantify particle generation upon implant insertion, 4 dental implants (Straumann USA LLC, 10 mm) were inserted in sawbone blocks of increasing densities, 10 PCF, 20 PCF, 30 PCF, and 40 PCF (pounds per cubic feet, PCF), simulating implantation in the bone. After insertion, each implant was removed from the block, which were sectioned for microscopic inspection. The internal surface of the sectioned blocks, the surface of the implants, and the compositions of the particles were analyzed with 3D microscopy (Keyence, VHX200), Scanning Electron Microscopy (JEOL 5600), and powder X‐ray (Bruker D8 Advance). 3D microscopy and Scanning Electron Microscopy revealed the presence of metal debris deposited in each density of sawbone . The amount of particles deposited was observed to decrease with increasing sawbone density. Powder X‐Ray Diffraction confirmed that particles generated were mainly composed of titanium. Therefore, this study illustrates how the insertion of dental implants may lead to the generation of metal particles in the encompassing tissue. This suggests that deformation of the implant surface and particle accumulation may start to develop in stages as early as insertion.Grant Funding Source: University of Texas at Dallas Startup Funds (Dr. Rodrigues)
Instrumentation for capture of high‐speed anatomical movement (923.1)
Authors: Sochor Mark , Heltzel Sara 
Published: June 2021

Objective: Describe the technique of instrumentation of the human body for capturing anatomic motion at high speed. A human body interacting with its environment is at risk for injury. Anatomic structures with viscoelastic properties do not behave in the same way at high speed. It's necessary to study these interactions when developing mechanical surrogates of the human body (crash test dummies). Way in which a crash dummy is able to replicate a human’s actual movement is called biofidelity.Methods: PMHS in this series were fresh frozen specimens thawed to room temperature. Instrumentation techniques which incorporate hardware into the spine and ribcage of the PMHS will be described. Video capture of these PMHS and the acceleration data were captured and compared in an automotive crash environment. Acceleration data filtered at industry standard and photo target tracking system compared to the post‐processed acceleration data. Force defection curves generated as well as excursion measurements for the head, thoracic spine, pelvis and lower extremities.Results: The PMHS moves similar to a live human subject in a high G environment as muscle reaction time is minimized and the baseline muscle tone is often overcome. Excursion of the PMHS head, thoracic spine and pelvis over several milliseconds shows the importance of anatomical movement in an acceleration environment.Conclusions: Instrumentation techniques have been developed. Techniques and motion capture are highly accurate and aid in developing surrogate tools for the motion of the human body for safety product development. Although PMHS do not have the baseline muscle tone of a live subject they do have realistic soft tissue strength (ligaments, tendons and other soft tissue load bearing structures). Accepted instrumentation techniques can help to describe how anatomical structures move relative to one another in environments the human body did not normally experience in it’s evolution.Grant Funding Source: National Highway Safety Administration
Structures, dynamics, and interactions with UBC9 of the RING and B1‐box domains of promyelocytic leukemia protein (938.1)
Authors: Huang Tai‐huang , Huang Shu‐Yu , Naik Mandar 
Published: June 2021

PML protein is mainly present inside the nucleus in the form of PML nuclear bodies (PML‐NB) and serves as anchoring point for various sumoylated transcription factors and regulators. It mediates activities, such as transcriptional regulation, antiviral defense, DNA replication, DNA repair, telomere lengthening, chromatin organization, cell cycle control, senescence, apoptosis, and tumor suppression. PML‐NB is associated with acute promyelocytic leukemia (APL). All known isoforms of PML have conserved N‐terminal RBCC region comprised of a RING finger domain followed by two B‐boxes and coiled‐coil region. The RING domain has been shown to possess SUMO E3 ligase activity and the B1‐box can be poly‐sumoylated. Both the RING domain and the B1‐box are zinc finger proteins. Surprisingly, only the structure of the RING domain was determined in 1995 and no information on the structure of other part of the molecule is known. Here we will present the solution NMR structures and dynamics of the RING domain and the B1 box, as well as their interactions with Ubc9, SUMO and SUMO substrates.Grant Funding Source: Supported by a Grants NSC 101‐2311‐B‐001‐025 from The National Science Council
Organization of protein factors on the carboxy terminal domain of RNA polymerase II in yeast (941.1)
Authors: Mosaheb Mohammad , Fuchs Stephen 
Published: June 2021

Organization of Protein Factors on the Carboxy Terminal Domain of RNA Polymerase II in Yeast Mohammad M. Mosaheb and Stephen M. Fuchs: Tufts University, Medford, MA, Department of Biology.The Carboxy Terminal Domain (CTD) of RNA Polymerase II (RNAPII) in yeast is made up of 26 heptad repeats with the sequence YSPTSPS. The heptad repeats have different phosphorylation patterns at their 3 serines at different stages of transcription which mediate the recruitment of specific protein factors required for transcription. Our goal is to find out how the protein factors organize themselves on the 26 repeats ‐ Do the protein factors have to bind to a specific range of repeats? Or can they bind anywhere on the CTD and still be functional. For this work, we divided the CTD into 3 segments of 8 heptad repeats and subsequently created variants in which the serines in one of three segments were replaced with alanine. Measuring yeast growth on plates we have demonstrated that repeats likely have non‐redundant function. We are currently isolating RNAPII complexes to biochemically identify difference in protein factor abundance in our three mutants. We are also creating 3 new mutants heptad repeats each one with only one of the 3 serines mutated, these new mutants will be helpful to decipher which one of the 3 serines is more important in recruiting our protein factor of interest.
The effects of histone glutathionylation on chromatin structure (942.5)
Authors: Blackshire Bradley 
Published: June 2021

The Effects of Histone Glutathionylation on Chromatin Structure DNA transcription is dependent on interactions between DNA and associated histone proteins. Modifications to histones have the potential to influence DNA transcription by promoting euchromatin structure, such as in the acetylation of histones, or promoting heterochromatin structure, such as in the methylation of histones. Recent work has increased our understanding of the consequences of histone modifications. In particular, a recent study demonstrated that cells exposed to nitrosative stress show an increase in histone glutathionylation, a redox sensitive modification. The current project focuses on the ramifications of glutathionylation of histones on chromatin structure and its potential to regulate gene transcription. We show that glutathionylation promotes heterochromatin structure, which may lead to a decrease in gene transcription. These results have broader significance as chromatin remodeling may play a role in aging and neurodegenerative diseases.Grant Funding Source: STEM Title V
Carbohydrates downregulates sodium‐dependent neutral amino acid transporter‐2 expression (946.5)
Authors: Ortiz‐Ortega Vicor , Mendez‐Garcia Ana Luisa , Noriega Lilia Guadalupe , Torres Nimbe , Tovar Armando Roberto 
Published: June 2021

SNAT has an important physiological role in the provision of amino acids that may enter the gluconeogenic pathway in liver. However, SNAT2 transcriptional regulation by carbohydrates has not been studied. The objective of this study was to determine the acute response to 70% sucrose diet (high sucrose diet, HSD) or 10% sucrose diet (low sucrose diet, LSD) on hepatic SNAT2 expression. Wistar rats fed HSD showed a decrease of hepatic SNAT2 mRNA and protein expression compared with rats fed LSD or fasted rats. Also, we found a decrease SNAT2 mRNA expression in rat hepatocytes primary culture or HepG2 cells incubated with 25 mM versus 5 mM glucose. SNAT2 promoter mapping showed a putative carbohydrate response element (ChoRE). A construct containing this site was ligated in a luciferase vector for functional studies in HepG2 cell line. Promoter activity was decreased when transfection was performed with 25 mM versus 5 mM glucose. Specific protein‐DNA complexes were detected by EMSA indicating that the carbohydrate response element‐binding protein (ChREBP) binds to ChoRE in the SNAT2 promoter. These results showed that sucrose‐fed rats decrease hepatic SNAT2 expression through ChREBP.Grant Funding Source: Supported by CONACyT 183037
Modeling ToxT to explain how cholera toxicity can be regulated by fatty acids: The 2014 Pingry SMART Team project (946.7)
Authors: Abbott Kathryn , Chow Kevin , Hong Brad , Kwon Emily , Newman Matthew , Robinson Jacob , Sander Mariel , Sander Mariel , Wu Rachel , Kull F. , D'Ausilio Morgan 
Published: June 2021

Infections of the enteric bacterium Vibrio cholerae cause the disease cholera and lead to severe dehydration and even death to those who ingest water contaminated with the organism. Two virulence factors are required for infection: the toxin‐corregulated pilus (TCP) and cholera toxin (CT). The production of both gene products is regulated by the transcription factor ToxT, a member of the AraC protein family. The structure of ToxT was solved by X‐ray crystallography and revealed a 16‐carbon fatty acid, cis‐palmitoleate, in the ligand binding pocket of the protein’s regulatory domain. Further analysis indicated that expression of both TCP and CT were reduced in the presence of cis‐palmitoleate and that binding of the fatty acid to ToxT prevented DNA binding and led to a reduction in virulence factor expression. Using the structure determined in this study, The Pingry School SMART (Students Modeling A Research Topic) Team, is using a 3D‐printer from the Milwaukee School of Engineering (MSOE) to model the interactions between ToxT and cis‐palmitoleate. Ligand binding by the regulatory domain of the ToxT leads to a change in conformation of the DNA‐binding domain, resulting in decreased interaction with DNA. Fatty acid regulation of ToxT‐DNA binding provides insight into the mechanism of controlling virulence gene expression in V. cholerae. Studies based on this research are currently investigating the structure and function of other AraC‐family members from a variety of infectious bacteria, seeking to determine if fatty acids may also be involved in regulation of virulence factor expression in other organisms.Grant Funding Source: NIH‐CTSA
Biochemical and biophysical insights into the function of the bHLH transcription factor TWIST2 (946.8)
Authors: Orengo‐Mercado Carmelo , Casasnovas Jose , Cadilla Carmen 
Published: June 2021

TWIST2 is a transcription factor of the basic Helix Loop Helix family, which binds DNA as homo or heterodimer to consensus sequences called E ‐ boxes. Mutations in TWIST2 cause a rare recessive disorder called Setleis Syndrome. To this date, no structural or functional assays have been published using recombinant TWIST2. First, we performed a bioinformatics analysis ranging from multiple sequence alignments to key structural features. These led us to perform a 3D structural prediction of TWIST2 using the Phyre2 server. In order to produce recombinant His tagged TWIST2, the TWIST2 cDNA was cloned into the pQET7 vector and expressed in BL21 pLysS cells. The protein was purified under native conditions by a two‐step purification via Ni‐NTA Affinity followed by Ion Exchange Chromatography. After purification, a band of the expected size of TWIST2 was observed in SDS‐PAGE. Western Blot analysis and Mass Spectrometry validated this finding. TWIST2 functionality was demonstrated by Electrophoretic Mobility Shift Assay (EMSA) with a known E‐box probe. Obtaining recombinant TWIST2 protein will allow future structural and functional assays. These assays will expand the knowledge of this transcription factor and its interactions with DNA to regulate its target genes.Grant Funding Source: Supported by NIH grants (2G12‐RR003051), (8G12‐MD007600) and (R25GM061838)
Isoaspartate accumulation in creatine kinase B in vivo and in vitro is associated with loss of enzymatic activity (949.1)
Authors: Dimitrijevic Aleksandra , Qin Zhenxia , Aswad Dana 
Published: June 2021

Formation of abnormal isoaspartyl (isoAsp) residues occurs frequently in proteins and peptides under physiological conditions, often resulting in the alteration of their structure and function. IsoAsp residues can be efficiently repaired by the action of protein L‐isoaspartyl O‐methyltransferase (PIMT), a cellular repair enzyme that catalyzes the conversion of isoAsp to normal Asp residues. The brain‐enriched isoform of creatine kinase (CK‐B) plays a key role in intracellular energy metabolism and is highly susceptible to isoAsp formation. We investigated the effect of isoAsp formation on CK‐B activity, both in vivo in PIMT‐deficient mice, and in vitro using aged recombinant CK‐B. Accumulation of isoAsp residues in vivo was associated with a significant decrease in CK‐B activity. In vitro aging of recombinant human CK‐B also resulted in isoAsp formation and loss of CK‐B activity. IsoAsp sites in aged, recombinant CK‐B were efficiently repaired in vitro by the action of PIMT. These results (1) corroborate previous finding that CK‐B is a major target of PIMT action in vivo, (2) demonstrate that isoAsp accumulation in CK‐B is associated with significant loss of function, and (3) suggest that loss of CK‐B function in vivo may contribute to the neuropathology and susceptibility to epileptic seizures that are characteristic of PIMT‐deficient mice.Grant Funding Source: Supported by NIH grant NS‐17269
The N‐terminal region of the Trypanosoma brucei Tim17 is critical for mitochondrial protein import (950.3)
Authors: Weems Ebony 
Published: June 2021

The protein translocases of the mitochondrial inner membrane in higher eukaryotes, TIM23‐17 and TIM22‐54, possess three homologous proteins, Tim17, Tim23, and Tim22. In contrast, Trypanosoma brucei, a parasitic protozoon that causes African trypanosomiasis, possesses a single homologue of this protein family, TbTim17. TbTim17 is a part of a large protein complex consisting of proteins unique to trypanosomes. In spite of a significant similarity in the secondary structure of TbTim17 with the Tim17/23/22 family proteins, we report here that the growth defect caused by TbTim17 knockdown in T. brucei could not be complemented by the expression of either Tim17, or Tim23, or Tim22 from Saccharomyces cerevisiae and vice versa, suggesting TbTim17 is significantly divergent in order to full‐fill the species‐specific functions. Bioinformatics analysis revealed that TbTim17 N‐terminus possesses a longer stretch of hydrophilic amino acids at this domain (~30 amino acids) relative to Tim17 proteins expressed in other eukaryotes. In order to investigate the function of this region we expressed a number of N‐terminal deletion mutants of TbTim17 in T. brucei, where endogenous TbTim17 was knockdown by RNA interference targeted to the 3’‐untranslated region of its transcript. We found that the growth defect caused by TbTim17 RNAi was completely rescued by ectopic expression of the full‐length TbTim17 (FL‐TbTim17) but not by the N‐terminal deletion mutants, 20TbTim17, and 30TbTim17. All of these mutants are expressed and properly targeted to mitochondrial membrane in T. brucei. However, the import of nucleus‐encoded mitochondrial proteins into the mitochondrion is significantly inhibited in the N‐terminal deletion mutants. Suggesting a critical role for this region in the import of mitochondrial proteins in T. brucei.Grant Funding Source: 2SC1GM081146, 5T32HL007737, 5T32AI007281, and 2R25GM059994
Carbonates are a new class of deubiquitinating enzyme inhibitors (952.5)
Authors: Long Marcus , Lawson Ann , Rozhansky Lior , Hedstrom Lizbeth 
Published: June 2021

Deubiquitinating enzymes (DUBs) have emerged as promising drug targets, but few small molecule DUB inhibitors have been identified. Herein we introduce carbonates as a novel class of mechanism‐based DUB inhibitors. Activity profiling was used to determine inhibitor potency and specificity in cell lysates. The most potent inhibitor, C17, has a preference for USP9x and USP7. In K562 cells, C17 (50 micromolar) causes the degradation of Bcr‐Abl kinase, as expected when USP9x is inhibited. In MCF7 cells, C17 (25 micromolar) causes the degradation of Mdm2 and upregulation of P53, as expected when USP7 is inhibited. We believe that carbonates will be useful tools for studying the ubiquitination pathways and provide a new strategy for the design of cysteine protease inhibitors.Grant Funding Source: Supported by the NIH R01 GM100921(LH), HHMI International Student Fellowship (MJCL).
Characterization of the mitochondrial function and genetics in the pathogenesis of collagen VI related disorders (958.1)
Authors: Angelin Alessia , Lin Chun Shi , Sharpley Mark , Derbeneva Olga , Potluri Prasanth , Bonaldo Paolo , Bernardi Paolo , Wallace Douglas 
Published: June 2021

Background: Alteration in the collagen VI protein causes Bethlem Myopathy and Ullrich Congenital Muscular Dystrophy. Mitochondrial dysfunction, ultrastructural defects, increased apoptosis and autophagy impairment are associated to muscle of young Col6a1‐/‐ mice and patients.Results: To clarify the pathophysiology of this disorder we are characterizing Col6a1‐/‐ mice at different ages. Preliminary studies show reduced cell growth, decreased respiratory capacity, increased ROS production and increased mitochondrial mass on myoblasts isolated from old Col6a1‐/‐ mice. Mutant cells show altered cytoskeleton structure that could explain why dysfunctional mitochondria accumulate and are not removed by autophagy. We are also determining if the progression of this myopathy is related to the accumulation of mtDNA mutations.Methods: We study: cell growth capacity, mitochondrial membrane potential and mass, oxygen consumption capacity, ROS production, mitochondrial dynamics and cytoskeleton structure in primary muscle cells; and skeletal muscle tissue properties with histological methods. To assess mtDNA mutations levels, we had developed a next generation sequencing protocol that avoids any PCR step in preparing the DNA prior to sequencing. This innovative approach is now being applied to various tissues, with particular reference to the diaphragm the most affected muscle.
Simultaneous analysis of urinary fructose and sucrose by isotope dilution tandem LCMS (959.14)
Authors: Franke Adrian , Custer Laurie , Li Xingnan 
Published: June 2021

Objective: Sugar intake has increased vastly in the US diet during past decades and has been associated with obesity, metabolic syndrome, type 2 diabetes, cardiovascular disease, and cancer. Measuring sugar intake by FFQ is not reliable and urinary fructose and sucrose excretion as a biomarker is recommended but existing methods for their analysis are complex, expensive or unreliable (GCMS, enzymatic kits, doubly labeled water). A simple liquid chromatography mass spectrometry (LCMS) method was therefore established for urinary fructose and sucrose.Methods: This study evaluated many extraction, chemical derivatization and electrospray ionization (ESI) tandem MS variations in positive and negative mode using isotope dilution and reversed, normal or reversed reversed phase LC protocols.Results: While sucrose was measurable reliably by many LCMS protocols myriads of interferences with fructose measurements could be avoided by derivatization of fructose to its dansyl hydrazone or by selective application of organic solvents during urine extraction.Conclusions: A reliable, simple, fast and inexpensive isotope dilution tandem ESI LCMS assay for fructose and sucrose was established requiring 20 uL or less of urine.Grant Funding Source: This research was supported by National Cancer Institute grants P30 CA71789.
Effects of avocado oil in brain mitochondrial ETC function and ROS generation in diabetic rats (960.5)
Authors: Ortiz‐Avila Omar , Hernandez‐De La Paz Lucio , Canizal‐Garcia Melina , Montoya‐Perez Rocio , Saavedra‐Molina Alfredo , Cortes‐Rojo Christian 
Published: June 2021

Diabetes mellitus is associated with functional and structural changes in the brain leading to neurodegeneration, with oxidative stress playing a role in the development of diabetic brain complications. In some cases, it has been reported that impaired function of the electron transport chain (ETC) may be involved in the development of diabetic encephalopathy and oxidative stress. Recently, we have reported that avocado oil supplementation has beneficial effects in kidney mitochondria during diabetes by increasing the resistance of the ETC to oxidative stress and decreasing ROS production in the complex III. Thus, the main goals of this work were to identify alterations in ETC function of brain mitochondria leading to ROS production in rats with 90‐days of STZ‐induced diabetes and the evaluation of the effects of avocado oil intake in these alterations. No alterations were found in the activity of any of the ETC complexes of diabetic rats. Avocado oil supplementation increases 1.2‐fold the activity of the complex III from diabetic rats and 3.5 times the activity of the complex II of normoglycemic rats. Despite no net changes in ROS generation were detected, a decrease in this parameter was identified in diabetic rats when ROS generation was normalized against complex III activity, with avocado oil further decreasing ROS production in the same group. These data suggest that 90 days of diabetes do not exert important changes in mitochondrial function of brain. However, early avocado supplementation may prevent further development of mitochondrial dysfunction in late stages of diabetes by improving the electron flow in the complex III and decreasing ROS generation.Grant Funding Source: Suuported by CONACYT (130638 to CCR) and CIC‐UMSNH (16.12 to CCR) grants