bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein‐DNA Interactome of the OxyR Oxidative‐Stress Transcription Factors in Aliivibrio fischeri
Authors: Castro-Martínez Alexander , Pinto-Sanchez Victoria I. , Rodriguez-Bonilla Laura M. , Flores-Cruz Zomary , Rodriguez-Martínez Jose A. 
Published: April 2020

Transcription factors (TFs) are sequence‐specific DNA‐binding proteins that dictate cell function by controlling selective usage of genomic information. One of the largest prokaryotic family of TFs is the LysR type transcriptional regulators (LTTRs). These TFs tend to regulate a diverse set of genes involved in virulence, metabolism, quorum sensing, and oxidative stress. Hydrogen peroxide (H2O2) is a well‐known cell damaging agent, which can lead to oxidative stress, disease, and important beneficial signaling roles. OxyR is a transcription factor with an N‐terminal DNA‐binding helix‐turn‐helix motif and a C‐terminal co‐inducer‐binding domain, that is involved in the defense mechanism against hydrogen peroxide‐induced oxidative stress. Although, different OxyR proteins share functional and sequence similarities across different bacterial species, they respond differently to hydrogen peroxide. The symbiotic relationship between Euprymna scolopes and Aliivibrio fischeri is dependent on the initial colonization survival of the bacteria in an environment rich reactive oxygen species. It has been documented that A. fischeri’s genome encodes two OxyR genes, OxyR1 and OxyR2. Studying OxyR1 and OxyR2 protein‐DNA interactomes will allow us to identify key differences and their possible roles in oxidative stress responses. Currently, we have over‐expressed and purified the full‐length OxyR1 and OxyR2 and their DNA binding domain. Protein functionality has been tested by Electric Mobility Shift Assay (EMSA), and High‐Throughput Systematic Evolution of Ligands by Exponential Enrichment (HT‐SELEX) will be used to determine the protein‐DNA interactomes of the OxyR1 and OxyR2. Genomic targets of OxyR1 and OxyR2 will be bioinformatically predicted once the DNA‐binding specificities are established.Support or Funding InformationNational Institutes of Health SC1GM127231.
Efficiency in Brain Removal Techniques: A Potentially Novel Approach
Authors: Robertson Ellen , Klender Sara , Mueller Caroline , Ferriby Andrew , Roth Alex , Batra Ranjan 
Published: April 2020

Dissection of the human brain is an important part of health professional education in the neuroscience curriculum. Therefore, it is critical that adequate protocols are utilized to preserve structures when removing brains from cadavers. Previous studies have looked at approaches to extracting the brain and associated structures from the cranial cavity which would best preserve these delicate structures. However, these methods require both extensive dissection experience and more time than suitable for routine use. The aim of this study was to determine the technique for brain removal that minimized the time required for the procedure while preserving key structures for future educational purposes.The time and ease for three aspects of brain extraction were assessed: removal of the calvaria, subsequent removal of the brain, and transection of the brainstem. Six dissectors (two faculty, four senior graduate students) with prior experience performed the removals. Each tested three calvaria‐removal approaches – circumferential only, circumferential plus a median cut, and circumferential plus a coronal cut. They also tested three approaches to brainstem transection—superiorly through the foramen magnum, inferiorly below C1 vertebra, or inferiorly after removal of an occipital wedge. The time for each procedure was recorded, and its ease was evaluated on a 5 point scale (1 easiest and 5 hardest). The combination of calvaria and brainstem approaches and the order of completion were randomized across dissectors and the 3 brains extracted by each. At the completion of brain removal, all brains were evaluated by two neuroscience course directors for utility in educational contexts. The evaluators rated structures on a list compiled from the laboratory handouts in the medical neuroscience course.Preliminary examination of the data suggests that removal of the calvaria using only the circumferential cut or using an additional coronal cut took about the same length of time, whereas performing circumferential and median cuts took somewhat longer. However, the ease of removal was greater when either the additional median or coronal cut was employed. Transecting the brainstem took less than a minute if performed through the foramen magnum or below C1, but it took substantially longer if the occipital wedge cut was executed. The ease of transection was greatest when performed below C1, and least when the occipital wedge was removed. There was no clear difference in overall quality of the brains removed by the various techniques.While there may be advantages to one or the other of the techniques for preservation of specific structures, it appears that all approaches tested were equivalent in yielding brains that could be used for educational purposes.
Effects of Lorcaserin on Opioid‐Induced Observable Behavior in Rhesus Monkeys
Authors: Borgatti Daniel , Bergman Jack , Kohut Stephen 
Published: April 2020

Serotonergic ligands that target the 5HT2‐family of receptors, such as the 5HT2C receptor agonist lorcaserin, have been shown to decrease several of the abuse‐related effects of opioids, including self‐administration and relapse‐related behavior. This suggests that lorcaserin may be an effective medication for the management of opioid use disorder. However, the impact of 5HT2C agonists on behaviors relevant to opioid withdrawal have not been reported. The objective of the present study was to determine whether lorcaserin alters behavioral signs indicative of opioid withdrawal in morphine‐dependent nonhuman primates. Adult rhesus monkeys (N=4; 3 males, 1 female) with histories of drug self‐administration received twice daily (0930 and 1700‐hr) morphine injections (intramuscularly) for a total daily dosage of 9.0 mg/kg/day over a 6–8‐month period. Behavioral observations were conducted by a blind observer over a 6.5 hr period on test days conducted twice per week. Spontaneous withdrawal was elicited by replacing the 0930‐hr morphine injection with saline while precipitated withdrawal was elicited by administering naltrexone (0.0032 and 0.01 mg/kg/inj) 3‐hr after morphine injections; test drugs were administered 15 min after saline or naltrexone. Results show that saline produced a time‐dependent increase in observable behavior throughout the observation period while morphine (1.0 and 4.5 mg/kg) dose‐dependently attenuated observable signs compared to saline, with the highest dose nearly eliminating withdrawal signs. Lorcaserin (0.3 and 1.0 mg/kg/inj) produced a modest decrease in observable signs (~30%) at the lowest dose but was ineffective at the higher dose. Naltrexone produced approximately 30% more observable signs compared to saline, particularly at the first timepoint (30 min), but this effect gradually dissipated over 3hr. Lorcaserin (1.0 mg/kg) attenuated the initial increase but was otherwise similar to naltrexone alone. Overall, these data suggest that lorcaserin does not appreciably alter opioid withdrawal signs.Support or Funding InformationSupported by NIH grant R01DA047130
Genetics in Action: Mutation of Chromoproteins in First‐Semester Introductory Biology
Authors: Walsh Susan Jennifer 
Published: April 2020

In contrast to fluorescent proteins, chromoproteins provide a quick, reliable way to assess phenotype in visible light. In this course‐based undergraduate research experience (CURE), students utilized two different strategies to mutate the chromoproteins aeBlue and tsPurple: either intentionally or randomly. After a journal club highlighting diversity in chromoproteins, the conservation of their chromophores, and the targeted mutation of amilCP, students designed their own primers for site‐directed mutagenesis of either the aeBlue chromophore itself or amino acids near the chromophore. As a complementary technique, students used isothermal, error‐prone PCR with manganese chloride to induce mutations in the tsPurple plasmid. Potentially mutated DNAs were transformed into bacteria, and candidates for mutation were selected based on a loss of color relative to bacteria expressing the parent vector. Students analyzed mutants by DNA sequencing and protein expression (via SDS‐PAGE) to verify how changes to protein sequence contributed to protein function. Based on the phenotypes from the random mutagenesis, students also identified novel mutations in the chromoprotein that prevented color development. Understanding of the project was assessed through laboratory notebooks, formal laboratory papers, and presentations. Overall, this project provided an engaging, straightforward, and affordable way to visualize the relationship between protein structure and function while teaching first‐year college students basic molecular biology techniques.Support or Funding InformationSoka University of America
Evidence that Sympathetic Activity is Increased Selectively to the Heart in a Mouse Model of Hypertrophic Cardiomyopathy
Authors: Larson Robert A. , Lu Yongjun , Chapleau Mark W. 
Published: April 2020

Hypertrophic cardiomyopathy (HCM), the most common genetic heart disease, is characterized by cardiac hypertrophy, fibrosis, and increased risk of arrhythmias and sudden death, even in the absence of heart failure. We have studied young (<20 wks) transgenic mice with cardiac‐specific expression of mutated alpha‐tropomyosin (Glu180Gly), an established model of HCM, to investigate autonomic mechanisms. In early experiments, abnormal heart rate and blood pressure responses to β‐adrenergic receptor blockade and ganglionic blockade indicated high cardiac accompanied by low vasomotor sympathetic tone in HCM vs. wild‐type (WT) mice. The aim of this study was to further characterize regional sympathetic activity in HCM vs. WT littermates by measuring expression/activity of tyrosine hydroxylase (TH, rate‐limiting enzyme for norepinephrine (NE) synthesis) and the norepinephrine transporter (NET) in sympathetic ganglia (stellate, superior cervical, celiac/mesenteric), and expression of β1 receptors in left ventricle (LV). Results (below) are expressed relative to WT (n=4 male mice each group). TH protein expression (Western blot) (standardized to neuronal content with PGP9.5) was significantly higher in stellate (cardiac) ganglia in HCM mice (HCM 162±12 vs. WT 100±7; p<0.05), but not significantly different in superior cervical (HCM 82±4 vs. WT 100±14; p>0.05) or celiac‐mesenteric (HCM 95±7 vs. WT 100±4; p>0.05) ganglia. TH/PGP9.5 protein expression was also higher in the LV of HCM (135±15) vs. WT (100±1) mice (p<0.05). LV β1 receptor protein expression was significantly lower in HCM (60±1) vs. WT (100±4) mice (p<0.05), consistent with increased local NE levels. NET protein (immunofluorescence) was lower in stellate ganglia from HCM mice vs. WT (n=3 mice per group, 3 sections/mouse, p<0.05). NET activity was assessed by measuring the rate of uptake of a fluorescent NET substrate (Molecular Devices) into individual sympathetic neurons isolated from stellate and superior cervical ganglia. NET activity measured in stellate neurons was significantly lower in HCM (4.5±0.3 a.u.*min−1, n=115 neurons, from 4 mice) vs. WT (5.3±0.4 a.u.*min−1, n=98 neurons, from 4 mice). NET activity in superior cervical ganglia did not differ between genotypes. In conclusion, increased TH expression (enhanced ‐NE synthesis) and decreased NET expression/activity (reduced NE reuptake) in stellate ganglia are consistent with increased cardiac sympathetic activity in HCM, whereas the lack of differences between HCM and WT in other sympathetic ganglia are consistent with normal sympathetic activity to non‐cardiac target organs in HCM.Support or Funding InformationNIH F32HL140880
Experimental Investigation of Profibrotic Cell Signaling in Pulmonary Arterial Adventitial Fibroblasts
Authors: Wang Ariel , Valdez-Jasso Daniela 
Published: April 2020

Pulmonary arterial adventitial fibroblasts (PAAFs) are important regulators of fibrotic vascular remodeling during pulmonary arterial hypertension (PAH). PAAFs can be activated into myofibroblasts that produce more extracellular matrix (ECM), which contributes significantly to pulmonary vascular remodeling and stiffening in disease progression. There are currently no therapies that reverse the matrix remodeling and vascular stiffening that occurs during PAH. In order to better identify treatments to target adventitial fibrosis, we sought to investigate the interplay between major pathways that have been reported to regulate myofibroblast transformation and ECM expression in PAAFs.Compared with other fibroblast types, there is a scarcity of experimental data on mechano‐signaling in PAAFs, therefore more in vitro experiments are needed to determine which pathways are crucial to creating a systems biology model that describes mechanosignaling in PAAFs.We have developed techniques to decellularize and reseed pulmonary arteries from Sprague‐Dawley rats to investigate the effects that purely the ECM have on the phenotypic transition of PAAFs. We surmise that pulmonary artery ECM alone from rats with PAH will have a significant impact on the transition of PAAFs into myofibroblasts and will investigate this difference using quantitative RT‐PCR. We will measure collagen I, collagen III expression, and alpha smooth muscle actin to measure the level of myofibroblast transition. In addition, levels of matrix proteins such as elastin and fibronectin will be measured via histology to characterize the level of fibrosis.Combining these results with a profibrotic signaling network model, we can use these methods to identify potential combinatorial therapeutics to prevent or inhibit wall remodeling to treat PAH.Support or Funding InformationThis work was partially funded by the American Heart Association Scientist Development Grant 16SDG29670010, and the National Institutes of Health NHLBI 1 T32 HL105373 and NHLBI 1 R01 HL137100.
Oroxylum indicum extract prevents chemotherapy‐induced cognitive impairment in mice
Authors: Pondugula Satyanarayana R. , Majrashi Mohammed , Almaghrabi Mohammed , Abbott Kodye L. , Govindarajulu Manoj , Ramesh Sindhu , Gill Kristina , Fahoury Eddie , Narayanan Natasha , Desai Darshini , Nadar Rishi , McElroy Edwin , Moore Timothy , Nagabhushanam Kalyanam , Majeed Muhammed , Dhanasekaran Muralikrishnan 
Published: April 2020

Chemotherapy‐induced cognitive impairment (CICI) is an emerging concern among cancer patients undergoing chemotherapy treatment. Several mechanisms including neuronal oxidative stress and mitochondrial dysfunction have been proposed as the underlying mechanisms of CICI. While a few synthetic and natural compounds with different mechanisms of action have been proposed for targeting the CICI, their beneficial effects are outweighed by severe adverse effects including reduced efficacy of chemotherapy drugs. Therefore, search for novel and safer neuroprotective avenues to target CICI is needed. We sought to determine whether Oroxylum indicum extract (OIE, Sabroxy®) prevents CICI in a rodent model by suppressing chemotherapy induced neuronal oxidative stress and mitochondrial dysfunction. Male C57BL/6J mice were injected intraperitoneally with saline or doxorubicin (2mg/kg) and cyclophosphamide (50mg/kg) once a week for 4 weeks. While control mice received powdered rodent food alone, OIE treatment group received the powdered rodent food mixed with OIE (250 or 500mg/kg) daily for 4 weeks. After the treatment period, the mice were assessed for cognitive function using novel object recognition, Y‐maze, and Morris water maze analyses. Biochemical assays were performed using brain tissues to determine the underlying mechanisms of CICI. While the chemotherapy treatment impaired the performance of the mice in the novel object recognition, Y‐maze and Morris water maze tests, OIE significantly prevented the chemotherapy impaired performance in these tests. Additionally, OIE treatment prevented the chemotherapy‐induced changes in oxidative stress and mitochondrial dysfunction in the cortex and rest of the brain. Mechanistically, OIE enhanced mitochondrial function and counteracted chemotherapy‐increased reactive oxygen species formation and lipid peroxidation. Furthermore, OIE treatment increased the monoamine oxidase activity in the cortex and rest of the brain. Our results support the hypothesis that neuronal mitochondrial dysfunction induced by doxorubicin and cyclophosphamide treatment is an underlying cause of CICI, and that OIE may be offered as an adjuvant therapeutic strategy to treat CICI.Support or Funding InformationOIE (Sabroxy®) and funding was provided by Sabinsa Corporation.
Evaluation of Novel Epibatidine Analogs in Rats Discriminating Nicotine
Authors: Wilkerson Jenny , Felix Jasmine , Restrepo Luis , Reeves Morgan , McMahon Lance 
Published: April 2020

Tobacco use is a persistent public health issue. One of every three cancer deaths is linked to tobacco use, including nearly 90% of all deaths related to lung cancer. Nicotine is the primary psychoactive component in tobacco, and nicotine has been identified as the primary compound responsible for maintaining tobacco dependence in humans. Drug discrimination is a pharmacologically selective bioassay, utilized in the past for elucidating the receptor pharmacology of nicotine. If a test compound shares discriminative stimulus effects with nicotine, then it might serve as an effective substitution pharmacotherapy. Epibatidine reliably substitutes for nicotine in the drug discrimination assay, but has a side‐effect profile that limits its therapeutic potential. Thus, considerable efforts are underway to produce derivatives of epibatidine. Here we tested three epibatidine derivatives, 2′‐fluoro‐3′‐(4‐nitrophenyl)deschloroepibatidine (RTI‐7527‐102; i.e., RTI‐102), 2′‐fluorodeschloroepibatidine (RTI‐7527‐36; i.e., RTI‐36), and 3′‐(3″‐dimethylaminophenyl)‐epibatidine (RTI‐7527‐76; i.e., RTI‐76). A total of 4 male and 4 female Sprague‐Dawley rats were trained on a fixed‐ratio 10 schedule to discriminate nicotine (0.32 mg/kg base) from vehicle. All compounds dose‐dependently substituted for nicotine, without significant decreases in response rates. The rank‐order potency in the discrimination assay was RTI‐36 > nicotine > RTI‐102 > RTI‐76. There is abundant evidence that the α4β2* subtype is of particular importance to the abuse potential of nicotine. Thus, we examined the relative contribution of the β2 subunit with the antagonist by dihydro‐β‐erythroidine (DHβE). DHβE antagonized the discriminative stimulus effects of nicotine. However, relative to antagonism of nicotine, DHβE produced less antagonism of RTI‐102, RTI‐36 and RTI‐76. Thus, it is likely that RTI‐102, RTI‐36 and RTI‐76 possess differing activity at nicotinic receptor subunits.Support or Funding InformationThis work was supported by the National Institutes of Health National Institute on Drug Abuse [DA25267] and [DA48353].
Comparing the DNA‐Binding Specificity of Glucocorticoid and Androgen Receptors
Authors: Henze Tyler , Boulanger Kyle , Pufall Miles A. , Hall Bonnie L. 
Published: April 2020

Prostate cancer is the second most common cancer among men, with an estimated 175,000 diagnoses expected in 2019. Androgen hormones fuel prostate tumor growth through the actions of the androgen receptor (AR), a member of the nuclear hormone family of transcription factors. Therapies for prostate cancer include surgery and inhibition of AR with antagonists. Patients, however, often relapse with castration‐resistant prostate cancer (CRPC) in which the cancer grows in the absence of AR ligand action. In some cases, the need for androgens is subverted by overexpression of the AR‐related glucocorticoid receptor (GR). GR effectively replaces AR by regulating genes that drive prostate growth and survival. We have previously used the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method along with the SelexGLM computational algorithm to demonstrate that GR and AR have similar, but distinct DNA sequence specificities. Upon overexpression, GR is able to bind genomic loci once preferentially bound by AR and regulate associated genes. To better understand differences in AR and GR DNA recognition, we are now measuring DNA sequence preferences of both AR and GR using the No Read Left Behind (NRLB) method. NRLB yields high resolution models of specificity after just one round of selection, allowing rapid screening of both wildtype and hybrid AR and GR DNA binding domains. We have over‐expressed and purified both the AR and GR DNA binding domains, and are designing hybrid mutants. Exploring the similarities and differences between AR, GR and the hybrid molecules should help us understand how GR might be playing a role in CRPC.Support or Funding Information• Grant: NSF:CAREER (MCB‐1552862) to M.A. Pufall
Essential Anatomy for General Internal Medicine in the Undergraduate Medical Curriculum
Authors: Latacha Kimberly , Keim Sarah , Harmon Derek , Marzban Hassan , Lopez Lisa , Topping Daniel , Royer Danielle , Carpenetti Tiffany , Downs Mary Beth , Davies David , Harrell Kelley , Brooks William , Cotter Meghan , McNary Thomas , Mork Amy , Wineski Lawrence , Lewis Steven , Giannaris Eustathia Lela , Farias Anna , Martindale Jim , Hankin Mark 
Published: April 2020

IntroductionTo prepare medical students for clinical training and practice, it is critical to understand the anatomical knowledge considered most important for different clinical specialties.AimTo address this issue, a consortium of anatomists in the US and Canada is collecting data from clinical educators in Internal Medicine clerkships and electives to identify the anatomy they consider essential.MethodsAn IRB‐approved, online survey (Qualtrics, Seattle, WA) was used to assess the importance of 98 anatomical topics in seven body regions. The study first examined the percentage of Internal Medicine clinical educators (clerkship/elective directors and attending physicians) that considered each anatomical region important to their specialty. Second, the study examined the rank assigned to each anatomical topic using an ordinal scale from 1 (not important) to 4 (essential).ResultsAt the time of abstract submission, data had been collected from 31 General Internal Medicine clinical educators at 16 medical schools and 43 Hospitalist Internal Medicine clinical educators at 16 medical schools. The percentage of clinical educators that considered each anatomical region important to their specialty were (highest‐to‐lowest): General Internal Medicine – Back (97%), Upper Limb (83%), Lower Limb (79%), Thorax (79%), Abdomen (79%), Pelvis & Perineum (76%), Head & Neck (79%); Hospitalist Internal Medicine – Back (87%), Abdomen (80%), Thorax (82%), Head & Neck (75%), Lower Limb (75%), Pelvis & Perineum (75%), and Upper Limb (61%). Further data analysis has identified the highest ranked anatomical topics in each body region for the General Internal Medicine and Hospitalist Internal Medicine clerkships/electives.Discussion and ConclusionThis database provides detailed information regarding the most clinically relevant anatomical topics as identified by General and Hospitalist Internal Medicine clinical educators. This information can aid in focusing preclinical learning to best prepare medical students for success in their undergraduate and graduate clinical experiences.