Browsing by Subject "Protein"
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Item ACTUAL AND PRESCRIBED ENERGY AND PROTEIN INTAKES FOR VERY LOW BIRTH WEIGHT INFANTS: AN OBSERVATIONAL STUDY(2012-10-11) Abel, Deborah Marie; Rickard, Karyl A.; Brady, Mary Sue; Engle, William A.; Ingram, David A.; Poindexter, Brenda B.Objectives: To determine (1) whether prescribed and delivered energy and protein intakes during the first two weeks of life met Ziegler’s estimated requirements for Very Low Birth Weight (VLBW) infants, (2) if actual energy during the first week of life correlated with time to regain birth weight and reach full enteral nutrition (EN) defined as 100 kcal/kg/day, (3) if growth velocity from time to reach full EN to 36 weeks’ postmenstrual age (PMA) met Ziegler’s estimated fetal growth velocity (16 g/kg/day), and (4) growth outcomes at 36 weeks’ PMA. Study design: Observational study of feeding, early nutrition and early growth of 40 VLBW infants ≤ 30 weeks GA at birth in three newborn intensive care units NICUs. Results: During the first week of life, the percentages of prescribed and delivered energy (69% [65 kcal/kg/day]) and protein (89% [3.1 g/kg/day]) were significantly less than theoretical estimated requirements. Delivered intakes were 15% less than prescribed because of numerous interruptions in delivery and medical complications. During the second week, the delivered intakes of energy (90% [86 kcal/kg/day]) and protein (102% [3.5 g/kg/day]) improved although the differences between prescribed and delivered were consistently 15%. Energy but not protein intake during the first week was significantly related to time to reach full EN. Neither energy nor protein intake significantly correlated with days to return to birth weight. The average growth velocity from the age that full EN was attained to 36 weeks’ PMA (15 g/kg/day) was significantly less than the theoretical estimated fetal growth velocity (16 g/kg/day) (p<0.03). A difference of 1 g/kg/day represents a total deficit of 42 - 54 grams over the course of a month. At 36 weeks’ PMA, 53% of the VLBW infants had extrauterine growth restriction, or EUGR (<10th percentile) on the Fenton growth grid and 34% had EUGR on the Lubchenco growth grid. Conclusions: The delivered nutrient intakes were consistently less than 15% of the prescribed intakes. Growth velocity between the age when full EN was achieved and 36 weeks’ PMA was 6.7% lower than Ziegler’s estimate. One-third to one-half of the infants have EUGR at 36 weeks’ PMA.Item Aldosterone-induced proteins in renal epithelia(1982-10-28) Blazer-Yost, Bonnie; Geheb, Michael A.; Preston, Alan; Handler, Joel; Cox, MalcolmSimilar aldosterone-induced proteins have been demonstrated in two renal epithelia, the urinary bladder of the toad, Bufo marinus, and epithelia formed by cells of the A6 line derived from the kidney of the toad, Xenopus laevis. The proteins are induced along with the stimulation of Na+ transport but their synthesis is not dependent on Na+ transport per se. In view of the similar characteristics of the aldosterone-induced proteins in these two different epithelia, we suggest that they may have an important role in aldosterone-induced Na+ transport.Item Defining protein expression in the kidney at large scale: from antibody validation to cytometry analysis(American Physiological Society, 2023) Sabo, Angela R.; Winfree, Seth; El-Achkar, Tarek M.; Medicine, School of MedicineItem Developing Novel Methods to Identify RNA-Associated Mechanisms for Inheritance(2020-11) Ettaki, Zacharia Nabil; Aoki, Scott T.; Georgiadis, Millie; Quilliam, LawrenceAnimals depend on inheriting non-genetic information early in life to grow and develop naturally. This inherited, non-genetic information was previously thought to be limited to DNA modifications and DNA binding proteins. But recent studies have expanded our understanding of inheritance to include RNA and RNA binding proteins. We currently lack methods to identify and enrich for RNA binding proteins that might be involved in providing non-genetic information from mother to daughter cells. Others have developed a method using modified enzyme tags to pulse-label proteins with small molecule fluorescent ligands and follow these proteins as they are inherited by cells. Here I characterized and tested the application of a fluorescent small molecule targeting antibody to enrich for these labeled proteins. I first tested the ability of this antibody to bind to fluorescent ligand-labeled enzymes. I determined that the antibody can efficiently bind to at least one of the labeled enzymes. Second, I determined crystallization conditions for the ligand binding antibody fragment. This thesis sets the stage for structure determination and to test whether this antibody can work in vivo to enrich for RNA binding proteins involved in the delivery of non-genetic information to cells.Item Diet and Diabetic Kidney Disease: Plant Versus Animal Protein(Springer, 2017-03) Moorthi, Ranjani N.; Vorland, Colby J.; Hill Gallant, Kathleen M.; Medicine, School of MedicinePURPOSE OF REVIEW: The goal of this review is to present an overview of the evidence on the effectiveness of plant-based diets in delaying progression of diabetic kidney disease (DKD). RECENT FINDINGS: The ideal quantity of dietary protein has been a controversial topic for patients with DKD. Smaller studies have focused on protein source, plant versus animal, for preventing progression. Limited evidence suggests that dietary patterns that focus on plant-based foods, those that are lower in processed foods, or those that are lower in advanced glycation end products (AGE) may be useful in prevention of DKD progression. Increasing plant-based foods, incorporating diet patterns that limit processed foods, or potentially lowering AGE contents in diets may be beneficial for dietary management of DKD. However, dietary studies specifically targeted at DKD treatment are sparse. Further, large trials powered to assess outcomes including changes in kidney function, end-stage kidney disease, and mortality are needed to provide more substantial evidence for these diets.Item High-nutrition biscuits to increase animal protein in diets of HIV-infected Kenyan women and their children: A study in progress(Food and Nutrition Bulletin, 2014-12-30) Ernst, Judith A.; Ettyang, Grace; Neumann, Charlotte G.Background. Preliminary evidence suggests that improved nutrition early in HIV infection may delay progression to AIDS and delay the initiation or improve the effectiveness of antiretroviral drug therapy. There are few studies that evaluate food-based interventions in drug-naïve, HIV-infected women and their children. Meat provides several nutrients identified as important in maintaining immune function and lean body mass. Objective. To design supplemental meat and soybean biscuits for use in a randomized trial examining the effect of meat in the diet of drug-naïve, HIV-infected rural Kenyan women on changes in weight, lean body mass, morbidity, nutritional status, and activities of daily living of the women and growth and development of their children. Methods. We designed three supplemental biscuits: one with added dried beef, another with added soybean flour, and a wheat biscuit to serve as a control biscuit to be used in a randomized feeding intervention in drug-naïve, HIV-infected rural Kenyan women and their children. The nutritional contents of the different types of biscuit were examined and compared. Results. The three biscuits were isocaloric. Meat biscuits provided more lysine, vitamin B12, and bioavailable zinc. Soybean biscuits provided more total and absorbable iron; however, higher fiber and phytate contents may inhibit nutrient absorption. Data analysis for clinical outcomes of the trial is ongoing. Conclusions. The “biscuit model” is useful for nutrition supplementation studies because it can be provided in a blinded and randomized fashion, safely and privately in a home under directly observed consumption by a highly stigmatized population. It is well received by adults and children, and the biscuits can be produced locally with available, simple, affordable technology.Item Identification of Nuclear and Cytoplasmic mRNA Targets for the Shuttling Protein SF2/ASF(PLOS, 2008-10-08) Sanford, Jeremy R.; Coutinho, Pedro; Hackett, Jamie A; Wang, Xin; Ranahan, William; Caceres, Javier F.; Biochemistry and Molecular Biology, School of MedicineThe serine and arginine-rich protein family (SR proteins) are highly conserved regulators of pre-mRNA splicing. SF2/ASF, a prototype member of the SR protein family, is a multifunctional RNA binding protein with roles in pre-mRNA splicing, mRNA export and mRNA translation. These observations suggest the intriguing hypothesis that SF2/ASF may couple splicing and translation of specific mRNA targets in vivo. Unfortunately the paucity of endogenous mRNA targets for SF2/ASF has hindered testing of this hypothesis. Here, we identify endogenous mRNAs directly cross-linked to SF2/ASF in different sub-cellular compartments. Cross-Linking Immunoprecipitation (CLIP) captures the in situ specificity of protein-RNA interaction and allows for the simultaneous identification of endogenous RNA targets as well as the locations of binding sites within the RNA transcript. Using the CLIP method we identified 326 binding sites for SF2/ASF in RNA transcripts from 180 protein coding genes. A purine-rich consensus motif was identified in binding sites located within exon sequences but not introns. Furthermore, 72 binding sites were occupied by SF2/ASF in different sub-cellular fractions suggesting that these binding sites may influence the splicing or translational control of endogenous mRNA targets. We demonstrate that ectopic expression of SF2/ASF regulates the splicing and polysome association of transcripts derived from the SFRS1, PABC1, NETO2 and ENSA genes. Taken together the data presented here indicate that SF2/ASF has the capacity to co-regulate the nuclear and cytoplasmic processing of specific mRNAs and provide further evidence that the nuclear history of an mRNA may influence its cytoplasmic fate.Item Impact of diet on hydrogen sulfide production: implications for gut health(Wolters Kluwer, 2023) Teigen, Levi; Biruete, Annabel; Khoruts, Alexander; Medicine, School of MedicinePurpose of review: Excessive hydrogen sulfide (H 2 S) production by the gut microbiota may contribute to the pathogenesis of multiple intestinal diseases, including colon cancer and ulcerative colitis. Therefore, understanding of dietary drivers of H 2 S production has potential implications for nutritional strategies to optimize gut health and treat intestinal diseases. Recent findings: Recent studies support a positive relationship between dietary protein intake and H 2 S production. However, protein rarely exists in isolation in the diet, and dietary fiber intake could reduce H 2 S production in humans and animals, even with ∼30% of calories derived from protein. Summary: These findings suggest that increased fiber intake may reduce H 2 S production irrespective of protein intake, enabling the ability to meet the metabolic demands of the illness while supporting gut health. Here we discuss two recent ulcerative colitis diet studies that illustrate this point.Item Influence of dietary protein on glomerular filtration before and after bariatric surgery: a cohort study(Elsevier, 2014-04) Friedman, Allon N.; Quinney, Sara K.; Inman, Margaret; Mattar, Samer G.; Shihabi, Zak; Moe, Sharon; Department of Medicine, IU School of MedicineBACKGROUND: Obesity-associated elevations in glomerular filtration rate (GFR) are common and may play a role in the development of kidney disease, so identifying the underlying mechanism is important. We therefore studied whether reductions in dietary protein intake, which is known to modulate GFR, explain why GFR decreases after bariatric surgery-induced weight loss. STUDY DESIGN: Cohort study with participants as their own controls. SETTING & PARTICIPANTS: 8 severely obese patients with normal kidney function were recruited from bariatric surgery centers in Indianapolis, IN. All participants were placed on a fixed-protein (50-g/d) diet for 1 week before and after a minimum of a 20-kg weight loss by bariatric surgery and were followed up closely by dieticians for adherence. PREDICTOR: Ad lib versus low-protein diet before versus after bariatric surgery. OUTCOME: Measured GFR, using repeated-measures analysis, was used to estimate the independent effects of diet and surgery. MEASUREMENT: GFR was measured using plasma iohexol clearance. RESULTS: A median of 32.9 (range, 19.5-54.4)kg was lost between the first presurgery visit and first postsurgery visit. Dietetic evaluations and urinary urea excretion confirmed that patients generally adhered to the study diet. GFRs on an ad lib diet were significantly higher before compared to after surgery (GFR medians were 144 (range, 114-178) and 107 (range, 85-147) mL/min, respectively; P=0.01). Although bariatric surgery (-26mL/min; P=0.005) and dietary sodium intake (+7.5mL/min per 100mg of dietary sodium; P=0.001) both influenced GFR, consuming a low-protein diet did not (P=0.7). LIMITATIONS: Small sample size; mostly white women; possible lack of generalizability. CONCLUSIONS: The decrease in GFR observed after bariatric surgery is explained at least in part by the effects of surgery and/or dietary sodium intake, but not by low dietary protein consumption.Item Small Angle Scattering Of Large Protein Units Under Osmotic Stress(2020-05) Palacio, Luis A.; Petrache, Horia I.; Cheng, Ruihua; Joglekar, Yogesh N.; Liu, Jing; Wassall, Stephen R.Large protein molecules are abundant in biological cells but are very difficult to study in physiological conditions due to molecular disorder. For large proteins, most structural information is obtained in crystalline states which can be achieved in certain conditions at very low temperature. X-ray and neutron crystallography methods can then be used for determination of crystalline structures at atomic level. However, in solution at room or physiological temperatures such highly resolved descriptions cannot be obtained except in very few cases. Scattering methods that can be used to study this type of structures at room temperature include small-angle x-ray and neutron scattering. These methods are used here to study two distinct proteins that are both classified as glycoproteins, which are a large class of proteins with diverse biological functions. In this study, two specific plasma glycoproteins were used: Fibrinogen (340 kDa) and Alpha 1-Antitrypsin or A1AT (52 kDa). These proteins have been chosen based on the fact that they have a propensity to form very large molecular aggregates due to their tendency to polymerize. One goal of this project is to show that for such complex structures, a combination of scattering methods that include SAXS, SANS, and DLS can address important structural and interaction questions despite the fact that atomic resolution cannot be obtained as in crystallography. A1AT protein has been shown to have protective roles of lung cells against emphysema, while fibrinogen is a major factor in the blood clotting process. A systematic approach to study these proteins interactions with lipid membranes and other proteins, using contrast-matching small-angle neutron scattering (SANS), small angle x-ray scattering (SAXS) and dynamic light scattering (DLS), is presented here. A series of structural reference points for each protein in solution were determined by performing measurements under osmotic stress controlled by the addition of polyethylene glycol-1,500 MW (PEG 1500) in the samples. Osmotic pressure changes the free energy of the molecular mixture and has consequences on the structure and the interaction of molecular aggregates. In particular, the measured radius of gyration (Rg) for A1AT shows a sharp structural transition when the concentration of PEG 1500 is between 33 wt% and 36 wt%. Similarly, a significant structural change was observed for fibrinogen when the concentration of PEG 1500 was above 40 wt%. This analysis is applied to a study of A1AT interacting with lipid membranes and to a study of fibrinogen polymerization in the presence of the enzyme thrombin, which catalyzes the formation of blood clots. The experimental approach presented here and the applications to specific questions show that an appropriate combination of scattering methods can produce useful information on the behavior and the interactions of large protein systems in physiological conditions despite the lower resolution compared to crystallography.