bluuebunny/crossref_metadata_2025 huggingface dataset:
CD16ahigh NK cell infiltration and spatial relationships with T cells and macrophages can predict improved progression-free survival in high grade ovarian cancer
Authors: Nersesian Sarah , Lee Stacey N. , Grantham Stephanie , Meunier Liliane , Communal Laudine , Arnason Thomas , Arnold Dirk , Nelson Brad H. , Mes-Messon Anne-Marie , Boudreau Jeanette E.
Published: June 2021

Background

High grade serous cancer (HGSC) remains a highly fatal malignancy with less than 50% of patients surviving 5 years after diagnosis. Despite its high mutational burden, HGSC is relatively refractory to checkpoint immunotherapy, suggesting that additional features of the cancer and its interactions with the immune system remain to be understood. Natural killer (NK) cells may contribute to HGSC control, but the role(s) of this population or its subsets in this disease are poorly understood.

Methods

We used a TMA containing duplicate treatment-naïve tumors from 1145 patients with HGSC and a custom staining panel to simultaneously measure macrophages, T cells and NK cells, separating NK cells based on CD16a expression. Using pathologist-validated digital pathology, machine learning, computational analysis and Pearson’s correlations, we quantitated infiltrating immune cell density, co-infiltration and co-localization with spatial resolution to tumor region. We compared the prognostic value of innate, general, and adaptive immune cell “neighborhoods” to define characteristics of HGSC tumors predictive for progression-free survival and used flow cytometry to define additional features of the CD16adim NK cell subset.

Results

NK cells were observed in >95% of tumor cores. Intrastromal localization of CD16alow and CD16ahigh NK cells was associated with shorter and longer progression-free survival, respectively. CD16ahigh NK cells most frequently co-localized with T cells and macrophages; their proximity was termed an “adaptive” neighborhood. We find that tumors with more area represented by adaptive immune cell neighborhoods corresponded to superior progression free survival. In contrast, CD16alow NK cells did not co-infiltrate with other immune cell types, and expressed the ectonucleotidases, CD39 and CD73, which have been previously associated with poor prognosis in patients with HGSC.

Conclusions

Progression-free survival for patients with HGSC may be predicted by the subset of NK cells within the tumor infiltrate (i.e. CD16ahigh vs. CD16alow). NK cell subtypes were associated predictable co-infiltrating and co-localizing leukocyte subsets, suggesting that their presence and activity may influence, or be influenced by the tumor microenvironment. Our data suggest that immunotherapeutic strategies for HGSC should consider the constitution of NK cell subsets and may benefit from mobilizing and activating CD16high NK cells.
Topological data analysis identifies emerging adaptive mutations in SARS-CoV-2
Authors: Bleher Michael , Hahn Lukas , Neumann Maximilian , Patiño-Galindo Juan Ángel , Carrière Mathieu , Bauer Ulrich , Rabadán Raúl , Ott Andreas
Published: June 2021

The COVID-19 pandemic has initiated an unprecedented worldwide effort to characterize its evolution through the mapping of mutations of the coronavirus SARS-CoV-2. The early identification of mutations that could confer adaptive advantages to the virus, such as higher infectivity or immune evasion, is of paramount importance. However, the large number of currently available genomes precludes the efficient use of phylogeny-based methods. Here we present CoVtRec, a fast and scalable Topological Data Analysis approach for the surveillance of emerging adaptive mutations in large genomic datasets. Our method overcomes limitations of state-of-the-art phylogeny-based approaches by quantifying the potential adaptiveness of mutations merely by their topological footprint in the genome alignment, without resorting to the reconstruction of a single optimal phylogenetic tree. Analyzing millions of SARS-CoV-2 genomes from GISAID, we find a correlation between topological signals and adaptation to the human host. By leveraging the stratification by time in sequence data, our method enables the high-resolution longitudinal analysis of topological signals of adaptation. We characterize the convergent evolution of the coronavirus throughout the whole pandemic to date, report on emerging potentially adaptive mutations, and pinpoint mutations in Variants of Concern that are likely associated with positive selection. Our approach can improve the surveillance of mutations of concern and guide experimental studies.
Cross-neutralizing activity against SARS-CoV-2 variants in COVID-19 patients: Comparison of four waves of the pandemic in Japan
Authors: Furukawa Koichi , Tjan Lidya Handayani , Sutandhio Silvia , Kurahashi Yukiya , Iwata Sachiyo , Tohma Yoshiki , Sano Shigeru , Nakamura Sachiko , Nishimura Mitsuhiro , Arii Jun , Kiriu Tatsunori , Yamamoto Masatsugu , Nagano Tatsuya , Nishimura Yoshihiro , Mori Yasuko
Published: June 2021

In March 2021, Japan is facing a 4th wave of SARS-CoV-2 infection. To prevent further spread of infection, sera cross-neutralizing activity of patients previously infected with conventional SARS-CoV-2 against novel variants is important but is not firmly established. We investigated the neutralizing potency of 81 COVID-19 patients’ sera from 4 waves of pandemic against SARS-CoV-2 variants using their authentic viruses. Most sera had neutralizing activity against all variants, showing similar activity against B.1.1.7 and D614G, but lower activity especially against B.1.351. In the 4th wave, sera-neutralizing activity against B.1.1.7 was significantly higher than that against any other variants, including D614G. The cross-neutralizing activity of convalescent sera was effective against all variants but was potentially weaker for B.1.351.
Early Prediction of In-Hospital Death of COVID-19 Patients: A Machine-Learning Model Based on Age, Blood Analyses, and Chest X-Ray Score
Authors: Garrafa E. , Vezzoli M. , Ravanelli M. , Farina D. , Borghesi A. , Calza S. , Maroldi R.
Published: June 2021

Background

To develop and validate an early-warning model to predict in-hospital mortality on admission of COVID-19 patients at an emergency department (ED).

Methods

In total, 2782 patients were enrolled between March 2020 and December 2020, including 2106 patients (first wave) and 676 patients (second wave) in the COVID-19 outbreak in Italy. The first-wave patients were divided into two groups with 1474 patients used to train the model, and 632 to validate it. The 676 patients in the second wave were used to test the model. Age, 17 blood analytes and Brescia chest X-ray score were the variables processed using a Random Forests classification algorithm to build and validate the model. ROC analysis was used to assess the model performances. A web-based death-risk calculator was implemented and integrated within the Laboratory Information System of the hospital.

Results

The final score was constructed by age (the most powerful predictor), blood analytes (the strongest predictors were lactate dehydrogenase, D-dimer, Neutrophil/Lymphocyte ratio, C-reactive protein, Lymphocyte %, Ferritin std and Monocyte %), and Brescia chest X-ray score. The areas under the receiver operating characteristic curve obtained for the three groups (training, validating and testing) were 0.98, 0.83 and 0.78, respectively.

Conclusions

The model predicts in-hospital mortality on the basis of data that can be obtained in a short time, directly at the ED on admission. It functions as a web-based calculator, providing a risk score which is easy to interpret. It can be used in the triage process to support the decision on patient allocation.
Encapsulated allografts preclude host sensitization and promote ovarian endocrine function in ovariectomized young rhesus monkeys and sensitized mice
Authors: Day James R. , Flanagan Colleen L. , David Anu , Hartigan-O’Connor Dennis J. , Mattos Barbosa Mayara Garcia de , Martinez Michele L. , Lee Charles , Barnes Jenna , Farkash Evan , Zelinski Mary , Tarantal Alice , Cascalho Marilia , Shikanov Ariella
Published: June 2021

Transplantation of allogeneic donor ovarian tissue holds great potential for female cancer survivors who often experience premature ovarian insufficiency. To avoid complications associated with immune suppression and to protect transplanted ovarian allografts from immune-mediated injury, we have developed an immuno-isolating hydrogel-based capsule that supports the function of ovarian allografts without triggering an immune response. Encapsulated ovarian allografts implanted in naïve ovariectomized BALB/c mice responded to the circulating gonadotropins without direct revascularization and maintained function for 4 months, as evident by regular estrous cycles and presence of antral follicles in the retrieved grafts. Repeated implantations of encapsulated mouse ovarian allografts did not sensitize naïve BALB/c mice in contrast to non-encapsulated controls, which was confirmed with undetectable levels of allo-antibody. Further, encapsulated allografts implanted in hosts previously sensitized by implantation of non-encapsulated allografts restored estrous cycles similarly to our results in naïve recipients. Next, we tested the translational potential and efficiency of the immune-isolating capsule in a rhesus monkey model by implanting encapsulated ovarian auto- and allografts in young ovariectomized animals. The encapsulated ovarian grafts survived and restored basal levels of urinary estrone conjugate and pregnanediol 3-glucuronide during the approximate 4-5 month observation period. We demonstrate, for the first time, that encapsulation of ovarian allografts prevents sensitization and protects the allograft from rejection in young rhesus monkeys and in sensitized mice.
Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer
Authors: Ravanmehr Vida , Blau Hannah , Cappelletti Luca , Fontana Tommaso , Carmody Leigh , Coleman Ben , George Joshy , Reese Justin , Joachimiak Marcin , Bocci Giovanni , Bult Carol , Rueter Jens , Casiraghi Elena , Valentini Giorgio , Mungall Christopher , Oprea Tudor , Robinson Peter N.
Published: June 2021

Inhibiting protein kinases (PKs) that cause cancers has been an important topic in cancer therapy for years. So far, almost 8% of more than 530 PKs have been targeted by FDA-approved medications and around 150 protein kinase inhibitors (PKIs) have been tested in clinical trials. We present an approach based on natural language processing and machine learning to the relations between PKs and cancers, predicting PKs whose inhibition would be efficacious to treat a certain cancer. Our approach represents PKs and cancers as semantically meaningful 100-dimensional vectors based on co-occurrence patterns in PubMed abstracts. We use information about phase I-IV trials inClinicalTrials.govto construct a training set for random forest classification. In historical data, associations between PKs and specific cancers could be predicted years in advance with good accuracy. Our model may be a tool to predict the relevance of inhibiting PKs with specific cancers.
Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States
Authors: Shao Rui , Kumar Banushree , Lidschreiber Katja , Lidschreiber Michael , Cramer Patrick , Elsässer Simon J.
Published: June 2021

Unique transcriptomes define naïve, primed and paused pluripotent states in mouse embryonic stem cells. Here we perform transient transcriptome sequencing (TT-seq) to de novo define and quantify coding and non-coding transcription units (TUs) in different pluripotent states. We observe a global reduction of RNA synthesis, total RNA amount and turnover rates in ground state naïve cells (2i) and paused pluripotency (mTORi). We demonstrate that elongation velocity can be reliably estimated from TT-seq nascent RNA and RNA polymerase II occupancy and observe a transcriptome-wide attenuation of elongation velocity in the two inhibitor-induced states. We also discover a relationship between elongation velocity and termination read-through distance. Our analysis suggests that steady-state transcriptomes in mouse ES cells are controlled predominantly on the level of RNA synthesis, and that signaling pathways governing different pluripotent states immediately control key parameters of transcription.
Tools, strains, and strategies to effectively conduct anaerobic and aerobic transcriptional reporter screens and assays in Staphylococcus aureus
Authors: Price Erin E. , Rudra Paulami , Norambuena Javiera , Román-Rodríguez Franklin , Boyd Jeffrey M.
Published: June 2021

Transcriptional reporters are reliable and time-tested tools to study gene regulation. In Staphylococcus aureus, β-galactosidase (lacZ)-based genetic screens are not widely used because of the necessity of selectable markers for strain construction and the production of staphyloxanthin pigment which obfuscates results. We describe a series of vectors that allow for markerless insertion of codon-optimized lacZ-based transcriptional reporters. The vectors encode for different ribosomal binding sites allowing for tailored lacZ expression. A ΔcrtM::kanR deletion insertion mutant was constructed that prevents the synthesis of staphyloxanthin, thereby permitting blue-white screening without the interference of carotenoid production. We demonstrate the utility of these vectors to monitor aerobic and anaerobic transcriptional activity. For the latter, we describe the use of a ferrocyanide-ferricyanide redox system (Fe(CN)63–/4–) permitting blue-white screening in the absence of oxygen. We also describe additional reporter systems and methods for monitoring transcriptional activity during anaerobic culture including a FAD-binding fluorescent protein (EcFbFP), alpha-hemolysin (hla), or lipase (geh). The systems and methods described are compatible with vectors utilized to create and screen high-density transposon mutant libraries.

Importance

Staphylococcus aureus is a human pathogen and a leading cause of infectious disease-related illness and death worldwide. For S. aureus to successfully colonize and invade host tissues, it must tightly control the expression of genes encoding for virulence factors. Oxygen tension varies greatly at infection sites and many abscesses are devoid of oxygen. In this study, we have developed novel tools and methods to study how and when S. aureus alters transcription of genes. A key advantage to these methods and tools is that they can be utilized in the presence and absence of oxygen. A better understanding of anaerobic gene expression in S. aureus will provide important insight into the regulation of genes in low oxygen environments.
Metabolomic analysis of diverse mice reveals hepatic arginase-1 as source of plasma arginase in Plasmodium chabaudi infection
Authors: Davis Nicole M. , Lissner Michelle M. , Massis Liliana M. , Richards Crystal L. , Chevée Victoria , Gupta Avni S. , Gherardini Frank C. , Monack Denise M. , Schneider David S.
Published: June 2021

Infections disrupt host metabolism, but the factors that dictate the nature and magnitude of metabolic change are incompletely characterized. To determine how host metabolism changes in relation to disease severity in murine malaria, we performed plasma metabolomics on eight Plasmodium chabaudi-infected mouse strains with diverse disease phenotypes. We identified plasma metabolic biomarkers for both the nature and severity of different malarial pathologies. A subset of metabolic changes, including plasma arginine depletion, match the plasma metabolomes of human malaria patients, suggesting new connections between pathology and metabolism in human malaria. In our malarial mice, liver damage, which releases hepatic arginase-1 (Arg1) into circulation, correlated with plasma arginine depletion. We confirmed that hepatic Arg1 was the primary source of increased plasma arginase activity in our model, which motivates further investigation of liver damage in human malaria patients. More broadly, our approach shows how leveraging phenotypic diversity can identify and validate relationships between metabolism and the pathophysiology of infectious disease.

Importance

Malaria is a severe and sometimes fatal infectious disease endemic to tropical and subtropical regions. Effective vaccines against malaria-causing Plasmodium parasites remain elusive, and malaria treatments often fail to prevent severe disease. Small molecules that target host metabolism have recently emerged as candidates for therapeutics in malaria and other diseases. However, our limited understanding of how metabolites affect pathophysiology limits our ability to develop new metabolite therapies. By providing a rich dataset of metabolite-pathology correlations, and by validating one of those correlations, our work is an important step toward harnessing metabolism to mitigate disease. Specifically, we showed that liver damage in P. chabaudi-infected mice releases hepatic arginase-1 into circulation, where it may deplete plasma arginine, a candidate malaria therapeutic that mitigates vascular stress. Our data suggest that liver damage may confound efforts to increase levels of arginine in human malaria patients.
Radiosynthesis and preclinical evaluation of a carbon-11 labeled PDE7 inhibitor for PET neuroimaging
Authors: Xiao Zhiwei , Sun Jiyun , Fujinaga Masayuki , Wei Huiyi , Zhao Chunyu , Haider Ahmed , Van Richard , Yamasaki Tomoteru , Zhang Yiding , Rong Jian , Hu Kuan , Chen Jiahui , Leon Erick Calderon , Hiraishi Atsuto , Wei Junjie , Xu Yi , Shao Yihan , Zhang Han-Ting , Xu Ying , Lloyd KC Kent , Wang Lu , Zhang Ming-Rong , Liang Steven
Published: June 2021

Background

Dysfunction of cyclic nucleotide phosphodiesterase 7 (PDE7) has been associated with excess intracellular cAMP concentrations, fueling pathogenic processes that are implicated in neurodegenerative disorders. The aim of this study was to develop a suitable PDE7-targeted positron emission tomography (PET) probe that allows non-invasive mapping of PDE7 in the mammalian brain.

Methods

Based on a spiro cyclohexane-1,4’-quinazolinone scaffold with known inhibitory properties towards PDE7, we designed and synthesized a methoxy analog that was suitable for carbon-11 labeling. Radiosynthesis was conducted with the respective desmethyl precursor using [11C]MeI. The resulting PET probe, codenamed [11C]26, was evaluated by cell uptake studies, ex vivo biodistribution and radiometabolite studies, as well as in vivo PET experiments in rodents and nonhuman primates (NHP).

Results

Target compound 26 and the corresponding phenolic precursor were synthesized in 2-3 steps with overall yields of 49.5% and 12.4%, respectively. An inhibitory constant (IC50) of 31 nM towards PDE7 was obtained and no significant interaction with other PDE isoforms were observed. [11C]26 was synthesized in high molar activities (170 - 220 GBq/µmol) with radiochemical yields of 34±7%. In vitro cell uptake of [11C]26 was 6-7 folds higher in PDE7 overexpressing cells, as compared to the controls, whereas an in vitro specificity of up to 90% was measured. Ex vivo metabolite studies revealed a high fraction of intact parent in the rat brain (98% at 5 min and 75% at 30 min post injection). Considerable brain penetration was further corroborated by ex vivo biodistribution and PET imaging studies – the latter showing heterogenic brain uptake. While marginal specific binding was observed by PET studies in rodents, a moderate, but dose-dependent, blockade was observed in the NHP brain following pretreatment with non-radioactive 26.

Conclusion

In this work, we report on the preclinical evaluation of [11C]26 (codename [11C]P7-2104), a PDE7-targeted PET ligand that is based on a spiroquinazolinone scaffold. [11C]26 displayed promising in vitro performance characteristics, a moderate degree of specific binding in PET studies with NHP. Accordingly, [11C]26 will serve as a valuable lead compound for the development of a new arsenal of PDE7-targeted probes with potentially improved in vivo specificity.
An automated method for precise axon reconstruction from recordings of high-density micro-electrode arrays
Authors: Buccino Alessio Paolo , Yuan Xinyue , Emmenegger Vishalini , Xue Xiaohan , Gänswein Tobias , Hierlemann Andreas
Published: June 2021

Neurons communicate with each other by sending action potentials through their axons. The velocity of axonal signal propagation describes how fast electrical action potentials can travel, and can be affected in a human brain by several pathologies, including multiple sclerosis, traumatic brain injury and channelopathies. High-density microelectrode arrays (HD-MEAs) provide unprecedented spatio-temporal resolution to extracellularly record neural electrical activity. The high density of the recording electrodes enables to image the activity of individual neurons down to subcellular resolution, which includes the propagation of axonal signals. However, axon recon-struction, to date, mainly relies on a manual approach to select the electrodes and channels that seemingly record the signals along a specific axon, while an automated approach to track multiple axonal branches in extracellular action-potential recordings is still missing.

In this article, we propose a fully automated approach to reconstruct axons from extracellular electrical-potential landscapes, so-called “electrical footprints” of neurons. After an initial electrode and channel selection, the proposed method first constructs a graph, based on the voltage signal amplitudes and latencies. Then, the graph is interrogated to extract possible axonal branches. Finally, the axonal branches are pruned and axonal action-potential propagation velocities are computed.

We first validate our method using simulated data from detailed reconstructions of neurons, showing that our approach is capable of accurately reconstructing axonal branches. We then apply the reconstruction algorithm to experimental recordings of HD-MEAs and show that it can be used to determine axonal morphologies and signal-propagation velocities at high throughput.

We introduce a fully automated method to reconstruct axonal branches and estimate axonal action-potential propagation velocities using HD-MEA recordings. Our method yields highly reliable and reproducible velocity estimations, which constitute an important electrophysiological feature of neuronal preparations.
Scalability of large neural network simulations via activity tracking with time asynchrony and procedural connectivity
Authors: Mascart Cyrille , Scarella Gilles , Reynaud-Bouret Patricia , Muzy Alexandre
Published: June 2021

We present a new algorithm to efficiently simulate random models of large neural networks satisfying the property of time asynchrony. The model parameters (average firing rate, number of neurons, synaptic connection probability, and postsynaptic duration) are of the order of magnitude of a small mammalian brain, or of human brain areas. Through the use of activity tracking and procedural connectivity (dynamical regeneration of synapses), both computational and memory complexities of this algorithm are proved to be theoretically linear with the number of neurons. These results are experimentally validated by sequential simulations of millions of neurons and billions of synapses running in few minutes using a single thread of an equivalent desktop computer.
Age-related increases in reaction time result from slower preparation, not delayed initiation
Authors: Hardwick Robert M , Forrence Alexander D. , Costello Maria Gabriela , Zackowski Kathy , Haith Adrian M
Published: June 2021

Recent work indicates that healthy younger adults can prepare accurate responses faster than their voluntary reaction times indicate, leaving a seemingly unnecessary delay of 80-100ms before responding. Here we examined how the preparation of movements, initiation of movements, and the delay between them are affected by ageing. Participants made planar reaching movements in two conditions. The ‘Free Reaction Time’ condition assessed the voluntary reaction times with which participants responded to the appearance of a stimulus. The ‘Forced Reaction Time’ condition assessed the minimum time actually needed to prepare accurate movements by controlling the time allowed for movement preparation. The time taken to both initiate movements in the Free Reaction Time and to prepare movements in the Forced Response condition increased with age. Notably, the time required to prepare accurate movements was significantly shorter than participants’ self-selected initiation times; however, the delay between movement preparation and initiation remained consistent across the lifespan (~90ms). These results indicate that the slower reaction times of healthy older adults are not due to an increased hesitancy to respond, but can instead be attributed to changes in their ability to process stimuli and prepare movements accordingly, consistent with age-related changes in brain structure and function.
Mathematical modeling of the effects of Wnt-10b on bone metabolism
Authors: Cook Carley V. , Islam Mohammad Aminul , Smith Brenda J. , Ford Versypt Ashlee N.
Published: June 2021

Bone health is determined by factors including bone metabolism or remodeling. Wnt-10b alters osteoblastogenesis through pre-osteoblast proliferation and differentiation and osteoblast apoptosis rate, which collectively lead to the increase of bone density. To model this, we adapted a previously published model of bone remodeling. The resulting model for the bone compartment includes differential equations for active osteoclasts, pre-osteoblasts, osteoblasts, osteocytes, and the amount of bone present at the remodeling site. Our alterations to the original model consist of extending it past a single remodeling cycle and implementing a direct relationship to Wnt-10b. Four new parameters were estimated and validated using normalized data from mice. The model connects Wnt-10b to bone metabolism and predicts the change in trabecular bone volume caused by a change in Wnt-10b input. We find that this model predicts the expected increase in pre-osteoblasts and osteoblasts while also pointing to a decrease in osteoclasts when Wnt-10b is increased.
Plasmodium falciparum Acetyl-CoA Synthetase is essential for parasite intraerythrocytic development and chromatin modification
Authors: Prata Isadora Oliveira , Galindo Cubillos Eliana Fernanda , Barbosa Deibs , Martins Joaquim , Setubal João Carlos , Wunderlich Gerhard
Published: June 2021

The malaria parasite Plasmodium falciparum possesses a unique Acetyl-CoA Synthetase (PfACS) which provides acetyl moieties for different metabolic and regulatory cellular pathways. We characterized PfACS and studied its role focusing on epigenetic modifications using the var gene family as reporter genes. For this, mutant lines to modulate plasmodial ACS expression by degron-mediated protein degradation or ribozyme induced transcript decay were created. Additionally, an ACS inhibitor was tested for its effectiveness and specificity in interfering with PfACS. The knockdown of PfACS or its inhibition led to impaired parasite growth. Decreased levels of PfACS also led to differential histone acetylation patterns, altered variant gene expression and concomitantly decreased cytoadherence of infected red blood cells containing knocked-down parasites. Further, ChIP analysis revealed the presence of PfACS in many loci in ring stage parasites, underscoring its involvement in the regulation of chromatin. Due to its significant differences to human ACS, PfACS seems an interesting target for drug development.
Proliferation maintains the undifferentiated status of stem cells: the role of the planarian cell cycle regulator Cdh1
Authors: Sato Yuki , Umesono Yoshihiko , Kuroki Yoshihito , Agata Kiyokazu , Hashimoto Chikara
Published: June 2021

The coincidence of cell cycle arrest and differentiation has been described in a wide variety of stem cells and organisms for decades, but the causal relationship is still unclear due to the complicated regulation of the cell cycle. Here, we used the planarian Dugesia japonica since it possesses a quite simple cell cycle regulation in which cdh1 is the only factor that arrests the cell cycle. When cdh1 was functionally inhibited, the planarians could not maintain their tissue homeostasis and could not regenerate their missing body parts. While the ablation of cdh1 caused pronounced propagation of the stem cells, the progenitor and differentiated cells were decreased. Further analysis indicated that the stem cells without cdh1 expression did not undergo differentiation even though they received ERK signaling activation as an induction signal. These results suggested that stem cells could not acquire differentiation competence without cell cycle arrest. Thus, we propose that cell cycle regulation determines the differentiation competence and that cell cycle exit to G0 enables stem cells to undergo differentiation.

Summary statement

By using planarians, which have quite simple cell cycle regulation, we revealed that stem cells with cell cycle progression could not undergo differentiation even though an induction signal was activated.
Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome
Authors: Kindschuh William F. , Baldini Federico , Liu Martin C. , Gerson Kristin D. , Liao Jingqiu , Lee Harry H. , Anton Lauren , Gajer Pawel , Ravel Jacques , Levy Maayan , Elovitz Michal A. , Korem Tal
Published: June 2021

Spontaneous preterm birth (sPTB) is a leading cause of maternal and neonatal morbidity and mortality, yet both its prevention and early risk stratification are limited. The vaginal microbiome has been associated with PTB risk, possibly via metabolic or other interactions with its host. Here, we performed untargeted metabolomics on 232 vaginal samples, in which we have previously profiled the microbiota using 16S rRNA gene sequencing. Samples were collected at 20-24 weeks of gestation from women with singleton pregnancies, of which 80 delivered spontaneously before 37 weeks of gestation. We find that the vaginal metabolome correlates with the microbiome and separates into six clusters, three of which are associated with spontaneous preterm birth (sPTB) in Black women. Furthermore, while we identify five metabolites that associate with sPTB, another five associate with sPTB only when stratifying by race. We identify multiple microbial correlations with metabolites associated with sPTB, including intriguing correlations between vaginal bacteria that are considered sub-optimal and metabolites that were enriched in women who delivered at term. We propose that several sPTB-associated metabolites may be exogenous, and investigate another using metabolic models. Notably, we use machine learning models to predict sPTB risk using metabolite levels, weeks to months in advance, with high accuracy. We show that these predictions are more accurate than microbiome-based and maternal covariates-based models. Altogether, our results demonstrate the potential of vaginal metabolites as early biomarkers of sPTB and highlight exogenous exposures as potential risk factors for prematurity.
Insights into rRNA processing and modification mapping in Archaea using Nanopore-based RNA sequencing
Authors: Grünberger Felix , Jüttner Michael , Knüppel Robert , Ferreira-Cerca Sébastien , Grohmann Dina
Published: June 2021

Similar to its bacterial and eukaryotic counterparts, ribosomal RNA maturation in archaea is a multi-step process requiring well-defined endo- and exoribonuclease activities. However, the detailed rRNA processing pathway in archaea remained elusive. Here, we employed long-read direct cDNA and direct RNA Nanopore-based sequencing to study rRNA maturation in three archaeal model organisms, namely the EuryarchaeaHaloferax volcaniiandPyrococcus furiosusand the CrenarchaeonSulfolobus acidocaldarius. Compared to standard short-read protocols, nanopore sequencing facilitates simultaneous readout of 5’- and 3’-positions, which is required for the classification of rRNA processing intermediates. More specifically, we i) accurately detect and describe rRNA maturation stages by analysis of terminal read positions of cDNA reads and thereupon ii) explore the stage-dependent installation of the KsgA-mediated dimethylations inHaloferax volcaniiusing basecalling and signal characteristics of direct RNA reads. Due to the single-molecule sequencing capacity of nanopore sequencing, we could detect hitherto unknown intermediates with high confidence revealing details about the maturation of archaea-specific circular rRNA intermediates. Taken together, our study delineates common principles and unique features of rRNA processing in euryarchaeal and crenarchaeal representatives, thereby providing a comprehensive picture of rRNA maturation pathways in archaea.
VirClust – a tool for hierarchical clustering, core gene detection and annotation of (prokaryotic) viruses
Authors: Moraru Cristina
Published: June 2021

Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called “megataxonomy of viruses”, recognizes five different viral realms, defined based on the presence of viral hallmark genes. Within the realms, viruses are classified into hierarchical taxons, ideally defined by their shared genes. Therefore, there is currently a need for virus classification tools based on such shared genes / proteins. Here, VirClust is presented – a novel tool capable of performing i) hierarchical clustering of viruses based on intergenomic distances calculated from their protein cluster content, ii) identification of core proteins and iii) annotation of viral proteins. VirClust groups proteins into clusters both based on BLASTP sequence similarity, which identifies more related proteins, and also based on hidden markow models (HMM), which identifies more distantly related proteins. Furthermore, VirClust provides an integrated visualization of the hierarchical clustering tree and of the distribution of the protein content, which allows the identification of the genomic features responsible for the respective clustering. By using different intergenomic distances, the hierarchical trees produced by VirClust can be split into viral genome clusters of different taxonomic ranks. VirClust is freely available, as web-service (virclust.icbm.de) and stand-alone tool.
Epigenetic features improve TALE target prediction
Authors: Erkes Annett , Mücke Stefanie , Reschke Maik , Boch Jens , Grau Jan
Published: June 2021

The yield of many crop plants can be substantially reduced by plant-pathogenic Xanthomonas bacteria. The infection strategy of many Xanthomonas strains is based on transcription activator-like effectors (TALEs), which are secreted into the host cells and act as transcriptional activators of plant genes that are beneficial for the bacteria.

The modular DNA binding domain of TALEs contains tandem repeats, each comprising two hyper-variable amino acids. These repeat-variable diresidues (RVDs) bind to a continuous DNA stretch (a target box) and determine the specificity of a TALE. All available tools for the prediction of TALE targets within the host plant suffer from many false positives. In this paper we propose a strategy to improve prediction accuracy by considering the epigenetic state of the host plant genome in the region of the target box. To this end, we extend our previously published tool PrediTALE by two epigenetic features: (i) We allow for filtering target boxes according to chromatin accessibility and (ii) we allow for considering the methylation state of cytosines within the target box during prediction, since DNA methylation may affect the binding specificity of RVDs. Here, we determine the epigenetic features from publicly available DNase-seq, ATAC-seq, and WGBS-seq data in rice.

We benchmark the utility of both epigenetic features separately and in combination, deriving ground-truth from RNA-seq infections studies in rice. We find an improvement for each individual epigenetic feature, but especially the combination of both. Having established an advantage in TALE target predicting considering epigenetic features, we use these data for promoterome and genome-wide scans by our new tool EpiTALE, leading to several novel putative virulence targets.

Our results suggest that it would be worthwhile to collect condition-specific chromatin accessibility data and methylation information when studying putative virulence targets of Xan-thomonas TALEs.
Development Of Novel Multiplex PCR For Rapid Diagnosis Of Coinfected Hemo-Parasites In Cattle
Authors: Kumar Pankaj , Kumar Abhay , Sarma Kamal , Sharma Paresh , Kumari Rashmi Rekha , Kumar Manish
Published: June 2021

A novel, rapid and specific multiplex polymerase chain reaction has been developed for the diagnosis of hemo-parasitic infection in bovine blood by three of the most common hemo-parasites. The reported method relied on the detection of the three different bovine hemoparasites isolated from red blood cells (RBCs) of cattle by conventional Giemsa stained blood smear (GSBS) and confirmed by multiplex PCR. The designed multiplex primer sets can amplify 205, 313 and 422 bp fragments of apocytochrome b, sporozoite and macroschizont 2 (spm2) and 16S rRNA gene for Babesia bigemina, Theileria annulata and Anaplasma marginale, respectively. This multiplex PCR was sensitive with the ability to detect the presence of 150 ng of genomic DNA. The primers used in this multiplex PCR also showed highly specific amplification of specific gene fragments of each respective parasite DNA without the presence of non-specific and non-target PCR products. This multiplex PCR system was used to diagnose GSBS confirmed blood samples (N=12) found infected or co-infected with hemoparasites. A comparison of the two detection methods revealed that 58.33% of specimens showed concordant diagnoses with both techniques. The specificity, positive predictive value and kappa coefficient of agreement was highest for diagnosis of B. bigemina and lowest for A. marginale. The overall Kappa coefficient for diagnosis based on GSBS for multiple pathogen compared to multiplex PCR was 0.56 slightly behind the threshold of 0.6 of agreement. Therefore, confirmation should always be made based on PCR to rule out false positive due to differences in subjective observations, stain particles and false negative due to low level of parasitaemia. The simplicity and rapidity of this specific multiplex PCR method make it suitable for large-scale epidemiological studies and for follow-up of drug treatments.
EEG-based visual deviance detection in freely behaving mice
Authors: Kat Renate , van den Berg Berry , Perenboom Matthijs JL , Schenke Maarten , van den Maagdenberg Arn MJM , Bruining Hilgo , Tolner Else A , Kas Martien JH
Published: June 2021

The mouse is widely used as an experimental model to study visual processing. To probe how the visual system detects changes in the environment, functional paradigms in freely behaving mice are strongly needed. We developed and validated the first EEG-based method to investigate visual deviance detection in freely behaving mice. Mice with EEG implants were exposed to a visual deviant detection paradigm that involved changes in light intensity as standard and deviant stimuli. By subtracting the standard from the deviant evoked waveform, deviant detection was evident as bi-phasic negativity (starting around 70 ms) in the difference waveform. Additionally, deviance-associated evoked (beta/gamma) and induced (gamma) oscillatory responses were found. We showed that the results were stimulus-independent by applying a “flip-flop” design and the results showed good repeatability in an independent measurement. Together, we put forward a validated, easy-to-use paradigm to measure visual deviance processing in freely behaving mice.
Nash equilibria in human sensorimotor interactions explained by Q-Learning
Authors: Lindig-León Cecilia , Schmid Gerrit , Braun Daniel A.
Published: June 2021

The Nash equilibrium concept has previously been shown to be an important tool to understand human sensorimotor interactions, where different actors vie for minimizing their respective effort while engaging in a multi-agent motor task. However, it is not clear how such equilibria are reached. Here, we compare different reinforcement learning models based on haptic feedback to human behavior in sensorimotor versions of three classic games, including the Prisoners’ Dilemma, and the symmetric and asymmetric matching pennies games. We find that a discrete analysis that reduces the continuous sensorimotor interaction to binary choices as in classical matrix games does not allow to distinguish between the different learning algorithms, but that a more detailed continuous analysis with continuous formulations of the learning algorithms and the game-theoretic solutions affords different predictions. In particular, we find that Q-learning with intrinsic costs that disfavor deviations from average behavior explains the observed data best, even though all learning algorithms equally converge to admissible Nash equilibrium solutions. We therefore conclude that it is important to study different learning algorithms for understanding sensorimotor interactions, as such behavior cannot be inferred from a game-theoretic analysis alone, that simply focuses on the Nash equilibrium concept, as different learning algorithms impose preferences on the set of possible equilibrium solutions due to the inherent learning dynamics.
Three recent sex chromosome-to-autosome fusions in aDrosophila virilisstrain with high satellite content
Authors: Flynn Jullien M. , Hu Kevin B. , Clark Andrew G.
Published: June 2021

The karyotype, or number and arrangement of chromosomes, has varying levels of stability across both evolution and disease. Karyotype changes often originate from DNA breaks near the centromeres of chromosomes, which generally contain long arrays of tandem repeats or satellite DNA.Drosophila virilispossesses among the highest relative satellite abundances of studied species, with almost half its genome composed of three related 7bp satellites. We discovered a strain ofD. virilisthat we infer recently underwent three independent chromosome fusion events involving the X and Y chromosomes, in addition to one subsequent fission event. Here we isolate, characterize and propose a timeline for the chromosome fusions in this strain which we believe demonstrates a remarkable karyotype instability. We discovered that one of the substrains with an X-autosome fusion has a X-to-Y chromosome nondisjunction rate 20x higher than theD. virilisreference strain (21% vs. 1%). Finally, we found an overall higher rate of DNA breakage in the substrain with higher satellite DNA compared to a genetically similar substrain with less satellite DNA. This suggests satellite DNA abundance may play a role in the risk of genome instability. Overall, we introduce a novel system consisting of a single strain with four different karyotypes, which we believe will be useful for future studies of genome instability, centromere function, and sex chromosome evolution.
Serotonergic Neurons Mediate Operant Conditioning in Drosophila Larvae
Authors: Klein Kristina T , Croteau-Chonka Elise C , Narayan Lakshmi , Winding Michael , Masson Jean-Baptiste , Zlatic Marta
Published: June 2021

Observed across species, operant conditioning facilitates learned associations between behaviours and outcomes, biasing future action selection to maximise reward and avoid punishment. To elucidate the underlying neural mechanisms, we built a high-throughput tracker for Drosophila melanogaster larvae, combining real-time behaviour detection with closed-loop optogenetic and thermogenetic stimulation capabilities. We demonstrate operant conditioning in Drosophila larvae by inducing a bend direction preference through optogenetic activation of reward-encoding serotonergic neurons. Specifically, we establish that the ventral nerve cord is necessary for this memory formation. Our results extend the role of serotonergic neurons for learning in insects as well as the existence of learning circuits outside the mushroom body. This work supports future studies on the function of serotonin and the mechanisms underlying operant conditioning at both circuit and cellular levels.
A capillary-based microfluidic device enables primary high-throughput room-temperature crystallographic screening
Authors: Sui Shuo , Mulichak Anne , Kulathila Raviraj , McGee Joshua , Filiatreault Danny , Saha Sarthak , Cohen Aina , Song Jinhu , Hung Holly , Selway Jonathan , Kirby Christina , Shrestha Om K. , Weihofen Wilhelm , Fodor Michelle , Xu Mei , Chopra Rajiv , Perry Sarah L.
Published: June 2021

A novel capillary-based microfluidic strategy to accelerate the process of small-molecule-compound screening by room-temperature X-ray crystallography using protein crystals is reported. The ultra-thin microfluidic devices are composed of a UV-curable polymer, patterned by cleanroom photolithography, and have nine capillary channels per chip. The chip was designed for ease of sample manipulation, sample stability and minimal X-ray background. 3D-printed frames and cassettes conforming to SBS standards are used to house the capillary chips, providing additional mechanical stability and compatibility with automated liquid- and sample-handling robotics. These devices enable an innovative in situ crystal-soaking screening workflow, akin to high-throughput compound screening, such that quantitative electron density maps sufficient to determine weak binding events are efficiently obtained. This work paves the way for adopting a room-temperature microfluidics-based sample delivery method at synchrotron sources to facilitate high-throughput protein-crystallography-based screening of compounds at high concentration with the aim of discovering novel binding events in an automated manner.
Simulating and benchmarking neutron total scattering instrumentation from inception of events to reduced and fitted data
Authors: Metz Peter C. , Huegle Thomas , Olds Daniel , Page Katharine
Published: June 2021

In the design and realization of modern neutron scattering instrumentation, particularly when designing beamline concepts from the ground up, it is desirable to fully benchmark against realistically simulated data. This is especially true for total scattering beamlines, where the future deliverable data is to be analysed in both reciprocal- and real-space representations, and needs must be carefully balanced to ensure sufficient range, resolution and flux of the instrument. An approach to optimize the design of neutron scattering instrumentation via a workflow including ray-tracing simulations, event-based data reduction, heuristic analysis and fitting against realistically simulated spectra is demonstrated here. The case of the DISCOVER beamline concept at the Spallation Neutron Source is used as an example. The results of the calculations are benchmarked through simulation of existing instrumentation and subsequent direct comparison with measured data. On the basis of the validated models, the ability to explore design characteristics for future beamline concepts or future instrument improvements is demonstrated through the examples of detector tube size and detector layout.