bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Lysin A from Two Novel Mycobacteriophages
Authors: Surendranathan Nandini 
Published: November 2023

As antibiotic resistant bacteria increase in prevalence, bacteriophage have been studied as an alternative to traditional antimicrobials. Through the Phage Hunters project funded by the Howard Hughes Medical Institute (HHMI), students have discovered over fifteen hundred novel bacteriophages that infect Mycobacterium smegmatis (M.Smeg), a bacterium related to Mycobacterium tuberculosis. At Montclair State University, the program has resulted in the isolation and genomic sequencing of numerous phage variants over the past five years. However, while multiple phages have been identified and sequenced, the genes required for their infectivity have not been studied as extensively. In order to gain a better understanding of how these bacteriophage function, this project has focused on the bioinformatic analysis and protein characterization of one gene, Lysin A, in two isolated bacteriophage, ShiVal and TeardropMSU. Lysin A is a protein that enables the virus to break out of the host and has the potential to serve as an antibiotic in its own right. ShiVal is part of the mycobacteriophage cluster B, the second largest group, while TeardropMSU is member of the mycobacteriophage cluster E. Structurally, Lysin A requires a murimidase homology sequence as well as a Zn+ binding site and peptidoglycan binding site that enables the enzyme to hydrolyze peptidoglycan. The bioinformatics data indicates that, while some of these critical regions appear in both sequences, there is only a three percent identity between Lysin A of the two bacteriophage which suggests that both lysins could be structurally different from one other. In addition to analyzing sequence comparisons between the two genes, Lysin A was directly isolated from ShiVal and TeardropMSU using PCR. TeardropMSU Lysin A was inserted into a cloning vector to allow for insertion into an expression vector. Protein expression and analysis of these two forms of the protein will allow us to clarify the mechanism of Lysin A activity and determine how the structural differences impact enzyme function.Support or Funding InformationI would like to thank the Science Honors Innovation Program (SHIP) and the department of Biology and Molecular Biology at Montclair State University.
Association of Acid Phosphatase‐1 (ACP1) Gene Polymorphism with MAI infection.
Authors: ANDAVOLU Radhika Gade , Al Sarabi Rubakovic Anastasia , Rodriguez Olivia Gade , Stafford Catherine 
Published: November 2023

Human acid phosphatases are normally found at low concentrations. However, pronounced changes in their synthesis occur in particular diseases, where unusually high or low enzyme expression is seen as part of the pathophysiological process. Acid Phosphatase locus 1 (ACP1) is a polymorphic enzyme controlled by a locus on chromosome 2 with three common codominant alleles: *A, *B, and *C. ACP1 shows two major isoforms, F and S. Genetic polymorphisms could contribute to natural resistance or susceptibility to the disease. Genetic screens in humans link polymorphisms in or near the ACP1 locus to a variety of inflammatory diseases including allergy and asthma. ACP1 is involved in activation, adhesion, and differentiation of T cells. Though few studies have shown the presence of ACP in human tissues, no studies have been reported linking ACP1 gene polymorphism to susceptibility to infections. In this study we investigate the role of ACP1 gene polymorphism in patients infected with Mycobacterium avium and normal healthy subjects. Mycobacterium avium complex (MAC) consists of two species: M avium and M intracellulare; because these species are difficult to differentiate, they are also collectively referred to as Mycobacterium avium‐intracellulare (MAI). Mycobacterium avium is an environmental microorganism which also exists in multiple hosts, including humans. M. avium can invade and replicate in immunocompromised hosts and also enhances permissiveness for HIV‐1 infection. DNA was extracted from blood and PCR‐RFLP method was used to detect ACP‐1 gene polymorphism. Our study showed high frequency of ACP AB haplotype (44%) in patients with infection than in individuals with no infection (24.8%) showing a significant association with infection (p<0.006). This is the first study to show an association of ACP1 gene with MAI. Our study highlights the role of gene/s polymorphism and their possible association with infection.Support or Funding InformationEisenhower Medical Center Research funds for Infectious disease.,
Targeting sigma factor controlled signaling pathways to modulate biofilm growth and composition
Authors: Ryno Lisa M , Brezel Emma R , Loewus Sarel J , Zheng Erica J 
Published: November 2023

Stress‐responsive transcription factors (TFs) and alternative sigma factor TFs control a multitude of downstream targets, some of which may have a direct impact on the formation of bacterial biofilm and the composition of the extracellular polymeric matrix (EPS) surrounding the biofilm. We explore the effect of moderate overexpression of several different alternative sigma factor TFs on biofilm growth using a variety of biochemical and analytical assays. Biofilm growth is monitored by a dye‐binding microtiter plate assay, and the EPS composition, specifically the concentration of proteins and polysaccharides, is monitored by colorimetric assays and FT‐IR spectroscopy. We monitor the known downstream targets of these TFs using quantitative real‐time PCR (qPCR) to confirm TF overexpression. Currently, we are exploring the impact of overexpressing sigma factors rpoH, normally upregulated upon heat shock, and rpoF, an alternative sigma factor responsible for the expression of chemotaxis receptors and flagellar assembly, on biofilm formation and composition.Support or Funding InformationThis work was supported by Oberlin College.
Suppression of biofilm formation in Staphylococcus aureus by targeting Staphylococcal accessory regulator X expression using siHybrids
Authors: Morrow Mikayla 
Published: November 2023

Nosocomial infections are becoming increasingly prevalent due to the ability of bacteria to adhere to implanted medical devices. Over 600,000 prosthetic joint replacements are performed yearly in the United States, with approximately 2% of those cases developing infections. The implantation of cardiac valves has increased by 42%, but with a corresponding 210% increased infection rate of Staphylococcus gram‐positive bacteria. S. aureus accounts for up to 73% of these infections. The ability of bacteria to adhere to the hard surfaces of medical devices is due to production of a biofilm, which is initiated by the secretion of polysaccharide intercellular adhesion (PIA) molecules. In Staphylococcal species, PIA production and regulation is controlled by the icaADBC (ica) operon, a sequence of four genes that are all involved in the production of PIA molecules. The icaA gene produces an N‐acetyl‐glucosaminyltransferase like protein, with the icaD gene product enhancing its activity. The icaC gene encodes a membrane protein that initiates the production of longer chains of polysaccharides and their translocation to the cell surface, while the icaB product is responsible for deacetylating the poly‐N‐acetylglucosamine ica transcript.The ica locus has several known activators and repressors. One of the best‐characterized factors is the staphylococcal accessory regulator A (sarA), which functions as an activator of the locus. Research has shown that when sarA transcripts are suppressed, biofilm growth is repressed. SarX is closely homologous to SarA and is believed to share similar, activating functions; however, the product of the sarX locus is not as well characterized. We investigated if sarX function can be suppressed through the use of sequence specific siHybrids, and if so, whether suppressing sarX has a repressing effect on biofilm development in Staphylococcus aureus. We hypothesized that suppression of sarX will cause repression of biofilm formation. S. aureus was passively transformed with siHybrids and the resulting biofilm growth was measured using crystal violet staining. RNA was isolated from transformed bacteria to determine if levels of sarX transcripts had changed. SiHybrid treatment groups were compared to three controls: an untreated S. aureus positive control, a sterile media negative control, and an E. coli negative control. The results indicated that repressing biofilm growth through the suppression of sarX transcripts with siHybrids led to a seventeen to forty percent decrease in biofilm formation. An ANOVA with a p‐value of 0.5 was used to determine significance. Inhibition of S. aureus at the molecular level, by targeting the RNA transcripts of the icaADBC activator, sarX, presents a novel treatment for nosocomial infections.
Understanding the mechanical stresses of sexually selected structures; is baculum remodelling influenced by the frequency of sex?
Authors: Dean Matthew , Schultz Nicholas G. , Huttenlocker Adam K 
Published: November 2023

In about 80% of mammalian species, males have a bone in their penis called a baculum. The baculum displays astonishing morphological diversity, likely driven by a combination of adaptive processes that may relate to male‐male competition and male‐female interactions, although specific function(s) remain unknown. Bones continuously remodel themselves in response to the magnitude and direction of stresses they experience. Characterization of such remodelling in the baculum may help uncover its function during copulation. Here we compare patterns of baculum remodeling in mice, comparing two treatments (regular sex versus no sex) to understand whether copulation strains the baculum. These studies are important for illuminating the mechanical forces imparted by structures thought to be important for sexual selection.Support or Funding InformationNational Institutes of Health R01‐GM098536
Microbial Masterpieces: Bacterial community profiling in the Hastings College art buildings
Authors: Athy Sienna , Tidwell Elizabeth , Laederach Alain , Solem Amanda 
Published: November 2023

Several large initiatives such as the Human Microbiome Project (NIH), the Earth Microbiome Project and Microbiology of the Built Environement (Alfred P. Sloan Foundation) as well as many smaller scale projects are exploring the composition and dynamics of bacterial communities to better understand how microbes impact our world from ecology to human health. The advent of high‐throughput sequencing techniques allows sequencing of the variable regions of the 16S rRNA gene from many samples. The 16S rRNA sequence is useful for differentiating between bacteria due to the fact that the gene is present in all bacteria, but contains variable regions. These 16S sequences can be used to identify the diversity and composition of Operational Taxonomic Units (OTUs) to characterize the bacterial community. Here we profile the bacterial communities found in the recently used Art building and the newly constructed Jackson Dinsdale Art Center on the Hastings College campus. Both Art buildings include different types of rooms such as faculty offices, a glass blowing studio and a painting studio. From the collected samples, DNA was extracted and PCR was used to amplify and isolate the 16S rRNA v4 sequence. These samples were then sent for high throughput sequencing for further analysis. This is an ongoing study; initial samples were collected shortly after construction finished and we plan to continue monitoring the bacterial community profiles in the Jackson Dinsdale Art Center periodically now that the facility is in use. The results will contribute to our overall understanding of the microbiology of the built environment in general and specifically at Hastings College.Support or Funding InformationThis work was supported by the Student Development Fund and the Excelsior Scholar program at Hastings College.
Association Between the Serum Metabolome and All‐Cause Mortality: A Prospective Analysis in the Alpha‐Tocopherol, Beta‐Carotene Cancer Prevention (ATBC) Study Cohort
Authors: Huang Jiaqi , Weinstein Stephanie J. , Moore Steven C. , Sampson Joshua N. , Albanes Demetrius 
Published: November 2023

Tobacco smoking, hypertension, hyperglycemia, overweight, and inactivity are the leading causes of mortality worldwide. Beyond these factors, prospective metabolomic profiling may help identify individuals at higher risk of death and point to molecular factors and biological pathways that have preventive potential. We conducted a serum metabolomic analysis of 667 men included as controls in 6 nested case‐control studies in the Alpha‐Tocopherol, Beta‐Carotene Cancer Prevention (ATBC) Study. During up to 28 years of follow‐up, there were 457 deaths, including 199 deaths from cardiovascular disease (CVD) and 112 deaths from cancer. Ultra‐high performance LC/MS and GC/MS (Metabolon, Inc., NC) identified 1,173 known metabolites, and 375 metabolites were retained for analysis after excluding those missing in ≥2 of the study sets. We modeled the relationship between each metabolite and risk of death by cox regression and report the set of metabolites where the False Discovery Rate (FDR) q‐value<0.02. We next split the data into training and test sets. Using only the training set, we selected those metabolites (N=14) with an FDR q‐value of <0.15 and included all selected metabolites in a multivariable cox regression. In the test set, we constructed a metabolomic score, where each individual's metabolite levels were weighted by the coefficients from the regression model, and categorized individuals into tertiles according to their score. All models were adjusted for mortality risk factors. 7‐Methylguanine, N‐acetylvaline, taurocholate, N‐acetyltryptophan, 5,6‐dihydrothymine, homocitrulline, dimethylglycine, myristoleate (14:1n5), palmitoleate (16:1n7), C‐glycosyltryptophan, taurochenodeoxycholate, 5‐dodecenoate (12:1n7), erythronate, N1‐methylguanosine, N‐formylmethionine, and hexanoylcarnitine yielded the strongest metabolite risk signals at a threshold of FDR q‐value <0.02 (0.05≤β≤0.07, and 2.0×10−6≤P≤4.6×10−4, respectively). The validation analysis in the test‐set showed that individuals in the 2nd and 3rd tertiles of the metabolite risk score experienced twice the mortality of those in the lowest tertile (2nd tertile score: HR=2.0, 95% CI: 1.2–3.2; 3rd tertile highest score: HR=2.2, 95% CI: 1.3–3.6). Our analysis identified several serum metabolites independently associated with overall mortality, as was their composite risk score, which replicated in the independent test‐set. The metabolite signals are associated with pathways related to CVD, physical activity, ageing, inflammation and nucleoside tumor markers.Research support: Intramural Research Program of the National Cancer Institute, NIH
The transmembrane sequences of amyloid precursor protein family members regulate their ectodomain shedding
Authors: Multhaup Gerhard , Schauenburg Linda , Mayer Magnus , Walter Corvin , Eravci Murat , Weise Chris , Liebsch Filip 
Published: November 2023

It has been shown that APP, APLP1 and APLP2 are similarly cleaved by different secretases. The prerequisite for shedding of those proteins by γ‐secretase is the initial cleavage by α‐ or β‐secretase, which released the soluble ectodomains. Here, we analyzed the soluble fragments in the conditioned media of HEK 293T cells overexpressing either APP, APLP1 or APLP2 under the treatment of different secretase inhibitors.Soluble fragments in the media of cells overexpressing APP, APLP1 and APLP2 were analyzed in the presence and absence of secretase inhibitors by Western blot using a variety of antibodies directed against individual domains of APP and APLPs. MS/MS analyses of APLP1 deletion mutants and of chimeric constructs allowed to differentiate between APLP1γ and APLP1α/β processing and to determine exact α‐, β‐ and γ‐cleavage sites.Interestingly, in the medium of APLP1‐overexpressing cells a larger soluble fragment appears that is recognized by an antibody directed against the Aβ‐like region of APLP1. The secretion of sAPLP1α/β occurred independent from inhibitor treatment whereas there is an inhibitor dependent secretion of endogenous sAPLP1γ. To enrich the fragment, the conditioned medium of SH‐SY5Y cells with or without treatment of γ‐secretase inhibitor was subjected to immunoprecipitation. MS/MS analysis revealed the exact cleavage site within the C‐terminal sAPLP1γ fragment.Our results reveal a novel secretion mechanism, which is specific for APLP1. Only this member of the APP protein family can be cleaved by γ‐secretase without the so far thought necessary proteolysis step of ectodomain shedding.Support or Funding InformationDFG, CIHR, NSERC
Pyruvate Carboxylase is Essential for Breast Cancer Metastasis in Vivo
Authors: Wilmanski Tomasz M , Shinde Aparna , Donkin Shawn S , Burgess John , Wendt Michael , Teegarden Dorothy 
Published: November 2023

Anaplerosis, or the replenishment of TCA cycle intermediates utilized for biosynthetic pathways, has recently emerged as an integral part of breast cancer cell metabolism. In particular, the enzyme pyruvate carboxylase (PC), responsible for facilitating pyruvate flux through oxaloacetate into the TCA cycle, has gained recognition as an essential component of breast tumor growth and metastatic capability. Therefore, the objective of the present studies was to investigate the role of PC in breast cancer utilizing the MCF10 model of breast cancer progression in vitro as well as in vivo utilizing metastatic murine 4T1 cells in immunocompetent Balb/C mice. PC mRNA expression was not significantly different between MCF10A untransformed and Harvey‐ras oncogene transfected cells (MCF10A‐ras), representing initiation. However metastatic MCF10CA1a cells, representing the latest stage in the model, had a 5.14(±0.21) fold higher PC mRNA abundance relative to both the MCF10A and MCF10A‐ras cells. In addition, PC overexpression achieved through transient transfection of a pCMV6‐PC plasmid increased cell migratory capability of both MCF10A‐ras (183%±46 relative to Neo control) and MCF10CA1a cells (191%±31 relative to Neo control), as measured by a Boyden Chamber migration assay. Interestingly, the same overexpression of PC in untransformed MCF10A cells resulted in their acquisition of a migratory phenotype in vitro (252%±34 relative to Neo vehicle). To test the role of PC in vivo, murine metastatic 4T1 breast epithelial cells expressing either PC silencing shRNA or a scramble control were engrafted onto the mammary fat pad of 6 week old Balb/C mice. Five weeks after engraftment, primary tumor and pulmonary metastasis were analyzed. Surprisingly, there was no difference in primary tumor size or volume between shPC and scramble control 4T1 breast epithelial cells. PC silencing, however, had a drastic impact on metastatic capability of cells with nearly complete inhibition of pulmonary metastasis (pulmonary mets per mouse of shPC#25=6±2 and shPC#28=8±4 scramble control=31±10). Together, these results suggest that PC plays an essential role in breast cancer progression, particularly in metastasis of cells from the primary tumor to distant secondary organs.Support or Funding InformationThis work was supported by a Project Development Team within the ICTSI NIH/NCRR (Grant Number UL1TR001108) and the National Institutes of Health, National Cancer Institute(R25CA128770) Cancer Prevention Internship Program. Additional support was received from the Indiana Elks Charities and the SIRG grant, both administered through the Purdue University Center for Cancer Research (Purdue University, West Lafayette, IN).
Cancer‐Specific Cell Death in Response to Palmitoylcarnitine is Associated with Increased Mitochondrial Hydrogen Peroxide
Authors: Turnbull Patrick C , Perry Christopher G. R. 
Published: November 2023

Rationale and HypothesisA benchmark of cancer cells is the reliance on glycolysis characterized by decreased mitochondrial oxidative phosphorylation (eg. Warburg effect). Recent evidence suggests that fatty acids (palmitoylcarnitine; PCarn) may force a shift to mitochondrial oxidative phosphorylation in HT29 colon cancer causing cell death, yet non‐cancer cells appear to be resistant. These results present the intriguing possibility that ‘lipid‐therapy’ might be well tolerated by healthy cells while retaining potency in cancer. However, the mechanism of lipid‐induced cancer cell death is not known. Glutathione is the main antioxidant found within the cell, we hypothesize that cell survival is determined by heterogeneity of basal intracellular glutathione. We theorize that cells with low basal glutathione will be more susceptible to elevated levels of mitochondrial H2O2 from beta‐oxidation of PCarn, whereas cells with higher glutathione will be more resistant to elevated levels of H2O2.Experimental approachWe developed a live cell kinetic assay to measure H2O2 emission in real time; using this assay we exposed three different cancer lines (HT29 colorectal adenocarcinoma, MCF7 breast adenocarcinoma and HepG2 hepatocellular carcinoma) and one non‐cancerous cell line (CCD841 colon epithelial cells) to increasing amounts of PCarn (25μM, 50μM 100μM) for 2, 24 and 48hrs. As a measure of cell proliferation, we adapted a BCA protein assay to digest adhered cells in‐well as a measure of total cell content.ResultsAfter 48hr incubation of 100μM PCarn, H2O2 emission increased in MCF7 (20%) and HT29 (170%), which corresponded to decreased protein contents of 20% and 50% respectively, thereby demonstrating a graded relationship between degree of H2O2 emission and reduction in cell content. HepG2 demonstrated increased H2O2 emission after 48hr incubation with 25μM (150% increase) and 50μM PCarn (218% increase) with a 50% reduction in protein content in both cases. In the non‐cancerous CCD841, we noticed an increase in H2O2 (115%) emission, despite no change in protein content. Collectively, this data suggests that increases in H2O2 production through PCarn oxidation is well tolerated by non‐cancerous cells, however cancer cells are unable to withstand the concomitant increase in mitochondrial H2O2 emission albeit in response to different PCarn concentrations. Future work will determine the manner by which these cancer‐specific redox‐cell death relationships are regulated by glutathione buffering.Support or Funding InformationFunding was provided to C.G.R.P. by National Science and Engineering Research Council (#436138‐2013) with infrastructure supported by Canada Foundation for Innovation, Ontario Research Fund and the James H. Cummings Foundation. P. C. T. was supported by an NSERC CGS‐D scholarship.