bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using targeted LC‐MS/MS‐based metabolomics to measure a broad constellation of bile acids/salts in disorders of human health
Authors: Horvath Thomas D. , Haidacher Sigmund J. , Hoch Kathleen M. , Engevik Melinda A. , Haag Anthony M. , Engevik Amy C. 
Published: May 2022

BackgroundBile is an important liver secretion which aids the digestion of fats in the intestine. Bile acids are the major organic solute component of bile and are synthesized from cholesterol in the liver and stored in the gallbladder. After secretion in the intestine, bile acids are re‐absorbed in the distal small intestine (ileum). Imbalances in the reabsorption of bile acids can lead to bile acid diarrhea when bile acid malabsorption occurs. Conversely, when there is an increase in bile acid absorption hepatic disorders such as nonalcoholic fatty liver disease can arise. A wide array of distinct bile acid structures have been identified in vertebrates. Developing and refining experimental tools to identify the role of bile acids in health and disease will enhance our ability to treat complex disorders impacting multiple organ systems.Methods & ResultsWe have expanded our existing reverse‐phase liquid chromatography‐tandem mass spectrometry (LC‐MS/MS)‐based targeted metabolomics method to accommodate a simple‐to‐use standards kit that includes reference standards for 16 bile acids/salts and their corresponding deuterated isotopologs as internal standards. LC‐MS/MS method enhancements include scheduled Selected‐Reaction Monitoring (sSRM) to reduce instrument duty cycle, and carefully tailored chromatographic conditions to resolve the following groups of structurally similar or isobaric bile acids/salts: i) Glycocholic Acid (GCA) and Taurocholic Acid (TCA); ii) Lithocholic Acid (LCA), Glycolithocholic Acid (GLCA), and Taurolithocholic Acid (TLCA); iii) isobaric Cholic Acid (CA) and beta‐Muricholic Acid (b‐MCA); iv) isobaric Ursodeoxycholic Acid (UDCA), Chenodeoxycholic Acid (CDCA), and Deoxycholic Acid (DCA); v) isobaric Glycoursodeoxycholic Acid (GUDCA), Glycochenodeoxycholic Acid (GCDCA), and Glycodeoxycholic Acid (GDCA); and vi) isobaric Tauroursodeoxycholic Acid (TUDCA), Taurochenodeoxycholic Acid (TCDCA), and Taurodeoxycholic Acid (TDCA). Our tissue processing and metabolite extraction procedures have been optimized for hepatic and fecal tissues. Individuals with inactivating mutations in the molecular motor, Myosin Vb, have severe diarrhea and often present with liver cholestasis. We used an animal model of loss of Myosin Vb to determine alterations in bile acid composition in the distal small intestine and liver. Whole segments of the ileum and liver were processed in methanol and analyzed by LC‐MS/MS.ConclusionWe have developed a targeted metabolomics method to accurately identify and quantify bile acids by LC‐MS/MS and this technique can be used to investigate changes in bile acid composition in gastrointestinal disorders.
Effects of a Treadmill Workstation on Coagulation Potential
Authors: DeJonge Sydney R. , Del Pozzi Andrew , Nagelkirk Paul R. 
Published: May 2022

IntroductionApproximately 2.7 million blood clot‐induced events occur each year, including most strokes and heart attacks. An upright, seated position reduces blood flow, promotes blood pooling, viscosity, and may active the coagulation system. Thus, occupational environments that include prolonged periods of seated work may contribute to the formation of a thrombus. Use of an active workstation may beneficially impact thrombolytic potential.PurposeTo observe the effects of low intensity walking at a treadmill workstation on changes in coagulation potential compared to use of a traditional, sedentary workstation.MethodsFive apparently healthy college‐aged students (n= 4 men, 1 woman; 22 ± 2 yrs; 27.3 ± 6.2 kg/m2) completed the same series of mental tasks at a sedentary workstation and while walking one mile‐per‐hour at a treadmill workstation. Blood samples were collected at baseline and immediately after completion of tasks and analyzed for the following: prothrombin time (PT), active partial thromboplastin time (APTT), factor VII (FVII), factor VIII (FVIII), and fibrinogen (FGN).ResultsThe walking condition elicited greater responses in FVII compared to the sedentary condition at baseline. Additionally, there was a non‐significant trend observed for FVIII. All data presented in Table 1.ConclusionLow intensity walking at a treadmill workstation can attenuate prothrombotic changes that are associated with completing tasks at a sedentary workstation.
Acquisition of a Senescence‐like Phenotype in Neurons Contributing to the Pathogenesis of Hepatic Encephalopathy Due to Chronic Liver Disease
Authors: Kobs Zachary A. , Williams Elaina , Chu Christopher , Petrescu Anca , An Suyeon , Venter Juliet , DeMorrow Sharon 
Published: May 2022

BackgroundHepatic encephalopathy resultant from chronic liver failure (Type C HE) is associated with neurological dysfunction and hyperammonemia. In HE, senescent markers have been found in astrocytes, but research into neuronal senescence has been limited. TGFb1 is one of the senescence‐associated secretory phenotype (SASP) factors released from senescent cells, and has been shown to be upregulated in the brain in Type A HE, but its role in Type C HE is unknown. The aim of this study was to assess the role of a senescence‐like phenotype in the pathogenesis of Type C HE.MethodsSD rats underwent bile duct ligation (BDL) surgery and C57BL/6 mice were treated with CCl4 for 16 wks to induce chronic liver failure. CCl4‐treated mice received a senolytic cocktail of Dasatinib and qercertin (D/Q via oral gavage) starting after 8 weeks of CCl4 injections. In parallel, human autopsy brain samples from patients with HE due to liver cirrhosis and age‐ and sex‐matched controls were used. Neurobehavioral testing to assess cognitive and neuromuscular function was performed. Markers of senescence (p21, p16, b‐galactosidase expression), SASPs (CCL2, TGFb1, and IL‐6) and neuroinflammation were assayed in the cerebellum and hippocampus by qPCR and immunohistochemistry.ResultsIn rodent models of HE and in human autopsy samples, markers of senescence and SASP were observed in neurons of the CA1 and dentate gyrus in the hippocampus and in the purkinje cell layer in the cerebellum, regions known for their involvement in learning and memory and motor control. Treatment with D/Q reduced the number of senescent neurons, and attenuated the cognitive deficits, the neuromuscular impairment, presence of ataxia and neuroinflammation observed in the mouse model of HE.ConclusionTaken together, these data suggest that the acquisition of a senescent‐like phenotype in neurons in the hippocampus and cerebellum in models of Type C HE may contribute to the pathogenesis of Type C HE. Taken together our data suggests that targeting the senescence‐like phenotype in HE may be a viable option for the development of novel therapeutic strategies.
Targeting Galanin Receptor Signaling as a Novel Therapeutic Strategy for the Treatment of Fatty Liver Disease
Authors: DeMorrow Sharon , Williams Elaina , An Su Yeon , Venter Julie , Choi Won Seog , Nadeem Yusra , Chu Christopher , Petrescu Anca 
Published: May 2022

BackgroundNon‐alcoholic fatty liver disease (NAFLD) is a common liver disease in the United States and is associated with dysregulated lipid metabolism and fat accumulation in hepatocytes (i.e. steatosis) leading to inflammation and fibrosis and cirrhosis. Galanin (Gal) is a neuropeptide with a role in food intake behavior and chronic upregulation of Gal is associated with increases in serum triglycerides, hyperinsulinemia, impaired glucose tolerance and hepatic steatosis. Targeting Gal receptor (GalR) signaling has been shown to have antifibrotic in models of cholestatic liver disease although the effects in NAFLD is unknown. The aim of this study was to evaluate the Gal/GalR axis in NAFLD and determined the effects of Gal Inhibition on the pathogenesis of NAFLD.MethodsC57Bl6 mice were fed a western diet (WD) consisting of high fat/high sugar/high cholesterol for a total of 16 weeks. At the 4 week time point, mice were treated with the GalR1/GalR2 antagonist, M40 (1 nmol, 3X per week for the duration of the experiment), or corresponding vehicle control. Serum and liver assays of Gal, triglycerides, and cholesterol were performed using commercially available kits. The expression of Gal, GalR1, GalR2, markers of steatosis (perilipin 2, PLIN2), biliary hyperplasia (cytokeratin 19, CK19), fibrosis (collagen type 1A1, Col1A1; α‐smooth muscle actin, α‐SMA) and inflammation (chemokine C‐C motif ligand 2, CCL2; tumor necrosis factor‐α, TNFα) by qPCR and immunostaining. Liver macrophages CD11b+ and CD68+ were quantified by immunohistochemistry (IHC). Liver lipid droplets (LD) were stained with Oil Red O. In vitro, HepG2 cells were used to assess the effects of M40 on palmitate (PA)‐induced LD formation.ResultsGal was significantly increased in the serum and liver of WD‐fed mice, with a corresponding increase in GalR1 and GalR2 expression. WD‐mice exhibited significant increase in serum transaminases, triglycerides and cholesterol compared to control mice, and M40 significantly reduced these indicators of liver injury. A drastic decrease in liver steatosis was also observed in M40‐treated WD‐mice compared to vehicle‐treated WD‐mice. M40 treatment also ameliorated WD‐induced increase in ductular reaction, fibrosis and liver inflammation in NAFLD mice. In vitro experiments confirmed that M40 decreased PA‐induced steatosis of HepG2.ConclusionsThe expression of Gal and its receptors GalR1 and GalR2, is enhanced in livers of mice on a WD. Treatment of WD‐fed mice with M40 reduces steatosis, intrahepatic biliary mass, fibrosis and inflammation. Therefore, targeting GalR1 and GalR2 may be a novel therapeutic option for the treatment of NAFLD.
Increased Neurovascular Vulnerability to Mild Traumatic Brain Injury in a Mouse Model of Marfan Syndrome
Authors: Curry Tala , Barrameda Mary E. , Bromberg Caitlin , Saber Maha , Rowe Rachel , Gonzales Rayna , Thomas Theresa C. , Esfandiarei Mitra 
Published: May 2022

Over 69 million traumatic brain injuries (TBIs) are reported annually worldwide, where the geriatric population are at greatest risk for prolonged morbidity and mortality. Cerebrovascular aging contributes to this increased vulnerability through extracellular matrix (ECM) impairment, vascular wall weakening and stiffening, blood‐brain barrier (BBB) permeability, and exacerbated cytokine production, yet the mechanisms behind these contributions are minimally investigated. In order to study these targets efficiently and with minimal variability, an animal model presenting these cerebrovascular alterations is required. Fibrillin‐1 (Fbn1) protein plays a role in elasticity and inflammation, and its mutation is known to lead to ECM impairment and vessel wall weakening induced by increased availability in transforming growth factor‐b (TGF‐b) and downstream production of matrix metalloproteinases (MMPs)‐2/‐9. In mice, this mutation induces vascular dysfunction by 6M of age and is a well‐established model of Marfan Syndrome.In this study, Fbn1+/‐ were utilized to test the hypothesis that Fbn1 mutation accelerates cerebrovascular rigidity, BBB permeability, and neurological alterations associated with aging, leaving the brain more vulnerable to diffuse TBI. In 6M‐ and 12M‐old Fbn1+/‐ and C57BL/6 wildtype (WT) male and female mice, posterior cerebral artery (PCA) blood flow (n=8‐10), PCA rupture point (N=3‐5/group), BBB permeability (N=2‐3/group), injury viability (N=5‐8/group), neurobehavioral severity scale (NSS) outcomes (N=10‐11/group), and microglial perturbation (N=1/group) were assessed.Our data shows that 6M‐old Fbn1+/‐ mice have decreased PCA blood flow (p<0.05), compromised PCA wall strength (p<0.05), increased BBB permeability (p<0.05), and elevated NSS scores (p<0.05) as compared to 6M‐old WT, and similar to 12M‐old WT mice. Preliminary investigation of iba‐1 staining for microglia, a supported assessment of neuroinflammation, suggests increased microglial activation in 6M‐old Fbn1+/‐ mice compared to age‐matched WT mice. To investigate vulnerability to mild TBI (mTBI), varying pulse pressures (1.11‐1.32atm) were applied to the brains of 6M‐old WT (1.25‐1.32atm) and Fbn1+/‐ (1.17‐1.21atm) mice using midline fluid percussion injury, where Fbn1+/‐ mice required lowered pressure to induce mTBI righting reflex times (5‐10 minutes).These data support that cerebrovascular aging contributes to outcome after TBI. Furthermore, this study demonstrates that Fbn1 mutation plays a critical role in the vulnerability of the aged brain to mTBI. Using this novel approach of a Marfan Syndrome mouse model that isolates cerebrovascular aging allows for the mechanistic study of potential Fbn1 downstream pathways that could serve as a therapeutic target for prevention and management of post‐concussive symptoms.
Renal Biomarker Evaluation using Data Integration in the Age of Precision Medicine
Authors: Prokop Jeremy W. 
Published: May 2022

Decades of work have given nephrology a handful of strong biomarkers of acute kidney injury (AKI), including clinical serum creatinine, blood urea nitrogen levels, and urine proteinuria. To refine the location of AKI to different regions of the nephron, proteins such as Albumin, NGAL, and KIM‐1 have been critical. Yet, many of our classical nephrology biomarkers are rarely evaluated considering broad patient pathologies and environmental factors such as viral infection. Millions of data points can inform on AKI in the data age. Thus, we have performed a systematic data analysis of ~10,000 blood sample precision transcriptomes for broad pathologies, ~200 RNA‐Seq samples for human AKI, the Comparative Toxicogenomics Database, Human Protein Atlas, GTEx, and our custom cell culture models of kidney response followed by advanced sequencing including direct RNA‐Seq. This data integration work elucidated biomarkers such as KIM‐1 can be elevated in blood due to viral infections and environmental contributors. In some patients, the elevation of KIM‐1 in the urine occurs due to blood activation and urine proteinuria instead of tubule secretion. However, refining KIM‐1 data with blood RNA‐Seq allows for identifying isoform switches that correlate to AKI and tubule damage.Further work in our data integration shows that RNA specific to tubule cells or podocytes can be observed in patient blood during AKI, suggesting a promising observable measure of detailed cell types damaged that may contribute to AKI. Finally, integrating our human GWAS and expression quantitative trait loci (eQTLs) for kidney traits elucidates the ability to map response eQTLs and mechanisms from easier to obtain blood samples that can be critical in defining AKI and chronic kidney diseases. Thus, continued revaluation of kidney biomarkers in the big data age can bring nephrology into the forefront of precision medicine.
Moderate‐to‐Vigorous Physical Activity and Time‐Restricted Eating are Predictors of Fat Mass Loss in Overweight and Obese Females Following an Eight‐Week Exercise and Dietary Intervention
Authors: Kotarsky Christopher J. , Johnson Nathaniel R. , Mahoney Sean J. , Mitchell Steven L. , Schimek Regina L. , Stastny Sherri N. , Hackney Kyle J. 
Published: May 2022

BackgroundThe American College of Sports Medicine recommends 300 minutes of moderate or 150 minutes of vigorous physical activity (MVPA) per week, in combination with proper nutrition, to obtain substantial health benefits and weight loss. Fasting dietary strategies, such as time‐restricted eating (TRE), combined with resistance exercise have been shown to reduce fat mass and maintain or increase lean mass. Concurrent exercise, the inclusion of aerobic and resistance exercise, and TRE may be a valid method for preserving lean mass during weight loss while simultaneously reducing disease risk and improving functional performance.ObjectiveThe purpose of this investigation was to determine whether average time spent in MVPA, an indicator of concurrent exercise training volume, was a predictor of fat mass loss in physically inactive overweight and obese females following an eight‐week dietary and concurrent exercise intervention, regardless of dietary group allocation. We hypothesized that MVPA will predict decreases in fat mass observed during the intervention.MethodsStepwise linear regression determined the relationship between MVPA and fat mass loss. A total of 18 females (mean ± SD; age 43.7 ± 7.3 years; BMI 29.7 ± 2.3 kgm2) were included in the analysis. Body and fat mass were assessed pre‐ and post‐exercise and dietary intervention using dual‐energy x‐ray absorptiometry. Dietary intakes were estimated using three‐day dietary logs and ESHA software at weeks one, four, and seven. Dietary group allocation was recorded as “1” for TRE and “0” for normal eating. Dietary group, age (years), height (cm), pre‐intervention body and fat mass (kg), average time spent in MVPA (min/week), average energy intake (kcal/day), and average carbohydrate, fat, and protein intake (g/day) were included in the analysis. Age was self‐reported and MVPA was assessed at weeks two, five, and eight using accelerometry.ResultsOur model explained 55.7% of the variance in fat mass changes (F2, 15= 9.424; p = 0.002). Stepwise analysis indicated that reductions in fat mass were predicted first by participation in TRE (β ± SE; ‐1.739 ± 0.451; p = 0.002) and then by time spent in MVPA (β ± SE; ‐0.004 ± 0.002; p = 0.044).ConclusionTime spent in MVPA and TRE were predictors of fat mass loss following eight weeks of dietary and concurrent exercise intervention. The significance of MVPA to the model indicates that concurrent exercise contributes to fat loss regardless of dietary pattern.
Synthesis and Conformational Analysis of APP O ‐Glycopeptides Bearing the Tn Antigen
Authors: Cudic Mare , Singh YashoNandini 
Published: May 2022

ObjectiveTo perform a conformational analysis of APP glycopeptides by CD spectroscopy and evaluate the impact of site specific mucin‐type O‐glycosylation and/or unique patterns of O‐glycan clusters proximal to secretase cleavage sites on the APP’s secondary structure.Alzheimer’s disease (AD) is characterized by the accumulation of the neurotoxic deposits of β‐amyloid peptide (Aβ) within the brain along with hyperphosphorylated and cleaved forms of the microtubule‐associated tau protein. Genetic, biochemical, and behavioral research suggest that physiologic generation of the Aβ forming fibrils stems from the proteolytic processing of the amyloid precursor protein (APP), a type 1 transmembrane glycoprotein, by β‐ and γ‐secretases. A small percent of AD is also caused by single genetic mutations that are passed down through families known as familial AD (FAD). The Swedish double mutation (Lys670Asn/Met671Leu), located near the N‐terminus region of Aβ results in a major increase in the total output of Aβ40 and Aβ42 by providing a better substrate for the β‐secretase enzyme. Recent findings suggest possible role of O‐glycosylation in APP’s proteolytic processing. However, due to the inherited complexity of protein glycosylation, the effect of O‐glycans on APP function, and its subsequent role in AD pathogenesis, remains challenging. Our preliminary data suggest that a unique type of O‐glycosylation, on the phenolic hydroxyl group of the tyrosine (Tyr681) can induce conformational change in APP and affect its proteolytic processing fate towards the amyloidogenic pathway. Intrigued by the number of mucin‐type O‐glycan sites that have been reported for APP in the proximity of β‐secretase site, we focused on three sites in this study, Thr663, Ser667 and Tyr681, modified with the simplest mucin‐type structure, O‐α‐GalNAc (Tn), to obtain an initial account of its direct impact on protein’s secondary structure. The APP glycopeptide models incorporating β‐ and α‐secretases sites, along with their Swedish‐double mutated versions, and the non‐glycosylated counterparts were synthesized by Fmoc solid phase peptide synthesis approach. Circular dichroism (CD) was used to analyze the secondary structure of peptides and evaluate the role of peptide environment on inducing conformational changes. The spectra were further analysed for secondary structure estimations by Beta Structure Selection (BeStSel) method, specifically designed for the analysis of beta sheet‐rich proteins. Our results show that conformation is strongly dependent on external conditions in the peptide environment such as buffer ions and solvent polarity as well as its internal modifications such as sequence length, O‐glycosylation, and Swedish mutation.
Altered gut microbiome structure and its association with inflammation markers in patients with Crohn’s disease in comparison to healthy siblings
Authors: Hu Jun , Cheng Sijing , Chen Wanning , Yao Jiayin , Li Yichen , Wang Wenxia , Huang Yibo , Zhu Lixin , Zhu Ruixin , Zhi Min 
Published: May 2022

BackgroundPrevious studies reported inconsistent results regarding altered gut microbiome in patients with Crohn's disease (CD), likely due to the large impact of genetic polymorphisms and environmental factors on the structure of the gut microbiota. We aim to investigate the altered microbiome in CD with a cohort that minimizes the impact of irrelevant genetic and environmental factors on the gut microbiota.MethodStool samples and clinical records were collected from 91 patients withCD and their healthy siblings in the Sixth Affiliated Hospital of Sun Yat‐sen University in Guangzhou, China, between March 2014 and December 2018. Fecal DNA was isolated and the V5‐V6 region of the 16S rRNA gene was sequenced on a MiSeq platform. Data was processed with QIIME2. Spearman analysis was performed to identify the microbial features correlated with inflammatory markers.ResultCompared to healthy siblings, CD patients exhibited reduced alpha diversities based on the metrics of Chao1, Shannon, and observed speciesat the ASV level (P<0.05). Beta diversity was significantly different between study groups according to UniFrac based principle coordinate analysis (P<0.001). Altered abundances were observed at various taxonomic levels comparing between CD patients and their healthy siblings, including increased abundance in Escherichia‐Shigella and Veillonella, and decreased abundance in Lachnospiraceae, Prevotella 9 and Faecalibacterium in CD patients. Spearman analysis identified significant correlations between Escherichia‐ Shigella and Lachnospiraceae with inflammatory markers erythrocyte sedimentation rate, C‐reactive protein, and white blood cell count (Fig.1).DiscussionBy comparing between CD patients with their siblings, the impact of the compounding genetic and environmental factors on the gut microbita was minimized. This approach allowed the identification of CD specific microbial fearures that are correlated with inflammatory markers. Further study along this line may establish CD specific microbial targets for diagnostic and therapeutic purposes.