bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and Characterization of Gamma‐Synuclein as a PCBP1‐Interacting Protein in Various Cancer Cell Lines
Authors: Ko Jane , Hunkele Amanda , Sultan Hamidah , Ikalina Faith , Liu Alexander , Nahar‐Gohad Pranjal 
Published: June 2021

PolyC binding protein1 (PCBP1), a transcriptional regulator of mu‐opioid receptor (MOR) gene, has multiple functions, which can be regulated by various protein‐protein interactions. Using PCBP1 as bait, a human brain cDNA library was screened via two‐hybrid system. One candidate clone was identified as g‐synuclein with glutamic acid (E) at the 110 position rather than valine (V). It was called g‐synuclein110E in here to differentiate from the 110V form. The interaction between PCBP1 and g‐synuclein110E was confirmed by in vivo validation and GST‐pull down assay. Confocal analysis showed g‐synuclein110E mainly expressed in the cytosol of neuronal NMB cells. Ectopic expression of g‐synuclein110E or 110V did not alter MOR mRNA level or hMOR promoter activity, suggesting no involvement of g‐synuclein in modulating hMOR expression. Co‐immunoprecipitation using anti‐PCBP1 antibody and lysates of NMB cells overexpressing g‐synuclein110E or 110V revealed a stronger band intensity of co‐immunoprecipitated 110E form than 110V form, indicating that the change of amino acid at the 110 position affected the interaction with PCPB1. Synuclein110E form was found in H292 (lung), HT29 (colon) and T47D (breast) cells, and co‐immunoprecipitation demonstrated that this physical interaction with PCPB1 also occurred in these cells. To further examine if different endogenous g‐synuclein forms were also present in various cancer cells, RT‐PCR using RNAs from different cell lines and a specific primer set for g‐synuclein were used. The full length of g‐synuclein PCR products were cloned into a cloning vector and then several clones were subjected to DNA sequencing. Different sequences were detected in certain cell lines. Overall, this study reports g‐synuclein110E as a new PCBP1‐interacting protein and provides some insight into its complex role.Support or Funding InformationConfocal microscope was acquired via the NSF grant. This research was supported by NIH research grant DA016673 and BioResearch Fund from Seton Hall University.
Probing the Role of Threonine‐221 and Lysine‐397 in ADP‐Glucose Pyrophosphorylase from Deinococcus radiodurans
Authors: Reynaga Janice , Szczeblowski Gabrielle , Salas Celeste , Le‐Pham Ashley , Ong Leo , Meyer Christopher R 
Published: June 2021

The knowledge gained from structure‐function studies of Adenosine Diphosphate Glucose Pyrophosphorylase (ADP‐glucose PPase), that serves as the rate‐limiting step in production of starch in plants and glycogen in bacteria, can inform protein engineering to generate a highly active enzyme. This enzyme is allosterically regulated by metabolites which serve as activators or inhibitors in accord with the organism's carbon metabolism pathways. An ADP‐glucose PPase form that was insensitive to feedback inhibition could enhance the biomass production of starch in plants, allowing for the efficient and economic use of starch as a renewable energy and food source. The enzyme of interest is derived from Deinococcus radiodurans (D. radiodurans), a microorganism that can withstand extreme growth conditions and ionizing radiation. Although studies on the enzyme from D. radiodurans are limited, the enzyme's characteristics of stability and altered regulation would be desirable to incorporate into an altered enzyme expressed in transgenic crops. The wild‐type D. radiodurans ADP‐glucose PPase is activated by fructose‐bisphosphate (FBP) and fructose‐6‐phosphate (F6P). The K397A and T221A enzymes were generated to further elucidate the role of amino acids in these regions on activity and regulation. Both enzymes were purified to near homogeneity by a procedure that included DEAE and phenyl sepharose chromatography. Preliminary studies indicate lower apparent binding affinity for activators and overall lower enzyme activity when alanine was substituted for lysine at position 397 (K397A), a position postulated to be near the allosteric site. These preliminary results demonstrate the importance of a positively charged amino acid at this position. The D. radiodurans enzyme harbors a threonine in a loop near the G1P binding site that is occupied by alanine in most ADP‐glucose PPases (amino acids 220–226: LTSMGIY). The T221A enzyme exhibited similar aparent affinity for the substrates ATP and G1P and co‐factor Mg but displayed a 50% reduction in activity in the absence of the activator FBP. However, the presence of the activator restores activity to the T221A enzyme, which is also more sensitive to other metabolites such as F6P, G6P, 3‐PGA, and sulfate. The T221 position appears to play a role in fold activation by metabolites as well as effector specificity. Complete kinetic and physical characerization of these enzymes is underway.Support or Funding InformationSupported in part by NSF and NSF BIO MCB grant #0448676.
Probing the role of the N‐terminus in the ADP‐Glucose Pyrophosphorylase from Thermodesulfovibrio yellowstonii
Authors: Yik Eric , Pushkarev Edward , Campbell Dylan , Diep Casey , Duran Nicholas , Nguyen Jackson , Orry Andrew , Meyer Christopher R 
Published: June 2021

Glucans serve as critical energy storage compounds in nearly all living organisms. Such renewable and biodegradable carbon sources are in demand now from industry as an eco‐friendly substitute for petroleum based products. ADP‐Glucose Pyrophosphorylase (ADPG PPase) is the enzyme that catalyzes the rate limiting step of glucan biosynthesis in plants and bacteria, respectively. The novel Thermodesulfovibrio yellowstonii (Td.y) ADPG PPase, from a thermophilic, sulfate‐reducing bacterium, has potential properties that could lead to engineering a very stable and highly active form which could increase the yield of starch. Further, sequence alignment data indicate that Td.y harbors varied amino acids in two conserved N‐terminal regions (glycine rich and RRAKPAV) that are known to be important for regulation and catalysis in other characterized ADPG PPases. The recombinant Wild‐type (WT) and variants (E15A, F23R, S25A) have been successfully purified by hydroxyapatite and size exclusion chromatography. In the case of E15A, preliminary data displayed similar velocity and similar apparent substrate affinity for ATP compared to WT, in the absence of effector molecules. However, in the presence of the activator PEP, E15A shows a ~7 fold increase in activity compared to 4 fold in WT. This suggests a role in regulation and binding of effector molecules. In the absence of effector molecules, preliminary data from F23R reveal a 4 fold decrease in activity and a ~2 fold decrease in apparent affinity for ATP compared to the WT. However, in the presence of effector molecules, ATP affinity was restored to WT values. In the presence of PEP and FBP, F23R displays a ~7 fold increase in activation compared to WT. The F23 position appears to play a role in structure or folding/allosteric regulation, which is also supported by molecular modeling. These results suggest a potential for altered binding of negatively charged metabolites due to increased positively charged residues in the postulated binding pocket. Kinetic data for the variant S25A reveals a Vmax ~3 fold higher than WT with a10‐fold higher apparent affinity for ATP compared to the WT as well as desensitization to effector molecules. This position in Td.y may play a role in setting the relative activity level that can be further attenuated by effectors. Along with kinetic analyses, initial crystallization trials are underway for variant S25A with initial crystals from different conditions diffracting to a resolution of ~3.96 Å. Results gathered from the WT and variants thus far confirm and extend the role of the two conserved regions for activity and regulation.Support or Funding InformationSupported in part by NSF and NSF BIO MCB grant #0448676.
Determinants of Variation in Trunk Morphology in Anthropoid Primates
Authors: Ward Carol V , Middleton Emily R. 
Published: June 2021

Bones of the torso are often used to infer postural and locomotor adaptation in fossil primates, based on inferred patterns of variation in overall torso form in extant primates and largely untested assumptions about how individual bones reflect the various forms. Observed variability of the bony pelvis, rib cage and vertebrae among taxa is most frequently hypothesized to reflect mobility and function of the upper and lower limbs. However, the degree of covariation among these torso elements and their relationships to factors other than limb function are poorly understood. To explore the determinants of variation in torso form, we quantified 3D torso shape from reconstructed CT scans of 57 anthropoid primates. We compared these data with linear and landmark data from the vertebrae, sterna, ribs, pelves, clavicles, scapulae and humeri of 256 anthropoids to determine patterns of relationships among torso skeletal elements. Finally, we conducted detailed analysis of integration patterns in the rib cages of 103 chimpanzees and 352 humans. Results reveal that the lower rib cage loosely follows pelvic form and is not as tightly integrated with upper rib cage shape as expected. Stiffness and control of the spine appears to be a much stronger determinant of pelvic form than previously recognized. Upper rib cage shape appears to relate to posture and perhaps other variables rather than locomotion or shoulder girdle morphology. There is also an unexpectedly weak relationship between the morphology of the upper rib cage and shoulder girdle. All together, there is more variation in overall torso shape and in its various components than previously recognized, which has implications for the reconstruction of locomotor behavior in fossil taxa and patterns of evolution in anthropoid primates.Support or Funding InformationNSF BCS 0716244, Leakey Foundation, Wenner Gren Foundation
An Inquiry‐based Exercise in Medicinal Chemistry: synthesis of a molecular library and screening for potential anti‐malarial and anti‐inflammatory compounds
Authors: Hall David J , Martin Charles G , Welford Michael , Debbert Stefan 
Published: June 2021

The development of new medicines holds particular fascination for chemistry, biochemistry, and biology students interested in a career in medicine or the life sciences. The identification and refinement of lead compounds to treat diseases requires researchers to be facile in a number of different disciplines including organic synthesis, biochemistry, cell biology, and molecular biology. We have developed an interdisciplinary, inquiry‐based laboratory spanning both organic chemistry and biochemistry classes that acquaints students with research in medicinal chemistry. The first part of the exercise takes place in the second semester of organic chemistry, where pairs of students design and execute their own multi‐step synthesis of a novel compound with anti‐inflammatory and/or anti‐malarial potential. Later, in first semester biochemistry, many of the same students then test these synthesized compounds for cytotoxicity, inhibition of the enzyme nitric oxide synthase and inhibition of the transcription factor NF‐kB. Learning outcomes, measured by the CURE survey, suggest that students participating in both classes had higher gains than the average student.Support or Funding InformationMonetary support for this project came from the Excellence in Science Fund of Lawrence University, NIH grant R15 AI065505‐01A1, and NSF grants 0521112 and CHE‐0923473, and the Sherman Fairchild Foundation.
A Redesigned Undergraduate Biochemistry Lab
Authors: Mills Jeffrey L. , Hart Kaitlin , Thurnherr Emily , O'Handley Suzanne F. , Bernstein Herbert J. , Craig Paul A. 
Published: June 2021

The need for a significant improvement in undergraduate STEM education has been broadly recognized. The primary purposes of this project are to (1) improve understanding of the process of training students to be effective scientists, (2) test the hypothesis that “undergraduate students can characterize proteins of unknown function as the central theme of their biochemistry teaching laboratory”, and (3) that actually doing hypothesis‐driven experimental science is a useful tool in training students to become an experimental scientist. We have incorporated authentic inquiry into an undergraduate biochemistry lab course. Students at RIT are combining computational (in silico) and wet lab (in vitro) techniques as they characterize proteins whose three‐dimensional structures are known but to which functional annotations have not been assigned. Following an initial pilot phase at RIT during the Fall 2015 semester, our curriculum will be implemented at five additional campuses (California Polytechnic, Hope, Oral Roberts, St. Mary's, and Ursinus). The feasibility of the proposed characterization protocols has already been successfully tested in an undergraduate research setting at RIT and Dowling College. Our students have used an internally developed program, ProMOL, to compare over 3000 PDB entries with “unknown function” against a library of known enzyme active site motif templates and have found 64 “good hits”. At the beginning of the semester, students selected one of these good hits and characterized it further with ProMOL and other well‐established in silico methods, such as DALI, Pfam, and BLAST. Following initial bioinformatics characterization, well‐established in vitro techniques for protein expression, purification, and validation of activity have been used. As this new curriculum is focused on research and discovery, it is reasonable to expect some of the students to produce novel results that will contribute to the field of structural biology, both as publications and as annotations to structural biology databases such as the Protein Data Bank.Support or Funding InformationThis project is supported by NSF IUSE 1503811.
Comparison of Selected Nutrients in Raw, Whole Egg from USDA Data Releases (1976 – 2010)
Authors: Somanchi Meena , Exler Jacob , Pehrsson Pamela Ruth 
Published: June 2021

BackgroundEggs are an important component of the US diet. The USDA released nutrient data for raw, whole eggs based on compilations in 1976, 1988–89, 2000–01 and 2010.MethodsThe 1976 compilation was primarily from literature data, the 1988–89 samples were from samples provided by egg producers nationwide, and the 2000–01 and 2010 samples were part of the Nutrient Data Laboratory (NDL) National Food and Nutrient Analysis Program (NFNAP).Except for the 1976 literature compilation, samples from the other years were analyzed by commercial and university laboratories approved by NDL for nutrient analysis of food samples.ResultsThere were only minor changes in total fat and protein, calcium, iron, phosphorus and sodium over this time period. There was a 22% decrease in cholesterol from 1976 to 1988–89, no significant change from 1988–89 to 2000–01. The mean cholesterol content decreased 51 mg/100 g (12%; p < 0.0001), from 423 mg/100 g in 2000–2001 to 372 (range 344–405) in 2010. Over the same period, average Vitamin D3 increased by 60%, to 2.05 mg [80 IU]/100 g (range 0.97–12.1). Samples from 2010 contained 0.65 mg 25‐OH‐D3/100 g (range 0.43–1.32).There was a 43% decrease in vitamin B12 from 1976 to 2010.ConclusionRecommendations on egg intake may allow for more eggs in the diet resulting in increase in egg consumption. USDA is planning on a future NFNAP sampling to monitor egg nutrients with a special interest in cholesterol, vitamin D3 and vitamin B12.Support or Funding InformationThis work was supported by the USDA Agricultural Research Service. Partial support was received from the National Institutes of Health, agreement #Y1CN5010, and from the Egg Nutrition Center
Characterizing Early Adolescent Food Waste using the Mobile Food Record
Authors: Banna Jinan C , Panizza Chloe , Boushey Carol , Delp Edward , Lim Eunjung 
Published: June 2021

BackgroundThe proportion of food that is plated, uneaten and thrown into the trash is known to be high in the school environment. To date, studies have not investigated the proportion of food waste in youth over 24‐hr periods in the U.S. The mobile food record (mFR) captures before and after images of eating occasions in real time and holds promise for evaluating food waste in diverse settings.PurposeTo assess the amount and type of food wasted in a multiethnic sample of early adolescent girls 9 to 13 yr residing in Oahu, Hawaii using the mFR.MethodsGirls (n=72) used the mFR for 3 days. A trained analyst reviewed all images with each participant. The amount of food consumed and left on the plate were estimated. Leftover food was further classified as thrown into the trash, saved to eat later, consumed by another person, eaten by a pet or other. Data were entered into the RapidCalc nutrition database to quantify waste by food groups.ResultsMean age was 10.8 and mean BMI z score was 0.04 (+/− 1.17). Girls identified as Asian (55.6%), non‐Hispanic white (36.1%) or other race (8.3%). All of participants’ mothers had a minimum of a 4‐yr college degree. The proportions of food plated and left uneaten were 12.1 % for vegetables, 10.6% for fruit, 10.2% for grains, 11.1% for meat/fish/poultry and 11.4% for dairy. The proportions of uneaten food thrown into the trash were 7.4% for vegetables, 7.8% for fruit, 6.1% for grains, 6.3% for meat/fish/poultry and 6.3% for dairy.ConclusionsFood waste over 3 days was considerably lower than food waste previously reported over the school lunch period alone. Food waste was nearly equivalent across food groups. This finding is in contrast to previous studies in the school setting indicating that waste of fruit and vegetables is significantly higher than other food groups. Studies in real time using technology over full days may better quantify waste among adolescents.Support or Funding InformationSupported by the USDA National Institute of Food and Agriculture, Hatch project, HAW02026‐H, Accession no. 1000090. Also supported by NIH grant U54MD007584.
Impact of Military Dining Facility Serving Modifications on the Nutritional Intake of Special Operations Personnel
Authors: Bukhari Asma S , Crombie Aaron P , McGraw Susan M , Champagne Catherine M , Ray Allen , Montain Scott J , Young Andrew J 
Published: June 2021

Military dining facilities (DFAC) aim to provide a nutrient dense diet that meets all nutritional needs of Warfighter customers, but meeting the nutritional needs of Special Operations Forces (SOF) personnel with high dietary energy and protein requirements can be challenging. The purpose of this study was to assess if an SOF garrison DFAC using tailored menu modification and employing customized nutrition labeling would provide adequate energy and protein while improving the nutrient density of food consumed by personnel enrolled in the small unit tactics iteration of the rigorous Special Forces Qualification Course. Menu modifications included increased availability of fruits, vegetables, fish, and healthy fats. The labeling strategy was focused on identifying performance‐facilitating versus performance‐limiting foods to influence diner choice in an ad libitum dining environment. We evaluated three independent but consecutive classes, at the same point during the course. Group one served as baseline (N=90), and groups two (N=112) and three (N=120) served as follow‐up to menu modification, and menu modification plus labeling interventions, respectively. Nutrient intake was estimated using digital photography of all participant trays before and after meals on two consecutive days of meals, and comparisons to reference standards, and nutrient density of foods consumed was assessed using the Healthy Eating Index (HEI). Compared to baseline, total HEI score increased (62.7±8.5 vs 52.6±9.2, p<0.01) and HEI across all domains increased except dairy (decreased) and vegetables (unchanged). Intakes of beta carotene and of high omega‐3 seafood increased while saturated fat intakes decreased (50±14 vs 69±22g·day−1, p<0.01). Total dietary energy intake decreased (4029±894 vs 4869±1099kcal·day−1, p<0.01), but was within guidelines for this population (125% of Military Dietary Reference Intakes), protein intakes were maintained at 2.0g·kg−1·day−1, sufficient for offsetting lean mass losses associated with periods of energy deficit. The decrease in dietary energy may be due to SOF personnel consuming less total fat (167 vs 205g·day−1, p<0.01), and carbohydrates (481 vs 581g·day−1, p<0.01). The observations indicate that modifications to the menu served to SOF personnel and employing customized nutrition labeling in the food service area can successfully increase the nutrient density and maintain adequate protein in the diets consumed by Warfighters dining ad libitum. The views expressed are those of the authors and do not reflect official policy of the Departments of the Army, Defense, or the U.S. Government.Support or Funding InformationThe study was funded by the US Army.
Consumption of Cultural and American‐style foods among Young Women of Cambodian Heritage
Authors: Nelson‐Peterman Jerusha L. , Sibeko Lindiwe , Cordeiro Lorraine S. 
Published: June 2021

ObjectiveRefugees have elevated chronic disease risk, which may be partially due to dietary changes over time with residence in the U.S. The dietary practices and health outcomes of children of refugees are not well studied. This study provides information that can guide practitioners and programs in promoting good long‐term health in refugee families.MethodsA cross‐sectional convenience sample of young women ages 15–35 YO of Cambodian heritage (primarily children of refugees) was conducted in Lowell, MA (n=107). Components of the survey that are relevant to this analysis were dietary practices and demographics. Fast food, vegetable, beverage, and grain consumption were measured through a qualitative, culture‐specific food frequency questionnaire. In analyses, special consideration was given to examining cultural food vs. American‐style food consumption within these categories. Descriptive statistics were calculated for dietary practices. Chi‐square analyses were used to assess relationship between food consumption and demographics for categorical variables and t‐tests were used to assess differences in mean for continuous variables.ResultsOver 60% of participants reported eating vegetables at least daily, and 67% reported eating fresh vegetables and/or fresh Cambodian herbs daily. A majority (62%) ate meals from Cambodian‐style quick stores (31%) or fast food restaurants at least once per week (31%). White rice was consumed at least daily by 71% of participants, while brown rice was consumed at least daily by 2%. More than 40% reported eating whole wheat bread at least weekly, with 31% consuming white bread at least weekly. Half (50%) consumed whole wheat bread, oatmeal, or brown rice at least weekly. Nearly half (47%) reported drinking some type of sugar sweetened beverage at least 2x/week. Women who had children at home were more likely to report eating vegetables daily (P=0.04), vegetables and herbs daily (P=0.02), and American‐style fast food weekly (P=0.01) than those without children. More acculturated respondents were less likely to eat vegetables and herbs daily than less acculturated respondents (P=0.05).ConclusionYoung women of Cambodian heritage provide us with a unique model for examining long‐term dietary practices of and determining strategies for interventions with children of refugees. Children of refugees must navigate the U.S. food environment, with strong influences from their heritage. Programs and practitioners seeking to promote long‐term health of refugees should focus on both healthful traditional foods and American foods and beverages, and may have enhanced success by targeting women with young children through a participatory approach that respects culture‐centric programming and foodways.Support or Funding InformationUniversity of Massachusetts Amherst Center for Agriculture, Food and the Environment and U.S. Department of Agriculture