bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tissue-Specific and Interorgan Metabolic Reprogramming Maintains Tolerance to Sepsis
Authors: Leitner Brooks P. , Lee Won D. , Zhu Wanling , Zhang Xinyi , Gaspar Rafael C. , Li Zongyu , Rabinowitz Joshua D. , Perry Rachel J. 
Published: October 2022

SummaryReprogramming metabolism is of great therapeutic interest for reducing morbidity and mortality during sepsis-induced critical illness1. Disappointing results from randomized controlled trials targeting glutamine and antioxidant metabolism in patients with sepsis have begged for both identification of new metabolic targets, and a deeper understanding of the metabolic fate of glutamine at the systemic and tissue-specific manner2–4. In critically ill patients versus elective surgical controls, skeletal muscle transcriptional metabolic reprogramming is comprised of reduced expression of genes involved in mitochondrial metabolism, electron transport, and glutamate transport, with concomitant increases in glutathione cycling, glutamine, branched chain, and aromatic amino acid transport. To analyze putative interorgan communications during sepsis, we performed systemic and tissue specific metabolic phenotyping in a murine polymicrobial sepsis model, cecal ligation and puncture. In the setting of drastically elevated inflammatory cytokines, we observed >10% body weight loss, >50% reductions in oxygen consumption and carbon dioxide production, and near full suppression of voluntary activity for the 48 hours following sepsis as compared to sham-operated controls. We found increased correlations in the metabolome between liver, kidney, and spleen, with drastic loss of correlations between the heart and quadriceps metabolome and all other organs, pointing to a shared metabolic signature within vital abdominal organs, and unique metabolic signatures for skeletal and cardiac muscle during sepsis. A lowered GSH:GSSG and elevated AMP:ATP ratio in the liver underlie the significant upregulation of isotopically labeled glutamine’s contribution to TCA anaplerosis and glutamine-derived glutathione biosynthesis; meanwhile, the skeletal muscle and spleen were the only organs where glutamine’s contribution to the TCA cycle was significantly suppressed. These results highlight tissue-specific mitochondrial reprogramming, rather than global mitochondrial dysfunction, as a mechanistic consequence of sepsis. Using a multi-omic approach, we demonstrate a model by which sepsis-induced proteolysis fuels the liver’s production of anaplerotic substrates and the antioxidant glutathione to sustain tolerance to sepsis.
Chemical potential measurements constrain models of cholesterol-phosphatidylcholine interactions
Authors: Shaw Thomas R. , Wisser Kathleen , Shaffner Taylor A. , Gaffney Anna D. , Machta Benjamin B. , Veatch Sarah L. 
Published: October 2022

ABSTRACTBilayer membranes composed of cholesterol and phospholipids exhibit diverse forms of non-ideal mixing. In particular, many previous studies document macroscopic liquid-liquid phase separation as well as nanometer-scale heterogeneity in membranes of phosphatidylcholine (PC) lipids and cholesterol. Here, we present experimental measurements of cholesterol chemical potential (μc) in binary membranes containing dioleoyl PC (DOPC), 1-palmitoyl-2-oleoyl PC (POPC), or dipalmitoyl PC (DPPC), and in ternary membranes of DOPC and DPPC, adapting a calibrated experimental protocol developed to measure μc in cells (Ayuyan and Cohen, Biophys. J. 114:904-918). μc is the thermodynamic quantity that dictates the availability of cholesterol to bind other factors, and notably must be equal between coexisting phases of a phase-separated mixture. It is simply related to concentration under conditions of ideal mixing but is found to be far from ideal for the majority of lipid mixtures investigated. Here we perform experimental measurements of μc, constraining thermodynamic models of membrane interactions. Our measurements are consistent with models involving cholesterol-phospholipid complexes, but only if complexes are more weakly bound than has been assumed in previous reports. Experimental measurements are also well described by regular solution theory and lattice models with pairwise interactions between components. We find that μc can vary by ~1.5 kBT at constant cholesterol mole-fraction implying a more than five-fold change in its availability for binding receptors and other reactions. These findings reinforce that μc depends on membrane composition overall, suggesting avenues for cells to alter the availability of cholesterol without varying cholesterol concentration.SIGNIFICANCEThe chemical potential of cholesterol (μc) reflects its availability to interact with other molecules. In a complex mixtures this chemical potential can vary dramatically even at fixed cholesterol concentration. In this report, we present measurements of μc in bilayer membranes composed of mixtures of cholesterol with one or two phospholipids. We find that μc in these mixtures depends strongly on the phospholipids that are present, with activity varying by a factor of more than five at fixed cholesterol concentration. This suggests that the availability of cholesterol in biological membranes could be tuned without altering cholesterol concentration directly, by adjusting the concentration of other lipid or protein components.
Osmotic pressure enables high yield assembly of giant vesicles in solutions of physiological ionic strengths
Authors: Cooper Alexis , Girish Vaishnavi , Subramaniam Anand Bala 
Published: October 2022

AbstractGiant unilamellar vesicles (GUVs) are micrometer scale minimal cellular mimics that are useful for synthetic biology and drug delivery. Unlike assembly in low-salt solutions, assembly of GUVs in solutions with ionic concentrations of 100-150 mM Na/KCl (salty solutions) is challenging. Chemical compounds deposited on the substrate or in the lipid mixture could assist in the assembly of GUVs. Here, we investigate quantitatively the effects of temperature and chemical identity of six assisting polymeric and small molecule compounds on the molar yields of GUVs composed of three different lipid mixtures using high resolution confocal microscopy and large dataset image analysis. All the polymers moderately increased the yields of GUVs either at 22 or 37 degrees Celsius, whereas the small molecule compound was ineffective. Low gelling temperature agarose is the singular compound that consistently produces yields of GUVs of greater than 10 %. We propose a free energy model of budding to explain the effects of polymers in assisting the assembly of GUVs. The osmotic pressure exerted on the membranes by the dissolved polymer balances the increased adhesion between the membranes, thus reducing the free energy for bud formation. Data obtained by modulating the ionic strength and ion valency of the solution shows that the evolution of the yield of GUVs support our model’s prediction. In addition, polymer specific interactions with the substrate and the lipid mixture effects yields. The uncovered mechanistic insight provides a quantitative experimental and theoretical framework to guide future studies. Additionally, this work shows a facile means for obtaining GUVs in solutions of physiological ionic strengths.
Multigenic resistance toXylella fastidiosain wild grapes (Vitissps.) and its implications within a changing climate
Authors: Morales-Cruz Abraham , Aguirre-Liguori Jonas , Massonnet Mélanie , Minio Andrea , Zaccheo Mirella , Cochetel Noe , Walker Andrew , Riaz Summaira , Zhou Yongfeng , Cantu Dario , Gaut Brandon S. 
Published: October 2022

AbstractXylella fastidiosais a bacterium that infects crops like grapevines, coffee, almonds, citrus and olives, causing economically devastating damage. There is, however, little understanding of the genes that contribute to resistance, the genomic architecture of resistance, and the potential role of climate in shaping resistance, in part because major crops like grapevines (V. vinifera) are not resistant to the bacterium. Here we studied a wild grapevine species,Vitis arizonica, that segregates for resistance toX. fastidiosa. Using genome-wide association, we identified candidate genes that mediate the host response toX. fastidiosainfection. We uncovered evidence that resistance requires genes from multiple genomic regions, based on data from breeding populations and from additionalVitisspecies. We also inferred that resistance evolved more than once in the wild, suggesting that wildVitisspecies may be a rich source for resistance alleles and mechanisms. Finally, resistance inV. arizonicawas climate dependent, because individuals from low (< 10°C) temperature locations in the wettest quarter were typically susceptible to infection, likely reflecting a lack of pathogen pressure in these climates. Surprisingly, climate was nearly as effective a predictor of resistance phenotypes as some genetic markers. This work underscores that pathogen pressure is likely to increase with climate, but it also provides genetic insight and tools for breeding and transforming resistant crops.
Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations
Authors: Thomasen F. Emil , Cuneo Matthew J. , Mittag Tanja , Lindorff-Larsen Kresten 
Published: October 2022

AbstractSpeckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.
High-throughput microgel biofabrication via air-assisted co-axial jetting for cell encapsulation, 3D bioprinting, and scaffolding applications
Authors: Pal Vaibhav , Singh Yogendra Pratap , Gupta Deepak , Alioglu Mecit Altan , Nagamine Momoka , Kim Myoung Hwan , Ozbolat Ibrahim T. 
Published: October 2022

AbstractMicrogels have recently received widespread attention for their applications in a wide array of domains such as tissue engineering, regenerative medicine, and cell and tissue transplantation because of their properties like injectability, modularity, porosity, and the ability to be customized in terms of size, form, and mechanical properties. However, it is still challenging to mass produce microgels with diverse sizes and tunable properties. Herein, we developed an air-assisted co-axial device (ACAD) for continuous production of microgels in a high-throughput manner. To test its robustness, microgels of multiple hydrogels and their combination, including alginate (Alg), gelatin methacrylate (GelMA) and Alg-GelMA, were formed at a maximum production rate of 65,000 microgels per sec while retaining circularity and a size range of 50-500 μm based on varying air pressure levels. The ACAD platform allowed single and multiple cell encapsulation with around 75% efficiency. These microgels illustrated appealing rheological properties such as yield stress, viscosity, and shear modulus for bioprinting applications. Specifically, Alg microgels have the potential to be used as a sacrificial support bath while GelMA microgels have potential for direct extrusion both on their own or when loaded in a bulk GelMA hydrogel. Generated microgels showed high cell viability (>90%) and proliferation over 7 days with their increased interactions with cells, particularly for GelMA microgels. The developed strategy provides a facile and rapid approach without any complex or expensive consumables and accessories for scalable high-throughput microgel production for cell therapy, tissue regeneration and 3D bioprinting applications.
N-terminal Domain Influences Steroid Activation of the Atlantic Sea Lamprey Corticoid Receptor
Authors: Katsu Yoshinao , Lin Xiaozhi , Ji Ruigeng , Chen Ze , Kamisaka Yui , Bamba Koto , Baker Michael E. 
Published: October 2022

AbstractLampreys are jawless fish that evolved about 550 million years ago at the base of the vertebrate line. Modern lampreys contain a corticoid receptor (CR), the common ancestor of the glucocorticoid receptor (GR) and mineralocorticoid receptor (MR), which first appear in cartilaginous fish, such as sharks. Until recently, 344 amino acids at the amino terminus of adult lamprey CR were not present in the lamprey CR sequence in GenBank. A search of the recently sequenced lamprey germline genome identified two CR sequences, CR1 and CR2, containing the 344 previously un-identified amino acids. CR1 also contains a novel four amino acid insertion in the DNA-binding domain (DBD). We studied corticosteroid and progesterone activation of CR1 and CR2 and found their strongest response was to 11-deoxycorticosterone and 11-deoxycortisol, the two circulating corticosteroids in lamprey. Based on steroid specificity, both CRs are close to elephant shark MR and distant from elephant shark GR. HEK293 cells that were transfected with full-length CR1 or CR2 and the MMTV promoter have about 3-fold higher steroid-mediated activation compared to HEK293 cells transfected with these CRs and the TAT3 promoter. Deletion of the amino-terminal domain (NTD) of lamprey CR1 and CR2 to form truncated CRs decreased transcriptional activation by about 70% in HEK293 cells that were transfected with MMTV, but increased transcription by about 6-fold in cells transfected with TAT3. This indicated that the promoter has an important effect on NTD regulation of transcriptional activation of the CR by steroids. Our results also indicate that the entire lamprey CR sequence is needed for an accurate determination of steroid-mediated transcription.
The protozoan commensal Tritrichomonas musculis is a natural adjuvant for mucosal IgA
Authors: Cao Eric Yixiao , Burrows Kyle , Chiaranunt Pailin , Popovic Ana , Zhou Xueyang , Xie Cong , Thakur Ayushi , Britton Graham , Spindler Matthew , Ngai Louis , Tai Siu Ling , Dasoveanu Dragos Cristian , Nguyen Albert , Faith Jeremiah J. , Parkinson John , Gommerman Jennifer L. , Mortha Arthur 
Published: October 2022

ABSTRACTImmunoglobulin(Ig) A antibodies are the most abundant antibodies supporting mucosal immune homeostasis and host-microbiota interactions. Driven by gut commensal microbes, IgA-secreting plasma cells (PC) differentiate through T cell-dependent (Td) or T cell independent (Ti) mechanisms. While commensal bacteria within the microbiota are known for their ability to promote IgA, the role of non-bacterial commensal microbes on the induction of IgA remains elusive. Here, we demonstrate that permanent colonization with the protozoan commensal Tritrichomonas musculis (T.mu) promotes T-cell dependent, IgA class-switch recombination and intestinal accumulation of IgA-secreting PC. T.mu colonization specifically drives the expansion of T follicular helper cells and a unique ICOS+ non-Tfh cell population, accompanied by an increase in germinal center B cells. Blockade of ICOS:ICOSL co-stimulation or MHCII-expression on B cells are central for the induction of IgA following colonization by T.mu, implicating a previously underappreciated mode of IgA induction following protozoan commensal colonization. Finally, the commensal T.mu further improves the induction of IgA-secreting plasma cells and their peripheral dissemination, even against non-protozoan, orally ingested antigens, identifying T.mu as natural adjuvant for IgA. Collectively, these findings propose a previously unknown, protozoa-driven mode of IgA induction that supports intestinal immune homeostasis even against non-microbial antigens.
Tumor Spheroids Layered in an Imageable Cancer Environment (T-SLICE): a novelin vitroplatform to study tumor biology
Authors: Pugh-Toole Morgan , Dawe Nicholas , Smith Andrew , Boudreau Jeanette E. , Leung Brendan M. 
Published: October 2022

AbstractCancer treatment is shifting towards precise medicine informed by tumor genetics and structural features. In recent years, it has become increasingly recognized that patient tumors—even those of the same tissue origin—can differ substantially between patients and respond differently to treatment. Given this, it is necessary to design therapies that target the heterogeneity of tumors. When investigating novel therapeutics in the laboratory, conventional cell culture models do not adequately recapitulate this heterogeneity and therefore may not accurately represent drug responses. Recent advances in miniaturized organ-on-a-chip models have been able to generate more complex microenvironments forin vitrostudies. However, many of these models do not resemble the scale of clinically relevant tumors and pose a high barrier to use because they are technically complex. To facilitate mechanistic studies of the tumor microenvironment (TME), we designed T-SLICE, a chip made using commercially available elastomers and designed to fit in a standard 6-well plate. This simple 3-D tumor model incorporates microfluidic principles into a fully customizable TME, wherein cells drive the formation of biochemical gradients akin to those observed within a real tumor. In T-SLICE, spheroids are seeded atop a monolayer of fibroblasts situated between two closely spaced coverslips (300-700 µm). The restrictive gap height limits the permeation of oxygen (O2) and hinders the removal of carbon dioxide (CO2) and metabolic waste, which leads to the generation of tumor-like hypoxic gradients. We demonstrate that T-SLICE establishes cell-driven oxygen gradients leading to the formation of a hypoxic core, with further impacts on cellular viability, mitochondrial membrane potential (MMP), and proliferation. T-SLICE cultures can be imaged live or fixed and stained for immunohistochemistry (IHC). These features of T-SLICE make it an accessible and faithful model of a tumor’s heterogeneity and open the possibility for more faithful testing of novel therapeutics in the context of a realistic TME.
An unbiased screen identified the Hsp70-BAG3 complex as a regulator of myosin binding protein C3
Authors: Thompson Andrea D. , Wagner Marcus J. , Rodriguez Juliani , Malhotra Alok , Roest Steve Vander , Lilienthal Ulla , Shao Hao , Yob Jaime M. , Prosser Benjamin L. , Helms Adam S. , Gestwicki Jason E. , Ginsburg David , Day Sharlene M. 
Published: October 2022

Structured AbstractObjectiveWe aim to identify regulators of myosin binding protein C3 (MyBP-C) protein homeostasis.BackgroundVariants in myosin binding protein C3 (MYBPC3) account for approximately 50% of familial hypertrophic cardiomyopathy (HCM). Most pathogenic variants in MYBPC3 are truncating variants that lead to reduced total levels of MyBP-C protein. Elucidation of the pathways that regulate MyBP-C protein homeostasis could uncover new therapeutic strategies that restore normal protein levels.MethodWe developed a high-throughput screen to identify compounds that can increase or decrease steady-state levels of MyBP-C in an induced pluripotent stem cell cardiomyocyte (iPSC-CM) model derived from a patient with HCM. To normalize results, we also monitored effects on myosin heavy chain (MYH) and focused on those molecules that selectively modulated MyBP-C levels.ResultsScreening a library of 2,426 known biologically active compounds, we identified compounds which either decreased (241/2426, 9.9%) or increased (29/2426, 1.2%) MyBP-C/MYH levels. After a rigorous validation process, including a counter screen for cellular toxicity, two compounds (JG98 and parthenolide) were confirmed as decreasing MyBP-C levels and no compounds were confirmed to increase MyBP-C levels. For further studies, we focused on JG98, which is an allosteric modulator of heat shock protein 70 (Hsp70), inhibiting its interaction with BAG domain co-chaperones. We found that genetic reduction of BAG3 phenocopies treatment with JG98 by reducing MyBP-C protein levels.ConclusionAn unbiased compound screen identified the Hsp70-BAG3 complex as a regulator of MyBP-C stability. Thus, approaches that stimulate this complex’s function may be beneficial in the treatment of HCM.Highlights-Hypertrophic cardiomyopathy (HCM) is commonly caused by pathogenic MYBPC3 variants that reduce total wild-type MyBP-C (the protein encoded by MYBPC3).-It is critical to understand the regulators of MyBP-C protein homeostasis to uncover novel therapeutic strategies.-We developed and executed a high-throughput chemical screen in iPSC-CMs to identify compounds which alter steady-state levels of MyBP-C protein, revealing two compounds, JG98 and parthenolide, that significantly reduced MyBP-C levels.-Validation studies suggest that the complex between heat shock protein 70 (Hsp70) and its co-chaperone BAG3 is a dynamic regulator of MyBP-C stability, suggesting that this axis could be a new therapeutic target for HCM.
Complex hybridization between deeply diverged fish species in a disturbed ecosystem
Authors: Banerjee Shreya M. , Powell Daniel L. , Moran Benjamin M. , Ramírez-Duarte Wilson F. , Langdon Quinn K. , Gunn Theresa R. , Vazquez Gaby , Rochman Chelsea , Schumer Molly 
Published: October 2022

AbstractOver the past two decades researchers have documented the extent of natural hybridization between closely related species using genomic tools. Many species across the tree of life show evidence of past hybridization with their evolutionary relatives. In some cases, this hybridization is complex – involving gene flow between more than two species. While hybridization is common over evolutionary timescales, some researchers have proposed that it may be even more common in contemporary populations where anthropogenic disturbance has modified myriad aspects of the environments in which organisms live and reproduce. Here, we develop a flexible tool for local ancestry inference in hybrids derived from three source populations and describe a complex, recent hybridization event between distantly related swordtail fish lineages (Xiphophorus) and its potential links to anthropogenic disturbance.Impact SummaryAs sequencing tools have advanced, we have found that barriers between animal species are more porous than once thought. Researchers have found evidence for hybridization between species throughout many branches of the tree of life. In some cases, these hybridization events can involve more than two species. Here, we develop a flexible and user-friendly tool that can be used to identify three-way hybrids and report the discovery of hybrids with ancestry from three swordtail (Xiphophorus) species from an anthropogenically impacted site on the Río Calnali in Hidalgo, Mexico. Researchers have studied hybrids between twoXiphophorusspecies along this river for decades, but this is the first documented case of hybridization involving three species. We explore hypotheses for what drove this hybridization event, including anthropogenic pollutants and reduced water quality.