bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contributions of adaptation and purifying selection to SARS-CoV-2 evolution
Authors: Neher Richard A 
Published: December 2022

Abstract
Continued evolution and adaptation of SARS-CoV-2 has led to more transmissible and immune-evasive variants with profound impacts on the course of the pandemic. Here I analyze the evolution of the virus over 2.5 years since its emergence and estimate the rates of evolution for synonymous and non-synonymous changes separately for evolution within clades—well-defined monophyletic groups with gradual evolution—and for the pandemic overall. The rate of synonymous mutation is found to be around 6 changes per year. Synonymous rates within variants vary little from variant to variant and are compatible with the overall rate of 7 changes per year (or $7.5 \times 10^{-4}$ per year and codon). In contrast, the rate at which variants accumulate amino acid changes (non-synonymous mutations) was initially around 12-16 changes per year, but in 2021 and 2022 it dropped to 6-9 changes per year. The overall rate of non-synonymous evolution, that is across variants, is estimated to be about 26 amino acid changes per year (or $2.7 \times 10^{-3}$ per year and codon). This strong acceleration of the overall rate compared to within clade evolution indicates that the evolutionary process that gave rise to the different variants is qualitatively different from that in typical transmission chains and likely dominated by adaptive evolution. I further quantify the spectrum of mutations and purifying selection in different SARS-CoV-2 proteins and show that the massive global sampling of SARS-CoV-2 is sufficient to estimate site-specific fitness costs across the entire genome. Many accessory proteins evolve under limited evolutionary constraints with little short-term purifying selection. About half of the mutations in other proteins are strongly deleterious.
Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer
Authors: Jindal Rashi , Nanda Abheepsa , Pillai Maalavika , Ware Kathryn E , Singh Divyoj , Sehgal Manas , Armstrong Andrew J. , Somarelli Jason A , Jolly Mohit Kumar 
Published: December 2022

AbstractAdvanced prostate cancer patients initially respond to hormone therapy, be it in the form of androgen deprivation therapy or second-generation hormone therapies, such as abiraterone acetate or enzalutamide. However, most men with prostate cancer eventually develop hormone therapy resistance. This resistance emerges in several ways, such as through genetic mutations, epigenetic mechanisms, or through non-genetic pathways, such as lineage plasticity along epithelial-mesenchymal or neuroendocrine-like axes. These mechanisms of hormone therapy resistance often co-exist within a single patient’s tumor and can overlap within a single cell. There exists a growing need to better understand how phenotypic heterogeneity and plasticity results from emergent dynamics of the regulatory networks governing androgen independence. Here, we investigated the dynamics of a regulatory network connecting the drivers of androgen receptor (AR) splice variant-mediated androgen independence and those of epithelial-mesenchymal transition. Model simulations for this network revealed four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR) and mesenchymal-sensitive (MS), with the latter phenotype occurring rarely. We observed that well-coordinated “teams” of regulators working antagonistically within the network enable these phenotypes. These model predictions are supported by multiple transcriptomic datasets both at single-cell and bulk levels, includingin vitroEMT induction models and clinical samples. Further, our simulations reveal spontaneous stochastic switching between the ES and MR states. Addition of the immune checkpoint molecule, PD-L1, to the network was able to capture the interactions between AR, PD-L1, and the mesenchymal marker SNAIL, which was also confirmed through quantitative experiments. This systems-level understanding of the driver of androgen independence and EMT could aid in understanding non-genetic transitions and progression of such cancers and help in identifying novel therapeutic strategies or targets.
Plastid double-strand RNA transgenes trigger small RNA-based gene silencing of nuclear-encoded genes
Authors: Bélanger Sébastien , Kramer Marianne C. , Payne Hayden A. , Slotkin R. Keith , Meyers Blake C. , Staub Jeffrey M. 
Published: December 2022

ABSTRACTPlastid transformation technology has been widely used to express traits of potential commercial importance, though the technology has been limited to traits that function while sequestered in the organelle. Prior research indicates that plastid contents can escape from the organelle, suggesting a possible mechanism for engineering plastid transgenes to function in other cellular locations. To test this hypothesis, we created tobacco plastid transformants that express a fragment of the nuclear-encodedPhytoene desaturase(PDS) gene capable of catalyzing post-transcriptional gene silencing if RNA escape to the cytoplasm occurs. We found multiple lines of direct evidence that plastid-encodedPDStransgenes affect nuclearPDSgene silencing: knockdown of the nuclear-encodedPDSmRNA and/or its apparent translational inhibition, biogenesis of 21-nucleotide (nt) phased small interfering RNAs (phasiRNAs), and pigment deficient plants. Furthermore, plastid-expressed double-stranded RNA (dsRNA) with no cognate nuclear-encoded pairing partner also produced abundant 21-nt phasiRNAs in the cytoplasm, demonstrating that a nuclear-encoded template is not required for siRNA biogenesis. Our results indicate that RNA escape from plastids to the cytoplasm occurs broadly, with functional consequences that include entry into the gene silencing pathway. Furthermore, we uncover a method to produce plastid-encoded traits with functions outside of the organelle and open new fields of study in plastid development, compartmentalization and small RNA biogenesis.
Novel Peptide Inhibitor of Human Tumor Necrosis Factor-α has Antiarthritic Activity
Authors: Sahu Debasis , Gupta Charu , Yennamalli Ragothaman , Sharma Shikha , Roy Saugata , Hasan Sadaf , Gupta Pawan , Sharma Vishnu Kumar , Kashyap Sujit , Kumar Santosh , Dwivedi Ved Prakash , Panda Amulya Kumar , Das Hasi Rani , Liu Chuan-Ju 
Published: December 2022

AbstractThe inhibition of tumor necrosis factor-α (TNFα) trimer formation renders it inactive for binding to its receptors thus mitigating the vicious cycle of inflammation. We designed a peptide (PIYLGGVFQ) that simulates a sequence strand of human TNFα monomer using a series ofin silicomethods, such as active site finding (Acsite), protein-protein interaction (PPI), docking studies (GOLD and Modeller) followed by molecular dynamics (MD) simulation studies. The MD studies confirmed the intermolecular interaction of the peptide with the TNFα. Fluorescence-activated cell sorting (FACS) and fluorescence microscopy revealed that the peptide effectively inhibited the binding of TNF to the cell surface receptors. The cell culture assays showed that the peptide significantly inhibited the TNFα-mediated cell death. In addition, the nuclear translocation of the nuclear factor kappa B (NFκB) was significantly suppressed in the peptide-treated A549 cells as observed in immunofluorescence and gel mobility-shift assays. Furthermore, peptide protected against joint damage in collagen-induced arthritis (CIA) mouse model as revealed in the microfocal-CT scans. In conclusion, this TNFα antagonist would be useful for the prevention and repair of inflammatory bone destruction and subsequent loss in the mouse model of CIA as well as human rheumatoid arthritis (RA) patients. This calls upon further clinical investigation to utilize its potential effect as an anti-arthritic drug.
Predicting the evolution of lung squamous cell carcinoma in situ using deep learning
Authors: Vigdorovits Alon , Olteanu Gheorghe-Emilian , Tica Ovidiu , Boros Monica , Pop Ovidiu 
Published: December 2022

AbstractLung squamous cell carcinomain situ(SCIS) is the pre-invasive precursor lesion of lung squamous cell carcinoma (SCC). Only half of these lesions progress to invasive cancer, while a third undergo spontaneous regression. The ability to predict the evolution of SCIS lesions can significantly impact the management of lung cancer patients.Here, we present the use of the deep learning (DL) approach in order to predict the progression of SCIS. The dataset consisted of 112 H&E stained whole slide images (WSI) that were obtained from the Image Data Resource public repository. The data set corresponded to tumors of patients who underwent biopsies of SCIS lesions and were subsequently followed up by bronchoscopy and CT to monitor for progression to SCC. We show that a deep convolutional neural network (DCNN) can predict if a SCIS lesion will progress to SCC. The model achieved a per-tile AUC of 0.78 (SD = 0.01) on the test set, an F1 score of 0.84 (SD = 0.05), and a sensitivity of 0.94 (SD = 0.01). Class activation maps were created in order to explore how the DCNN made decisions.To our knowledge, this study is the first to demonstrate that DL has the ability to predict the evolution of SCIS from H&E WSI. DL has the potential to be used as a low-cost method that could provide prognostic information for patients with preinvasive lesions.
Variable organization of symbiont-containing tissue across planthoppers hosting different heritable endosymbionts
Authors: Michalik Anna , Franco Diego C. , Deng Junchen , Szklarzewicz Teresa , Kobiałka Michał , Stroiński Adam , Łukasik Piotr 
Published: December 2022

AbstractSap-feeding hemipteran insects live in associations with diverse heritable endosymbiotic bacteria and fungi that provide essential nutrients deficient in their diets. These symbionts typically reside in bacteriomes, dedicated organs made up of specialized cells termed bacteriocytes. The bacteriome organization varies between insect clades that are ancestrally associated with different microbes. As these symbioses evolve and additional microorganisms complement or replace the ancient associates, the organization of the symbiont-containing tissue becomes even more variable.Planthoppers (Hemiptera: Fulgoromorpha) are ancestrally associated with bacterial symbiontsSulciaandVidania, but in many of the planthopper lineages, these symbionts are now accompanied or have been replaced by other heritable bacteria (e.g.,Sodalis, Arsenophonus, Purcelliella) or fungi. We know the identity of many of these microbes, but the symbiont distribution within the host tissues and the bacteriome organization have not been systematically studied using modern microscopy techniques.Here, we combine light, fluorescence, and transmission electron microscopy with phylogenomic data to compare symbiont tissue distributions and the bacteriome organization across planthoppers representing 15 families. We identify and describe seven primary types of symbiont localization and seven types of the organization of the bacteriome. We show thatSulciaandVidania, when present, occupy distinct bacteriomes distributed within the body cavity. The more recently acquired gammaproteobacterial and fungal symbionts generally occupy separate groups of cells organized into distinct bacteriomes or mycetomes, distinct from those withSulciaandVidania. They can also be localized in the cytoplasm of fat body cells. Alphaproteobacterial symbionts colonize a wider range of host body habitats:Asaia-like symbionts often colonize the host gut lumen, whereasWolbachiaandRickettsiaare usually scattered across tissues and cell types, including bacteriocytes containing other symbionts, bacteriome sheath, fat body cells, gut epithelium, as well as hemolymph. However, there are exceptions, including Gammaproteobacteria that share bacteriome withVidania, or Alphaproteobacteria that colonizeSulciacells.We discuss how planthopper symbiont localization correlates with their acquisition and replacement patterns and the symbionts’ likely functions. We also discuss the evolutionary consequences, constraints, and significance of these findings.
Targeting Damaged Collagen for Intra-Articular Delivery of Therapeutics using Collagen Hybridizing Peptides
Authors: Luke E. N. , Na Bhuket P. Ratnatilaka , Yu S. M. , Weiss J. A. 
Published: December 2022

AbstractThe objective of this study was to investigate the potential of collagen hybridizing peptides (CHPs), which bind to denatured collagen, to extend the retention time of near-infrared fluorophores (NIRF) following intra-articular (IA) injection in rat knee joints. CHPs were synthesized with a NIRF conjugated to N-terminus. Male Sprague-Dawley rats were assigned to one of four experimental groups: healthy, CHP; osteoarthritis (OA), CHP; healthy, scrambled-sequence CHP (sCHP), which has no collagen binding affinity; or OA, sCHP. Animals in the OA groups received an IA injection of monosodium iodoacetate to induce OA. All animals then received the corresponding CHP injection. Animals were imaged repeatedly over two weeks using anin vivofluorescence imaging system. Joint components were isolated and imaged to determine CHP binding distribution. Safranin-O and Fast Green histological staining was performed to confirm the development of OA. CHPs were found to be retained within the joint following IA injection in both healthy and OA animals for the full study period. In contrast, sCHPs were cleared within 24-48 hours. CHP signal was significantly greater (p<0.05) in OA joints when compared to healthy joints. At the two-week end point, multiple joint components retained CHPs, including cartilage, meniscus, and synovium. CHPs extended the retention time of NIRFs following IA injection in healthy and OA knee joints by binding to multiple collagenous tissues in the joint. These results support the pursuit of further research on CHP based therapeutics for IA treatment of OA.
Genome-wide association reveals novel insights into the molecular mechanisms regulating stem volume inPinus taeda
Authors: Aono Alexandre Hild , Bajay Stephanie Karenina , Francisco Felipe Roberto , de Souza Anete Pereira 
Published: December 2022

AbstractPinus taeda(loblolly pine [LP]) is a long-lived tree species and one of the most economically significant forest species. Among growth traits, volume is the most widely considered trait in tree improvement programs. However, deciphering the genetic variants responsible for growth trait variations in conifers, such as LP, is particularly challenging due to the vast size and intricate complexity ofPinusgenomes. We present a comprehensive genetic analysis of LP, focusing on markers associated with stem volume variation, to elucidate the molecular mechanisms governing high-performance phenotypes. We used a population of 1,692 individuals phenotyped for stem volume and genotyped these individuals using sequence capture probes. To conduct genome-wide associations, we utilized both genome-wide association study (GWAS) analysis and machine learning (ML) approaches. The markers identified in association with volume were found to be linked with the genes assembled from three distinct transcriptomes. These genes were subsequently used to construct gene coexpression networks, and through topological evaluations, we identified key genes with potential regulatory roles within stem volume configurations. Using a set of 31,589 SNPs, we defined 7 GWAS-associated SNPs and 128 ML-associated markers, all of which were correlated with multiple genes involved in diverse biological functions. Gene coexpression analysis revealed a group of 270 genes potentially associated with the regulation of genetic material. Key genes directly implicated in the regulation of growth and response to stress were identified, and inferences about their impact on pine development were subsequently elucidated. Our study not only offers insights into SNPs associated with stem volume but also elucidates a subset of genes characterized by unique regulatory features. These findings significantly advance our understanding of the genetic factors influencing growth traits, reveal candidate genes for future functional studies, and contribute to a broader comprehension of the genetic architecture underlying volume traits in LP.
Leptospermum extract (QV0) suppresses pleural mesothelioma tumour growthin vitroandin vivoby mitochondrial dysfunction associated apoptosis
Authors: Shi Huaikai , Zhang Le , Yu Ta-Kun , Zheng Ling , Ke Helen , Johnson Ben , Rath Emma , Lee Kenneth , Klebe Sonja , Kao Steven , Qin Karl Lijun , Pham Hong Ngoc Thuy , Vuong Quan , Cheng Yuen Yee 
Published: December 2022

AbstractPleural mesothelioma (PM) is a highly aggressive, fast-growing asbestos-induced cancer with limited effective treatments. There has been an interest in using naturally occurring anticancer agents derived from plant materials for the treatment of PM. However, it is unclear if aqueous extract from theLeptospermum polygalifolium(QV0) has activity against PM. Here we investigated the anti-cancer property of QV0in vitroandin vivo.Animals treated with Defender®(QV0 dietary supply) exhibited a reduced tumour size over 30 days, which was associated with an average extended of seven days mouse life. There was no liver toxicity, nor increased blood glucose post-treatment in animals treated with Defender®. Moreover, QV0 suppressed the growth of 13 cancer cell lines in a dose-dependent manner, effective at concentrations as low as 0.02% w/v. This response was found to be associated with inhibited cell migration, proliferation, and colony formation, but without evident cell cycle alteration. We observed mitochondrial dysfunction post QV0 treatment, as evidenced by significantly decreased basal and maximal oxygen consumption rates. Significantly enhanced tumour apoptosis was observed in the Defender®-treated animals, correlating with mitochondrial dysfunction. To the best of our knowledge, this study constitutes the first demonstration of an improved host survival (without adverse effects) response in a QV0-treated PM mouse model, associated with an evident inhibition of PM cell growth and mitochondrial dysfunction-related enhancement of tumour apoptosis.ImportanceA major problem with cancer chemotherapy or immunotherapy is the severe adverse effects associated with normal tissue damage. PM is known to be treatment resistant and has poor a prognosis, therefore new therapeutic treatment options are urgently needed. In the present study, we explored the potential utility of aLeptospermumextract (QV0) as a treatment option for mesothelioma. We demonstrated for the first time that QV0 exhibits an anti-tumour response in mesothelioma, without any associated adverse effects observed in the PM mouse model. These findings provide a rationale for early-stage clinical trials. We anticipate that prospective translational research will lead to the clinical implementation of a novel QV0-based treatment strategy that will ultimately benefit PM patients.
Ribosomal s6 kinase (RSK) is a mediator of aquaporin 2 S256 phosphorylation and membrane accumulation after EGFR inhibition with erlotinib
Authors: Babicz Richard Samuel Edward , Cheung Pui W. , Baylor Noah , Bouley Richard , Brown Dennis 
Published: December 2022

AbstractVasopressin (VP) activates PKA, resulting in phosphorylation and membrane accumulation of aquaporin-2 (AQP2). Epidermal growth factor receptor (EGFR) inhibition with erlotinib also induces AQP2 membrane trafficking with a phosphorylation pattern similar to VP, but without increasing PKA activity. Here, we identify the ribosomal s6 kinase (RSK) as the final mediator phosphorylating AQP2 in this novel, erlotinib-induced pathway. We found that RSK was expressed in medullary principal cells in rat kidneys. RSK inhibition with BI-D1870 or siRNA blocked erlotinib-induced AQP2 S256 phosphorylation and membrane trafficking. CRISPR-generated RSK knockout cells failed to show increased S256 phosphorylation in response to erlotinib. Like PKA, RSK was able to phosphorylate AQP2 S256in vitro. Stimulation of PDK1, a known activator of RSK, caused AQP2 S256 phosphorylation and membrane accumulation similar to erlotinib and VP. We conclude that RSK is the terminal kinase phosphorylating AQP2 at S256 upon EGFR inhibition by erlotinib.
General stain deconvolution of histopathology images with physics-guided deep learning
Authors: Chen Jianan , Liu Lydia Y. , Han Wenchao , Wang Dan , Cheung Alison M. , Tsui Hubert , Martel Anne L. 
Published: December 2022

AbstractAdvances have been made in the use of deep learning to extract quantitative and predictive information from digital pathology slides, yet many barriers remain before clinical translation and deployment. In particular, models need to be generalizable despite the wide variations in image characteristics due to inter-scanner variability and differences in slide preparation protocols. This has led to an interest in stain deconvolution methods that could correct for the variability in image appearances. However, most existing stain deconvolution methods were developed and validated on specific datasets and perform poorly on unseen data. We developed Physics-Guided Deep Image Prior network for Stain deconvolution (PGDIPS), a method that combines a novel optical physics model and a self-supervised deep neural network to perform deconvolution for various classes and any number of stains, without the need of training data. PGDIPS outperformed state-of-the-art approaches for the deconvolution of conventional stain combinations, enabled analysis of previously unsupported special stains, and provided superior interpretability by explicitly encoding representations for stain properties and the light transmittance/absorbance process. PGDIPS is publicly available as an end-to-end off-the-shelf tool that does not require data curation, domain knowledge or high computation power.
Competition between chemoattractants causes unexpected complexity and can explain negative chemotaxis
Authors: Dowdell Adam , Paschke Peggy , Thomason Peter , Tweedy Luke , Insall Robert H. 
Published: December 2022

AbstractNegative chemotaxis, where eukaryotic cells migrate away from repellents, is important throughout biology, for example in nervous system patterning and resolution of inflammation. However, the mechanisms by which molecules repel migrating cells are unknown. Here, we use a combination of modelling and experiments with Dictyostelium cells to show that competition between different ligands that bind to the same receptor leads to effective chemorepulsion. 8-CPT-cAMP, widely described as a simple chemorepellent, is inactive on its own, and only repels cells if it interacts with the attractant cAMP. If cells degrade either competing ligand, the pattern of migration becomes more complex; cells may be repelled in one part of a gradient but attracted elsewhere, leading to populations moving in different directions in the same assay, or converging in an arbitrary place. More counterintuitively still, two chemicals can each attract cells on their own, but repel cells when combined together. We have thus identified a new mechanism that drives reverse chemotaxis, verified by mathematical models and experiments with real cells, and important anywhere several ligands compete for the same receptors.