bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acute repair of meniscus root tear partially restores joint displacements as measured with MRI and loading in a porcine knee
Authors: Meadows Kyle D. , Peloquin John M. , Markhali Milad I. , Zgonis Miltiadis H. , Schaer Thomas P. , Mauck Robert L. , Elliott Dawn M. 
Published: February 2023

AbstractThe meniscus serves important load-bearing functions and protects the underlying articular cartilage. Unfortunately, meniscus tears are common and impair the ability of the meniscus to distribute loads, greatly increasing the risk for developing osteoarthritis. Therefore, surgical repair of the meniscus is a frequently performed procedure; however, this repair does not always prevent osteoarthritis. This is hypothesized to be due to altered joint loading post injury and repair, where the functional deficit of the meniscus prevents it from performing its role of distributing forces. However, many studies of meniscus function required opening the joint, which alters kinematics. The objective of this study was to use novel MRI methods to image the intact joint under axial load and measure the acute meniscus and femur displacements in an intact joint, after a meniscus root tear, and after suture repair in the porcine knee, a frequently used in vivo model. We found that anterior root tear led to large meniscus and femur displacements under physiological axial loading, and that suture anchor repair reduced these displacements, but did not fully restore intact joint kinematics. After tear and repair, the anterior region of the meniscus moved posteriorly and medially as it was forced out of the joint space under loading, while the posterior region had small displacements as the posterior attachment acted as a hinge about which the meniscus rotated in the axial plane. This technique can be applied to evaluate the effect of knee injuries and to develop improved repair strategies to restore joint kinematics.
SCCA1/SERPINB3 promotes suppressive immune environment via STAT-dependent chemokine production, blunting the therapy-induced T cell responses
Authors: Chen Liyun , Shi Victoria , Wang Songyan , Freeman Rebecca , Ruiz Fiona , Jayachandran Kay , Zhang Jin , Cosper Pippa , Sun Lulu , Luke Clifford J. , Spina Catherine , Grigsby Perry W. , Schwarz Julie K. , Markovina Stephanie 
Published: February 2023

AbstractRadiotherapy is a commonly used cancer treatment; however, patients with high serum squamous cell carcinoma antigen (SCCA1/SERPINB3) are associated with resistance and poor prognosis. Despite being a strong clinical biomarker, the modulation of SERPINB3 in tumor immunity is poorly understood. We investigated the microenvironment of SERPINB3 high tumors through RNAseq of primary cervix tumors and found thatSERPINB3was positively correlated withCXCL1/8, S100A8/A9and myeloid cell infiltration. Induction of SERPINB3in vitroresulted in increased CXCL1/8 and S100A8/A9 production, and supernatants from SERPINB3-expressing cultures attracted monocytes and MDSCs. In murine tumors, the orthologuemSerpinB3apromoted MDSC, TAM, and M2 macrophage infiltration contributing to an immunosuppressive phenotype, which was further augmented upon radiation. Radiation-enhanced T cell response was muted in SERPINB3 tumors, whereas Treg expansion was observed. A STAT-dependent mechanism was implicated, whereby inhibiting STAT signaling with ruxolitinib abrogated suppressive chemokine production. Patients with elevated pre-treatment serum SCCA and high pSTAT3 had increased intratumoral CD11b+ myeloid cell compared to patients with low SCCA and pSTAT3 cohort that had overall improved cancer specific survival after radiotherapy. These findings provide a preclinical rationale for targeting STAT signaling in tumors with high SERPINB3 to counteract the immunosuppressive microenvironment and improve response to radiation.
Adipocyte lipin 1 is positively associated with metabolic health in humans and regulates systemic metabolism in mice
Authors: LaPoint Andrew , Singer Jason M. , Ferguson Daniel , Shew Trevor M. , Renkemeyer M. Katie , Palacios Hector , Field Rachael , Shankaran Mahalakshmi , Smith Gordon I. , Yoshino Jun , He Mai , Patti Gary J. , Hellerstein Marc K. , Klein Samuel , Brestoff Jonathan R. , Finck Brian N. , Lutkewitte Andrew J. 
Published: February 2023

AbstractDysfunctional adipose tissue is believed to promote the development of hepatic steatosis and systemic insulin resistance, but many of the mechanisms involved are still unclear. Lipin 1 catalyzes the conversion of phosphatidic acid to diacylglycerol (DAG), the penultimate step of triglyceride synthesis, which is essential for lipid storage. Herein we found that adipose tissueLPIN1expression is decreased in people with obesity compared to lean subjects and lowLPIN1expression correlated with multi-tissue insulin resistance and increased rates of hepatic de novo lipogenesis. Comprehensive metabolic and multi-omic phenotyping demonstrated that adipocyte-specificLpin1-/-mice had a metabolically-unhealthy phenotype, including liver and skeletal muscle insulin resistance, hepatic steatosis, increased hepatic de novo lipogenesis, and transcriptomic signatures of nonalcoholic steatohepatitis that was exacerbated by high-fat diets. We conclude that adipocyte lipin 1-mediated lipid storage is vital for preserving adipose tissue and systemic metabolic health and its loss predisposes mice to nonalcoholic steatohepatitis.
Evolution of reproductive isolation in a long-term evolution experiment withDrosophila melanogaster: 30 years of divergent life history selection
Authors: Robinson Chloe E , Thyagarajan Harshavardhan , Chippindale Adam K 
Published: February 2023

ABSTRACTWe ask if three decades and over 1 500 generations of divergent life history selection on age at reproduction has resulted in the evolution of reproductive isolation (RI) between laboratory populations ofDrosophila melanogaster. We tested for premating, postmating-prezygotic and postzygotic reproductive isolation between 3 replicate population pairs. Large evolved differences in body size between selection treatments suggested the potential for prezygotic barriers driven by sexual selection or physical incompatibilities between the sexes. Although a simple prediction would be preference for larger size, creating directional isolation, our results from individual mate choice trials indicate that populations from both selection treatments show a marked bias towards homotypic mate choice; indicative of prezygotic RI driven by sexual selection or sexual conflict. Hybridization between the focal populations resulted in the production of viable adult flies with intermediate size and developmental traits. We observed a suggestive but statistically non-significant trend of fitness decline in the F2 generation of hybrids, but no significant evidence suggesting the evolution of postmating-prezygotic or postzygotic RI. Our findings are in accord with extant literature that posits that premating RI evolves before postmating forms of RI.
Red-purple Andean potato polyphenols have an anti-neuroblastoma effectin vitrovia apoptosis through mitochondria
Authors: Silveyra María Ximena , Andreu Adriana Balbina 
Published: February 2023

AbstractAndean potatoes (Solanum tuberosumssp.andigena) are a good source of dietary polyphenols, such as phenolic acid and flavonoids. These polyphenols have several beneficial effects on human health due to their antioxidant properties. Previously, we demonstrated that polyphenol extracts from Andean potato tubers exerted a concentration-dependent cytotoxic effect in human neuroblastoma cells. However, the mechanisms involved in this cytotoxic activity were not explored. Here we show that Santa María tuber’s polyphenols activated a programmed cell death by caspase-independent apoptosis. We found that polyphenols induced cell and nucleus morphology changes and slightly affected the cell cycle. Furthermore, the polyphenols altered the neuroblastoma cells’ homeostasis redox and mitochondrial function, increasing the levels of apoptotic cells. Finally, we showed that neither Bcl-2 nor caspase-3 was involved in this mechanism of death. Our results confirmed that Santa María tuber’s polyphenols are bioactive compounds with mitochondria as a target and contribute to revalorizing Andean potatoes as a functional food. These findings demonstrated that they would be a good source of anti-tumor compounds that would induce tumor cell death even in apoptotic-resistant tumors, opening new therapeutic avenues.
EMBER multi-dimensional spectral microscopy enables quantitative determination of disease- and cell-specific amyloid strains
Authors: Yang Hyunjun , Yuan Peng , Wu Yibing , Shi Marie , Caro Christoffer D. , Tengeiji Atsushi , Yamanoi Shigeo , Inoue Masahiro , DeGrado William F. , Condello Carlo 
Published: February 2023

AbstractIn neurodegenerative diseases proteins fold into amyloid structures with distinct conformations (strains) that are characteristic of different diseases. However, there is a need to rapidly identify amyloid conformationsin situ. Here we use machine learning on the full information available in fluorescent excitation/emission spectra of amyloid binding dyes to identify six distinct different conformational strainsin vitro, as well as Aβ deposits in different transgenic mouse models. Our EMBER (excitation multiplexed bright emission recording) imaging method rapidly identifies conformational differences in Aβ and tau deposits from Down syndrome, sporadic and familial Alzheimer’s disease human brain slices. EMBER hasin situidentified distinct conformational strains of tau inclusions in astrocytes, oligodendrocytes, and neurons from Pick’s disease. In future studies, EMBER should enable high-throughput measurements of the fidelity of strain transmission in cellular and animal neurodegenerative diseases models, time course of amyloid strain propagation, and identification of pathogenic versus benign strains.SignificanceIn neurodegenerative diseases proteins fold into amyloid structures with distinct conformations (strains) that are characteristic of different diseases. There is a need to rapidly identify these amyloid conformationsin situ. Here we use machine learning on the full information available in fluorescent excitation/emission spectra of amyloid binding dyes to identify six distinct different conformational strainsin vitro, as well as Aβ deposits in different transgenic mouse models. Our imaging method rapidly identifies conformational differences in Aβ and tau deposits from Down syndrome, sporadic and familial Alzheimer’s disease human brain slices. We also identified distinct conformational strains of tau inclusions in astrocytes, oligodendrocytes, and neurons from Pick’s disease. These findings will facilitate the identification of pathogenic protein aggregates to guide research and treatment of protein misfolding diseases.
Light sheet autofluorescence lifetime imaging with a single photon avalanche diode array
Authors: Samimi Kayvan , Desa Danielle E. , Lin Wei , Weiss Kurt , Li Joe , Huisken Jan , Miskolci Veronika , Huttenlocher Anna , Chacko Jenu V. , Velten Andreas , Rogers Jeremy D. , Eliceiri Kevin W. , Skala Melissa C. 
Published: February 2023

AbstractSingle photon avalanche diode (SPAD) array sensors can increase the imaging speed for fluorescence lifetime imaging microscopy (FLIM) by transitioning from laser scanning to widefield geometries. While a SPAD camera in epi-fluorescence geometry enables widefield FLIM of fluorescently labeled samples, label-free imaging of single-cell autofluorescence is not feasible in an epi-fluorescence geometry because background fluorescence from out-of-focus features masks weak cell autofluorescence and biases lifetime measurements. Here, we address this problem by integrating the SPAD camera in a light sheet illumination geometry to achieve optical sectioning and limit out-of-focus contributions, enabling fast label-free FLIM of single-cell NAD(P)H autofluorescence. The feasibility of this NAD(P)H light sheet FLIM system was confirmed with time-course imaging of metabolic perturbations in pancreas cancer cells with 10 s integration times, andin vivoNAD(P)H light sheet FLIM was demonstrated with live neutrophil imaging in a zebrafish tail wound, also with 10 s integration times. Finally, the theoretical and practical imaging speeds for NAD(P)H FLIM were compared across laser scanning and light sheet geometries, indicating a 30X to 6X frame rate advantage for the light sheet compared to the laser scanning geometry. This light sheet system provides faster frame rates for 3D NAD(P)H FLIM for live cell imaging applications such as monitoring single cell metabolism and immune cell migration throughout an entire living organism.
An electrochemical approach for rapid, sensitive, and selective detection of dynorphin
Authors: Conway Sineadh M. , Kuo Chao-Cheng , Gardiner Woodrow , Wu Rui-Ni , Thang Loc V. , Gereau Graydon B. , Cirrito John R. , Yuede Carla M. , McCall Jordan G. , Al-Hasani Ream 
Published: February 2023

AbstractThe endogenous opioid peptide systems are critical for analgesia, reward processing, and affect, but research on their release dynamics and function has been challenging. Here, we have developed microimmunoelectrodes (MIEs) for the electrochemical detection of opioid peptides using square-wave voltammetry. Briefly, a voltage is applied to the electrode to cause oxidation of the tyrosine residue on the opioid peptide of interest, which is detected as current. To provide selectivity to these voltammetric measurements, the carbon fiber surface of the MIE is coated with an antiserum selective to the opioid peptide of interest. To test the sensitivity of the MIEs, electrodes are immersed in solutions containing different concentrations of opioid peptides, and peak oxidative current is measured. We show that dynorphin antiserum-coated electrodes are sensitive to increasing concentrations of dynorphin in the attomolar range. To confirm selectivity, we also measured the oxidative current from exposure to tyrosine and other opioid peptides in solution. Our data show that dynorphin antiserum-coated MIEs are sensitive and selective for dynorphin with little to no oxidative current observed in met-enkephalin and tyrosine solutions. Additionally, we demonstrate the utility of these MIEs in anin vitrobrain slice preparation using bath application of dynorphin as well as optogenetic activation of dynorphin release. Future work aims to use MIEsin vivofor real-time, rapid detection of endogenous opioid peptide release in awake, behaving animals.
Optimizing anesthesia and delivery approaches for dosing into lungs of mice
Authors: Seo Yurim , Qiu Longhui , Magnen Mélia , Conrad Catharina , Moussavi-Harami S. Farshid , Looney Mark R , Cleary Simon J 
Published: February 2023

AbstractMicrobes, toxins, therapeutics and cells are often instilled into lungs of mice to model diseases and test experimental interventions. Consistent pulmonary delivery is critical for experimental power and reproducibility, but we observed variation in outcomes between handlers using different anesthetic approaches for intranasal dosing into mice. We therefore used a radiotracer to quantify lung delivery after intranasal dosing under inhalational (isoflurane) versus injectable (ketamine/xylazine) anesthesia in C57BL/6 mice. We found that ketamine/xylazine anesthesia resulted in delivery of a greater proportion (52±9%) of an intranasal dose to lungs relative to isoflurane anesthesia (30±15%). This difference in pulmonary dose delivery altered key outcomes in models of viral and bacterial pneumonia, with mice anesthetized with ketamine/xylazine for intranasal infection with influenza A virus orPseudomonas aeruginosadeveloping more robust lung inflammation responses relative to control animals randomized to isoflurane anesthesia. Pulmonary dosing efficiency through oropharyngeal aspiration was not affected by anesthetic method and resulted in delivery of 63±8% of dose to lungs, and a non-surgical intratracheal dosing approach further increased lung delivery to 92±6% of dose. Use of either of these more precise dosing methods yielded greater experimental power in the bacterial pneumonia model relative to intranasal infection. Both anesthetic approach and dosing route can impact pulmonary dosing efficiency. These factors affect experimental power and so should be considered when planning and reporting studies involving delivery of fluids to lungs of mice.Graphical abstract
Computational evaluation of light propagation in cylindrical bioreactors for optogenetic mammalian cell cultures
Authors: Minami Shiaki A. , Shah Priya S. 
Published: February 2023

AbstractOptogenetic control of cellular pathways and gene circuits in mammalian cells is a new frontier in mammalian genetic engineering. As a low-cost, tunable, and reversible input, light is highly adept at spatiotemporal, orthogonal regulation of cellular behavior. However, light is absorbed and scattered as it travels through media and cells, and the applicability of optogenetics in larger mammalian bioreactors has not been determined. In this work, we computationally explore the size limit to which optogenetics can be applied in cylindrical bioreactors at relevant height-to-diameter ratios for mammalian cell culture. We model the propagation of light using the radiative transfer equation and consider changes in reactor volume, absorption coefficient, scattering coefficient, and scattering anisotropy. We observed sufficient light penetration for activation for bioreactor sizes of up to 80,000 L with maximal cell densities, with decreasing efficiency for larger bioreactors. For a 100,000 L bioreactor, we determined that lower cell densities of up to 1.5·107cells/mL can be supported. We conclude that optogenetics can be applied to bioreactors at an industrial scale and may be a valuable tool for specific biomanufacturing applications.
Identifying Human Specific Adverse Outcome Pathways of Per- and Polyfluoroalkyl Substances Using Liver-Chimeric Humanized Mice
Authors: Robarts Dakota R. , Paine-Cabrera Diego , Kotulkar Manasi , Venneman Kaitlyn K. , Gunewardena Sumedha , Corton J. Christopher , Lau Christopher , Foquet Lander , Bial Greg , Apte Udayan 
Published: February 2023

AbstractBackgroundPer- and polyfluoroalkyl substances (PFAS) are persistent organic pollutants with myriad adverse effects. While perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS) are the most common contaminants, levels of replacement PFAS, such as perfluoro-2-methyl-3-oxahexanoic acid (GenX), are increasing. In rodents, PFOA, PFOS, and GenX have several adverse effects on the liver, including nonalcoholic fatty liver disease.ObjectiveWe aimed to determine human-relevant mechanisms of PFAS induced adverse hepatic effects using FRG liver-chimeric humanized mice with livers repopulated with functional human hepatocytes.MethodsMale humanized mice were treated with 0.067 mg/L of PFOA, 0.145 mg/L of PFOS, or 1 mg/L of GenX in drinking water for 28 days. Liver and serum were collected for pathology and clinical chemistry, respectively. RNA-sequencing coupled with pathway analysis was used to determine molecular mechanisms.ResultsPFOS caused a significant decrease in total serum cholesterol and LDL/VLDL, whereas GenX caused a significant elevation in LDL/VLDL with no change in total cholesterol and HDL. PFOA had no significant changes in serum LDL/VLDL and total cholesterol. All three PFAS induced significant hepatocyte proliferation. RNA-sequencing with alignment to the human genome showed a total of 240, 162, and 619 differentially expressed genes after PFOA, PFOS, and GenX exposure, respectively. Upstream regulator analysis revealed inhibition of NR1D1, a transcriptional repressor important in circadian rhythm, as the major common molecular change in all PFAS treatments. PFAS treated mice had significant nuclear localization of NR1D1.In silicomodeling showed PFOA, PFOS, and GenX potentially interact with the DNA-binding domain of NR1D1.DiscussionThese data implicate PFAS in circadian rhythm disruption via inhibition of NR1D1. These studies show that FRG humanized mice are a useful tool for studying the adverse outcome pathways of environmental pollutants on human hepatocytes in situ.
A Zymography technique to study amino acid activation by aminoacyl tRNA synthetases (aaRS): A broad spectrum, high-throughput tool to screen activities of aaRS and their “Urzyme” variants
Authors: Patra Sourav Kumar , Carter Charles W. 
Published: February 2023

AbstractAmino acyl tRNA synthetases or aaRSs play a key role in assuring the precision of protein translation. They are highly specific for their cognate amino acid and cognate tRNA substrates during protein synthesis, utilizing ATP to ensure that proper assignments are made between amino acid and anticodon. Specific aaRS for each amino acid are present in all cells. We describe a new zymography technique to qualitatively visualize and semi-quantitatively determine the amino acid activation capacity of each type of aaRS molecule by indirect colorimetric detection of released pyrophosphates during the formation of aminoacyl-AMP. Protein samples containing aaRS are subjected to Native PAGE, followed by incubation in buffer containing cognate amino acid and ATP for sufficient time to generate pyrophosphates (PPi) which are then converted to inorganic phosphates by pyrophosphatase treatment. Finally, the generated and localized phosphates around the aaRS protein inside the gel can be visualized after staining by ammonium molybdate and malachite green solution. This technique has been validated by inspecting the substrate specificities of specific aaRSs. This zymography technique is sufficiently sensitive to detect and authenticate activities of much (i.e., ~10-5-fold) less active aaRS “Urzymes”, to study alteration of activities of aaRS by various intrinsic or extrinsic factors and to screen aaRS-specific antimicrobial drugs.
SATB2 loss in inflammatory bowel disease-associated small intestinal metaplasia of the distal colon
Authors: Zeineldin Maged , Larman Tatianna C. 
Published: February 2023

AbstractEpithelial metaplasia is a common adaptation to chronic inflammatory processes and can be associated with increased risk of dysplasia and cancer. The distal colon of patients with inflammatory bowel disease (IBD) commonly shows crypt architectural distortion and Paneth cell metaplasia (PCM), and IBD patients also carry increased risk of colitis-associated dysplasia and cancer (CAC). Loss of SATB2 expression (Special AT-rich binding 2 protein, a colon-restricted chromatin remodeler) has recently been shown to distinguish colitis-associated dysplasia and CAC from sporadic disease. Here we report non-diffuse heterogeneous patterns of SATB2 loss across non-dysplastic distal colon biopsies from IBD patients (n=20). This cohort was specifically curated to include biopsies with well-developed histologic features of villiform growth and PCM. Notably, CDX2 was strongly expressed and P53 showed a wild-type immunolabeling pattern across our non-dysplastic cohort, regardless of SATB2 immunolabeling pattern. Our findings fit with recent murine studies in which colon-specificSatb2deletion resulted in histologic conversion of colonic mucosa to small intestinal-like mucosa, including emergence of villi and Paneth cells. Taken together, we show that SATB2 loss is associated with a preneoplastic metaplastic response to chronic injury in human IBD and chronic colitis, reframing PCM more broadly as small intestinal metaplasia. We propose that inflammation-associated SATB2 loss mediates a remodeled chromatin landscape permissive for dysplasia and CAC.