bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oral mTOR Inhibition Limits And Reduces Actinic Keratosis And Cutaneous Squamous Cell Carcinoma In A UVB-Induced Mouse Model
Authors: Booty MG , Komalo B , Hosny A , Headland SE , Fernandez-Figueras MT , Nguyen AM , Cousin W , Heinrich J , Nicolaisen L , DeVay RM , White B , Elabd C 
Published: November 2022

ABSTRACTActinic keratosis (AK) is a skin disease that is characterized by clinical and subclinical cutaneous lesions in sun-exposed areas. It is a considerable burden due to its high occurrence in middle-aged and older populations, as well as its propensity to progress to invasive cutaneous squamous cell carcinoma. The mammalian target of rapamycin (mTOR) pathway is critical in carcinogenesis and tumor development, and it has been shown to be over-activated during skin tumorigenesis, particularly upon ultraviolet (UV) radiation exposure, the key risk factor for AK. However, the ability of mTOR inhibitors to treat AK is not well documented. Herein, we evaluated the effect of oral mTOR inhibitorsin vitroandin vivoand found that mTOR inhibitors lower keratinocyte cell proliferationin vitroand both clear and prevent AK and cutaneous squamous cell carcinoma (cSCC) in a UV-B induced SKH1 hairless mouse model of disease. mTOR inhibition reduced the number and size of skin lesions and the frequency of cSCC, resulting in a considerable reduction in disease severity. mTOR inhibition prevented lesion occurrence in areas of field cancerization, without affecting epidermal thickness, keratinocyte proliferationin vivo, or the presence of p53+ cells. Our findings indicate that, when appropriately dosed, oral mTOR inhibitors provide a safe home-based systemic treatment alternative with significant benefits to patients over current topical treatment options.
Machine-learning based detection of adventitious microbes in T-cell therapy cultures using long read sequencing
Authors: Strutt James P. B. , Natarajan Meenubharathi , Lee Elizabeth , Teo Denise Bei Lin , Sin Wei-Xiang , Cheung Faye Ka-Wai , Chew Marvin , Thazin Khaing , Barone Paul W. , Wolfrum Jacqueline M. , Williams Rohan B. H. , Rice Scott A. , Springs Stacy L. 
Published: November 2022

AbstractAssuring that cell therapy products are safe before releasing them for use in patients is critical. Currently, compendial sterility testing for bacteria and fungi can take 7-14 days. The goal of this work was to develop a rapid untargeted approach for the sensitive detection of microbial contaminants at low abundance from low volume samples during the manufacturing process of cell therapies. We developed a long-read sequencing methodology using Oxford Nanopore Technologies MinION platform with 16S and 18S amplicon sequencing to detect USP<71> organisms and other microbial species. Reads are classified metagenomically to predict the microbial species. We used an extreme gradient boosting machine learning algorithm (XGBoost) to first assess if a sample is contaminated and second, determine whether the predicted contaminant is correctly classified or misclassified. The model was used to make a final decision on the sterility status of the input sample. An optimised experimental and bioinformatics pipeline starting from spiked species through to sequenced reads allowed for the detection of microbial samples at 10 CFU / mL using metagenomic classification. Machine learning can be coupled with long read sequencing to detect and identify sample sterility status and microbial species present in T-cell cultures, including the USP<71> organisms to 10 CFU / mL.ImportanceThis research presents a novel method for rapidly and accurately detecting microbial contaminants in cell therapy products, which is essential for ensuring patient safety. Traditional testing methods are time-consuming, taking 7-14 days, while our approach can significantly reduce this time. By combining advanced long read Nanopore sequencing techniques and machine learning, we can effectively identify the presence and types of microbial contaminants at low abundance levels. This breakthrough has the potential to improve the safety and efficiency of cell therapy manufacturing, leading to better patient outcomes and a more streamlined production process.
Assessing the impact of pedigree quality on the validity of quantitative genetic parameter estimates
Authors: Mawass Walid , Milot Emmanuel 
Published: November 2022

AbstractInvestigating the evolutionary dynamics of complex traits in nature requires the accurate assessment of their genetic architecture. Using a quantitative genetic (QG) modeling approach (e.g., animal model), relatedness information from a pedigree combined with phenotypic measurements can be used to infer the amount of additive genetic variance in traits. However, pedigree information from natural systems is not perfect and might contain errors or be of low quality. Published sensitivity analyses revealed a limited impact of expected error rates on parameter estimates. However, natural systems will differ in many respects (e.g., mating system, data availability, pedigree structure), thus it can be inappropriate to generalize outcomes from one system to another. French-Canadian (FC) genealogies are extensive and deep-rooted (up to 9 generations in this study) making them ideal to study how the quality and properties (e.g., errors, completeness) of pedigrees affect QG estimates. We conducted simulation analyses to infer the reliability of QG estimates using FC pedigrees and how it is impacted by genealogical errors and variation in pedigree structure. Broadly, results show that pedigree size and depth are important determinants of precision but not of accuracy. While the mean genealogical entropy (based on missing links) seems to be a good indicator of accuracy. Including a shared familial component into the simulations led to on average a 46% overestimation of the additive genetic variance. This has crucial implications for evolutionary studies aiming to estimate QG parameters given that many traits of interest, such as life history, exhibit important non-genetic sources of variation.
Mutual Annotation-Based Prediction of Protein Domain Functions with Domain2GO
Authors: Ulusoy Erva , Doğan Tunca 
Published: November 2022

AbstractMotivationIdentifying unknown functional properties of proteins is an important task for understanding their roles in both health and disease states. The domain composition of a protein can reveal critical information in this context, as domains are structural and functional units that dictate how the protein should act at the molecular level. The expensive and time-consuming nature of wet-lab experimental approaches prompted researchers to develop computational strategies for predicting biomolecular functions. Biological ontologies, such as the Gene Ontology (GO), which provide a standardized vocabulary of information about biological entities, are frequently employed in protein function prediction.ResultsIn this study, we proposed a new method called Domain2GO that predicts associations between protein domains and GO terms, thus redefining the problem as domain function prediction, using documented protein-level GO annotations together with proteins’ domain content. To obtain reliable associations, co-annotation patterns of domains and GO terms in the same proteins are examined using statistical resampling. An ablation study was conducted to compare the predictive performance of various implementations of Domain2GO, differing from each other by the utilized statistical measure (e.g., information theory inspired similarity measures and the ones calculated by the expectation-maximization algorithm). As a use-case study, examples selected from the finalized domain-GO term mappings were evaluated for their biological relevance via a literature review. Then, we applied the proposed method to predict presently unknown protein functions by propagating domain-associated GO terms to proteins annotated with these domains. For protein function prediction performance evaluation and comparison against other methods, we employed Critical Assessment of Function Annotation 3 (CAFA3) challenge datasets. The results demonstrated the high potential of Domain2GO, particularly for predicting molecular function and biological process terms, along with advantages such as producing interpretable results and having exceptionally low computational costs. The approach presented here can be extended to other ontologies and biological entities in order to investigate unknown relationships in complex and large-scale biological data.Availability and implementationThe source code, datasets, results, and user instructions for Domain2GO are available athttps://github.com/HUBioDataLab/Domain2GO.
Mosquito bites and stages specific antibody responses againstPlasmodium falciparumin southern Ghana
Authors: Kwapong Sebastian Shine , Asare Kwame Kumi , Kusi Kwadwo Asamoah , Pappoe Faustina , Ndam Nicaise , Tahar Rachida , Poinsignon Anne , Amoah Linda Eva 
Published: November 2022

AbstractBackgroundThe human host elicits specific immune responses after exposure to various life stages of the malaria parasite as well as components of mosquito saliva injected into the host during a mosquito bite. This study describes differences in IgG responses against antigens derived from the sporozoite (PfCSP), asexual stage parasite (PfEBA175) and the gametocyte (Pfs230) in addition to anAnopheles gambiaesalivary gland antigen (gSG6-P1) in two communities in Ghana with similar blood stage malaria parasite prevalence.MethodologyThis study used archived plasma samples collected from an earlier cross-sectional study that enrolled volunteers aged from 6 months to 70 years from Simiw, peri-urban community (N=347) and Obom, rural community (N=291). An archived thick and thin blood smear for microscopy was used for the estimation ofPlasmodiumparasite density and species and DNA extraction from blood spots andP. falciparumconfirmation was performed using PCR. This study used the stored plasma samples to determine IgG antibody levels toPlasmodium falciparumandAnophelessalivary antigens using indirect ELISA.ResultsIndividuals from Simiw had significantly higher levels of IgG against mosquito gSG6-P1 (median (95%CI)) (2.590 (2.452-2.783) ng/mL) compared to those from Obom (2.119 (1.957-2.345) ng/mL), p<0.0001. Both IgG responses against Pfs230proC (p=0.0006), and PfCSP (p=0.002) were significantly lower in volunteers from Simiw compared to the participants from Obom. The seroprevalence of PfEBA-175.5R (p=0.8613), gSG6-P1 (p=0.0704), PfCSP (p=0.7798) IgG were all similar in Obom and Simiw. However, Pfs230 seroprevalence was significantly higher at Obom compared to Simiw (p=0.0006). Spearman correlation analysis showed no significant association between IgG responses against gSG6-P1, PfCSP, Pfs230proC and PfEBA-175.5R and parasite density at both Obom and Simiw (p>0.05).ConclusionIn conclusion, malaria transmission dynamics is highly complex. The similar malaria transmission intensity identified in the two communities resulted from a different combination of vector, environmental and host factors. With one community likely having a higher prevalence of uninfected mosquitoes and the other a larger reservoir of gametocyte carriers.
The Ribosome Maturation Factor Rea1 utilizes nucleotide independent and ATP-hydrolysis driven Linker remodelling for the removal of ribosome assembly factors
Authors: Busselez Johan , Koenig Geraldine , Klos Torben , Sosnowski Piotr , Marechal Nils , Gizardin-Fredon Hugo , Cianferani Sarah , Dominique Carine , Henry Yves , Henras Anthony , Schmidt Helgo 
Published: November 2022

SummaryThe ribosome maturation factor Rea1 (or Midasin) catalyses the removal of assembly factors from large ribosomal subunit precursors to promote their export from the nucleus to the cytosol. Rea1 consists of nearly 5000 amino-acid residues and belongs to the AAA+ protein family. It consists of a ring of six AAA+ domains from which the ≈ 1700 amino-acid residue linker emerges that is subdivided into stem, middle and top domains. A flexible and unstructured D/E rich region connects the linker top to a MIDAS (metal ion dependent adhesion site) domain, which is able to bind the assembly factor substrates. Despite its key importance for ribosome maturation, the Rea1 mechanism driving assembly factor removal is still poorly understood. Here we demonstrate that the Rea1 linker is essential for assembly factor removal. It rotates and swings towards the AAA+ ring following a complex remodelling scheme involving nucleotide independent as well as nucleotide dependent steps. ATP-hydrolysis is required to engage the linker with the AAA+ ring and ultimately with the AAA+ ring docked MIDAS domain. The interaction between the linker top and the MIDAS domain allows force transmission for assembly factor removal.
Cryo-EM structure of the chain-elongating E3 ligase UBR5
Authors: Hodáková Zuzana , Grishkovskaya Irina , Brunner Hanna L. , Bolhuis Derek L. , Belačić Katarina , Schleiffer Alexander , Kotisch Harald , Brown Nicholas G. , Haselbach David 
Published: November 2022

ABSTRACTUBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT E3 ligase has recently been identified as an important regulator of oncogenes, e.g., MYC, but little is known about its structure or mechanisms of substrate engagement and ubiquitination. Here, we present the cryo-EM structure of the human UBR5, revealing a building block of an antiparallel dimer which can further assemble into larger oligomers. The large helical scaffold of the dimer is decorated with numerous protein-interacting motifs for substrate engagement. Using cryo-EM processing tools, we observe the dynamic nature of the domain movements of UBR5, which allows the catalytic HECT domain to reach engaged substrates. We characterise the proteasomal nuclear import factor AKIRIN2 as an interacting protein and propose UBR5 as an efficient ubiquitin chain elongator. This preference for ubiquitinated substrates permits UBR5 to function in several different signalling pathways and cancers. Together, our data expand on the limited knowledge of the structure and function of HECT E3s.
SEPepQuant enables comprehensive protein isoform characterization in shotgun proteomics
Authors: Dou Yongchao , Yi Xinpei , Olsen Lindsey K. , Zhang Bing 
Published: November 2022

AbstractShotgun proteomics is essential for protein identification and quantification in biomedical research, but protein isoform characterization is inhibited by the extensive number of peptides shared across proteins, hindering our understanding of protein isoform regulation and their roles in normal and disease biology. We systematically assess the challenge and opportunities of shotgun proteomics-based protein isoform characterization usingin silicoand experimental data, and then present SEPepQuant, a graph theory-based approach to enable isoform characterization. Using published data from one induced pluripotent stem cell study and two human hepatocellular carcinoma studies, we demonstrate the ability of SEPepQuant in addressing the key limitations of existing methods, providing more comprehensive proteome characterization, identifying hundreds of isoform-level regulation events, and facilitating streamlined cross-study comparisons. Our analysis provides solid evidence to support a widespread role of protein isoform regulation in normal and disease processes, and SEPepQuant has broad applications to biological and translational research.
IGF2BP2 is Induced by Stress in the Heart and Mediates Dilated Cardiomyopathy
Authors: Krumbein Miriam , Oberman Froma , Cinnamon Yuval , Golomb Mordechai , May Dalit , Vainer Gilad , Belzer Vitali , Meir Karen , Fridman Irina , Haybaeck Johannes , Poelzl Gerhard , Kehat Izhak , Beeri Ronen , Kessler Sonja , Yisraeli Joel K. 
Published: November 2022

AbstractThe IGF2BP family of RNA binding proteins consists of three paralogs that regulate intracellular RNA localization, RNA stability, and translational control. Although IGF2BP1 and 3 are oncofetal proteins, IGF2BP2 expression is maintained in many tissues, including the heart, into adulthood. Previous studies indicated that IGF2BP2 is upregulated in cardiomyocytes during cardiac stress and remodelling and returns to normal levels in recovering hearts. These results raise the possibility that IGF2BP2 might play an adaptive role during cardiac stress and recovery. Using a conditional, inducible transgenic mouse line, we found that enhanced expression of an IGF2BP2 transgene in newborn or adult hearts leads to dilated cardiomyopathy (DCM) and death within 3-4 weeks. Downregulation of the transgene after 2 weeks, however, rescues these mice, with complete recovery by 12 weeks. Hearts overexpressing IGF2BP2 downregulate sarcomeric and mitochondrial proteins and have fragmented mitochondria and elongated, thinner sarcomeres. Consistent with these results, IGF2BP2 is upregulated in patients with DCM or after myocardial infarction. These results suggest that IGF2BP2 may be an attractive target for therapeutic intervention in DCM.
Catching more air: A method to spatially quantify aerial triazole resistance inAspergillus fumigatus
Authors: Kortenbosch Hylke H. , van Leuven Fabienne , van den Heuvel Cathy , Schoustra Sijmen S. , Zwaan Bas J. , Snelders Eveline 
Published: November 2022

ABSTRACTAirborne triazole-resistant spores of the human fungal pathogenAspergillus fumigatusare a significant human health problem as the agricultural use of triazoles has selected for cross-resistance to life-saving clinical triazoles. However, how to measure the health risk posed by these inhaled spores remains unclear. Here, we describe a method for cost-effective wide-scale outdoor air sampling to measure both spore abundance as well as antifungal resistance fractions. We show that prolonged outdoor exposure of sticky seals placed in delta traps, when combined with a two-layered cultivation approach, can consistently yield sufficient colony-forming units (CFUs) for the quantitative assessment of aerial resistance levels at a spatial scale that was up to now unfeasible. When testing our method in a European pilot sampling of 12 regions, we demonstrate that the triazole-resistant fraction of airborne spores is widespread and varies between 0 and 0.1 for itraconazole (∼4 mg/L) and voriconazole (∼2 mg/L). This method facilitates the assessment of health risks by pinpointing potential hot- and coldspots of environmental resistance selection. This efficient and accessible air sampling protocol opens up extensive options for fine-spatial sampling and surveillance studies.IMPORTANCEAspergillus fumigatusis an opportunistic fungal pathogen which humans and other animals are primarily exposed to through inhalation. Due to the limited availability of antifungals, resistance to the first choice class of antifungals, the triazoles, inA. fumigatuscan make infections by this fungus untreatable and uncurable. Here we describe and validate a method that allows for the quantification of airborne resistance fractions and quick genotyping ofA. fumigatusTR-types. Our pilot study provides proof of concept of the suitability of the method for use by citizen scientists for large-scale spatial air sampling. Spatial air sampling opens up extensive options for surveillance, health-risk assessment, and studying the ecology ofA. fumigatusand the development of triazole resistance.
Shigellainduces epigenetic reprogramming of zebrafish neutrophils
Authors: Gomes Margarida C. , Brokatzky Dominik , Bielecka Magdalena K. , Wardle Fiona C. , Mostowy Serge 
Published: November 2022

SUMMARYTrained immunity is a long-term memory of innate immune cells, generating an improved response upon re-infection.Shigellais an important human pathogen and inflammatory paradigm for which there is no effective vaccine. Using zebrafish larvae we demonstrate that afterShigellapriming neutrophils are more efficient at bacterial clearance. We observe thatShigella-induced protection is non-specific and long-lasting, and is unlike training by BCG and β-glucan. Analysis of histone ChIP-seq on primed neutrophils revealed thatShigellatraining deposits the active H3K4me3 mark on promoter regions of 1612 genes, significantly changing the epigenetic landscape of neutrophils towards enhanced microbial recognition and mitochondrial ROS production. Finally, we demonstrate that mitochondrial ROS plays a key role in enhanced antimicrobial activity of trained neutrophils. It is envisioned that signals and mechanisms we discover here can be used in other vertebrates, including humans, to suggest new therapeutic strategies involving neutrophils to control bacterial infection.
Nuclei isolation protocol from diverse angiosperm species
Authors: Li Chenxin , Wood Joshua C. , Deans Natalie C. , Jarrell Anne Frances , Martin Dionne , Mailloux Kathrine , Wang Yi-Wen , Buell C. Robin 
Published: November 2022

AbstractThe ability to generate intact nuclei is crucial to the success of a variety of genomics experiments, such as Assay for Transposase-Accessible Chromatin using sequencing (ATAC- seq), Cleavage Under Targets and Tagmentation (CUT&Tag), and nuclei-based single cell sequencing (e.g., single nuclei ATAC-seq and single nuclei RNA-seq). For plants, the presence of the cell wall presents significant challenges in the isolation of nuclei from tissues. Here, we report an optimized nuclei isolation protocol that can be adapted for diverse angiosperm species, including maize, soybean, tomato, potato, and wheat, starting from fresh or frozen tissues. Nuclei release is achieved through chopping tissue on ice, where a key parameter affecting nuclei integrity is the concentration of detergent TritonX-100 in the nuclei isolation buffer. The method is simple, quick, and largely centrifugation-free, in which debris is removed by serial filtration. Initial nuclei release and filtration can be performed within 20 min. Fluorescence activated nuclei sorting is then used for final nuclei purification to remove other organelles such as plastids. The protocol uses 500 mg or less plant tissue as input and typically yields at least 100,000 – 200,000 purified nuclei per sample, a common input amount for downstream experiments. Throughout the protocol, we provide guidelines for optimization if performing nuclei isolation from a given species and tissue for the first time.