bluuebunny/crossref_metadata_2025_split huggingface dataset:
Craniofacial Growth Studies and Craniofacial Growth
Authors: Sherwood Richard J , McNulty Kieran P , Valiathan Manish , Duren Dana L , Knigge Ryan P , Hardin Anna M , Oh Hee Soo , Leary Emily V 
Published: June 2021

Current understandings of human craniofacial growth are based on multiple historic longitudinal growth studies. The extent to which regional variation in growth patterns is present among the various growth studies even within the United States, however, is not well understood. The aim of this study is to compare growth patterns across six of the nation's largest growth studies.Lateral cephalographs were examined from the historical archives of the Denver Growth Study, Iowa Growth Study, and Oregon Growth Study (available via the AAOF Legacy Collection) as well as the Fels Longitudinal Study, the Michigan Growth Study, and the Bolton‐Brush Growth Study. A set of 44 two‐dimensional landmarks were collected on longitudinal series from participants 6–22 years old. A total of 5,622 cephalographs from 726 males and 5,514 cephalographs from 723 females were assessed. Fifth order polynomials were used to evaluate growth of 11 linear craniofacial measures for each growth study and by sex. Rates of growth and associated growth milestones were calculated from polynomial models and compared across study and by sex. In addition, geometric morphometric analyses were used to assess ontogenetic shape differences among studies using a regression of the shape variables on log centroid size, pooled by study, with subsequent evaluation of residual variation.Growth curves for the separate studies roughly parallel each other yet show differences in the timing of growth milestones and adult morphology. In general, for each linear trait participants in the Denver study are smaller and participants in the Iowa and Michigan studies are larger than participants in other studies at the same chronological age. Timing of onset and peak growth is similar in all 11 craniofacial measures, although trait values at those growth milestones differ by study. Preliminary results from the geometric morphometric analysis identify a common ontogenetic pattern shared across studies but demonstrate that, for a given size, individuals from the Denver study are more advanced along the common shape trajectory relative to other studies. Although ontogenetic trajectories are roughly similar, overall shape differences are present between study populations.Variations in growth and overall morphology among these six longitudinal growth study populations demonstrate regional differences in the rate and timing of growth that may be attributable to the ancestry and environmental conditions of study participants. Further study of the mechanisms for these differences in growth will improve the accuracy of craniofacial growth predictions, thereby improving the efficacy of growth modification interventions in pediatric craniofacial treatment.Support or Funding InformationFunding: NIH/NIDCR R03‐DE021435; NIH/NIDCR R01 DE024732This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
SPECC1L‐Deficient Cells Show Impaired Collective Cell Migration Attributes that are Rescued by Upregulation of PI3K‐AKT Pathway
Authors: Saadi Irfan , Goering Jeremy , Isai Dona Greta , Hall Everett , Wilson Nathan , Kosa Edina , Wenger Luke , Umar Zaid , Yousaf Abdul Rehman , Czirok Andras 
Published: June 2021

Clefts of the lip and/or palate (CL/P) are common anomalies that occur in 1/700 live births. Pathogenic SPECC1L variants identified in patients with rare atypical clefts and syndromic CL/P suggest the gene plays a primary role in face and palate development. Null mutants are lethal at embryonic day 9.5 with defective neural tube closure and cranial neural crest cell delamination. Hypomorphic Specc1lΔ200 mutants die perinatally, but do not show cleft palate. Specc1lnull/Δ200 compound mutants resulted in transient oral adhesions, subepidermal blebbing, and a delay in palate elevation. Palate development requires extensive mesenchymal remodeling especially during palatal shelf elevation. We posit that this remodeling involves collective cell migration (CCM) of neural crest derived palate mesenchymal cells. Live time‐lapse microscopy was performed to visualize in vitro wound‐repair assays with SPECC1L‐deficient U2OS osteosarcoma and primary mouse embryo palatal mesenchyme (MEPM) cells. SPECC1L‐deficient cells consistently showed delayed wound closure. Directional movement of neighboring cells is a hallmark of CCM. In wound‐repair assays, an increase in movement parallel to the direction of wound front propagation results can be measured as an attribute of CCM. Tracking of individual trajectories of SPECC1L deficient cells during wound‐repair indeed shows an increase in cell movement perpendicular to the direction of wound closure. This diminished directionality causes delayed wound closure even though cells are adequately motile. We previously demonstrated SPECC1L to be a novel regulator of PI3K‐AKT signaling, with in vitro and in vivo SPECC1L deficiency exhibiting reduced PI3K‐AKT signaling. Indeed, wound closure delay, and the underlying CCM defect, in SPECC1L‐deficient U2OS and MEPM cells can be rescued by activation of the PI3K‐AKT signaling pathway using 740 Y‐P small molecule activator. Our data are the first to show CCM attributes in MEPM cells, and propose that MEPM cells can be used to model mesenchymal remodeling during palatal shelf elevation. We also show a novel role for SPECC1L in CCM through modulation of P13K‐AKT signaling.Support or Funding InformationThis project was supported in part by the National Institutes of Health grants DE026172 (I.S.). Core support and pilot funding was also provided by National Institutes of Health Center of Biomedical Research Excellence (COBRE) grant (P20 GM104936), Kansas IDeA Network for Biomedical Research Excellence (INBRE) grant (P20 GM103418), and Kansas Intellectual and Developmental Disabilities Research Center (IDDRC) grant (P30 HD 002528).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Validating and Optimizing A Combination of INTACT and FACS Techniques for the Isolation of Mouse Astrocyte Nuclei Upon Ablation of the Atrx Intellectual Disability Gene
Authors: Jiang Yuxuan , Pena Ortiz Miguel A. , Jiang Yan , Bérubéé Nathalie G 
Published: June 2021

The ATRX gene codes for the ATRX chromatin remodelling protein, which interacts with DAXX protein to deposit histone variant H3.3 at telomeres and pericentromeric heterochromatin. Mutations of the ATRX gene cause intellectual disability. One noticeable example is the ATRX syndrome, which is characterized by distinctive craniofacial features, severe developmental delays, intellectual disability, and mild‐to‐moderate anemia. It is therefore apparent that the ATRX gene likely plays an important role in the central nervous system (CNS). An astrocyte is a cell type that, by the most conservative survey, has the same abundance as neurons in the human brain. However, unlike neurons, astrocyte function is far less understood, and its role other than a supporting function was not known until a decade ago, when astrocytes were discovered to actively participate in higher neuronal processing through the tripartite synapse. The specific role of ATRX in astrocytes has never been reported before. A challenge of elucidating ATRX function in astrocyte is a lack of an optimized technique to isolate a reasonable number of highly enriched Atrx‐ablated astrocyte nuclei for various sequencing purposes, including ChiP‐seq and RNA‐seq. This project aims to fulfill such research demand by validating and optimizing the Isolation of Nuclei Tagged in Specific Cell Types (INTACT) technique with mouse brain tissue at postnatal day 30. By adjusting various experimental conditions such as tissue homogenization time, the concentration of octylphenoxy poly(ethyleneoxy)ethanol (IGEPAL) in buffer solutions, the dilution ratio of the tissue homogenate and the centrifugation time, a total nuclei yield of 90% was obtained. The structural integrity of nuclei was verified by laser microscopy with nuclei sample stained with 4′,6‐diamidino‐2‐phenylindole (DAPI). However, subsequent enrichment of GFP‐tagged AtrxF/y; Cre+/−;Sun1‐GFP+/− nuclei using anti‐G‐protein coated magnetic bead, as per the original INTACT protocol, is plagued with non‐specific binding of less than 32% specificity. To improve the enrichment factor, a preliminary investigation was performed to validate the use of Florescent‐Assisted Cell Sorting (FACS) to enrich Sun1GFP‐tagged nuclei from the previously‐produced total nuclei preparation. A 92% enrichment of GFP‐tagged nuclei was obtained, demonstrating the promising potential of a combined INTACT‐FACS technique to effectively isolate structurally‐sound nuclei from transcriptionally‐sensitive cell types, within a complex and intermingled tissue environment.Support or Funding InformationThis work was supported by a Dean's Undergraduate Research Opportunity Program award to Yuxuan Jiang and the Canadian Institutes for Health Research MOP#142369.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Co‐expression Network Analysis of Altered lncRNAs and mRNAs in Diabetic Cardiomyopathy using Human iPSC‐derived Cardiomyocytes
Authors: DHANASEKARAN ANURADHA , PANT TARUN , MISHRA MANOJ , BAI XIAOWEN , GE ZHI‐DONG , BOSNJAK ZELJKO 
Published: June 2021

IntroductionMounting evidence in the past have substantiated the role of long‐non coding RNAs (lncRNAs) in diabetic cardiomyopathy (DCM). However, the pathogenesis of DCM remains unknown.AimThis study aimed to investigate the effect of the pro‐diabetic stimulus on the profile of lncRNAs and mRNAs, and the underlying co‐expression signaling network associated with DCM disease pathogenesis.ResultsOut of 40,173 lncRNAs and 20,730 mRNAs being screened, 1582 mRNAs and 2046 lncRNAs were differentially regulated (fold change>2.0, P<0.05) between DCM and control group of which more than half were intergenic and antisense lncRNAs. The subgroup analysis revealed more than 411 lncRNAs being co‐expressed with neighboring genes. To further investigate the potential regulatory role of these lncRNAs in gene regulation and the pathogenesis of DCM we constructed lncRNA‐mRNA co‐expression network which showed overall 48,155 significant co‐expression network connections. Moreover, in the DCM derived network, we had a comparatively greater number of nodes and connections than that in the control group. Majority of the dysregulated mRNAs of DCM co‐expression network were significantly enriched for the GO terms including actomyosin structure organization (GO:0031032), muscle contraction (GO:0006936), membrane raft assembly (GO:0001765), drinking behavior (GO:0042756), Focal adhesion (GO:0005925), skeletal muscle tissue development (GO:0007519), and cell‐matrix adhesion (GO:0007160) which have been associated with DCM in the past.ConclusionThis is the first study to investigate the genome‐wide lncRNA expression profile and co‐expression patterns with mRNA in DCM using microarray technology. These results provide comprehensive data about the pathways and regulatory mechanisms associated with DCM and indicate that lncRNAs may play a crucial role in DCM.Support or Funding InformationThis work was supported, in part, by a National Institutes of Health research grant P01GM 066730 (to Dr. Bosnjak) from the United States Public Health Services, Bethesda, Maryland, USA & DST‐UKEIRI DST/INT/UK/P‐50/2012 (to Dr. Anuradha Dhanasekaran) from the Department of Science and Technology, New Delhi, India.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Regulation of RpoS by RbsD in Escherichia coli
Authors: Peterson Celeste , Dorlean Shaina , Parsons Dylan , Tran Thomas , Dey Arup 
Published: June 2021

In stressful environments, RpoS a stationary phase regulator, accumulates in E. coli and induces a state of dormancy. A screen for regulators of RpoS was carried out with an overexpression DNA library and an RpoS’‐’LacZ fusion. Overexpression of the rbsD gene, which codes for a ribose pyranase necessary for efficient metabolism of ribose, was found to reduce RpoS levels. We next used a series of LacZ fusions and RT‐qPCR to determine how rbsD affects RpoS. We found that rpoS mRNA levels were modestly lowered in the rbsD overexpressed strain. However, a much larger effect was seen in the post‐transcriptional level as determined by an RpoS’‐’LacZ protein fusion. Furthermore the effect of overexpression of rbsD was diminished in a fusion that did not have the RpoS untranslated hairpin loop. In summary overexpression of rbsD resulted in decreased RpoS translation in a manner that depended on the RpoS hairpin loop.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Long noncoding RNAs in immune response and inflammation
Authors: Mandal Subhrangsu S , Obaid Monira 
Published: June 2021

The mammalian immune system orchestrates innate and adaptive immune responses that are complex biochemical processes regulated by various protein and lipid mediators such as cytokines, chemokines, hormones, growth factors, and others. The emerging evidences suggest that non‐coding RNAs (ncRNAs) play vital roles in regulation of immune responses. In a recent study, we discovered that lncRNA HOTAIR plays critical roles in immune response and inflammation. HOTAIR expression is induced in immune cells (macrophages) upon treatment with lipopolysaccharide (LPS) or peptidoglycan, which are components of bacterial cell membrane. HOTAIR is required for LPS‐induced expression of cytokines and pro‐inflammatory genes. HOTAIR regulates activation of NF‐κB and its target gene (IL‐6 and iNOS) expression via facilitating the degradation of IκBα. Thus, HOTAIR appear to be a critical player in NF‐κB activation in macrophages suggesting its potential functions in inflammatory and immune response. Beyond HOTAIR, we also performed RNA‐Seq analysis on macrophages and identified novel lncRNA associated with immune response and inflammation. Overall, lncRNA appear to be play critical roles in immune response and inflammation and are misregulated in inflammatory disease.Support or Funding InformationNational Institute of Health‐ 1R15HL142032This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Structural polymorphism in actin filaments modulates gelsolin binding
Authors: Lee Myeongsang , Kang Hyeran 
Published: June 2021

The conformational states of actin filaments determine their biological functions and numerous actin binding proteins tightly control filament structure. Gelsolin is an actin regulatory protein that remodels actin cytoskeleton by severing and capping the barbed‐end of an actin filament. A recent study demonstrates that actin filaments exist in multiple conformations with varying tilted states, suggesting structural polymorphism in the filament. Yet, it is unknown how polymorphic nature of actin filament structure affects gelsolin binding. Here we investigated the interactions between the segment 1 domain of gelsolin and filaments with distinct structural states identified in the recent experimental study, utilizing molecular docking and the explicit molecular dynamics (MD) simulations. Our simulation results show that the filaments with different tilted states influence the binding modes of gelsolin segment‐1 domain. Analysis on buried area and the number of hydrogen bonds in the actin‐binding interface indicate that distinct filament structure results in different binding affinities of gelsolin. Distributions of salt‐bridge interactions between actin subunit and gelsolin may explain molecular basis of the filament structure‐dependent gelsolin binding affinities. This study suggests that structural polymorphism in actin filaments may play an important role in modulating interactions between actin filaments and binding proteins.Support or Funding InformationThis study was supported by the UCF start‐up fund and In‐House grant for Hyeran Kang. We acknowledge the computational time from UCF stokes cluster.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Yeast Polygalacturonase Activity is Resistant to Extreme Temperature and pH
Authors: Caspers Mary Lou 
Published: June 2021

Polygalacturonase cleaves the α1–4 galactosidic bonds of polygalacturonic acid (PG), a major component of fruit mucilage, to produce galacturonic acid. A unit of polygalacturonase activity is defined as the number of mmol of galacturonic acid produced per min at pH 5.0. Polygalacturonase is stable to submersion in a boiling water bath for 1 hour or 10 minutes at 200 °C. When the polygalacturonase assay is conducted at a pH 3 or 14, no loss of activity is noted. Addition of 0.3 M β‐mercaptoethanol abolishes polygalacturonase activity and so this concentration of β‐mercaptoethanol is used as an assay control. Dithiothreitol is able to reduce polygalacturonase activity in a dose‐dependent manner. A 38 % reduction in enzyme activity is seen at 81 mM dithiothreitol and this increases to 95 % inhibition at 162 mM dithiothreitol. Tris(2‐carboxyethyl)phosphine at 50 mM completely inhibits polygalacturonase activity. β‐Mercaptoethanol, dithiotheitol and tris(2‐carboxyethyl)phosphine all reduce the disulfide bonds formed between the side chains of cysteine residues. This suggests that the resistance of polygalacturonase to denaturation by high temperature and acid or base is due to the stabilization of its tertiary structure by disulfide bonds. (I gratefully acknowledge the work of Melissa L. Zuteck, Edwin A. Gay, Joshua Henning, Ayah Bakri, Bianca Yaldo and Glenn R. Oppenlander who assisted in this work while undergraduates.)Support or Funding InformationI thank the Department of Chemistry and Biochemistry, University of Detroit Mercy for support of this projectThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Initial characterization of DszA for the high throughput validation of rationally designed DszC mutants
Authors: Sanchez Misael , Truong Sharon , Vey Jessica 
Published: June 2021

Sulfur dioxide production through fossil fuel combustion is a negative contributor to atmospheric pollution and human health. Currently, the preferred method for the removal of sulfur containing compounds from fossil fuels is though hydrodesulfurization. This process however, continues to be costly and inefficient in targeting certain common aromatic organosulfur contaminants like dibenzothiophene (DBT). Fortunately, the biodesulfurization (BDS) pathways in R. erythropolis and other bacterial species have shown promise in the removal of sulfur from such organosulfur compounds. However, improvements are still necessary for this pathway to become competitive and industrially applicable. Our current laboratory objectives are to rationally design the BDS pathway in R. erythropolis to decrease substrate specificity, starting with the first enzyme in the pathway DszC. To facilitate high‐throughput validation of our rationally designed DszC mutants, we will generate a strain of E. coli that harbors the three downstream biodesulfurization genes (DszA, DszB, and DszD). Here, we present our preliminary overexpression and biochemical characterization of the other enzymes in the BDS pathway, focusing on DszA, a flavin‐dependent monooxygenase. DszA crystals have also been produced and are being optimized for co‐crystallization with dibenzothiophene sulfone (DBTO2) substrate to accurately identify the substrate active site.Support or Funding InformationResearch Initiative for Science Enhancement (RISE), National Institute of Health (NIH), California State University NorthridgeThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Insights into gasdermin pore formation from the structure of a pre‐pore
Authors: Xia Shiyu , Ruan Jianbin , Fu Tian‐Min , Wu Hao 
Published: June 2021

Downstream of inflammasome activation, gasdermin D (GSDMD) mediates IL‐1β secretion and pyroptosis by forming membrane pores. Structural investigation into GSDMD pore formation will provide new mechanistic knowledge about the GSDM family and facilitate the treatment of GSDMD‐associated diseases. We hypothesize a dynamic model where upon caspase cleavage of autoinhibited GSDMD, GSDMD‐NTs dissociate from GSDMD‐CTs for lipid binding and oligomerization into a pre‐pore, followed by β‐barrel insertion to form a membrane pore. In light of our recently resolved structure of the mouse GSDMA3 membrane pore, we aim to determine the structure of a GSDM pre‐pore. We arrest the pore formation process at the pre‐pore stage by generating a GSDMA3 mutant defective in membrane insertion while functional in lipid binding and oligomerization. Cryo‐electron microscopy (Cryo‐EM) analysis reveals a pre‐pore conformation where GSDMA3‐NT subunits oligomerize into a soluble ring without extended transmembrane β strands.Support or Funding InformationThis work was supported by US NIH grant DP1HD087988 (H.W.), R01Al124491 (H.W.), and Charles A. King Trust Postdoctoral Fellowship Program (J.R.). We thank the University of Massachusetts Cryo‐EM Core Facility and NCI National Cryo‐EM Facility for data collection.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Elucidating the Intermolecular Interactions of a Cataract‐Causing Protein: γB Crystallin
Authors: Faraone Julia , Bushunow Symeon , Fadden Aaron , Mills Jeffrey L , Thurston George , Michel Lea Vacca 
Published: June 2021

Gamma crystallin proteins can be found in the eye lens, helping to maintain transparency through their intermolecular interactions. Because crystallins remain in the lens after their initial synthesis, mutations caused by prolonged exposure to environmental stresses can have permanent consequences, including aggregation and liquid‐liquid phase separation of the crystallins. These structural deviations can cause clouding of the lens, a condition known as cataracts. With the use of light scattering and nuclear magnetic resonance (NMR) spectroscopy, we aim to study the detailed interactions between crystallins. We have expressed and isolated recombinant bovine Gamma B crystallin protein in Escherichia coli and performed T1/T2 NMR experiments to measure the longitudinal and transverse relaxation times of the protein. These experiments allowed us to analyze the crystallins in terms of the attractive forces between molecules and how those forces change with the manipulation of environmental conditions (temperature, pH). Analysis of our current data suggests higher rates of intermolecular interaction at higher concentrations of crystallins and lower temperatures.Support or Funding InformationRIT and NIH Grant EY018249This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.