bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS
Authors: Mitchell David , Cotter Jennifer , Saleem Irfana , Mustoe Anthony M. 
Published: April 2023

ABSTRACTChemical probing experiments have transformed RNA structure analysis, enabling high-throughput measurement of base-pairing in living cells. Dimethyl sulfate (DMS) is one of the most widely used structure probing reagents and has played a prominent role in enabling next-generation single-molecule probing analyses. However, DMS has traditionally only been able to probe adenine and cytosine nucleobases. We previously showed that, using appropriate conditions, DMS can also be used to interrogate base-pairing of uracil and guaninesin vitroat reduced accuracy. However, DMS remained unable to informatively probe guanines in cells. Here, we develop an improved DMS mutational profiling (MaP) strategy that leverages the unique mutational signature of N1-methylguanine DMS modifications to enable robust, high-fidelity structure probing at all four nucleotides, including in cells. Using information theory, we show that four-base DMS reactivities convey greater structural information than comparable two-base DMS and SHAPE probing strategies. Four-base DMS experiments further enable improved direct base-pair detection by single-molecule PAIR analysis, and ultimately support RNA structure modeling at superior accuracy. Four-base DMS probing experiments are easily performed and will broadly facilitate improved RNA structural analysis in living cells.
Programmed ribosomal frameshifts, and how to find them
Authors: McNair Katelyn , Salamon Peter , Edwards Robert A. , Segall Anca M. 
Published: April 2023

AbstractOne of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a slippery sequence, shifting the ribosome into one of the other two alternate reading frames. The alternate frame has different codons, so different amino acids are added to the peptide chain, but more importantly, the original stop codon is no longer in-frame, so the ribosome can bypass the stop codon and continue to translate the codons past it. This produces a longer version of the protein, a fusion of the originalin-frameamino acids, followed by all the alternate frame amino acids. There is currently no automated software to predict the occurrence of these programmed ribosomal frameshifts (PRF), and they are currently only identified by manual curation. Here we present the first machine-learning based method to detect and predict the presence of PRFs in all types of coding genes and taxa with an accuracy exceding 90%.
Is neglect of self-clearance biassing TB vaccine impact estimates?
Authors: Scarponi Danny , Clark Rebecca A , Weerasuriya Chathika , Emery Jon C , Houben Rein MGJ , White Richard G , McCreesh Nicky 
Published: April 2023

AbstractBackgroundMathematical modelling has been used extensively to estimate the potential impact of new tuberculosis vaccines, with the majority of existing models assuming that individuals with Mycobacterium tuberculosis (Mtb) infection remain at lifelong risk of tuberculosis disease. Recent research provides evidence that self-clearance of Mtb infection may be common, which may affect the potential impact of new vaccines that only take in infected or uninfected individuals. We explored how the inclusion of self-clearance in models of tuberculosis affects the estimates of vaccine impact in China and India.MethodsFor both countries, we calibrated a tuberculosis model to a scenario without self-clearance and to various scenarios with self-clearance. To account for the current uncertainty in self-clearance properties, we varied the rate of self-clearance, and the level of protection against reinfection in self-cleared individuals. We introduced potential new vaccines in 2025, exploring vaccines that work in uninfected or infected individuals only, or that are effective regardless of infection status, and modelling scenarios with different levels of vaccine efficacy in self-cleared individuals. We then estimated the relative incidence reduction in 2050 for each vaccine compared to the no vaccination scenario.FindingsThe inclusion of self-clearance increased the estimated relative reductions in incidence in 2050 for vaccines effective only in uninfected individuals, by a maximum of 12% in China and 8% in India. The inclusion of self-clearance increased the estimated impact of vaccines only effective in infected individuals in some scenarios and decreased it in others, by a maximum of 14% in China and 15% in India. As would be expected, the inclusion of self-clearance had minimal impact on estimated reductions in incidence for vaccines that work regardless of infection status.InterpretationsOur work suggests that the neglect of self-clearance in mathematical models of tuberculosis vaccines does not result in substantially biased estimates of tuberculosis vaccine impact. It may, however, mean that we are slightly underestimating the relative advantages of vaccines that work in uninfected individuals only compared to those that work in infected individuals.
Qualitative evaluation of the use of modelling in resource allocation decisions for HIV and TB
Authors: Bowring Anna L , ten Brink Debra , Martin-Hughes Rowan , Fraser-Hurt Nicole , Cheikh Nejma , Scott Nick 
Published: April 2023

AbstractIntroductionGlobally, resources for health spending, including HIV and tuberculosis (TB), are constrained, and a substantial gap exists between spending and estimated needs. Optima is an allocative efficiency modeling tool that has been used since 2010 in over 50 settings to generate evidence for country-level HIV and TB resource allocation decisions. This evaluation assessed the utilization of modeling to inform financing priorities from the perspective of country stakeholders and their international partners.MethodsIn October-December 2021, the World Bank and Burnet Institute led 16 semi-structured small-group virtual interviews with 54 representatives from national governments and international health and funding organizations. Interviews probed participants’ roles and satisfaction with Optima analyses and how model findings have had been used and impacted resource allocation. Interviewed stakeholders represented nine countries and 11 different disease program-country contexts with prior Optima modeling analyses. Interview notes were thematically analyzed to assess factors influencing the utilization of modeling evidence in health policy and outcomes.ResultsCommon influences on utilization of Optima findings encompassed the perceived validity of findings, health system financing mechanisms, the extent of stakeholder participation in the modeling process, engagement of funding organization, socio-political context, and timeliness of the analysis. Utilizing workshops can facilitate effective stakeholder engagement and collaboration.Model findings were often used conceptually to localize global evidence and facilitate discussion. Secondary outputs included informing strategic and financial planning, funding advocacy, grant proposals, and influencing investment shifts.ConclusionAllocative efficiency modeling has supported evidence-informed decision making in numerous contexts and enhanced the conceptual and practical understanding of allocative efficiency. Most immediately, greater involvement of country stakeholders in modeling studies and timing studies to key strategic and financial planning decisions may increase the impact on decision making. Better consideration for integrated disease modeling, equity goals, and financing constraints may improve relevance and utilization of modeling findings.
Divergent pattern of development in rats and humans
Authors: campos Wanda , Iorri Tomas , Presti Antonella , Grimson Rafael , Vázquez-Borsetti Pablo 
Published: April 2023

AbstractRattus norvegicusis the second most used laboratory species and the most widely used model in neuroscience. Nonetheless, there is still no agreement regarding the temporal relationship of development between humans and rats. We addressed this question by examining the time required to reach a set of homologous developmental milestones in both species. With this purpose, a database was generated with data collected through a bibliographic survey. This database was in turn compared with other databases about the same topic present in the literature. Finally, the databases were combined, covering for the first time the entire development of the rat including the prenatal, perinatal, and postnatal periods. This combined database includes 497 individual dates for both species. The developmental relationship between humans and rats was better fit by a logarithmic function than by a linear function. Also, an inflection point close to birth becomes evident after the logarithmic transformation of the data. The predictions of the proposed model were compared with other estimators historically used to calculate developmental relationships, such as growth in brain weight, finding a notorious discrepancy. As development progresses, an increase in the dispersion of the data is observed. Until now, developmental relationships have been interpreted as a univocal equivalence. In this work, is proposed an alternative interpretation where the age of one species is translated into a range of ages in the other.
A Shared Pathogenic Mechanism for Valproic Acid and SHROOM3 Knockout in a Brain Organoid Model of Neural Tube Defects
Authors: Takla Taylor N. , Luo Jinghui , Sudyk Roksolana , Huang Joy , Walker J. Clayton , Vora Neeta L. , Sexton Jonathan Z. , Parent Jack M. , Tidball Andrew M. 
Published: April 2023

ABSTRACTNeural tube defects (NTDs) including anencephaly and spina bifida are common major malformations of fetal development resulting from incomplete closure of the neural tube. These conditions lead to either universal death (anencephaly) or life-long severe complications (spina bifida). Despite hundreds of genetic mouse models having neural tube defect phenotypes, the genetics of human NTDs are poorly understood. Furthermore, pharmaceuticals such as antiseizure medications have been found clinically to increase the risk of NTDs when administered during pregnancy. Therefore, a model that recapitulates human neurodevelopment would be of immense benefit to understand the genetics underlying NTDs and identify teratogenic mechanisms. Using our self-organizing single rosette spheroid (SOSRS) brain organoid system, we have developed a high-throughput image analysis pipeline for evaluating SOSRS structure for NTD-like phenotypes. Similar to small molecule inhibition of apical constriction, the antiseizure medication valproic acid (VPA), a known cause of NTDs, increases the apical lumen size and apical cell surface area in a dose-responsive manner. This expansion was mimicked by GSK3β and HDAC inhibitors; however, RNA sequencing suggests VPA does not inhibit GSK3β at these concentrations. Knockout of SHROOM3, a well-known NTD-related gene, also caused expansion of the lumen as well as reduced f-actin polarization. The increased lumen sizes were caused by reduced cell apical constriction suggesting that impingement of this process is a shared mechanism for VPA treatment and SHROOM3-KO, two well-known causes of NTDs. Our system allows the rapid identification of NTD-like phenotypes for both compounds and genetic variants and should prove useful for understanding specific NTD mechanisms and predicting drug teratogenicity.
Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes
Authors: Zhou Xinrui , Seow Wan Yi , Ha Norbert , Cheng Teh How , Lingfan Jiang , Boonruangkan Jeeranan , Goh Jolene Jie Lin , Prabhakar Shyam , Chou Nigel , Chen Kok Hao 
Published: April 2023

AbstractHigh-dimensional, spatially resolved analysis of intact tissue samples promises to transform biomedical research and diagnostics, but existing spatial omics technologies are costly and labor-intensive. We present FISHnCHIPs for highly sensitivein situprofiling of cell types and gene expression programs. FISHnCHIPs achieves this by simultaneously imaging ∼2-35 co-expressed genes that are spatially co-localized in tissues, resulting in similar spatial information as single-gene FISH, but at ∼2-20-fold higher sensitivity. Using FISHnCHIPs, we imaged up to 53 gene modules from the mouse kidney and mouse brain, and demonstrated high-speed, large field-of-view profiling of a whole tissue section. FISHnCHIPS also revealed spatially restricted localizations of cancer-associated fibroblasts in a human colorectal cancer biopsy. Overall, FISHnCHIPs enables robust and scalable spatial transcriptomics analysis of tissues with normal physiology or undergoing pathogenesis.
A Gene-expression Module Identifies Circulating Immune Cells with Enhanced Recruitment to Sites of Inflammation
Authors: Sinha Debajyoti , Laurent Thomas , Broquet Alexis , Fourgeux Cynthia , Letellier Thibault , Tilly Gaelle , Bruneau Sarah , Ville Simon , Bouchet-Delbos Laurence , Brancherau Julien , Kerleau Clarisse , Brouard Sophie , Blancho Gilles , Giral Magali , Josien Regis , Danger Richard , Roquilly Antoine , Degauque Nicolas , Poschmann Jeremie 
Published: April 2023

AbstractCirculating immune cells are critical mediators of inflammation upon recruitment to tissues, yet how their gene expression state influences this recruitment is not well understood. Here, we report longitudinal single-cell transcriptome profiling of peripheral blood mononuclear cells in patients undergoing kidney transplantation rejection. We identify a novel gene expression module, termed ALARM (early activation transcription factor module), associated with transcriptional regulation, homing, and immune activation across multiple immune cell types. Circulating cells expressing this module are significantly reduced in patients experiencing graft rejection, a finding confirmed in a pig model of acute kidney transplantation rejection. Correspondingly, module expression is markedly increased in kidney grafts undergoing rejection, indicating preferential recruitment of ALARM-expressing cells to the inflamed tissue.Within this module, we identify the receptor CXCR4 and its ligand CXCL12, expressed in the graft, as a likely mechanism for recruitment. In vitro transwell assays combined with scRNA-seq reveal that this CXCR4-CXCL12 interaction is critical for T cell migration and upregulation of CD69, an early activation marker, and is accompanied by a metabolic switch towards glycolysis. Further exploration of publicly available transcriptomic data demonstrates that this module is generally expressed in healthy individuals and is strongly associated with responses to infection, including SARS-CoV-2 infection. This finding is further supported by experiments in a pneumonia mouse model, which confirm the recruitment of CXCR4-expressing T cells during lung infection. Moreover, we find that module expression is predictive of immune-mediated diseases.In summary, we have identified a key gene expression module in circulating immune cells that orchestrates their preferential recruitment to inflamed tissues, metabolic reprogramming, promoting tissue residency and effector functions. These insights advance our understanding of immune cell recruitment and activation mechanisms in transplant rejection and infectious diseases, with potential implications for therapeutic interventions.
Dimerisation of European robin cryptochrome 4a
Authors: Hanić Maja , Antill Lewis M. , Gehrckens Angela S. , Schmidt Jessica , Görtemaker Katharina , Bartölke Rabea , El-Baba Tarick J. , Xu Jingjing , Koch Karl W. , Mouritsen Henrik , Benesch Justin L. P. , Hore P. J. , Solov’yov Ilia A. 
Published: April 2023

AbstractHomo-dimer formation is important for the function of many proteins. Although dimeric forms of cryptochromes (Cry) have been found by crystallography and were recently observedin vitrofor European robin Cry4a, little is known about the dimerisation of avian cryptochromes and the role it could play in the mechanism of magnetic sensing in migratory birds. Here we present a combined experimental and computational investigation of the dimerisation of robin Cry4a resulting from covalent and non-covalent interactions. Experimental studies using native mass spectrometry, mass spectrometric analysis of disulphide bonds, chemical cross-linking and photometric measurements show that disulphide-linked dimers are routinely formed, the most likely cysteines being C317 and C412. Computational modelling and molecular dynamics simulations were used to generate and assess a number of possible dimer structures. The relevance of these findings to the proposed role of Cry4a in avian magnetoreception is discussed.
Identification of microbial communities and their removal efficiency of multiple pharmaceutical micropollutants combined in Membrane-Bioreactors
Authors: Suleiman Marcel , Demaria Francesca , Zimmardi Cristina , Kolvenbach Boris , Corvini Philippe 
Published: April 2023

AbstractPharmaceuticals are of concern to our planet and health as they can accumulate in the environment. The impact of these biologically active compounds on ecosystems is hard to predict and information on their biodegradation is necessary to establish sound risk assessment. Microbial communities are promising candidates for the biodegradation of pharmaceuticals such as ibuprofen, but little is known yet about their degradation-capacity of multiple micropollutants at higher concentrations (100 mg/L). In this work, microbial communities were cultivated in lab-scale Membrane Bioreactors (MBRs) exposed to increasing concentrations of a mixture of six micropollutants (ibuprofen, diclofenac, enalapril, caffeine, atenolol, paracetamol). Key players of biodegradation were identified using a combinatorial approach of 16S rRNA sequencing and analytics. Microbial community structure changed with increasing pharmaceutical intake (from 1 mg/L to 100 mg/L) and reached a steady-state during incubation for 7 weeks on 100 mg/L. HPLC analysis revealed a fluctuating but significant degradation (30-100%) of five pollutants (caffeine, paracetamol, ibuprofen, atenolol, enalapril) by an established and stable microbial community mainly composed ofAchromobacter,Cupriavidus,PseudomonasandLeucobacter. By using the microbial community from MBR1 as inoculum for further batch culture experiments on single micropollutants (400 mg/L substrate, respectively), different active microbial consortia were obtained for each single micropollutant. Microbial genera potentially responsible for degradation of the respective micropollutant were identified, i.e.Pseudomonassp. andSphingobacteriumsp. for ibuprofen, caffeine and paracetamol,Sphingomonassp. for atenolol, andKlebsiellasp. for enalapril. Our study demonstrates the feasibility of cultivating stable microbial communities capable of degrading simultaneously a mixture of highly concentrated pharmaceuticals in lab-scale MBRs and the identification of microbial genera potentially responsible for the degradation of specific pollutants.Graphical abstract
Physical interaction between MSL2 and CLAMP assures direct co-operativity and prevents competition at composite binding sites
Authors: Eggers Nikolas , Gkountromichos Fotios , Krause Silke , Campos-Sparr Aline , Becker Peter B. 
Published: April 2023

AbstractMSL2, the DNA-binding subunit of theDrosophiladosage compensation complex, cooperates with the ubiquitous protein CLAMP to bind MSL recognition elements (MREs) on the X chromosome. We explore the nature of the cooperative binding to these GA-rich, composite se-quence elements in reconstituted naïve embryonic chromatin.We found that the cooperativity requires physical interaction between both proteins. Remarkably, disruption of this interaction does not lead to indirect, nucleosome-mediated cooperativity as expected, but to competition. The protein interaction apparently not only increases the affinity for composite binding sites, but also locks both proteins in a defined dimeric state that prevents competition.High Affinity Sites of MSL2 on the X chromosome contain variable numbers of MREs. We find that the cooperation between MSL2/CLAMP is not influenced by MRE clustering or arrangement, but happens largely at the level of individual MREs.The sites where MSL2/CLAMP bind stronglyin vitrolocate to all chromosomes and show little overlap to an expanded set of X-chromosomal MSL2in vivobinding sites generated by CUT&RUN. Apparently, the intrinsic MSL2/CLAMP cooperativity is limited to a small selection of potential sitesin vivo. This restriction must be due to components missing in our reconstitution, such asroX2lncRNA.
Differential Expression of 5’-tRNA Fragments in Circulating Preeclampsia Syncytiotrophoblast Vesicles Drives Macrophage Inflammation
Authors: Cooke William Robert , Jiang Peiyong , Ji Lu , Bai Jinyue , Jones Gabriel Davis , Lo Y. M. Dennis , Redman Christopher , Vatish Manu 
Published: April 2023

AbstractBackgroundThe relationship between placental pathology and the maternal syndrome of preeclampsia is incompletely characterised. Mismatch between placental nutrient supply and fetal demands induces stress in the syncytiotrophoblast, the layer of placenta in direct contact with maternal blood. Such stress alters the content and increases the release of extracellular vesicles (STB-EVs) into the maternal circulation. We have previously shown 5’-tRNA fragments (5’-tRFs) constitute the majority of small RNA in STB-EVs in healthy pregnancy. 5’-tRFs are produced in response to stress. We hypothesised STB-EV 5’-tRF release might change in preeclampsia.MethodsWe perfused placentas from eight women with early-onset preeclampsia and six controls, comparing small RNA expression in STB-EVs. We used membrane-affinity columns to isolate maternal plasma vesicles and investigate placental 5’-tRFsin-vivo. We quantified 5’-tRFs from circulating STB-EVs using a placental alkaline phosphatase immunoassay. 5’-tRFs and scrambled RNA controls were added to monocyte, macrophage and endothelial cells in culture to investigate transcriptional responses.Results5’-tRFs constitute the majority of small RNA in STB-EVs from both preeclampsia and normal pregnancies. >900 small RNA fragments are differentially expressed in preeclampsia STB-EVs. Preeclampsia-dysregulated 5’-tRFs are detectable in maternal plasma, where we identified a placentally-derived load. 5’-tRF-Glu-CTC, the most abundant preeclampsia-upregulated 5’-tRF in perfusion STB-EVs, is also increased in preeclampsia STB-EVs from maternal plasma. 5’-tRF-Glu-CTC induced inflammation in macrophages but not monocytes. The conditioned media from 5’’-tRF-Glu-CTC-activated macrophages reduced eNOS expression in endothelial cells.ConclusionsIncreased release of syncytiotrophoblast-derived vesicle-bound 5’-tRF-Glu-CTC contributes to preeclampsia pathophysiology.