bluuebunny/crossref_metadata_2025_split huggingface dataset:
pGpG-signaling regulates virulence and global transcriptomic targets inErwinia amylovora
Authors: Kharadi Roshni R. , Hsueh Brian Y. , Waters Christopher M. , Sundin George W. 
Published: January 2024

AbstractCyclic-di-GMP (c-di-GMP) is a critical bacterial second messenger that enables the physiological phase transition inErwinia amylovora, the phytopathogenic bacterium that causes fire blight disease. C-di-GMP generation is dependent on diguanylate cyclase enzymes while the degradation of c-di-GMP can occur through the action of phosphodiesterase (PDE) enzymes that contain an active EAL and/or a HD-GYP domain. The HD-GYP-type PDEs, which are absent inE. amylovora, can directly degrade c-di-GMP into two GMP molecules. PDEs that contain an active EAL domain, as found in all active PDEs inE. amylovora,degrade c-di-GMP into pGpG. The signaling function of pGpG is not fully understood in bacterial systems. A transcriptomic approach revealed that elevated levels of pGpG inE. amylovoraimpacted several genes involved in metabolic and regulatory functions including several type III secretion and extracellular appendage related genes. The heterologous overexpression of an EAL or HD-GYP-type PDE in different backgroundE. amylovorastrains with varying c-di-GMP levels revealed that in contrast to the generation of pGpG, the direct breakdown of c-di-GMP into GMP by the HD-GYP-type PDE led to an elevation in amylovoran production and biofilm formation despite a decrease in c-di-GMP levels. The breakdown of c-di-GMP into pGpG (as opposed to GTP) also led to a decrease in virulence in apple shoots. The expression ofhrpSwas significantly increased in response to the breakdown of c-di-GMP into pGpG. Further, our model suggests that a balance in the intracellular ratio of pGpG and c-di-GMP is essential for biofilm regulation inE. amylovora.Importancec-di-GMP is the keystone molecule for regulating the transition from motility to biofilm formation in most bacteria. Interestingly, there are two distinct enzymatic phosphodiesterase (PDE) domains, termed EAL and HD-GYP, that degrade c-di-GMP. EAL domains cleave one bond of the cyclic ring to generate pGpG while HD-GYP enzymes cleave c-di-GMP to two GMP molecules. A central question regarding c-di-GMP signaling is has whether or not pGpG itself functions as a signaling molecule. Here we demonstrate in the plant pathogenErwinia amylovorathat pGpG specifically regulates genes and contributes to biofilm formation and disease progression.
A Cytological F1 RNAi Screen for Defects inDrosophila melanogasterFemale Meiosis
Authors: Gilliland William D. , May Dennis P. , Bowen Amelia O. , Conger Kelly O. , Elrad Doreen , Marciniak Marcin , Mashburn Sarah A. , Presbitero Gabrielle , Welk Lucas F. 
Published: January 2024

AbstractGenetic screens for recessive alleles induce mutations, make the mutated chromosomes homozygous, and then assay those homozygotes for the phenotype of interest. When screening for genes required for female meiosis, the phenotype of interest has typically been nondisjunction from chromosome segregation errors. As this requires that mutant females be viable and fertile, any mutants that are lethal or sterile when homozygous cannot be recovered by this approach. To overcome these limitations, our lab has screened the VALIUM22 collection produced by the Harvard TRiP Project, which contains RNAi constructs targeting genes known to be expressed in the germline in a vector optimized for germline expression. By driving RNAi with GAL4 under control of a germline-specific promoter (nanosormat-alpha4), we can test genes that would be lethal if knocked down in all cells, and by examining unfertilized metaphase-arrested mature oocytes, we can identify defects associated with genes whose knockdown results in sterility or causes other errors besides nondisjunction.We screened this collection to identify genes that disrupt either of two phenotypes when knocked down: the ability of meiotic chromosomes to congress to a single mass at the end of prometaphase, and the sequestration of Mps1-GFP to ooplasmic filaments in response to hypoxia. After screening >1450 lines of the collection, we obtained multiple hits for both phenotypes, identified novel meiotic phenotypes for genes that had been previously characterized in other processes, and identified the first phenotypes to be associated with several previously uncharacterized genes.
Venturicidin A affects the mitochondrial membrane potential and induces kDNA loss inTrypanosoma brucei
Authors: Hauser Dennis , Kaiser Marcel , Mäser Pascal , Albisetti Anna 
Published: January 2024

AbstractNeglected tropical diseases caused by trypanosomatid parasites have devastating health and economic consequences, especially in tropical areas. New drugs or new combination therapies to fight these parasites are urgently needed. Venturicidin A, a macrolide extracted fromStreptomyces, inhibits the ATP synthase complex of fungi and bacteria. However, its effect on trypanosomatids is not fully understood. In this study, we tested venturicidin A on a panel of trypanosomatid parasites using Alamar Blue assays and found it to be highly active againstTrypanosoma bruceiandLeishmania donovani, but much less so againstTrypanosoma evansi. Using fluorescence microscopy we observed a rapid loss of the mitochondrial membrane potential inT. bruceibloodstream forms upon venturicidin A treatment. Additionally, we report the loss of the mitochondrial DNA in approximately 40 to 50% of the treated parasites. We conclude that venturicidin A targets the ATP synthase ofT. brucei, and we suggest that this macrolide could be a candidate for antitrypanosomatid drug repurposing, drug combinations, or medicinal chemistry programs.
Fluorescence Lifetime Imaging for Quantification of Targeted Drug Delivery in Varying Tumor Microenvironments
Authors: Verma Amit , Pandey Vikas , Sherry Catherine , James Christopher , Matteson Kailie , Smith Jason T. , Rudkouskaya Alena , Intes Xavier , Barroso Margarida 
Published: January 2024

ABSTRACTRationaleTrastuzumab (TZM) is a monoclonal antibody that targets the human epidermal growth factor receptor (HER2) and is clinically used for the treatment of HER2-positive breast tumors. However, the tumor microenvironment can limit the access of TZM to the HER2 targets across the whole tumor and thereby compromise TZM’s therapeutic efficacy. An imaging methodology that can non-invasively quantify the binding of TZM-HER2, which is required for therapeutic action, and distribution within tumors with varying tumor microenvironments is much needed.MethodsWe performed near-infrared (NIR) fluorescence lifetime (FLI) Forster Resonance Energy Transfer (FRET) to measure TZM-HER2 binding, usingin vitromicroscopy andin vivowidefield macroscopy, in HER2 overexpressing breast and ovarian cancer cells and tumor xenografts, respectively. Immunohistochemistry was used to validatein vivoimaging results.ResultsNIR FLI FRETin vitromicroscopy data show variations in intracellular distribution of bound TZM in HER2-positive breast AU565 and AU565 tumor-passaged XTM cell lines in comparison to SKOV-3 ovarian cancer cells. Macroscopy FLI (MFLI) FRETin vivoimaging data show that SKOV-3 tumors display reduced TZM binding compared to AU565 and XTM tumors, as validated byex vivoimmunohistochemistry. Moreover, AU565/XTM and SKOV-3 tumor xenografts display different amounts and distributions of TME components, such as collagen and vascularity. Therefore, these results suggest that SKOV-3 tumors are refractory to TZM delivery due to their disrupted vasculature and increased collagen content.ConclusionOur study demonstrates that FLI is a powerful analytical tool to monitor the delivery of antibody drug tumor both in cell cultures and in vivo live systems. Especially, MFLI FRET is a unique imaging modality that can directly quantify target engagement with potential to elucidate the role of the TME in drug delivery efficacy in intact live tumor xenografts.
Comparing DOACs with warfarin in AF patients with chronic kidney disease or valvular disease: A systematic review and meta-analysis
Authors: Liang Aileen , Wang Cathy , Iansavichene Alla E , Lazo-Langner Alejandro 
Published: January 2024

AbstractObjectiveTo analyze the safety and efficacy of different direct oral anticoagulant agents (DOACs) compared to warfarin in patients with concomitant atrial fibrillation (AF) and valvular disease or concomitant AF and chronic kidney disease (CKD).MethodsWe conducted literature searches in MEDLINE, Embase, and EBM Reviews to examine randomized-controlled trials (RCTs) and non-RCTs that included the aforementioned patient populations treated with warfarin or DOAC (rivaroxaban, dabigatran, apixaban, or edoxaban) and assessed outcomes of bleeding, stroke, or systemic/arterial thromboembolism. Meta-analysis was performed for eligible studies using the Mantel-Haenszel method random-effects model.Results3,172 studies were screened and 154 studies were selected after two levels of screening. Meta-analysis showed that, in patients with concomitant AF and CKD, DOAC was associated with reduced bleeding in non-RCTs (OR 0.65, 95% Cl [0.49, 0.86], p=0.003), particularly in more severe CKD (eGFR < 60mL/min/1.73m2). Apixaban in particular was associated with reduced bleeding (OR 0.52, 95% Cl [0.44, 0.63], p<0.00001) and stroke incidence (OR 0.60, 95% Cl [0.41, 0.87], p=0.007). In patients with concomitant AF and valvular disease, DOAC was associated with reduced bleeding (OR 0.75, 95% CI [0.57, 0.97], p=0.03) and stroke incidence (OR 0.66, 95% CI [0.47, 0.93], p=0.02) in non-RCTs.ConclusionOur study studied populations that are typically excluded from large-scale anticoagulation studies and our findings suggest that DOACs may be superior to warfarin both in the prevention of thromboembolic event and in the reduction of bleeding risks in patients with concomitant CKD or valvular disease.
Somatic mutations in Alzheimer-associated tetraploid neurons
Authors: López-Sánchez Noelia , Rábano Alberto , Frade José M. 
Published: January 2024

AbstractAn early pathological process affecting the brain of Alzheimer’s disease (AD) is the reactivation of the cell cycle in neurons followed by somatic neuronal tetraploidization (NT). NT also increases with age, and ageing has been shown to correlate with the accumulation of DNA somatic mutations. In this study, we have evaluated the presence of somatic mutations including single nucleotide variants (SNVs) and indels in genomic DNA from tetraploid neurons obtained from the parietal cortex of AD patients, compared with diploid neurons from control individuals and AD patients. Here we show that, in contrast to somatic indels, the proportion of somatic SNVs (sSNVs) significantly increases in the exome of tetraploid neurons, having increased levels of T to C (A to G) transitions, a type of mutation that is associated with oxidative stress. This finding correlates with the over-representation of sSNVs in genes involved in oxidative stress response and DNA repair, suggesting that these alterations exacerbate oxidative DNA damage in tetraploid neurons. sSNVs affecting cancer-related (CR) genes showed a greater molecular pathogenicity score compared with those from a random sample of genes. We propose that neuronal tetraploidy is stochastically triggered through a CR mechanism in neurons whose DNA repair genes become mutated in an oxidative stress scenario. This mechanism likely participates in the etiology of AD.
Testing microbial biomining from asteroidal material onboard the International Space Station
Authors: Santomartino Rosa , Blanco Giovanny Rodriguez , Gudgeon Alfred , Hafner Jason , Stirpe Alessandro , Waterfall Martin , Cayzer Nicola , Pichevin Laetitia , Calder Gus , Birkenfeld Kyra R. , Waajen Annemiek C. , McLaughlin Scott , Mariani Alessandro , Balsamo Michele , Neri Gianluca , Eades Lorna J. , Cockell Charles S. 
Published: January 2024

AbstractExpanding human space exploration beyond Earth’s orbit necessitates efficient technologies for self-sustainable acquisition of local resources to overcome unviable resupply missions from Earth. Potential source of materials are asteroids, some of which contain valuable metals, such as platinum group elements.The BioAsteroid experiment, performed onboard the International Space Station, tested the use of microorganisms (bacteria and fungi) to carry out mining of useful elements from asteroidal material (L-chondrite) under microgravity, in support of a long-term human presence in space. The fungusPenicillium simplicissimum, enhanced the mean release of palladium, platinum and other elements from the meteorite material in microgravity, compared to non-biological leaching. However, there was large variability in the results. For many elements, non-biological leaching under microgravity was enhanced compared to terrestrial gravity, while bioleaching was unaffected. Metabolomics results revealed clear patterns that highlight the influence of space conditions on the microbial metabolism, particularly forP. simplicissimum. We identified the presence of carboxylic acids, and molecules of potential biomining and pharmaceutical interest, enhanced in microgravity.These results show a non-trivial effect of microgravity on bioleaching, highlighting the requirement of an optimal combination of microorganism(s), rock substrate, and conditions for successful biomining, both in space and Earth.
Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems
Authors: Giannantoni Leonardo , Bardini Roberta , Savino Alessandro , Di Carlo Stefano 
Published: January 2024

AbstractBackgroundThe Biology System Description Language (BiSDL) is an accessible, easy-to-use computational language for multicellular synthetic biology. It allows synthetic biologists to represent spatiality and multi-level cellular dynamics inherent to multicellular designs, filling a gap in the state of the art. Developed for designing and simulating spatial, multicellular synthetic biological systems, BiSDL integrates high-level conceptual design with detailed low-level modeling, fostering collaboration in the Design-Build-Test-Learn cycle. BiSDL descriptions directly compile into Nets-Within-Nets (NWNs) models, offering a unique approach to spatial and hierarchical modeling in biological systems.ResultsBiSDL’s effectiveness is showcased through three case studies on complex multicellular systems: a bacterial consortium, a synthetic morphogen system and a conjugative plasmid transfer process. These studies highlight the BiSDL proficiency in representing spatial interactions and multi-level cellular dynamics. The language facilitates the compilation of conceptual designs into detailed, simulatable models, leveraging the NWNs formalism. This enables intuitive modeling of complex biological systems, making advanced computational tools more accessible to a broader range of researchers.ConclusionsBiSDL represents a significant step forward in computational languages for synthetic biology, providing a sophisticated yet user-friendly tool for designing and simulating complex biological systems with an emphasis on spatiality and cellular dynamics. Its introduction has the potential to transform research and development in synthetic biology, allowing for deeper insights and novel applications in understanding and manipulating multicellular systems.
Death Incidents Following Transcatheter Edge-to-Edge Repair (TEER) With the MitraClip Device: Analysis of 10-years Post-marketing Death Reports from the Manufacturer and User Facility Device Experience (MAUDE) Registry
Authors: Sun Xing-he , Zhao Yi-fei , Li Yan 
Published: January 2024

AbstractBackgroundThe MitraClip device (Abbott), an FDA-approved transcatheter apparatus, is employed for the management of mitral regurgitation (MR) among patients deemed at high risk for surgical interventions. We analyzed reports in the FDA MAUDE database to evaluate the safety trend in fatal complications associated with MitraClip implantation in the last decade.MethodsWe searched the publicly accessible Manufacturer and User Facility Device Experience (MAUDE) database for reports of deaths and injuries associated with MitraClip implantation from October 2013 to September 2023. Duplicate reports were excluded. The Cochran-Armitage test was used to analyze the trend in proportion of fatal events.ResultsIn the 10 year period after FDA approval, a total of 927 death reports and 9211 injury reports were recorded by the MAUDE database. 592 death reports were included for analysis after excluding duplicates and reports from other sources. The most frequently reported complications were MR (26.69%), tissue damage (24.16%) and hypotension (22.13% ). The most common device-related problems were incomplete coaptation (14.70%), difficult to remove (6.42%), and failure to adhere or bond/positioning failure(4.90%). Most deaths (76.94%) occurred within one year of implantation. The proportion of reported fatal events showed a significant declining trend from 15.9% in 2014-2015 to 3.5% in 2020-2021 (p<0.0001).ConclusionsAnalysis of the MAUDE database suggests a decline in reported fatal events associated with MitraClip implantation over time, which may reflect increasing experience with the device. However, passive reporting has limitations including underreporting and incomplete data. Further studies are needed to better characterize the safety profile and complication rates of MitraClip implantation in real-world practice.
Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape
Authors: Santinello B , Sun R , Amjad A , Hoyt SJ , Ouyang L , Courret C , Drennan R , Leo L , Larracuente AM , Core L , O’Neill RJ , Mellone BG 
Published: January 2024

AbstractCentromeres depend on chromatin containing the conserved histone H3 variant CENP-A for function and inheritance, while the role of centromeric DNA repeats remains unclear. Retroelements are prevalent at centromeres across taxa and represent a potential mechanism for promoting transcription to aid in CENP-A incorporation or for generating RNA transcripts to maintain centromere integrity. Here, we probe into the transcription and RNA localization of the centromere-enriched retroelementG2/Jockey-3(hereafter referred to asJockey-3) inDrosophila melanogaster, currently the onlyin vivomodel with assembled centromeres. We find thatJockey-3is a major component of the centromeric transcriptome and produces RNAs that localize to centromeres in metaphase. Leveraging the polymorphism ofJockey-3and ade novocentromere system, we show that these RNAs remain associated with their cognate DNA sequences incis, suggesting they are unlikely to perform a sequence-specific function at all centromeres. We show thatJockey-3transcription is positively correlated with the presence of CENP-A, and that recentJockey-3transposition events have occurred preferentially at CENP-A-containing chromatin. We propose thatJockey-3contributes to the epigenetic maintenance of centromeres by promoting chromatin transcription, while inserting preferentially within these regions, selfishly ensuring its continued expression and transmission. Given the conservation of retroelements as centromere components through evolution, our findings have broad implications in understanding this association in other species.
Multi-condensate state as a functional strategy to optimize the cell signaling output
Authors: Chattaraj Aniruddha , Shakhnovich Eugene I 
Published: January 2024

AbstractThe existence of multiple biomolecular condensates inside living cells is a peculiar phenomenon not compatible with the predictions of equilibrium statistical mechanics. In this work, we address the problem of multiple condensates state (MCS) from a functional perspective. We combined Langevin dynamics, reaction-diffusion simulation, and dynamical systems theory to demonstrate that MCS can indeed be a function optimization strategy. Using Arp2/3 mediated actin nucleation pathway as an example, we show that actin polymerization is maximum at an optimal number of condensates. For a fixed amount of Arp2/3, MCS produces a greater response compared to its single condensate counterpart. Our analysis reveals the functional significance of the condensate size distribution which can be mapped to the recent experimental findings. Given the spatial heterogeneity within condensates and non-linear nature of intracellular networks, we envision MCS to be a generic functional solution, so that structures of network motifs may have evolved to accommodate such configurations.
Deciphering the co-evolutionary dynamics of L2 β-lactamases via Deep learning
Authors: Zhu Yu , Gu Jing , Zhao Zhuoran , Chan A W Edith , Mojica Maria F. , Hujer Andrea M. , Bonomo Robert A. , Haider Shozeb 
Published: January 2024

AbstractL2 β-lactamases, a serine-based class A β-lactamases expressed byStenotrophomonas maltophiliaplays a pivotal role in antimicrobial resistance. However, limited studies have been conducted on these important enzymes. To understand the co-evolutionary dynamics of L2 β-lactamase, innovative computational methodologies, including adaptive sampling molecular dynamics simulations, and deep learning methods (convolutional variational autoencoders and BindSiteS-CNN) explored conformational changes and correlations within the L2 β-lactamase family together with other representative class A enzymes including SME-1 and KPC-2. This work also investigated the potential role of hydrophobic nodes and binding site residues in facilitating the functional mechanisms. The convergence of analytical approaches utilized in this effort yielded comprehensive insights into the dynamic behaviour of the β-lactamases, specifically from an evolutionary standpoint. In addition, this analysis presents a promising approach for understanding how the class A β-lactamases evolve in response to environmental pressure and establishes a theoretical foundation for forthcoming endeavours in drug development aimed at combating antimicrobial resistance.SynopsisDeep learning is used to reveal the dynamic co-evolutionary patterns of L2 β-lactamases.Analysis of hydrophobic nodes and binding site residues provides a detailed understanding of both local and global dynamic evolution, which explain the functional divergences.The employment of two distinct deep learning models, the Convolutional Variational Autoencoder (CVAE) and BindSiteS-CNN, facilitates the investigation of conformational shifts, thereby depicting the dynamic evolution of L2 β-lactamases.The effectiveness of CVAE and BindSiteS-CNN in dynamic classification is corroborated with selected features.Abstract Figure