bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating the GADPH‐Sir2 interaction in S. cerevisiae (763.2)
Authors: Palmer Claire 
Published: June 2021

The yeast glyceraldehyde‐phosphate dehydrogenase (GAPDH), Tdh3, has been found to interact with the silencing protein Sir2 in S. cerevisiae. Sir2 is a protein deacetylase that removes acetyl groups from the tails of histones H3 and H4. Deacetylated histones are associated with more densely packed chromatin and thus, transcriptional silencing. The Sir2‐GAPDH interaction is being investigated in order to further understand this connection between metabolism and gene silencing. We are interested in determining what part of Sir2 is necessary for this interaction with Tdh3. To this end, Sir2 mutant strains for use in coimmunoprecipitation experiments have been created. We hope to identify strains in which coimmunoprecipitation of Sir2 with Tdh3 is unsuccessful, indicating that these strains are missing a part of Sir2 that is essential for Tdh3 interaction. We are also investigating the possibility that Sir2 could be interacting with Tdh3 in its capacity as a deacetylase. A previous genetic screen suggests that Sir2 may also interact with two ribosomal proteins, Rpl22a and Rps7a. Tdh3, a similar GAPDH protein, Tdh2, Rpl22a and Rps7a are therefore being tested for acetylation by immunoprecipitatation and probing with an anti‐acetyl lysine antibody. Thus far, no evidence of acetylation on Tdh3 has been observed. However, further experiments are necessary to confirm this result. Finally, to better understand Tdh3’s role in silencing, we are creating a library of Tdh3 mutants defective for promoting silencing.Grant Funding Source: Supported by National Science Foundation
Protein splicing of a temperature‐dependent intein from an extreme thermophile (768.10)
Authors: Siegart Nicolle , Colelli Kathryn , Williams Jennie , Reitter Julie , Mills Kenneth 
Published: June 2021

Inteins are intervening polypeptides that self‐catalyze their own excision from the flanking polypeptides, or exteins, in a process called protein splicing. We are studying an intein that interrupts genes from the archaebacteria Pyrococcus abyssi. The Pyrococcus abyssi (Pab) PolII intein only splices at elevated temperatures. The intein contains an N‐terminal cysteine and is preceded by an asparagine in the N‐extein at the ‐1 position. We have shown that protein cleavage occurs independent of the canonical splicing mechanism when the protein contains an alanine in place of the cysteine and an aspartate in place of the asparagine. In addition, we created a split version of the intein to determine whether when split into two fragments and recombined, the intein is capable of undergoing trans splicing.Grant Funding Source: Supported by the National Science Foundation, the Dreyfus Foundation, and The BD Corporation
Structural analysis of human carbonic anhydrase II and a thermophillic intein (768.3)
Authors: Haley Daniel , Siegart Nicolle , Reitter Julie , Mills Kenneth 
Published: June 2021

We are interested in various structural aspects of human Carbonic Anhydrase II (hCAII) and the Pyrococcus horikoshii PolII intein (Pho PolII). A combination of analyses including x‐ray crystallography and biochemical assays will be used to study each of the two proteins. We will compare the activity and structure of hCAII to hCAII where the active‐site zinc ions have been replaced with rhenium. Additionally, we will assay both zinc and rhenium hCAII for enzymatic functionality using a p‐NPA hydrolysis assay. Thus far, we have optimized expression in E. coli and purification of hCAII and have assayed for functionality. Our goal with the PolII intein is to obtain structures for the unspliced precursor and the excised intein in order to do structural comparisons. Our lab has recently crystallized the precursor and my focus is on the intein. The PolII precursor, which comes from a sea‐dwelling, thermophillic archaea, was mutated so that a stop codon preceded the poly‐His tag at the C‐terminal end of the intein before expression and purification were optimized. In order to isolate the intein from its remaining N‐extein, we used DTT to facilitate N‐terminal cleavage and will use size exclusion chromatography to separate the products.Grant Funding Source: Supported by the National Science Foundation under grant MCB‐1244089 and by the Dreyfus Foundation.
Protein splicing of an intein from the extreme halophile Halobacterium salinarum (768.9)
Authors: Jaramillo Mario , Nicastri Michael , Reitter Julie , Mills Kenneth 
Published: June 2021

Protein splicing is the self‐catalyzed excision of an intervening polypeptide (intein) from flanking polypeptides (exteins), concomitant with the ligation of the extein. An intein in the archaebacterium Halobacterium salinarum (Hsa) interrupts the DNA Polymerase II. We have observed that the Hsa intein splices poorly in Escherichia coli cells, unlike two highly related inteins found in Pyrococcus abyssi and Methanoculleus marisnigri, which are not halophilic. To test if splicing activity depends on salinity, we altered the expression conditions by varying the salinity of the growth media and of in vitro activity assays. Future experiments will involve in vivo techniques by over‐expressing the intein and the flanking exteins into Hsa, and by using antibodies to detect possible splicing of the native protein.Grant Funding Source: Supported by the National Science Foundation under grant MCB‐1244089 and by the Dreyfus Foundation
Discovery of a unique starch degradation system in the thermophilic red alga Cyanidioschyzon merolae (769.18)
Authors: Husodo Satrio , Gentry Matthew 
Published: June 2021

Starch is a key component in many aspects of daily life, including nutrition, biofuel production, and industrial processing: 50‐80% of daily caloric intake comes from starch; >20% of corn starch produced in the U.S. is converted to ethanol; and starch is a cheap and renewable industrial feedstock for producing paper, textiles, adhesives, plastics, and pharmaceuticals. Starch is comprised of glucose chains that intertwine into double helices that pack together to make starch insoluble and inaccessible to most enzymes, including the amylases that release its energy cache. Starch‐based feedstocks are generated by modifying starch using physical, chemical, and enzymatic methods. Physical modifications include cyclic heating/cooling between 50°C and >100°C. The addition of acids and bases to this process both catalyzes glucan chain hydrolysis and converts insoluble starch to a structure that improves accessibility of glucan chains to amylases. Alternatively, plants utilize an orchestrated reversible phosphorylation system to efficiently solubilize the starch surface, a process that can be mimicked to improve in vitro starch degradation. We recently discovered a unique dikinase‐phosphatase system in the thermophilic red alga Cyanidioschyzon merolae that is integral for starch degradation and different from systems seen in Kingdom Plantae. First, we defined the evolutionary phylogeny of this unique system. We cloned the genes, purified the enzymes from a recombinant expression system, and defined their kinetics and substrate specificities. Lastly, we demonstrated that these enzymes dramatically increase in vitro starch degradation of amylases. Collectively, this study provides a basis for understanding how glucan kinases and phosphatases function at the molecular level.Grant Funding Source: NSF#1252345
Probing conformational changes with multiwavelength collisional quenching (769.6)
Authors: Bell Ellis , Barkdoll‐Weil Forest , Metz Carlos , Varnes Philip , Bartle Emily , Li Chun 
Published: June 2021

Collisional quenching approaches using neutral or charged quencher molecules has long been used to indicate conformational changes in proteins Here we introduce a novel approach to collisional quenching using multiwavelength analysis of spectral data collected at two different excitation wavelengths with a variety of small molecule and protein test fluorophores. The results show that not only can detailed information about the local environment of tryptophans in proteins be obtained (even proteins with multiple tryptophans), but information is derived resulting from tyrosine‐tryptophan resonance energy transfer in proteins… Using Acrylamide, Iodide and Cesium collisional quenchers with both tyrosine and tryptophan derivatives and with model proteins with one or more tryptophans we demonstrate the utility of the approach for defining the local environment and changes induced by ligand binding, Furthermore, during the course of these studies we revealed that pi‐cation effects disrupt resonance energy transfer between tryptophan (acting as either donor or acceptor) and other moieties in the protein.This work was supported by NSF Grants MCB‐104995 and MCB 0448905 to EBGrant Funding Source: Supported by NSF Grants MCB‐104995 and MCB 0448905 to EB
Probing the role of the N‐terminus of Thermodesulfovibrio yellowstonii ADPglcuose pyrophosphorylase in allosteric regulation (769.9)
Authors: Yik Eric , Susoeff Michael , Kaur Sandeep , Dua Gautam , Holling Jaqueline , Meyer Christopher 
Published: June 2021

ADPGlucose Pyrophosphorylase (ADPG PPase) catalyzes the rate‐limiting step of glucan biosynthesis in plants and bacteria. The successful engineering of ADPG PPase will allow for the production of more renewable and biodegradable carbon. Thermodesulfovibrio yellowstonii (Td.y) ADPG PPase shows only ~30% identity to other bacterial forms of the enzyme; at positions E15, F18, F23, S25, and S28 the Td.y enzyme differs from consensus in the glycine rich (positions 9‐17) and KRAKPAV regions (positions 23‐29), areas known to play roles in activity and allosteric regulation. These positions were targeted for mutagenesis and the enzymes purified using hydroxyapitite and DEAE chromatography. For wild‐type (WT), kinetic studies revealed a Vmax of 5.3 U/mg and S0.5 values of 4.0 mM, 13.9 mM, and 1.2 mM for ATP, Mg, and G1P, respectively. Metabolites PEP, G6P, and 3PGA increased the Vmax by 1.5‐3 fold and decreased the S0.5 values for ATP by 4.2, 10.3, and 3.8 fold, respectively. Initial kinetics for the variant S25A gave a Vmax ~3 fold higher and a 10‐fold lower S0.5 value for ATP compared to WT. S25 in Td.y may play a role in setting the activity level in the absence of effectors. Further experiments are being conducted to fully characterize S25A and other variants, particularly with respect to allosteric regulation. Efforts are also underway to crystallize these enzymes to solve the three dimensional structures.Grant Funding Source: NSF Grant 0448676 and a CSUPERB Presidential Commission Grant
Effects of alcohol on the outer hair cell protein Prestin (775.2)
Authors: Minten Elizabeth 
Published: June 2021

Prestin, a transmembrane motor protein, is a member of the SLC26 family and is highly expressed in mammalian outer hair cells located in the cochlea. Outer hair cells, in response to changes in membrane potentials, adjust in length and rigidity. The production of these mechanical changes is thought to amplify the vibrations in the cochlea, increasing hearing sensitivity in mammals by 100‐fold. Since its identification in 2000, prestin has been found to be the motor protein in outer hair cells and is necessary for electromotility of the outer hair cell and for cochlear amplification.At this point, while the structure of prestin remains a mystery, previous experiments have indicated that prestin is sensitive to the levels of cholesterol in the cell membrane. Alcohols, which are also known modulators of lipid bilayer properties, could have the potential to have an impact on prestin function. It has been established that the link between the nonlinear capacitance of prestin and its electromotility is a surrogate measure of prestin function. Therefore, the effects of six alcohols ‐ ethanol, butanol, pentanol, hexanol, nonanol, and decanol, were each assessed at differing concentrations using patch‐clamp electrophysiology on HEK cells expressing prestin. The alcohols were chosen to have chain lengths smaller than 13, as alcohols with chain lengths above this cutoff have been shown to have limited biological activity and low solubility in cell buffers. All six of the alcohols tested showed either a depolarizing or polarizing effect.Grant Funding Source: Supported by NSF, RICE University
Creation of tPA conjugated dendrimer nanoparticles (780.4)
Authors: Paliwal Vipin 
Published: June 2021

A drug delivery system was created using nanoparticles called dendrimers. Tissue plasminogen activator (tPA), a clot busting drug given to stroke patients was covalently bonded to dendrimers using surface active organic functional groups including carboxylic acids, amines, and alcohol. Methods included esterification using a heterobifunctional coupling agent EDC (1‐ethyl‐3[3‐dimethylaminpropyl]carbodiimide hydrochloride. A fourth generation dendrimer (hydroxyl‐terminated poly(amidoamine) PAMAM dendrimers (G4‐OH) with 64 binding sites was chosen to bind the human tPA protein molecule (molecular mass of 72 kDa). Several dilutions of dendrimer were tested to achieve the best drug‐nanoparticle stoichiometric ratio and avoid overcrowding. Upon completion of the synthesis the drug‐dendrimer conjugate was purified using centrifugal filtration. The tPA‐dendrimer complex was tested for clot dissolving activity using an in vitro Thrombin assay. It was concluded that Succinamic acid functionalized dendrimer at a 1:1 drug to nanoparticle ratio was found to have the highest clot dissolving activity when compared to control tPA standard. This tPA‐dendrimer conjugate could be more effective, quicker reacting than tPA drug alone and may find use in treating stroke, pulmonary embolism and heart attack patients.Grant Funding Source: National Science Foundation
Census tract income levels and outdoor physical activity opportunities for families with preschoolers (806.19)
Authors: Li Cheng , Martin‐Biggers Jennifer , Cheng Carolyn , Byrd‐Bredbenner Carol 
Published: June 2021

The near home environment influences the PA and sedentary behaviors of adults and children. A valid, reliable, and easy to use self‐report assessment of the PA environment of homes with preschoolers was used to determine availability and accessibility of PA equipment and space in yards (areas immediately outside the home) and neighborhood PA facilities (e.g., playgrounds, low‐cost recreation centers). Scores for yard and neighborhood PA availability and accessibility were compared to the CTIL of the home’s address using 1‐way ANOVA. Homes (n=44) were categorized in low, middle, moderate, and upper CTIL (9%, 9%, 57%, 25%). Significant (p<.05) group differences were found for yard accessibility score and neighborhood availability score, but not for others. Post hoc tests indicated that the highest CTIL homes had more accessible yard PA equipment and space than lower CTIL homes. Highest CTIL homes also had significantly more neighborhood PA availability than lowest CTIL homes and neared significance for neighborhood accessibility (p=0.08). CTIL, as proxies for income, indicate that income disparities affect the PA availability and accessibility of families with preschoolers, and likely are a contributor to differences in obesity rates by income. Thus, eliminating “playground deserts” could be an important step in reducing obesity rates in CTIL areas.Grant Funding Source: Supported by USDA, National Institute of Food and Agriculture, Grant Number 2011‐68001‐30170
Feasibility and effectiveness of in‐home behavioral economic strategies to increase vegetable intake among low‐income children (808.18)
Authors: Leak Tashara , Swenson Alison , Vickers Zata , Reicks Marla 
Published: June 2021

Poor dietary behaviors put children at risk for obesity. The purpose of this intervention is to determine which behavioral economic strategies increase vegetable consumption among low‐income children (9‐12 years) in the Minneapolis/St. Paul metropolitan area. Caregivers (n=44) are randomly assigned 6 (of 10) in‐home behavioral economic strategies; one new strategy/week to be completed at 3 dinner meals for a total of 6 weeks. An example strategy is to make vegetables more available and visible than other foods during dinner. Intervention and control group (n=20) caregivers record child vegetable intake at 3 dinner meals and report intakes weekly to a trained researcher via telephone or in person. Researchers also inquire about barriers (e.g. lack of availability) and facilitators (e.g. time) for implementing strategies. Child vegetable liking, vegetable home inventory data, and three 24‐dietary recalls are also collected at baseline and immediately after the intervention. Most children reported liking more than 5 vegetable types; often the same vegetables available in the home and prepared by caregivers at dinner meals. Mean vegetable intake is being compared for each strategy across intervention and control groups to determine the effectiveness of each. The 6 most effective will be incorporated into the Cooking Matters for Families nutrition education program to increase vegetable intake among children.Grant Funding Source: Supported by NIFA 2014‐00403
Hummus (H)/garbanzo bean (GB) consumption is associated with increased nutrient intake, better diet quality, and lower body mass index in adult participants (19+ y) from the NHANES (2003‐2010) (810.15)
Authors: O'Neil Carol , Nicklas Theresa , Fulgoni Victor 
Published: June 2021

The association between H/GB consumption with nutrient intake, dietary quality, and weight parameters was examined in adults using data from NHANES (2003‐2010). Consumers (n=264) were defined as having any amount of H/GB during either 24‐hour diet recall. Means and ANOVA (covariate adjusted) were determined using appropriate sample weights; significance was p<0.05. Diet quality was calculated using the Healthy Eating Index‐2005 (HEI). Fiber (24.4±0.7 v 10.1±0.1 g/d), PUFA (19.5±0.4 v 17.3±0.1 g/d), vitamins A (787±42 v 640±6 RAE mcg/d), E (10.1±0.5 v 7.5±1.01 mcg/d), and C (119±8 v 86.4±4.3 mg/d), folate (627±16 v 547±4 mcg/d), magnesium (385±13 v 292±4 mg/d), potassium 3103±59 v 2697±12 mg/d), and iron (17.4±0.5 v 15.8±0.1 mg/d) intake was higher in consumers. Total fat (76.4±4.5 v 80.4±0.3 g/d), SFA (22.4±0.7 v 26.6±0.1 g/d), and cholesterol (227±8 v 288±2 mg/d) were lower in consumers. Consumers had higher HEI scores (62.2±1.3 v 51.9±0.2). BMI (26.4±0.5 v 28.6±0.1) and waist circumference (92.2±1.3 v 97.9±0.3 cm) were lower in consumers.Consumers were 43% less likely to be overweight or obese and had a 48% reduced risk of increased waist size. H/GB consumption was associated with better nutrient intake, diet quality and weight parameters in adults.Grant Funding Source: Supported by Sabra Dipping Co., LLC., and USDA.
Normality of adult dietary protein requirement distribution (820.11)
Authors: Ross Richard , McCabe George , Campbell Wayne , Johnson Craig 
Published: June 2021

Nitrogen balance data consistently suggest that the dietary protein requirement of adult humans follows a lognormal distribution. In contrast, statistical theory and the associated physiology imply that the protein requirement for healthy adults is normally distributed. The objective of this research was to reconcile this apparent conflict. An errors‐in‐variables simulation was conducted with parameters drawn from nitrogen balance data obtained in a study of 42 healthy adults (age 21‐81 years) who consumed controlled diets with protein intakes of 0.50, 0.75, and 1.00 g protein•kg‐1•d‐1 during three randomized 18‐day trials. Simulation results indicate that even when the true distribution of the protein requirement is normal, the observed (estimated) distribution is lognormal. Parameter estimates for the normal distribution obtained from the simulation enable policy decisions that more accurately reflect the distribution of the protein requirement in the adult population.Grant Funding Source: Supported by NIH R01 AG15750 and USDA 98‐35200‐6151
Characterization of muscle plasticity in a neotropical migrant, Dumetella carolinesis (gray catbird) (878.2)
Authors: DeMoranville Kristen , Corder Keely , Russell Dave , Huss Janice , Schaeffer Paul 
Published: June 2021

This study focuses on how avian migration is facilitated by changes in organismal metabolism, muscle structure, and muscle metabolism. These specific migratory changes were examined across the annual cycle on‐an organismal level by investigating whole body oxidative capacity (ability to use energy) and, on a tissue level by characterizing muscle tissue size and oxidative capacity. In order to quantify whole body oxidative capacity, summit metabolism was measured to determine the peak oxygen consumed by each individual. Birds were euthanized and the pectoralis (flight muscle) and gastrocnemius (leg muscle) were removed and weighed. Mitochondrial content of the muscle was quantified by measuring enzyme activity via citrate synthase and cytochrome oxidase assays to determine oxidative capacity of the muscles. Summit metabolism and flight muscle mass were greatest during southward migration compared to temperate breeding and tropical wintering. The Gray Catbird displays phenotypic plasticity during migration compared to non‐migratory periods suggesting that augmentation of the flight muscle and increased metabolism are necessary for migration.Grant Funding Source: Supported by NSF #IOS‐1257455 to PJS
AltitudeOmics: the effect of high altitude ascent and acclimatisation on cerebral blood flow regulation (885.1)
Authors: Fan Jui‐Lin , Subudhi Andrew , Evero Oghenero , Bourdillon Nicolas , Kayser Bengt , Julian Colleen , Panerai Ronney , Lovering Andrew , Roach Robert 
Published: June 2021

Adequate oxygen supply to the brain is critical to maintain brain function. Hypoxia presents a unique challenge in maintaining sufficient cerebral oxygen delivery (DO2). We assessed by ultrasound cerebral blood flow (CBF: internal carotid, vertebral arteries and middle cerebral artery velocity [MCAv]) and arterial blood pressure (index of cerebral autoregulation; CA) during rest and hypercapnic breathing (MCAv‐CO2 slope; index of cerebrovascular function) in 21 healthy subjects at sea‐level (SL) and upon arrival at 5260m (ALT1) and after 16 days of acclimatisation (ALT16). Cerebral DO2 was calculated as the product of arterial oxygen content (CaO2) and flow in each respective artery and summed to estimate global CBF. Global CBF increased ~70% upon arrival at ALT1 (P<0.05) and returned to SL values at ALT16 as a result of changes in cerebral vascular resistance. A reciprocal pattern in CaO2 maintained global cerebral DO2 across acclimatisation. MCAv‐CO2 slope was elevated by ~79% upon arrival at ALT1 and further increased by ~89% at ALT16 (P<0.05). Indexes of CA were reduced upon arrival at ALT1 (P<0.05), but did not change with acclimatisation at ALT16 (P>0.10). Cerebral DO2 was well maintained upon acute exposure and acclimatisation to hypoxia. Cerebrovascular function was enhanced with acclimatisation to high altitude, but these changes did not mitigate the reduction in CA associated with hypoxic exposure.Grant Funding Source: Supported by U.S. Department of Defense