bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and assessment of a machine learning tool for predicting emergency admission in Scotland
Authors: Liley James , Bohner Gergo , Emerson Samuel R. , Mateen Bilal A. , Borland Katie , Carr David , Heald Scott , Oduro Samuel D. , Ireland Jill , Moffat Keith , Porteous Rachel , Riddell Stephen , Rogers Simon , Thoma Ioanna , Cunningham Nathan , Holmes Chris , Payne Katrina , Vollmer Sebastian J. , Vallejos Catalina A. , Aslett Louis J. M.
Published: August 2021

Emergency admissions (EA), where a patient requires urgent in-hospital care, are a major challenge for healthcare systems. The development of risk prediction models can partly alleviate this problem by supporting primary care interventions and public health planning. Here, we introduce SPARRAv4, a predictive score for EA risk that will be deployed nationwide in Scotland. SPARRAv4 was derived using supervised and unsupervised machine-learning methods applied to routinely collected electronic health records from approximately 4.8M Scottish residents (2013-18). We demonstrate improvements in discrimination and calibration with respect to previous scores deployed in Scotland, as well as stability over a 3-year timeframe. Our analysis also provides insights about the epidemiology of EA risk in Scotland, by studying predictive performance across different population sub-groups and reasons for admission, as well as by quantifying the effect of individual input features. Finally, we discuss broader challenges including reproducibility and how to safely update risk prediction models that are already deployed at population level.
Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis
Authors: Smith Byron J. , Piceno Yvette , Zydek Martin , Zhang Bing , Syriani Lara Aboud , Terdiman Jonathan P. , Kassam Zain , Ma Averil , Lynch Susan V. , Pollard Katherine S. , El-Nachef Najwa
Published: August 2021

Fecal microbiota transplant is a promising therapy for ulcerative colitis. Parameters maximizing effectiveness and tolerability are not yet clear, and it is not known how import the transmission of donor microbes to patients is. Here (clinicaltrails.gov: NCT03006809) we have tested the effects of antibiotic pretreatment and compared two modes of maintenance dose delivery, capsules versus enema, in a randomized, pilot, open-label, 2×2 factorial design with 22 patients analyzed with mild to moderate UC. Clinically, the treatment was well-tolerated with favorable safety profile. Of patients who received antibiotic pretreatment, 6 of 11 experienced remission after six weeks of treatment, versus 2 of 11 non-pretreated patients (odds ratio: 1.69, 95% confidence interval: -0.25 to 3.62). No significant differences were found between maintenance dosing via capsules versus enema. In exploratory analyses, microbiome turnover at both the species and strain levels was extensive and significantly more pronounced in the pretreated patients. Associations were also revealed between taxonomic turnover and changes in the composition of primary and secondary bile acids. Together these findings suggest that antibiotic pretreatment contributes to microbiome engraftment and possibly clinical effectiveness, and validate longitudinal strain tracking as a powerful way to monitor the dynamics and impact of microbiota transfer.
Improving QSAR Modeling for Predictive Toxicology using Publicly Aggregated Semantic Graph Data and Graph Neural Networks
Authors: Romano Joseph D. , Hao Yun , Moore Jason H.
Published: August 2021

Quantitative Structure-Activity Relationship (QSAR) modeling is the most common computational technique for predicting chemical toxicity, but a lack of methodological innovations in QSAR have led to underwhelming performance. We show that contemporary QSAR modeling for predictive toxicology can be substantially improved by incorporating semantic graph data aggregated from open-access public databases, and analyzing those data in the context of graph neural networks (GNNs). Furthermore, we introspect the GNNs to demonstrate how they can lead to more interpretable applications of QSAR, and use ablation analysis to explore the contribution of different data elements to the final models’ performance.
Mesoderm-Derived PDGFRA+Cells Regulate the Emergence of Hematopoietic Stem Cells in the Dorsal Aorta
Authors: Chandrakanthan Vashe , Rorimpandey Prunella , Zanini Fabio , Chacon Diego , Kang Young Chan , Knezevic Kathy , Huang Yizhou , Qiao Qiao , Oliver Rema A. , Unnikrishnan Ashwin , Carter Daniel R. , Lee Brendan , Brownlee Chris , Power Carl , Mendez-Ferrer Simon , Enikolopov Grigori , Walsh William , Göttgens Berthold , Taoudi Samir , Beck Dominik , Pimanda John E.
Published: August 2021

Mouse hematopoietic stem cells (HSCs) first emerge at embryonic day 10.5 (E10.5) on the ventral surface of the dorsal aorta, by endothelial-to-hematopoietic transition (EHT). We investigated whether cells with mesenchymal stem cell-like activity, which provide an essential niche for long-term HSCs (LT-HSCs) in the bone marrow, reside in the aorta- gonad-mesonephros (AGM) and contribute to the structural development of the dorsal aorta and EHT. Using transgenic mice, we demonstrate a lineage hierarchy for AGM stromal cells and traced the E10.5/E11.5 aortic endothelium and HSCs to mesoderm derived (Mesp1) PDGFRA+stromal cells (Mesp1derPSCs).Mesp1derPSCs dominate the sub-endothelial and ventral stroma in the E10.5–E11.5 AGM but by E13.5 were replaced by neural crest (Wnt1) derived PDGFRA+stromal cells (Wnt1derPSCs). Co-aggregating non-hemogenic embryonic and adult endothelial cells withMesp1derPSCs but not withWnt1derPSCs resulted in activation of a hematopoietic transcriptional program in endothelial cells accompanied by EHT and generation of LT-HSCs. Dose-dependent inhibition of PDGFRA signalling or BMP, WNT, NOTCH signalling interrupted this reprogramming event. This partnership between endothelial cells and AGMMesp1derPSCs could potentially be harnessed to manufacture LT-HSCs from endothelium.
Development of Functional Connectome Gradients during Childhood and Adolescence
Authors: Xia Yunman , Xia Mingrui , Liu Jin , Liao Xuhong , Lei Tianyuan , Liang Xinyu , Zhao Tengda , Shi Ziyi , Sun Lianglong , Chen Xiaodan , Men Weiwei , Wang Yanpei , Pan Zhiying , Luo Jie , Peng Siya , Chen Menglu , Hao Lei , Tan Shuping , Gao Jiahong , Qin Shaozheng , Gong Gaolang , Tao Sha , Dong Qi , He Yong
Published: August 2021

Connectome mapping studies have documented a principal primary-to-transmodal gradient in the adult brain network, capturing a functional spectrum which ranges from perception and action to abstract cognition. However, how this gradient pattern develops and whether its development is linked to cognitive growth, topological reorganization, and gene expression profiles remain largely unknown. Using longitudinal resting-state functional magnetic resonance imaging data from 305 children (ages 6-14), we describe substantial changes in the primary-to-transmodal gradient between childhood and adolescence, including emergence as the principal gradient, expansion of global topography, and focal tuning in primary and default-mode regions. These gradient changes are mediated by developmental changes in network integration and segregation, and are associated with abstract processing functions such as working memory and expression levels of calcium ion regulated exocytosis, synaptic transmission, and axon and synapse part related genes. Our findings have implications for understanding connectome maturation principles in normal development and developmental disorders.

Teaser

Our study reported the maturation of the core connectome gradient and its association with cognitions and genes expression.
Antibody-mediated neutralization of authentic SARS-CoV-2 B.1.617 variants harboring L452R and T478K/E484Q
Authors: Wilhelm Alexander , Toptan Tuna , Pallas Christiane , Wolf Timo , Goetsch Udo , Gottschalk Rene , Vehreschild Maria JGT , Ciesek Sandra , Widera Marek
Published: August 2021

The capacity of convalescent and vaccine-elicited sera and monoclonal antibodies (mAb) to neutralize SARS-CoV-2 variants is currently of high relevance to assess the protection against infections.

We performed a cell culture-based neutralization assay focusing on authentic SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.427/B.1.429 (Epsilon), all harboring the spike substitution L452R.

We found that authentic SARS-CoV-2 variants harboring L452R had reduced susceptibility to convalescent and vaccine-elicited sera and mAbs. Compared to B.1, Kappa and Delta showed a reduced neutralization by convalescent sera by a factor of 8.00 and 5.33, respectively, which constitutes a 2-fold greater reduction when compared to Epsilon. BNT2b2 and mRNA1273 vaccine-elicited sera were less effective against Kappa, Delta, and Epsilon compared to B.1. No difference was observed between Kappa and Delta towards vaccine-elicited sera, whereas convalescent sera were 1.5-fold less effective against Delta, respectively. Both B.1.617 variants Kappa (+E484Q) and Delta (+T478K) were less susceptible to either casirivimab or imdevimab.

In conclusion, in contrast to the parallel circulating Kappa variant, the neutralization efficiency of convalescent and vaccine-elicited sera against Delta was moderately reduced. Delta was resistant to imdevimab, which however, might be circumvented by a combination therapy with casirivimab together.
Interpretable multi-stream ensemble learning for radiographic pattern recognition
Authors: Ferreira José Raniery , Cardenas Diego Armando Cardona
Published: August 2021

Chest radiography (CXR) remains an essential component to evaluate lung diseases. However, it is crucial nowadays to include computer-based tools to aid physicians in the early detection of chest abnormalities. Therefore, this work proposed deep ensemble models to improve the CXR evaluation, interpretability, and reproducibility. Five convolutional neural networks and six different processed image inputs yielded an AUC of 0.982. Furthermore, ensemble learning could produce more reliable outcomes as it did not consider the information of only one method. Moreover, the ensemble strategy balanced the most critical factors from each model to perform a more consistent classification. Finally, class activation and gradient propagation maps allowed locally visualizing CXR regions that most activate neurons from the trained models and explaining practically which areas of the CXR correlated to the model output.
Slow expanders invade by forming dented fronts in microbial colonies
Authors: Lee Hyunseok , Gore Jeff , Korolev Kirill S.
Published: August 2021

Most organisms grow in space, whether they are viruses spreading within a host tissue or invasive species colonizing a new continent. Evolution typically selects for higher expansion rates during spatial growth, but it has been suggested that slower expanders can take over under certain conditions. Here, we report an experimental observation of such population dynamics. We demonstrate that the slower mutants win not only when the two types are intermixed at the front but also when they are spatially segregated into sectors. The latter was thought to be impossible because previous studies focused exclusively on the global competitions mediated by expansion velocities but overlooked the local competitions at sector boundaries. We developed a theory of sector geometry that accounts for both local and global competitions and describes all possible sector shapes. In particular, the theory predicted that a slower, but more competitive, mutant forms a dented V-shaped sector as it takes over the expansion front. Such sectors were indeed observed experimentally and their shapes matched up quantitatively with the theory. In simulations, we further explored several mechanism that could provide slow expanders with a local competitive advantage and showed that they are all well-described by our theory. Taken together, our results shed light on previously unexplored outcomes of spatial competition and establish a universal framework to understand evolutionary and ecological dynamics in expanding populations.

Significance

Living organisms never cease to evolve, so there is a significant interest in predicting and controlling evolution in all branches of life sciences from medicine to agriculture. The most basic question is whether a trait should increase or decrease in a given environment. The answer seems to be trivial for traits such as the growth rate in a bioreactor or the expansion rate of a tumor. Yet, it has been suggested that such traits can decrease rather than increase during evolution. Here, we report a mutant that outcompeted the ancestor despite having a slower expansion velocity. To explain this observation, we developed and validated a theory that describes spatial competition between organisms with different expansion rates and arbitrary competitive interactions.
Hotair and Malat1 Long Noncoding RNAs regulate Bdnf Expression and Oligodendrocyte Precursor Cells Differentiation
Authors: Khani-Habibabadi Fatemeh , Zare Leila , Sahraian Mohammad Ali , Javan Mohammad , Behmanesh Mehrdad
Published: August 2021

BDNF has remarkable protective roles in the central nervous system to ensure neurons and glial cells survival and proper functions. The regulatory processes behind the BDNF expression have not been revealed completely. Here, it was explored whetherMalat1andHotairlncRNAs play roles in the regulation ofBdnfexpression level, modification of fingolimod downstream pathway, and oligodendrocytes precursor cells maturation. ByHotairandMalat1downregulation, their regulatory mechanism onBdnfexpression was investigated. Immunostaining and RT-qPCR assays were employed to assess the effects of fingolimod and lncRNAs on OPCs maturation. The results represented thatHotairandMalat1lncRNAs may regulate Bdnf expression in primary glial cells significantly, and also can coordinate fingolimod stimulatory effect onBdnfexpression. Furthermore,Malat1may have a role in the last stages of the intrinsic oligodendrocyte myelination. Here it was demonstrated that these lncRNAs have critical roles in theBdnflevel, fingolimod mechanism of action, and OPCs maturation. Understanding the regulatory mechanism of neurotrophins leads to a better comprehension of the neurodegenerative disorders pathogenesis and designing more effective treatments.
Who is the best surrogate for germ stem cell transplantation in fish?
Authors: Franěk Roman , Cheng Yu , Fučíková Michaela , Kašpar Vojtěch , Xie Xuan , Shah Mujahid Ali , Linhart Otomar , Šauman Ivo , Pšenička Martin
Published: August 2021

Surrogate reproduction technology in fish has potential for aquaculture as well as endangered species preservation and propagation. Species with some unfavourable biological characteristics for culturing such as a late maturation or a large body size are ideal candidates for surrogate reproduction using smaller and faster-maturing host. One of the general prerequisites for the successful surrogacy and the pure donor-derived gamete production is the sterility of the host. Various sterilization methods have been developed and used in fish surrogacy; however, a direct comparison of available methods is missing. Such a knowledge gap hinders choice for the surrogate in various fish species, including those in high commercial demand such as tuna or sturgeons, where is a particular limitation from the point of the live material availability and difficulty to perform a high throughput assessment of different surrogates. Yet, large sturgeons or tuna species are one of the most prominent candidates for surrogacy. Zebrafish was utilized in this study as a model species to answer whether and to which extent different sterilization strategies can affect the surrogacy. Germ cell-depleted recipients (produced using knockdown of dead end gene), triploid recipients, and zebrafish x pearl danio hybrid recipients were tested as they represent the most frequently used types of surrogates. Spermatogonia isolated from vas::EGFP transgenic strain were intraperitoneally transplanted into swim-up 5-day old zebrafish. Transplantation success, survival, gonadal development, and reproductive output of the fish was analyzed. Germ cell-depleted recipients with empty gonads were identified as the most convenient among tested sterilization methods considering surrogacy induction success and reproductive output. The present study stands as significant aid for selecting suitable surrogates in various fish species.
Neutrophilic inflammation promotes SARS-CoV-2 infectivity and augments the inflammatory responses in airway epithelial cells
Authors: Calvert BA , Quiroz EJ , Lorenzana Z , Doan N , Kim S , Senger CN , Wallace WD , Salomon MP , Henley J , Ryan AL
Published: August 2021

In response to viral infection, neutrophils release inflammatory mediators as part of the innate immune response, contributing to pathogen clearance through virus internalization and killing. Pre-existing co- morbidities correlating to incidence of severe COVID-19 are associated with chronic airway neutrophilia. Furthermore, examination of COVID-19 explanted lung tissue revealed a series of epithelial pathologies associated with the infiltration and activation of neutrophils, indicating neutrophil activity in response to SARS- CoV-2 infection. To determine the impact of neutrophil-epithelial interactions on the infectivity and inflammatory responses to SARS-CoV-2 infection, we developed a co-culture model of airway neutrophilia. SARS-CoV-2 infection of the airway epithelium alone does not result in a notable pro-inflammatory response from the epithelium. The addition of neutrophils induces the release of proinflammatory cytokines and stimulates a significantly augmented pro-inflammatory response subsequent SARS-CoV-2 infection. The resulting inflammatory response is polarized with differential release from the apical and basolateral side of the epithelium. Additionally, the integrity of the epithelial barrier is impaired with notable epithelial damage and infection of basal stem cells. This study reveals a key role for neutrophil-epithelial interactions in determining inflammation and infectivity in response to SARS-CoV-2 infection.
SIGNR1 promotes immune dysfunction in systemic candidiasis by modulating neutrophil lifespan via T cell-derived histones and G-CSF
Authors: Ioannou Marianna , Hoving Dennis , Aramburu Iker Valle , De Vasconcelos Nathalia M. , Temkin Mia I. , Wang Qian , Vernardis Spyros , Demichev Vadim , Tsourouktsoglou Theodora-Dorita , Boeing Stefan , Goldstone Robert , David Sascha , Stahl Klaus , Bode Christian , Ralser Markus , Papayannopoulos Venizelos
Published: August 2021

The mechanisms regulating immune dysfunction during sepsis are poorly understood. Here, we show that neutrophil-derived myeloperoxidase delays the onset of immune dysfunction during systemic candidiasis by controlling microbes captured by splenic marginal zone (MZ) macrophages. In contrast, SIGNR1-mediated microbe capture accelerates MZ colonization and immune dysfunction by triggering T cell death, T cell-dependent chromatin release and the synergistic induction of G-CSF by histones and fungi. Histones and G-CSF promote the prevalence of immature Ly6Glowneutrophils with defective oxidative burst, by selectively shortening the lifespan of mature Ly6Ghighneutrophils. Consistently, T cell deficiency, or blocking SIGNR1, G-CSF or histones delayed neutrophil dysfunction. Furthermore, histones and G-CSF in the plasma of sepsis patients, shortened neutrophil lifespan and correlated with neutrophil mortality markers associated with a poor prognosis. Hence, the compromise of internal antimicrobial barrier sites drives neutrophil dysfunction by selectively modulating neutrophil lifespan via pathogenic T cell death, extracellular histones, and G-CSF.
Diauxic lags explain unexpected coexistence in multi-resource environments
Authors: Bloxham William , Lee Hyunseok , Gore Jeff
Published: August 2021

How the coexistence of species is affected by the presence of multiple resources is a major question in microbial ecology. We experimentally demonstrate that differences in diauxic lags, which occur as species deplete their own environments and adapt their metabolisms, allow slow-growing microbes to stably coexist with faster-growing species in multi-resource environments despite being excluded in single-resource environments. In our focal example, an Acinetobacter species (Aci2) competitively excludes Pseudomonas aurantiaca (Pa) on alanine and on glutamate. However, they coexist on the combination of both resources. Experiments reveal that Aci2 grows faster but Pa has shorter diauxic lags. We establish a tradeoff between Aci2’s fast growth and Pa’s short lags as their mechanism for coexistence. We model this tradeoff to accurately predict how environmental changes affect community composition. We extend our work by surveying a large set of competitions and observe coexistence nearly three times as frequently when the slow-grower is the fast-switcher. Our work illustrates a potentially common mechanism for the emergence of multi-resource coexistence despite single-resource competitive exclusions.
A Systematic Comparison of Differential Analysis Methods for CyTOF Data
Authors: Arend Lis , Bernett Judith , Manz Quirin , Klug Melissa , Lazareva Olga , Baumbach Jan , Bongiovanni Dario , List Markus
Published: August 2021

Cytometry techniques are widely used to discover cellular characteristics at single-cell resolution. Many data analysis methods for cytometry data focus solely on identifying subpopulations via clustering and testing for differential cell abundance. For differential expression analysis of markers between conditions, only few tools exist. These tools either reduce the data distribution to medians, discarding valuable information, or have underlying assumptions that may not hold for all expression patterns.

Here, we systematically evaluated existing and novel approaches for differential expression analysis on real and simulated CyTOF data. We found that methods using median marker expressions compute fast and reliable results when the data is not strongly zero-inflated. Methods using all data detect changes in strongly zero-inflated markers, but partially suffer from overprediction or cannot handle big datasets. We present a new method, CyEMD, based on calculating the Earth Mover’s Distance between expression distributions that can handle strong zero-inflation without being too sensitive.

Additionally, we developed CYANUS, a user-friendly R Shiny App allowing the user to analyze cytometry data with state-of-the-art tools, including well-performing methods from our comparison. A public web interface is available at https://exbio.wzw.tum.de/cyanus/.
Mechanism of hyperproteinemia-induced blood cell homeostasis imbalance in an animal model
Authors: Wang Guang , Wang Yongfeng , Li Jianglan , Peng Ruji , Liang Xinyin , Chen Xuedong , Jiang Guihua , Shi Jinfang , Si-ma Yanghu , Xu Shiqing
Published: August 2021

Hyperproteinemia is a metabolic disorder associated with increased plasma protein concentration (PPC). It is often clinically complicated by malignant diseases or severe infections. Research on the molecular mechanism of High PPC (HPPC) is scant. Here, an animal model of primary hyperproteinemia was constructed in an invertebrate, Bombyx mori, to investigate the effect of HPPC on circulating blood cells. We showed that HPPC affected blood cell homeostasis and enhanced blood cell phagocytosis, leading to increased reactive oxygen species levels, and induced programmed cell death that depended on the endoplasmic reticulum-calcium ion signaling pathway. HPPC induced the proliferation of blood cells, mainly granulocytes, by activating the JAK/STAT signaling pathway. Supplementation with endocrine hormone active substance 20E significantly reduced the impact of HPPC on blood cell homeostasis. Herein, we reported a novel signaling pathway by which HPPC affected blood cell homeostasis, which was different from hyperglycemia, hyperlipidemia, and hypercholesterolemia. In addition, we showed that down-regulation of gene expression of the hematopoietic factor Gcm could be used as a potential early monitoring index for hyperproteinemia.

Highlights

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HPPC induced proliferation of circulating blood cells through the JAK/STAT pathway, leading to a significant increase in the proportion of granulocytes.

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Supplementing endocrine hormone 20E improved hematopoietic function and restored the homeostasis of circulating blood cells through modulation of the JAK/STAT signaling pathway.

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HPPC induced PCD in blood cells through the endoplasmic reticulum-calcium ion release signaling pathway.

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Down-regulation of the gene expression of the hematopoietic factor Gcm could be used as a potential early monitoring index for hyperproteinemia.
Molecular basis for redox control by the human cystine/glutamate antiporter System xc-
Authors: Parker Joanne L. , Deme Justin C. , Kolokouris Dimitrios , Kuteyi Gabriel , Biggin Philip C. , Lea Susan M. , Newstead Simon
Published: August 2021

Cysteine plays an essential role in cellular redox homeostasis as a key constituent of the tripeptide glutathione (GSH). A rate limiting step in cellular GSH synthesis is the availability of cysteine. However, circulating cysteine exists in the blood as the oxidised di-peptide cystine, requiring specialised transport systems for its import into the cell. System xc- is a dedicated cystine transporter, importing cystine in exchange for intracellular glutamate. To counteract elevated levels of reactive oxygen species in cancerous cells system xc- is frequently upregulated, making it an attractive target for anticancer therapies. However, the molecular basis for ligand recognition remains elusive, hampering efforts to specifically target this transport system. Here we present the cryo-EM structure of system xc- in both the apo and glutamate bound states. Structural comparisons reveal an allosteric mechanism for ligand discrimination, supported by molecular dynamics and cell-based assays, establishing a mechanism for cystine transport in human cells.
The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth
Authors: Boezio Giulia L. M. , Gollin Josephine , Zhao Shengnan , Priya Rashmi , Mansingh Shivani , Guenther Stefan , Fukuda Nana , Gunawan Felix , Stainier Didier Y. R.
Published: August 2021

The epicardium, the outermost layer of the heart, is an important regulator of cardiac regeneration. However, a detailed understanding of the crosstalk between the epicardium and myocardium during development requires further investigation. Here, we generated three models of epicardial impairment in zebrafish by mutating the transcription factor genestcf21andwt1a, and by ablatingtcf21+epicardial cells. Notably, all three epicardial-impairment models exhibit smaller ventricles. We identified the initial cause of this phenotype as defective cardiomyocyte growth, resulting in reduced cell surface and volume. This failure of cardiomyocytes to grow is followed by decreased proliferation and increased abluminal extrusion. By temporally manipulating its ablation, we show that the epicardium is required to support ventricular growth during early cardiac morphogenesis. By transcriptomic profiling of sorted epicardial cells, we identified reduced expression of FGF and VEGF ligand genes intcf21-/-hearts, and pharmacological inhibition of these signaling pathways partially recapitulated the ventricular growth defects. Thus, the analysis of these epicardial-impairment models further elucidates the distinct roles of the epicardium during cardiac morphogenesis and the signaling pathways underlying epicardial-myocardial crosstalk.
Phox2bmutation mediated byAtoh1expression impaired respiratory rhythm and ventilatory responses to hypoxia and hypercapnia
Authors: Ferreira Caroline B. , Silva Talita M. , Silva Phelipe E. , Czeisler Catherine , Otero Jose J. , Takakura Ana C. , Moreira Thiago S.
Published: August 2021

Retrotrapezoid nucleus (RTN) neurons are involved in central chemoreception and respiratory control. Lineage tracing studies demonstrate RTN neurons to be derived fromPhox2bandAtoh1expressing progenitor cells in rhombere 4.Phox2bexon 3 mutations cause congenital central hypoventilation syndrome (CCHS), producing an impaired respiratory response to hypercapnia and hypoxia. Our goal was to investigate the extent to which a conditional mutation ofPhox2bwithinAtoh1-derived cells might affect a) respiratory rhythm; b) ventilatory responses to hypercapnia and hypoxia and c) number of RTN-chemosensitive neurons. Here, we used a transgenic mouse line carrying a conditionalPhox2bΔ8mutation activated by cre-recombinase. We crossed them withAtoh1Cremice. Ventilation was measured by whole body plethysmograph during neonate and adult life. In room air, experimental and control groups showed similar basal ventilation; however,Atoh1Cre/Phox2bΔ8increased breath irregularity. The hypercapnia and hypoxia ventilatory responses were impaired in neonates. In contrast, adult mice recovered ventilatory response to hypercapnia, but not to hypoxia. Anatomically, we observed a reduction of the Phox2b+/TH−expressing neurons within the RTN region. Our data indicates that conditionally expression ofPhox2bmutation byAtoh1affect development of the RTN neurons and are essential for the activation of breathing under hypoxic and hypercapnia condition, providing new evidence for mechanisms related to CCHS neuropathology.
Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: A case study of an urothelial cancer cohort analyzed in the Galaxy framework
Authors: Föll Melanie Christine , Volkmann Veronika , Enderle-Ammour Kathrin , Wilhelm Konrad , Guo Dan , Vitek Olga , Bronsert Peter , Schilling Oliver
Published: August 2021

Background

Mass spectrometry imaging (MSI) derives spatial molecular distribution maps directly from clinical tissue specimens. This allows for spatial characterization of molecular compositions of different tissue types and tumor subtypes, which bears great potential for assisting pathologists with diagnostic decisions or personalized treatments. Unfortunately, progress in translational MSI is often hindered by insufficient quality control and lack of reproducible data analysis. Raw data and analysis scripts are rarely publicly shared. Here, we demonstrate the application of the Galaxy MSI tool set for the reproducible analysis of an urothelial carcinoma dataset.

Methods

Tryptic peptides were imaged in a cohort of 39 formalin-fixed, paraffin-embedded human urothelial cancer tissue cores with a MALDI-TOF/TOF device. The complete data analysis was performed in a fully transparent and reproducible manner on the European Galaxy Server. Annotations of tumor and stroma were performed by a pathologist and transferred to the MSI data to allow for supervised classifications of tumor vs. stroma tissue areas as well as for muscle-infiltrating and non-muscle invasive urothelial carcinomas. For putative peptide identifications, m/z features were matched to the MSiMass list.

Results

Rigorous quality control in combination with careful pre-processing enabled reduction of m/z shifts and intensity batch effects. High classification accuracy was found for both, tumor vs. stroma and muscle-infiltrating vs. non-muscle invasive tumors. Some of the most discriminative m/z features for each condition could be assigned a putative identity: Stromal tissue was characterized by collagen type I peptides and tumor tissue by histone and heat shock protein beta-1 peptides.

Intermediate filaments such as cytokeratins and vimentin were discriminative between the tumors with different muscle-infiltration status. To make the study fully reproducible and to advocate the criteria of FAIR (findability, accessibility, interoperability, and reusability) research data, we share the raw data, spectra annotations as well as all Galaxy histories and workflows. Data are available via ProteomeXchange with identifier PXD026459 and Galaxy results viahttps://github.com/foellmelanie/Bladder_MSI_Manuscript_Galaxy_links.

Conclusion

Here, we show that translational MSI data analysis in a fully transparent and reproducible manner is possible and we would like to encourage the community to join our efforts.
Interactions of the Trypanosoma brucei brucei zinc-finger-domain protein ZC3H28
Authors: Bishola Tania , Clayton Christine
Published: August 2021

In Trypanosoma brucei and related Kinetoplastids, regulation of gene expression occurs mostly post-transcriptionally, and RNA-binding proteins play a critical role in the regulation of mRNA and protein abundance. Trypanosoma brucei ZC3H28 is a 114 KDa cytoplasmic mRNA-binding protein with a single C(x)7C(x)5C(x)sH zinc finger at the C-terminus and numerous proline-, histine- or glutamine-rich regions. We here show that N-terminally tagged ZC3H28 copurifies ribosomes, various RNA-binding proteins, and the translation initiation complex EIF4E4/EIF4G3. ZC3H28 is preferentially associated with long RNAs that have low complexity sequences in their 3’-untranslated regions. When tethered to a reporter mRNA, ZC3H28 increased the mRNA level without a corresponding increase in protein expression; this suggests that it stabilized the reporter but at the same time suppressed its translation. Indeed, there was a clear negative correlation between ZC3H28 mRNA binding and ribosome density. After ZC3H28 depletion, the relative levels of ribosomal protein mRNAs increased while levels of some long mRNAs decreased, but there is no overall correlation between binding and RNAi effects on mRNA abundance. We speculate that ZC3H28 might be implicated in stabilizing poorly-translated mRNAs.
PRC1 Sustains the Memory of Neuronal Fate Independent of PRC2 Function
Authors: Sawai Ayana , Pfennig Sarah , Bulajić Milica , Miller Alexander , Khodadadi-Jamayran Alireza , Mazzoni Esteban O. , Dasen Jeremy S.
Published: August 2021

Polycomb repressive complexes (PRCs) 1 and 2 maintain stable cellular memories of early fate decisions by establishing heritable patterns of gene repression. PRCs repress transcription through histone modifications and chromatin compaction, but their roles in neuronal subtype diversification are poorly defined. We unexpectedly found that PRC2 is dispensable to preserve the morphogen-induced positional fates of spinal motor neurons (MNs), while PRC1 is essential for the specification of segmentally-restricted subtypes. Mutation of the core PRC1 componentRing1in mice leads to increased chromatin accessibility and ectopic expression of a broad variety of fates determinants, including Hox transcription factors, while neuronal class-specific features are maintained. Loss of MN subtype identities inRing1mutants is due to the suppression of Hox networks by derepressed caudalHoxgenes. These results indicate that PRC1 can function independently ofde novoPRC2-dependent histone methylation to maintain chromatin topology and transcriptional memory at the time of neuronal differentiation.
isotracer: An R package for the analysis of tracer addition experiments
Authors: Bruneaux Matthieu , López-Sepulcre Andrés
Published: August 2021

Tracer addition experiments, particularly using isotopic tracers, are becoming increasingly important in a variety of studies aiming at characterizing the flows of molecules or nutrients at different levels of biological organization, from the cellular and tissue levels, to the organismal and ecosystem levels.

We present an approach based on Hidden Markov Models (HMM) to estimate nutrient flow parameters across a network, and its implementation in the R package isotracer.

The isotracer package is capable of handling a variety of tracer study designs, including continuous tracer drips, pulse experiments, and pulse-chase experiments. It can also take into account tracer decay when radioactive isotopes are used.

To illustrate its use, we present three case studies based on published data and spanning different levels of biological organization: a molecular-level study of protein synthesis and degradation inArabidopsis thaliana, an organismal-level study of phosphorus incorporation in the eelgrassZostera marina, and an ecosystem-level study of nitrogen dynamics in Trinidadian montane streams.

With these case studies, we illustrate how isotracer can be used to estimate uptake rates, turnover rates, and total flows, as well as their uncertainty. We also show how to perform model selection to compare alternative hypotheses.

We conclude by discussing isotracer’s further applications, limitations, and possible future improvements and expansions.
A Capped Tudor Domain within a Core Subunit of the Sin3L/Rpd3L Histone Deacetylase Complex Binds Nucleic Acids
Authors: Marcum Ryan Dale , Hsieh Joseph , Giljen Maksim , Zhang Yongbo , Radhakrishnan Ishwar
Published: August 2021

Chromatin-modifying complexes containing histone deacetylase (HDAC) activities play critical roles in the regulation of gene transcription in eukaryotes. These complexes are thought to lack intrinsic DNA-binding activity, but according to a well-established paradigm, they are recruited via protein-protein interactions by gene-specific transcription factors and post-translational histone modifications to their sites of action on the genome. The mammalian Sin3L/Rpd3L complex, comprising more than a dozen different polypeptides, is an ancient HDAC complex found in diverse eukaryotes. The subunits of this complex harbor conserved domains and motifs of unknown structure and function. Here we show that Sds3, a constitutively associated subunit critical for the proper functioning of the complex, harbors a type of Tudor domain that we designate the capped Tudor domain (CTD). Unlike canonical Tudor domains that bind modified histones, the Sds3 CTD binds to nucleic acids that can form higher-order structures such as G-quadruplexes, and shares similarities with the knotted Tudor domain of the Esa1 histone acetyltransferase (HAT) that was previously shown to bind single-stranded RNA. Our findings expand the range of macromolecules capable of recruiting the Sin3L/Rpd3L complex and draws attention to potentially new roles for this HDAC complex in transcription biology.
LoFTK: a framework for fully automated calculation of predicted Loss-of-Function variants
Authors: Alasiri A. , Karczewski K. J. , Cole B. , Loza B. , Moore J. H. , van der Laan S. W. , Asselbergs F. W. , Keating B. J. , van Setten J.
Published: August 2021

Motivation

Loss-of-Function (LoF) variants in human genes are important due to their impact on clinical phenotypes and frequent occurrence in the genomes of healthy individuals. Current approaches predict high-confidence LoF variants without identifying the specific genes or the number of copies they affect. Moreover, there is a lack of methods for detecting knockout genes caused by compound heterozygous (CH) LoF variants.

Results

We have developed the Loss-of-Function ToolKit (LoFTK), which allows efficient and automated prediction of LoF variants from both genotyped and sequenced genomes. LoFTK enables the identification of genes that are inactive in one or two copies and provides summary statistics for downstream analyses. LoFTK can identify CH LoF variants, which result in LoF genes with two copies lost. Using data from parents and offspring we show that 96% of CH LoF genes predicted by LoFTK in the offspring have the respective alleles donated by each parent.

Availability and implementation

LoFTK is an open source software and is freely available to non-commercial users at https://github.com/CirculatoryHealth/LoFTK

Contact

j.vansetten@umcutrecht.nl

Supplementary information

Supplementary data are available at Bioinformatics online.
ADrosophilaRNAi screen reveals conserved glioblastoma-related adhesion genes that regulate collective cell migration
Authors: Kotian Nirupama , Troike Katie M. , Curran Kristen N. , Lathia Justin D. , McDonald Jocelyn A.
Published: August 2021

Migrating cell collectives are key to embryonic development but also contribute to invasion and metastasis of a variety of cancers. Cell collectives can invade deep into tissues, leading to tumor progression and resistance to therapies. Collective cell invasion is also observed in the lethal brain tumor glioblastoma, which infiltrates the surrounding brain parenchyma leading to tumor growth and poor patient outcomes.Drosophilaborder cells, which migrate as a small cell cluster in the developing ovary, are a well-studied and genetically accessible model used to identify general mechanisms that control collective cell migration within native tissue environments. Most cell collectives remain cohesive through a variety of cell-cell adhesion proteins during their migration through tissues and organs. In this study, we first identified cell adhesion, cell junction, and associated regulatory genes that are expressed in human brain tumors. We performed RNAi knockdown of theDrosophilaorthologs in border cells to evaluate if migration and/or cohesion of the cluster was impaired. From this screen, we identified eight adhesion genes that disrupted border cell collective migration upon RNAi knockdown. Bioinformatics analyses further demonstrated that subsets of the orthologous genes were elevated in the margin and invasive edge of human glioblastoma patient tumors. These data together show that conserved cell adhesion and adhesion regulatory proteins with potential roles in tumor invasion also modulate collective cell migration. This dual screening approach for adhesion genes linked to glioblastoma and border cell migration thus may reveal conserved mechanisms that drive collective tumor cell invasion.
Pseudomonas aeruginosa C-terminal processing protease CtpA assembles into a hexameric structure that requires activation by a spiral-shaped lipoprotein binding partner
Authors: Hsu Hao-Chi , Wang Michelle , Kovach Amanda , Darwin Andrew J. , Li Huilin
Published: August 2021

Pseudomonas aeruginosa CtpA is a carboxyl terminal-processing protease that partners with the outer membrane lipoprotein LbcA to degrade at least five cell wall-associated proteins, four of which are cell wall hydrolases. This activity plays an important role in supporting P. aeruginosa virulence in a mouse model of acute pneumonia. However, almost nothing is known about the molecular mechanisms underlying CtpA and LbcA function. Here, we used structural analysis to show that CtpA alone assembles into an inactive hexamer comprising a trimer of dimers, which limits its substrate access and prevents nonspecific degradation. The adaptor protein LbcA is a right-handed open spiral with 11 tetratricopeptide repeats, which might wrap around a substrate to deliver it to CtpA for degradation. By structure-guided mutagenesis and functional assays, we also showed that the interfaces of the CtpA trimer-of-dimers, and an N-terminal helix of LbcA, are important for LbcA-mediated substrate degradation by CtpA both in vitro and in vivo. This work improves our understanding of the molecular mechanism of a CTP within the C-terminal processing peptidase-3 group.

IMPORTANCE

Carboxyl-terminal processing proteases (CTPs) are found in all three domains of life. In bacteria, some CTPs have been associated with virulence, raising the possibility that they could be theraputic targets. However, relatively little is known about their molecular mechanisms of action. In Pseudomonas aeruginosa, CtpA supports virulence by working in complex with the outer membrane lipoprotein LbcA to degrade cell wall hydrolases. Here, we report structure-function analyses of CtpA and LbcA, which reveals that CtpA assembles into an inactive hexamer comprising a trimer of dimers. LbcA is monomeric, with an N-terminal region important for binding to and activating CtpA, followed by a spiral structure composed of 11 tetratricopetide repeats, which could wrap around a substrate for delivery to CtpA. This work provides the first structure of a CTP-3 group member, revealing a unique mutimeric arrangement and insight into how this important proteolytic system functions.
Comparative analysis of machine learning and evolutionary optimization algorithms for precision tissue culture ofCannabis sativa: Prediction and validation ofin vitroshoot growth and development based on the optimization of light and carbohydrate sources
Authors: Pepe Marco , Hesami Mohsen , Small Finlay , Jones Andrew Maxwell Phineas
Published: August 2021

Micropropagation techniques offer opportunity to proliferate, maintain, and study dynamic plant responses in highly controlled environments without confounding external influences, forming the basis for many biotechnological applications. With medicinal and recreational interests forCannabis sativaL. growing, research related to the optimization ofin vitropractices is needed to improve current methods while boosting our understanding of the underlying physiological processes. Unfortunately, due to the exorbitantly large array of factors influencing tissue culture, existing approaches to optimizein vitromethods are tedious and time-consuming. Therefore, there is great potential to use new computational methodologies for analysing data to develop improved protocols more efficiently. Here, we first tested the effects of light qualities using assorted combinations of Red, Blue, Far Red, and White spanning 0-100 μmol/m2/s in combination with sucrose concentrations ranging from 1-6 % (w/v), totaling 66 treatments, onin vitroshoot growth, root development, number of nodes, shoot emergence, and canopy surface area. Collected data were then assessed using multilayer perceptron (MLP), generalized regression neural network (GRNN), and adaptive neuro-fuzzy inference system (ANFIS) to model and predictin vitro Cannabisgrowth and development. Based on the results, GRNN had better performance than MLP or ANFIS and was consequently selected to link different optimization algorithms (genetic algorithm, biogeography-based optimization, interior search algorithm, and symbiotic organisms search) for prediction of optimal light levels (quality/intensity) and sucrose concentration for various applications. Predictions ofin vitroconditions to refine growth responses were subsequently tested in a validation experiment and data showed no significant differences between predicted optimized values and observed data. Thus, this study demonstrates the potential of machine learning and optimization algorithms to predict the most favourable light combinations and sucrose levels to elicit specific developmental responses. Based on these, recommendations of light and carbohydrate levels to promote specific developmental outcomes forin vitro Cannabisare suggested. Ultimately, this work showcases the importance of light quality and carbohydrate supply in directing plant development as well as the power of machine learning approaches to investigate complex interactions in plant tissue culture.