bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prebiotics and Probiotics Maintain the Intestinal Barrier Function
Authors: Ducray Henri Alexandre Giblot , Globa Ludmila , Pustovyy Oleg , Vodyanoy Vitaly , Sorokulova Iryna 
Published: June 2021

The intestinal barrier function is crucial in maintaining the host's homeostasis, as it acts as the first protective barrier between the lumenal content and circulation. Disruptions to this protective barrier have been linked to various pathological conditions. Excessive permeability can lead to tissue damage, systemic inflammation, and even organ failure. Studies have shown that the gut microbiota and its metabolites have an essential role in the regulation of the intestinal barrier function. Negative alterations to the gut microbiota, known as dysbiosis, have been shown to be a factor involved for the increased barrier permeability. Thus, restoration of the gut microbiota can provide a novel approach for the prevention of adverse effects caused by the loss of this protective barrier. The main goal of this study was to evaluate the efficacy of a prebiotic and probiotic in maintaining the intestinal barrier integrity during heat stress.Animals were pre‐treated by oral gavage with Bacillus subtilis probiotic strain, a yeast fermentate product having prebiotic properties, or phosphate buffered saline (PBS) prior to exposure to heat stress. Control rats received identical treatments, but without the exposure to stressor. The results demonstrated that heat stress lead to significant changes to the intestinal barrier in the stressed animals pre‐treated with PBS, causing significant decreases in villi height and total mucosal thickness, and reduced expression of tight junction proteins. The level of lipopolysaccharides in serum also significantly increased in those animals. All registered adverse effects were prevented in stressed animals pre‐treated with the probiotic and prebiotic. Analysis of the gut microbiota revealed significant disruption of microbial composition only in the stressed rats pre‐treated with PBS. These results demonstrate the high efficacy of the prebiotic and probiotic in preventing the loss of the intestinal barrier function. We can speculate that the beneficial modulation of the gut microbiota could be a valuable approach for prevention of stress‐related adverse effects.Support or Funding InformationThis work was supported by Auburn University funds.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Clinical implications of the cleido‐occipitalis cervicalis muscle: A muscular variant of the trapezius muscle
Authors: Maslowski Doug J. , Snyder Sean B. , Pellis Zachary , Petrone Ashley B. , Zdilla Matthew J. , Lambert H. Wayne 
Published: June 2021

Anatomical variation in the supraclavicular region is unusual, aside from the scalene muscles. This report presents a left‐sided cleido‐occipitalis cervicalis muscle found during routine dissection of an 87 year‐old female body donor. The variant muscle traveled from the occipital bone as part of the trapezius muscle, before deviating from the trapezius to descend inferiorly in the neck to insert into the superior and posterior aspect of the middle of the clavicle. As it traveled inferiorly towards the clavicle, the variant muscle passed immediately superficial to the transverse cervical artery. The muscle was innervated by the accessory nerve (or CN XI). With regard to clinical relevancy during imaging and physical examination, the cleido‐occipitalis cervicalis muscle may appear to be an arterial aneurysm, thrombosed vein, lymphovenous malformation, neck cyst, tumor, enlarged lymph node, or other soft tissue pathology. Within the literature, it has been reported that it may be difficult to distinguish the cleido‐occipitalis cervicalis muscle from the levator claviculae muscle, which is a more common muscular variant within the lateral cervical triangle. Furthermore, the presence of the cleido‐occipitalis cervicalis may present difficulty in the management of clavicular fractures— the most common type of bone fracture.Support or Funding InformationWVU Initiation to Research Opportunities (INTRO) ProgramThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Alternative mechanisms of ribosome stalling rescue in the gram‐negative bacterium Francisella tularensis
Authors: Srinivas Pooja , Goralski Tyler D. P. , Keiler Kenneth C. , Dunham Christine M. 
Published: June 2021

The number of new antibiotics being developed has plateaued, particularly compared to the sharp increase in antibiotic‐resistant bacteria plaguing humanity. Many current antibiotics target the bacterial ribosome, but have cross‐reactivity with eukaryotic ribosomes, causing host toxicity. One approach to prevent this is the identification and development of antibiotics that target bacterial‐specific pathways, such as ribosome stalling rescue. At any given moment, 5–10% of E. coli ribosomes are stalled. Stalled ribosome complexes arise when the ribosome halts during translation, which may arise due to the absence of an in‐frame stop codon, depletion of aminoacyl‐tRNAs, or proline‐rich motifs. Trans‐translation, found in 99.9% of bacterial species, is the main rescue pathway for stalled complexes that arise due to no in‐frame stop codon. Most bacteria remain viable without trans‐translation because they encode additional rescue systems, such as Alternative Rescue Factor A and B (ArfA and ArfB). The pathogenic bacterium F. tularensis appears to only encode trans‐translation factors, but trans‐translation deletion strains remain viable. How does F. tularensis survive without known ribosome rescue mechanisms present? Transposon mutagenesis data from the Keiler lab identifies a novel release factor, ArfT, which allows F. tularensis survival in the absence of trans‐translation. In vitro translation assays find that ArfT facilitates peptidyl‐tRNA hydrolysis with both RF1 and RF2, in contrast to the model of ArfA‐RF2‐mediated rescue in other well‐studied systems. These data suggest that ArfT‐mediated ribosome rescue occurs via a novel mechanism. Our results indicate that F. tularensis 70S‐ArfT stalled complexes have an increase of RF1 binding, suggesting a novel mechanism of recognition by RF1. Future studies include structural and biochemical characterization of the molecular mechanism of ArfT and release factor binding to stalled F. tularensis 70S ribosome complexes. These studies will provide new insights on the fundamental mechanism and role of ribosome rescue in bacteria.Support or Funding InformationT32‐GM008602 R01‐GM093278‐09S1 R01‐GM121650‐02This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Methylation of Ded1 Affects Its Role in Translation
Authors: Murvin Mickey , Yang Banruo , D'Alessandro Alec , Freniere Christian , Hilliker Angie 
Published: June 2021

Ded1p is an essential ATP‐dependent RNA helicase involved in translation initiation through association with translation factors such as eIF4A and eIF4G (1, 2), nuclear export and accumulation of stress granules. We are interested in how a post translational modification (PTM) of Ded1, methylation, modulates these roles of Ded1. The methyltransferase Hmt1 methylates Ded1 at four arginine residues in the N and C terminus (3). Methylation strengthens the interaction between Ded1 and Npl3, a protein involved in nuclear export (3). However, it is unclear how methylation impacts Ded1 in translation.To test Ded1 methylation in vivo, we mutated the four methylated arginines to either alanine or lysine. Methylation of Ded1p is not required for normal cell growth, making it unlikely that Ded1 methylation is required for global translation. However, Ded1 is important for the translation of many mRNAs, especially those with highly structured 5′ UTRs (8). We find a reporter with the highly structured CLG1 5′ UTR is not efficiently translated by a Ded1 methylation mutant, suggesting Ded1 methylation may be important for the translation of specific mRNAs.However, as the arginines are mutated, we cannot rule out another role for these arginines aside from methylation. In order to directly test the effect of Ded1 methylation on translation, we will purify recombinant wild type Ded1 protein with or without co‐expression with Hmt1. Translation efficiency of recombinant methylated versus unmethylated Ded1 protein will be tested in vitro using both simple and highly structured 5′ UTRs, such as CLG1, before a luciferase reporter. We will also perform helicase assays to test the impact of Ded1 methylation on its biochemical function.Since Ded1 interacts with other proteins through the N or C terminus, it is possible that methylation influences Ded1‐protein interactions. We use a conditional two‐hybrid assay in E. coli (3) to test the effect of methylation on Ded1's binding partners. We show methylation strengthens the known interaction between Ded1 and eIF4A. A novel interaction between Ded1 and Xrn1 and a reported oligomerization of Ded1 (4) has been validated through immunoprecipitation. Furthermore, we will test the effects of methylation on known Ded1 interactions with other translation factors such as eIF4G and eIF4E (2, 5) and RNA exporters such as Gle1 and XpoI (6, 7). Besides testing Ded1 interactions with a single binding partner, we will also test interactions between Ded1 and a combination of two different initiation factors. Ded1 is required for translation of >600 mRNAs in yeast (8). Our investigation further elucidates how methylation regulates Ded1 and its effect on mRNA translation.Support or Funding InformationNIH R15 GM128068‐01; HHMI; Arts & Sciences (UR); Smart FellowshipThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Ensemble Docking of Potential BACE1 Inhibitors for Alzheimer's Disease
Authors: Guevara Johnny , Zahran Mai 
Published: June 2021

A wealth of evidence suggests that inhibiting β‐secretase 1 (BACE1) can delay or halt the progression of Alzheimer's disease (AD). Studies have shown that small molecules able to interact with the asp dyad and the flap in the active site of BACE1 can promote inhibition. In our previous published work, six potential BACE1 inhibitors (1–6) were designed, synthesized, and evaluated by pIC50 measures obtained from in vitro FRET inhibition assays. The aim of this work was to implement an in silico ensemble docking approach to study the binding mechanism between 1–6 and flexible conformations of BACE1. We performed a 50 ns molecular dynamics (MD) simulation of a free BACE1 structure to generate an ensemble of flexible BACE1 conformations and docked 1–6 to each conformation in the ensemble. Docking results revealed 3, 5, and 1 exhibiting the most favorable binding affinities across all dockings, while retaining binding orientations relative to the catalytic asp dyad sustained by hydrogen bonds, as well as exhibiting stabilizing hydrophobic and pi‐pi interactions to flap residues. MMGBSA residue decomposition analysis further revealed residues ASP32, ASP228, and TYR71 as the main contributors for binding of 3, 5, and 1 to BACE1. Conversely, 2, 4 and 6 exhibited less favorable binding affinities and as a result formed fewer interactions to critical active site residues responsible for BACE1 inhibition. In addition, the Pearson correlation coefficient (R) values between computational binding affinity and experimental pIC50 values across all dockings, R < −0.75, showed a strong correlation between computational and experimental results. Overall, our computational results support our experimental results, provide crucial information about the binding mechanism behind our potential six BACE1 inhibitors, and highlight the importance of addressing receptor flexibility in docking simulations.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Effect of Azadirachtin on Bacterial Biofilm Formation
Authors: Kaverimanian Vishnu , Heuertz Rita 
Published: June 2021

Due to the overuse of currently available antibiotics, bacteria are rapidly evolving resistance to modern medical treatments. Because of this fact, it is important to find alternative antimicrobic agents for which bacteria have not yet developed resistance. To compound this problem, it has been identified that bacteria living in biofilms (as aggregates protected by extracellular polymeric matrix) can be up to 1000 times more antibiotic‐resistant than their planktonic counterparts. The NIH has reported that up to 80% of chronic and 65% of all human infections are biofilm‐associated. One major therapeutic alternative to modern antibiotics is phytochemicals (plant‐derived compounds). A phytochemical of interest, azadirachtin, is derived from the neem tree (Azadirachta indica) which has been historically used in the Indian subcontinent as an herbal remedy for many ailments including those caused by parasites and bacteria. A significant source of infection in hospitals is Staphylococcus aureus which is known for emerging antimicrobic resistance and tendency to form biofilms. The purpose of my project was to identify if azadirachtin inhibits biofilm formation. In order to determine the effects of azadirachtin on biofilm, a microplate biofilm quantitative assay was performed. S. aureus that were methicillin resistant (MRSA, 4 different strains) or susceptible (MSSA, 3 different strains) were assessed. Bacteria were first inoculated into tryptic soy broth (TSB) and incubated (37°C, overnight). Afterwards, bacteria were standardized to a spectrophotometric A590 of 0.1–0.2 growth. Once standardized, the bacteria were transferred to 96‐well microplates with/without azadirachtin (0–0.8 mM) and incubated (37°C, 20 h). Following incubation, bacteria were killed with glutaraldehyde and microplates were washed (three times with dH2O). Subsequently, crystal violet (0.1% aqueous) was added to stain the biofilm. Excess dye was removed by washing (three times with dH2O) and stained biofilm was solubilized (8% acetic acid). Solubilized biofilm was quantitated by A590 readings. Results indicated that azadirachtin had no significant (p<0.05) effect on mean biofilm amounts for MRSA and MSSA biofilm formation. As azadirachtin appears to elicit no anti‐biofilm effect on the Gram positive S. aureus, our next step will be to ascertain its effect on Gram negative Pseudomonas aeruginosa biofilm.Support or Funding InformationFinancial support for VK was received from the DeNardo Education and Research Foundation.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Amygdalin improves burn wound healing in diabetic rats
Authors: Haidar Hanine , Lauricella Marianna , Jurjus Rosalyn , Daouk Hisham , Leone Angelo , Capello Francesco , Eid Assaad , Jurjus Abdo 
Published: June 2021

IntroductionThe skin has a unique plasticity and regenerative abilities which are partly impaired in diabetics. On the other hand, amygdalin or vitamin B17 has an array of functions affecting inflammation and cell regeneration.AimThis study aimed to assess the effect of amygdalin on burn wound healing in diabetic ratsMaterials and methodsSixty‐four male Sprague‐Dawley rats were subjected to burn according to standard published models. Diabetes was induced by sterptozocin and treatment by vitamin B17 followed every other day for 28 days, the duration of the experiment. Biopsies were taken on days 1, 3, 7, 14, and 28 for light microscopy evaluation and cytokines modulation.ResultsHistological assessment of the burn wounds showed a remarkable improvement in earlier healing, smaller wound area and a better scar in the amygdalin treated group. In addition, a significant decrease in the inflammatory cytokines (IL‐1α, Il‐6 and IL‐12) was noted.ConclusionAmygdalin improved burn wound healing in diabetic rats, in quality and time.Support or Funding InformationPh D Program (University of Palermo and American University of Beirut)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Insulin‐like Growth Factor‐1 Receptor Signaling Regulates Adult Tendon Growth Through ERK1/2‐dependent Tenocyte Proliferation and Initiation of Protein Synthesis
Authors: Disser Nathaniel P , Sugg Kristoffer B , Kharaz Yalda Ashraf , Talarek Jeffrey R , Comerford Eithne , Mendias Christopher L 
Published: June 2021

Tendon fibroblasts, or tenocytes, are the main cell type in tendon and serve to synthesize and maintain collagen fibrils and other extracellular matrix proteins within the tissue. Despite the high prevalence of tendon injury, the underlying biological mechanisms of postnatal tendon growth and repair are not well understood. Insulin‐like growth factor (IGF‐1) signaling is stimulated by growth hormone (GH) and promotes the growth and development of many different tissue types. While IGF‐1 is a potent hypertrophic signaling molecule in skeletal muscle, less is known about the role of IGF‐1 in tendon biology. Therefore, the purpose of this study was to determine the importance of IGF‐1 signaling in postnatal tendon growth. Our hypothesis was that IGF‐1 signaling is required for the response of tendon to a mechanical load stimulus. To test this hypothesis, we used both in vitro studies of cultured tenocytes, and in vivo studies using genetically modified mice that allowed us to delete the IGF‐1 receptor (IGF1R) specifically in tenocytes. Treatment of tenocytes in vitro with IGF‐1 increased the expression of Mki67 transcript levels after 24 hours, and resulted in activation of the Akt and ERK1/2 pathways. When tenocyte proliferative activity was measured, cells treated with IGF‐1 displayed increased proliferation compared to controls, but inhibition of ERK prevented the IGF‐1‐mediated increase in cell proliferation and Mki67 (Ki67) expression. Inhibition of Akt signaling did not impact tenocyte proliferation or Mki67 expression. In addition, treatment of tenocytes with IGF1 increased the rate of protein synthesis and ribosomal RNA expression. Analysis of mechanically overloaded plantaris tendons in vivo revealed significantly reduced size of the neotendon matrix which forms around the original tendon in response to mechanical loads, and total tendon cross‐sectional area (CSA) at 14 days in the IGF‐1 knockdown mice compared to the controls. This was accompanied by decreased number of proliferating cells and proteins involved in cell proliferation and initiation of translation, as measured by proteomic analysis. The results of this work support IGF‐1 signaling as a fundamental component of postnatal tendon growth in response to mechanical loading, specifically through the regulation of ERK1/2‐dependent tenocyte proliferation and initiation of protein synthesis. Further studies of the growth factors and proteins involved, and the potential to evaluate IGF‐1 to promote tendon regeneration, are warranted.Support or Funding InformationNIH R01‐AR063649 and F32‐AR067086.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Effect of Norepinephrine on Gut Bacterial Community Structure and Function
Authors: Menon Rani , Fitzsimmons Ben , Vanajakumari Manoj U , Lee Kyongbum , Jayaraman Arul 
Published: June 2021

Metabolites produced by both the microbial community and the host are present in the gastrointestinal tract environment. Several metabolites have been identified as important mediators of different physiological functions in the host. Small molecules and metabolites produced by commensal bacteria resident in the gastrointestinal tract can both promote and attenuate colonization of pathogens and inflammation. However, interactions between different metabolites in the GI tract and their net effect on the host are poorly understood. We hypothesized that NE promotes EHEC virulence by altering the microbial community structure and function to facilitate colonization. An in vitro anaerobic batch culture system was used to investigate the effect of NE on the microbial community structure and function. Cecal contents from 6–8 week‐old mice (n = 7) were both collected and cultured anaerobically in Gut Microbiota Medium (GMM) with or without NE (500μM) at 37°C for seven days. Exposure to NE increased the diversity of the bacterial community (p < 0.05, Mann‐Whitney test), as determined from 16S rRNA sequencing. Genera containing facultative pathogens and reported with pro‐inflammatory roles like Hathewaya, Clostridium and Streptococcus were highly abundant in the NE group while beneficial bacterial genera like Lactobacillus were decreased in abundance with NE treatment. Untargeted LC‐MS metabolomics showed significant changes in the levels of metabolites derived from aromatic amino acids. Targeted LC‐MS metabolomics analysis confirmed that the tryptophan metabolites indole and 5‐hydroxyindole were significantly decreased and tyramine was increased with NE treatment (p < 0.05, Wilcoxon test). Integration of metabolomic and metagenomic data using partial least squares regression (PLS‐R) showed correlation between the downregulation of indole and indole producing bacteria in the presence of NE. NE also down‐regulated the expression of the enzyme Tryptophanase A (TnaA) that is required for the conversion of dietary tryptophan to indole, in both nonpathogenic E. coli and EHEC. These results suggest that NE can modulate the microbial community composition and metabolite output to potentially increase pathogen colonization and infection.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.