bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression of wheat eukaryotic initiation factor (eIF) 3 in E. coli
Authors: Wilkerson Chris , Cho Peter , Mu Kathy , Shie Jessica , Tzeng Shinetin , Fontenot Miles , Koythong Tamisa , Lay Erica , Browning Karen S. , Choy Grace 
Published: June 2021

The eukaryotic initiation factor 3 (eIF3) complex is comprised of 13 non‐identical subunits. eIF3 interacts with several other initiation factors and controls the assembly of the 40S ribosomal subunit on mRNA. It would be useful to express the subunits for eIF3 in E. coli and purify a functional complex for further analysis. A Freshman Research Initiative (FRI) group prepared de novo all the subunits for wheat eIF3 in a format that optimized codon usage for E. coli. The goal was to clone all 13 eIF3 subunits into three plasmid cassettes for simultaneous expression and self‐assembly into the functional eIF3 complex. The FRI has students from the spring of the freshman year to the fall of the sophomore years participate in goal oriented research. Over a period of 2 years, FRI students prepared coding regions by overlap extension PCR of oligonucleotides, cloned the PCR products into vectors and showed expression of the individual subunits in E. coli. The 13 subunits were cloned into one of three plasmids, pET22b (subunits i,g,h,f), pRSFDuet‐1 (subunits c,d,l,k,e), and pACYCDuet‐1 (a,b, m). Each of the subunits in the plasmids were shown to express. Additional orientations will be tested for optimized expression of the complex.Grant Funding Source: NSF
Structural studies of an RNA aptamer‐with high affinity for the B. anthracis ribosomal protein S8.
Authors: Davlieva Milya G , Doneske James , Michnicka Malgorzata , Nikonowicz Edward P. , Shamoo Yousif 
Published: June 2021

The bacterial S8 protein is a ribosomal protein which binds to the 16S rRNA in the central domain and plays a critical role in 30S ribosomal subunit assembly. An RNA aptamer with high affinity for B. anthracis S8 protein was developed using the SELEX methodology and crystals of the complex were obtained. To understand how S8/RNA recognition occurs for this apatamer, we are determining the structure of the complex by X‐ray crystallography.Diffraction data for the S8/RNA crystal were collected to 2.6Å resolution at the Advanced Light Source synchrotron (Berkeley, CA). The crystal belonged to the space group P212121 with unit cell parameters a= 55.41 b=59.27 c=92.25Å, α=90, β= 90, γ=90. The data were processed using the program d*TREK with Rmerge=9.2 % and completeness = 99.9 %. A molecular replacement solution for S8/RNA complex was found with the program Phaser for MR from the CCP4 suite using S8 protein (unpub.data) as a search model. The initial solution suggested one monomer per asymmetric unit consistent with a Matthews coefficient of 3.2 (65% solvent). The molecular replacement solution was further confirmed by the initial (2Fo‐Fc) maps generated using Coot that clearly indicated electron density for the RNA aptamer. A model is being constructed for the protein‐RNA complex.This work was supported by NSF (0641792) to Y.S. and The Robert A. Welch Foundation (C‐1584 to Y.S. and C‐1277 to E.P.N.) and NIH(U54 AI057156).
Vitamin D Status in Overweight and Obese Individuals During A Controlled Calorie Restricted Intervention
Authors: Piccolo Brian D , Gertz Erik R , Hall Laura , Cheema Minnu , Woodhouse Leslie , Souza Elaine , Keim Nancy L. , Adams Sean H , Stephensen Charles B , Van Loan Marta D 
Published: June 2021

Vitamin D deficiency is common in obese subjects and status may be improved with dietary interventions. We examined serum 25(OH)D in overweight and obese individuals enrolled in a controlled calorie restricted intervention. Serum samples from overweight and obese (BMI = 28–37) subjects (F=53, M=18), participating in a study examining dairy's role in weight and fat loss, were taken pre‐ and post‐intervention. Participants were randomly assigned to either a high dairy (HD: 3–4 servings; average 333IU D) or low dairy (LD: ≤ 1 serving/d, average 151 IU D) for 12 wks. Energy balance was achieved in wks 1–3 followed by 12wk of 500 kcal/d reduction. All foods were supplied by the metabolic food lab. Outcome variables were body weight (WT), body fat (BF) determined by DXA and serum 25(OH)D measured by RIA. When controlling for total body fat mass, ANOVA showed a significant treatment effect with a greater increase in the %change of serum 25(OH)D in the high dairy group (27.27 ± 37.47 nmol; p = 0.05) compared to the low dairy group(13.16 ± 32.7 nmol; p = .09). The inclusion of 3–4 servings of vitamin D fortified dairy rich foods in a moderate energy restricted diet may contribute to an improved vitamin D status in overweight and obese individuals.Funding: National Dairy Council; USDA, ARS, WHNRC; DairyCouncil of California; CTSC, CCRC University of California (1M01RR19975‐01), and National Center for Medical Research (UL1 RR024146).
Effect of Zinc Supplementation on Diarrhea and Malaria Morbidity in Adults in Rural Kenya
Authors: Scrimgeour Angus G , Lukaski Henry C , Polhemus Mark E , Otieno Lucas , McGraw Susan M , Young Andrew J , Bovill Maria E 
Published: June 2021

Zinc (Zn) supplementation has been associated with reductions in the incidence and severity of diarrheal diseases and malaria in young children, but not in adults. We evaluated the potential role of Zn for treatment of diarrhea and malaria in adults living in western Kenya, a malaria and HIV‐prevalent setting.MethodsA double‐blind, RCT was conducted in 500 adults (18–55 yr of age), supplemented daily with 20 mg elemental Zn (as Zn‐sulphate) or placebo for 3 months. Trace elements and indices of inflammation (ferritin and CRP) were determined before and after the study.ResultsAt baseline, 33% of subjects were Zn‐deficient (<65μg/dL). Plasma Zn increased by 18.5% in subjects receiving Zn (P<0.0001), and did not change in the placebo group (P=0.30). Zn‐supplementation did not modify Ca, Cu, Fe, Mg, Mn, Se, ferritin or CRP values, and did not decrease overall diarrhea or malaria indices. However, compared to placebo, Zn supplementation decreased diarrhea prevalence (−48%, P=0.20), incidence (−50%, P=0.17), and malaria prevalence (−26%, P=0.06) in co‐infected adults (malaria and HIV‐positive).ConclusionsIn Kenya, Zn decreased diarrhea and malaria morbidity in co‐infected adults, but not in malaria‐only, HIV‐only, or “healthy” subjects. The observation is biologically plausible, has potential for public health impact, and should be explored in future studies.Study funded by the U.S. Army MRMC
Intake of added sugars is not associated with weight measures in children 6 to 18 years: NHANES 2003–2006
Authors: O'Neil Carol E , Nicklas Theresa A , Zanovec Michael , Liu Yan 
Published: June 2021

The association between intakes of added sugars and weight measures in children continues to be under scrutiny because the evidence is inconclusive. This study examined the association between intake of added sugars and five weight measures using a nationally representative sample of children. NHANES, 2003–2006, 24‐hour recall data from children aged 6–18 years (n = 3,136) were used in the analyses. USDA's definition of added sugars and MyPyramid Equivalents Database were used to estimate daily intake. Multiple linear regression and squared partial correlation coefficients were used to estimate the strength of association between weight, body mass index, waist circumference, triceps skinfold, and subscapular skinfold as dependent variables with added sugars as the independent variable. Covariates included age, gender, race‐ethnicity, poverty income ratio, total energy intake (kcals), and physical activity. Mean intake of added sugars was 21 tsp accounting for 16% of total kcals. The percent variance explained in the weight measures ranged from 18%–59%; with none of the variance explained by intakes of added sugars. No significant associations were observed between intakes of added sugars and weight measures. Results are limited to cross‐sectional comparisons and the assessment measures used. Additional longitudinal studies are needed to confirm the findings.Funding: USDA
Undergraduate research and active learning opportunities in biochemistry at UNL
Authors: Matejka Stephanie Lynn , Jimenez Ignacio , Bailey Cheryl 
Published: June 2021

At large universities and some smaller institutions, not all undergraduate biochemistry majors are involved in a research project. This is unfortunate, since the scientific method and research process provides an excellent learning opportunity. Three models are currently being implemented to provide alternate opportunities to undergraduate life science majors at the University of Nebraska, Department of Biochemistry. These include the Genomics Education Partnership and the Joint Genomic Institute Annotation Collaborative Tool, both undergraduate research classes. In addition, short bioinformatics modules have been implemented in existing laboratory and large traditional lecture classes, to facilitate a mini research experience for a large number of students. We report methods, implementation strategies, student assessment results, and confidence in project findings.Supported by HHMI and NSF
Subdivision of the echinoderm nervous system as defined by antibody probes
Authors: Diaz‐Balzac Carlos A. , Lázaro‐Peña María I. , García‐Arrarás José E. 
Published: June 2021

Echinoderms are an enigmatic group of deuterostomes that present some unusual properties in many cells and organs, including those of the nervous system. Nonetheless, studies of their nervous system have lagged behind when compared to those in other invertebrates groups due to the lack of nervous system markers. We have now used 8 commercially available antibodies and 3 antibodies produced by our group, which specifically label nervous system components in the echinoderms, to study the neuroanatomy of the sea cucumber Holothuria glaberrima. Our studies have produced three important findings. First, each antibody labels specific regions of the radial nerve, suggesting that the radial nerve cord is subdivided into distinct regions with specialized tracts or networks. Second, the level of complexity of the enteric nervous system is higher than described in the past, since our antibodies label many more cells and nerves than previously documented. Third, labeling of the different muscular tissues showed the presence of a large number of nerve fibers that appear to be innervating the muscle fibers, thus identifying the possible motor pathway that innervates the echinoderm muscles system. By combining our observations, we have begun to assemble a map of the neural circuitry of the holothurians. Our findings suggest that the echinoderm nervous system is more similar to that of other deuterostomes than previously thought.Grant Funding Source: This work was supported by NSF (IBN‐0110692) and NIH‐MBRS (S06GM08102). CADB was funded by the UPR‐RP MARC Program (5T34GM007821) and MILP was funded by the UPR‐RP RISE Program (2R25GM061151). We also acknowledge partial support from NIH‐RCMI (RRO‐3641‐01) and the University of Puerto Rico.
Investigating the structural flexibility of intrinsically disordered proteins
Authors: Grese Laura Nicole , Stanley Christopher , Rowe Erica , O'Neill Hugh , Berthelier Valerie 
Published: June 2021

Intrinsically disordered proteins (IDPs) either possess an unstructured domain or are fully disordered until recognizing a target binding partner, upon which a coupled folding‐binding event occurs. Exactly how this mechanism is linked to protein signaling and recognition is still poorly understood, primarily because the structural flexibility of IDPs limits the number of suitable characterization techniques. We are using circular dichroism (CD) spectroscopy and small‐angle neutron scattering (SANS) to investigate IDP regions of the transcription co‐activator: CREB binding protein (CBP), and its interactions with the binding partner: activator for thyroid hormone and retinoid receptors (ACTR). CBP is essential to several biological processes such as embryonic development, growth control, and homeostasis, and its dysfunction is implicated in Huntington's disease and some cancers. CD spectroscopy allows us to study changes in protein secondary structure. With SANS we are able to directly probe structural changes on the nanometer length‐scale and in solution, which is essential for capturing the flexibility of IDP structures. SANS experiments have been performed using the BioSANS instrument at HFIR, ORNL to characterize the CBP‐ACTR complex. Ultimately, this research should provide new possibilities for the study of disordered protein regions and yield unique insights into the mechanism of IDP function.This research is supported by a Laboratory Directed Research and Development (LDRD) grant from Oak Ridge National Laboratory, managed by UT‐Battelle for the Department of Energy.
Mechanical Ventilation and Sepsis Impair Protein Metabolism in the Diaphragm of Neonatal Pigs
Authors: Srivastava Neeraj , Gazzaneo Maria C , Torrazza Roberto Murgas , Suryawan Agus , Nguyen Hanh V , El‐Kadi Samer W , Fiorotto Marta L , Davis Teresa A , Orellana Renan A 
Published: June 2021

Mechanical ventilation (MV) impairs diaphragmatic function and diminishes the ability to wean from ventilatory support in adult humans. In normal neonatal pigs, animals that are highly anabolic, endotoxin (LPS) infusion induces sepsis, reduces peripheral skeletal muscle protein synthesis rates, but increases protein synthesis in the diaphragm. To determine whether MV and sepsis lead to protein catabolism in the diaphragm, neonatal pigs (n=5–6/group) were subjected to MV and infused with LPS (0 and 10 μg•kg−1•hr−1), as well as dextrose and a balanced amino acid mixture. After 9 hours, fractional protein synthesis rates and translation and degradation signals were determined in diaphragm muscle. Compared to controls, MV alone decreased protein synthesis in the diaphragm by 16%, and this effect was not further aggravated by the addition of LPS. MV alone and in the presence of LPS decreased eIF4G·eIF4E association and eIF4G phosphorylation in similar proportion when compared to controls. MV alone increased MURF‐1 abundance by 240% and by 340% in the presence of LPS. These findings suggest that MV induces diaphragmatic wasting due to both decreased protein synthesis and increased proteolysis, and the presence of sepsis enhances the MV‐associated induction of proteosomal degradation. NIH AR51563, NIH AR44474, and USDA 6250‐51000‐040Grant Funding Source: NIH AR51563, NIH AR44474, and USDA 6250‐51000‐040
eMentoring for Diversity in the Biosciences
Authors: Porush David , Elekonich Michelle 
Published: June 2021

MentorNet (www.mentornet.net) is a 12‐yr‐old nonprofit organization devoted to helping women and minorities in science and engineering at 100 campuses achieve their career goals. Our vision is a level playing field for all talented students and a diversified global workforce in these most crucial fields. We provide a Web‐based program, refined by years of research and study (funded by NSF and others), that matches proteges with mentors and guides their one‐on‐one relationship for an extended period. We track data on our participants very closely and have recently seen an upsurge in students in the biosciences.In this presentation, we will describe how the program works in exemplary fashion at one institution ‐ in Las Vegas; report our findings about the bioscience ementoring to date, discuss their implications, and solicit feedback about how we can further refine and adapt our program to serve the needs of bioscience students and professions.
Association of Bone Mineral Density with Lean Mass and Fat Mass
Authors: Hooshmand Shirin , Chai Sheau C. , Saadat Raz L. , Arjmandi Bahram H. 
Published: June 2021

Obese individuals hold an increased risk of chronic diseases such as CVD. We reported that a relationship exists between BMI and indices of CVD risk in postmenopausal women. To investigate the relationship between BMI and chronic diseases, we measured CRP level, a marker of inflammation, in 132 postmenopausal women. Participants were divided into three groups based on their BMI values: 1) normal (18.5–24.9); 2) overweight (25–29.9); and 3) obese (>30). BMI was positively correlated with CRP. In addition, overweight and obese individuals had higher serum levels of CRP compared to individuals with normal BMI. In contrast to existing relationship of higher BMI and higher incidence of chronic diseases, studies have shown that osteoporosis is the only chronic disease that has negative correlation with BMI. To investigate this relation, we evaluated the correlation between BMI and BMD in this population. BMI was positively correlated with BMD which means a negative correlation with osteoporosis; however, when we examined the correlation between BMD and components of body composition including fat mass and lean mass; BMD was highly correlated with lean mass but not with fat mass. Although these data supports the notion that individuals with higher BMI have lower risk of osteoporosis, break down of body composition clearly demonstrate that the credit for this correlation should be given to lean mass and not fat mass.Grant Funding Source: USDA
Effect of maternal methyl diet on epigenetic changes and mammary carcinogenesis in offspring
Authors: Bae Sajin , Cho Kyongshin , Mabasa Lawrence , Walters Mark William , Park Chung S 
Published: June 2021

Maternal nutrition influences the offspring's growth and metabolism while also affecting the susceptibility to diet‐related diseases such as cancer in adulthood. Lipotropes (choline, methionine, folic acid, and vitamin B12) play a role in DNA methylation, an epigenetic mechanism controlling the expression of genes involved in cell growth and metabolism. We studied the effects of a maternal lipotrope‐additive diet (LAD) on epigenetic changes and mammary cancer risk in female rat offspring. Dams were fed either a control diet (CD) or LAD during gestation and lactation. Their female offspring were weaned onto the CD and used for: 1) analysis of DNA methylation and gene expression in mammary tissues, and 2) a mammary carcinogenesis experiment using nitrosomethylurea. We observed a significant increase of 22% in global DNA methylation and a tendency toward decreased mRNA expression of the DNA methyltransferase1 gene in the LAD group. The offspring of the LAD‐fed dams also showed an increased latency period of 17%, along with decreased tumor incidence (27%), tumor numbers (57%), and tumor volume (33%). Our study suggests in utero and early postnatal exposure to LAD increases global DNA methylation in mammary glands, while also reducing mammary tumorigenesis. Future studies will be required to establish the detailed mechanisms responsible. Supported in part by a US Department of Defense grant.Grant Funding Source : U.S. Department of Defense
Low‐dose endotoxemia as a human model of inflammation
Authors: Flock Mike R , Skulas-Ray Ann C , Prabhu K. Sandeep , Fleming Jennifer A , Kris-Etherton Penny M 
Published: June 2021

Inflammation is important in the pathology of many diseases. We examined the safety and efficacy of a low dose in vivo endotoxin challenge (0.6 ng/kg intravenous lipopolysaccharide) for inducing inflammation in humans. Healthy men (n=6) were randomized to a 2‐period, saline placebo‐controlled, crossover design. Blood samples were taken at 0 (pre‐injection), 1, 2, 3, 4, 6, 12, 24, 48, 72, and 120 hours post‐injection. All meals were standardized and controlled for the first 12 hours. A mixed linear model demonstrated a treatment by time interaction for TNF‐α, IL‐6, and hs‐CRP (p < 0.0001 for all) and post hoc analyses, after adjustment for multiple comparisons, indicated several time specific differences (p < 0.05). TNF‐α increased versus placebo at 1, 2, 3, and 4 hours post‐injection (19.8 vs 0.9, 27.9 vs 0.9, 13.4 vs 0.9, and 7.1 vs 0.9 pg/mL, respectively). Similarly, IL‐6 increased at 2, 3, and 4 hours versus placebo (21.7 vs 0.9, 25.1 vs 2.0, and 16.4 vs 2.7 pg/mL, respectively). Serum hs‐CRP increased at 12, 24, 48, and 72 hours versus placebo (9.3 vs 0.7, 16.7 vs 0.7, 8.3 vs 0.8, and 4.6 vs 1.2 mg/dL, respectively). Our findings demonstrate the safety and efficacy of a low dose endotoxin challenge to induce inflammation as evident by increases in TNF‐α, IL‐6, and hs‐CRP. Thus, the endotoxemia model can be used to characterize metabolic changes during inflammation and identify interventions to ameliorate inflammation.Grant Funding Source: USDA
Suppression of Skeletal Muscle Inflammation by Muscle Stem Cells
Authors: Proto Jonathan , Lu Aiping , Imbrogno Kayla , Tang Ying , Robbins Paul , Wang Bing , Huard Johnny 
Published: June 2021

Recently, we have reported that intramuscular (i.m.) injection of muscle‐derived stem cells (MDSCs) heterozygous for the NF‐kB subunit p65 (p65+/−) reduces host inflammation and fiber necrosis following muscle injury more so than wild type (WT) MDSC injection. In vitro inflammation assays demonstrated that MDSCs secrete factors that modulate cytokine expression in LPS‐activated macrophages, and genetic reduction of p65 enhances this effect. We have also found that the anti‐inflammatory protein hepatocyte growth factor is more highly expressed in p65+/−cells. In order to investigate the impact of these observations in vivo, we performed i.m. injections of WT or p65+/−MDSCs into WT mouse muscle 24 hrs post injury. We followed cell fate at 1, 3, and 7 days post‐injection. At 24 hrs we observed a higher number of engrafting WT cells, but a higher percentage of proliferating (Ki67+) p65+/− MDSCs. By 3, and 7 days, the number of p65+/−MDSCs exceeded that of WT cells. These preliminary results suggest a novel role for NF‐kB in stem cells, one in which the anti‐inflammatory properties of MDSCs are regulated by NF‐kB via growth factor expression and cell proliferation kinetics.Grant Funding Source: Department of Defense
Recombinant erythropoietin administration reduces exercise‐induced deline in regional cerebral oxygenation at 4500 m
Authors: Muza Stephen Raymond , Jones Juli E. , Fulco Charles S. , Beidleman Beth A. , Staab Janet E. 
Published: June 2021

At high altitude, exercise‐induced arterial desaturation decreases regional cerebral oxygenation (rO2Hb). Erythropoietin (EPO) potentiates endothelium‐mediated dilation of isolated, perfused rat middle cerebral arteries. To determine if EPO administration in humans mitigated the decreased cerebral rO2Hb during exercise within the first 3 h at 4500 m eight healthy male lowlanders received a subcutaneous injection of either EPO (600 IU/Kg) or a placebo (PLA) (0.9% NaCl) ~12 hr prior to ascent in a hypobaric chamber in a double‐blind, cross‐over study. We measured frontal lobe rO2 Hb by NIRS, arterial saturation (SaO2) by pulse oximetry, and PetO2 and PetCO2 by metabolic cart during rest and 50 W cycling. At 4500 m, serum EPO levels were (mean ± SD) 6 ± 2 and 720 ± 273 mU/ml for PLA and EPO trials, respectively. From rest‐to‐ exercise SaO2 decreased similarly in both trials (PLA: −6 ± 4 and EPO: −8 ± 4%), but rSO2 declined less in EPO (PLA: −2.12 ± 1.93 and EPO: −1.47 ± 2.40 μM, p=0.027), while rest and exercise PetO2 and PetCO2 were similar for both trials.Conclusionsince PO2 and PCO2 were constant and not likely changing cerebral vasomotor activity, the smaller exercise‐induced decline in rO2Hb following EPO administration supports the hypothesis that increasing circulating EPO potentiates dilation of cerebral blood vessels at high altitude. Funding: USAMRMC. Authors’ views; not official U.S. Army or DoD policy.