bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overcoming PARP inhibitor resistance by inducing a homologous recombination repair defective phenotype with ATR, CHK1 and WEE1 inhibitors
Authors: Smith Hannah L , Willmore Elaine , Prendergast Lisa , Curtin Nicola J 
Published: July 2023

AbstractPurposePARP inhibitors (PARPi) are effective in homologous recombination repair (HRR) defective (HRD) cancers. To (re)sensitise HRR proficient (HRP) tumours to PARPi combinations with other drugs are being explored. Our aim was to determine the mechanism underpinning the sensitisation to PARPi by inhibitors of cell cycle checkpoint kinase ATR, CHK1 and WEE1.Experimental designA panel of HRD and HRP cells (including matched BRCA1 or 2 mutant and corrected pairs) and ovarian cancer ascites cells were used. Rucaparib (PARPi) induced replication stress (RS) and HRR (immunofluorescence microscopy for γH2AX and RAD51 foci, respectively), cell cycle changes (flow cytometry), activation of ATR, CHK1 and WEE1 (Western Blot for pCHK1S345, pCHK1S296 and pCDK1Y15, respectively) and cytotoxicity (colony formation assay) was determined, followed by investigations of the impact on all of these parameters by inhibitors of ATR (VE-821, 1 μM), CHK1 (PF-477736, 50 nM) and WEE1 (MK-1775, 100 nM).ResultsRucaparib induced RS (3 to10-fold), S-phase accumulation (2-fold) and ATR, CHK1 and WEE1 activation (up to 3-fold), and VE-821, PF-477736 and MK-1775 inhibited their targets and abrogated these rucaparib-induced cell cycle changes in HRP and HRD cells. Rucaparib activated HRR in HRP cells only and was (60-1,000x) more cytotoxic to HRD cells. VE-821, PF-477736 and MK-1775 blocked HRR and sensitised HRP but not HRD cells and primary ovarian ascites to rucaparib.ConclusionsOur data indicate that, rather than acting via abrogation of cell cycle checkpoints, ATR, CHK1 and WEE1 inhibitors cause an HRD phenotype and hence synthetic lethality with PARPi.
Label-free imaging of DNA interactions with 2D materials
Authors: Sülzle Jenny , Yang Wayne , Shimoda Yuta , Ronceray Nathan , Mayner Eveline , Manley Suliana , Radenovic Aleksandra 
Published: July 2023

AbstractTwo-dimensional (2D) materials offer potential as substrates for biosensing devices, as their properties can be engineered to tune interactions between the surface and biomolecules. Yet, not many methods can measure these interactions in a liquid environment without introducing labeling agents such as fluorophores. In this work, we harness interferometric scattering (iSCAT) microscopy, a label-free imaging technique, to investigate the interactions of single molecules of long dsDNA with 2D materials. The millisecond temporal resolution of iSCAT allows us to capture the transient interactions and to observe the dynamics of unlabeled DNA binding to a hexagonal boron nitride (hBN) surface in solution for extended periods (including a fraction of 10%, of trajectories lasting longer than 110 ms). Using a Focused Ion Beam (FIB) technique to engineer defects, we find that DNA binding affinity is enhanced at defects; when exposed to long lanes, DNA binds preferentially at lane edges. Overall, we demonstrate that iSCAT imaging is a useful tool to study how biomolecules interact with 2D materials, a key component in engineering future biosensors.
msqrob2PTM: differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level
Authors: Demeulemeester Nina , Gébelin Marie , Gomes Lucas Caldi , Lingor Paul , Carapito Christine , Martens Lennart , Clement Lieven 
Published: July 2023

AbstractIn the era of open-modification search engines, more post-translational modifications than ever can be detected by LC-MS/MS-based proteomics. This development can switch proteomics research into a higher gear, as PTMs are key in many cellular pathways important in cell proliferation, migration, metastasis and ageing. However, despite these advances in modification identification, statistical methods for PTM-level quantification and differential analysis have yet to catch up. This absence can partly be explained by the inherently low abundance of many PTMs and the confounding of PTM intensities with its parent protein abundance.Therefore, we have developed msqrob2PTM, a new workflow in the msqrob2 universe capable of differential abundance analysis at the PTM, and at the peptidoform level. The latter is important for validating PTMs found as significantly differential. Indeed, as our method can deal with multiple PTMs per peptidoform, there is a possibility that significant PTMs stem from one significant peptidoform carrying another PTM, hinting that it might be the other PTM driving the perceived differential abundance.Our workflows can flag both Differential Peptidoform (PTM) Abundance (DPA) and Differential Peptidoform (PTM) Usage (DPU). This enables a distinction between direct assessment of differential abundance of peptidoforms (DPA) and differences in the relative usage of peptidoforms corrected for corresponding protein abundances (DPU). For DPA, we directly model the log2-transformed peptidoform (PTM) intensities, while for DPU, we correct for parent protein abundance by an intermediate normalisation step which calculates the log2-ratio of the peptidoform (PTM) intensities to their summarized parent protein intensities.We demonstrated the utility and performance of msqrob2PTM by applying it to datasets with known ground truth, as well as to biological PTM-rich datasets. Our results show that msqrob2PTM is on par with, or surpassing the performance of, the current state-of-the-art methods. Moreover, msqrob2PTM is currently unique in providing output at the peptidoform level.
The receptor binding domain of SARS-CoV-2 spike protein fused with the type IIbE. coliheat-labile enterotoxin A subunit as an intranasal booster after mRNA vaccination
Authors: Hsieh He-Chin , Chen Chung-Chu , Chou Pin-Han , Liu Wen-Chun , Wu Suh-Chin 
Published: July 2023

AbstractThe outbreak of SARS-CoV-2 infections had led to the COVID-19 pandemic which has a significant impact on global public health and the economy. The spike (S) protein of SARS-CoV-2 contains the receptor binding domain (RBD) which binds to human angiotensin-converting enzyme 2 receptor. Numerous RBD-based vaccines have been developed and recently focused on the induction of neutralizing antibodies against the immune evasive Omicron BQ.1.1 and XBB.1.5 subvariants. In this preclinical study, we reported the use of a direct fusion of the type IIbEscherichia coliheat-labile enterotoxin A subunit with SARS CoV-2 RBD protein (RBD-LTA) as an intranasal vaccine candidate. The results showed that intranasal immunization with the RBD-LTA fusion protein in BALB/c mice elicited potent neutralizing antibodies against the Wuhan-Hu-1 and several SARS-CoV-2 variants as well as the production of IgA antibodies in bronchoalveolar lavage fluids (BALFs). Furthermore, the RBD-LTA fusion protein was used as a second-dose booster after bivalent mRNA vaccination. The results showed that the neutralizing antibody titers elicited by the intranasal RBD-LTA booster were similar to the bivalent mRNA booster, but the RBD-specific IgA titers in sera and BALFs significantly increased. Overall, this preclinical study suggests that the RBD-LTA fusion protein could be a promising candidate as a mucosal booster COVID-19 vaccine.
Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome
Authors: Cozzolino Kira , Sanford Lynn , Hunter Samuel , Molison Kayla , Erickson Benjamin , Courvan Meaghan C.S. , Jones Taylor , Ajit Deepa , Galbraith Matthew D. , Espinosa Joaquin M. , Bentley David L. , Allen Mary A. , Dowell Robin D. , Taatjes Dylan J. 
Published: July 2023

AbstractHyperactive interferon (IFN) signaling is a hallmark of Down syndrome (DS), a condition caused by trisomy 21 (T21); strategies that normalize IFN signaling could benefit this population. Mediator-associated kinases CDK8 and CDK19 drive inflammatory responses through incompletely understood mechanisms. Using sibling-matched cell lines with/without T21, we investigated Mediator kinase function in the context of hyperactive IFN in DS over a 75min - 24h timeframe. Activation of IFN-response genes was suppressed in cells treated with the CDK8/CDK19 inhibitor cortistatin A (CA), via rapid suppression of IFN-responsive transcription factor (TF) activity. We also discovered that CDK8/CDK19 affect splicing, a novel means by which Mediator kinases control gene expression. To further probe Mediator kinase function, we completed cytokine screens and metabolomics experiments. Cytokines are master regulators of inflammatory responses; by screening 105 different cytokine proteins, we show that Mediator kinases help drive IFN-dependent cytokine responses at least in part through transcriptional regulation of cytokine genes and receptors. Metabolomics revealed that Mediator kinase inhibition altered core metabolic pathways in cell type-specific ways, and broad up-regulation of anti-inflammatory lipid mediators occurred specifically in kinase-inhibited cells during hyperactive IFNγ signaling. A subset of these lipids (e.g. oleamide, desmosterol) serve as ligands for nuclear receptors PPAR and LXR, and activation of these receptors occurred specifically during hyperactive IFN signaling in CA-treated cells, revealing mechanistic links between Mediator kinases, lipid metabolism, and nuclear receptor function. Collectively, our results establish CDK8/CDK19 as context-specific metabolic regulators, and reveal that these kinases control gene expression not only via TFs, but also through metabolic changes and splicing. Moreover, we establish that Mediator kinase inhibition antagonizes IFN signaling through transcriptional, metabolic, and cytokine responses, with implications for DS and other chronic inflammatory conditions.
Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis
Authors: von der Dunk Samuel H. A. , Hogeweg Paulien , Snel Berend 
Published: July 2023

AbstractThe complex eukaryotic cell resulted from a merger between simpler prokaryotic cells, yet the relative timing and the role of the mitochondrial endosymbiosis with respect to other eukaryotic innovations has remained under dispute. Although expansion of the regulatory repertoire has been inferred from phylogenetic studies, gene regulation has not been taken into account in current scenarios of the mitochondrial endosymbiosis which mostly focus on the complementary energetic and ecological perspectives. The endosymbiotic state introduced several unique challenges to cells such as coordination of host and symbiont cell cycles and its disruption by leaking gene products and DNA fragments between host and symbionts. To investigate how these unique challenges impacted genome and network evolution during eukaryogenesis, we study a constructive computational model where two simple cells are forced into an obligate endosymbiosis.Across multiplein silicoevolutionary replicates, we observe the emergence of different mechanisms for the coordination of host and symbiont cell cycles, stabilizing the endosymbiotic relationship. The most commonly evolved mechanism, implicit control, works without signaling between host and symbiont. Signaling only evolves under the influence of leaking gene products, while such regulatory interference is inherently harmful. In the fittest evolutionary replicate, the host controls the symbiont cell cycle entirely through signaling, mimicking the regulatory dominance of the nucleus over the mitochondrion that evolved during eukaryogenesis.
Theoretical principles explain the structure of the insect head direction circuit
Authors: Aceituno Pau Vilimelis , Dall’Osto Dominic , Pisokas Ioannis 
Published: July 2023

AbstractTo navigate their environment, insects need to keep track of their orientation. Previous work has shown that insects encode their head direction as a sinusoidal activity pattern around a ring of neurons arranged in an eight-column structure. However, it is unclear whether this sinusoidal encoding of head direction is just an evolutionary coincidence or if it offers a particular functional advantage. To address this question, we establish the basic mathematical requirements for direction encoding and show that it can be performed by many circuits, all with different activity patterns. Among these activity patterns, we prove that the sinusoidal one is the most noise-resilient, but only when coupled with a sinusoidal connectivity pattern between the encoding neurons. We compare this predicted optimal connectivity pattern with anatomical data from the head direction circuits of the locust and the fruit fly, finding that our theory agrees with experimental evidence. Furthermore, we demonstrate that our predicted circuit can emerge using Hebbian plasticity, implying that the neural connectivity does not need to be explicitly encoded in the genome of the insect but rather can emerge during development. Finally, we illustrate that in our theory, the consistent presence of the eight-column organisation of head direction circuits across multiple insect species is not a chance artefact but instead can be explained by basic evolutionary principles.
Dual targeting of hepatocyte DGAT2 and stellate cell FASN alleviates nonalcoholic steatohepatitis in mice
Authors: Yenilmez Batuhan , Harney Shauna , DiMarzio Chloe , Kelly Mark , Min Kyounghee , Echeverria Dimas , Bramato Brianna M. , Jackson Samuel O. , Reddig Keith , Kim Jason K. , Khvorova Anastasia , Czech Michael P. 
Published: July 2023

AbstractNonalcoholic steatohepatitis (NASH) is a malady of multiple cell types associated with hepatocyte triglyceride (TG) accumulation, macrophage inflammation, and stellate cell-induced fibrosis, with no approved therapeutics yet available. Here, we report that stellate cell fatty acid synthase (FASN) in de novo lipogenesis drives the autophagic flux that is required for stellate cell activation and fibrotic collagen production. Further, we employ a dual targeting approach to NASH that selectively depletes collagen through selective stellate cell knockout of FASN (using AAV9-LRAT Cre in FASNfl/flmice), while lowering hepatocyte triglyceride by depleting DGAT2 with a GalNac-conjugated, fully chemically modified siRNA. DGAT2 silencing in hepatocytes alone or in combination with stellate cell FASNKO reduced liver TG accumulation in a choline-deficient NASH mouse model, while FASNKO in hepatocytes alone (using AAV8-TBG Cre in FASNfl/flmice) did not. Neither hepatocyte DGAT2 silencing alone nor FASNKO in stellate cells alone decreased fibrosis (total collagen), while loss of both DGAT2 plus FASN caused a highly significant attenuation of NASH. These data establish proof of concept that dual targeting of DGAT2 plus FASN alleviates NASH progression in mice far greater than targeting either gene product alone.
Effects of sexual dimorphism and estrous cycle onC. difficileinfections in rodent models
Authors: Phan Jacqueline R. , Washington McKenzie , Do Dung M. , Mata Tiffany V. , Niamba Maria , Heredia Efren , Soriano Robert , Hassan Chandler , Cross Chad L. , Abel-Santos Ernesto 
Published: July 2023

AbstractClostridioides difficileinfection (CDI) is responsible for the majority of identifiable hospital-related antibiotic-associated diarrhea. Susceptibility to CDI and severity of disease varies depending on a variety of factors such as aggressive use of broad-spectrum antibiotics, age, and immune status. Epidemiological studies have consistently shown that female patients are more at risk for CDI than their male counterparts. In this study, we show that female mice developed more severe CDI than males when challenged with spores from three differentC. difficilestrains. CDI sexual dimorphism was still apparent when animals were placed under diet conditions that exacerbated CDI severity. Unlike male mice, females undergo the estrous cycle. Thus, female mice were challenged withC. difficilespores when they were at the estrus, metestrus, diestrus, late diestrus/early proestrus, proestrus, or late proestrus/early estrus stages. Animals were scored for CDI sign severity while continuously monitoring their estrous cycle stages. The resulting data showed a striking spike in CDI severity when animals were in proestrus the day before sign scoring. In contrast, animals who were in estrus the day before sign scoring were protected from CDI. Prophylactic treatment of CDI also showed sexual dimorphism with females responding better to treatment than males. Interestingly, infection sexual dimorphism was reversed in hamsters, with male hamsters developing more severe CDI signs than females. In conclusion, we have shown that mice recreate many of the conditions of sexual dimorphism of human CDI.
Missing-link fold reveals the evolutionary pathway between RNA polymerase and ribosomal proteins
Authors: Yagi Sota , Tagami Shunsuke 
Published: July 2023

AbstractNumerous molecular machines are required to drive the central dogma of molecular biology. However, the means by which such numerous proteins emerged in the early evolutionary stage of life remains enigmatic. Many of them possess small β-barrel folds with different topologies, represented by DPBB conserved in DNA and RNA polymerases, and RIFT, OB, and SH3 in ribosomal proteins. Here, we discovered that the previously reconstructed ancient DPBB sequence could also adopt a novel β-barrel fold named DZBB, which shares similarities with RIFT and OB. Indeed, DZBB could be transformed into them through simple engineering experiments. Furthermore, the OB designs could be converted into SH3 by circular-permutation. These results indicate that these β-barrels diversified quickly from a common ancestor at the beginning of the central dogma evolution.
Mycorrhizal symbiont provides growth benefits in host plants via phosphate and phenylpropanoid metabolism
Authors: Chen Cheng-Yen , Naqvi Naweed I. 
Published: July 2023

SummaryUsing functional interaction assays,Tinctoporellus speciesisolate AR8 was identified as a plant growth-promoting fungus from Arabidopsis roots.Confocal microscopy revealed interstitial growth and intracellular endophytic colonization within root cortex by AR8 hyphae prior to induction of beneficial effects.AR8 improved plant growth and fitness across a broad range of monocot and dicot host species. AR8 solubilized inorganic phosphate and enabled macronutrient phosphorus assimilation into the host plants, and the resultant growth promotion required an intact phosphate starvation response therein.Metabolomics analysis identified a highly specific subset of primary and secondary metabolites such as sugars, organic acids, sugar alcohols, amino acids, and phenylpropanoids, which were found to be essential for the plant growth-promoting activities of AR8.trans-Cinnamic acid was identified as a novel AR8-induced plant growth promoting metabolite.
Community-based volunteering in response to Covid-19: people, process and planning
Authors: MacInnes Julie , Jones Bridget , Frere-Smith Kat , Abrahamson Vanessa , Eida Tamsyn , Sharp Rebecca , Gage Heather , Wilson Patricia 
Published: July 2023

PurposeThe Covid-19 pandemic saw a dramatic rise in the number of people volunteering to support older people shielding at home. This study aimed to determine the processes by which volunteers were rapidly engaged in their communities and their impact on the older people who were supported and health and social care services.Design/methodology/approachThe study took place in South East England between May–August 2020. Semi-structured interviews were conducted with 88 participants including health and social care practitioners (n = 12), leaders of voluntary, community and social enterprise (VCSE) organisations (n = 25), volunteers (n = 26) and older people receiving volunteer support (n = 25). Policy and procedure documents were sourced from the VCSE organisation leaders. Data were analysed thematically according to a framework method.FindingsThe authors identified key themes of People, Process and Planning. People: volunteers had a significant, positive impact on older people in their communities, with volunteers themselves, also benefiting. Process: VCSE organisations needed to work together and with health and care providers to avoid gaps and duplication of services. VCSE organisations were able to act quickly, by-passing many complex operational procedures. However, there was a need to ensure the safety of both volunteers and older people. Planning: Looking forward, there were concerns about the long-term funding of VCSE organisations and the availability of volunteers.Originality/valueThis study took place during the first wave of the pandemic, hence, it provides a snapshot of how voluntary organisations operated at this time and highlights the importance of integration with health and care statutory services.
Gender balance in the workforce and abortion attitudes: A cross‐national time‐series analysis
Authors: Fernández Juan J. , Valiente Celia , Jaime‐Castillo Antonio M. 
Published: July 2023

AbstractThis article explores the relationship between gender balance in the workforce and attitudes towards abortion worldwide. Studies on macro‐level conditions related to abortion attitudes overlook the role of gender balance in the workforce—specifically the degree of female representation in a country's workforce. There are strong reasons why this factor could shape abortion attitudes. We argue that such a gender balance creates necessary conditions to break with traditional, anti‐abortion ideology and facilitates dissemination and public acceptance of pro‐choice views. We test this argument with two different datasets ‐ the Integrated Values Survey and three waves of the International Social Survey Programme—along with two outcomes: general tolerance towards abortion and tolerance towards abortion for pregnant women of low income. Using three‐level random intercept models and multiple controls for individual and country‐level conditions, the results support our hypothesis: In countries with higher gender balance in the workforce, individuals display higher tolerance towards abortion.