bluuebunny/crossref_metadata_2025_split huggingface dataset:
Full‐thickness Engineered Skin Tissue with 3D Biomimetic Micro‐topography
Authors: Yu Jonelle , Korkmaz Emrullah , LeDuc Philip , Ozdoganlar Burak 
Published: November 2023

Many native tissues possess three‐dimensional (3D) micro‐topographies that have evolved to be more biologically functional. As one of the functional features, dermal papillae, 3D undulated interface between epidermis and dermis in skin is centered on increased interface area, resulting in, for instance, reinforced mechanical contact, enhanced thermal conductivity, and improved biomolecular transportation. To reserve the micro‐topographies in engineered skin tissues would bring tremendous advances to patient‐specific skin transplantation (for higher graft take rate and shorter recovery time) and organ‐on‐a‐chip development (for more accurate disease models and drug screening). To accomplish this, various approaches have been developed in academic researches. However, those approaches only achieved the topographies as 2D rectangular channels, 2D sine wave channels, or 3D taper pillars, which have not mimicked precisely the natural topographies of dermal papillae.Here we developed 3D undulated topographies at multiple micro‐scales on hydrogel spongy scaffolds for mimicking dermal papillae by using coupled 3‐axis micro‐milling and micro‐molding approaches. We micro‐milled master molds with 3D sine wave matrix, where the structure possesses continuous curvature in all directions, to mimick the undulated topographies in native skin. We afterwards accomplished hydrogel porous scaffolds with the 3D undulated surface, which was transferred from master molds by micro‐molding and lyophilization. We finally examined cell‐scaffold interfacial response by culturing fibroblasts on the undulated surfaces. As a result, the hydrogel porous scaffolds replicated the precise master molds without obvious distortion or shrinkage. The cells grew and migrated along the micro‐patterned scaffolds over 7 days with very few dead cells. Our biological engineering approach applied to tissue scaffolds paves the way to fabricate more 3D structurally realistic artificial tissues in areas such as organ repair and organ‐on‐a‐chip applications, which are applicable to biological functions such as cell‐cell interactions and cell signaling.
Bisphenol‐A and 17‐β Estradiol Alter Colon Microbial Metabolites and Exacerbate Dextran Sodium Sulfate‐Induced Colitis in Mice
Authors: DeLuca Jennifer A.A. , Menon Rani , Riordan Rebekah , Allred Kimberly F. , Jayaraman Arul , Allred Clinton D. 
Published: November 2023

Inflammatory bowel diseases (IBDs), including Crohn's disease (CD) and ulcerative colitis (UC), differ in their responses to estrogen status in female patients. Previous studies investigating the role of 17‐β estradiol (E2) in animal models of both CD and UC have shown anti‐inflammatory or pro‐inflammatory responses, respectively. E2 has been reported to worsen disease activity scores in the Dextran Sodium Sulfate (DSS)‐induced colitis model. Additionally, data from DSS models suggest changes in intestinal microbes play a role in inflammation initiation and exacerbation of colitis. Bisphenol‐A (BPA) has been shown to exert estrogenic activity in the colon and alter intestinal function at relatively low doses, but the role that xenoestrogens such as BPA play in colonic inflammation is poorly described. We investigated the ability of E2 and BPA to exacerbate colonic inflammation and alter microbial metabolites in an acute DSS‐induced colitis model in vivo. Treatment with DSS and E2 resulted in 100% mortality, while DSS and BPA co‐treatment resulted in 67% mortality. Body weight decreased significantly in E2 mice, indicating worsened disease severity. BPA treatment also resulted in reduced body weight. Rectal bleeding and fecal consistency scores were most severe in E2 treated mice, but BPA treatment also worsened these scores. DSS treatment significantly decreased colon length and increased colon inflammation score. Inflammation score was worsened in BPA treated animals in the presence and absence of DSS. Alterations in the levels of tryptophan‐derived metabolites were determined using LC‐MS metabolomics and identified unique patterns of metabolites associated with BPA exposure. To further assess the effects of BPA on non‐transformed colonocytes, cell number, cell cycle, and apoptosis were measured in vitro in young adult mouse colonocytes (YAMCs). BPA at concentrations of 1 μM and 10 nM reduced cell number similarly to 1 nM E2. Apoptosis was increased in E2 treated cells, but not in BPA treated cells. Collectively, these data suggest BPA can alter cellular function of nonmalignant colonocytes and exacerbate inflammation in vivo which may be associated with changes in microbiota‐derived metabolites.Support or Funding InformationFunding was provided by the Center for Translational Environmental Health Research through National Institute of Environmental Health Sciences grant number P30ES023512.
Genetic Variations at 15 Forensically Relevant Microsatellite Loci (STRs) in the Three Major Ethno‐Linguistic Population Groups in Nigeria
Authors: Agbo Benedict Usman , Ebuehi Osaretin Albert Taiwo , de Osuntoki Akinniyi A 
Published: November 2023

This study is to identify genetic markers that will show distinct genetic variability among the three major ethno‐linguistic population groups in Nigeria that can help establish ethnic origin of forensic evidential materials. Samples from 315 unrelated individuals representing the three populations; ‘Hausa’, ‘Ibo’ and ‘Yoruba’ were analyzed using 15 Microsatellite loci (STRs) from Applied Biosystems. Analyses of inter‐ and intra‐population diversity were carried out using average heterozygosity, allele range (base pair), most frequent allele per a locus, Fixation index (Fst), Forensic and Paternity parameters. Multi‐locus genotype frequencies were utilized for testing conformity with Hardy‐Weinberg equilibrium (HW). 7 loci was found to conform to Hardy Weinberg equilibrium after X2 analysis. However, Bonferoni corrections show all loci to be in HW equilibrium, equally, exact test showed all loci to be in conformity with HW. Forensic and paternity parameters across the loci showed adequate discriminatory power for forensic identification of individuals as well as sufficient exclusionary power for parentage analysis. Average heterozygosity Fixation Index and Nei's standard genetic distance gave the least distance between the Ibo and Yoruba ethic groups. Allele frequency distribution comparisons at all loci analyzed show substantially no significant difference at 5% level of confidence between the Nigerian population and the FBI African American population allele frequencies. Ethnically blinded test from twenty samples among the three ethnic groups show a high degree of certainty in ethnic origin inferences from unknown samples. The study show Genetic variations between the three populations with marked phylogenetic relationships.Support or Funding InformationUniversity of Lagos, Lagos Nigeria
Role of the ELL complex in transcriptional regulation in S. pombe
Authors: Gopalan Sneha , Gibbon Dana , Seidel Chris , Zhang Ying , Florens Laurence , Washburn Michael , Conaway Joan , Conaway Ronald 
Published: November 2023

The ELL family of transcription elongation factors can suppress the transient pausing of Pol II at each step of nucleotide addition during transcription, thereby stimulating the overall rate of transcription. ELL‐associated factors (EAFs) bind directly to ELL and are positive regulators of ELL elongation activity. ELL and EAF have been implicated in the release of RNA pol II from promoter proximal pausing by an unknown mechanism. Orthologs of ELL and EAF were not identified in fungi until recently. Previous data from our lab identified genes in S. pombe similar to ELL and EAF, which have no obvious orthologs in S. cerevisiae. SpELL and SpEAF also interact with each other to form a heterodimer and can positively regulate transcription by RNA pol II. We identified proteins interacting with SpELL and SpEAF by immunoprecipitation followed by Multidimensional Protein Identification Technology (MudPIT). Proteomic analyses revealed an uncharacterized sequence orphan protein that associates strongly with both ELL and EAF. Biochemical analysis using recombinant proteins confirmed that this protein binds directly to ELL and forms a ternary complex with ELL and EAF. ChIP‐seq experiments suggest that all three proteins co‐localize at genes with high RNA pol II occupancy. Synthetic Genetic Array (SGA), a high‐throughput technique for exploring genetic interactions, was performed on the deletion mutants lacking the genes encoding ELL, EAF and the novel ELL‐interacting protein. Preliminary data analysis suggests that these genes may interact genetically with overlapping set of genes.Support or Funding Information
Characterization of the SUN Domain Protein Mps3 Function in Gene Expression
Authors: Antoniacci Lisa , Lukasak Rebecca 
Published: November 2023

The yeast nuclear envelope protein Mps3 functions in several aspects of chromosome metabolism such as sister chromatid cohesion, telomere clustering, and DNA damage repair. In addition, Mps3 physically and functionally interacts with the histone variant Htz1. Htz1 was previously identified as a histone variant that prevents DNA from forming silent heterochromatin as a way to regulate transcription. Because of the involvement of both of these genes in chromosome metabolism, it is hypothesized that they may function in regulating gene expression. In order to assess genome expression wild type yeast, mps3‐3, mps3‐5, and an htz1Δ strain were examined for genome wide expression levels in both asynchronously and synchronized growing cells. The data generated was analyzed for both up‐regulation and down‐regulation of gene expression in comparison to the wild type strain. Identification of expression differences between the wild type and mutant strains would suggest a function for Mps3 and Htz1 in gene expression.Support or Funding InformationShierling Endowed Chair Marywood University
Fine‐tuning of FACT by the ubiquitin proteasome system in regulation of transcriptional elongation
Authors: Bhaumik Sukesh R. , Sen Rwik , Ferdoush Jannatul , Kaja Amala 
Published: November 2023

FACT (facilitates chromatin transcription), an evolutionarily conserved histone chaperone involved in transcription and other DNA transactions, is upregulated in cancers, and its downregulation is associated with cellular death. However, it is not clearly understood how FACT is fine‐tuned for normal cellular functions. We find that the FACT subunit Spt16 is ubiquitylated by San1 (an E3 ubiquitin ligase) and degraded by the 26S proteasome. Enhanced abundance of Spt16 in the absence of San1 impairs transcriptional elongation. Likewise, decreased abundance of Spt16 also reduces transcription. Thus, an optimal level of Spt16 is required for efficient transcriptional elongation, which is maintained by San1 via ubiquitylation and proteasomal degradation. Consistently, San1 associates with the coding sequences of active genes to regulate Spt16's abundance. Further, we find that enhanced abundance of Spt16 in the absence of San1 impairs chromatin reassembly at the coding sequence, similarly to the results seen following inactivation of Spt16. Efficient chromatin reassembly enhances the fidelity of transcriptional elongation. Taken together, our results demonstrate for the first time a fine‐tuning of FACT by an ubiquitin proteasome system in promoting chromatin reassembly in the wake of elongating RNA polymerase II and transcriptional elongation, thus revealing novel regulatory mechanisms of gene expression.Support or Funding InformationNational Institutes of Health (2R15GM088798‐02) and American Heart Association (15GRNT25700298).
Role of chromatin remodeling and spacing factor 1 in histone H2A ubiquitination mediated gene silencing
Authors: Wang Hengbin , Zhang Zhuo , Jones Amanda E , Renfrow Matthew B , Liu Chuan Fa , An Woojin , Luo Jianjun , Wu Wei , Kang Yue , Tong Yufeng 
Published: November 2023

Posttranslational modification of histones plays important regulatory roles in chromatin‐based nuclear processes. Histone H2A ubiquitination (H2Aub) is a predominate modification and has been primarily linked to gene silencing; however, the mechanism by which H2Aub achieves the gene silencing function remains unclear. Here we report the identification of RSF1 (remodeling and spacing factor 1), a subunit of the RSF (remodeling and spacing factor) complex, as a novel H2Aub binding protein which mediates the repressive function of H2Aub on gene expression. RSF1 preferentially associates with H2Aub‐enriched nucleosomes through a previously uncharacterized region designated as the ubiquitinated H2A binding (UAB) motif. RSF1 specifically interacts with H2Aub nucleosomes and the UAB motif is required for RSF1 to interact with H2Aub nucleosomes in vitro and in vivo. Genes regulated by RSF1 overlap significantly with genes regulated by RNF2 or Ring1B, the catalytic subunit of Polycomb repressive complex 1 (PRC1), in both human and mouse cells. Strikingly, virtually all overlapped genes show changes in the same direction. RSF1 binds to gene promoter regions, and over 85% of H2Aub enriched genes, including the classic PRC1‐target Hox genes, are co‐bound by RSF1. Reduction H2Aub levels by Ring1B knockout resulted in a significant reduction of RSF1 binding. RSF1 knockout did not affect RNF2/Ring1B or H2Aub levels but resulted in re‐expression of H2Aub target genes, accompanied by a reduction in the spacing and stability of H2Aub‐containing nucleosomes. Finally, the direct role of RSF1 in H2Aub‐mediated gene silencing was demonstrated by chromatin based in vitro transcription assay. Therefore, this study identifies RSF1 as a novel H2Aub binding protein and reveals that H2Aub represses gene expression by maintaining a regular spaced, stable nucleosome array at promoter regions through RSF1.Support or Funding InformationHengbin Wang is a Leukemia and Lymphoma Scholar.
Determination of Altered Bromodomain Function of Cancer‐Associated Missense Mutations in Polybromo‐1
Authors: Goetz Christopher , Dykhuizen Emily , Smith Brian 
Published: November 2023

Bromodomains are chromatin interaction modules of approximately 110 amino acids that bind acetyl‐lysine residues on histones and other nuclear proteins. Bromodomains target transcriptional proteins and their associated protein complexes to specific gene loci on chromatin, and thus influence transcriptional activity of selected genes. Humans encode 61 bromodomains distributed among 46 bromodomain‐containing proteins, one of these proteins, Polybromo‐1 (PBRM1), contains six tandem bromodomains and is a subunit of the Polybromo‐1‐BRG‐Associated‐Factors (PBAF) chromatin remodeling complex. Missense mutations in PBRM1 cluster in the bromodomains and are present in many cancers. In particular, PBRM1 is mutated in approximately 40% of the sequenced cases of Renal Clear Cell Carcinoma, the most aggressive and lethal subtype of renal cell carcinomas. However, the functional consequences of these missense PBRM1 bromodomain mutations was unknown. Here, we compiled 178 missense mutations located within the PBRM1 bromodomains through analysis of cancer databases including Cancer Driver Mutation, COSMIC, and IntOgen. To determine the consequences these missense mutations have on PBRM1 bromodomain function, we developed a high‐throughput ThermoFluor assay using an acetyl‐lysine mimetic, 1‐methyl‐2‐quinolinone, which mimics the acetyl‐lysine: bromodomain interaction through formation of a hydrogen bond between its N‐methyl amide moiety and a conserved asparagine residue found in the acetyl‐lysine binding pocket of bromodomains. The ThermoFluor assay simultaneously quantifies both bromodomain thermal stability and the ability of the bromodomains to bind acetyl‐lysine residues by measuring the shift in melting temperature of mutant and wild‐type bromodomains in the presence or absence of the acetyl‐lysine mimic ligand. The thermal shift data strongly correlates with dissociation constants measured by isothermal titration calorimetry (ITC), rendering the ThermoFluor assay a rapid and quantitative way to assess bromodomain function for a large number of mutations. Our preliminary data shows that cancer‐associated PBRM1 bromodomain mutants exhibit altered stability (to varying degrees) in the presence of the acetyl‐lysine mimetic in comparison with the wild‐type PBRM1 bromodomains. This research provides insights into function of the PBRM1 bromodomains under normal conditions and during cancer development and may lead to novel methods to selectively target missense mutations in PBRM1 as potential therapeutics.Support or Funding InformationAmerican Heart Association Scientist Development Grant 15SDG25830057 Medical College of Wisconsin Research Affairs Committee American Cancer Society Institutional Research Grants #14‐247‐29‐IRG and #86‐004‐26‐IRG Advancing a Healthier Wisconsin Endowment
Complementary roles of Pseudomonas aeruginosa condensins in global chromosome organization
Authors: Bhowmik Bijit Kumar , Rybenkov Valentin V 
Published: November 2023

Condensins play a crucial role in global chromosome maintenance and organization in all forms of life. In bacteria, condensins contribute to proper resolution and segregation of sister chromatids following replication. Atypically, Pseudomonas aeruginosa strain PAO1 expresses two condensins, the canonical SMC‐ScpAB complex and the unconventional MksBEF. These two proteins belong to two different super‐families of condensins. Here we investigated the roles of SMC‐ScpAB and MksBEF in chromosome segregation of PAO1.Pseudomonas aeruginosa condensin mutants, ΔmksB and Δsmc were constructed using homologous recombination. To visualize different loci on the chromosome, arrays of tetO operators were inserted into pre‐determined positions of P. aeruginosa chromosome and used as a binding target for TetR‐CFP chimera. TetR‐CFP was expressed from a plasmid under an IPTG inducible lacUV5 promoter. Individual chromosomal loci were then observed using fluorescence microscopy while cellular morphology was characterized using phase‐contrast microscopyPAO1 chromosome segregation initiated from a unique origin (oriC), progressed bidirectionally and terminated at the site‐specific recombination site dif, responsible for the resolution of daughter chromosomes. Notably, the oriC and dif sites are asymmetrically positioned on the PAO1 chromosome. As a result, the left arm is about 1.6 times longer than the right arm. Thus, segregation along the arms proceeds with unequal rates.In newly born cells, the oriC was located close to mid‐cell, whereas dif site was located close to the new pole. Following replication, oriC split into two foci, relocated to the quarter positions and remained there for the rest of cell cycle. In contrast, dif site was pulled from the pole, towards the mid‐cell and split at the very end of cell cycle. We found two macrodomains on the left arm of the chromosome. Deletion of mksB did not change the longitudinal organization of PAO1 chromosome. At the same time, the sequence of chromosome segregation remained unchanged in ΔmksB cells. However, the timing of segregation of chromosomal loci were significantly altered. Interestingly, one of the macrodomains was dispersed in ΔmksB cells. Deletion of smc had a more dramatic effect. It markedly altered segregation of oriC while most of the chromosome was disorganizedOur findings indicate that both SMC and MksB contribute to the global chromosome organization in P aeruginosa. SMC and MksB has complementary but non‐overlapping roles in chromosome segregation. While SMC is required for timely segregation of oriC region, MksB ensures compactness of the chromosome.Support or Funding InformationThis work was supported by the award OCAST HR 14–042.
Methylation status of the gene encoding Akt2 in cinnamon extract treated MCF‐7 cells
Authors: Hill Matthew , Bulko Rachel , Aulthouse Amy , Kinder David , Stockert Amy 
Published: November 2023

The role of epigenetics in cancer development and progression has exponentially grown in recent years. Polyphenolic compounds from green tea and other sources have been demonstrated to alter methylation status in a variety of genes, including those linked to cancer. Our studies suggest similar results may be possible from treatment of cells with cinnamon extract. We selected the MCF‐7 breast cancer cell line to explore the effects of cinnamon treatment on DNA methylation patterns. Following confirmation of total methylation changes we selected genes of interest in cancer development to complete methylation specific PCR aimed at determining the effects of gene specific methylation changes in cinnamon treated cells. Akt2 signaling can play a major role in different signaling pathways to prevent cellular apoptosis and lead to prolonged cell life. Research also demonstrates variable localization of the Akt2 protein, with confirmed identification in both the cytoplasm and the nucleus. Preliminary results in the lab demonstrate the potential for aqueous cinnamon extract to methylation the Akt2 gene in MCF‐7 cells, potentially decreasing expression of the protein. Here we will present our results demonstrating the methylation change on Akt2 upon cinnamon extract treatment as well as further characterize effects of cinnamon on Akt2 expression and localization. Collection of treated and untreated cells under various treatment regimes will allow further methylation analysis, RNA extraction followed by quantitative PCR to evaluation expression of Akt2. Additionally we will perform Western blot analysis on cytoplasmic and nuclear proteins to determine both protein expression and localization.Support or Funding InformationDepartments of Pharmaceutical and Biomedical Sciences and Biological and Allied Health Sciences, Ohio Northern University
MCF‐7 Morphological changes upon treatment with aqueous cinnamon extract
Authors: Bulko Rachel , Aljahani Rawan , Aulthouse Amy , Kinder David , Stockert Amy 
Published: November 2023

Epigenetics has emerged as a key component in both the prevention and the development of various cancers. Polyphenolic compounds from a variety of sources have been explored as potential epigenetic modifiers for both methyaltion and acetylation. Furthermore, studies exploring extracts versus individual components have demonstrated up to 50% more activity when treating cells with the full extract rather than select components. Our studies suggest a similar synergistic effect when treating MCF‐7 breast cancer cells with aqueous cinnamon extract. These cells exhibit a proliferative response when exposed to heightened endogenous estrogen and progesterone. Upon administration of certain natural substances, however, proliferation can be lowered significantly. Simulating potential cancer treatments in vitro can be accomplished with this cell line, since it has characteristics of metastatic breast cancer. Visible changes in cell morphology, including shrinking and becoming rotund, can be observed in the MCF‐7 cells treated with cinnamon extract. Similar results have been obtained from trials involving turmeric and curcumin, which researchers believe may be due to the qualities of the polyphenol levels that exist in these organic compounds. Here we present results of a morphological study involving treatment of MCF‐7 cells with cinnamon extract and or various components identified in the extract. We report changes in cell shape, with treated cells adopting a round shape rather and polygonal which is not induced by changes in monolayer attachment. We also see a significant difference in cell size upon cinnamon treatment. We explored changes in methylation patterns from extracted DNA and selected target genes of interest, FoxO1 and GSK3beta for anaylsis by methylation specific PCR.Support or Funding InformationDepartments of Pharmaceutical and Biomedical Sciences and Biological and Allied Health Sciences, Ohio Northern University.