bluuebunny/crossref_metadata_2025_split huggingface dataset:
Macrophage depletion impairs neonatal tendon regeneration
Authors: Howell Kristen L. , Kaji Deepak A. , Montero Angela , Yeoh Kenji , Nasser Philip , Huang Alice H. 
Published: January 2021

ABSTRACTTendons are dense connective tissues that transmit muscle forces to the skeleton. After adult injury, healing potential is generally poor and dominated by scar formation. Although the immune response is a key feature of healing, the specific immune cells and signals that drive tendon healing have not been fully defined. In particular, the immune regulators underlying tendon regeneration are almost completely undetermined due to a paucity of tendon regeneration models. Using a mouse model of neonatal tendon regeneration, we screened for immune-related markers and identified upregulation of several genes associated with inflammation, macrophage chemotaxis, and TGFβ signaling after injury. Depletion of macrophages using AP20187 treatment of MaFIA mice resulted in impaired functional healing, reduced cell proliferation, reduced ScxGFP+ neo-tendon formation, and altered tendon gene expression. Collectively, these results show that inflammation is a key component of neonatal tendon regeneration and demonstrate a requirement for macrophages in effective functional healing.
Oxidative stress alters transcript localization of disease-causing genes in the retinal pigment epithelium
Authors: Kaczynski Tadeusz J. , Au Elizabeth D. , Farkas Michael H. 
Published: January 2021

AbstractNuclear retention is a mechanism whereby RNA transcripts are held in the nucleus to maintain a proper nuclear-to-cytoplasmic balance or as a stockpile for use in responding to stimuli. Many mechanisms are employed to determine whether transcripts are retained or exported to the cytoplasm, though the extent to which tissue- or cell-type, stressors, or disease pathogenesis affect this process remains unclear. As the most biochemically active tissue in the body, the retina must mitigate endogenous and exogenous stressors to maintain cell health and tissue function. Oxidative stress, believed to contribute to the pathogenesis, or progression, of age-related macular degeneration (AMD) and inherited retinal dystrophies (IRDs), is produced both internally from biochemical processes, as well as externally from environmental insult. To evaluate the effect of oxidative stress on transcript localization in the retinal pigment epithelium (RPE), we performed poly-A RNA sequencing on nuclear and cytoplasmic fractions from induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE) cells exposed to hydrogen peroxide, as well as untreated controls. Under normal conditions, the number of mRNA transcripts retained in the nucleus exceeded that found in studies of other tissues. Further, the nuclear-to-cytoplasmic ratio of transcripts is altered following oxidative stress, as is the retention of genes associated with AMD, IRDs, and those important for RPE physiology. These results provide a retention catalog of all expressed mRNA in iPSC-RPE under normal conditions and after exposure to hydrogen peroxide, offering insight into one of the potential roles oxidative stress plays in the progression of visual disorders.
Substantial intraspecific variation in energy budgets: biology or artefact?
Authors: Potter Tomos , Reznick David N , Coulson Tim 
Published: January 2021

AbstractDynamic energy budget (DEB) models provide a mechanistic description of life-histories in terms of fluxes of energy through biological processes. In these models, life-histories are a function of environmental conditions and of fundamental traits of the organism relating to the acquisition, allocation, and use of energy.These traits are described by the parameters of the DEB model, which have been estimated for over 2500 species. Recent work has aimed to compare species on the basis of differences in DEB parameters.We show that caution is required in such analyses, because (i) parameter estimates vary considerably as an artefact of the types of data used to fit the models, and (ii) there is substantial intraspecific variation in parameter values, reflecting biological differences among populations.We show that similar patterns of growth and reproduction can be reproduced with very different parameter sets. Our results imply that direct comparison of DEB parameters across populations or species may be invalid. However, valid comparisons are possible if differences in the types of data used to fit the models are taken into account.We estimated DEB parameters for 16 populations of Trinidadian guppy, identifying differences in resource allocation and metabolic rate consistent with evolved life-history differences among these populations.Variation in parameter values was substantial: if intraspecific variation in DEB parameters is greater than currently measured levels of interspecific variation, the detection of broad-scale patterns in energy budgets across species will be challenging.
A co-culture microplate for real-time measurement of microbial interactions
Authors: Jo Charles , Bernstein David B. , Vaisman Natalie , Frydman Horacio M. , Segrè Daniel 
Published: January 2021

AbstractThe dynamic structures of microbial communities emerge from the complex network of interactions between their constituent microbial organisms. Quantitative measurements of these microbial interactions are important for understanding and engineering microbial community structure. Here, we present the development and application of the BioMe plate, a redesigned microplate device in which pairs of wells are separated by porous membranes. BioMe facilitates the measurement of dynamic microbial interactions and integrates easily with standard laboratory equipment. We first applied BioMe to recapitulate recently characterized, natural symbiotic interactions between bacteria isolated from theD. melanogastergut microbiome. Specifically, the BioMe plate allowed us to observe the benefit provided by twoLactobacillistrains to anAcetobacterstrain. We next explored the use of BioMe to gain quantitative insight into the engineered obligate syntrophic interaction between a pair ofE. coliamino acid auxotrophs. We integrated experimental observations with a mechanistic computational model to quantify key parameters associated with this syntrophic interaction, including metabolite secretion and diffusion rates. This model also allowed us to explain the slow growth observed for auxotrophs growing in adjacent wells, by demonstrating that under the relevant range of parameters, local exchange between auxotrophs is essential for efficient growth. The BioMe plate provides a scalable and flexible approach for the study of dynamic microbial interactions.
Oncofly: A CURE for Cancer
Authors: Reed Floyd A. , de Couet H. Gert 
Published: January 2021

AbstractCourse-based Undergraduate Research Experiences (CURE’s) are emerging as a means to engage large numbers of undergraduate students in meaningful inquiry-based research activities. We describe here a simple laboratory exercise as part of an undergraduate genetics course that illustrates the contributions of oncogenes and tumor suppressors to the formation of neoplasms in an invertebrate model system. In addition, students were challenged to investigate whether flies reared on a diet containing a variety of additives display a higher number of invasive tumors in the larval abdomen.The goal of the exercise was to (i) familiarize students with the multigenic origin of the cancer phenotype, to (ii) introduce some of the fundamental molecular cancer hallmarks, and to (iii) highlight the significance of invertebrate model systems in biomedical research. Furthermore, (iv) students learn to execute a molecular test for transgenic produce and (v) apply statistical tools to test a simple hypothesis.We evaluated student learning and changes in opinions and attitudes relating to environmental versus genetic causes of cancer and several common misconceptions using a questionnaire before and after completing the exercise.Overall, significant improvements in the rate of factually correct responses and reductions in uncertainty were demonstrated. Although resistance to change was apparent in regard to identifying some risk factors, there was clear learning and understanding of the core concepts of carcinogenesis and the utility of basic research with model organisms.
Institutional Differences in the Stewardship and Research Output of United States Herbaria
Authors: Garretson Alexis 
Published: January 2021

AbstractPublic policy decisions regarding institutional frameworks that govern the stewardship of biodiversity data at public and private institutions are an area of increasing importance. Museums, government agencies, and academic institutions across the United States maintain collections of biological specimens and information critical to scientific discovery. One subset of these natural history collections are herbaria, or collections of preserved plant matter and their associated data. In this study, I evaluate the current state of the digitization and databasing of herbariums contributing data to the SEInet Regional Network of North American Herbaria, and assess the impact of characteristics, particularly institution type (cultural sector institutions, public universities, private universities, or public land institutions), on the metrics of herbaria richness, digitization, and research usage. The results of this study suggest that institution type is significantly associated with the size, diversity, and digitization efforts of a herbarium collection. Specifically, cultural sector institutions tend to have larger and more diverse collections, followed by public and private universities, and finally public land institutions. Additionally, as herbarium size and richness increases, the research output of associated staff also increases. These results highlight that some institutions, particularly larger institutions located at universities or cultural sector institutions, may be better supported in the curation, stewardship, and digitization of large collections, allowing long-term access to the associated biodiversity data. Smaller institutions at public land institutions may need additional support in these endeavors, and may represent an area of unmet needs for digitization and curatorial funding and resources.
Impact of gene annotation choice on the quantification of RNA-seq data
Authors: Chisanga David , Liao Yang , Shi Wei 
Published: January 2021

AbstractRNA sequencing is currently the method of choice for genome-wide profiling of gene expression. A popular approach to quantify expression levels of genes from RNA-seq data is to map reads to a reference genome and then count mapped reads to each gene. Gene annotation data, which include chromosomal coordinates of exons for tens of thousands of genes, are required for this quantification process. There are several major sources of gene annotations that can be used for quantification, such as Ensembl and RefSeq databases. However, there is very little understanding of the effect that the choice of annotation has on the accuracy of gene expression quantification in an RNA-seq analysis. In this paper, we present results from our comparison of Ensembl and RefSeq human annotations on their impact on gene expression quantification using a benchmark RNA-seq dataset generated by the SEquencing Quality Control (SEQC) consortium. We show that the use of RefSeq gene annotation models led to better quantification accuracy, based on the correlation with ground truths including expression data from >800 real-time PCR validated genes, known titration ratios of gene expression and microarray expression data. We also found that the recent expansion of the RefSeq annotation has led to a decrease in its annotation accuracy. Finally, we demonstrated that the RNA-seq quantification differences observed between different annotations were not affected by the use of different normalization methods.
Molecular mechanism of ACAD9 in mitochondrial respiratory complex 1 assembly
Authors: Xia Chuanwu , Lou Baoying , Fu Zhuji , Mohsen Al-Walid , Vockley Jerry , Kim Jung-Ja P. 
Published: January 2021

AbstractACAD9 belongs to the acyl-CoA dehydrogenase family, which catalyzes the α-β dehydrogenation of fatty acyl-CoA thioesters. Thus, it is involved in fatty acid β-oxidation (FAO). However, it is now known that the primary function of ACAD9 is as an essential chaperone for mitochondrial respiratory complex 1 assembly. ACAD9 interacts with ECSIT and NDUFAF1, forming the mitochondrial complex 1 assembly (MCIA) complex. Although the role of MCIA in the complex 1 assembly pathway is well studied, little is known about the molecular mechanism of the interactions among these three assembly factors. Our current studies reveal that when ECSIT interacts with ACAD9, the flavoenzyme loses the FAD cofactor and consequently loses its FAO activity, demonstrating that the two roles of ACAD9 are not compatible. ACAD9 binds to the carboxy-terminal half (C-ECSIT), and NDUFAF1 binds to the amino-terminal half of ECSIT. Although the binary complex of ACAD9 with ECSIT or with C-ECSIT is unstable and aggregates easily, the ternary complex of ACAD9-ECSIT-NDUFAF1 (i.e., the MCIA complex) is soluble and extremely stable. Molecular modeling and SAXS studies of the MCIA complex identified the possible interaction sites between the three assembly factors and binding sites for other assembly factors, including complex 1 subunits. Furthermore, we have mapped over 40 currently known pathogenic mutation sites onto the homology-modeled ACAD9 structure, giving us the structural basis for their involvement in diseases that result from complex 1 deficiency.
Fibrinolysis influences SARS-CoV-2 infection in ciliated cells
Authors: Hou Yapeng , Ding Yan , Nie Hongguang , Ji Hong-Long 
Published: January 2021

AbstractRapid spread of COVID-19 has caused an unprecedented pandemic worldwide, and an inserted furin site in SARS-CoV-2 spike protein (S) may account for increased transmissibility. Plasmin, and other host proteases, may cleave the furin site of SARS-CoV-2 S protein and γ subunits of epithelial sodium channels (γ ENaC), resulting in an increment in virus infectivity and channel activity. As for the importance of ENaC in the regulation of airway surface and alveolar fluid homeostasis, whether SARS-CoV-2 will share and strengthen the cleavage network with ENaC proteins at the single-cell level is urgently worthy of consideration. To address this issue, we analyzed single-cell RNA sequence (scRNA-seq) datasets, and found the PLAU (encoding urokinase plasminogen activator), SCNN1G (γENaC), and ACE2 (SARS-CoV-2 receptor) were co-expressed in alveolar epithelial, basal, club, and ciliated epithelial cells. The relative expression level of PLAU, TMPRSS2, and ACE2 were significantly upregulated in severe COVID-19 patients and SARS-CoV-2 infected cell lines using Seurat and DESeq2 R packages. Moreover, the increments in PLAU, FURIN, TMPRSS2, and ACE2 were predominately observed in different epithelial cells and leukocytes. Accordingly, SARS-CoV-2 may share and strengthen the ENaC fibrinolytic proteases network in ACE2 positive airway and alveolar epithelial cells, which may expedite virus infusion into the susceptible cells and bring about ENaC associated edematous respiratory condition.
Site-directed crosslinking identifies the stator-rotor interaction surfaces in a hybrid bacterial flagellar motor
Authors: Terashima Hiroyuki , Kojima Seiji , Homma Michio 
Published: January 2021

AbstractThe bacterial flagellum is the motility organelle powered by a rotary motor. The rotor and stator elements of the motor are embedded in the cytoplasmic membrane. The stator units assemble around the rotor, and an ion flux (typically H+or Na+) conducted through a channel of the stator induces conformational changes that generate rotor torque. Electrostatic interactions between the stator protein PomA inVibrio(MotA inEscherichia coli) and the rotor protein FliG have been suggested by genetic analyses, but have not been demonstrated directly. Here, we used site-directed photo- and disulfide-crosslinking to provide direct evidence for the interaction. We introduced a UV-reactive amino acid,p-benzoyl-L-phenylalanine (pBPA), into the cytoplasmic region of PomA or the C-terminal region of FliG in intact cells. After UV irradiation,pBPA inserted at a number of positions formed a crosslink with FliG. PomA residue K89 gave the highest yield of crosslinks, suggesting that it is the PomA residue nearest to FliG. UV-induced crosslinking stopped motor rotation, and the isolated hook-basal body contained the crosslinked products.pBPA inserted to replace residues R281 or D288 in FliG formed crosslinks with theEscherichia colistator protein, MotA. A cysteine residue introduced in place of PomA K89 formed disulfide crosslinks with cysteine inserted in place of FliG residues R281 and D288, and some other flanking positions. These results provide the first demonstration of direct physical interaction between specific residues in FliG and PomA/MotA.
Topoisomerase 2β induces DNA breaks to regulate human papillomavirus replication
Authors: Kaminski Paul , Hong Shiyuan , Kono Takeyuki , Hoover Paul , Laimins Laimonis 
Published: January 2021

AbstractTopoisomerases regulate higher order chromatin structures through the transient breaking and re-ligating of one or both strands of the phosphodiester backbone of duplex DNA. TOP2β is a type II topoisomerase that induces double strand DNA breaks at topological-associated domains (TADS) to relieve torsional stress arising during transcription or replication. TADS are anchored by CTCF and SMC1 cohesin proteins in complexes with TOP2β. Upon DNA cleavage a covalent intermediate DNA-TOP2β (TOP2βcc) is transiently generated to allow for strand passage. The tyrosyl-DNA phosphodiesterase TDP2 can resolve TOP2βcc but failure to do so quickly can lead to long-lasting DNA breaks. Given the role of CTCF/SMC1 proteins in the HPV life cycle we investigated if TOP2β proteins contribute to HPV pathogenesis. Our studies demonstrated that levels of both TOP2β and TDP2 were substantially increased in cells with high risk HPV genomes and this correlated with high amounts of DNA breaks. Knockdown of TOP2β with shRNAs reduced DNA breaks by over 50% as determined through COMET assays. Furthermore this correlated with substantially reduced formation of repair foci such as γH2AX, pCHK1 and pSMC1 indicative of impaired activation of DNA damage repair pathways. Importantly, knockdown of TOP2β also blocked HPV genome replication. Our previous studies demonstrated that CTCF /SMC1 factors associate with HPV genomes at sites in the late regions of HPV31 and these correspond to regions that also bind TOP2β. This study identifies TOP2β as responsible for enhanced levels of DNA breaks in HPV positive cells and as a regulator of viral replication.
The Conundrum of Giglio Island: unraveling the dynamics of an apparent resistance to COVID-19 – A descriptive study
Authors: Bognanni Antonio , Schiaffino Armando , Pimpinelli Fulvia , Donzelli Sara , Celesti Ilaria , Strano Sabrina , Solari Elena , Schiaffino Giorgia , Solari Gabriele , Solari Domenico , Delbue Serena , Rigoni Marta , Nollo Giandomenico , Muti Greta E. , Schünemann Giovanna E.U. Muti , Schünemann Holger J , Blandino Giovanni , Morrone Aldo , Muti Paola 
Published: January 2021

AbstractObjectivesDespite an extensive risk of exposure to COVID-19, the residents of Giglio Island, Italy, did not develop any symptom of SARS-CoV-2. The present study aims to characterize the nature of exposure and to describe the local population dynamics underlying its apparent resistance to COVID-19.MethodsWe conducted seroprevalence screening from April 29 to May 3, 2020 across the three main settlements on the island. We invited the adult resident population, present on the island to undergo testing by rapid serologic assay and to provide a sample of saliva for molecular validation. We monitored the participation through the official municipality residents’ list. Serologic testing was performed using a COVID-19 IgG/IgM rapid test while molecular analyses were carried out by Allplex 2019-nCoV Assay (Seegene).ResultsA total of 634 residents out of 748 (84.8%) present at the time, and 89 non-residents underwent serological testing. 364 males and 359 females with a median age of 58.5 years. The serological screening identified one positive, asymptomatic subject. The Nucleic Acid Amplification Tests did not yield any positive result.ConclusionDespite extensive exposure to SARS-CoV-2, only one new asymptomatic infection occurred in this population. This may be due to unknown protective factors or chance. On the basis of this first descriptive study, using its population as a reference model, further investigations will be conducted to characterize the summer period exposure and to test the advanced hypotheses, focusing on the evaluation of a possible cross-reactivity to SARS-CoV-2 from exposure to endemic viruses.
Tuberculosis biomarkers discovered using Diversity Outbred mice
Authors: Koyuncu Deniz , Niazi M. Khalid Khan , Tavolara Thomas , Abeijon Claudia , Ginese Melanie , Liao Yanghui , Mark Carolyn , Gower Adam C , Gatti Daniel M , Kramnik Igor , Gurcan Metin , Yener Bülent , Beamer Gillian 
Published: January 2021

AbstractBackgroundBiomarker discovery for pulmonary tuberculosis (TB) may be accelerated by modeling human genotypic diversity and phenotypic responses toMycobacterium tuberculosis(Mtb). To meet these objectives, we use the Diversity Outbred (DO) mouse population and apply novel classifiers to identify informative biomarkers from multidimensional data sets.MethodTo identify biomarkers, we infected DO mice with aerosolizedMtbconfirmed a human-like spectrum of phenotypes, examined gene expression, and inflammatory and immune mediators in the lungs. We measured 11 proteins in 453Mtb-infected and 29 non-infected mice. We have searched all combinations of six classification algorithms and 239 biomarker subsets and independently validated the selected classifiers. Finally, we selected two mouse lung biomarkers to test as candidate biomarkers of active TB, measuring their diagnostic performance in human sera acquired from the Foundation for Innovative New Diagnostics.FindingsDO mice discovered two translationally relevant biomarkers, CXCL1 and MMP8 that accurately diagnosed active TB in humans with > 90% sensitivity and specificity compared to controls. We identified them through the two classifiers that accurately diagnosed supersusceptible DO mice with early-onset TB: Logistic Regression using MMP8 as a single biomarker, and Gradient Tree Boosting using a panel of 4 biomarkers (CXCL1, CXCL2, TNF, IL-10).InterpretationThis work confirms that the DO population models human responses and can accelerate discovery of translationally relevant TB biomarkers.FundingSupport was provided by NIH R21 AI115038; NIH R01 HL145411; NIH UL1-TR001430; and the American Lung Association Biomedical Research Grant RG-349504.