bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic plasticity and genetic differentiation drive troglomorphic character development in European cave loach
Authors: Behrmann-Godel Jasminca , Roch Samuel , Böhm Alexander , Jolles Jolle , Brinker Alexander 
Published: February 2023

AbstractUsing a cross-fostering experiment, we provide evidence for the contribution of both genetic differentiation and phenotypic plasticity to troglomorphic character development in the recently discovered cave form ofBarbatula barbatula, an evolutionarily young lineage and first cavefish described in Europe, the northernmost record. We established reproducing populations of cave- and surface-dwelling loaches to produce cave, surface, and hybrid offspring and reared the F1 fish in a common garden setting in total darkness (DD) to simulate cave conditions as well as under the natural photoperiod (DL). We observed significant differences in the occurrence and extent of typical troglomorphic target characters among the offspring groups. Regardless of rearing conditions, cave fish exhibited smaller eyes, lighter body coloration, longer barbels, and larger olfactory epithelium than seen in surface fish. Hybrids in both rearing conditions generally showed an intermediate level of these traits. Surface and hybrid DD fish differed from the DL groups, resembling the cave fish phenotype in several traits, including eye size and body pigmentation. In contrast, cave and hybrid DL fish groups resembled surface fish phenotypes. Results confirmed that troglomorphic traits arise from heritable genetic differentiation of cave from surface forms and that phenotypic plasticity contributes to the process of adaptation to novel light conditions.
Bacillus subtilisengineered for aerospace medicine: a platform for off-planet production of pharmaceutical peptides
Authors: Vallota-Eastman Alec , Bui Cynthia , Williams Philip M. , Valentine David L. , Loftus David , Rothschild Lynn 
Published: February 2023

1.AbstractBiologics, such as pharmaceutical peptides, have notoriously short shelf lives, insufficient for long-duration space flight missions to the Moon or Mars. To enable the sustainable presence of humans on the Moon or Mars, we must develop methods for on-site production of pharmaceutical peptides in space, a concept we callAstropharmacy. Here, we present proof-of-concept for the first step needed: a low-mass system for pharmaceutical production designed to be stable in space. To demonstrate feasibility, we engineered strains of the space-hardy spore-forming bacterium,Bacillus subtilis, to secrete two pharmaceutical peptides important for astronaut health: teriparatide (an anabolic agent for combating osteoporosis) and filgrastim (an effective countermeasure for radiation-induced neutropenia). We found that the secretion peptides from thewalMandyoqHgenes ofB. subtilis168 worked well for secreting teriparatide and filgrastim, respectively. In consideration of the TRISH challenge to produce a dose equivalent in 24 hours, dried spores of our engineered strains were used to produce 1 dose equivalent of teriparatide from a 2 mL culture and 1 dose equivalent of filgrastim from 52 mL of culture in 24 hours. Further optimization of strain growth conditions, expression conditions, and promoter sequences should allow higher production rates to be achieved. These strains provide the template for future optimization efforts and address the first step in theAstropharmacy, capable of on-site production, purification, and processing of biopharmaceutical compounds in platforms amenable for use in space.
Mass Spectrometry Reveals that Oxysterols are Secreted from Non-Alcoholic Fatty Liver Disease Induced Organoids
Authors: Kømurcu Kristina Sæterdal , Wilhelmsen Ingrid , Thorne James L , Karl Krauss Stefan Johannes , Haakon Wilson Steven Ray , Aizenshtadt Aleksandra , Røberg-Larsen Hanne 
Published: February 2023

AbstractOxysterols are potential biomarkers for liver metabolism that are altered under disease conditions such as non-alcoholic fatty liver disease (NAFLD). We here apply sterolomics to organoids used for disease modeling of NAFLD. Using liquid chromatography-mass spectrometry with on-line sample clean-up and enrichment, we establish that liver organoids produce and secrete oxysterols. We find elevated levels of 26-hydroxycholesterol, an LXR agonist and the first oxysterol in the acidic bile acid synthesis, in medium from steatotic liver organoids compared to untreated organoids. Other upregulated sterols in medium from steatotic liver organoids are dihydroxycholesterols, such as 7α,26–dihydroxycholesterol, and 7α,25-dihydroxycholesterol. Through 26-hydroxycholesterol exposure to human stem cell-derived hepatic stellate cells, we observe a trend of expressional downregulation of the pro-inflammatory cytokine CCL2, suggesting a protective role of 26-hydroxycholesterol during early-phased NAFLD disease development. Our findings support the possibility of oxysterols serving as NAFLD indicators, demonstrating the usefulness of combining organoids and mass spectrometry for disease modeling and biomarker studies.Graphical abstract
Real-time monitoring of cell surface protein arrival with split luciferases
Authors: Fischer Alexandra A.M. , Baaske Julia , Römer Winfried , Weber Wilfried , Thuenauer Roland 
Published: February 2023

AbstractEach cell in a multicellular organism permanently adjusts the concentration of its cell surface proteins. In particular, epithelial cells tightly control the number of carriers, transporters and cell adhesion proteins at their plasma membrane. However, the sensitively measuring the cell surface concentration of a particular protein of interest in live cells and in real time represents a considerable challenge.Here, we introduce a novel approach based on split luciferases, which uses one luciferase fragment as tag on the protein of interest and the second fragment as supplement to the extracellular medium. Once the protein of interest arrives at the cell surface, the luciferase fragments complement and generate luminescence. We compared the performance of split Gaussia luciferase and split Nanoluciferase by using a system to synchronize biosynthetic trafficking with conditional aggregation domains. The best results were achieved with split Nanoluciferase, for which luminescence increased more than 6000-fold upon recombination. Furthermore, we showed that our approach can separately detect and quantify the arrival of membrane proteins at the apical and basolateral plasma membrane in single polarized epithelial cells by detecting the luminescence signals with a microscope, thus opening novel avenues for characterizing the variations in trafficking in individual epithelial cells.SynopsisWe present here a novel method to determine the arrival of a membrane protein of interest at the cell surface in real time and with sufficient sensitivity to achieve single-cell resolution. This allows measuring detailed kinetics of plasma membrane trafficking and thus to detect also minor changes in protein sorting and intracellular trafficking. Furthermore, the single-cell sensitivity of the method will enable to systematically characterize variations in trafficking between neighboring cells within a multicellular organism.
Arsenic is a potent co-mutagen of ultraviolet light
Authors: Speer Rachel M. , Nandi Shuvro P. , Cooper Karen L. , Zhou Xixi , Yu Hui , Guo Yan , Hudson Laurie G. , Alexandrov Ludmil B. , Liu Ke Jian 
Published: February 2023

ABSTRACTEnvironmental co-exposures are widespread and are major contributors to carcinogenic mechanisms. Two well-established environmental agents causing skin cancer are ultraviolet radiation (UVR) and arsenic. Arsenic is a known co-carcinogen that enhances UVR’s carcinogenicity. However, the mechanisms of arsenic co-carcinogenesis are not well understood. In this study, we utilized primary human keratinocytes and a hairless mouse model to investigate the carcinogenic and mutagenic properties of co-exposure to arsenic and UVR.In vitroandin vivoexposures revealed that, on its own, arsenic is neither mutagenic nor carcinogenic. However, in combination with UVR, arsenic exposure has a synergistic effect leading to an accelerated mouse skin carcinogenesis as well as to more than 2-fold enrichment of UVR mutational burden. Notably, mutational signature ID13, previously found only in UVR-associated human skin cancers, was observed exclusively in mouse skin tumors and cell lines jointly exposed to arsenic and UVR. This signature was not observed in any model system exposed purely to arsenic or purely to UVR, making ID13 the first co-exposure signature to be reported using controlled experimental conditions. Analysis of existing genomics data from basal cell carcinomas and melanomas revealed that only a subset of human skin cancers harbor ID13 and, consistent with our experimental observations, these cancers exhibited an elevated UVR mutagenesis. Our results provide the first report of a unique mutational signature caused by a co-exposure to two environmental carcinogens and the first comprehensive evidence that arsenic is a potent co-mutagen and co-carcinogen of UVR. Importantly, our findings suggest that a large proportion of human skin cancers are not formed purely due to UVR exposure but rather due to a co-exposure of UVR and other co-mutagens such as arsenic.
The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation
Authors: Long Trevor , Bhattacharyya Tapas , Repele Andrea , Naylor Madison , Nooti Sunil , Krueger Shawn , Manu  
Published: February 2023

AbstractThe upregulation of gene expression by enhancers depends upon the interplay between the binding of sequence-specific transcription factors (TFs) and DNA accessibility. DNA accessibility is thought to limit the ability of TFs to bind to their sites, while TFs can increase accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events underlying the modulation of gene expression during cellular differentiation remain unknown for the vast majority of genes. We investigated the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of an important neutrophil gene,Cebpa, during macrophage-neutrophil differentiation. Reporter genes were integrated in a site-specific manner in PUER cells, which are progenitors that can be differentiated into neutrophils or macrophagesin vitroby activating the pan-leukocyte TF PU.1. Time series data show that two enhancers upregulate reporter expression during the first 48 hours of neutrophil differentiation. Surprisingly, there is little or no increase in the total accessibility, measured by ATAC-Seq, of the enhancers during the same time period. Conversely, total accessibility peaks 96 hrs after PU.1 activation—consistent with its role as a pioneer—but the enhancers do not upregulate gene expression. Combining deeply sequenced ATAC-Seq data with a new bias-correction method allowed the profiling of acces-sibility at single-nucleotide resolution and revealed protected regions in the enhancers that match all previously characterized TF binding sites and ChIP-Seq data. Although the accessibility of most positions does not change during early differentiation, that of positions neighboring TF binding sites, an indicator of TF occupancy, did in-crease significantly. The localized accessibility changes are limited to nucleotides neighboring C/EBP-family TF binding sites, showing that the upregulation of enhancer activity during early differentiation is driven by C/EBP-family TF binding. These results show that increasing the total accessibility of enhancers is not sufficient for upregulating their activity and other events such as TF binding are necessary for upregulation. Also, TF binding can cause upregulation without a perceptible increase in total accessibility. Finally, this study demonstrates the feasibility of comprehensively mapping individual TF binding sites as footprints using high coverage ATAC-Seq and inferring the sequence of events in gene regulation by combining with time-series gene expression data.
Machine learning investigation of gene expression datasets revealsTP53mutant-like AML with wild typeTP53and poor prognosis
Authors: Lee Yoonkyu , Baughn Linda B. , Myers Chad L. , Sachs Zohar 
Published: February 2023

AbstractAcute myeloid leukemia (AML) withTP53mutations (TP53Mut) has poor clinical outcomes with 1-year survival rates of less than 10%. We investigated whether this AML subtype harbors a distinct gene expression profiling (GEP), what this GEP reveals aboutTP53MutAML pathophysiology, and whether this GEP is prognostic inTP53wild type (TP53WT) AML.We applied a supervised machine-learning approach to assess whether a uniqueTP53MutGEP could be detected. Using the BEAT-AML dataset, we randomly divided the samples into training and testing datasets, while the TCGA dataset was reserved as a validation dataset. We trained a ridge regression machine learning model to classifyTP53MutandTP53WTcases. This model was highly accurate in distinguishingTP53MutversusTP53WTcases in both the test and validation data sets. Additionally, we noted a cohort ofTP53WTsamples with high ridge regression scores and poor overall survival, suggesting share clinical and GEP features withTP53MutAML. We defined theseTP53WTsamples asTP53mutant-like (TP53Mut-like) AMLs. We trained a second ridge regression model to specifically detectTP53Mut-like samples in the BEAT AML dataset and found that TCGA data also harborsTP53Mut-like samples. TheTP53Mut-like samples in the TCGA also have a worse OS rate thanTP53WTcases. Using drug sensitivity data from 122 small molecules in the BEAT AML dataset, we foundTP53Mut-like AMLs have distinct drug sensitivity patterns compared toTP53WT. Finally, we identified a 25 gene signature that can identifyTP53Mut-like cases. This signature could be used clinically to identify this novel subset of poor-prognosis AML.
Identifying High Priority Ethical Challenges for Precision Emergency Medicine - A Nominal Group Study
Authors: Rose Christian , Shearer Emily , Woller Isabela , Foster Ashley , Ashenburg Nicholas , Kim Ireh L. , Newberry Jennifer 
Published: February 2023

AbstractOBJECTIVEPrecision medicine is a rapidly progressing avenue to providing the right care to the right patient at the right time and spans all medical fields and specialties. However, given its reliance on computation and timely, accurate information, actualizing precision medicine within the emergency department and its “anyone, anywhere, anytime” approach presents unique challenges which could exacerbate disparities rather than improve care.METHODSWe performed a qualitative, nominal group technique study of emergency physicians with prior knowledge of precision medicine concepts to identify high priority ethical concerns facing the implementation of precision medicine in the emergency department.RESULTSTwelve emergency physicians identified 91 ethical concerns which were organized into a framework with three major themes: values, privacy, and justice. The framework identified the need to address these themes across three time points of the precision medicine process: acquisition of data, actualization in the care setting, and after effects of its use.CONCLUSIONSPrecision medicine may help to improve the quality of care provided in the emergency department, but significant hurdles exist. Our framework helps to identify high-yield ethical concerns that could serve as focus areas for future research and policy in order to guide the effective implementation of precision medicine in the emergency department.
Multilevel determinants of Covid-19 vaccine hesitancy and undervaccination among marginalized populations in the United States: A scoping review
Authors: Newman Peter A. , Nyoni Thabani , Allan Kate , Fantus Sophia , Dinh Duy , Tepjan Suchon , Reid Luke , Guta Adrian 
Published: February 2023

AbstractBackgroundAmid persistent disparities in Covid-19 vaccination, we conducted a scoping review to identify multilevel determinants of Covid-19 vaccine hesitancy (VH) and undervaccination among marginalized populations in the U.S.MethodsWe utilized the scoping review methodology developed by the Joanna Briggs Institute and report all findings according to PRISMA-ScR guidelines. We developed a search string and explored 7 databases to identify peer-reviewed articles published from January 1, 2020–October 31, 2021, the initial period of U.S. Covid-19 vaccine avails.comability. We combine frequency analysis and narrative synthesis to describe factors influencing Covid-19 vaccination among marginalized populations.ResultsThe search captured 2,496 non-duplicated records, which were scoped to 50 peer-reviewed articles: 11 (22%) focused on African American/Black people, 9 (18%) people with disabilities, 4 (8%) justice-involved people, and 2 (4%) each on Latinx, people living with HIV/AIDS, people who use drugs, and LGBTQ+ people. Forty-four articles identified structural factors, 36 social/community, 27 individual, and 40 vaccine-specific factors. Structural factors comprised medical mistrust (of healthcare systems, government public health) and access barriers due to unemployment, unstable housing, lack of transportation, no/low paid sick days, low internet/digital technology access, and lack of culturally and linguistically appropriate information. Social/community factors including trust in a personal healthcare provider (HCP), altruism, family influence, and social proofing mitigated VH. At the individual level, low perceived Covid-19 threat and negative vaccine attitudes were associated with VH.DiscussionThis review indicates the importance of identifying and disaggregating structural factors underlying Covid-19 undervaccination among marginalized populations, both cross-cutting and population-specific—including multiple logistical and economic barriers in access, and systemic mistrust of healthcare systems and government public health—from individual and social/community factors, including trust in personal HCPs/clinics as reliable sources of vaccine information, altruistic motivations, and family influence, to effectively address individual decisional conflict underlying VH as well as broader determinants of undervaccination.
Design of logistics Indicators for Monitoring the Covid-19 Vaccination Process in Colombia
Authors: Velasco Nubia , Herrera Andrea , Trujillo-Diaz Johanna , Amaya Ciro-Alberto , González-Uribe Catalina , Hernandez Estefania 
Published: February 2023

AbstractThe vaccine supply chain (VSC) integrates all the activities from production to dispensing. It is characterized by its complexity and low responsiveness, highlighting the importance of defining key performance indicators (KPIs). The design science research methodology was used to develop 38 KPIs, which were grouped into humanitarian and technological dimensions. The former includes demographic, epidemiological, and vaccination indicators, while the latter is classified into five groups according to the echelons of the supply chain. Public and private health organizations and research groups validated the indicators. They were calculated and recorded daily to monitor the logistics progress of the National Vaccination Plan against covid-19 in Colombia. These tailored KPIs, made it possible to evaluate and compare the results of the execution and effectiveness of public policies, and to redefine the strategies, showing that the logistics point of view helps identify the impact of good practices and transfer them promptly.
Influence of HIV-1 genomic RNA on the formation of Gag biomolecular condensates
Authors: Monette Anne , Niu Meijuan , Maldonado Rebecca Kaddis , Chang Jordan , Lambert Gregory S. , Flanagan John M. , Cochrane Alan , Parent Leslie J. , Mouland Andrew J. 
Published: February 2023

SummaryBiomolecular condensates (BMCs) play an important role in the replication of a growing number of viruses, but many important mechanistic details remain to be elucidated. Previously, we demonstrated that pan-retroviral nucleocapsid (NC) and the HIV-1 pr55Gag(Gag) proteins phase separate into condensates, and that HIV-1 protease (PR)-mediated maturation of Gag and Gag-Pol precursor proteins yield self-assembling BMCs having HIV-1 core architecture. Using biochemical and imaging techniques, we aimed to further characterize the phase separation of HIV-1 Gag by determining which of its intrinsically disordered regions (IDRs) influence the formation of BMCs and how the HIV-1 viral genomic RNA (gRNA) could influence BMC abundance and size. We found that mutations in the Gag matrix (MA) domain or the NC zinc finger motifs altered condensate number and size in a salt-dependent manner. Gag BMCs were also bimodally influenced by the gRNA, with a condensate-promoting regime at lower protein concentrations and a gel dissolution at higher protein concentrations. Interestingly, incubation of Gag with CD4+T cell nuclear lysates led to the formation of larger BMCs as compared to much smaller ones observed in the presence of cytoplasmic lysates. These findings suggests that the composition and properties of Gag-containing BMCs may be altered by differential association of host factors in nuclear and cytosolic compartments during virus assembly. This study significantly advances our understanding of HIV-1 Gag BMC formation and provides a foundation for future therapeutic targeting of virion assembly.
Energy Coupling and Stoichiometry of Zn2+/H+Antiport by the Cation Diffusion Facilitator YiiP
Authors: Hussein Adel , Fan Shujie , Lopez-Redondo Maria , Kenney Ian , Zhang Xihui , Beckstein Oliver , Stokes David L. 
Published: February 2023

ABSTRACTYiiP is a prokaryotic Zn2+/H+antiporter that serves as a model for the Cation Diffusion Facilitator (CDF) superfamily, members of which are generally responsible for homeostasis of transition metal ions. Previous studies of YiiP as well as related CDF transporters have established a homodimeric architecture and the presence of three distinct Zn2+binding sites named A, B, and C. In this study, we use cryo-EM, microscale thermophoresis and molecular dynamics simulations to address the structural and functional roles of individual sites as well as the interplay between Zn2+binding and protonation. Structural studies indicate that site C in the cytoplasmic domain is primarily responsible for stabilizing the dimer and that site B at the cytoplasmic membrane surface controls the structural transition from an inward facing conformation to an occluded conformation. Binding data show that intramembrane site A, which is directly responsible for transport, has a dramatic pH dependence consistent with coupling to the proton motive force. A comprehensive thermodynamic model encompassing Zn2+binding and protonation states of individual residues indicates a transport stoichiometry of 1 Zn2+to 2-3 H+depending on the external pH. This stoichiometry would be favorable in a physiological context, allowing the cell to use the proton gradient as well as the membrane potential to drive the export of Zn2+.