bluuebunny/crossref_metadata_2025_split huggingface dataset:
Base Editor Scanning Reveals Activating Mutations of DNMT3A
Authors: Garcia Emma M. , Lue Nicholas Z. , Liang Jessica K. , Lieberman Whitney K. , Hwang Derek D. , Woods James , Liau Brian B. 
Published: April 2023

AbstractDNA methyltransferase 3A (DNMT3A) is ade novocytosine methyltransferase responsible for establishing proper DNA methylation during mammalian development. Loss-of-function (LOF) mutations to DNMT3A, including the hotspot mutation R882H, frequently occur in developmental growth disorders and hematological diseases, including clonal hematopoiesis (CH) and acute myeloid leukemia (AML). Accordingly, identifying mechanisms that activate DNMT3A is of both fundamental and therapeutic interest. Here, we applied a base editor mutational scanning strategy with an improved DNA methylation reporter to systematically identify DNMT3A activating mutations in cells. By integrating an optimized cellular recruitment strategy with paired isogenic cell lines with or without the LOF hotspot R882H mutation, we identify and validate three distinct hyperactivating mutations within or interacting with the regulatory ADD domain of DNMT3A, nominating these regions as potential functional target sites for pharmacological intervention. Notably, these mutations are still activating in the context of a heterozygous R882H mutation. Altogether, we showcase the utility of base editor scanning for discovering functional regions of target proteins.SynopsisUsing base editor mutagenesis and a DNA methylation reporter optimized to find activating mutations, we identify novel hyperactivating mutations in DNMT3A that suggest new mechanisms of allosteric control.
Novel lytic and lysogenic cyanophages predicted to infectMicrocoleusassociated with anatoxin-producing benthic mats
Authors: Valadez-Cano Cecilio , Reyes-Prieto Adrian , Lawrence Janice 
Published: April 2023

AbstractProliferations of toxic benthic cyanobacteria are increasingly being reported around the world. Of particular concern areMicrocoleus-dominated mats associated with anatoxin production that have resulted in dog fatalities. Although the impact of cyanophages has been demonstrated in planktonic systems, their role in the population dynamics of benthic cyanobacteria has received little attention. Here we use metagenomics to explore phage presence in benthic mats from the Wolastoq|Saint John River (WR; New Brunswick, Canada) and Eel River (ER; California, US). Our survey recovered multiple viral-like sequences associated with different putative bacterial hosts, including two cyanophage genomes with apparently different replication strategies. A lysogenic cyanophage (predicted as a prophage) was found integrated in the genomes ofMicrocoleussp. 3 recovered from five ER mat samples. This Microcoleus phage is related to previously described Phormidium phage counterparts. Also, we recovered lytic cyanophages from WR and ER mats dominated by anatoxin-producingMicrocoleus, which was predicted as the putative host. Despite the geographical distance between WR and ER, the lytic Microcoleus phage genomes recovered from each river have similar sizes (circa 239 Kbp) and share similar gene content with high sequence identity. Phylogenetic analysis suggests that these lytic Microcoleus phages are distant from any other cyanophage previously described. Our results constitute the first report of cyanophages predicted to infect and therefore influence the population dynamics of mat-formingMicrocoleusspp. associated with anatoxin production.
Effect of Intermittent Pneumatic Compression on Preventing Deep Vein Thrombosis Using Microfluidic Vein Chip
Authors: Dai Hongtao , Chai Senlin , Xu Wei , Yao Yao , Tang Wenlai , Shi Jianping , Yang Ji quan , Jiang Qing , Zhu Liya 
Published: April 2023

AbstractDeep vein thrombosis (DVT) is a common disease often occurring in the lower limb veins of bedridden patients. Intermittent pneumatic compression (IPC) has been considered an effective approach to solve this problem. In our previous research, 264 patients were randomly treated either with IPC for one or eight hours per day. The incidence of severe venous thrombosis was significantly lowered in the IPC group than in the control group. However, it is still a chanllenge to real-time monitoring the blood flow and thrombus formation process during IPC operation periods. Here we made a microfluidic vein chip with valves embedded in a flexible channel that can mimic the compression of vessels by IPC contractrion. Driven by inlet blood velocity obtained clinally, numerical simulation were conducted to identify the shear stress and laminar pressure distribution in the vein. The obtained results showed that the thrombus formation can be reduced with Higher compressive pressure and smaller time interval. 24s interval time and 40mmHg maximum contractive pressure was considered to be the most appropriate parameters for DVT prevention. This vein chip offers a new approachin vitroto observe the working mechanism of IPC device, offering important data for its further clinical standard regulation.
Risk of new-onset Long Covid following reinfection with SARS-CoV-2: community-based cohort study
Authors: Bosworth Matthew L. , Shenhuy Boran , Walker A. Sarah , Nafilyan Vahé , Alwan Nisreen A. , O’Hara Margaret E. , Ayoubkhani Daniel 
Published: April 2023

AbstractBackgroundLittle is known about the risk of Long Covid following reinfection with SARS-CoV-2. We estimated the likelihood of new-onset, self-reported Long Covid after a second SARS-CoV-2 infection, and compared to a first infection.MethodsWe included UK COVID-19 Infection Survey participants who tested positive for SARS-CoV-2 between 1 November 2021 and 8 October 2022. The primary outcome was self-reported Long Covid 12 to 20 weeks after each infection. Separate analyses were performed for those <16 years and ≥16 years. We estimated adjusted odds ratios (aORs) for new-onset Long Covid using logistic regression, comparing second to first infections, controlling for socio-demographic characteristics and calendar date of infection, plus vaccination status in those ≥16 years.ResultsOverall, Long Covid was reported by those ≥16 years after 4.0% and 2.4% of first and second infections, respectively; the corresponding estimates among those <16 years were 1.0% and 0.6%. The aOR for Long Covid after second compared to first infections was 0.72 (95% confidence interval: 0.63–0.81) for those ≥16 years and 0.93 (0.57–1.53) for those <16 years.ConclusionsThe risk of new-onset Long Covid after a second SARS-CoV-2 infection is lower than that after a first infection for those ≥16 years, though there is no evidence of a difference in risk for those <16 years. However, there remains some risk of new-onset Long Covid after a second infection, with around 1 in 40 of those ≥16 years and 1 in 165 of those <16 years reporting Long Covid after a second infection.
Selenium reduction of ubiquinone via SQOR suppresses ferroptosis
Authors: Lee Namgyu , Park Sung Jin , Lange Mike , Tseyang Tenzin , Doshi Mihir B. , Kim Tae Yong , Song Yoseb , Kim Dong In , Greer Paul L. , Olzmann James A. , Spinelli Jessica B. , Kim Dohoon 
Published: April 2023

AbstractThe canonical biological function of selenium is in the production of selenocysteine residues of selenoproteins, and this forms the basis for its role as an essential antioxidant and cytoprotective micronutrient. Here, we demonstrate that selenium, via its metabolic intermediate hydrogen selenide, efficiently donates its electrons to ubiquinone to form ubiquinol in the mitochondria through catalysis by sulfide quinone oxidoreductase (SQOR). Hydrogen selenide is superior to hydrogen sulfide as an electron donor owing to its larger valence shell. We show that this mechanism, independently of selenoprotein production, protects against ferroptosis via ubiquinol production in a manner that depends on xCT mediated selenide formation and SQOR activity. Our findings identify a regulatory mechanism against ferroptosis that implicates SQOR and expands our understanding of selenium in biology.
Efficient Fisher Information Computation and Policy Search in Sampled Stochastic Chemical Reaction Networks through Deep Learning
Authors: Badolle Quentin , Berrada Gabrielle , Khammash Mustafa 
Published: April 2023

AbstractMarkov jump processes constitute the central class of Chemical Reaction Network models used to account for the intrinsic stochasticity observed in the dynamics of molecular species abundance throughout Molecular Biology. These models are specified in a parametric form, and their identification requires the use of inference procedures, and in particular the estimation of the Fisher Information. Here, a fast and accurate computation method is introduced in the case of partial observations at discrete time points, based on the use of a Mixture Density Network. We also demonstrate how this Neural Network can be used to perform fast policy search. The efficiency of these approaches is illustrated on a set of examples, and is compared to that of the current state-of-the-art.
Extracellular thiamine concentration influences thermogenic competency of differentiating neck area-derived human adipocytes
Authors: Vinnai Boglárka Ágnes , Arianti Rini , Győry Ferenc , Fésüs László , Kristóf Endre 
Published: April 2023

AbstractBrown adipose tissue (BAT) dissipates energy in the form of heat majorly via the mitochondrial uncoupling protein 1 (UCP1). The activation of BAT, which is enriched in the neck area and contains brown and beige adipocytes in humans, was considered as a potential therapeutic target to treat obesity. Therefore, finding novel agents that can stimulate the differentiation and recruitment of brown or beige thermogenic adipocytes are important subjects for investigation. The current study investigated how the availability of extracellular thiamine (vitamin B1), an essential cofactor of mitochondrial enzyme complexes that catalyze key steps in the catabolism of nutrients, affects the expression of thermogenic marker genes and proteins and subsequent functional parameters duringex vivoadipocyte differentiation. Therefore, we differentiated primary human adipogenic progenitors that were cultivated from subcutaneous (SC) or deep neck (DN) adipose tissues in the presence of gradually increasing thiamine concentrations during their 14 day long differentiation program. Higher thiamine levels resulted in increased expression of thiamine transporter 1 and 2 both at mRNA and protein levels in human neck area-derived adipocytes. Gradually increasing concentrations of thiamine led to increased basal, cAMP-stimulated, and proton-leak respiration along with elevated mitochondrial biogenesis of the differentiated adipocytes. The extracellular thiamine availability during adipogenesis determined the expression levels of UCP1, PGC1a, CKMT2, and other browning-related genes and proteins in primary SC and DN-derived adipocytes in a concentration-dependent manner. Providing abundant amounts of thiamine further increased the thermogenic competency of the adipocytes. Our study raises the possibility of a novel strategy with long-term thiamine supplementation, which can enhance the thermogenic competency of differentiating neck area-derived adipocytes for preventing or combating obesity.
Cell specificity of adeno-associated virus (AAV) serotypes in human cortical organoids
Authors: Stanton Morgan M. , Hariani Harsh N. , Sorokin Jordan , Taylor Patrick M. , Modan Sara , Rash Brian G. , Rao Sneha B. , Enriquez Luigi , Quang Daphne , Hsu Pei-Ken , Paek Justin , Owango Dorah , Castrillo Carlos , Nicola Justin , Ramkumar Pavan , Lash Andy , Flanzer Douglas , Shah Kevan , Kato Saul , Skibinski Gaia 
Published: April 2023

AbstractHuman-derived cortical organoids (hCOs) recapitulate cell diversity and 3D structure found in the human brain and offer a promising model for discovery of new gene therapies targeting neurological disorders. Adeno-associated viruses (AAVs) are the most promising vehicles for non-invasive gene delivery to the central nervous system (CNS), but reliable and reproduciblein vitromodels to assess their clinical potential are lacking. hCOs can take on these issues as they are a physiologically relevant model to assess AAV transduction efficiency, cellular tropism, and biodistribution within the tissue parenchyma, all of which could significantly modulate therapeutic efficacy. Here, we examine a variety of naturally occurring AAV serotypes and measure their ability to transduce neurons and glia in hCOs from multiple donors. We demonstrate cell tropism driven by AAV serotype and hCO donor and quantify fractions of neurons and astrocytes transduced with GFP as well as overall hCO health.
Single-Cell Transcriptomes and Immune Repertoires Reveal the Cell State and Molecular Changes in Pemphigus Vulgaris
Authors: Duan Shumin , Li Qionghua , Wang Fei , Kuang Wenjing , Dong Yunmei , Liu Dan , Wang Jiongke , Li Wei , Chen Qianming , Zeng Xin , Li Taiwen 
Published: April 2023

ABSTRACTThe etiology and pathogenesis of pemphigus vulgaris (PV) are closely related to both immune cells and epithelial cells, but the specific subtypes of immune cells involved in PV and their roles are not yet fully understood. Additionally, the specific functions and mechanisms of first-line treatment glucocorticoids on cell types of PV remain to be elucidated. We performing 5’ single-cell RNA sequencing, combined with V(D)J enrichment on buccal mucosal lesions and peripheral blood samples from treatment-naïve patients with PV, in conjunction with post-treatment peripheral blood samples obtained after oral prednisone treatment. Our findings suggest that IL-1α signaling pathway, myeloid antigen presenting cells, inflammatory CD8+ Trm, and dysfunctional CD4+ Treg are crucial in PV. Our results were also supported by immunohistochemical assays. Furthermore, our results show that prednisone has a significant impact on monocytes and MAIT, but a limited effect on CD4+ Treg. Finally, we provide CDR3 amino acid sequence data of BCR that may be used as therapeutic targets. In conclusion, this study provides a comprehensive understanding of PV, particularly in the mucosal-dominant type, and the effect of GCs on PV, which could effectively lead to the development of new therapeutic strategies.
Parting the cellular sea: electrotaxis evoked directional separation of co-cultured keratinocytes and fibroblasts
Authors: Leal José , Shaner Sebastian , Jedrusik Nicole , Savelyeva Anna , Asplund Maria 
Published: April 2023

AbstractBioelectric communication plays a significant role in several cellular processes and biological mechanisms, such as division, differentiation, migration, cancer metastasis, or wound healing. The flow of ions through cellular walls and the gradients generated thereby evoke this signaling as electric fields (EFs) form across membranes, and their changes act as cues for cells. An EF is natively generated towards the wound center during epithelial wound healing, aiming to align and guide cell migration, particularly of keratinocytes, fibroblasts, and macrophages. While this phenomenon, known as electrotaxis, has been extensively investigated across many cell types, it is typically explored one cell type at a time, which does not accurately represent cellular interactions during complex biological processes. Here we show the co-cultured electrotaxis of epithelial keratinocytes and fibroblasts with a salt-bridgeless microfluidic approach for the first time. The electrotactic response of these cells was first assessed in mono-culture to establish a baseline, resulting in a characteristic anodic migration for keratinocytes and cathodic for fibroblasts. Both cell types retained their electrotactic properties in co-culture leading to clear cellular partition. The methods leveraged herein can pave the way for future co-culture electrotaxis experiments where the concurrent influence of cell lines can be thoroughly investigated.
Uptake without inactivation of human adenovirus type 2 byTetrahymena pyriformisciliates
Authors: Olive Margot , Daraspe Jean , Genoud Christel , Kohn Tamar 
Published: April 2023

AbstractHuman adenoviruses are ubiquitous contaminants of surface water. Indigenous protists may interact with adenoviruses and contribute to their removal from the water column, though the associated kinetics and mechanisms differ between protist species. In this work, we investigated the interaction of human adenovirus type 2 (HAdV2) with the ciliateTetrahymena pyriformis. In co-incubation experiments in a freshwater matrix,T. pyriformiswas found to efficiently remove HAdV2, with ≥ 4 log10removal over 72 hours. Neither sorption onto the ciliate nor secreted compounds contributed to the observed loss of infectious HAdV2. Instead, internalization was shown to be the dominant removal mechanism, resulting in the presence of viral particles inside food vacuoles ofT. pyriformis,as visualized by transmission electron microscopy. The fate of HAdV2 once ingested was scrutinized and no evidence of virus digestion was found over the course of 48 hours. This work shows thatT. pyriformiscan exert a dual role on microbial water quality: while they remove infectious adenovirus from the water column, they can also accumulate and potentially protect infectious viruses from exposure to environmental or engineered stressors.Environmental significanceHuman viruses are ubiquitous contaminants of surface water. The fate of human viruses, once discharged into the environment, is modulated by indigenous microorganisms in the surrounding water body. Among microorganisms, the role of protists in controlling virus persistence has been overlooked. Here, we investigate the interactions of the ciliateTetrahymena pyriformiswith human adenovirus type 2. We demonstrate thatT. pyriformiscan serve as a sink of adenovirus from the water column, but also act as a reservoir and potential protective barrier for infectious viruses against stressors.T. pyriformisciliates are among the most abundant protists in surface waters. Understanding this dual role of protists is important for assessing and maintaining microbial water quality and infection risks.
A novel high-throughput assay identifies small molecules with activity against persister cells
Authors: Petersen Maiken Engelbrecht , Hansen Liva Kjær , Kelly Nicholas M. , Wood Thomas Keith , Jørgensen Nis Pedersen , Østergaard Lars Jørgen , Meyer Rikke Louise 
Published: April 2023

AbstractPersister cells are a subpopulation of transiently antibiotic tolerant bacteria, which are believed to be the main cause of relapsing bacterial infections. Due to the importance of persister cells in human infections, there is a need for new antibiotics that kill bacteria independently of their activity. However, high-throughput assays to screen for drugs with such activity are missing. This is partly due to the transient nature of the phenotype, which makes it is difficult to prepare a concentrated population of persister cells that remain inactive during incubation with antibiotics in standard growth media.The purpose of this study was to develop a simple and high-throughput assay to identify compounds with antimicrobial activity against persister cells during a 24 h incubation period. Subsequently, this assay was used to screen a selection of small molecules with hypothesized antimicrobial activity.The fraction ofS. aureusthat tolerate bactericidal concentrations of ciprofloxacin were defined as persister cells. We first quantified how the cell concentration, growth phase, antibiotic concentration, duration of antibiotic exposure, and presence/absence of nutrients during antibiotic exposure affected the fraction of persister cells in a population. After optimizing these parameters, we compared our approach to generate persister cells, to a process that generated persister cells by a short exposure to rifampicin. Finally, we used the optimised protocol to identify molecular structures that have anti-persister activity by performing screening on initially compound fragments and then selecting compounds that incorporated the fragments that displayed activity.We show that exponential- and stationary-phase cultures transferred to nutrient-rich media only contain a small fraction (0.001 to 0.07 %) of persister cells that tolerated 10, 50 and 100 × MIC ciprofloxacin. Exponential-phase cultures displayed a bi-phasic time-kill curve, which plateaued after 5 h exposure, while stationary phase cultures displayed a low, but constant death rate at 50 and 100 × MIC ciprofloxacin. Inducing the persister phenotype with a short rifampicin treatment resulted in 100% persister cells when evaluated after ≤5 h exposure to ciprofloxacin. However, after longer incubation times, cells resumed activity and lost their tolerance to ciprofloxacin. Tolerance was only maintained in the majority of the population for the full 24 h incubation period if cells were transferred to a carbon-free minimal medium before exposure to ciprofloxacin. We conclude that keeping cells starved in a carbon-free medium enables generation of high concentrations ofS. aureuscells that tolerate 50 × MIC ciprofloxacin, and we find this protocol easily applicable for rapid screening of anti-persister drugs that act on dormant or non-dividing cells.
Virus-induced overexpression of heterologous FT for efficient speed breeding in tomato
Authors: Deng Yingtian , Yarur-Thys Antonia , Baulcombe David 
Published: April 2023

ABSTRACTPotato Virus X (PVX) vectors expressing theArabidopsis thaliana FTor tomatoFTorthologSINGLE-FLOWER TRUSS(SFT) accelerated tomato flowering time by 14-21d and increased by 2-3 fold the number of flowers and ripe fruit compared with non-infected or empty vector-infected plants. TheArabidopsisFT was more effective than the tomato orthologue and there was no alteration of the plant architecture, leaf, flower, or fruit morphology. The virus is not transmitted to the next generation and viral vectors with expression of a heterologous FT will be a useful approach to speed breeding in tomato and other species.