bluuebunny/crossref_metadata_2025 huggingface dataset:
Sugar‐sweetened beverage intake is associated with fatty liver in the Framingham Offspring Study (267.3)
Authors: Ma Jiantao , Fox Caroloine , Speliotes Elizabeth , Hoffmann Udo , Smith Caren , Saltzman Edward , Jacques Paul , McKeown Nicola
Published: June 2021

Nonalcoholic fatty liver disease (NAFLD) affects 20‐30% of US adults, yet its underlying cause is unknown. Excess intake of sugar‐sweetened beverages (SSB), the largest source of added sugar intake in the American diet, is a potential risk factor for NAFLD. We examined the cross‐sectional association between SSB intake and fatty liver in members of the Framingham Offspring cohort (n=1,061; 57% women; mean age 59 y). Liver fat was measured using CT scan, and fatty liver was defined as a liver to phantom ratio <0.33. Cumulative intakes of SSB and diet soda were estimated from FFQ collected at 3 exam cycles over 7 years. Participants were defined as SSB non‐consumers or consumers (3 categories: 1 drink/mo to <1 drink/wk, 1 drink/wk to < 1 drink/d, and 蠅1 drink/d). Participants were also categorized into 4 groups according to diet soda intake as described above. Covariates examined included age, sex, BMI, smoking status, energy intake, alcohol intake, dietary fiber, total fat, and fruit and vegetable intake. After multivariate adjustment, 14.3% (95%CI: 9.1, 19.5%) of non‐SSB consumers and 26.9% (95%CI: 19.5, 34.2%) of daily SSB consumers had fatty liver, P for trend =0.02. No significant association was observed between diet soda intake and fatty liver. In this study sample, daily SSB consumers had nearly 2 fold higher prevalence of fatty liver compared to non‐SSB consumers.

Grant Funding Source: Supoorted by the NIH/NHLIBI's Framingham Heart Study, Boston University School of Medicine, and USDA
Tissue distribution and metabolism of 5‐demethylnobiletin after its long‐term dietary administration in mice (270.5)
Authors: Wang Minqi , Zheng Jinkai , Song Minyue , Gao Zili , Xu Fei , Cai Xiaokun , Wu Xian , Xiao Hang
Published: June 2021

5‐demethylnobiletin (5‐DN), a citrus‐derived polymethoxyflavone, has many beneficial bioactivities. However, its tissue distribution and metabolism remain unclear, which limits its better utilization as a nutraceutical ingredient. In this study, CD‐1 mice were fed with 5‐DN in diet for 20 weeks, and then the levels of 5‐DN and its major metabolites i.e. 5, 3'‐didemethylnobiletin (M1), 5, 4'‐didemethylnobiletin (M2) and 5, 3', 4'‐tridemethylnobiletin (M3) in different tissues were determined by HPLC. Our result showed that 5‐DN was extensively metabolized to form glucuronide/sulfate conjugates of M1, M2, M3, with M2 as the most abundant, in small intestine (SI). The levels of these metabolites were much higher in distal SI than in proximal SI, whereas much lower levels of these metabolites were found in the bile. These results suggested that both phase I and phase II metabolism of 5‐DN occurred predominantly in the SI enterocytes rather than in the liver. Further more, we observed that the metabolites of 5‐DN almost exclusively exist as unconjugated forms in the cecum and colon, which is contributed to deconjugation by microbiome. Despite the low plasma levels of 5‐DN found in the mice, much higher levels of 5‐DN were observed in tissues such as brain, lung, liver, spleen, muscle and kidney. This is the first report on the tissue distribution and metabolism of 5‐DN after long‐term oral consumption in mice.

Grant Funding Source: Supported by NIH, AICR and USDA
Nutrition education improves behaviors without accompanying improvements in dietary guideline recognition among rural 4th and 5th graders (273.7)
Authors: Bea Jennifer , Bawden Margine , Islas Aleya , Hartz Vern , Martinez Stephanie , Alves Joyce , Misner Scottie
Published: June 2021

Dietary guidelines are designed to reduce the burden of obesity and related health problems. Our aim was to measure change in knowledge and behavior related to USDA dietary guidelines following nutrition education of rural, low‐income, 4th and 5th graders. Eight Apache County, AZ classrooms volunteered to participate; each received three, 45‐minute, education sessions related to USDA recommendations over 2‐3 weeks (N=139 pre, 121 post). Anonymous self‐report behavior and knowledge questionnaires were administered to the children prior to and following the class series. Descriptive statistics were computed for student demographics and consumption of fruits, vegetables, grains, and milk on the prior day. Paired t‐tests were used to evaluate change in weighted classroom averages. Seventy‐six percent were 4th graders, 52% male. Identification of USDA‐recommended milk type increased by 12% (p<0.0001), while knowledge of other recommendations did not improve. Reported consumption of lower fat milk, whole grains, vegetables, and fruit significantly increased (p蠄0.01). The percent of students active during morning break and lunchtime significantly increased (p<0.02). Minutes of afterschool physical activity did not change, but minutes of sedentary time decreased (p=0.01). These data suggest that acute changes in target behaviors are possible in this age group, despite the absence of increased knowledge.

Grant Funding Source: USDA HI050073, NIH P30CA023074
Superoxide dismutase protects against effects of eNOS uncoupling in early‐stage aortic valve disease (278.6)
Authors: Farrar Emily , Huntley Geoffrey , Butcher Jonathan
Published: June 2021

Objective: Oxidative stress (OxS) is known to contribute to late stages of aortic valve disease (AVD), but its role in early‐stage valve inflammation and as a driver of valve pathology has not been investigated. Here we show that inflammation drives increased OxS via eNOS uncoupling. Using an ex vivo model of AVD, we show that superoxide dismutase can block the downstream effects of eNOS uncoupling and mitigate later‐stage valve degeneration.

Methods and Results: We first observed evidence of eNOS uncoupling in the endothelium of calcified human aortic valve leaflets, which had elevated dihydroethidium staining for superoxide in endothelial cells both near and distal to the primary nodule. We then used a 3‐D in vitro system to show that inflammatory cytokine TNF‐α caused increased superoxide, free radicals, and hydrogen peroxide in aortic valve endothelial cells, as soon as 15 minutes after treatment. The excess oxidative stress due to TNF‐α decreased VEC nitric oxide secretion, lowered eNOS and VE‐cadherin protein levels, and increased expression of inflammatory adhesion molecules (VCAM1, ICAM1). Addition of eNOS co‐factor tetrahydrobiopterin (BH4) mitigated the increases in OxS caused by TNF‐α, demonstrating the eNOS uncoupling was the primary pathophysiological mechanism at play. Using an ex vivo system of porcine aortic valve leaflets cultured for 21 days, we screened the ability of BH4, catalase, and superoxide dismutase (SOD) to decrease the endothelial OxS effects caused by TNF‐α. We found that all three antioxidants mitigated the effects of TNF‐α and improved endothelial function, but SOD showed the most significant reduction in protein levels of myofibroblastic protein α‐smooth muscle actin and VCAM1.

Conclusions: These results present endothelial inflammatory oxidative stress as a new mechanism that connects early valve pathology with later stages of degeneration. Targeting these mechanisms via tailored antioxidant therapy could provide new avenues for treatment of CAVD.

Grant Funding Source: Supported by NIH HL110328, NSF CBET‐0955172
Patching the leaky pipeline at two points (29.2)
Authors: Ortiz Phillip , Breton Kristian , Duncan‐Poitier Johanna , Groome Meghan , Lansing Jill , Moore Gaylen , Paulsson Kristine , Rossi Elizabeth , Smith Nakesha , Wortel Stephanie
Published: June 2021

The United States is facing a crisis in education ‐‐ not enough students are being trained in the areas of science, technology, engineering and mathematics (the STEM disciplines) to support and foster economic growth. To respond, the State University of New York (SUNY) and the New York Academy of Sciences (The Academy) are collaborating to train SUNY graduate students and post‐doctoral fellows to deliver mentoring and STEM content to underserved middle‐school children in afterschool programs. Since 2010, as part of the Afterschool STEM Mentoring Program, the Academy has successfully trained graduate students within the New York City area, and to date they have reached >7,000 middle school students with curricula in areas such as genetics, mathematics, and space science. At the suggestion of SUNY Chancellor Nancy Zimpher, who also serves as the Chair of the Academy's Board of Governors, we have developed a collaboration in which SUNY graduate students and post‐doctoral fellows learn pedagogy and content via an online course, and then are placed in underserved afterschool programs in New York State. This online course was developed by faculty and SUNY ESC. After a thorough evaluation of the course, curriculum, and methods the goal is for this program to be replicated throughout the United States. In it's first year ~30 graduate and post‐doctoral students from three SUNY campuses (CNSE, IT, and Downstate) reached ~200 middle‐school aged children. To date we are able to demonstrate improvements in (1) mentors' teaching skills and confidence, and career perceptions, (2) students' content knowledge, attitudes, self‐efficacy and interest, and (3) curricula, mentor practice and support. As we enter the second year of the project we have added three additional campuses. In the near future we hope to expand the program to reach other groups of college students and pre‐college mentees.

Grant Funding Source: National Science Foundation
Aligning and using assessments in gateway courses for Biochemistry and Molecular Biology majors (348.5)
Authors: Bell Ellis
Published: June 2021

Biochemistry and Molecular Biology majors rarely take introductory courses in the discipline of “biochemistry and molecular biology” during the first year or two of their undergraduate degree program, more usually taking introductory courses in biology, chemistry, mathematics and physics before taking “biochemistry” in their junior year. To foster the interdisciplinary approaches to the life sciences recommended by recent reports such as Vision & Change a hierarchy of foundational concepts and skills drawn from those expected of graduating majors in biochemistry and molecular biology should be presented and assessed during the first two years of an undergraduate curriculum. It is suggested that these should include foundational concepts of the basic sciences (biology, chemistry and physics), mathematics skills necessary for data analysis and modeling, and process of science skills including using the primary literature, hypothesis development and proposal writing. These areas should be introduced in the context of examples drawn from big picture areas of the molecular life sciences and should focus on foundational concepts of the five critical content areas, evolution, matter and energy transformation, homeostasis, information flow and macromolecular structure and function. Such courses can be either “blended” introductory courses or stand‐alone courses specific for biochemistry and molecular biology majors. This work is supported by a grant from the National Science Foundation: NSF 0957205 to EB
Foods contributing to fruit and vegetable intakes of U.S. adults: What We Eat In America, NHANES 2009‐2010 (369.3)
Authors: Hoy M. , Goldman Joseph , Bowman Shanthy , Moshfegh Alanna
Published: June 2021

Fruits and vegetables that are consumed as individual foods such as apples or tomatoes are also ingredients in mixture foods such as apple pie or pizza. Using 1‐day food intakes for adults 20+ years (n=5762) from What We Eat In America (WWEIA), NHANES 2009‐2010, this study compared fruit and vegetable intakes from the Food Patterns Equivalents Database 2009‐2010 to WWEIA Food Categories (FC) to determine contribution of all foods including mixtures to total fruit and vegetable intakes. The estimated mean Total Fruit intake of adults was ~1 cup equivalent per day, most from fruits and 100% fruit juices (63 and 27% respectively). WWEIA FCs contributing 蠅5% to Total Fruit intake were apples (17%), citrus juices (16%), bananas (12%), other fruits and fruit salads (8%), other fruit juices (8%), melons (7%), berries (6%) and citrus fruits (5%). The estimated mean Total Vegetable intake of males and females was 1.7 and 1.5 cup equivalents per day, respectively, most from vegetables and mixed dishes (61 and 25%, respectively). WWEIA FCs contributing 蠅5% to Total Vegetable intake were white potatoes (17%), vegetable combinations (11%), lettuce/lettuce salads (10%), tomatoes (6%), meat, poultry, fish‐ and grain‐based mixed dishes (8% and 5% respectively), and soups (5%). These data can inform about dietary patterns of adults in the U.S. and guide nutrition education and consumer messages for increasing fruit and vegetable intake.

Grant Funding Source: Suppported by USDA Agricultural Research Service
Effect of height adjustable desks on standing time, discomfort, and productivity of office workers with sedentary occupations (37.8)
Authors: Roemmich James
Published: June 2021

Sedentary jobs promote weight gain and health risks. Interrupting sitting with standing is protective against sitting‐related health risks. However, standing for portions of the workday will not be accepted if it reduces comfort or productivity. This study determined the initial changes from baseline (conventional sitting height desk) to 1‐week after receiving a height adjustable desk for sitting/standing times, steps (activPAL), musculoskeletal discomfort (Nordic questionnaire), productivity (questionnaires 3x/day for 3 d), and energy intake (3 d ASA24 recall) in 13 men and women. Subjects were 33‐66y and not provided with direction to change behavior or behavioral goals. Height adjustable desk installation decreased workday sedentary min (6.7±0.3 vs 4.0±0.3 hr/d) and increased standing time (2.2±0.2 vs 4.9±0.3 hr/d). These changes were accompanied by decreased tiredness and increased perceptions of amount and quality of work completed and overall work performance and no changes in musculoskeletal discomfort or energy intake. Non‐work step number, standing time, and sedentary time were not changed. Height adjustable desks increase standing without further behavioral intervention and is accompanied by greater perceived work performance. Increased work‐time standing is not compensated for by decreased non‐work standing or greater energy intake.

Grant Funding Source: Sponsored by USDA 5450‐51000‐049‐00D
Healthful cultural foods and safety nets: experiences of immigrant and Puerto Rican families in Massachusetts (380.5)
Authors: Peterman Jerusha , Cordeiro Lorraine
Published: June 2021

Objective: (1) To understand the perceptions of, access to, and utilization of healthful cultural foods and safety nets in immigrant and Puerto Rican families. (2) To assess the overlap between healthful cultural foods and safety nets in these families.

Methods: Focus groups were held with Puerto Ricans and immigrants from the Dominican Republic (3 groups, 16 participants) and with Cambodian (9 focus groups, 66 participants) and Brazilian (2 focus groups, 16 participants) immigrants in Massachusetts. Directed content analysis was used to identify themes about perceptions, access, and utilization for healthful cultural foods and safety nets. Overlapping themes were identified between healthful cultural foods and safety nets.

Results: Participants from all groups valued healthful cultural foods. Cambodians and Brazilians considered American‐style foods less healthful than cultural foods, while Latinas identified some cultural foods as less healthful. All groups were able to access healthful cultural foods but some found it challenging to afford them. Cambodians worried about quality and safety. Cambodians and Latinas reported using safety nets such as food stamps (SNAP), WIC, families, and food pantries. They reported that while both SNAP and WIC helped them afford healthful cultural foods, benefits were inadequate, and that food quality decreased over the month.

Conclusions: Intervention programs targeted to these populations should build on current knowledge and practices that value healthful cultural foods and take into consideration barriers. Barriers to accessing and utilizing government safety nets such as SNAP and WIC appear to limit diet quality at some points in the month for immigrant and Puerto Rican families.

Grant Funding Source: USDA National Institute of Food and Agriculture, Projects MAS00991 and MAS00994
Sodium to potassium ratio and food choices of U.S. adults (384.7)
Authors: Rhodes Donna , Parker Elizabeth , Goldman Joseph , Gaine P Coutney , Moshfegh Alanna
Published: June 2021

The relationship between sodium (Na) and potassium (K) has been studied extensively; however, research is limited on the range of intake of sodium to potassium ratio (Na/K) consumed in the U.S. The purpose of this research was to examine the typical ranges of Na, K, and Na/K and the food choices contributing to Na and K across different ratios. Study sample included nationally representative data for adult (20+yr) males (n=5450) and females (n=5731) participating in What We Eat in America (WWEIA) NHANES 2007‐2010. Dietary intake data were obtained from an in‐person 24‐hour recall collected using the 5‐step USDA Automated Multiple‐Pass Method. WWEIA Food Categories were used to define food and beverages as consumed. Mean Na/K was 1.5 (0.01) for males and 1.4 (0.01) for females. Fewer than 2% of adults met the recommended Na/K of 0.49 (2300mg Na/4700mg K). Distribution of Na/K at the 10th, 25th, 50th, 75th and 90th percentile was 0.8, 1.0, 1.4, 1.8, and 2.2, respectively for males; and 0.7, 1.0, 1.3, 1.7 and 2.1 for females. Among individuals with Na/K <1.0 vs Na/K 蠅 1.0, milk and dairy foods contributed 8% vs 6% of daily Na and 12% vs 9% of daily K. Mixed dishes contributed 22% vs 31% of daily Na and 11% vs 20% of daily K, respectively. Fruit and vegetables contributed 12% vs 6% of total daily Na and 25% vs 18% of daily K. These data highlight the importance of food choices to achieve improved sodium to potassium ratios in the U.S. population.

Grant Funding Source: ARS,USDA with partial support from ILSI North America
Community food environment and early childhood BMI: baseline findings from the Hawaii Children’s Healthy Living Program (390.5)
Authors: Fialkowski Marie , Li Fenfang , Butel Jean , Nigg Claudio , Braun Kathryn , Johnson Kathleen , Tachibana Alvin , Wilkens Lynne , Novotny Rachel
Published: June 2021

Community food environment (CFE) is an important determinant of health, especially obesity. Factors of the CFE (including availability and quality of fruits/vegetables [F/V], store advertisement, community readiness for change [CR], and store walkability) were assessed in 4 communities in Hawai‛i participating in the Children’s Healthy Living Program community randomized trial to describe CFE variables in association with early childhood (2‐8 y) body mass index (BMI). Anthropometric measurements were collected in all communities (n=598); BMI percentiles and z scores were calculated using CDC 2000 growth curves. CFE factors, except CR, were measured in 29 stores. CR was measured by survey of 29 community members knowledgeable of the CFE. Spearman correlations were calculated for mean BMI‐z score and CFE variables. Mean BMI z‐score = 0.59 (SD=0.20) while means of CR = 5.25 (SD=0.4), FV availability = 4.9 (SD=2.8), FV quality = 5.2 (SD=2.6) and store walkability = 11.1 (SD 9.3). BMI z‐score and CR (r=‐0.98, p<0.001) were negatively correlated in addition to mean BMI z‐score and store walkability (r=‐0.45, p=0.04). Positive correlations were found between BMI z‐score and store exterior healthy ads (r=0.40, p=0.03); FV availability (r=0.59, p<0.001); and FV quality (r=0.62, p<0.001). Further study, including more Pacific communities and the examination of additional factors, may influence these associations.

Grant Funding Source: Supported by the Agriculture and Food Research Initiative Grant no. 2011‐68001‐30335 from the USDA
Conceptual assessment of physiology: development of a concept inventory for homeostasis (531.13)
Authors: McFarland Jenny , Michael Joel , Wenderoth Mary Pat , Modell Harold , Wright Ann , Cliff William
Published: June 2021

Homeostasis is an important core principle for undergraduate physiology students to understand and apply. Assessment of student conceptual understanding of homeostasis is important for teaching and learning, especially formative assessment to reveal students’ incomplete understanding and ‘misconceptions’. We engaged in a 3‐step process to develop a Conceptual Assessment of Physiology (CAP) instrument for homeostasis. First, a conceptual framework for homeostasis that identifies component ideas appropriate for undergraduate physiology was developed and validated by a cohort of faculty at 2‐ & 4‐year colleges, universities & medical schools. Second, common student conceptions regarding homeostasis and its component ideas were identified (from physiology students and faculty). Third, multiple‐choice questions to assess important homeostasis component ideas were developed and tested in student interviews. These questions were then vetted by a cohort of faculty from diverse institutions and students in physiology courses. We will present the CAP questions on homeostasis, the physiology faculty data on the appropriateness of these questions for undergraduate students, and the results of initial testing with students. The questions will be linked to the conceptual framework and student conceptions & incomplete understandings. Supported by NSF DUE‐1043443.

Grant Funding Source: Supported by NSF DUE‐1043443.
What visual representations of homeostasis do faculty use? (531.14)
Authors: Wright Ann , Michael Joel , McFarland Jenny , Modell Harold , Cliff William , Wenderoth Mary Pat
Published: June 2021

Physiology faculty have identified homeostasis as one of the core concepts their students must understand and apply. Visual representations of physiological processes are important for teaching and learning in physiology. What visual representations of homeostasis do faculty employ to help students understand this core concept? 40 Anatomy & Physiology faculty were asked to draw the representation of homeostasis that they use with their students. They were also asked to describe what might be missing from their drawing and to describe possible misconceptions that could arise. Analysis of the results obtained suggests that physiology instructors and textbook authors sometimes convey inaccurate and incomplete models of homeostasis. Supported by NSF DUE‐1043443.
Regulation of neural crest cell emigration in turtle embryos (541.9)
Authors: Gochnauer Heather , Smith Matthew , Rice Ritva , Cebra‐Thomas Judith
Published: June 2021

Turtle plastron bones develop by intramembranous ossification, suggesting that they are derived, like the facial bones, from neural crest cells. Using cell‐labeling and neural tube explant cultures, we have shown that cells expressing neural crest markers emerge from the trunk neural tube in the turtle Trachemys scripta for a greatly extended period compared other model amniotes. The neural crest cells that emerge in a second wave, well beyond the stage of neural crest emigration in chick or mouse embryos, appear to migrate ventrally to form an ectomesenchymal dermis that gives rise to the bones of the plastron. The specification of premigratory neural crest cells and the epithelial‐mesenchymal transition that produces migratory neural crest cell is controlled by a gene regulatory network including the transcription factors Snail2, FoxD3, Sox9, and Sox10. We are currently examining the expression of markers of premigratory and early migratory neural crest cells to examine whether the premigratory domain persists during the period in between the early and late migratory phases. If the expression of these markers persist throughout this period, it will suggest that the premigratory region is maintained, and that the lack of neural crest cell migration may be due to the lack of a supportive environment. In contrast, if these genes are only expressed during the periods of active neural crest cell emigration, then the second wave of neural crest cell migration would require a second inductive signal not found in chick embryos.

Grant Funding Source: NSF
The Cdc13‐Stn1‐Ten1 complex stimulates Pol α activity by promoting the primase‐to‐polymerase switch (548.2)
Authors: Lue Neal
Published: June 2021

The Cdc13‐Stn1‐Ten1 complex stimulate Pol α activity by promoting the primase‐to‐polymerase switch Neal F. Lue1. 1Weill Medical College of Cornell University, New York, NY 10065 Emerging evidence suggests that Cdc13‐Stn1‐Ten1 (CST), an evolutionarily conserved RPA‐like ssDNA‐binding complex, may regulate Pol α activity at telomeres constitutively, and at other genomic locations under conditions of replication stress. However, the detailed mechanisms and the extent of evolutionary conservation are not understood. In this study, I examined the mechanisms of Pol α stimulation by CST using purified complexes derived from Candida glabrata. In the presence of physiologic concentrations of ribonucleotides and deoxyribonucleotides, CST did not enhance either the RNA primase or the DNA polymerase reaction, but rather augmented the efficiency of the primase‐to‐polymerase switch. In addition, CST simultaneously shortened the RNAs and lengthened the DNAs in the chimeric products synthesized by Pol α. Stn1, the most conserved subunit of CST, was alone capable of Pol α stimulation. Both the N‐terminal OB fold and the C‐terminal winged‐helix domains of Stn1 can separately bind the Pol12 subunit of the Pol α complex, and separately mediate Pol α activity enhancement. Overall, the findings suggest that Stn1 makes multiple, functionally important contacts with Pol12, causing an altered conformation of the Pol α‐primase complex capable of more efficient “handoff” of the RNA‐DNA hybrid from the primase to the polymerase. This mode of Pol α regulation has not been described before. Thus, the current report provides new mechanistic and evolutionary insights on a conserved pathway of Pol α regulation that is critical for genome stability.

Grant Funding Source: NIH, NSF
A conservative isoleucine to leucine mutation causes major rearrangements and cold‐sensitivity in KlenTaq1 DNA polymerase (551.1)
Authors: Wu Eugene , Walsh Amanda , Materne Emma , Kornberg Emily , Zielinski Bryan , Barnes Wayne , Kermekchiev Milko
Published: June 2021

Assembly of polymerase chain reactions at room temperature can sometimes lead to low yields or unintentional products due to mispriming. Mutation of isoleucine 707 to leucine in DNA polymerase I from Thermus aquaticus substantially decreases its activity at room temperature without compromising its ability to amplify DNA. To understand why a conservative change to the enzyme over 20Å from the active site can have a large impact on its activity at low temperature, we solved the X‐ray crystal structure of the large (5´‐to‐3´exonuclease‐deleted) fragment of Taq DNA polymerase containing the cold‐sensitive mutation (Cs3C KlenTaq1) in the ternary (E‐DNA‐ddNTP) and binary (E‐DNA) complexes. The Cs3C KlenTaq1 ternary complex was identical to the wild‐type in the closed conformation except for the mutation and a rotamer change in a nearby phenylalanine 749, suggesting that the enzyme should remain active. However, soaking out of the nucleotide substrate at low temperature results in an altered binary complex made possible by the rotamer change at F749 near the tip of the polymerase O‐helix. Surprisingly, two adenosines in the 5´‐template overhang fill the vacated active site by stacking with the primer strand, thereby blocking the active site at low temperature. Replacement of the two overhanging adenosines with pyrimidines substantially increased activity at room temperature, confirming the importance of base stacking. These results explain the cold sensitivity phenotype of the I707L mutation in KlenTaq1 and serve as an example of a large conformational change affected by a conservative mutation.

Grant Funding Source: WMB supported by SBIR grant R44 GM6081002A1 and 1R21HG006291
Proteasome‐mediated degradation of TATA binding protein (TBP2) in Haloferax volcanii (556.1)
Authors: Fu Xian
Published: June 2021

Gene transcription and proteolysis are two processes that have seemingly nothing in common: transcription is the first step in the life of any protein and proteolysis is last. However, we show that TATA binding protein (TBP2), one of the general transcription factors in Haloferax volcanii is degraded in proteasome‐mediated way. To be specific, TBP2 levels are increased by either chemical inhibition or genetic depletion of catalytic 20S core particles of proteasomes. In addition, TBP2 levels are higher in AAA+ ATPases proteasome‐activating nucleotidase (PAN) and cell division cycle 48 (cdc48) mutant strains compared with wild‐type strain suggesting TPB2 turnover by proteasome also requires AAA+ ATPases which closely related to the regulatory particle triple‐A ATPases (Rpt) of eukaryotic 26S proteasomes. Interestingly, like ubiquitin‐proteasome system in eukaryotic the recent described small ubiquitin‐like archaeal modifier proteins (SAMPs), its activating enzyme, E1 like UbaA, and the potential de‐ubiquitin enzyme (JAMM2) seem to be involved in TBP2 degradation based on the fact TBP2 level are much higher in those mutant strains than wild‐type strain, although evidences also suggest the presence of a SAMP‐independent pathway for TBP2 degradation. Overall, these findings first open a window for disclosing interactions among transcription initiation, SAMP and proteasome systems in archaea.

Grant Funding Source: NIH R01 GM057498 and DOE DE‐FG02‐05ER15650
Peroxygenase and oxidase activities of dehaloperoxidase‐hemoglobin from Amphitrite ornata (580.1)
Authors: Ghiladi Reza , McCombs Nikolette
Published: June 2021

The marine globin dehaloperoxidase‐hemoglobin (DHP) from Amphitrite ornata was found to catalyze the H2O2‐dependent oxidation of monohaloindoles, a previously unreported class of substrate for DHP. Using 5‐Br‐indole as a representative substrate, the major monooxygenated products were found to be 5‐Br‐2‐oxindole and 5‐Br‐3‐oxindolenine. Isotope labeling studies confirmed that the oxygen atom incorporated was derived exclusively from H2O2, indicative of a previously unreported peroxygenase activity for DHP. Peroxygenase activity could be initiated from either the ferric or oxyferrous states with equivalent substrate conversion and product distribution. It was found that 5‐Br‐3‐oxindole, a precursor of the product 5‐Br‐3‐oxindolenine, readily reduced the ferric enzyme to the oxyferrous state, demonstrating an unusual product‐driven reduction of the enzyme. As such, DHP returns to the globin‐active oxyferrous form after peroxygenase activity ceases. Reactivity with 5‐Br‐3‐oxindole in the absence of H2O2 also yielded 5,5’‐Br2‐indigo above the expected reaction stoichiometry under aerobic conditions, and O2‐concentration studies demonstrated dioxygen consumption. Non‐enzymatic and anaerobic controls both confirmed the requirements for DHP and molecular oxygen in the catalytic generation of 5,5’‐Br2‐indigo, and together suggest a novel oxidase activity for DHP.

Grant Funding Source: Supported by the National Science Foundation CHE‐1150709
Mechanistic and computational studies on C‐N bond oxidation in D‐amino acids catalyzed by D‐arginine dehydrogenase Y53F and Y249F (584.4)
Authors: Gannavaram Swathi , Sirin Sarah , Gadda Giovanni
Published: June 2021

Pseudomonas aeruginosa D‐arginine dehydrogenase (PaDADH) is a flavin dependent enzyme that can be classified as a member of D‐amino acid oxidase, sarcosine oxidase, and related enzyme families. It catalyzes the oxidation of D‐amino acids except D‐aspartate, D‐glutamate and glycine, to imino acids. Mechanistic details of C‐N bond oxidations of D‐amino acids by PaDADH are still elusive. Multiple mechanistic possibilities such as carbanion, hydride transfer and polar nucleophilic mechanisms could be considered. Previous work on PaDADH showed that NH and CH bond cleavages during amine oxidation are asynchronous with no further details available on the chemical mechanism. Here, we mutated two conserved active site residues Y53 and Y249 to phenylalanine in an attempt to reveal the mechanistic details of amine oxidation via pH profiles and deuterium isotope effects on rapid reaction kinetics. To further minimize mechanistic possibilities, QM/MM methodology was used to probe the relative local electrophilicity of key FAD sites within PaDADH active site. Our results are consistent with D‐amino acid oxidation occurring through the direct transfer of a hydride ion from the substrate to FAD without stabilization of reaction intermediates or FAD‐derived adducts, in which the active site tyrosines do not have a direct role in catalysis in PaDADH.

Grant Funding Source: NSF MCB‐1121695 (G.G.) and a GSU Molecular Basis for Disease Fellowship (S.G.).
Human rhinovirus elicits differential cytokine response and signal transduction pathways in human macrophages as a function of viral receptor stimulation (609.2)
Authors: Hall David , Schuler Bryce , Schreiber Michael , Li LuYuan , Raugi Dana , Kingdon Megan , Smith Cosonya , Hameister Chelsea , Mokry Michal , Racaniello Vincent
Published: June 2021

Major‐ and minor‐group rhinoviruses enter their host by binding to the cell surface molecules ICAM‐1 and LDL‐R, respectively, which are present on both macrophages and epithelial cells. Although epithelial cells are the primary site of productive HRV infection, previous studies have implicated macrophages in establishing the cytokine dysregulation that occurs during rhinovirus‐induced asthma exacerbations. Upon closer examination in human primary macrophages, differential signaling pathway activation was observed between major‐ and minor‐group rhinovirus upon initial HRV binding, indicating a discordant receptor‐dependent response to these rhinovirus types. Differential phosphorylation of kinases (p38, JNK, ERK5) and transcription factors (ATF‐2, CREB, CEBP‐beta) was observed between the major‐ and minor‐ group HRV treatments. Furthermore, major‐ and minor‐ group HRV elicited differential production of the asthma‐relevant cytokines CCL20, CCL2, and IL‐10. This is the first report of genetically similar viruses eliciting dissimilar cytokine release, transcription factor phosphorylation, and MAPK activation from macrophages. These results suggest that receptor dependence plays a role in establishing the inflammatory microenvironment initiated in part by monocytic‐lineage cells in the human airway upon exposure to rhinovirus.

Grant Funding Source: Supported by the McNair Program, NIH R15 AI065505‐01A1,NSF 0521112, Excellence in Science Fund
Promoting concept driven teaching strategies in biochemistry and molecular biology through concept assessments: a regional workshop in Boston (618.16)
Authors: Fox Kristin , Roecklein‐Canfield Jennifer
Published: June 2021

A workshop was held on January 11, 2014, at Simmons College in Boston, MA, to design assessments and learning strategies for concepts in Biochemistry and Molecular Biology Education. The workshop included faculty from a variety of institutions in the northeast. Before the meeting faculty filled out a survey indicating which of the recently‐published learning objectives, developed as part of the NSF‐RCN UBE grant referenced in the title, they were most interested in developing assessments for. Using this information, small groups of faculty were organized and each group worked to develop both an exam‐type question and a scoring rubric for the question. Once these had been developed, the groups re‐convened to list the knowledge from allied fields that is required to successfully answer the question. Finally, they worked together to design a student‐centered learning strategy that would prepare students to answer the question correctly. The assessments, rubrics and activities that were developed will be available for the community to use.

Grant Funding Source: Supported by NSF Grant #DBI‐0957205
Undergraduate research ő a key to advancing interest in STEM (618.40)
Authors: Carroll Margaret , Skeete Dereck , Catapane Edward
Published: June 2021

In 2006 Medgar Evers College received an NSF grant (0622197 of the DUE Program) designed to increase the number of students earning BS degrees in Biology and Environmental Science. The goals of our STEP into Science program were to: recruit new students and non‐STEM students into Biology or Environmental Sciences; improve retention by providing academic, financial and mentoring support; foster integration of research and technology to better equip majors to be successful applicants to graduate/professional programs; and increase the number of students graduating with BS degrees. We use peer recruiters to attract more high school, transfer, and non‐science college students into STEM majors and place emphasis on undergraduate research experiences to increase the quality and retention of science majors through their BS degree. Since the inception of the program, STEM enrollment more than doubled. Our program evaluations consistently showed that a key factor in our successful recruitment and retention was student involvement in undergraduate research activities. The number of majors actively engaged in research has risen more than 90% with a concurrent increase in student research presentations at scientific conference, and an 87% increase in the number of students receiving external research internships and travel awards to attend national conferences. STEM graduates have also increased and many of them are continuing on to Masters and Doctoral programs in STEM and hopefully will ultimately enter rewarding careers in the science enterprise.

Grant Funding Source: NIH‐ 2R25GM06003, NSF‐ 0622197, NYSED‐ 0516041071
Digital exhaust: an analysis of students’ interactions with online learning tools (618.42)
Authors: Mueller Dustin , Offerdahl Erika , Boyer Jeff
Published: June 2021

Learning management systems (LMS) such as Blackboard, Desire2Learn, and WebCT have become ubiquitous on college campuses. At a minimum, these platforms are an efficient way to provide access to course materials (e.g. course notes, syllabus, study guides) to all students. But the real power of LMS is in their potential to provide online tools to engage students outside of class in ways that support and reinforce the learning that occurs during class. When students interact with these online tools, they leave behind a digital “exhaust” that is collected in access logs. This clickstream data can be analyzed for patterns of student behavior from which we can make inferences about student learning. The overarching goal of this project was to analyze clickstream data associated with a large‐enrollment, introductory biochemistry course for science majors. Specifically, we analyzed students’ access logs related to their use of weekly Progress Checks. Progress checks are a series of online assessment tools released weekly to students that gauge their acquisition of key biochemical principles and skills as well as introducing them to upcoming material to be covered in class. We hypothesized that successful students would exhibit different clickstream patterns than non‐successful students. We gathered clickstream data, student performance data on in‐class activities, quizzes, and exams, incoming GPA, and pre/post assessment data. These data were analyzed for patterns of interaction that would help flag students who are not performing adequately within a course (i.e., an early warning system) to proactively target and support student learning.

Grant Funding Source: Supported by the NSF
Best practices in direct nutrition education for low‐income audiences: educator characteristics, training, and monitoring (625.1)
Authors: MacKinnon Chloe , Auld Garry , Baker Susan
Published: June 2021

The project objective was to identify best practices in nutrition education for low‐income audiences. Best practices are evidence‐based elements or strategies that have shown effectiveness in achieving outcomes. Utilizing best practices increases stakeholder confidence that programs will be effective in helping low‐income participants make positive nutrition‐related behavior changes. A seven‐member expert panel identified best practices criteria via telephone and electronic correspondence; the criteria were confirmed via literature review. Five criteria were identified as characteristics inherent to the success of the educator in community‐based nutrition education programs. These include expertise in both content and teaching methods, a thorough understanding of performance expectations, and the ability to relate to the target audience. Three criteria were identified for training and monitoring of educators throughout employment. Best practices criteria for educator characteristics, training, and monitoring are useful for program leaders at the state and local level and may promote consistency and efficacy within and across low‐income nutrition education programs.

Grant Funding Source: Supported by the National Institute of Food and Agriculture no. 2012‐48757‐20337
Apples/apple products consumption is associated with a better nutrient intake profile, better diet quality, and lower risk of obesity in children (2‐18 yrs): National Health and Nutrition Examination Survey (NHANES) 2001‐2010 (626.16)
Authors: Nicklas Theresa , Rodriguez Gabriela , O'Neil Carol , Fulgoni Victor
Published: June 2021

The association between apples/apple product (A/AP) consumption with nutrient intake, diet quality, and risk of obesity was examined in children using data from NHANES (2001‐2010). Consumers (n=3,482) were defined by consumption of any amount of apple, applesauce, or 100% apple juice using a 24‐hour diet recall. ANOVA (covariate adjusted) were conducted using appropriate sample weights. Logistic regression was used to determine odds ratios. Diet quality was calculated using the Healthy Eating Index‐2010 (HEI). Mean intake of total sugars (133±1 v 143±1 g/d), dietary fiber (12.2±0.1 v 15.0±0.2 g/d), magnesium (226±1 v 243±2 mg/d), and potassium (2149±16 v 2408±29 mg/d) was higher (p <0.01) in apple consumers than in non‐consumers. Intake of added sugars (21.3±0.2 v 17.8±0.3 tsp/d), SFA (26.3±1.5 v 24.6±0.2 g/d), and sodium (3172±20 v 3079±23 was lower (p <0.01) in A/AP consumers than non‐consumers. The total HEI score was higher (50.7±0.4 v 40.8±0.3) in A/AP consumers than non‐consumers. The percentage of obese children was lower among A/AP consumers (12.9%) compared to non‐consumers (17.6%). Risk of obesity was 25% lower in apple consumers but not significant among consumers of applesauce or 100% apple juice. Total consumption was associated with better nutrient intake, diet quality and weight parameters in children and consumption of A/AP should be encouraged.

Grant Funding Source: Supported by: Dr. Pepper Snapple Group, Inc & USDA
Reduced IL‐10 production contributes to impaired NK cytotoxicity in old mice fed a high folic acid diet (638.3)
Authors: Sawaengsri Hathairat , Wang Junpeng , Reginaldo Christina , Smith Donald , Wu Dayong , Meydani Simin , Selhub Jacob , Paul Ligi
Published: June 2021

Natural killer (NK) cells are important for immunity against malignant and virally infected cells. High folic acid intake, which may be linked with higher risk of colon cancer, was associated with lower NK activity in older women. To study the underlying mechanisms, we created a mouse model and found that aged mice fed a high folic acid (HFA) diet had reduced NK activity. In this study, we determined if expression of cytokines that are known to activate NK activity (IL‐10, IFN‐γ, TNF‐α) are affected by a HFA diet in aged mice.

Female C57BL/6 mice (16 mo) were fed a control (1x RDA folic acid) or a HFA diet (20x RDA folic acid) for 3 months. Splenocytes were collected and stimulated with LPS for 24 h for ex vivo production of IL‐10, IFN‐γ, and TNF‐α determined by cytometric bead array.

In HFA mice, IL‐10 production was 50.7% less than that of the control mice (P=0.028) but no differences were found in IFN‐γ and TNF‐α production. Since IL‐10 activates NK cells, we examined whether addition of IL‐10 to the splenocyte cultures would restore NK activity in the HFA group. We found that NK activity increased for both groups (P<0.01), but the HFA group had larger percent increase in NK activity as compared to control mice (P=0.058). These results indicate that IL‐10 restored the lower NK activity in aged mice fed a HFA diet.

These findings suggest the decreased NK activity due to a high folic acid diet may in part be due to impaired IL‐10 secretion.

Grant Funding Source: Supported by USDA contract # 51520‐008‐045 and HNRCA Pilot grant
Methods of sustaining dietary ketosis in Sprague‐Dawley rats (643.5)
Authors: Kesl Shannon , Poff Angela , Ward Nathan , Fiorelli Tina , Ari Csilla , D'Agostino Dominic
Published: June 2021

The ketogenic diet (KD) has been successfully used to treat pediatric refractory epilepsy since the 1920s and is currently being investigated as an adjunct treatment for cancer and neurological disorders. The therapeutic efficacy of the ketogenic diet results from an elevation of blood ketones. Concerns regarding this treatment include low compliance due to restrictive diet and adverse effects on blood lipids. We hypothesized ketone precursor supplementation would elevate blood ketone levels to therapeutic ranges (2‐5mM) without need for dietary restriction. We tested the effects of the following ketone precursors on blood glucose, ketones, and lipids with a 28‐day dose escalation study in male Sprague‐Dawley rats: R,S‐1,3‐Butandiol (BD), a mineral (Na+/K+) salt of β‐hydroxybutyrate (βHB) (SO), medium chain triglyceride (MCT) oil (MO), SO+MO 1:1 mixture (SM), acetoacetate ketone ester (KE), and control (H2O) (n 蠅8). Days 1‐14, rats received a daily 5g/kg intragastric gavage, and days 15‐28 rats received a 10g/kg dose of their respective test substances. BD and KE rats were not increased to 10g/kg based on previous toxicology studies and were administered a 5g/kg dose for the duration of the study. Once weekly, whole blood samples (10 μl) were acquired for analysis of glucose and βHB at 0, 0.5, 1, 4, 8, and 12 hours after test substance administration, or until βHB returned to baseline. At day 1 and 28, 10 μL of whole blood were collected to measure triglycerides, total cholesterol, and HDL concentration. At days 1, 7, 14, 21 and 28 substances significantly decreased blood glucose and elevated βHB without dietary restriction. There were no significant elevations in the lipid panel for any of the substances.

Grant Funding Source: Funded by the Office of Naval Research