bluuebunny/crossref_metadata_2025_split huggingface dataset:
Basicranial and temporal bone morphology of a sample of early human fossils
Authors: Smith Heather F 
Published: June 2021

Extensive debate has centered around the location and timing of the initial speciation events of humans and the subsequent microevolution and migratory routes that lead to their dispersal around the world. Several early human fossils preserve portions of the temporal bone and other aspects of the basicranium, the morphology of which has been found to reflect genetic distances and population history reliably in humans. Thus, the analysis of these regions in early fossil Homo sapiens can inform our interpretations of their relationships to each other and to specific modern human populations.Eighteen ectocranial landmarks from the temporal bone and basicranium were digitized on 14 early Anatomically Modern Human fossils and casts and 9 Neandertals. A modern human sample of 13 populations was also measured for comparative purposes. Compared to the modern sample, the early humans were more variable in morphology, suggesting that the fossil sample reflects a greater genetic diversity than humans today, who have undergone a genetic bottleneck. In a multidimensional scaling plot, the fossil specimens also do not cluster together morphologically. The Neandertal specimens fell outside the cluster of early and modern Homo sapiens, and did not share closer relationships with the human specimens from the same continent than from elsewhere.This study was supported by NSF BCS‐0622570 and the Wenner‐Gren Foundation.Grant Funding Source: n/a
Computational approach to investigate the catalytic chemical reaction mechanism of glyoxysomal Malate Dehydrogenase
Authors: Guterres Hugo , Bell Ellis 
Published: June 2021

Geometry optimization calculation was used to find the minimum total energy and structure of the transition state during conversion of malate to oxaloacetate. During the reaction proton abstraction to H220 in the active site, and hydride transfer to NAD occur. Our primary goal was to develop a computational approach to examine the effects of active site and second sphere mutations in the activity of gMDH. Gaussian 03W was used to build the structure of the compounds, arrange their symmetry, and run the geometry optimization calculations. A truncated model including Histidine 220, malate and NAD was used to analyze the effect of the catalytic base. The result shows an imaginary frequency which indicates the presence of the transition state. The geometry structure of the transition state confirms the hydride transfer but the proton transfer is disoriented. This suggests that amino acids around the active site play important roles in facilitating the hydride and proton transfer. We have finished the transition state energy for the native gMDH and are working to find the total energy for transition state of mutants gMDH to facilitate the study of second sphere mutations.This work is supported by NSF Grant MCB 0448905 to EB.
Structure‐function studies of the regulatory bicarbonate binding in H. influenzae carbonic anhydrase: a functional reversion of allostery using multiple site mutations
Authors: Hoffmann Katherine M. , Rowlett Roger S. 
Published: June 2021

Type II β‐carbonic anhydrases are metalloenzymes that catalyze the conversion of carbon dioxide to bicarbonate using a characteristic closed four‐side chain coordination sphere for the active site Zn ion. Non‐catalytic bicarbonate binding sites have been discovered in some type II β‐CAs 8 Å away from the active site. A network of seven hydrogen bonds holds the inhibitory bicarbonate in place, and kinetic studies confirm cooperative inhibition by bicarbonate at sufficient levels. A comparison of bicarbonate‐bound HICA with type I β‐CAs lacking the non‐catalytic bicarbonate binding site reveals a number of principal interactions that might be responsible for the allosteric regulation of HICA. W39 provides a direct, stabilizing hydrogen bond to the inhibitory bicarbonate, a one‐residue shift of proline 48 changes an influential backbone orientation of the 44–48 loop, and a G41 residue makes additional room in the allosteric binding site compared to a conserved Ala in non‐allosteric β‐CAs. Individual site mutants of W39 have revealed predictable decreases in cooperativity consistent with the loss of a stabilizing hydrogen bond to the bicarbonate. Structure function studies of compound site mutants, however, abrogate the binding of inhibitory bicarbonate in the crystalline state even at high concentrations.This work is supported by NSF grant CHE‐0819686 and MCB‐0741396.
Tumor necrosis factor is necessary, but not sufficient, for castration induced prostate regression
Authors: Davis Jennifer Sarah , Nastiuk Kent L , Krolewski John J 
Published: June 2021

Tumor necrosis factor (TNF) is a pro‐inflammatory cytokine that plays a vital role in immune responses. TNF is also a potent apoptotic stimulus in vitro. However, few reports have demonstrated a physiologic role for TNF induced apoptosis in vivo. Employing high field MRI (magnetic resonance imaging) to measure mouse prostate volume, we demonstrate that the extent of castration induced prostate regression is significantly reduced in mice null for either the TNF or TNFR1 genes. Wild type (WT) mice receiving soluble TNFR2 prior to castration exhibit a nearly identical reduction of prostate regression. Additionally, membrane‐bound TNF protein and TNF mRNA levels increase in the ventral lobe of rat prostate following castration. When injected into the peritoneum of TNF−/− mice at the time of castration, soluble TNF is able to restore normal levels of prostate regression. However, WT mice receiving soluble TNF in the absence of castration do not exhibit prostate regression, indicating that TNF alone is not sufficient, but must act in the context of additional castration induced signals. These findings support a physiologic role for TNF in prostate regression following androgen withdrawal. Understanding this role may lead to novel therapies for prostate cancer.J.S. Davis is supported by DOD Pre‐doctoral Training Grant #PC073208.
When Reduction Leads to Expansion: A Simple Native PAGE Gel Enzyme Assay Experiment as a Starting Point for Other Structure‐Function Investigations
Authors: Hazzard James Taylor , Pasalic Dario , Edwards Sarah , Friedrich Kenneth 
Published: June 2021

A simple assay on native PAGE gel for two E. coli enzymes, purified by undergraduates in a biochemistry laboratory, provides an excellent springboard for more sophisticated investigations on protein structure. They perform colorimetric assays on b‐galactosidase (b‐gal) using ortho‐nitrophenyl‐b‐galactosidase in a buffer containing b‐mercaptoethanol (BME) and on alkaline phosphatase (AP) using FAST RED TR/Naphthol AS‐MX reagent. Half of the class assays for b‐gal first and AP second; the other half of the class reverses the order. Results differ because the former group reduces two disulfide bonds which are essential for AP activity, only observing activity for b‐gal, while the latter sees activity for both enzymes.This simple PAGE experiment leads the students to the question: Is loss of activity due to protein denaturation? Answering this question raises more sophisticated investigations, including BME dialysis, intrinsic fluorescence spectroscopy of AP tryptophan residues, ANS fluorescence spectroscopy, and circular dichroism. These can be offered as special projects to laboratory groups who report their findings to the entire class, providing a holistic approach to investigating the relationship between loss of activity and protein denaturation. Initial data and results from our laboratory course will be presented. This work supported in part by a grant from NSF (DUE 0837398 to JTH).
Investigation of ω‐hydroxylation of tocopherols by CYP4F2 and by rat liver slices
Authors: Farley Sherry M. , Leonard Scott W. , Mustacich Debbie J. , Labut Edwin M. , Traber Maret G. 
Published: June 2021

The ω‐hydroxylation of 2S‐α‐tocopherol (2S, 4′RS, 8′RS α‐tocopherol) and deuterated (d2)‐ γ‐tocopherol (d2‐γ‐T), relative to d6‐RRR‐α‐tocopherol (d6‐α‐T) was studied. Rat liver slices were incubated with d6‐α‐T, d2‐γ‐T, or 2S‐α‐T and their metabolism to 13′‐OH was measured by LC‐MS/MS. Although uptake of each form by liver slices was comparable, 2S‐α‐T and d2‐γ‐T were more readily metabolized to 13′‐OH (39 ± 15 pmol/g and 42 ± 5, respectively, p<0.01), than was d6‐α‐T (17 ±2). When these tocopherols were incubated with microsomes expressing human recombinant CYP4F2, there was greater production (p<0.001) of d2‐γ‐T‐13′‐OH (0.36 ± 0.05 pmol 13′‐OH/pmol CYP4F2) compared to d6‐α‐T‐13′‐OH (0.08 ± 0.02); however, there was no preference for 2S‐α‐T over d6‐α‐T. These data indicate that CYP4F2‐mediated ω‐hydroxylation does not differentiate between side chain stereoisomers and that structural differences in the chroman ring are more influential. This study also suggests that other factors present in liver slices, such as selectivity of α‐T transfer protein, are responsible in regulating metabolism of natural versus synthetic α‐T.Grant Funding Source: NIH, ODS, Archer Daniels Midland, and USDA
Oxidative stress status of high prolific sows during pregnancy and lactation
Authors: Berchieri‐Ronchi Carolina Bragiola , Zhao Yan , Correa Camila Renata , Ferreira Ana Lucia dos Anjos , Yeum Kyung‐Jin , Kim Sung Woo 
Published: June 2021

Sows are highly prolific with insufficient nutrient intake during late pregnancy and lactation periods causing a severe catabolic condition. Antioxidant status and oxidative DNA damage were determined in blood samples collected during the course of gestation and lactation in multiparous sows (parity 3 and 4). Blood samples were collected from sows (n=5) at d 30, 60, 90 and 110 of pregnancy, d 3, 10, and 18 of lactation, and d 5 postweaning. Lymphocytes were isolated from the fresh blood and cryopreserved in each time point. Lymphocyte DNA damage was analyzed by alkaline single cell gel electrophoresis (comet assay) to determine the single and double strand brakes, plasma total antioxidant performance (TAP) using fluorometry and endogenous antioxidant by a HPLC system with UV detection. The comet assay showed lower (p<0.01) endogenous DNA damage at d 30 of pregnancy (21%) as compared with those of the other time points (38 to 47%). On the other hand, TAP was lower (p<0.05) during d 30 to 90 of pregnancy as compared with that of d 10 of lactation. Plasma α‐tocopherol concentration was lower (p<0.05) at d 110 of pregnancy as compared with d 30 of pregnancy. The current study indicates that there is a systemic oxidative stress during the pregnancy and antioxidant nutrients can be reduced in the mother pig during the end of the pregnancy and that oxidative DNA damage can be elevated during the pregnancy, which can be sustained until the end of lactation period.[Supported by CAPES 0635‐09, NCPC 09M69MF1, USDA 1950‐51000‐065‐08S]
INGESTION OF DEOXYNIVALENOL REDUCES DIET‐INDUCED OBESITY IN THE MOUSE
Authors: Flannery Brenna , Amuzie Chidozie , Ulrich Allison , Romsos Dale , Pestka James 
Published: June 2021

Deoxynivalenol (DON) is a Fusarium mycotoxin that has been long known to suppress weight gain of monogastric animals. We tested the hypothesis that DON consumption will reduce weight and adiposity in diet‐induced obese (DIO) mice. Female B6C3F1 mice were fed 60% kcal high fat diet (HFD) for 8 wk to induce obesity. They were then regrouped and fed HFD containing either 0, 2, 5,10 or ppm DON for an additional 8 wk. Animals fed HFD containing 5 ppm and 10 ppm DON exhibited reductions in body weights of 16% and 23%, respectively, while periuterine fat pad weights of the DON 10 ppm HFD group were reduced by 40%. Insulin like growth factor acid labile subunit (IGFALS) was reduced by 20 and 42% in the 5 and 10 ppm DON‐fed mice, respectively. In subsequent experiments, we determined that DIO mice fed DON exhibited reduced food intake and that these animals regained weight upon removal of DON from the diet. Taken together, our data indicate that DON attenuated weight and adiposity in DIO mice in a reversible manner and that this corresponded to both decreased food intake and deregulation of the growth hormone axis.This material is based upon work supported by the U.S. Department of Agriculture, under Agreement No. 59‐0790‐4‐119 and by PHS Grant ES03358
Greater fruit and vegetable intake is associated with increased bone mass in older Puerto Ricans
Authors: Bhupathiraju Shilpa N , Lichtenstein Alice H , Dawson‐Hughes Bess , Tucker Katherine L 
Published: June 2021

Puerto Ricans, a group with documented health disparities, are the largest Hispanic sub‐group in Massachusetts. Yet, little is known about diet and bone health in this high risk population. We determined the association of fruit and vegetable (FV) intake (servings/day) with bone mineral density (BMD) among 613 Puerto Rican adults, aged 45–75 years. BMD at the lumbar spine (L2‐L4) and proximal femur were measured using dual energy X‐ray absorptiometry. FV intake was assessed using a food frequency questionnaire. Multiple linear regression showed significant positive associations of FV intake with BMD of the femoral neck (β=0.011, P=0.004), trochanter (β=0.010, P=0.009), and lumbar spine (β=0.015, P=0.01). Analyses were adjusted for age, sex, BMI, smoking, drinking status, season of BMD measurement, energy intake, calcium and vitamin D intake, servings of meat and fish, current estrogen use, physical activity, diabetes, blood pressure, and household income. The observed positive association between FV intake and BMD supports findings in other populations adding support to the notion that FV are important to bone health. Compounds and nutrients in FV can potentially neutralize acid production without depending on the buffering effects of bone minerals. Further, their antioxidant and anti‐inflammatory properties may also play an important role.Grant Funding Source: NIH P01 AG023394 and USDA ARS contract 58‐1950‐7‐707
Improved nutrient intake and diet quality with 100% fruit juice consumption in children: NHANES 2003–2006
Authors: O'Neil Carol E , Fulgoni Victor L , Zanovec Michael , Nicklas Theresa A 
Published: June 2021

Fruit juice (FJ) consumption has recently been viewed as a sweetened beverage with little regard to its nutrient contribution to the diet. NHANES, 2003–2006, data were used to examine the association of 100% FJ consumption with nutrient intake and diet quality in children ages 2–5 y (n=1,665) and 6–12 y (n=2,446). Mean usual intakes, standard errors, and regression analyses (juice independent variable; vitamins/minerals and Healthy Eating Index‐2005 [HEI] were dependent variables) were determined using sample weights. Mean daily intake of 100% FJ was 5.76 ± 0.17oz (2–5 y) and 2.59 ± 0.37oz (6–12 y); 29% (2–5 y) and 43% (6–12 y) did not consume 100% FJ on the day of the recall. In children 2–5 y, magnesium (p=0.004), potassium (p<0.001), vitamin C (p<0.0001), and HEI (p<0.0001) (specifically whole fruit and whole grain) increased linearly and added sugars decreased linearly (p<0.0001) with higher levels of FJ consumption; in children 6–12y, magnesium (p<0.0001), calcium (p<0.0001), potassium (p<0.0001), dietary fiber (p<0.0001), vitamin C (p<0.0001) and HEI (p<0.0001) increased linearly and added sugars decreased linearly (p<0.0001) with higher intakes of FJ. On average, 100% FJ consumption did not exceed the American Academy of Pediatrics’ recommendation for children and was associated with increased consumption of key nutrients and better diet quality in children.Funding: USDA and Juice Products Association.
Construction and Validation of a DNA Combinatorial Library of 2E8 Combinations Designed for Solving Satisfiability Problems in Biomolecular Computing
Authors: Waters Colin , Bellomo Lea , Pogozelski Wendy 
Published: June 2021

DNA is being investigated as a tool for biomolecular computing. Some of these biomolecular computing methods require the creation of combinatorial libraries. We have developed a method for creating combinatorial libraries of nearly any size. We demonstrate creation of library of 28 or 256 distinct DNA strands of 128bp, made by linking eight 16‐mer oligomers together. Each 16‐base oligomer has one of two possible sequences. One sequence is designated as “true” and the other as “false”. In computing terms, each library strand has eight variables with values of true or false (corresponding to 1 or 0 in a binary system). Every possible combination of the eight linked true or false strands (variables) yields 28 or 256 distinct library strands. The library was constructed by a series of primer extension and ligation steps. We used a variety of PCR‐based methods and gel electrophoresis to demonstrate that the sequences in the library have the expected length and composition.This work was funded by NSF, the Camille and Henry Dreyfus Foundation, the Geneseo Student Association and the Geneseo Association.
Enhancing iron bioavailability of maize using a Caco2 cell/quantitative trait loci model
Authors: Lung'aho Mercy , Hoekenga Owen , Tako Elad , Glahn Raymond 
Published: June 2021

Iron deficiency is an important public health problem that is estimated to affect over one‐half the world population. Improving the nutritional quality of staple food crops such as maize, by developing varieties with high bioavailable iron represents a sustainable and cost effective approach to alleviating iron malnutrition. The aim of our study was to use a Caco‐2 cell/quantitative trait loci (QTL) model to discover the genes that influence maize grain iron concentration and amount of bioavailable iron. After several breeding cycles guided by measurements of Fe bioavailability with the Caco‐2 cell model, we identified two maize lines with identical grain iron concentration (20 ppm), but one line contained double the amount of bioavailable iron (p < 0.001). Three QTL were found to influence the bioavailability of iron in the two maize lines. Blood hemoglobin data from a poultry model confirmed the results of the Caco‐2 cell model. Some of the lines screened using the Caco‐2 cell/QTL model have been grown at multiple locations and data show a genotype × environment (G×E) interaction. We conclude that conventional breeding can significantly improve iron bioavailability in maize grain and that the G×E effect plays a major role in Fe bioavailability. Human feeding trials should be conducted to determine the efficacyof consuming the high bioavailability maize.Source of research support: United States Department of Agriculture, Cornell University
Iron status and serine hydroxymethyltransferase (SHMT) activity and abundance in pre‐ and postmenopausal women
Authors: Reddy Manju B. , Zhou Ying , Chen Dan , Alekel D. Lee , Hansen Christine M. 
Published: June 2021

To explore relationships between iron status and lymphocyte SHMT activity (ACT) and abundance (ABN), 118 postmenopausal women (54.3 y) enrolled in SIRBL (Soy Isoflavones for Reducing Bone Loss) study and 105 young women (21.2 y) were studied. Serum ferritin, folate, and vitamin B‐12, plasma total homocysteine (tHcy) and pyridoxal phosphate (PLP), lymphocyte SHMT ACT and ABN were determined. Subjects in the first (4.8 ng/mL; 93% premenopausal) and fifth (92.6 ng/mL; 98% postmenopausal) quintiles of serum ferritin were compared. The fifth quintile had higher median BMI (25 vs 22 kg/m2; p<0.02), plasma PLP (p<0.0001), total homocysteine (p<0.05), and SHMT ABN (p<0.0001), but significantly lower SHMT ACT (p<0.02) than first quintile.

Ferritin quintile
Folate ng/mL
B‐12 pg/mL
PLP nmol/L
tHcy nmol/L
SHMT ACT cpm/ug protein
SHMT ABN relative density

First (n)
14.2 (45)
597 (45)
61.7 (45)
6.4 (45)
43.6 (27)
1.1 (21)

Fifth (n)
13.1 (45)
521 (45)
93.9 (45)
6.6 (45)
13.0 (14)
12.3 (31)

Increased iron status may enhance SHMT expression, favoring thymidine synthesis over Hcy remethylation, thus warranting further investigation.Funded by USDA Special Grant, NWRC, Iowa State University.
Effective Bioactive Treatment for Ewing Sarcoma
Authors: Randolph Priscilla , Ibrahim Salam A. , Holmes‐McNary Minnie 
Published: June 2021

Ewing sarcoma (EWS) is a rare form of bone cancer that is found primarily in Caucasian children and young adults. Ewing sarcoma is characterized as a highly malignant tumor that is found in both bone and soft tissues. However, when EWS is detected early the overall survival rate is 60%. Current treatment has been limited to chemotherapy, radiation and surgery or a combination of these treatment modalities.Previous research by our lab and others demonstrate the beneficial cancer prevention properties of trans‐Resveratrol (RES) a bioactive nutrient. These former studies are the impetus for our present studies. Therefore, we hypothesize that RES will be an effective combinatorial treatment for EWS.Our studies with human‐derived EWS cells show significant apoptotic cell death and differential gene expression during exposure with either TNF‐alpha, RES, irradiation (IRR) alone or in combination. Our studies clearly demonstrate an effective alternative treatment modality for EWS. Supported in part by NSF‐AGEP (PR), United States Department of Agriculture (USDA‐SI, PR), Faculty Initiated Grant (MHM), College of Arts and Sciences.Grant Funding Source: NCAT, USDA
Effects on mood and satiety of 4 days of partial energy deficit (60%) or energy excess (150%)
Authors: McGraw Susan M. , DeGroot David W , Ely Matthew R , Karl James P , Young Andrew J , Lieberman Harris R 
Published: June 2021

We previously demonstrated that up to 48‐h of near total calorie deprivation does not affect mood or cognitive performance but does alter satiety. In this study we examined effects of partial energy deficiency (ED) and overfeeding (OF) on mood and satiety. Volunteers (10M, 4F, age 22 ± 2 yr, BMI 25.0 ± 3.8) underwent 4 days of EB, 4 days of ED (60% of energy balance (EB)), and 4 days of OF (150% of EB) in the laboratory. Macronutrient composition, daily activities and total energy expenditure were held constant. ED reduced self‐reported vigor compared to EB (p=0.02) as assessed by the Profile of Mood (POMS) state but OF had no effect on mood (Table). Both ED and OF affected perception of satiety as assessed with the SLIM questionnaire, with OF increasing satiety and ED decreasing it (p<0.001). This study indicates substantial, sustained underfeeding adversely affects mood but overfeeding does not, and that OF and ED both alter perception of hunger.
Mean POMS scores.

T
D
A
V
F
C
TOT

EB
2.98 ±3.1
1.24 ±2.2
1.86 ±2.3
16.7 ±8.6
2.88 ±4.7
3.24 ±2.2
−4.52 ±17.0

ED
3.67 ±2.3
1.57 ±2.1
2.02 ±2.8
12.8 ±9.0*
2.95 ±3.4
3.95 ±2.4
1.38 ±14.8

OF
2.60 ±2.0
0.67 ±1.1
0.81 ±1.6
13.76 ±9.5
3.43 ±4.1
3.74 ±2.4
−2.52 ±14.3

T, tension‐anxiety; D, depression‐dejection; A, anger‐hostility; V, vigor; F, fatigue; C, confusion;
TOT, Total mood score.
= Significantly different P=0.02 than EB

Funded by MRMC