bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Collaboration between the ASBMB and Course Source to Promote the Use of Active Learning Strategies in BMB Courses
Authors: Fox Kristin M , Grover Neena 
Published: November 2023

Over the last few years workshops have been held around the country to develop a set of core concepts for undergraduates completing a major in biochemistry and molecular biology. These concepts and associated learning goals have been published at: www.asbmb.org/education/teachingstrategies/foundationalconcepts/. A second aim of the project was to develop a network of faculty interested in improving the education of undergraduates. This was accomplished by involving the community of BMB educators from a wide variety of institutions. To date, more than 700 participants from 475 institutions have been involved. This year the workshops were adapted to develop in‐class materials that encourage active learning approaches. These materials are designed to guide students toward mastering one or more of the earning goals related to the core concepts. We will provide several examples of activities developed at the workshops. In order to make these activities available to the BMB community at large, we have set up a collaboration with Course Source (coursesource.org), an online, open‐access journal. The activities will be peer‐reviewed by members of the BMB community, and linked with the learning goals that have already been developed. In order to make this a robust resource, we encourage members of the BMB community to submit activities they have developed. Most materials used in classes are eligible for publication on Course Source: from detailed case studies to short, 15‐min. in‐class activities that teach a single concept. These activities should have been tested in at least one class, but detailed data on outcomes is not required for publication on Course Source.Support or Funding InformationSupported by NSF RCN‐UBE grant #0957205
Collaborative Undergraduate Research Laboratory (CURL): Engaging Students in Research Using Yeast Molecular Genetics
Authors: Munshi Azad Hossain , Johnson Tracy L. 
Published: November 2023

A growing body of data suggests that undergraduate research enhances the learning experience of students in science, technology, engineering and mathematics (STEM). Moreover, these data also show that engaging undergraduate students in research enhances student learning outcomes and the likelihood of their retention in science. We have developed a course, the CURL, to engage freshman undergraduate students in research‐based scientific learning. The course was constructed to eliminate the need for prerequisite courses by blending classroom learning and hands‐on laboratory experiments so that students reinforce their understanding of the material by applying it to solve real‐world research problems. The students performed the experiments in pairs, built their own hypotheses, and presented their work both orally and in written form.The research problem we addressed was to understand the role of DExH/D‐box ATPases in pre‐mRNA splicing. To this end, the CURL students carried out a screen to identify suppressors of the yeast temperature sensitive (ts) mutant prp2‐1 using a yeast transposon library. Prp2 is a DExH/D‐box ATPase and an essential component of the splicing machinery. Suppressor screening has not been previously carried out, so we anticipate that the results of the screen could lead to novel insights into the mechanism of Prp2 activity, which could be pursued beyond the course and would be of interest to the broader scientific community. The mutant prp2‐1 cells grow at the permissive temperature (25°C) but are unable to grow at the non‐permissive temperature (35°C). We have isolated a number of suppressors of prp2‐1, which grow at the non‐permissive temperature and suppress the splicing defects of prp2‐1 mutant when cells are grown at 35°C. Identification of the suppressors is being performed by next generation sequencing. This study provides first‐year undergraduate students with a rigorous, guided research experience with the goal of enhancing their self‐identification as researchers, while simultaneously addressing a fundamental scientific question.Support or Funding InformationThis works is supported by HHMI (HHMI program award to T.L.J)
Transformation and Assessment Mapping of a Course Undergraduate Research Experience
Authors: Clase Kari , Zissimopoulos Angelika 
Published: November 2023

Course undergraduate research experiences (CURE) can help engage a large number of students in a research experience and address valuable learning outcomes. It is a challenge to develop learning outcomes and design assessments to measure both student learning gains and the impact of the research experience. Many different types of CURES exist and the research objectives, implementation, assessments and student experiences are diverse. Recent papers have highlighted the importance of assessing the impact of CURES and the alignment of specific outcomes with specific components of the CURE. The objective of our study was to transform an existing CURE for undergraduate students at a large land grant institution. Learning outcomes and objectives were developed and assessment mapping was performed for the CURE through a course redesign program on campus. The course transformation was guided by overall university core learning outcomes and the research framework and recommendations for course undergraduate research experiences.Participants included approximately 80 students from primarily science and engineering majors within their second year of study. Within the two course CURE, students engaged in activities to help them think like scientists including weekly troubleshooting of experiments, documenting their laboratory progress in an electronic lab notebook, annotating genomes using authentic bioinformatics tools, and communicating their data and results using both traditional and virtual technologies. Students also learned how to collaborate and share data using virtual resources in addition to practical laboratory skills. A virtual group tool was used to help manage and assess student teams. Opportunities were also provided for both undergraduate and graduate students to build leadership and teaching experiences by serving as undergraduate peer leaders or graduate student teaching assistants in the CURE.Both qualitative and quantitative assessment data supports that the CURE transforms students’ view of the process of research and science, increases student confidence to pursue and secure additional opportunities in industry, government and academia, and improves learning outcomes. Students’ perception of the classroom learning environment, and their degree of competence, relatedness, autonomy, and perceived knowledge transfer scale were positive. Due to the increased demand for the course, we are currently exploring the scale up of the CURE to multiple laboratory sections and also further refining the assessments to better address desired learning outcomes of systems thinking and quantitative literacy.Support or Funding InformationSupport for the project was provided by the Provost Office, Polytechnic Institute, College of Agriculture and College of Science at Purdue University and by Howard Hughes Medical Institute through the Science Education Alliance.
Creating Authentic Research Experiences For Student Engagement And Success
Authors: Makhluf Huda A. 
Published: November 2023

Undergraduate research experiences are considered high impact educational practices. In a laboratory course for pre‐health sciences, students collected household toothbrushes and cultured bacterial isolates while learning microbial aseptic techniques on selective and differential media. Students were also asked to formulate their own scientific questions and hypotheses. Research methodology, data collection and analysis were emphasized throughout the course. We tested the hypothesis that adapting an authentic research approach to our curriculum could lead to increased student satisfaction and enhanced learning. To that end, we performed a preliminary assessment of the Classroom Undergraduate Research Experience using pre and post surveys and collected student artifacts for assessment.Students found that up to half of toothbrushes stored in bathrooms were contaminated with fecal matter, but when sterilized in a home dishwasher or had leftover toothpaste on them prior to culturing yielded no colony growth. The results triggered lively discussions on oral flora, hygiene and proper storage of toothbrushes to avoid fecal contamination. Students were shocked that there would be fecal traces on their toothbrushes albeit while living in a microbial world. Student engagement ‐ by doing relevant and current research activities ‐ and subsequently student satisfaction were increased compared to a control class.Support or Funding InformationSource: The intentional educational design of this activity was based on a presentation (primary source) at the 2015 General Meeting of the American Society for Microbiology held May 31‐June 2, 2015 in New Orleans, Louisiana.
Do the TWIST: Transcription and Regulation of Estrogen Receptor Operon
Authors: Krishnaswamy Aditya , Eshleman Campbell , Fortier Abigail , Kahn Maya , Kepner Alisa , Naderi Aurian , Om Seyun , Baxley Ann , Link Tina , Nowak Scott 
Published: November 2023

Twist is a 202‐residue basic helix‐loop‐helix (HLH) transcription factor encoded by the TWIST1 gene. Known Twist functions in humans include the generation of stem cells and regulation of the tumor suppressor protein E‐cadherin. In Twist gene, nonsense or duplication, rather than missense, mutations comprise a majority of errors. The majority of mutations linked to cancer progression are missense mutations located in the first exon of the gene, which subsequently impacts the DNA binding (HLH) domain. Correspondingly, these mutations result in a loss of function, as observed in Saethre‐Chotzen Syndrome. Further, elevated Twist levels are predictive of poor overall survival in patients with breast cancer. Twist is thought to hyperactivate histone deacetylase in breast cancer tumors, which subsequently suppresses the activity of the Estrogen Receptor (ER) gene promoter, and leads to tumor formation. For this project, the research team designed a three‐dimensional model of the Twist protein to investigate how the structure of the protein affects the function of this critical regulator of a variety of cancers.Support or Funding InformationWalton High School SMART (Students Modeling a Research Topic) Team is sponsored by Milwaukee School of Engineering.
Characterization of rare oncogenic mutations in the kinase domain of Epidermal Growth Factor Receptor (EGFR)
Authors: Ruan Zheng , Katiyar Samiksha , Kannan Natarajan 
Published: November 2023

Epidermal growth factor receptor (EGFR) is activated by a variety of oncogenic mutations, many of which map to the intracellular protein kinase domain. While several recurrent mutations in the kinase domain are well characterized, mining of the Protein Kinase Ontology (ProKinO), which relates mutations to key functional motifs, reveals recurrent, but poorly characterized mutations in key functional regions. R776H and M766T are two such mutations in the alphaC‐beta4 and regulator spine of EGFR. We recently showed that the R776H functions as a “superacceptor” when paired with WT EGFR and exerts lateral phosphorylation activity (2). Molecular dynamics simulations identified a critical auto‐inhibitory interaction mediated by R776 that is relieved in the R776H mutant (2). M766T, on the other hand, activates EGFR by disrupting the inactive hydrophobic packing between the C‐helix and DFG motif, and stabilizing a water mediated hydrogen bond with the K745‐E762 salt bridge, formation of which is critical for kinase activation. Our experimental and computational studies provide new insights into kinase mutational activation and framework for identifying and characterizing rare drivers in the cancer kinome.Support or Funding InformationFunding for N.K. from the American Cancer Society (RSG‐10‐ 188‐01‐TBE), Georgia Cancer Coalition (GCC) and University of Georgia is acknowledged. This study was supported in part by resources and technical expertise from the Georgia Advanced Computing Resource Center, a partnership between the University of Georgia's Office of the Vice President for Research and Office of the Vice President for Information Technology.
Iron Nutritional Status of Overweight and Obese Subjects. Relation with BMI and Inflammation
Authors: Zago Liliana , Pandolfo Marcela , Carbia Claudio , Lardo Mabel , Weisstaub Adriana , Felipoff Ana Lia , Dupraz Hernán , Presner Natalia , Perdomo Clara , Río María Esther , Infantino Carlos González 
Published: November 2023

Iron deficiency is one of the most prevalent nutritional problems in the world. There is evidence that the prevalence is even higher in overweight and obese individuals. As part of a project in which the relationship between nutritional deficiencies and obesity are studied, we evaluate nutritional status of iron, its relationship to diet and presence of inflammation in 175 overweight and obese subjects, from which, 14 consumers of vitamin and mineral supplements were discarded. The final group were 130 female (F) and 31 males (M). There were 46 overweight (OW), 58 Obese (Ob) degree I, 27 Ob II and 30 Ob III. Iron was assessed through measurements of hemoglobin (Hb), hematocrit (Hct), serum iron (SI), total iron binding capacity (TIBC) and transferrin saturation (TS %). The following levels were considered compatible with iron deficiency: Hb <12 g/dl in F and <13 g/dl in M; Hematocrit <36% in F and <40% in M; SI <60 mg/dl in both sexes; TIBC >400 mg/dl and TS% <20%. Inflammation was assessed by ultrasensitive C‐Reactive Protein (CRPu), which can detect low levels of inflammation, considered a risk factor for cardiovascular disease. Iron intake was estimated by using food frequency data analyzed by SARA program (Health Ministry of Argentina). Deficit values occurred in 5.0% of cases by Hct, 6.2% by Hb, 9.3% by SI, 10.6% by TIBC and 16.8% by TS%, being those last values taken for further analysis. As expected, deficit values from fertile age women (22%) were higher than that from postmenopausal (15%), which were similar to men (13%). When data were divided into OW, Ob I, Ob II and Ob III groups, a gradient of percentage of subjects with low TS% values were obtained: 8.7%, 15.5%, 22.2% and 26.7% (P=0.0275). No differences among mean iron intake of 4 groups were obtained, but a higher level of inflammation with a greater degree of obesity was founded: mean±SD CRPu was 2.6±1.9 in OW, 3.9±3.4 in Ob I, 6.6±5.6 in Ob II and 6.8±4.3 in Ob III (P<0.0001; ANOVA). When data were divided into CRPu quartiles, subjects with iron deficiency were 7.1%, 20.0%, 21.1% and 19.5% for quartiles 1 to 4, being only the first quartile different from the others. The obtained results indicate that incidence of iron deficiency was associated with the degree of obesity. The higher degree of inflammation of obese subjects justify in part iron deficiency, but the association between iron deficiency and obesity was stronger than that between iron deficiency and inflammation.Support or Funding InformationSupported by UBACyT 20720130100006BA
The Trend of Korean Staple Food Intake and Prevalence of Obesity in Korean Adults: the Korean National Health and Nutrition Examination Survey (KNHANES) 1998–2012
Authors: Kim Seong‐Ah , Ha Kyungho , Kim Jiyoon , Paik Hee Young , Joung Hyojee 
Published: November 2023

Over the past several decades, South Korea's rapid socioeconomic growth resulted in lifestyle changes, such as diet that has led to an increase in obesity rates. This study was performed to identify the longitudinal trend of staple food intake and prevalence of obesity in Korean adults using the dietary survey data from Korean National Health and Nutritional Examination Survey (KNHANES) 1998–2012.We used a 24‐hr dietary recall and anthropometric data from 54,042 people aged over 20 who participated in KNHANES 1998, 2001, 2005, 2007–2009, and 2010–2012. The 16 kinds of cooked rice were selected from the previous research as main Korean traditional staple dishes and foods.During the period 1998–2012, the average intake from grains and cooked rice decreased in both gender: for grains and cooked rice, from 1343.7, 1056.4 kcal to 1265.9, 936.6 kcal in men (p < 0.0001); and, 1122.8, 843.8 kcal to 1004.1, 699.6 kcal in women (p < 0.0001), respectively. Also the proportion of the total energy intake from grain and cooked rice decreased in both gender: for grains and cooked rice, from 63.5, 51.1% to 57.5, 44.0% in men (p < 0.0001); and, 66.2, 51.8% to 61.3, 43.9% in women (p < 0.0001). Among the cooked rices, cooked white rice (ssalbap) was the most contributing dish to the total energy intake, followed by rice with assorted grains (japgokbap). The caloric intake from cooked white rice was decreased from 587.9 kcal/day in 1998 to 244.2 kcal/day in 2012, but the caloric intake from rice with assorted grains intake increased gradually from 145.2 kcal/day in 1998 to 309.5 kcal/day in 2012.The average body mass index (BMI) and the prevalence of obesity (BMI≥25kg/m2) increased markedly in men and slightly in women during this period. Obese men and women showed a different pattern in energy intake from grains and rice; a higher proportion of total energy consumption from grains and rice was shown in obese men (p < 0.0001) while a lower proportion was found in obese women (p < 0.0001).These results showed distinct consumption trends of Korean traditional staple dishes, depending on the obesity status and gender. Our findings are waiting for further research to examine the association between intake of staple food and the prevalence of obesity or other chronic diseases.Support or Funding InformationThis work is carried out with the support of ‘Research Program for Agricultural Science and Technology Development’, National Academy of Agricultural Science, Rural Development Administration, Republic of Korea (Project No. PJ011637022015).
Oregano Essential Oil and Carvacrol reduce Cryptosporidium parvum infectivity of HCT‐8 Cells
Authors: GAUR SHASHANK , Kuhlenschmidt Theresa B , Kuhlenschmidt Mark S , Andrade Juan E 
Published: November 2023

Lipid‐based nutrition supplements (LNS) are commonly used to treat moderate acute undernutrition in children. However, existing LNS products mainly focus on providing nutrients and do not address other immediate causes of undernutrition, such as parasitic infection and gut inflammation. Enteric parasites are known to reduce nutrient digestion and absorption, cause chronic gut inflammation, iron deficiency anemia, protein‐energy malnutrition, and reduce growth and cognitive development in children. Oregano essential oil (OEO) is known to have anti‐bacterial and anti‐fungal activity, however its anti‐parasitic properties are poorly understood. This study systemically investigated the effect of OEO and its main bioactive, carvacrol (CV), on prevention of Cryptosporidium parvum infectivity of HCT‐8 (human colon carcinoma) cells in vitro, for potential incorporation of these bioactives into LNS products. HCT‐8 cells were seeded (1 × 106) in 96‐well microtiter plates until confluency (2 days). HCT‐8 cell viability at various concentrations of either OEO or CV was measured using a Live/Dead cell imaging kit. Confluent HCT‐8 cell monolayers were seeded with C. parvum oocytes (1 × 104) in two modalities: 1) 4 h co‐culture of C. parvum oocysts, cells and several dosages (0 μg/mL to 250 μg/mL) of CV or OEO in complete medium, followed by PBS washing and replacement with bioactive‐free media; and 2) 4 h co‐culture of C. parvum oocysts and cells alone, followed by PBS washing and treatment with several dosages (0 μg/mL to 250 μg/mL) of CV or OEO. In either modality, plates were incubated at 37°C and 5% CO2, and after 2‐day incubation, cells and C. parvum were fixed with methanol: acetic acid solution (9:1 v/v). Infectivity was assessed via immunofluorescence detection using C. parvum‐specific antibody staining (Sporo‐Glo™) and phase contrast/fluorescent microscopy. Deformation of cell monolayers and loss of cell viability was found at 50 μg/mL CV, whereas no loss in cell viability was observed in cells treated with OEO at dosages as high as 125 μg/mL (containing similar concentrations of CV). In modality 1 experiments, cells simultaneously treated with C. parvum and various dosages of OEO or CV presented similar amounts of infection after 4 h incubation as those cells treated with C. parvum alone. In modality 2 experiments, after 2‐day treatment with bioactives, a 50% reduction in C. parvum infectivity was observed at 25 μg/mL of CV and at 125 μg/mL of OEO. C. parvum is one of the most resilient enteric parasites and prevalent in most of the developing world. Incorporation of OEO or CV into LNS formulas may provide double benefit to at risk populations afflicted by undernutrition and gut infection living in low‐income settings.Support or Funding InformationIndian Council of Agricultural Research (ICAR), India
Caffeine Consumption and its Association with Mitochondrial Specific Oxidative Stress in People Living with HIV in the Miami Adult Studies on HIV Cohort
Authors: Ramamoorthy Venkataraghavan , Campa Adriana , Sales Sabrina , Rubens Muni , Fleetwood Christina , Stewart Tiffanie , Alvarado Glenda , Khan Hafiz , Liuzzi Juan P. , George Florence , Baum Marianna 
Published: November 2023

ObjectiveHigh caffeine consumption has been associated with compromised serum antioxidant nutrients in people living with HIV (PLWH). This could adversely affect mitochondrial oxidative status. This study examines the relationship between caffeine consumption and a marker of mitochondrial oxidative stress.MethodsAfter consenting 130 PLWH on stable antiretroviral therapy recruited from the Miami Adults Studies on HIV (MASH) cohort, caffeine intake was measured using standardized questionnaires. Blood was drawn for mitochondrial‐specific 8‐oxo‐2′‐deoxyguanosine (mt‐specific 8‐oxo‐dG), a marker of mitochondrial oxidative stress. CD4 cell counts and HIV viral load were obtained from medical records with written permission from participants. SPSS version 21 was used for statistical analyses. More than 250 mg of caffeine intake or the equivalent of 3–4 cups of coffee daily was considered the cut‐off point for high consumption. This study was approved by the Florida International University Institutional Review Board.ResultsMean age of this group was 47.9 ± 6.4 years, 60.8% were men, and 75.4% were Black. Mean caffeine intake was 337.63 ± 304.97 mg/day. Levels of mt‐specific 8‐oxo‐dG were higher in participants reporting >250 mg/day of caffeine consumption (0.40±0.34 vs 0.54±0.40 ΔCt [=Ct2 – Ct1], P=0.049). High caffeine consumption was significantly correlated with high mt‐specific 8‐oxo‐dG levels (r=0.212, P=0.028), and significantly predicted higher mt‐specific 8‐oxo‐dG levels (β=0.693, P=0.049), adjusting for CD4 counts and viral load.ConclusionHigh caffeine intake adversely affected mitochondrial‐specific oxidative status in PLWH in the MASH cohort. Further studies are needed to elucidate the bio‐chemical mechanisms for these adverse effect.Support or Funding InformationFunded by NIDA and FIU Graduate School Dissertation Year Fellowship.