bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatiotemporal Dynamics of Vcam1 Regulates Cholangiocarcinoma Mass Expansion and Tumor Dissemination under Growth-suppressive Peritumoral Myofibroblasts
Authors: Tian Cheng , Li Liyuan , Pan Qingfei , Xu Beisi , Li Yizhen , Fan Li , Brown Anthony , Morrison Michelle , Dey Kaushik , Yang Jun J. , Yu Jiyang , Glazer Evan S , Zhu Liqin 
Published: January 2023

ABSTRACTIntrahepatic cholangiocarcinoma (iCCA) is characterized by its highly desmoplastic stroma. Myofibroblasts (MFs) are present both within the tumor mass (intratumoral MFs, iMFs) and at the tumor border (peritumoral MFs, pMFs). Using a spheroid-based coculture system, we show that the initial iCCA-pMF contact is growth suppressive to the tumor cells. However, prolonged iCCA-pMF interaction elicits significant tumor cell invasion and dissemination. We find that vascular cell adhesion molecule-1 (Vcam1) level is elevated in tumor cells in contact with pMFs but low in disseminated tumor cells both in vitro and in vivo. A gene regulatory network analysis of mouse and patient iCCA tumors andVcam1knockout (Vcam1KO) demonstrate a heavy involvement of Vcam1 in epithelial-to-mesenchymal transition. WhileVcam1KOhas only a limited impact on tumor cell growth in their monoculture,Vcam1KOspheroids exhibit instant dissemination and a severe growth defect when cocultured with pMFs. When transplanted into the liver,Vcam1KOiCCA cells show a similar increase in dissemination but a significant defect in establishing primary and metastatic tumors. Incomplete blocking of Vcam1 in vivo reduces the size but increase the number of metastatic lesions. Overall, our study shows a spatiotemporal regulation of iCCA growth and dissemination by pMFs in a Vcam1-dependent manner.
Global scale phylogeography of functional traits and microdiversity inProchlorococcus
Authors: Ustick Lucas J. , Larkin Alyse A. , Martiny Adam C. 
Published: January 2023

AbstractProchlorococcusis the most numerically abundant photosynthetic organism in the surface ocean. TheProchlorococcushigh-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenomically assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenomically assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype’s phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity inProchlorococcus.
Path analysis reveals that corticosterone mediates gluconeogenesis from fat-derived substrates during acute stress in songbirds
Authors: Fokidis H. Bobby 
Published: January 2023

AbstractGlucocorticoids (e.g., corticosterone or CORT in birds) mobilize energy reserves during stress to aid survival. Stress liberates glucose (GLU) by glycogenolysis, but with glycogen depletion, gluconeogenesis of fat and protein sources predominates. Songbirds have higher metabolic rates and GLU concentrations than mammals and likely rely more on fat and protein stores during stress. We tested this hypothesis in four songbird species using path analysis to model the interrelationships between CORT and energy metabolites both at baseline and after acute stress. Individuals in better condition had higher triglyceride and CORT levels at baseline than individuals in poor body condition, and these differences became more pronounced with stress. Free CORT (the fraction unbound to circulating proteins) was associated with more GLU and free glycerol at baseline, but the former relationship was lost after acute stress. This suggests a shift from a combination of glycogenolysis and gluconeogenesis to solely the latter with acute stress. Glucose levels were also associated with uric acid indicating that birds obtain GLU during stress from gluconeogenesis of mostly fat-derived substrates. This provides a previously elusive functional link between body condition and the stress response, and suggests songbirds are more susceptible to stress challenges during energy-limiting conditions than mammals.
in vivoquantitative FRET small animal imaging: intensity versus lifetime-based FRET
Authors: Smith Jason T. , Sinsuebphon Nattawut , Rudkouskaya Alena , Michalet Xavier , Intes Xavier , Barroso Margarida 
Published: January 2023

ABSTRACTFörster Resonance Energy Transfer (FRET) microscopy is used in numerous biophysical and biomedical applications to monitor inter- and intramolecular interactions and conformational changes in the 2–10 nm range. FRET is currently being extended toin vivooptical imaging, its main application being in quantifying drug-target engagement or drug release in animal models of cancer using organic dye or nanoparticle-labeled probes. Herein, we compared FRET quantification using intensity-based FRET (sensitized emission FRET analysis with the 3-cube approach using an IVIS imager) and macroscopic fluorescence lifetime (MFLI) FRET using a custom system using a time-gated ICCD, for small animal opticalin vivoimaging. The analytical expressions and experimental protocols required to quantify the productfDEof the FRET efficiencyEand the fraction of donor molecules involved in FRET,fD, are described in detail for both methodologies. Dynamicin vivoFRET quantification of transferrin receptor-transferrin binding was acquired in live intact nude mice upon intravenous injection of near infrared-labeled transferrin FRET pair and benchmarked againstin vitroFRET using hybridized oligonucleotides. Even though bothin vivoimaging techniques provided similar dynamic trends for receptor-ligand engagement, we demonstrate that MFLI FRET has significant advantages. Whereas the sensitized emission FRET approach using the IVIS imager required 9 measurements (6 of which are used for calibration) acquired from three mice, MFLI FRET needed only one measurement collected from a single mouse, although a control mouse might be needed in a more general situation. Based on our study, MFLI therefore represents the method of choice for longitudinal preclinical FRET studies such as that of targeted drug delivery in intact, live mice.WHY IT MATTERSFRET measurements in live animals open a unique window into drug-target interaction monitoring, by sensing the close proximity between a donor and acceptor-labeled molecular probes. To perform these measurements, a 3-cube fluorescent intensity measurement strategy can be adopted, as is common forin vitroFRET microscopy studies. However, it is challenging to translate this already cumbersome approach toin vivosmall animal imaging. Here, we compare this standard approach, for which we provide a revised analytical framework, to a conceptually much simpler and more powerful one based on fluorescence lifetime measurements. Our results demonstrate that the technical challenge ofin vivofluorescence lifetime macroscopic imaging is well worth surmounting to obtain quantitative, whole-animal information regarding molecular drug-target engagement.
The circadian clock is required for rhythmic lipid transport in theDrosophilahemolymph in interaction with diet, photic condition and feeding
Authors: Amatobi Kelechi M. , Ozbek-Unal Ayten Gizem , Schäbler Stefan , Deppisch Peter , Helfrich-Förster Charlotte , Mueller Martin J , Wegener Christian , Fekete Agnes 
Published: January 2023

AbstractModern lifestyle often is at odds with endogenously driven rhythmicity, which can lead to circadian disruption and metabolic syndrome. One signature for circadian disruption is a diminished or altered cycling of metabolites in the circulating tissue reflecting the current metabolic status.Drosophilais a well-established model in chronobiology, but day-time dependent variations of transport metabolites in the fly circulation are poorly characterized. Here, we sampled fly hemolymph throughout the day and analysed diacylglycerols (DGs), phosphoethanolamines (PEs) and phosphocholines (PCs) using LC-MS. In wildtype flies kept on sugar-only medium under a light-dark cycle, all transport lipid species showed a synchronized bimodal oscillation pattern with maxima at the beginning and end of the light phase which were impaired inperiod01clock mutants. In wildtype flies under constant dark conditions, the oscillation became monophasic with a maximum in the middle of the subjective day. In strong support of clock-driven oscillations, levels of DGs, PEs and PCs peaked once in the middle of the light phase under time-restricted feeding independent of the time of food intake. Rearing of wildtype flies on lipid-containing standard medium masked the rhythmic alterations of hemolymph lipid levels. Our data suggest that the circadian clock aligns daily oscillations of DGs, PEs and PCs in the hemolymph to the anabolic siesta phase, whith a strong influence of light on phase and modality. This finding opens the question whether and to what extent the circadian regulation of transport lipid levels in the hemolymph contributes to the health of the fly.
RAMEN Unveils Clinical Variable Networks for COVID-19 Severity and Long COVID Using Absorbing Random Walks and Genetic Algorithms
Authors: Xiong Yiwei , Wang Jingtao , Shang Xiaoxiao , Chen Tingting , Fraser Douglas D. , Fonseca Gregory , Rousseau Simon , Ding Jun 
Published: January 2023

AbstractThe COVID-19 pandemic has significantly altered global socioeconomic structures and individual lives. Understanding the disease mechanisms and facilitating diagnosis requires comprehending the complex interplay among clinical factors like demographics, symptoms, comorbidities, treatments, lab results, complications, and other metrics, and their relation to outcomes such as disease severity and long term outcomes (e.g., post-COVID-19 condition/long COVID). Conventional correlational methods struggle with indirect and directional connections among these factors, while standard graphical methods like Bayesian networks are computationally demanding for extensive clinical variables. In response, we introduced RAMEN, a methodology that integrates Genetic Algorithms with random walks for efficient Bayesian network inference, designed to map the intricate relationships among clinical variables. Applying RAMEN to the Biobanque québécoise de la COVID-19 (BQC19) dataset, we identified critical markers for long COVID and varying disease severity. The Bayesian Network, corroborated by existing literature and supported through multi-omics analyses, highlights significant clinical variables linked to COVID-19 outcomes. RAMEN’s ability to accurately map these connections contributes substantially to developing early and effective diagnostics for severe COVID-19 and long COVID.
Volumetric Printing across Melt Electrowritten Scaffolds Fabricates Multi-Material Living Constructs with Tunable Architecture and Mechanics
Authors: Größbacher Gabriel , Bartolf-Kopp Michael , Gergely Csaba , Bernal Paulina Nuñez , Florczak Sammy , de Ruijter Mylène , Groll Jürgen , Malda Jos , Jüngst Tomasz , Levato Riccardo 
Published: January 2023

ABSTRACTMajor challenges in biofabrication revolve around capturing the complex, hierarchical composition of native tissues. However, individual 3D printing techniques have limited capacity to produce composite biomaterials with multi-scale resolution. Volumetric bioprinting recently emerged as a paradigm-shift in biofabrication. This ultra-fast, light-based technique sculpts cell-laden hydrogel bioresins into three-dimensional structures in a layerless fashion, providing unparalleled design freedom over conventional bioprinting. However, it yields prints with low mechanical stability, since soft, cell-friendly hydrogels are used. Herein, for the first time, the possibility to converge volumetric bioprinting with melt electrowriting, which excels at patterning microfibers, is shown for the fabrication of tubular hydrogel-based composites with enhanced mechanical behavior. Despite including non-transparent melt electrowritten scaffolds into the volumetric printing process, high-resolution bioprinted structures were successfully achieved. Tensile, burst and bending mechanical properties of printed tubes were tuned altering the electrowritten mesh design, resulting in complex, multi-material tubular constructs with customizable, anisotropic geometries that better mimic intricate biological tubular structures. As a proof-of-concept, engineered vessel-like structures were obtained by building tri-layered cell-laden vessels, and features (valves, branches, fenestrations) that could be resolved only by synergizing these printing methods. This multi-technology convergence offers a new toolbox for manufacturing hierarchical and mechanically tunable multi-material living structures.
Functional Overlap of Inborn Errors of Immunity and Metabolism Genes Define T Cell Immunometabolic Vulnerabilities
Authors: Patterson Andrew R. , Needle Gabriel A. , Sugiura Ayaka , Chi Channing , Steiner KayLee K. , Fisher Emilie L. , Robertson Gabriella L. , Bodnya Caroline , Markle Janet G. , Gama Vivian , Rathmell Jeffrey C. 
Published: January 2023

SUMMARYInborn Errors of Metabolism (IEM) and Immunity (IEI) are Mendelian diseases in which complex phenotypes and patient rarity can limit clinical annotations. Few genes are assigned to both IEM and IEI, but immunometabolic demands suggest functional overlap is underestimated. We applied CRISPR screens to test IEM genes for immunologic roles and IEI genes for metabolic effects and found considerable crossover. Analysis of IEM showed N-linked glycosylation and thede novohexosamine synthesis enzyme,Gfpt1, are critical for T cell expansion and function. Interestingly,Gfpt1-deficient TH1 cells were more affected than TH17 cells, which had increasedNagkfor salvage UDP-GlcNAc synthesis. Screening IEI genes showed the transcription factorBcl11bpromotes CD4+T cell mitochondrial activity andMcl1expression necessary to prevent metabolic stress. These data illustrate a high degree of functional overlap of IEM and IEI genes and point to potential immunometabolic mechanisms for a previously unappreciated set of these disorders.HIGHLIGHTSInborn errors of immunity and metabolism have greater overlap than previously knownGfpt1deficiency causes an IEM but also selectively regulates T cell subset fateLoss ofBcl11bcauses a T cell deficiency IEI but also harms mitochondrial functionMany IEM may have immune defects and IEI may be driven by metabolic mechanisms
Double-strand breaks induce inverted duplication chromosome rearrangements by a DNA polymerase δ and Rad51-dependent mechanism
Authors: Al-Zain Amr , Nester Mattie R. , Symington Lorraine S. 
Published: January 2023

ABSTRACTInverted duplications, also known as foldback inversions, are commonly observed in cancers and are the major class of chromosome rearrangement recovered from yeast cells lacking Mre11 nuclease. Foldback priming at naturally occurring inverted repeats is one mechanism proposed for the generation of inverted duplications. However, the initiating lesion for these events and the mechanism by which they form has not been fully elucidated. Here, we show that a DNA double-strand break (DSB) induced near natural short, inverted repeats drives high frequency inverted duplication in Sae2 and Mre11-deficient cells. We find that DNA polymerase δ proof-reading activity acts non-redundantly with Rad1 nuclease to remove heterologous tails formed during foldback annealing. Additionally, Pol32 is required for the generation of inverted duplications, suggesting that Pol δ catalyzes fill-in synthesis primed from the foldback to create a hairpin-capped chromosome that is subsequently replicated to form a dicentric isochromosome. Stabilization of the dicentric chromosome after breakage involves telomere capture by non-reciprocal translocation mediated by repeat sequences and requires Rad51.
In vitro and in vivo Antioxidant potential of aqueous and hydroethanolic extracts leaves ofDracaena deistelianaEng. (Dracacenaceae)
Authors: Feudjio Huguette Bocanestine Laure , Chekem Goka Marie Stéphanie , Djeguemtar Josias , Kamsu Gabriel Tchuente , Sokoudjou Jean Baptiste , Famen Louis-Claire Ndel , Kodjio Norbert , Gatsing Donatien 
Published: January 2023

ABSTRACTEnterobacteria such as those of the genusSalmonellaexpress the oxyR gene that codes for several proteins that allow it to resist free radicals. This resistance ofSalmonellais often at the origin of an overproduction of these free radicals that can lead to oxidative stress. To investigate the antioxidant activity in vitro (aqueous and hydroethanolic extracts in vivo (of the 55% hydroethanolic extract) of Dracaena deisteliana leaves in albino rats of Wistar strain previously infected with the Salmonella strain Typhi ATCC 6539. Thein vitroantioxidant activity of these extracts was determined by studying their anti-radical power with DPPH•, then their iron-reducing power and determining their flavonoids and total phenols content.In vivoantioxidant activity was determined in plasma and tissues of albino rats of wistar strain aged between 8 and 10 weeks previously infected withSalmonellatyphi ATCC 6539. These infected rats concurrently received daily doses ofDracaena deistelianaextract (10, 20 and 51.84 mg/kg) or ciprofloxacin (14 mg/kg) as positive control, for 15 days. At the end of the treatment period, the animals were sacrificed and blood, liver, kidney, heart, lung, spleen testis and ovaris were collected for evaluation of antioxidants parameters, which included malondialdehyde, nitric oxide, catalase and peroxidase, as well as biological responses. Regardingin vitroantioxidant tests, the 65% hydroethanolic extract showed an anti-radical activity with DPPH• superior to that of all hydroethanolic extracts at 100 μg/ml. However, the infused showed lower antiradical activity than all extracts at 12.5 and 200 μg/ml concentrations. The 55% hydroethanolic extract had the best IC50of (11.99 μg/ml). The iron reducing power of this extract was higher than the other extracts at 200 μg/ml. The highest levels of flavonoids and total phenols were obtained respectively with the 55% and 95% hydroethanolic extract. The hydroethanol extract ofDracaena deisteliana(10, 20 and 51.84 mg/kg) cured the infected rats between the 9th and 13th day of treatment. The extract also significantly reduced (p < 0.05) blood malondialdehyde and nitric oxide levels, and significantly increased (p >0.05) the activity of catalase and peroxidase in the infected rats. The results suggest that leaves extract ofDracaena deistelianacontains antisalmonella and antioxidant substances, which could be used for the treatment of typhoid fever and another salmonellosis. In addition, 55% hydroethanolic extract of this plant possesses antisalmonella activity and reduces the state of oxidative stress caused by S. typhi during rat’s infection.
Targeting the intestinal circadian clock by meal timing ameliorates gastrointestinal inflammation
Authors: Niu Yunhui , Heddes Marjolein , Altaha Baraa , Birkner Michael , Kleigrewe Karin , Meng Chen , Haller Dirk , Kiessling Silke 
Published: January 2023

AbstractObjectiveImpaired clock genes expression has been observed in biopsy samples from patients with inflammatory bowel disease (IBD). Disruption of circadian rhythms, which occurs in shift workers, has been linked to an increased risk of gastrointestinal diseases, including IBD. The intestinal clock balances gastrointestinal homeostasis by regulating the microbiome. Here we characterize intestinal immune functions in mice lacking the intestinal clock and IBD-relevant mouse model under different feeding conditions to describe the functional impact of the intestinal clock in the development of gastrointestinal inflammation.DesignTissues and fecal samples from intestinal clock-deficient mice (Bmal1IEC-/-) and mouse models for colitis (IL-10-/-,Bmal1IEC-/-xIL-10-/-, dextran sulfate sodium (DSS) administration) under ad libitum and restricted feeding (RF) conditions were used to determine the causal role of the intestinal clock for colitis.ResultsInIL-10-/-mice, inflammation correlated with disrupted colon clock genes expression. Genetic loss of intestinal clock functions promoted DSS and IBD inflammatory phenotypes and dramatically reduces survival, and colonization with disease-associated microbiota in germ- freeBmal1IEC-/-hosts increased their inflammatory responses, demonstrating the causal role of colonic clock disruption and the severity of IBD. RF inIL-10-/-mice restored the colon clock and related immune functions, improved the inflammatory responses and rescued the histopathological phenotype. In contrast, RF failed to improve IBD symptoms inBmal1IEC-/-xIL-10-/-demonstrating the significance of the colonic clock to gate the effect of RF.ConclusionWe provide evidence that inflammation-associated intestinal clock dysfunction triggers host immune imbalance and promotes the development and progression of IBD-like colitis. Enhancing intestinal clock function by RF modulates the pathogenesis of IBD and thus could become a novel strategy to ameliorate the symptoms in IBD patients.
Co-transplantation with mesenchymal stem cells and endothelial cells improvise islet engraftment and survival in STZ treated hyperglycemic mice
Authors: Naqvi Raza Ali , Naqvi Afsar 
Published: January 2023

AbstractThough intra-portal islet transplantation demonstrated as best suited strategy for the reversal of hyperglycemia without the threat of iatrogenic hyperglycemia in type 1 diabetes (T1D) in patients, the inferior quality of post-transplantation (tx) vascularization needs to be addressed for the maximization of post-tx islet survival. Therefore, in this study, we have first generated MSCs and endothelial progenitor cells (EPC) from mice bone marrow by in house optimized protocol and then 3-D co-cultured them with mice islets. Secretion of in the culture supernatant suggested the pro-angiogenic nature of 3D cultured mice islets. After 5 days post-tx of these pro-angiogenic islets in the omental pouch of syngeneic mice led to: 1) restoration of normoglycemia, 2) secretion of mouse C-peptide and 3) induction of angiogenic factors after 3 days of post-tx. The induction of angiogenic factors was done by RT-qPCR of omental biopsies. Importantly, pro-angiogenic islet recipient mice also demonstrated the clearance of glucose within 75 min, reflecting their efficient function and engraftment. Our results highlights needs of 3-D co-culture islets for superior quality post-tx islet vasculature and better engraftment – crux to improvise the challenges associated with post-tx islet vascularization and functions.