bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing Diet Quality Based on a Dietary Screening Tool and the DASH Diet Index in Obese, Older Women
Authors: Beebe Nowen Elizabeth , Manganti Steven , Katkowski Lynn , Benson Marisa , Delmonico Matthew J , Lofgren Ingrid E 
Published: June 2021

Diet quality impacts chronic disease risk and can be measured by the Dietary Screening Tool (DST) and the Dietary Approaches to Stop Hypertension (DASH) Index, however little research has compared these two methods. A 16‐week randomized clinical trial examined the additive impact of Tai Chi (TC) in obese, older women. Subjects completed a food frequency questionnaire (FFQ) and a DST. The FFQ output was converted to the DASH diet score. The DST provided a summary score. DST and DASH Diet scores were compared at baseline and post intervention using the following risk categories: <25th percentile as at risk, ≥25th
–<75th percentile as possible risk, and ≥75th percentile as not at risk. “At risk” and “possible risk” categories were combined and compared to “not at risk.” Thirteen women received modified DASH Diet Education (DE) and 14 women received TC in addition (TC+DE). Mean ages were 62.6 ± 5.9 y for DE and 60.4 ± 6.0 y for TC+DE. The number of participants in each risk category from the two questionnaires at baseline were compared and significant differences were seen as determined by fisher's exact test (p =.01). Though not significant, from baseline to post, those subjects classified as “not at risk” via DST increased from 4 to 15 versus from 5 to 7 via DASH score. Discrepancies between the classifications of risk may be because the DST measures diet patterns and the FFQ reflects nutrient intake.Research supported by the USDA.Grant Funding Source: USDA
Hand grip strength and estimates of body composition in HIVinfected rural Kenyan women
Authors: Ernst Judith Ann , Ettyang Grace , Johnson Cynthia , Siika Abraham , Nyandiko Winstone , Neumann Charlotte 
Published: June 2021

ObjectiveTo compare hand grip (HG) strength with estimates of body composition (BC) in HIV+ women.MethodsIn 256 drug naïve women (WHO Stage 1 or 2; CD4 cell count > 250 cells/uL), isometric strength was evaluated from HG measures using standardized technique and compared to BC estimates. The muscle areas of the mid upper‐arm, mid‐thigh, and mid‐calf, and sum of fat skin folds (SF) were calculated with standard equations using body circumferences and SF. Predicted values of fat‐free mass (FFM), % body fat and total body water (TBW) from bioelectrical impedance analysis were calculated with standardized equations.ResultsThe mean (SD) for age and CD4 were 36.7(8.1) yrs and 533(229) cells/uL respectively. Significant correlations (p<0.001) were found between HG measures (right and left) and estimates of muscle area on the arm, thigh and calf, FFM and TBW and (p<0.005) between HG (left) and body mass index; correlations were not significant with fat mass estimates.ConclusionsHG strength was related to estimates of lean mass at baseline, in drug naïve asymptomatic HIV+ rural Kenyan women enrolled in an 18 month randomized food intervention measuring the impact of beef vs soy vs wheat biscuit supplements on nutrition status. The trial is near completion, with positive acceptance of the biscuits. Supported by USAID Grant No. PCE‐G‐00‐98‐00036‐00, 1R01HD57646‐01A1 (CFDA #93.865) and Heifer Project International.
Maturation of protein kinase C masks its C1 domains
Authors: Antal Corina Elena , Skovsø Søs , Newton Alexandra C. 
Published: June 2021

Protein kinase C (PKC) is important in proliferation and apoptosis, and its misregulation can give rise to cancer. PKC is processed by a series of ordered phosphorylations that are crucial in structuring it for catalysis; thus, understanding conformational changes that occur during maturation and activation of PKC are paramount. PKC contains tandem C1 domains that bind the lipid diacylglycerol (DAG), or the functional analogs, phorbol esters, an event that releases the autoinhibitory pseudosubstrate thereby activating PKC. Using FRET‐based methods, we show that unprocessed PKCs translocate to plasma membrane upon phorbol ester stimulation with a half time 6 times faster than wild‐type. This fast rate is mimicked by a construct of PKC's tandem C1 domains suggesting that both C1 domains are exposed in unprocessed PKC and become masked upon maturation. We propose a model for maturation in which unprimed PKC is in an open conformation with C1 domains exposed and the pseudosubstrate out of the active site. Upon maturation, PKC exists in a closed conformation with both C1 domains masked. Following intracellular Ca2+ release, PKC's C2 domain mediates translocation of PKC to membranes; subsequent binding of one of the C1 domains to DAG provides the energy to remove the pseudosubstrate, allowing phosphorylation of downstream targets.This work was supported by NIH GM43154 to ACN, and NSF DGE1144086 and NIH T32 GM007752 to CEA.
Effects of Hypoxia on Growth and Biomechanics in Limb Bones of Alligator mississippiensis
Authors: Lujan Susan L. , Owerkovicz Tomasz , Elsey Ruth M. , Hicks James W. , Middleton Kevin M. 
Published: June 2021

Microanatomy and cross sectional geometry of limb bones are often used to infer life history and locomotor ability of fossil vertebrates based on study of their extant relatives; often the extreme variations in atmospheric oxygen that occurred over geologic time (oxygen levels 30% or more during the Permian, 15% in the Triassic) are not considered. As hypoxia is known to inhibit growth in vertebrates, while hyperoxia may be permissive, such comparisons between extinct and modern taxa merit investigation. As members of Archosauria, a clade with a long evolutionary history, alligators are excellent models to test for effects of environmental oxygen on skeletal growth and biomechanics. We incubated eggs and reared hatchlings in hypoxic (16% O2) and hyperoxic (26%, 31%, 36% O2) conditions. After sacrifice, femora were used in whole‐bone morphometric measurements and preparation of transverse mid‐diaphyseal ground sections. For comparison, traits were standardized to femur length. Cross sectional area, second moment of area, and polar moment of inertia scaled with isometry in alligators reared in chronic hypoxia, but with negative allometry in hyperoxic groups. The stouter femora of hypoxic animals exhibited greater resistance to compression, bending and torsion than predicted. Caution in evaluation of paleohistological data and consideration of oxygen availability is suggested.Supported by NSF IOS‐0922756.
Identification of a nucleosomal region required for the proper distribution of the transcription elongation factor Spt16 across transcribed genes in Saccharomyces cerevisiae
Authors: Duina Andrea Angelo , Nguyen Trang Hoai , Wharton William , Harper Jennifer Aileen 
Published: June 2021

In eukaryotic cells, DNA associates with several proteins to form a compacted structure referred to as chromatin. The basic unit of chromatin is the nucleosome, a particle consisting of a stretch of DNA wrapped around the histone octamer, itself composed of pairs of four core histone proteins: histones H2A, H2B, H3 and H4. In previous studies we described a mutant of histone H3 – H3‐L61W – that causes abnormal accumulation of Spt16 at the 3′ ends of transcribed genes. We now report that a mutation in histone H4 – H4‐R36A – causes a similar defect in Spt16 association with chromatin during transcription. Genetic evidence indicates that the H3‐L61W and H4‐R36A mutations affect Spt16 function through a common mechanism and an inspection of the crystal structure of the core nucleosome particle revealed that the H3‐L61 and H4‐R36 residues are located in close proximity to each other. These results suggest that a nucleosomal region defined by H3‐L61 and H4‐R36 plays a key role in ensuring proper Spt16 interactions with genes. We propose a model in which the region defined by these residues participates in a signal required for Spt16 to properly disengage from genes following the transcription process.This material is based upon work supported by the National Science Foundation under grant No. 0919241.
Damage‐induced association of Rap1p with an internal binding site stimulates de novo telomere addition
Authors: Friedman Katherine Louise , Platts Margaret H. , Obodo Udochukwu C. , Paul Shira R. , Velkovsky Stoycho M. , Eli Ilham M. 
Published: June 2021

At a low rate, sites of chromosome breakage in yeast are “healed” through telomere addition by the enzyme telomerase. While de novo telomere addition is normally repressed, it may serve to prevent chromosome loss in the face of irreparable damage. To address this possibility, we have sought factors that positively regulate telomerase action at chromosome breaks. Our study utilizes a “hotspot” for de novo telomere addition on yeast chromosome 5. This ~80 bp region contains TG‐rich sequences with similarity to yeast telomeric repeats. We find that function of the Rap1/Rif1/Rif2 complex is required for most de novo telomere addition within and flanking the hotspot. While this complex normally associates with telomeres to negatively regulate telomere length, Rap1/Rif1/Rif2 appears to stimulate telomere addition at ends with little or no telomeric sequence. Mutation of a putative Rap1p binding site at the centromere‐proximal end of the hotspot abolishes telomere addition, even though most of the TG‐rich sequences remain. Chromatin‐immunoprecipitation experiments demonstrate that Rap1p associates with hotspot DNA, but only after a chromosome break is induced telomere‐proximal to the hotspot. We suggest that Rap1p binds to internal chromosomal sites as a response to DNA damage and stimulates de novo telomere addition on a subset of broken ends to mediate damage tolerance.Funded by the National Science Foundation.
Iron induced eukaryotic initiation factor/ mRNA binding affinity change
Authors: Ma Jia , Khan Mateen A. , Merrick William C. , Haldar Suranjana , Theil Elizabeth C. , Goss Dixie J. 
Published: June 2021

Cellular iron metabolism is regulated by expression of iron responsive element (IRE) containing‐mRNA to control iron related protein levels (e.g. ferritin). The cytoplasmic iron regulatory proteins, IRPs, bind to iron response element (IRE) mRNAs, which represses IRE‐mRNA translation. IRE‐RNA binds to Fe2+ (in the absence of oxygen to prevent insoluble oxides) and the iron metabolite change the IRE‐RNA conformation resulting in decreased IRP (repressor) binding and increased eIF4F (enhancer) binding. eIF4F binds IRE‐RNA with high affinity (Kd=39.8±5.6nM) and further eIF4F: IRP competitively binds to IRE‐mRNA. eIF4G, a component of eIF4F, is also found to bind to the IRE‐RNA. The eIF4G middle domain binding affinity to the ferrtin IRE is lower than eIF4F and IRE binding doses not respond to metal concentration changes. While the eIF4G middle domain contains the RNA binding domain, additional protein domains and/or initiation factors (e.g. eIF4A, eIF4E) are necessary for functioning of the iron metabolite IRE‐ribo regulator.This work is supported in whole or in part, by National Institutes of Health Grants DK20251 (D.J.G. and E.C.T.) and National Science Foundation Grant MCB 0814051 (D.J.G.)
Conditional protein splicing of inteins with a non‐canonical C‐terminal glutamine
Authors: Nicastri Michael C. , Xega Kristina , Reitter Julie N. , Mills Kenneth V. 
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. The reaction begins with an amide‐thioester rearrangement of the peptide bond that links the N‐extein to the intein. Next, the intein either proceeds to splice, or, if downstream steps are prevented, the thioester can be cleaved. We have examined inteins interrupting PolII proteins in both Methanoculleus marisnigri (Mma) and Methanospirillum hungatei (Mhu). Both inteins have C‐terminal Gln in place of the highly conserved Asn. We have observed that the inteins promote mostly N‐terminal cleavage with the native Gln, but promotes some protein splicing with mutation to the conserved Asn. Also, when expressed under oxidizing conditions, the Mma PolII intein accumulates unspliced precursor, which can be induced to undergo N‐terminal cleavage upon in vitro incubation with 1,4‐dithiothreitol. This suggests that a disulfide bond, perhaps between the terminal Cys residues, could regulate the initiation of protein splicing.This material is based upon work supported by the National Science Foundation under grant MCB‐0950245 and by the Camille and Henry Dreyfus Foundation.
Non‐canonical inteins: Protein splicing by alternate mechanisms
Authors: Mills Kenneth V. , Reitter Julie N. , Connor Katherine R. , Nicastri Michael C. , Urbanski Laura M. , Williams Jennie E. , Colelli Kathryn M. , Savidis George , Marieni Michelle D. 
Published: June 2021

Protein splicing is the post‐translational excision of an intervening polypeptide (intein) from its flanking domains (the exteins), concomitant with extein ligation. The first step of splicing is an amide‐to‐thioester rearrangement of the peptide bond linking the N‐extein and intein. Class three inteins bypass this step. The Clostridium thermocellum TerA intein is class three, whereas the Thermobifida fusca Tfu2914 intein is a traditional intein despite having class three sequence motifs. The third step of splicing is Asn cyclization coupled to cleavage of the peptide bond linking the intein and C‐extein. Both the Methanoculleus marisnigri (Mma) and the Pyrococcus abyssi (Pab) PolII inteins promote efficient splicing with C‐terminal Gln in place of Asn. The activity of the Mma PolII intein may be regulated by disulfide bond formation. The Pab PolII intein splices only at elevated temperatures, allowing for isolation of a stable precursor and study each step of splicing in vitro. An NMR solution structure of the Pab PolII intein reveals a particularly rigid structure, a disordered loop absent in a highly similar P. horikoshii intein, and a β‐hairpin specific to thermophilic inteins.This material is based upon work supported by the National Science Foundation under grant MCB‐0950245 and the Camille and Henry Dreyfus Foundation.
Potassium channels on natural killer cells in the presence of breast carcinoma cells
Authors: Koshy Shyny , Wu Danli , Tajhya Rajeev , Hu Xueyou , Odejimi Abiola , Yotnda Patricia , Beeton Christine 
Published: June 2021

Natural Killer (NK) cells are cytotoxic lymphocytes that play an important role in immune defense against viruses and cancer. Reduced NK cell activity has been associated with tumor resistance and metastasis in breast cancer. Our overall objective is to determine the phenotype and function of potassium channels on human NK cells in presence of breast cancer cells. We have found that human NK cells express two types of potassium channels, namely Kv1.3 and KCa3.1. The potassium channel phenotype did not vary with expression levels of CD16 and CD56 but it did differ between adherent and non‐adherent NK cells following cytokine‐induced activation. Blocking Kv1.3 and KCa3.1 channels differentially affected the proliferation, degranulation, and adhesion to fibronectin and tumor cells by adherent and non‐adherent human NK cells in vitro and differentially affected their ability to destroy tumors in vivo.This work was funded in part by grants from the American Heart Association (0665009Y) and the Department of Defense (BC096018) to Christine Beeton.
The Role of PkcA in Septum Formation in Aspergillus nidulans
Authors: Henley Jordan Larissa , Jackson-Hayes Loretta , Hill Terry , Loprete Darlene , Dawodu Omolola , Delbove Clair , Poullard Ashely 
Published: June 2021

Fungi of the Aspergillus genus can causes serious illnesses to those with compromised immune systems. PkcA in Aspergillus nidulans is important in formation of the cell wall and septa, which are both necessary for the invasive nature of the fungus. Elucidating PkcA's role in cell wall synthesis can be accomplished by understanding which domains facilitate specific functions of PkcA. Wild type PkcA localizes to growing hyphal tips and septation sites. To determine which domains are important for localization, green fluorescent protein tagged, domain deleted PkcA were constructed. The domains that are vital to A. nidulans maintenance of cell wall integrity were separately identified by growing the domain deleted stains in the presence of the cell wall stressor calcofluor white. We have determined that the localization signal and the domain responsible for proper function are distinct and essential domains.This research was funded by NSF grant RUI‐0742907 and The Merck Institute for Science Education.This research from the Jackson Heart Study is supported by NIH contracts N01‐HC‐95170, N01‐HC‐95171, and N01‐HC‐95172 provided by the National Heart, Lung, and Blood Institute and the National Center for Minority Health and Health Disparities
Increased expression of heat shock proteins in skeletal muscle induces autophagy
Authors: Mestril Ruben , Ju Jeong-Sun 
Published: June 2021

PURPOSETo determine if heat shock proteins (hsp) are involved in autophagy in mouse skeletal muscle.METHODSTo determine whether an hsp activator stimulates autophagy in skeletal muscle, CB6F1 wild‐type mice were i.p. injected with 17‐DMAG (a hsp activator, 10 mg/kg) daily for 6 days with and without colchicine (autophagy inhibitor, 0.4 mg/kg/day) administration in the last 2 days to measure in vivo autophagic flux in skeletal muscle. In order to induce autophagy, mice were also treated with rapamycin (10 mg/kg i.p.) for 2 days with and without 2 days of colchicine administration. Tibialis anterior muscles were excised and p62/SQSTM1 and LC3 II (autophagic marker proteins) were analyzed by Western blot.RESULTSWestern blots show that p62 protein levels were significantly decreased (~50%; P<0.05) in 17‐DMAG and rapamycin treated mouse skeletal muscles. The LC3 II protein levels were increased even further when degradation was inhibited by colchicine in 17‐DMAG treated mice by ~2‐fold (P<0.01), similar results were obtained with rapamycin.CONCLUSIONOur study suggests that the heat shock proteins enhance autophagy in mouse skeletal muscle under basal and induced conditions, the precise mechanism by which the hsps regulate autophagy still needs to be clarified.This research was supported by an award from the USAMRMC.
A new model of acute respiratory distress syndrome due to smoke inhalation and cutaneous burns in swine
Authors: Ivey Katherine Marie , Batchinsky Andriy , Langer Thomas , Belenkiy Slava , Necsiou Corina , Vecchi Vittoria , Salinas Jose , Cancio Leopoldo 
Published: June 2021

ObjectiveTo develop a clinically relevant model of severe acute respiratory distress syndrome (ARDS) in swine with the aim to test therapeutic interventions.MethodsUnder intravenous anesthesia (ketamine, midazolam), female swine (44.8 ± 1.9kg) underwent tracheostomy, line placement, exposure to 30L of smoke, and a 40% total body surface area full‐thickness flame burn. Animals were monitored for 7 days with one‐on‐one ICU care. Post burn resuscitation using lactated Ringer's was guided by a computerized algorithm. At onset of ARDS [PaO2:FiO2 ratio (PFR) < 200], the injury group (IG, n=5) received low‐tidal volume ventilation per ARDSNet guidelines. Time controls (TC, n=2) were uninjured. Data are means; statistics by T‐test or Wilcoxon 2‐sample test.ResultsPost‐injury carboxyhemoglobin level in IG was 89.8 ± 1.4% with onset of ARDS at 22 ± 1.7 hrs post‐injury. Survival time was lower in IG (65 ± 14 hrs) compared with TC (168 hrs, p<0.0001). Peak airway pressure in IG increased above 30cm H2O 6 hrs after injury (p<0.02). PFR in IG decreased below 200 at 24hr post‐injury (p<0.01) and remained lower than TC until the end of study.ConclusionsWe have created a clinically relevant porcine model of ARDS within 24 hrs of smoke and thermal injuries. Future work includes validation of various interventions for ARDS management.Source of support: U.S. Army Institute of Surgical Research
Semi‐automated Quantitative CT‐scan Analysis For In Vivo Lung Weight Measurement
Authors: Vecchi Vittoria , Langer Thomas , Batchinsky Andriy , Ivey Katherine , Walker Kerfoot , Necsoiu Corina , Belenkiy Slava , Dimitri Rachael , Lucas Michael , Leon Alisa , Salinas José , Cancio Leopoldo 
Published: June 2021

IntroductionAcute Respiratory Distress Syndrome (ARDS) is characterized by impairment of gas exchange, lung edema and diffuse density changes on computed tomography (CT). We sought to measure lung weight through a simplified, semi‐automated method of quantitative CT scan analysis (qCT) in order to quantify lung edema.MethodsChest CT scans were performed in 6 pigs (46±2 kg). Five pigs had ARDS due to smoke inhalation and 40% total body surface area cutaneous burn; 1 was a healthy control. CT images were reconstructed at 2 mm thickness with a step of 20 mm, yielding 15±2 images per series. Lung weight was estimated with image‐analysis software (Maluna, Goettingen, Germany) assuming 1.06 as lung‐specific weight. After necropsy, lungs were weighed on a balance to assess agreement between qCT and post‐mortem lung weight via Bland‐Altman analysis.ResultsLung weights ranged from 237 to 1463 g (mean 1003 g) at necropsy and from 356 to 1411 g (mean 1066 g) at qCT. A high correlation (r2=0.98, p=0.0001) was observed between the two methods. Bland‐Altman analysis showed a bias of −63.5 g with limits of agreement of 60 and −186.ConclusionsLung weight can be accurately measured in vivo via qCT. Quantitative CT analysis may be a useful tool to evaluate and monitor the time course of lung edema in ARDS.Source of research support: Institute of Surgical Research, Fort Sam Houston, TX
Structural analysis of an intein from an extreme thermophile
Authors: Williams Jennie E. , Reitter Julie N. , Mills Kenneth V. 
Published: June 2021

Protein splicing is a post‐translational event by which an intervening polypeptide, the intein, facilitates its own excision from the flanking polypeptides, the exteins, and the ligation of the exteins. We have studied the structure of two inteins that interrupt the DNA PolII from the extreme thermophiles Pyrococcus abyssi (Pab) and Pyrococcus horikoshii (Pho). The two inteins have 71% sequence identity. Solutions to the NMR structure of the Pab PolII intein revealed a long flexible loop in an otherwise rigid protein; the sequence corresponding to this loop is absent in the Pho intein. We have used susceptibility to digestion by the thermostable protease thermolysin to show that the Pho intein is more rigid than the Pab intein. The Pho intein also is less active at low temperature than the Pab intein. Perhaps due to this increased rigidity, we were able to identify crystallization conditions for the Pho PolII intein. Our first crystals give diffraction data to about 2.9 Å; we hope to optimize crystallization conditions and solve the structure in collaboration with colleagues at the Wadsworth Center. We also hypothesize that the flexible loop may play a role in mechanism‐linked conformational changes that might help to coordinate the steps of splicing.This material is based upon work supported by the National Science Foundation under grant MCB‐0950245 and by the Camille and Henry Dreyfus Foundation.