bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic Dissection of the Spindle Assembly Checkpoint
Authors: Garcia Yenni Alejandra , Velasquez Erick , Gao Lucy , Whitelegge Julian , Torres Jorge 
Published: June 2021

Human cell division is a critical process that ensures the accurate transmission of the genetic material from one mother cell to two cells. The mitotic Spindle Assembly Checkpoint (SAC) ensures the fidelity of this process by responding to errors in microtubule‐kinetochore attachment and tension, and arresting the cells in prometaphase to allow time to repair the errors before progressing into anaphase. The SAC core proteins include MAD2, MAD1, BUB1, BUBR1, and BUB3. To gain insight into the protein associations that are critical for regulating the SAC in a spatial‐temporal manner, we have employed a label‐free proximity‐based association mapping approach. We have generated BIOID2 stable cell lines for all of the core SAC proteins and the BioID2 tag alone as our control. We have verified the inducible expression of these BioID2 tagged SAC proteins and their localization to the kinetochore region at the time when the SAC is active. We have performed purifications from mitotic arrested cells and have generated proximity association networks for these SAC proteins. Although, proteomic approaches, like BioID2, have been widely used to identify novel cellular pathway components and to interrogate their functions, a common problem that we and other researchers face is what to call a “Hit” and what to call a “contaminant” in mass proteomic data, therefore we have developed a statistical proteomic pipeline in R that 1) is user friendly and 2) can be used to analyze mass proteomic data with any lab specific control and lab specific conditions to generate statistically significant results to inform on hits vs. contaminants. We have analyzed our proximity‐based purifications with this new computational approach and have identified known and novel associations. Our current and future work is focused on better understanding these identified associations by validating them, and assessing their roles in the activation and maintenance of the SAC pathway.Support or Funding Information1. NSF MCB1243645(JZT), NIH R01GM117475‐01 (JZT),2. USHHS Ruth L. Kirschtein Institutional National Research Service Award #T32 CA009056 (YAG)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Thinking Outside the Informatics Box: Computed Chemical Properties for Protein Function Annotation
Authors: Ondrechen Mary Jo , Mills Caitlyn L. , Ruffner Lydia A. , Beuning Penny J. 
Published: June 2021

There are now over 14,000 Structural Genomics (SG) protein structures deposited in the Protein Data Bank (PDB) and most of these are of unknown or uncertain biochemical function. Reliable computational methods for the prediction of the function of protein structures is an important current need. Typically, functions are assigned using informatics‐based approaches. The annotation of protein function by automated means has led to high rates of misannotations in some databases. Here we present a complementary and powerful approach based on computed chemical properties of the individual residues in a protein structure. Partial Order Optimum Likelihood (POOL) is used to predict the residues in the query protein structure that are important for catalysis. Typically these include the residues in the first layer that make direct contact with the substrate molecule(s) and also some residues in the second and third layers that play supporting roles in the catalytic process. Then, for proteins of known biochemical function, Graph Representation of Active Sites for Prediction of Function (GRASP‐Func) establishes local arrays of POOL‐predicted residues that are common to proteins of the same function. Then local arrays of POOL‐predicted residues of the query (SG) protein are aligned with those of the proteins of known function for the different functional types. These alignments, each SG protein against each functional family, are scored in order to predict the most likely function of the SG proteins. Results are reported for the SG members of the Ribulose Phosphate Binding Barrel (RPBB), Clp‐Crotonase, and Haloacid Dehalogenase superfamilies. While we find the SG proteins in the RPBB superfamily to be well annotated, we predict very high annotation error rates (about 70%) in the Clp‐Crotonase superfamily. Of particular interest are cases of predicted misannotation, where our prediction differs from that of the assigned function. Experimental testing of our predictions is performed by direct biochemical assays to verify our predictions.Support or Funding InformationNational Science Foundation under grant number CHE‐1305655, MathWorks, Inc. and a PhRMA Foundation Fellowship awarded to CLM.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Novel metabolome and breath platforms to trace microbiome contribution to host metabolism
Authors: Assadi‐Porter Fariba M , Tonelli Marco , Regan Matthew D , Carey Hannah V 
Published: June 2021

Host diet influences the structure and function of the microbiota in species that regularly consume food. To measure the functional contribution of microbiotas, we developed a metabolome‐microbiome platform (MMP) and novel stable isotopic labeling to trace microbiotas' metabolism in breath, cecum, and host tissues. We combined cavity ringdown spectroscopy to measure real‐time breath biomarkers and NMR‐based metabolomics to analyze metabolome profiles in tissues. We applied MMP to hibernating ground squirrels to assess the role of bacterial metabolism contributing to seasonal changes in diet. Previously, we showed that the long‐term fast of hibernation decreases relative abundance of bacterial taxa that are adept at degrading abundant plant glycans in summer versus their reduction in winter. Here, we determined the functional significance of seasonally changing microbiotas by gavaging Spring and Summer squirrels and aroused hibernators in Winter with 13C‐labeled complex and simple carbohydrates, and comparing against their respective intraperitoneal and antibiotics applications. Measurement of 13CO2/12CO2(δ13C) in breath was used as an index of bacterial degradation of 13C‐substrates and linked to observed changes in 1H‐[13C]‐metabolome profiles. Compared with robust responses in Summer changes in δ13C after 13C‐inulin gavage in hibernators were nearly abolished, whereas squirrels in Early Winter and Spring showed variable responses consistent with their transitional microbiotas. Metabolome profiles mirrored seasonal changes in 13C‐labeled short‐chain fatty acids. These suggest that during hibernation, the gut microbiota gradually loses the capacity to degrade a plant‐derived glycan, and a shift away from taxa that prefer dietary substrates. The results suggest MMP is a powerful tool in analysis of host‐microbe relationships.Support or Funding InformationSupported by funds from NSF (IOS1558044), UW‐Madison Graduate and Veterinary Medicine.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Lipidomic Analysis of Media from Castration and Drug Resistant Prostate Cancer Cells
Authors: Mansoura Maryam , Ingram Lishann M. , Cummings Brian S. 
Published: June 2021

Castration‐resistant prostate cancer (CRPC) is a severe, metastatic form of prostate cancer (PCa). Several treatment modalities have been approved during the past decade by the FDA for treating CRPC patients. Unfortunately, a high percentage of patients fail to respond to these treatments for several reasons, including developing resistance. One reason for these failures is inadequate methods that allow for accurate staging of PCa. This poses a diagnostic problem that limits our ability to create a patient‐centered treatment plan. We addressed this problem by testing the hypothesis that an association exists between circulating lipids and clinical outcomes of CRPC. This hypothesis is based on recent studies demonstrating a correlation between plasma lipids and CRPC prognosis. To understand this correlation, we used in vitro models of non‐cancerous, hormone‐sensitive, and drug‐resistant CRPC cell lines combined with quantitative lipidomic analysis to study the correlation between CRPC and lipid profiles. An untargeted approach indicated that media from hormone sensitive cells (LNCaP), and CRPC cells (DU145) had lower relative abundance of glycerophospholipids, as compared to a non‐cancer cell model (PNT2). However, drug resistant cells (DU145 DR) and their media had a higher abundance of glycerophospholipids such as phosphatidylinositol (PI), phosphatidic acid (PA), and phosphatidylserine (PS) as compared to parent control (DU145). These data confirm previous in vivo findings and suggest that the lipidomic profiles of PCa cells lines mirror lipidomic profiles in the plasma of PCa patients. Further, these data provide an in vitro model to investigate the molecular mechanisms mediating lipidomic changes during the progression of drug resistant PCa.Support or Funding InformationNational Institute of Biomedical Imaging and Bioengineering NIBIB (EB0160100), Department of Defense Prostate Cancer Research Program Idea Development Award (PC150431 GRANT11996600)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Dual Roles of Reactive Oxygen Species in Exacerbated Proinflammatory Effects of Caveolin‐2 Deficiency in Ischemia/Reperfusion and the Anti‐inflammatory Effects of Ethanol Preconditioning
Authors: Wang Meifang , Wang Derek , Liu Yajun , Sowa Grzegorz , Korthuis Ronald 
Published: June 2021

Caveolin‐2 (Cav‐2), a member of caveolin protein family, is ubiquitously co‐expressed ubiquitously with caveolin‐1 (Cav‐1) in vascular endothelial cells. Cav‐2 interacts with Cav‐1 to form a hetero‐oligomeric complex within caveolae. In contrast with the extensively studied Cav‐1 including the functional role of Cav‐l expressed in ECs in ischemic injury, much less is known regarding the effects of Cav‐2. We hypothesized that (i) genetic deletion of Cav‐2 (CAV‐2 KO) would promote proinflammatory effects in the absence of I/R in wild‐type (WT) mice; (ii) postischemic inflammation will be exacerbated in CAV‐2 KO mice compared to WT animals; (iii) the proinflammatory effects induced by I/R are due to generation of reactive oxygen species (ROS) in CAV‐2 KO mice; and (iv) ingestion of ethanol at low to moderate levels (EPC) 24 hours prior to ischemia (45 min) followed by reperfusion (60 min) (I/R) will limit postischemic inflammation in CAV‐2 KO mice by a ROS‐dependent mechanism. Intravital fluorescence microscopy was used to visualize leukocyte rolling (LR) and adhesion (LA) in single postcapillary venules of the small intes­tine. Prior to I/R, male CAV‐2 KO mice were treated with EPC, MnTBAP (cell‐permeable SOD mimetic) 1 hour prior to I/R, or MnTBAP 20 minutes prior to EPC, respectively, with postcapillary venular LR and LA quantified during the first hour of reperfusion. Our data shown that LR and LA were markedly elevated in male CAV‐2 KO mice under baseline condition relative to that noted in WT animals. I/R‐induced LR and LA were increased to a greater extent in CAV‐2 KO mice compared to WT animals. These postischemic increases in LR and LA were abolished by treatment with EPC or by exposure to MnTBAP 1 hour prior to I/R. MnTBAP pretreatment 20 minutes prior to EPC also abolished the protective effects of EPC. These results indicate that genetic deletion of CAV‐2 produces proinflammatory effects under baseline conditions and exacerbates these effects after I/R by a ROS‐dependent mechanism. Antecedent EPC prevents the proinflammatory responses to I/R in CAV‐2 KO mice. This protective effect of EPC was initiated by ROS.Support or Funding InformationNIH: R01‐AA022108, R01‐HL081860; DOD: W81XWH‐15‐1‐0624.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The effect of maternal high fat diet on offspring muscle regeneration
Authors: Mikovic Jasmine , Islam Rabia , Lamon Séverine 
Published: June 2021

BackgroundSkeletal muscle fibres are post‐mitotic cells. As such, they exclusively rely on regenerative processes to restore muscle structure and function when damage has occurred through direct trauma or everyday tasks. Skeletal muscle quality relies on its development during the pre‐natal period. Foetal muscle development is a highly plastic process that is influenced by the intrauterine environment. Maternal behaviour, such as diet or exercise, can alter this environment. Using a maternal high fat diet model, we fed C57Bl/6 female mice with a low or high fat diet prior to and during gestation and lactation. The offspring were then switched to a low or high fat diet. We assessed whether maternal diet hindered offspring muscle regeneration after injury, and whether post‐natal diet could reverse these effects.ResultsAdiposity levels were higher in C57Bl/6 female mice consuming a high fat diet. There was no difference in offspring weight born to lean or obese dams at weaning; however, in adulthood, offspring born to obese dams were smaller than their control counterparts regardless of post‐natal diet. Markers of muscle regeneration including Pax7, MyoG, Myf5 and MRF4 were downregulated in offspring born to an obese mother or fed a high‐fat diet when compared to offspring experiencing normal growth.ConclusionAn obesogenic maternal diet negatively affects offspring muscle growth and markers of muscle regeneration. These effects could not be offset by offspring diet, highlighting the importance of the pre‐natal environment in muscle development and function.Support or Funding InformationAustralian Research Council (DE150100538)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Mechanical Characterization of Frozen and Freshly‐Isolated Human Brain Tumors
Authors: Stewart Daniel , Marsh Erica , Simmons Renee , Simmons Chelsey 
Published: June 2021

IntroductionTissue banks are a common human tissue source for oncology researchers, and common pathobiological assays have been optimized to accommodate previously frozen tissue. However, emerging interest in tissue mechanics to motivate tissue‐on‐a‐chip applications necessitate additional optimization for and understanding of mechanical changes with prolonged storage. Here, we seek to compare the mechanical properties of previously frozen to freshly‐isolated human brain tumors.MethodsAll human tumor samples were collected and data analyzed under University of Florida Institutional Review Board‐approve protocols. Meningioma samples were isolated from patients and stored at −80°C for 2 or 5 years before thawing in DMEM at room temperature and characterizing with a custom‐built indentation system within 30 min after thawing. Indentation and subsequent analysis of samples was performed fresh, never frozen tissue (1). Briefly, samples were indented and allowed to undergo stress‐relaxation until a quasi‐static state was reached. The steady‐state modulus was then determined by fitting the data to the Standard Linear Solid viscoelastic model, which represents the quasi‐static properties of the sample. Freshly‐isolated human tumor and normal mouse brain data was originally published in PLoS ONE in 2017 (1). Statistics were performed with a Wilcoxon non‐parametric test with multiple comparisons. Values are reported as median ± median absolute deviation.Results and DiscussionFreshly‐isolated human meningioma samples were about twice as stiff (2.83±1.26 kPa, Figure 1) as frozen meningiomas stored for 2 or 5 years (1.15±0.26 kPa and 0.97±0.54 kPa, respectively, p<0.0003). These findings are similar to those in the literature comparing showing that frozen tissue is softer than the freshly isolated counterparts (2, 3). The change in the mechanical properties of previously frozen tissue may reflect disruption of the extracellular matrix (ECM) architecture and cellular fidelity due to expansion and contraction of ice crystals during a freeze/thaw cycle (4). Future work will investigate changes in the ECM structure via SEM and immunostaining to correlate ECM structure and mechanical properties, allowing for a better understanding of cryogenically‐stored tissue.Support or Funding InformationWe gratefully acknowledge support from the Florida Center for Brian Tumor Research for human tissue coordination and collection, and funding support from Medtronic and NSF Award No. 1711543This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Sensitivity of Trabecular Mapping to Sliding Semilandmark Placement
Authors: Russell C. Kinley , Cunningham Deborah L. , Wescott Daniel J. , Gleiber Devora S. , Sylvester Adam D. 
Published: June 2021

Analyses of bone microstructure based on single volumes of interest (VOIs) are limited in their ability to quantify variation in trabecular properties across a joint. Geometric morphometric methods can overcome these limitations by utilizing sliding semilandmarks to locate multiple VOIs within a trabecular structure. Variation in the placement of semilandmarks, however, may change collected bone parameter values. Here we quantify the effect of intraobserver error in delineating the articular surface on sliding semilandmark placement and sampled trabecular properties.Proximal tibiae of 12 individuals that are part of the Texas State University Donated Skeletal Collection were scanned using micro‐computed tomography at the Forensic Anthropology Center at Texas State. Original grey scale image stacks were converted to binary images, and surface models of the exterior bone surface were created. Medial condyles were trimmed from their full surface models three times over a period of weeks. Sliding semilandmarks (n=141) were distributed on the condyle surfaces and then slid to minimize the bending energy of the thin‐plate spline function relative to the updated Procrustes average. Each sliding semilandmark was then used to locate a single VOI just deep to the cortical shell. To investigate the effect of landmark placement on trabecular bone parameters, each VOI was moved 0.5–1.5 mm to one of 10 neighboring positions. Bone volume fraction (BV/TV) and trabecular thickness (Tb.Th) were calculated for each VOI at each of the 11 positions. VOIs that moved outside the trabecular structure were removed from further analyses. 10,000 randomized combinations of the 11 positions of each VOI were created and correlations between bootstrap samples were calculated.Sliding semilandmark placement differed by 0.27 mm on average. Landmarks most affected by intraobserver error were those placed along the edge of the condylar surface (mean = 0.38 mm), while those on the interior portion of the condyle were affected less (mean = 0.21 mm). Sampled BV/TV and Tb.Th vary with VOI position, although there is a strong correlation among the 11 sampled values for BV/TV (r=0.83) and Tb.Th (r=0.80). These results suggest that VOI positions calculated from sliding semilandmarks provide consistent information about bone microstructure even when VOI placement is forced to deviate beyond average variation in sliding landmark position.Support or Funding InformationThis work was supported in part by instrumentation funded by the NSF under grant NSF: MRI 1338044.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Neanderthal Eustachian tube morphology lowered population‐wide fitness and contributed to extinction
Authors: Pagano Anthony Santino , Marquez Samuel , Laitman Jeffrey T. 
Published: June 2021

Among modern humans, otitis media (benign otitis media with effusion and acute otitis media, AOM) is the second most common pediatric clinical conditions. Acute otitis media is a fatal disease that can result in meningitis and pneumonia if untreated. Osteological signs of this disease may be found in erosion patterns on the middle ear ossicles, ossification of the tympanic membrane, and a lack of mastoid pneumatization. Recent studies report that nearly all known Neanderthal ossicles exhibit erosion patterns consistent with chronic AOM. To account for the anatomical basis of this apparent disease susceptibility, we assessed the morphological configuration of the cartilaginous Eustachian tube (CET) and dilator tubae (DT) musculature among a modern human growth series ranging from newborns to adults (n=442) and a sample of Neanderthals (La Chapelle aux Saints 1, La Ferrassie 1, Forbes Quarry 1, Saccopastore 1, Guattari 1) and mid‐Pleistocene pre‐Neanderthals (Atapuerca 5 and Steinheim 1). We performed morphometric analysis of the bony upper respiratory tract boundaries. A total of 31 bilateral and midline 3D landmarks were used and coordinate data were subjected to Procrustes‐fitting for geometric morphometric analysis and calculation of univariate measures.Neanderthals exhibited tall narrow choanae and greater overall robusticity. La Ferrassie 1 and Forbes Quarry 1 possessed extremely infant‐like CET orientation relative to the Frankfurt Horizontal Plane while other specimens had adult‐like or intermediate orientation. Choanal orientation among all Neanderthals was horizontal as among human infants. This trait occurred alongside a relatively adult‐like elongation and vertical orientation of the DT whereas the pre‐Neanderthals were distinguished primarily by an extremely short DT relative to Neanderthals and modern humans.The morphological configuration of Neanderthals was unlike any modern human population or growth stage. Differences between these groups appear to be species‐level with Neanderthals retaining infant‐like horizontal orientation of both the choanae and (among some) CET into adulthood. Neanderthal children were probably susceptible to AOM for longer periods of development. While modern human children experience steep reduction in disease occurrence at approximately six years of age with changes in both CET length and orientation, Neanderthal children would have remained susceptible as there was no such growth change in CET orientation. This could have impacted population‐wide fitness when sympatric modern humans invaded Neanderthal habitats and competed for limited resources. AOM should thus be considered among the many potential factors involved in the extinction of the Neanderthals.Support or Funding InformationNational Science Foundation, Grant number 1128901This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.