bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anthropometric Evaluation of Body Composition and Foot Arches of African and European Women
Authors: Akambase Jonas Atulebire , Kokoreva Tatyana Valerevna , Gurova Olga Aleksandrovna , Odiase Benedict Efosa , Okediden Chris Ufuoma , Akambase Joseph Atule 
Published: June 2021

Anthropometry is the branch of ergonomics that deals with body shape and size. The parts of the human body varies in size and in shape, thus, there is a need to take these variations into consideration whenever a product is designed for their use. The absence of the application of ergonomics principles could result musculoskeletal disorders. Evolutionary development of humans over the years has produced erect posture among humans necessary for their functionality and effective interaction with their immediate environment. The sole of the human foot has evolved to attain an arch and a three‐point support, which supports the body from either falling back or front. The foot is complex in structure and by function. It plays a major role in keeping the body in balance and steady. Body composition is the proportion of fat and fat‐free mass in the body. However, the fat and non‐essential body fat can be excessively stored in the body and may tend to be unhealthy to the human body and the foot. In this study we aim to preliminarily evaluate the relationship between body composition and anthropometric features of the foot, among women from African and European origin. A total of 150 feet of young women from African and European origin between the ages of 18 and 27 were recruited for the study. The required anthropometric parameters were measured. The shtriter index, a Russian method to determining height of foot arches was used, and body composition examined using BMI. The data were analysed using T‐test and regression analysis. The respective parameters for African and European women were measured: mean Height (H) of 159.6±0.54 and 164.3±0.69, (p<0.05), Body Mass Index (BMI) 24.5±0.40 and 21.1±0.25 (p<0.05), Foot Length (FL) 22.6±0.14 and 22.8±0.13 (p>0.05), Foot Width (FW) 8.3±0.07 and 8.4±0.05 (p>0.05), Length of Medial Longitudinal Arch (LMLA) 14.2±0.12 and 13.5±0.10 (p<0.05), and Width of Posterior Transverse Arch (WPTA) 3.4±0.13 and 2.5±0.12 (p<0.05). For African women, 51% of the total number of feet were FAF (Flat‐Arch Foot) and LAF (Low‐Arch Foot); 33% – VHAF (Very High‐Arched Foot) and HAF (High‐Arched Foot). European women recorded 18% – FAF and LAF; 74% – VHAF and HAF. The research revealed significance difference in the anthropometric parameters of the foot between women from the African and European origin. We speculate that the significant difference in the former is due to the significant difference in their body composition. Reasons for the significant difference in some of the anthropometric parameters of the foot were attributed to factors such as environment, genetics, and origin of race.Support or Funding InformationResearch supported by the Department of Human Anatomy at RUDN University, Moscow, RussiaThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Structural Biochemistry and the Opioid Crisis: Using the Primary Literature to Teach Core Concepts and Underscore the Societal Relevance of Biochemical Research
Authors: LOCHNER JANIS 
Published: June 2021

Macromolecular structure, interactions and dynamics are essential underpinnings of an education in biochemistry. Biochemists often convey these core concepts by systematically probing the structure function relationship of archetypal proteins. G‐protein–coupled receptors are the largest class of signaling receptors in the genome and the target of over 30% of marketed drugs. The mu opioid receptor (MOR) is a member of this influential receptor family and constitutes the main opioid target for the management of pain. Insight into opioid action has been facilitated by acquiring structures of the MOR in inactive and agonist‐induced active states. Importantly, these structures enabled the application of structure‐based approaches to drug discovery in a quest to find an ideal opioid that elicits analgesia but fails to trigger the respiratory depression associated with the epidemic of opioid‐induced deaths.To provide an authentic learning experience, a primary literature module that explores the structure function of the MOR, and the ongoing work on developing optimized opioids as well as non‐opioid analgesics was integrated into our undergraduate biochemistry class. Students in the class undertook a deep reading of the primary papers detailing MOR structure and then addressed questions on the mode of ligand engagement and signal transduction in a think‐pair‐share method during class time. In a subsequent class session, teams of students critically assessed findings from published studies on designing ‘biased’ opioids that activate signaling pathways relevant to analgesia, but not those that produce unwanted effects. To complement this focus on the biochemistry of opioid analgesics, primary papers that detail the development of non‐opioid alternatives for the pharmacological treatment of pain were probed. Since humans with loss‐of‐function mutations in the gene that codes for the sodium channel subtype Nav1.7 exhibit complete insensitivity to pain, a literature review session focused on the diverse biochemical approaches being used to develop potent, selective inhibitors of Nav1.7. This literature module succeeded in illuminating the contemporary relevance of structural biochemistry by delving into the molecular interactions relevant to the escalating opioid crisisThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Developing a 3D Physical Model of 16S rRNA m1A1408 Methyltransferase, NpmA to Enhance Student Understanding of the Mechanisms of Resistance to Aminoglycosides
Authors: Toledo Silvia , Renn Jaxon , Rosenthal Caleb , Robinson Ashley , Bygd Madison , Ademola‐Green Dami , Martinez‐Vaz Betsy 
Published: June 2021

Aminoglycosides are broad‐spectrum antibiotics common in clinical, veterinary, and agricultural settings and are often reserved for treating severe bacterial infections. With antibiotic resistance becoming a global crisis, understanding the mechanisms by which bacteria attain such resistance is more urgent than ever. One such mechanism specific to aminoglycosides is ribosomal modification by methyltransferases (RMTases). RMTases pose a significant threat as they grant simultaneous resistance to various aminoglycosides and are transmitted between species. The purpose of this project was to develop a 3D physical model of NpmA, an RMTase that confers blanket resistance to aminoglycoside antibiotics by transferring a methyl group to the A1408 nucleotide in helix 44 of the 30S ribosomal subunit. Methylation of A1408 makes helix 44 unrecognizable to these antibiotics. Database searches and sequence alignments were performed to identify conserved amino acids and structural features important in the catalytic mechanism of NpmA. Details of the protein structure and its interaction with helix 44 were obtained by analyzing the Protein Databank File 4OX9. To construct the physical model, the structure file (4OX9) was imported into Jmol and modified into a format suitable for 3D printing using scripts created by undergraduate researchers. The 3D model features NpmA interacting with rRNA and S‐adenosyl‐L‐methionine, the methyl group donor for the methylation reaction. The physical model also highlights key amino acids such as Arg207, E146, Trp107 and Trp197, which are critical to flip A1408 from helix 44 and position it into the enzyme's active site prior to methylation. A Jmol tutorial was created to complement the 3D model and assess students' learning of the structure and function of NpmA. Initial assessment of this activity showed improvement of students' protein visualization abilities, and computational skills. Future work will focus on field‐testing the complete exercise in a microbiology course to evaluate the impact of the 3D model on students' understanding of the mechanisms of antimicrobial resistance.Support or Funding InformationThis project was supported by NSF‐DUE 1725940 awarded to the CREST (Connecting Researchers, Educators, and Students) ProjectThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Managing course embedded research projects of any size using the Open Science Framework
Authors: Berndsen Christopher 
Published: June 2021

The large biochemistry lecture section is not an environment where course‐embedded research projects are found. However, large lecture sections offer the opportunity to expose a large number of students with diverse backgrounds to an open, collaborative research experience. CUREs, while relatively common in biochemistry and molecular biology laboratory settings, are seen infrequently in lecture settings because of constraints on instructor time, access to projects, and having resources to manage a large research project. I will describe the implementation of a lecture‐based research activity that has been used in Biochemistry sections of over 100 students and was managed within the Open Science Framework (OSF). The research project reinforces concepts of biomolecule structure and mechanism through analyzing and modeling understudied areas of the biochemical literature. While performing this project over the course of the semester, students learn to search through scientific databases, analyze biomolecule structure, effectively convey scientific information in visual/text formats, and perform modeling to predict and explore the biomolecule structure‐function connection. OSF facilitates project management by serving as a central repository for the storage of data and hosts resources for analyzing results, collaboration between participants, describing conclusions, and dissemination of final project. This latter feature helps students develop public portfolios of their work for gaining employment or admission to graduate/professional school. Thus using the Open Science Framework to manage a course‐based research project aids students in learning the entire research cycle and developing professional materials to benefit their careers. In eight semesters of executing this project in my classroom, the activity has involved nearly 500 students and the data generated have been included in three peer‐reviewed publications.All software and guides are free to use and are available through the internet, thereby reducing the cost burden and opening access to classrooms of all levels and resources. Instructor produced materials for this project including guides for using software/servers and OSF are available for use or adaptation through the Open Science Framework and the presenter's website. Moreover, new contributions and collaborations are welcome.Support or Funding InformationThe Thomas F. and Kate Miller Jeffress Memorial Trust, Bank of America, TrusteeThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Integrating a Research‐Based Experience in the Biochemistry I Laboratory: From Separation of Colored Compounds to Protein Purification
Authors: Sherrer Shanen M. , Mertz Pamela S. 
Published: June 2021

As part of our CUR Transformations Project work within the Department of Chemistry and Biochemistry, we aimed to create an additional research‐based experience for the Biochemistry I laboratory course. We designed a series of chromatography experiments that focus on careful observation, experimental design, data interpretation, and presentation skills. Students first work with three different types of columns during a two‐week chromatography lab. The first week they work with two mixtures of colored compounds, each mixture contains 3 out of the 5 compounds. These two mixtures are run through gel filtration, anion exchange, and cation exchange columns. Students analyze their observations in week 1 to design a purification scheme for separation of all 5 colored compounds together in one mixture in week 2. After finishing the two‐week lab, students write a paper based on their results in the format of Nature Methods. Following this experiment, students start a 3‐week lab where they design a scheme to separate two unknown colorless proteins in a mixture. They are given the following information: isoelectric points for both proteins, one of the two proteins has a 6x histidine‐tag, and the 260 nm extinction coefficient of the tagged protein. Students then choose a cation exchange, anion exchange, or an affinity column to use for protein separation. Students analyze their chromatography procedure by using the Bradford reagent to detect protein in column fractions, denaturing gel electrophoresis to assess purification and determine molecular weights of the two proteins, and a western blot to verify identity of one of the proteins using an antibody to 6x histidine‐tags. Lastly, students present their results to their peers in week 4.Support or Funding InformationWe would like to acknowledge support for this CUR Transformations project through NSF DUE IUSE grant # 16‐25354.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Ataxia telangiectasia and Rad3‐related kinase (ATR) may prevent replication stress in planarian during regeneration
Authors: Sawyer Nathaniel , Tirgar Reyhaneh , Shamoon Ushna , Akpati Lois , Nguyen Lillian , Nam Edward A 
Published: June 2021

S. mediterranea is a planarian with extensive regenerative ability which requires substantial cell division. However, DNA replication stress occurs every cell division and must be resolved. From yeast to man, an evolutionary conserved DNA replication stress response (RSR) is essential for life. The RSR is a signal transduction pathway regulated by Ataxia telangiectasia and Rad3‐related kinase (ATR) and Checkpoint 1 kinase (CHK1) to respond to replication stress. However, the RSR has not been established in planarian nor do we know if it functions in regeneration. We hypothesize that ATR may be essential for regeneration. Preliminary results show reduced regenerative ability in the presence of hydroxyurea (HU), a replication stress inducing agent. However, low concentrations (2mM) did not attenuate regeneration, indicating that ATR and the RSR may be present and able to overcome replication stress. To test this, we treated amputated tails with HU, ATR inhibitor (ATRi), and a combination of both. In 2mM HU, tails regenerated similarly to control. We observed only a one day delay in regeneration with ATRi alone. However, ATRi and 2mM HU in combination prevented planarian regeneration completely. This synergistic effect suggests that ATR is significant in the response to replication stress during regeneration. To obtain genetic evidence, we are in the process of knocking down ATR as well as other RSR genes like CHK1, WRN, etc. Further determining the importance of RSR genes in planarian will elucidate the conserved components and allow us to understand how ATR and the RSR contributes to the incredible regenerative abilities in planarian.Support or Funding InformationThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Modulation of gene expression by Salvia hispanica seed extract in MC3T3 cells
Authors: Mendez Daisy May , Rey Maximo , Hernandez Tomas , Vel Jaysonn , Sanchez Diego , Nair Saraswathy , Banu Jameela 
Published: June 2021

Postmenopausal bone loss weakens bones and make them fragile and easily susceptible to fractures. Available therapies have severe side effects increasing the need for new therapeutic agents that can be effective in protecting bone loss and have less‐side effects. Recently, Salvia hispanica (SH) is reported to have several health benefits and high calcium levels. Our studies using a rodent model for postmenopausal bone loss showed bone protective properties, we decided to determine the influence of SH seed extract on osteogenic gene expression.We cultured MC3T3 cells, differentiated them into osteoblast and treated them with Salvia hispanica (SH) seed extract at optimal concentration. Cells were harvested, for gene expression studies, RNA was isolated using Purezol RNA isolation reagent (BioRad). cDNA was synthesized using standard methods. The cDNA was assessed for the expression of genes related to osteogenesis in real‐time RT‐PCR using gene specific primers and Taqman assays. Alkaline phosphatase, BMPr2, osteocalcin, osteopontin, DCAT (inhibitor of beta catenin – wnt signaling pathway) and Type 1 collagenase.Alkaline phosphatase increased (58%) when treated with SH seed extract while type 1 collagen (18%), Bgl (19%), BMP2r (80%) decreased in the SH group. The expression of DCAT1, an antagonist of b‐catenin, also significantly decreased (75%) after treatment with SH. This suggests that SH may act via the Wnt signaling pathway to modulate bone metabolism.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Decoding Melanoma Antigen Gene (MAGE) Expression
Authors: Colemon Ashley , Ramanathan Saumya 
Published: June 2021

Melanoma Antigen Genes (MAGEs) are a family of tumor‐associated genes whose protein products share a MAGE‐homology domain (MHD). Type I MAGEs are physiologically restricted in expression to the germline, specifically to the testis, however, they are aberrantly re‐expressed in a wide variety of cancers. Their expression often correlates with poor patient prognosis. There is a significant gap in knowledge regarding the regulatory mechanisms that cause this aberrant expression of Type I MAGEs. The overall goal of this project is to understand these regulatory mechanisms. We have tested the hypothesis that like many germline genes, the expression of the MAGE‐A gene family is regulated by promoter or DNA Methylation. Using DNA Methyltransferase inhibitor 5‐azacytidine, we determined that MAGE‐A gene expression can be controlled by CpG methylation. This data was validated by complementary bioinformatics analysis using the UCSC Genome browser methylome datasets showing conserved differentially methylated positions within the respective promoter regions of target MAGE‐As. In order to test the effect of the aberrant expression, we then introduced MAGE‐A genes into “normal” cells and tested deviations from known phenotypes. We discovered that when expressed several MAGE‐A genes can act as single‐gene drivers of cell proliferation and anchorage‐independent growth. Taken together our data indicate that MAGE‐A genes are expressed by epigenetic mechanisms, specifically CpG methylation and their aberrant expression in cancer is not happenstance but results in providing cells with a proliferative advantage.Support or Funding Information

R25 Bridge to the Doctorate Grant‐1R25GM107754
NSF Implementation Award to L.L. # NSF HRD 1332284 Fisk University Implementation Award
NSF Research Initiation Award to S.R. #HRD1764201
This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Conserved mechanisms of transcriptional pausing regulate diverse RNA polymerases
Authors: Palo Michael Z. , Mishanina Tatiana V. , Landick Robert 
Published: June 2021

Transcription of DNA into RNA requires multi‐subunit RNA polymerases (RNAPs) in all forms of life. Pausing is an important regulatory feature of RNAPs that facilitates formation of RNA structures and the process of termination in bacteria. The elemental pause is an offline state of RNAP caused by conformational rearrangements and may be a precursor to longer‐lived backtracked and RNA hairpin‐stabilized pausing. While the backtrack pause has been well‐characterized in eukaryotes, biochemical data describing the elemental pause are lacking and hairpin‐stabilized pausing has not been described. As these last two types of pausing are important for the proper regulation of transcription in prokaryotes, it is important to know whether they are conserved in eukaryotes. Using in vitro transcription assays on synthetic oligonucleotide scaffolds, we investigated the response of Saccharomyces cerevisiae RNA polymerase II (Pol II) to the consensus elemental pause and his hairpin‐stabilized pause sequences from Escherichia coli. We demonstrate that RNA duplexes can form within the Pol II elongation complex and modulate pausing behavior. These duplexes can also halt transcription elongation in a manner analogous to intrinsic terminator hairpins found in prokaryotes. We also characterize the previously‐described HIV‐1 TAR pause as a consensus elemental pause sequence, confirming that features of the elemental pause are conserved from bacteria to mammals. These data show that aspects of pausing as a form of transcriptional regulation are conserved from bacteria to mammals, and guide the search for novel examples of elemental and hairpin‐modulated pauses in eukaryotes.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.