bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene editing in the Chagas disease vectorRhodnius prolixusby Cas9-mediated ReMOT Control
Authors: Lima Leonardo , Berni Mateus , Mota Jamile , Bressan Daniel , Julio Alison , Cavalcante Robson , Macias Vanessa , Li Zhiqian , Rasgon Jason L. , Bier Ethan , Araujo Helena 
Published: August 2023

AbstractRhodnius prolixusis currently the model vector of choice for studying Chagas disease transmission, a debilitating disease caused byTrypanosoma cruziparasites. Despite the broad use of double-stranded RNA interference for the knockdown of gene function inR. prolixus, transgenesis and gene editing protocols are still lacking. Here we tested Receptor-Mediated Ovary Transduction of Cargo (ReMOT Control) and direct parental injection of CRISPR (DIPA-CRISPR) for the maternal delivery of CRISPR/Cas9 elements to developingR. prolixusoocytes, and strategies for the identification of insertions/deletions (indels) in target loci of resulting gene-edited G0 nymphs. We demonstrate successful ReMOT Control-mediated gene editing of the eye color markersRp-scarletandRp-white, and the cuticle color markerRp-yellow,with highest effectiveness obtained using the ovary-targeting BtKV ligand. These results provide proof-of-concepts for generating somatic mutations inR. prolixusand potentially for generating germline edited lines in triatomines. Our studies also suggest that optimal strategies for recovery of mutations include performing multiple gRNA injections and the use of visible phenotypes such as those displayed in theRp-scarlet, Rp-whiteandRp-yellowloci for future Co-CRISPR experiments. These results will lay the foundation for gene editing protocols for triatomines and could lead to the development of novel control strategies for vectors of Chagas disease.Author SummaryRhodnius prolixusis an insect vector of the protozoanTrypanossoma cruzi, causative agent of debilitating Chagas disease. To fight the spread of the disease, it has been suggested that biological control of the insect should be attempted. Gene editing by the novel CRISPR methodology holds great promise in this sense, as it enables to target almost any gene in the genome for mutagenesis, thus allowing the control of insect physiology and reproduction. Here we have tested protocols for the delivery of CRISPR reagents as an attempt to enable genome editing of the vector. Our results show that maternal delivery of CRISPR by the ReMOT Control method is efficient for mutating eye and cuticle color genes in the resulting nymphs, generating edited animals with red eyes, white eyes or a yellow cuticle. This is the first report of gene editing in a vector of Chagas disease and should lay the basis to produce modified animals either unable to carry theT. cruziparasite or to reproduce.
Combination Treatment to Improve Mucociliary Transport ofPseudomonas aeruginosaBiofilms
Authors: Rouillard Kaitlyn R. , Esther Christopher P. , Kissner William J. , Plott Lucas M. , Bowman Dean W. , Markovetz Matthew R. , Hill David B. 
Published: August 2023

AbstractPeople with muco-obstructive pulmonary diseases such as cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) often have acute or chronic respiratory infections that are difficult to treat due in part to the accumulation of hyperconcentrated mucus within the airway. Mucus accumulation and obstruction promote chronic inflammation and infection and reduce therapeutic efficacy. Bacterial aggregates in the form of biofilms exhibit increased resistance to mechanical stressors from the immune response (e.g., phagocytosis) and chemical treatments including antibiotics. Herein, combination treatments designed to disrupt the mechanical properties of biofilms and potentiate antibiotic efficacy are investigated against mucus-grownPseudomonas aeruginosabiofilms and optimized to 1) alter biofilm viscoelastic properties, 2) increase mucociliary transport rates, and 3) reduce bacterial viability. A disulfide bond reducing agent (tris(2-carboxyethyl)phosphine, TCEP), a surfactant (NP40), a biopolymer (hyaluronic acid, HA), a DNA degradation enzyme (DNase), and an antibiotic (tobramycin) are tested in various combinations to maximize biofilm disruption. The viscoelastic properties of biofilms are quantified with particle tracking microrheology and transport rates are quantified in a mucociliary transport device comprised of fully differentiated primary human bronchial epithelial cells. The combination of the NP40 with hyaluronic acid and tobramycin was the most effective at increasing mucociliary transport rates, decreasing the viscoelastic properties of mucus, and reducing bacterial viability. Multimechanistic targeting of biofilm infections may ultimately result in improved clinical outcomes, and the results of this study may be translated into future in vivo infection models.Author SummaryOne of the major challenges associated with chronic respiratory infections in cystic fibrosis and chronic obstructive pulmonary disease is difficult to treat biofilms that form in hyperconcentrated mucus. Biofilms are mechanically robust due to an exterior polymeric matrix that protects from the immune response and antibiotics. Antibiotics like tobramycin alone have little impact on the biofilm matrix, but disruption of viscous mucus and the biofilm architecture has previously been shown to improve antibiotic efficacy. Combination treatments must be used to break up mucus and biofilms and simultaneously kill bacteria. The most promising combination in this study includes the surfactant NP40, the biopolymer hyaluronic acid, and the antibiotic tobramycin which together decreased biofilm viscosity, reduced bacterial load, and increased mucociliary transport rates. The results from this study may be translated to an infected animal study for eventual clinical trials.
Proteogenomic characterization reveals antitumor mechanisms of intrahepatic cholangiocarcinoma
Authors: Wang Weibing , Xu Shifeng 
Published: August 2023

AbstractDiagnosing and managing intrahepatic cholangiocarcinoma (iCCA) poses a significant oncological hurdle as it is a deadly form of liver cancer.A significant role is played by nonapoptotic regulatory cell death (NRCD) in the tumor immune microenvironment (TME) of iCCA. Nevertheless, the precise functions of NRCD-associated genes (NRGs) in the tumor microenvironment (TME) are still not well understood. Transcriptomics, proteomic analysis, and single-cell RNA analysis were utilized to distinguish two NRG-related clusters in iCCA patients from the FU-iCCA cohort in this study. We have shown the clear disparities in immune traits and predictive categorization among two groups. To address the risk stratification and prognosis prediction, a prognostic signature model called NPS (NRG-related risks core prognostic signature model) was created using the FU-iCCA cohort. The validation of the NRG-associated risk score in prognosis and immunotherapy confirmed its predictive capabilities. In iCCA patients with high-risk, the secretion of CP and TGF-β proteins strengthened the enriched TGF-β signaling network between CD4+ T cells and erythroid cells. Patients exhibiting a low-risk score demonstrated improvement in the effector function of CD4+ T cells, resulting in a more favorable reaction to chemotherapy medications. The NPS-risk score showed a significant negative correlation with the IC50 values of four drugs (Trametinib, CI-1040, X17-ACC, and PD-0325901). From these findings, it can be inferred that a clear connection exists between the NRG and the TME in iCCA. Additionally, the risk score has the potential to act as a reliable prognostic indicator, offering advantageous outcomes for chemotherapy and immunotherapy. This could aid in making informed clinical decisions for patients with iCCA.
Effect of foot position during plantarflexion on the neural drive to thegastrocnemiiin runners with Achilles tendinopathy
Authors: Fernandes Gabriel L. , Orssatto Lucas B. R. , Shield Anthony J. , Trajano Gabriel S. 
Published: August 2023

AbstractRunners with Achilles tendinopathy (AT) have reduced neural drive to thegastrocnemius lateralis(GL). This study investigated if the strategy of pointing feet-inward (feet-in) during isometric plantarflexion would increasegastrocnemius lateraliselectromyography root mean square amplitude (RMS) and motor unit discharge rates, compared to feet-in neutral position (feet-neutral), in runners with Achilles Tendinopathy (AT). High-density electromyograms were recorded fromgastrocnemius lateralisandmedialis, during 20-sfeet-inandfeet-neutralisometric heel raise, in runners with (n=18) and without (n=19) AT. Duringfeet-in, GL RMS was higher duringfeet-inin both groups and GM RMS was lower only duringfeet-inin the AT. Conversely, motor unit discharge rates were lower duringfeet-inin GL (p<0.001) and in GM in the AT group. The AT group had lowertriceps suraeendurance during single leg heel raise. In summary,feet-inincreases GL RMS in both groups, conversely reducing motor unit discharge rates in the AT group, compared tofeet-neutral. Additionally,feet-inreduces GM RMS and motor unit discharge rates only in the AT group, compared tofeet-neutral. This would shift thegastrocnemius lateralis/medialisratio excitation, favouringgastrocnemius lateralis. Nonetheless, while this strategy holds promise, it remains uncertain whether performing plantarflexion exercise with feet pointed inwards would provide additional benefits for the treatment of runners with Achilles tendinopathy. Our findings suggest that the increased GL RMS duringfeet-inis effective in increasing GL excitation but not as consequence of increased MUDR and, but it might be a result of recruitment of more motor units.
CD61 identifies a superior population of aged murine hematopoietic stem cells and is required to preserve quiescence and self-renewal
Authors: Skinder Natalia , Fernández Irene Sanz , Dethmers-Ausema Albertien , Weersing Ellen , de Haan Gerald 
Published: August 2023

AbstractAging leads to a decline in function of hematopoietic stem cells (HSCs) and increases susceptibility to hematological disease. We found CD61 to be highly expressed in aged HSCs. Here we investigate the role of CD61 in identifying distinct subpopulations of aged HSCs and assess how expression of CD61 affects stem cell function. We show that HSCs with high expression of CD61 are functionality superior and retain self-renewal capacity in serial transplantations. A population of aged HSCs with highest CD61 expression is functionally comparable to young HSCs. These CD61HighHSCs display a notably higher quiescence compared to their CD61Lowcounterparts. We also show that CD61Highand CD61LowHSCs are transcriptomically distinct populations within aged HSCs. Collectively, our research identifies CD61 as a key player in maintaining stem cell quiescence during aging, ensuring the preservation of their functional integrity and potential. Moreover, CD61 emerges as a marker to prospectively isolate a superior, highly dormant population of young and aged HSCs, making it a valuable tool both in fundamental and clinical research.HighlightsCD61 expression marks a functionally superior population of long-term hematopoietic stem cells and plays a pivotal role in the maintenance of aged LT-HSCs by regulating their dormancyAged LT-HSCs with high expression of CD61 are functionally comparable to their young counterparts
Pairing interacting protein sequences using masked language modeling
Authors: Lupo Umberto , Sgarbossa Damiano , Bitbol Anne-Florence 
Published: August 2023

AbstractPredicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids within protein chains. It also captures inter-chain coevolution, despite being trained on single-chain data. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. Starting from sequences paired by DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer. It also achieves competitive performance with using orthology-based pairing.Significance statementDeep learning has brought major advances to the analysis of biological sequences. Self-supervised models, based on approaches from natural language processing and trained on large ensembles of protein sequences, efficiently learn statistical dependence in this data. This includes coevolution patterns between structurally or functionally coupled amino acids, which allows them to capture structural contacts. We propose a method to pair interacting protein sequences which leverages the power of a protein language model trained on multiple sequence alignments. Our method performs well for small datasets that are challenging for existing methods. It can improve structure prediction of protein complexes by supervised methods, which remains more challenging than that of single-chain proteins.
Cigarette smoking promotes the spread of antimicrobial resistance in the human lung and the environment
Authors: Fang Peiju , Konyali Diala , Fischer Emily , Mayer Robin Pascal , Huang Jin , Elena Alan Xavier , Orzechowski Gerit Hartmut , Tony-Odigie Andrew , Kneis David , Dalpke Alexander , Krebs Peter , Li Bing , Berendonk Thomas U. , Klümper Uli 
Published: August 2023

AbstractWhile immediate health risks of cigarette smoking are well-established, indirect health impacts of cigarette-derived pollutants through proliferation of antimicrobial resistance (AMR) among bacteria remain understudied. Here, exposure to cigarette smoke condensate at relevant concentrations resulted in >2-fold elevated transfer rates of a multi-drug-resistance encoding plasmid betweenPseudomonasstrains in artificial lung sputum medium. This effect was connected to elevated reactive oxygen species production as part of the bacterial stress response when exposed to cigarette-derived toxicants. Similar results were obtained under exposure to cigarette ash leachate in environmental medium. Further, used cigarette filters enriched in toxic residues were submerged in a wastewater stream, and colonized by altered microbial communities compared to unused filters. These communities were significantly enriched in pathogens and AMR. Hence, filters could facilitate hitchhiking of high-risk bacteria to novel environments. We demonstrate that cigarette-derived compounds can promote the spread of AMR within the human lung and natural environments.
Met58 and di-acidic motif located at C-terminal region of SARS-CoV-2 ORF6 plays a crucial role in its structural conformations
Authors: Kumar Prateek , Saumya Kumar Udit , Bhardwaj Taniya , Giri Rajanish 
Published: August 2023

AbstractDespite being mostly neglected in structural biology, the C-terminal Regions (CTRs) are studied to be multifunctional in humans as well as in viruses. Their role in cellular processes such as trafficking, protein-protein interactions, and protein-lipid interactions are known due to their structural properties. In our previous findings on SARS-CoV-2 Spike and NSP1 proteins, the C-terminal regions (CTRs) are observed to be disordered and experimental evidence showed a gain of structure properties in different physiological environments. In this line, we have investigated the structural dynamics of CTR (residues 38-61) of SARS-CoV-2 ORF6 protein, disrupting bidirectional transport between the nucleus and cytoplasm. Like Spike and NSP1-CTR, the ORF6-CTR is also disordered in nature but possesses gain of structure properties in minimal physiological conditions. As per studies, the residue such as Methionine at 58thposition in ORF6 is critical for interaction with Rae1-Nup98. Therefore, along with M58, we have identified a few other mutations from the literature and performed extensive structure modelling and dynamics studies using computational simulations. The exciting revelations in CTR models provide evidence of its structural flexibility and possible capabilities to perform multifunctionality inside the host.
GalNAc-siRNA Mediated Knockdown of Ketohexokinase Versus Systemic, Small Molecule Inhibition of its Kinase Activity Exert Divergent Effects on Hepatic Metabolism in Mice on a HFD
Authors: Park Se-Hyung , Fadhul Taghreed , Conroy Lindsey R. , Clarke Harrison , Sun Ramon C. , Wallenius Kristina , Boucher Jeremie , O’Mahony Gavin , Boianelli Alessandro , Persson Marie , Martinez Genesee J. , Hinds Terry D. , Divanovic Senad , Softic Samir 
Published: August 2023

SUMMARYConsumption of diets high in sugar and fat are well-established risk factors for the development of obesity and its metabolic complications, including non-alcoholic fatty liver disease. Metabolic dysfunction associated with sugar intake is dependent on fructose metabolism via ketohexokinase (KHK). Here, we compared the effects of systemic, small molecule inhibition of KHK enzymatic activity to hepatocyte-specific, GalNAc-siRNA mediated knockdown of KHK in mice on a HFD. Both modalities led to an improvement in liver steatosis, however, via substantially different mechanisms. KHK knockdown profoundly decreased lipogenesis, while the inhibitor increased the fatty acid oxidation pathway. Moreover, hepatocyte-specific KHK knockdown completely prevented hepatic fructose metabolism and improved glucose tolerance. Conversely, KHK inhibitor only partially reduced fructose metabolism, but it also decreased downstream triokinase. This led to the accumulation of fructose-1 phosphate, resulting in glycogen accumulation, hepatomegaly, and impaired glucose tolerance. In summary, KHK profoundly impacts hepatic metabolism, likely via both kinase-dependent and independent mechanisms.HIGHLIGHTSKHK knockdown or inhibition of its kinase activity differently target hepatic metabolism.KHK inhibitor increases F1P and glycogen accumulation as it also lowers triokinase.KHK knockdown completely prevents hepatic fructose metabolism and lipogenesis.E of wild type, but not mutant, kinase dead KHK-C increases glycogen accumulation.
Re-education of myeloid immune cells to reduce regulatory T cell expansion and impede breast cancer progression
Authors: Gamage Hashni Epa Vidana , Shahoei Sayyed Hamed , Albright Samuel T. , Wang Yu , Smith Amanda J. , Farmer Rachel , Fink Emma C. , Jacquin Elise , Weisser Erin , Bautista Rafael O. , Henn Madeline A. , Schane Claire P. , Nelczyk Adam T. , Ma Liqian , Gupta Anasuya Das , Bendre Shruti V. , Nguyen Tiffany , Tiwari Srishti , Krawczynska Natalia , He Sisi , Tjoanda Evelyn , Chen Hong , Sverdlov Maria , Gann Peter H. , Boidot Romain , Vegran Frederique , Fanning Sean W. , Apetoh Lionel , Hergenrother Paul J. , Nelson Erik R. 
Published: August 2023

AbstractImmune checkpoint blockade (ICB) has revolutionized cancer therapy but has had limited utility in several solid tumors such as breast cancer, a major cause of cancer-related mortality in women. Therefore, there is considerable interest in alternate strategies to promote an anti-cancer immune response. We demonstrate that NR0B2, a protein involved in cholesterol homeostasis, functions within myeloid immune cells to modulate the NLRP3 inflammasome and reduce the expansion of immune-suppressive regulatory T cells (Treg). Loss of NR0B2 increased mammary tumor growth and metastasis. Small molecule agonists, including one developed here, reduced Tregexpansion, reduced metastatic growth and improved the efficacy of ICB. This work identifies NR0B2 as a target to re-educate myeloid immune cells providing proof-of-principle that this cholesterol-homeostasis axis may have utility in enhancing ICB.Brief SummaryImmune therapy has been disappointing for breast cancer. NR0B2 within myeloid immune cells reduces the expansion of Tregs, a highly immune suppressive subtype historically challenging to target. NR0B2 within myeloid immune cells represses the inflammasome, leading to reduced Tregexpansion and subsequent tumor growth/metastasis. Activation of NR0B2 with small molecule agonists, including one developed herein, attenuates tumor growth and metastasis in murine models of mammary cancer.
Seasonal effects of long-term warming on ecosystem function and bacterial diversity
Authors: Shinfuku Melissa S. , Domeignoz-Horta Luiz A. , Choudoir Mallory J. , Frey Serita D. , Mitchell Megan F. , Ranjan Ravi , DeAngelis Kristen M. 
Published: August 2023

1AbstractAcross biomes, soil biodiversity promotes ecosystem functions. However, whether this relationship will be maintained under climate change is uncertain. Here, using two long-term soil warming experiments, we investigated how warming affects the relationship between ecosystem functions and bacterial diversity across seasons, soil horizons, and warming duration. Soils were sampled from these warming experiments located at the Harvard Forest Long-Term Ecological Research (LTER) site, where soils had been heated +5 °C above ambient for 13 or 28 years at the time of sampling. We assessed seven measurements representative of different ecosystem functions and nutrient pools. We also surveyed bacterial community diversity. We found that ecosystem function was significantly affected by season, with autumn samples having higher function than summer samples. The effect of warming on bacterial diversity was similarly affected by season, where warming in the summer was associated with decreased bacterial evenness in the organic horizon. Despite the decreased bacterial diversity in the warmed plots, we found that the relationship between ecosystem function and bacterial diversity was unaffected by warming or warming duration. Our findings highlight that season is a consistent driver of ecosystem function as well as a modulator of climate change effects on bacterial community diversity.
Population interconnectivity shapes the distribution and complexity of chimpanzee cumulative culture
Authors: Gunasekaram Cassandra , Battiston Federico , Padilla-Iglesias Cecilia , van Noordwijk Maria A. , Manica Andrea , Betranpetit Jaume , Whiten Andrew , van Schaik Carel P. , Vinicius Lucio , Migliano Andrea Bamberg 
Published: August 2023

AbstractWhile cumulative culture is a hallmark of hominin evolution, its origins can be traced back to our common ancestor with chimpanzees. Here we investigate the evolutionary origins of chimpanzee cumulative culture, and why it remained incipient. To trace cultural transmission among the four chimpanzee subspecies, we compared between-population networks based on genetic markers of recent migration and shared cultural traits. We show that limited levels of interconnectivity favored the emergence of a few instances of cumulative culture in chimpanzees. As in humans, cultural complexification likely happened in steps, with between-community transmission promoting incremental changes and repurposing of technologies. We propose that divergence in social patterns led to increased between-group mobility inHomo, propelling our lineage towards a trajectory of irreversible dependence on cultural exchange and complexification.One-Sentence SummaryPopulation interconnectivity through migration explains the origins of chimpanzee cumulative culture and why it remained incipient