bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved functional recovery following spinal cord compression in rats treated with losartan is associated with reduced T cell influx into the injury site
Authors: Jones T Bucky , Robbins Emily , Hanyu‐Deutmeyer Aaron , Jones Carleton 
Published: June 2021

Inhibition of the renin‐angiotensin system (RAS) is neuroprotective in a variety of CNS disorders, including Parkinson disease, Alzheimer disease and stroke. One proposed mechanism for protective effects of RAS inhibition is modulation of inflammation. Post‐injury inflammation has been implicated in degenerative cascades initiated by mechanical trauma to the spinal cord, thus we sought to determine whether a similar protective effect of RAS inhibition would occur following spinal cord injury (SCI). Rats were treated with losartan or vehicle (i.p., sid), beginning one day after lateral compression SCI. Functional recovery was assessed using a standardized scale. Rats were sacrificed at 7, 14 or 28 days post injury (dpi) and the tissues processed for PCR or immunohistochemical analyses. We show that rats treated with losartan have improved functional recovery compared to vehicle‐treated rats, beginning at 5 dpi. Quantitative PCR revealed that treatment with losartan decreased the intraspinal expression of CCL5, a chemokine that promotes T cell infiltration into tissues. Decreased expression of CCL5 was associated with a significant decrease in the number of T cells within the injury site at 7 dpi and maintained to 28 dpi. Collectively, these data suggest that beneficial effects of RAS inhibition in this spinal cord injury model may be due to a reduction in the T cell response within the injury site.This study was supported by MWU Office of Research and Sponsored Programs (E.R., A.H‐D.), MWU College of Health Sciences (CBJ), and Arizona College of Osteopathic Medicine (TBJ).
Improving Biofuel Production with Metagenomics and Synthetic Biology
Authors: Witt Evan , Forsberg Kevin , Ellison Tyler , Dantas Gautam 
Published: June 2021

The Department of Energy has expressed considerable interest in the production of biofuels from lignocellulose. Lignocellulose represents the largest terrestrial carbon source on Earth, but cannot be broken down without a combination of acids, industrial chemicals and heat. Only after treatment with these harsh conditions can the sugars within lignocellulose be made available for conversion into fuels (i.e. ethanol or isobutanol) by engineered strains of Escherichia coli.Unfortunately, this treatment process also creates compounds that inhibit bacterial growth and limit the potential output of biofuels.We have shown that genes isolated from soil metagenomes can confer tolerance to the products of biofuel production, which include fuels like ethanol and isobutanol, and the toxic products from lignocellulose treatment (e.g. furfural, ferulic acid, and others). Increasing tolerance to these byproducts can theoretically increase the yield of biofuel producing strains of E. coli, which is our ultimate goal.We aim to demonstrate the viability of a workflow combining synthetic biology and metagenomics to address innumerable challenges in industry and bioremediation. This workflow is not only versatile and adaptable, but also scalable, and could have tremendous economic and environmental potential.
Genetic deletion of an instability motif in the Tristetraprolin (TTP) transcript increases TTP mRNA stability and protein expression and provides protection against inflammatory diseases
Authors: Patial Sonika , Blackshear Perry 
Published: June 2021

ObjectiveTristetraprolin (TTP) is an mRNA binding protein that binds to AU‐rich elements (AREs) in the 3′‐untranslated regions (3′UTR) of specific mRNAs, such as tumor necrosis factor (TNF) mRNA, and increases their rates of deadenylation and turnover. TTP mRNA also contains AREs within its own 3′UTR that are partly responsible for its own instability. The objective of this study was to test the hypothesis that increased TTP mRNA stability, and the resulting increased TTP protein expression, may provide protection against inflammatory diseases.ResultsUsing knock‐in technology, a novel TTP mouse line (TTPΔARE) was generated in which 136 bases in the 3′UTR AU‐rich region of TTP mRNA were deleted. TTPΔARE mice developed and reproduced normally, and exhibited no phenotypic or histopathological abnormalities. TTP mRNA stability was found to be significantly enhanced in bone marrow‐derived macrophages (BMDMs) and mouse embryonic fibroblasts (MEFs) isolated from TTPΔARE mice. Moreover, TTP protein expression was increased in unstimulated and LPS‐stimulated BMDMs, and in various mouse tissues. In addition, LPS‐induced expression of TTP target mRNAs, particularly TNF and Il‐1β mRNAs, was significantly reduced in TTPΔARE BMDMs. TTPΔARE mice exhibited reduced skin inflammation in an experimental model of psoriasis, and were completely protected from collagen antibody‐induced arthritis.ConclusionsOur data demonstrate that modestly increased levels of TTP in mouse cells and tissues are protective against certain inflammatory disease models. These data may have implications for the development of therapeutic strategies to target chronic inflammatory diseases via enhancing TTP expression.
Structural Bioinformatics and Molecular Dynamics of p53 Tumor Suppressor Protein
Authors: Thayer Kelly , Slaw Benjamin , Han In , Quinn Taylor 
Published: June 2021

In carrying out its tumor suppressor function, p53 binds to cognate DNA regulatory sites throughout the genome. While many of the binding sites contain a recognizable consensus, other binding sites exist which lack this, making this an interesting system for understanding the potential role of indirect readout in the binding event. In order to study this, we are constructing additive energy models based on hydrogen bond contacts and the presence of the TG DNA base pair step. The simplest model simply counts how many of the crystallographic bonds are available for a particular DNA sequence based on H‐bond donor and acceptor groups, and the model is made increasingly complex through refinements including distance dependence and angle of the H‐bonds. Based on the score from the additive model, clustering of experimentally determined DNA binding sites led to the identification of five distinct classes of binding sites, which we hypothesize represent distinct modes of binding. To further investigate this hypothesis, we have carried out molecular dynamics simulations of the p53 protein complexed with DNA representative of the different clusters, as well as engineered sequences expected to have interesting mechanical properties. Furthermore, we have examined molecular dynamics involving lys120, a key residue interacting with the DNA. Our results shed light on the dynamic interaction of p53 and its binding sites and suggest novel means by which the recognition process may occur. This mechanistic understanding lays groundwork that informs the development of more robust cancer therapeutics.Funding: Vassar College Spring 2014 Research Committee Award from the Emily Abbey Fund, the Christian A. Johnson Endeavor Foundation, and the Elise Nichols and Margaret Sawyer Biochemistry Research Fellowship
Profiling of Lipids Expression Along the Rostral and Caudal Axis After Spinal Cord Injury: Matrix Assisted Laser Desorption/Ionization Approach
Authors: Adam Amna , Salzet Michel , Devaux Stephanie 
Published: June 2021

Spinal cord injury (SCI) causes alteration in lipid composition and migration of lipids between the gray and white matter regions of spinal cord. Studying the prominent and region‐specific lipids in injured spinal cords can possibly lead to clinical understanding of the specific role each class of lipid plays in the inflammation process after SCI. Utilization of Matrix Assisted Laser Desorption/Ionization (MALDI)‐TOF/TOF coupled with FlexImaging and ClinProTools software for statistical analysis was imployed as a method to identify lipids that demonstrate interesting behavior post SCI. Furthermore, shotgun analysis using Q Exactive performed to possibly characterize interesting lipids.Using MALDI‐Mass Spectrometry, the region‐specificity of lipid expression and alteration in injured spinal cord were identified with progression of time. Rat tissues from 3, 7, 10 days post SCI were imaged in both negative and positive mode and revealed that visualization of region‐specific lipid is best carried in the positive reflector mode. Shotgun analysis using Orbitrap allowed for approximate characterization of the lipids with m/z ratio identified using MALDI imaging. Taking all together the data suggests that in the positive reflector mode, there is a difference in the expression in rostral and caudal region, and glycerophospholipids is possibly the most prominent class of lipid in both gray and white matter region of spinal cord post SCI.
Cellular mechanisms by which alcohol promotes HIV protease inhibitor‐induced liver lipotoxicity
Authors: Hinton Michael , Pandak William , Hylemon Phillip , Zhou Huiping 
Published: June 2021

The development of highly‐active‐antiretroviral therapy(HAART) has allowed management of HIV and extended the lives of those infected. Alcohol abuse, which is very common in HIV‐1 infected patients, is one of the most important co‐morbid risk factors for liver injury and has been associated with the occurrence of serious metabolic syndrome and subsequent discontinuation of HAART in HIV patients. We have identified endoplasmic reticulum (ER) stress‐induced proapoptotic factor CHOP as an important factor underlying HIV PI‐induced inflammation and hepatic lipotoxicity. However, little is known about the mechanistic pathways by which alcohol promotes HIV PI‐induced hepatic lipotoxicity. The aim of this study was to determine if inhibition of CHOP expression prevents alcohol‐ and HIV PI‐induced apoptosis and dysregulation of lipid metabolism.MethodsPrimary hepatocytes from wild type or CHOP‐/‐ mice were treated with individual HIV PIs with or without alcohol. Activation of the key genes responsible for lipid metabolism was determined by real time RT‐PCR and Western Blot.ResultsCHOP‐/‐ mice prevent ethanol and HIV PI‐induced dysregulation of key genes involved in lipid metabolism in hepatocytes. CHOP‐/‐ hepatocytes treated with alcohol showed decreased biosynthesis of cholesterol, fatty acid, and bile acid.ConclusionsActivation of the ER stress‐induced proapoptotic factor CHOP is a key cellular mechanism underlying alcohol and HIV PI‐induced hepatotoxicity. CHOP expression is key for alcohol and HIV PI‐induced dysregulation of key genes involved in lipid metabolism in hepatocytes.
Fluorescent Labeling of the Carbohydrate Backbone of Peptidoglycan to Track Degradation In Vivo
Authors: Wang Yiben , Leimkuhler‐Grimes Catherine 
Published: June 2021

Microbe associated molecular patterns (MAMPs) are detected via Toll‐ and Nod‐like receptors. Upon their activation, inflammatory molecules are produced in cells. One specific example of a MAMP is muramyl dipeptide (MDP), a small fragment of the bacterial cell wall peptidoglycan. Synthetic MDP has been shown to elicit an immune response by activating nucleotide‐binding oligomerization domain‐containing protein 2 (Nod2). However it is still unclear how MDP, with its unusual stereochemistry, is released from the peptidoglycan. Furthermore, it is unknown if there are other peptidoglycan fragments that can activate the innate immune system. The main objective of this study is to investigate the possibility of using peptidoglycan O‐acetyltransferase B (PatB) to fluorescently label the peptidoglycan to track the generation of these immunostimulatory fragments. PatB acetylates the sixth hydroxyl position of N‐acetylmuramic acid (MurNAc), one of the two alternating sugar units of the peptidoglycan backbone, to block the cleavage of the peptidoglycan by lysozyme and other lytic transglycosylases. We aim to hijack this modification pathway to fluorescently label the peptidoglycan. To this end, we optimized the expression and purification of PatB. Initial in vitro studies using PatB and tri‐N‐acetylglucosamine (GlcNAc)3, the other sugar unit, as the acceptor shows that we are able to install a variety of functional groups, including an alkyl derivative, at the sixth hydroxyl group. The alkyl handle will allow for fluorescent labeling of the peptidoglycan through Click chemistry. We are currently working towards observing the degradation of fluorescently labeled peptidoglycan in vivo.Funding for this project has been provided by NIH COBRE grants and the NIH‐CBI T32 Training Grant.
Molecular Screening for Antagonists of HIV‐1 Viral Infectivity Factor Enables Drug Discovery
Authors: Salter Jason , Bennett Ryan , Morales Guillermo , Smith Harold 
Published: June 2021

HIV‐1 Viral infectivity factor (Vif) is a viral accessory protein that is absolutely required for HIV‐1 infection in CD4+ T cells, macrophages and dendritic cells due largely to its role in recruiting antiretroviral factors of the APOBEC3 family to an E3 ligase complex for polyubiquitination and proteasomal degradation. Oligomerization of Vif is essential for APOBEC3G degradation and for the HIV‐1 life‐cycle but the mechanism of action and molecular oligomeric interface are unknown.Vif oligomerization is mediated by a conserved 161PPLP164 motif, but the crystal structure of Vif (PDB 4N9F) revealed the burial of the PPLP motif between N and C‐terminal domains. The sole Vif‐Vif crystal contact involves the conserved 40YRHHY44 motif, potentially implicating its involvement in a biological Vif oligomeric interface. The YRHHY motif is also essential for A3G degradation. Thus, inhibition of Vif‐dependent A3G degradation and HIV infectivity by PPLP peptidomimetics may be allosteric. OyaGen has identified a small molecule Vif dimerization antagonist through a novel in‐cell HTS quenched‐FRET assay. Here we show that this hit, BRD25, disrupts Vif oligomerization, reduces APOBEC3G degradation, and decreases HIV infectivity. Fluorescence anisotropy was used to show that BRD25 reduces the size of purified Vif in a dose‐dependent manner, consistent with oligomer disruption. In silico docking of BRD25 with the crystal structure of Vif reveals a potential binding site consistent with its role in disruption of Vif oligomerization and A3G degradation. These data demonstrate the availability of protein‐protein interactions as novel drug targets in HIV infected cells.
Role of the U2AF Homology Motif in Human Tat‐SF1 as a Cofactor for HIV‐1 Splicing
Authors: Loerch Sarah , Kielkopf Clara 
Published: June 2021

The HIV‐1 life cycle relies on controlled ratios of unspliced and alternatively spliced mRNAs. Human Tat‐SF1 is a requisite host factor for the regulation of HIV‐1 RNA splicing. It is known that Tat‐SF1 associates with the U2 small nuclear ribonucloprotein particle (snRNP) of the spliceosome. However, the underlying mechanisms by which Tat‐SF1 affects HIV‐1 RNA splicing remain elusive.The core U2 snRNP protein subunit SF3b155 comprises five tryptophan‐containing motifs, termed U2AF ligand motifs (ULM) interspersed with regulated phosphorylation sites. Our lab has shown previously that the SF3b155 ULMs are recognized by splicing factors containing a small globular domain named U2AF homology motif (UHM). Based on sequence homology, we identified a putative UHM in Tat‐SF1. We hypothesize that this UHM provides a phosphorylation‐sensitive link between this alternative splicing factor and the splicing machinery via SF3b155.To investigate the Tat‐SF1 UHM interactions with SF3b155 and the role of phosphorylation, we determined the crystal structures of the Tat‐SF1 UHM in complex with a minimal phosphorylated SF3b155 ULM and for comparison the unphosphorylated and apo‐forms at 1.7 Å, 1.9 Å, and 1.1 Å, respectively. The apo‐Tat‐SF1 UHM displays a canonical UHM‐fold. The complex with the phosphorylated ULM reveals that the phosphorylation site is located closely above the plane of an aromatic residue. This suggests a reduced affinity of phosphorylated SF3b155 for the UHM due to electrostatic repulsion between the phosphate‐anion and the π‐cloud of the aromatic side chain. We are currently testing the phosphorylation‐sensitivity and significance of these Tat‐SF1 UHM/SF3b155 ULM‐interactions for HIV‐1 infectivity in vivo.
Effect of Curcumin and Silymarin in Combination Exerts Synergistic Inhibition of Colon Cancer Cell Proliferation
Authors: Montgomery Amanda , Daniel Nalini , Ezekiel Uthayashanker 
Published: June 2021

Consumption of a diet rich in phytochemicals is efficacious in inhibiting colon cancer. Curcumin is the major component of the spice turmeric, and silymarin, the bioactive component of milk thistle, is used as a supplement for liver disease. We studied the antiproliferative effect of curcumin alone and silymarin alone or the combination of curcumin and silymarin using the colon cancer cell lines DLD‐1, HCT116 and LoVo. Curcumin inhibited colon cancer cell proliferation in a concentration dependent manner, whereas silymarin showed significant inhibition only at the highest concentration assessed. We found synergistic effects when curcumin was held at a constant concentration (12.5 µM) and the silymarin concentration was varied. Pre‐exposure studies were conducted using DLD‐1 cells with curcumin alone followed by different concentrations of silymarin or silymarin alone followed by different concentrations of curcumin. Results indicated that curcumin sensitized silymarin effect whereas silymarin did not sensitize curcumin effect. The outcome of this research study shows that combinations of phytochemicals could prevent or eliminate colon cancer initiation and/or progression.AM is supported by DeNardo Foundation Fellowship.
The Majority of Athletes Participating in Winter Multisport Events and Ironman Fail to Meet Recommended Intakes for Endurance Sports
Authors: Masson Genevieve , Lamarche Benoit 
Published: June 2021

Participating in endurance sports requires optimal nutrition, with particular focus on dietary carbohydrates (CHO). Yet, little is known regarding dietary intakes of athletes involved in multisport endurance events. The objective of this observational study was to evaluate the nutritional habits of non‐elite athletes participating in winter triathlon (snowshoeing, skating and cross‐country skiing), winter pentathlon (winter triathlon sports + cycling and running), Ironman (IM‐ swimming, cycling, running) and half‐distance Ironman (IM70.3). A total of 151 athletes (44 women and 107 men) competing in a winter triathlon, winter pentathlon or in one of the IM and IM70.3 events were included in the analysis. Participants completed an online validated food frequency questionnaire. Other questionnaires assessing training habits, socio‐demographic information and sport food and supplements use were also completed. Athletes (21‐66 years) trained on average (±SD) 11.8±1.7 hours per week. Average energy intake was 3257±1091 kcal with higher energy intakes (p<0.001) reported by IM athletes compared to other groups. A significantly higher proportion of men achieved the recommended intakes of proteins (1.6 g/kg of body weight) compared with women (72.0 vs. 54.6%, p=0.04). On the other hand, small proportions of both men (37.4%) and women (27.3%, p=0.24 for difference between gender) meet the recommended CHO intakes for endurance athletes (7g/kg of body weight). Our data suggest that a majority of athletes involved in endurance multisport events fail to reach the minimal recommended intakes for CHO, highlighting the need for targeted education in this area.Funding:Natural Sciences and Engineering Research Council of Canada
Post‐Prandial Changes in Bone Turnover after High Saturated Fat Challenge Meals
Authors: Rogers Tara , Demmer Elieke , Rivera Nancy , Gertz Erik , Zivkovic Angela , Smilowitz Jennifer , German J , Van Loan Marta 
Published: June 2021

Biomarkers of bone turnover fluctuate over the course of a day; these fluctuations are exaggerated with food intake. The effect of foods with differing fatty acid profiles on this phenomenon is unknown. We compared bovine milk saturated fatty acids (SFA) to plant‐based SFA on post‐prandial bone metabolism in overweight/obese subjects. Adult subjects (n=20) participated in a randomized controlled trial, consuming 2 isocaloric high fat meals (dairy cheese sandwich vs. vegan sandwich plus palm oil) separated by a 1‐2 week washout period. Blood samples were collected at baseline, 1, 3, and 6 hrs post‐prandial. Bone resorption marker C‐terminal telopeptide of type 1 collagen (CTx) and bone formation marker cross‐linked C‐telopeptide of type 1 collagen (C1CP) were measured by ELISA. Spearman's Correlation analyses showed that C1CP and CTx were significantly correlated at baseline for both treatments (dairy: rs=0.585, p=0.007; palm oil: rs=0.630, p=0.003). These correlations remained significant at all time points for palm oil, but not dairy, suggesting a potentially more potent effect of dairy SFA. However, ANOVA revealed no significant effects of time or treatment on C1CP. CTx significantly decreased from baseline to 3 hrs after both dairy (p<0.0001) and palm oil (p<0.01), but there was no significant treatment effect. Differences in SFA composition between dairy and palm oil did not affect the postprandial response of CTx and C1CP in this study.Funding:National Dairy Council
THE EFFECT OF CONSUMPTION OF FAT‐FREE DAIRY PRODUCTS OVER EIGHT WEEKS ON BODY WEIGHT, WAIST CIRCUMFERENCE AND SATIETY HORMONES IN OVERWEIGHT AND OBESE INDIVIDUALS
Authors: El Khoury Dalia , Huot Pedro , Barkhordari Nazanin , Smith Chris , Wad Mukta , Goff H Douglas , Anderson G Harvey 
Published: June 2021

Increasing dairy consumption may be an alternative to weight loss diets. Therefore, we compared the effects of adding 4 servings per day of fat‐free and low‐fat dairy products to an energy restricted (ER, 500 kcal) diet over 8 weeks on body weight, waist circumference and satiety hormones in overweight/obese individuals. 36 overweight/obese men and women (age: 46±1.19 years; BMI: 30.4±0.46 kg/m2) completed the study. By week 8, all participants reduced weight (‐1.13±0.38 kg; P<0.01) and waist circumference (‐0.70±0.19 cm; P=0.001). Consumption of dairy reduced fasting levels of HbA1c compared with the ER group at week 4 (P=0.006) and week 8 (P=0.065). Furthermore, in women, dairy (32.1±2.8 ng/ml; n=10) led to higher fasting leptin levels than ER diet (23.1±2.0 ng/ml; n=11) at week 8 (P=0.016). By week 8, mean fasting PYY increased in the dairy group (4.06±5.76 pg/ml; n=12), whereas it decreased in the ER group (‐9.19±3.06 pg/ml; n=10) from baseline (P=0.07). There were no differences in glucose area under the curve (AUC) (P=0.33) between the dairy (226±24 mmol/l; n=16) and the ER group (266±33 mmol/l; n=14), and no differences in insulin AUC (dairy: 3735±693 μIU/ml; n=17; ER: 2212±487 μIU/ml; n=15; P=0.09), at week 8. Ghrelin levels were not affected by diet over the 8 weeks. Adding fat‐free and low‐fat dairy products reduced body weight and waist circumference similar to the ER diet but had mixed effects on metabolic measures.Supported by Natural Sciences and Engineering Research Council of Canada‐Collaborative Research and Development Grant, Dairy Farmers of Ontario and Kraft Canada Inc.