bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interactions between Campylobacter jejuni and AB5 toxins in the gut
Authors: Szymanski Christine M. , Patry Robert T. , Stahl Martin , Sacher Jessica C , Vallance Bruce A. 
Published: November 2023

Campylobacter jejuni is a ubiquitous commensal in chickens, but a major cause of human diarrheal disease worldwide. To avoid immune detection by its host, most C. jejuni isolates express human ganglioside‐mimicking lipooligosaccharide (LOS) structures and it has been shown that host recognition of these antigens as non‐self results in the development of Guillain‐Barré syndrome. In addition to immune evasion, expression of ganglioside mimics in C. jejuni has been associated with improved host cell invasion and resistance to human serum. Although only positive benefits for ganglioside mimic expression have been described for C. jejuni, the organism has the ability to quickly switch off the mimicry through a phase‐variable galactosyltransferase, CgtB, involved in LOS biosynthesis. Vibrio cholerae secretes the bacteriophage‐encoded cholera toxin (CT) which binds to GM1 ganglioside structures on human cells as well as to C. jejuni GM1 ganglioside‐mimics. Enterotoxigenic Escherichia coli secretes heat‐labile enterotoxin I (LT), which also binds to these structures. Since C. jejuni, V. cholerae and E. coli can co‐infect the same niche, we examined the effects of these AB5 toxins on C. jejuni biology in order to determine if this relationship could represent a new mechanism for interpathogen competition in the intestine. We demonstrate that CT and LT specifically bind only to C. jejuni strains expressing GM1 mimics. Interestingly, our experiments show that addition of CT or LT to C. jejuni strains expressing GM1‐mimicking LOS partially clears cell growth on agar. LOS from bacteria remaining inside these zones of clearance was isolated and compared to LOS from untreated bacteria. SDS‐PAGE and silver staining of the LOS showed the loss of a band from the exposed cells compared to untreated cells, and Western blot analysis revealed reduced binding of LOS to CT. Sequencing cgtB in these two groups demonstrated that this enzyme is “on” or “off” in the unexposed group, while cgtB in the CT‐ and LT‐treated cells showed a frameshift mutation, causing premature truncation of the galactosyltransferase. Examination of an engineered E. coli strain expressing GM1 mimics shows that CT is capable of binding to the mimicking cells without inducing growth clearance, pointing toward a Campylobacter‐specific mechanism of action. These results suggest that CT and LT have a negative influence on C. jejuni and could contribute to competition between these pathogens. Further studies describing the interactions between these zoonotic pathogens, the resident gut microbiome and poultry will be described.Support or Funding InformationCMS is an Alberta Innovates Technology Futures iCORE Strategic Chair in Bacterial Glycomics.
Potential of Hyperspectral Imaging for Label‐free Tissue and Pathology Classification
Authors: Deal Joshua Andrew , Favreau Peter , Weber David , Rich Tom , Leavesley Silas 
Published: November 2023

The ultimate goal of this project is to develop a novel imaging system that allows classification of both normal and pathogenic tissues based on fluorescence excitation spectra. Current imaging diagnostic techniques have limited capacity to classify normal tissue or detect pathogenic states. In vivo imaging suffers from poor signal to noise ratios and excessive data acquisition times while most alternative imaging techniques offer little molecular specificity. Our previous research has shown that excitation scanning hyperspectral imaging produces image data with high signal to noise ratios, fast acquisition times, and the potential to determine molecular composition. Here, we present data comparing characteristic spectral signatures for a range of tissue types. These data serve as a basis for establishing normal tissue spectra and characterizing molecular composition per tissue type. Tissues from Sprague Dawley rats were collected as 2 cm cubes and stored in cold PBS. Immediately following harvest, a custom inverted microscope (TE‐2000, Nikon Instruments) with a Xe arc lamp and an array of thin film tunable filters (VersaChrone, Semrock, Inc.) were used to collect hyperspectral image data from each sample. Scans utilized excitation wavelengths from 360nm to 600nm in 5nm increments. Three fields of view were recorded for each sample. Hyperspectral images were analyzed with custom Matlab scripts including linear spectral unmixing (LSU), principal component analysis (PCA), and Gaussian mixture modeling (GMM). Spectra were examined for potential characteristic features such as unique intensity peaks at specific wavelengths or ratios between intensity peaks. The resultant spectra vary among tissues types, which alludes to a unique spectral signature per tissue type. Additionally, excitation spectra appear to be a mixture of pure endmembers with commonalities in multiple tissue types, potentially identifiable through GMM. These results suggest that most tissues have common molecules and that intensity ratios of these molecules may serve as a signature for characterizing tissue composition. In addition, variations in signatures could indicate a change in molecular composition coincident with changes in pathology. Thus, excitation scanning hyperspectral imaging may be a potential diagnostic tool with the ability to distinguish tissues of varying pathology.Support or Funding InformationThis work is supported by P01HL066299 and the Abraham Mitchell Cancer Research Fund.
EXPEL: A Novel Non‐Destructive Method for Mining Soluble Tumor Biomarkers
Authors: Turtoi Andrei , Costanza Brunella , Peulen Olivier , Bellahcène Akeila , De Pauw Edwin , Detry Olivier , Delvenne Philippe , Castronovo Vincent 
Published: November 2023

The search for biomarkers able to detect and evaluate disease such as cancer at an early stage, or to predict resistance and response to therapies, has been and remains a major challenge. Despite very important progresses in all fields of omics technologies, the success of discovery of clinically valuable biomarkers is surprisingly disappointing. Difficult mining of secreted proteins in biological fluids poses the first major hurdle, mainly because the concentration of interesting proteins in serum or urine is generally very low. The second key limitation in the field is the inaccessibility of tissue specimens from early lesions. Those are routinely required in their integrity for the complete histological evaluation in the clinical routine, leaving no residual material for research (e.g. colonic polyps). Here we present an innovative procedure that we have named EXPEL, which entirely overcomes these limitations. It makes any tissue, regardless of its size, available for both omics research and histological investigation. Our original device and approach extracts soluble tumor biomarkers and small metabolites within few minutes and without altering the tissue morphology. For this purpose a small tissue biopsy is incubated in a slightly hypertonic extraction buffer while subjected to alternating pressure. Upon extraction the tissue is fixed in formalin and can be used for histological analysis. The soluble extract is further prepared for proteomic and metabolomic analysis. In a proof of concept study we have extracted and analyzed soluble biomarkers from human colorectal carcinoma liver metastases (N=10) as well as primary colorectal tumors (N=10). Immunohistochemistry (IHC)‐based validation demonstrates that EXPEL procedure does not alter tissue morphology or any subsequent molecular and pathological tests. The comparison of proteins and metabolites identified in tumor lesions with those found in adjacent normal tissues revealed a promising group of novel and differentially expressed targets. Their potential usefulness as diagnostic or predictive markers is currently being explored in larger cohort of patients using IHC on tissue and ELISA on blood samples.Support or Funding InformationThe present work has been supported by FNRS Televie grant and funding from Mithra Pharma Co.
Single‐cell biomarker detection identifies heterogeneity within cancer populations
Authors: Weldon Don , Williams Yuko , Patel Amish 
Published: November 2023

Understanding a complex biological system such as a cancerous tumor is already a difficult endeavor. Further, this complexity is compounded given the multiple cell subpopulations found in cancer tissue (e.g., cancer stem cells), broadly described as tumor heterogeneity. The significance of tumor heterogeneity is best understood when examined at the cellular level, where distinct differences in gene expression, signaling pathways, nutrient requirements can contribute to a diverse and dynamic microenvironment, which has already been implicated as a key factor in chemotherapy resistance. With so many distinct factors at play performing bulk measurements on a subset of cells will limit the ability to understand key differences which exist at the single cell level.Traditional methods tend to measure RNA expression globally, with cell lysis and fixation steps resulting in a loss of key information about individual cells, making it challenging to properly assay the genetic heterogeneity within cell populations. Analyzing the relationships between gene expression and biological processes involved in the development and progression of cancer requires analysis at single cell resolution. We have developed a single cell biomarker tool for sequence‐specific detection of gene expression in live cells without altering viability or inherent biology. In addition to detection of cellular heterogeneity within researchers’ samples, the live single cell compatibility enables enrichment and further characterization of cell subpopulations based on RNA expression through Fluorescent Activated Cell Sorting (FACS).Here, we describe live single cell detection of cancer biomarkers within heterogeneous cell models. Breast cancer cell lines were co‐cultured in specific ratios to mimic heterogeneous breast cancer populations. Subsequent characterization of the populations was performed by both flow cytometry using fluorescent live‐cell RNA detection probes, and quantitative real‐time PCR. Additionally, we analyzed miR‐221 expression in a mixture of T47D and MDA‐MB‐231 breast cancer cell lines, which allowed us to sort the two cell types based on differential expression of this microRNA. Subsequently after culturing the sorted cells we were able to perform downstream IHC analysis of vimentin and E‐cadherin, two protein markers known to be associated with the epithelial‐to‐mesenchymal transition during tumor progression.Single cell analysis of populations with varied gene expression allows a better understanding of the inherent differences that exist within the population. The ability to identify differences in gene expression within live cells allows scientists to formulate novel questions and design experiments that better address the importance of gene expression heterogeneity in normal and disease states. This is particularly true in cancer where alterations in gene expression within specific cell subpopulations can play a role in resistance to standard drug therapies.
Regulation of p65‐β‐catenin Complex And Its Targets in Liver Injury And Regeneration
Authors: Nejak‐Bowen Kari , Cornuet Pamela K , Monga Satdarshan P 
Published: November 2023

We have previously reported the identification of a complex between β‐catenin and the p65 subunit of NF‐κB. Further, we have shown that β‐catenin sequesters p65 in the cytosol to prevent it from translocating to the nucleus, and that lack of p65‐β‐catenin complex in liver‐specific β‐catenin knockout (KO1) mice enhances survival due to enhanced p65 nuclear translocation and activation. To determine the signaling pathways regulating this complex during acute liver injury, we injected galactosamine (GalN) followed by lipopolysaccharide (LPS), which activates the TNF‐α pathway, into liver‐specific LRP5‐6 double KO mice (KO2) and wild‐type littermate controls (WT). Unlike KO1, KO2 phenocopy WT and show comparable morbidity, apoptosis, liver weight to body weight ratio, and alanine aminotransferase (ALT) levels. This is due to existence of the β‐catenin‐p65 complex in KO2 as opposed to its absence in KO1. These observations also suggest that the β‐catenin‐p65 association is autonomous of Wnt signaling since lack of LRP5‐6 in hepatocytes prevents Wnt communication to β‐catenin. Treatment of Hep3B hepatoma cells with TNF‐α, or of WT mice with GalN/LPS, induced dissociation of the β‐catenin‐p65 complex, implicating TNF‐α signaling in the regulation of this association. Since cyclin D1 is a target of both NF‐κB and β‐catenin, we next examined the role of the p65‐β‐catenin complex in hepatocyte proliferation. In hepatoma cells, TNF‐α induced p65 reporter activity; however, it had no effect on either TOPflash or cyclin D1 reporter. Further, while β‐catenin suppression decreased both cyclin D1 reporter activity and cell proliferation, these functions were unchanged in the presence of p65 siRNA. We then characterized the association and expression of NF‐κB and β‐catenin during liver regeneration and demonstrated translocation of these two proteins in the nucleus within hours after partial hepatectomy, which preceded a 2.5‐fold increase in cyclin‐D1 mRNA. However, using inducible NF‐κB lacZ reporter mice, we found p65 activity to be confined exclusively to the NPC compartment during liver regeneration. Thus we conclude that hepatocyte proliferation is independent of p65 but requires β‐catenin, and that p65 and β‐catenin activation are occurring in disparate cell types during early liver regeneration. The distinct roles of β‐catenin and p65 in proliferation and survival, respectively, offer opportunities for manipulation of this complex to optimize regenerative therapies.Support or Funding InformationThis study was funded by NIH grants 1R01DK62277 to SPSM and by the American Liver Foundation's Thomas E. Starzl, MD Postdoctoral Research Fellowship to KNB.
Synonymous Codon Changes in Measles (HMV) and Canine Distemper (CDV) Viral Nucleic Acid Sequences Result in Gene‐Specific Changes in Levels of Viral Protein Expression
Authors: Uhl Elizabeth W , Osborn Michelle L , Michel Frank J , Hogan Robert J 
Published: November 2023

The purpose of this study was to characterize the effects of human and canine codon optimization on expression of viral proteins from HMV and CDV nucleic acid sequences. All the codon changes made were synonymous in that the amino acid coded for was unchanged. The human and canine CUB optimized HMV and CDV sequences had increased nucleic acid and codon identity as compared to the WT sequences. Protein expression from human and canine CUB optimized and sub‐optimized constructs of the N, F, M, H and P/C proteins was assessed in transfected human (293 HEK) and canine (A‐72) cells using fluorescence, Cellomic and, for proteins for which antibodies were available, western analysis.Results1) codon optimization increased protein expression of HMV and CDV N and F proteins in both cell lines; 2) synonymous codon changes did not affect expression of the HMV and CDV P and C and the HMV M proteins, but both optimization and sub‐optimization to canine CUB increased expression of the CDV M protein in human cells; 3) synonymous codon changes increased expression of the HMV H protein in both cell lines, but did not significantly affect CDV H protein expression. Overall both CUB optimization and sub‐optimization affected protein expression independent of viral infection in ways that varied with the gene and cell type, and differed between HMV and CDV. These results indicate that synonymous codon changes in viral nucleic acid sequences can alter protein expression in a variety of ways, some of which are likely to impact viral pathogenicity.Support or Funding InformationThis project was sponsored by the Department of Defense Threat Reduction Agency. The content of the information does not necessarily reflect the position or the policy of the federal government, and no official endorsement should be inferred.
Brainstem pathology induces peripheral changes correlating with hippocampal markers of Alzheimer's disease in animal model
Authors: Filipcik Peter , Cente Martin , Zorad Stefan , Fecik Miroslav , Novak Michal 
Published: November 2023

Alzheimer's disease (AD) and related tauopathies are difficult to diagnose in early phase and their diseases modifying treatment is still missing. Epidemiological studies indicate relationships between AD and level of leptin in blood. However, the mechanistic link behind this association is not yet defined. Here, we investigated the link between selected metabolic parameters including leptin and pathogenic markers of neurodegeneration in a transgenic rat model of AD.Brains of transgenic rats expressing human truncated tau protein, whose primary sequence was designed according to AD‐core tau protein, were analysed in pre‐symptomatic and terminal phase of disease. The data were correlated with biochemical parameters such as glucose, insulin and lipids in plasma. We found that development of AD pathology leads to reduction of body weight accompanied with significant decrease in level of plasma leptin in transgenic animal model of sporadic AD. The plasma leptin inversely and significantly correlates with amount of hippocampal tau proteins hyperphosphorylated on several AD‐specific epitopes. Moreover, the strong inverse correlation between the load of neurofibrillary pathology and peripheral levels of leptin was observed.We provide a molecular evidence and experimental confirmation for association of circulating leptin and early stage of neurofibrillary degeneration in hippocampus, thus leptin could serve as a convenient peripheral biomarker, which can help to recognize an early phase of neurodegeneration.This study was supported by research grants:Slovak research and development agency APVV‐0677‐12 and VEGA 2/0147/16
Utilizing Interdisciplinary Research Experiences and Learning Communities To Engage Students in the Natural Sciences and Mathematics
Authors: Kruchten Anne 
Published: November 2023

Faculty in the biology, chemistry, math, and physics departments at Linfield College have developed an interdisciplinary STEM community through an annual iFOCUS camp for incoming students and student‐led learning communities. In August 2012, iFOCUS (Interdisciplinary First‐Year Orientation Camp for Undergraduate Sciences) engaged ten new Linfield students in collaborative research projects with Linfield faculty for a week before classes began in the fall. Primary goals for this pilot program included increasing the recruiting and retention of STEM majors, developing interdisciplinary problem solving skills through modeling and practice, and enhancing the intellectual opportunities for STEM faculty. In the fall of 2013, the first learning community was led by students interested in the field of genomics. We now report on the successes of four years of iFOCUS camp and three years of learning communities, including an increase of iFOCUS students registering for multiple STEM courses and an increase in the involvement of first year students in our research programs. We will also discuss plans for the future development of interdisciplinary science at Linfield.Support or Funding InformationFunding for this program was provided by the Hearst Foundations, Inc., and the Rose E Tucker Charitable Trust.
Geometry in Cell Biology
Authors: Lin Danielle , West Lori 
Published: November 2023

A goal of our research is to demonstrate to students the integration of geometry in biology. In order to do so, we developed an activity where elementary students can apply mathematical concepts in their biology laboratory sessions. In these activities, students first view cells using a compound light microscope. The cells are onion root tip mitosis cells. Then, using Geometer's SketchPad, they survey parallel and perpendicular lines as well as angles. In another activity, they consider a single cell and consider whether the cell is symmetrical. We demonstrated these activities to 4th and 5th grade elementary teachers. The teachers’ response was very positive. Although this experiment was developed with elementary teachers in mind, we feel that extensions of this exercise would be well suited in secondary and higher education.Support or Funding InformationThese activities were funded by the Tennessee Higher Education Commission Improving Teacher Quality program.
Comparison of High Fidelity Patient Simulation on the Retention of Physiology Concepts Over Summer Break
Authors: Jones Adriana , Harris David 
Published: November 2023

It is well known that medical students experience significant knowledge loss over long breaks such as summer. Likewise, active learning methods, where students are involved in doing things and thinking about things, have been shown to improve retention of material versus passive learning. Therefore, high fidelity patient simulations (HFPS) which are an engaging, active learning activity, may promote better long term retention of physiology covered. The purpose of this study is to determine if medical students’ long‐term retention of physiology concepts is enhanced through the use of HFPS.MethodsQuestions from the midterm of the physiology module were selected from topics covered by HFPS or other methods (lecture or computer based instruction) with similar averages and difficulties. 2nd year medical students were recruited to take a formative set of different questions comparing physiology topics covered in HFPS vs other teaching methods about 6 months later. Student scores from the formative questions were compared with performance on the midterm to determine knowledge loss.ResultsForty of about 120 students participated in the formative test in Year 2 six months later.DiscussionDeveloping ways to prevent knowledge loss and facilitate retention of material in students should become part of a “best practices” approach for faculty. Active learning methods such as HFPS may be an avenue to facilitate better and more efficient learning of physiology material.
Quantitative and Qualitative Analysis of Medical Students’ Research Output in Six Developing Countries
Authors: Obad Adam S. , Albarqawi Haneen T. , Eshaq Abdulaziz M. , Hoilat Hudie N. , Al‐Khateeb Abdulrahman A. , Fothan Ahmed M. , AlSaffar Alaa H. , Al‐Najjar Wedad M. , Bakather Abdulrahman M. , Shareef Mohammad A. , Khan Tehreem A. , AlAmodi Abdulhadi A. 
Published: November 2023

BackgroundPublishing in peer‐review journals is among the useful outcomes resulting from participating in medical research. In particular, medical students perceive it as important aspect of improving employment chances and associated with long term academic career success. There is lack in studies with objective measure assessing the medical students’ research output in developing countries. This study aims to investigate the quantity and quality of medical students’ research output in the Gulf Cooperation Council countries (GCC).Methodsabstracts presented by medical students in the medical students GCC conference were subject to analysis. Abstracts which propagated into full‐length articles were subject to further demographic analysis in which information in regard to type of study, field of study, country of origin, mode of presentation and journal's impact factor were collected.Results798 abstracts were studies, and 19% (n=155) were found to be published for all the GCC countries with average impact factor of 1.85 ± 0.26 (SE). Countries which recorded the highest conversion rats in descending order were Saudi Arabia, United Arab of Emirates, Oman, Bahrain and Kuwait. Moreover, basic biomedical and clinical research topics were to be likely more publishable than community oriented and medical education related topics.Conclusioneffective efforts should be promoted to encourage more medical students” research output in the GCC countries with focusing on qualitative aspects too to reach the numbers reported by developed countries.