bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate estimation of cell-type resolution transcriptome in bulk tissue through matrix completion
Authors: Wang Weixu , Zhou Xiaolan , Yao Jun , Wen Haimei , Wang Yi , Sun Mingwan , Zhang Chao , Tao Wei , Zou Jiahua , Ni Ting 
Published: July 2021

AbstractSingle cell RNA-seq (scRNA-seq) has been widely used to uncover cellular heterogeneity, however, the constraints of cost make it impractical as a routine on large patient cohorts. Here we present ENIGMA, a method that accurately deconvolute bulk tissue RNA-seq into single cell-type resolution given the knowledge gained from scRNA-seq. ENIGMA applies a matrix completion strategy to minimize the distance between mixture transcriptome and weighted combination of cell type-specific expression, allowing quantification of cell type proportions and reconstruction of cell type-specific transcriptome. The superior performance of ENIGMA was validated in simulated and realistic datasets, including disease-related tissues, demonstrating its ability in novel biological findings.
STEM CELL TECHNOLOGY PROVIDES NOVEL TOOLS TO UNDERSTAND HUMAN VARIATION IN Plasmodium falciparum MALARIA
Authors: Pance Alena , Ling Bee , Mwikali Kioko , Koutsourakis Manousos , Agu Chukwuma , Rouhani Foad , Ponstingl Hannes , Montandon Ruddy , Law Frances , Rayner Julian C. 
Published: July 2021

ABSTRACTPlasmodium falciparum interacts with several human cell types during their complex life cycle, including erythrocytes and hepatocytes. The enuclated nature of erythrocytes makes them inaccessible to genetic tools, which in turn makes studying erythrocyte proteins involved in malaria invasion and development particularly difficult. Here we overcome this limitation using stem cell technology to develop a universal differentiation protocol for in vitro derivation of erythrocytes from a variety of stem cell lines of diverse origin. This allows manipulation of erythrocytic genes and examination of their impact on the parasite by flow cytometric detection of parasite haemozoin. Deletion of Basigin, the essential receptor for P. falciparum, abrogates invasion, while other less studied proteins such as ATP2B4 have a minor effect. Reprogramming of induced pluripotent stem cells from α-thalassemia primary samples shows reduced infection levels, demonstrating this approach is useful for understanding the effect of natural human polymorphisms on the disease.
High-throughput single-cell TCR - pMHC dissociation rate measurements performed by an autonomous microfluidic cellular processing unit
Authors: Jammes Fabien , Schmidt Julien , Coukos George , Maerkl Sebastian J. 
Published: July 2021

AbstractWe developed an integrated microfluidic cellular processing unit (mCPU) capable of autonomously isolating single cells, perform, measure, and on-the-fly analyze cell-surface dissociation rates, followed by recovery of selected cells. We performed proof-of-concept, high-throughput single-cell experiments characterizing pMHC-TCR interactions on live CD8+ T cells. The mCPU platform analyzed TCR-pMHC dissociation rates with a throughput of 50 cells per hour and hundreds of cells per run, and we demonstrate that cells can be selected, enriched, and easily recovered from the device.
Proper migration of lymphatic endothelial cells requires survival and guidance cues from arterial mural cells
Authors: Peng Di , Ando Koji , Gloger Marleen , Skoczylas Renae , Mochizuki Naoki , Betsholtz Christer , Fukuhara Shigetomo , Koltowska Katarzyna 
Published: July 2021

ABSTRACTThe migration of lymphatic endothelial cells (LECs) is key for the development of the complex and vast lymphatic vascular network that pervades most of the tissues in an organism. In zebrafish, arterial intersegmental vessels together with chemokines have been shown to promote lymphatic cell migration from the horizontal myoseptum (HM). Here we found that LECs departure from HM coincides with the emergence of mural cells around the intersegmental arteries, raising the possibility that arterial mural cells promote LEC migration. Our live imaging and cell ablation experiments revealed that LECs migrate slower and fail to establish the lymphatic vascular network in the absence of arterial mural cells. We determined that mural cells are a source for the C-X-C motif chemokine 12 (Cxcl12a and Cxcl12b) and vascular endothelial growth factor C (Vegfc). We showed that ERK, a downstream component of Vegfc-Vegfr3 singling cascade, is activated in migrating LECs and that both chemokine and growth factor signalling is required for the robust migration. Furthermore, Vegfc-Vegfr3 has a pro-survival role in LECs during the migration. Together, the identification of mural cells a source for signals that guide LEC migration and survival will be important in the future design for rebuilding lymphatic vessels in the disease contexts.
Epileptiform GluN2B–driven excitation in hippocampus as a therapeutic target against temporal lobe epilepsy
Authors: Gorlewicz Adam , Pijet Barbara , Orlova Krstina , Kaczmarek Leszek , Knapska Ewelina 
Published: July 2021

AbstractNMDAR is an ionotropic glutamate receptor critically involved in excitatory synaptic transmission. The receptor properties are strongly determined by its subunit composition. One of the NMDAR subunits is GluN2B, which displays restricted and spatially different from other subunits expression in the mature brain. GluN2B–containing NMDARs are present in the hippocampus – a structure playing a major role in temporal lobe epilepsy (TLE). However, the contribution of GluN2B to pathophysiology of TLE has not been fully explored. Here, we report the functional alterations of GluN2B–containing NMDAR receptors in the hippocampus in distinct mouse models of temporal lobe epilepsy. In particular, we show the impact of GluN2B on excitatory feedback in granule cells. Based on these results, we propose a mechanism–oriented effective antiepileptic strategy that selectively antagonizes GluN2B–containing NMDARs with ifenprodil, a well–known GluN2B antagonist. Collectively, our research identifies GluN2B as one of the pivotal factors in pathogenesis of temporal lobe epilepsy and associated recurrent seizures. Furthermore, our study indicates the prospective antiepileptic properties of ifenprodil in TLE.
Evaluation of FRET X for Single-Molecule Protein Fingerprinting
Authors: de Lannoy Carlos , Filius Mike , van Wee Raman , Joo Chirlmin , de Ridder Dick 
Published: July 2021

AbstractSingle-molecule protein identification is a novel, as of yet unrealized concept with potentially groundbreaking applications in biological research. We propose a method called FRET X (Förster Resonance Energy Transfer via DNA eXchange) fingerprinting, in which the FRET efficiency is read out between exchangeable dyes on protein-bound DNA docking strands, and accumulated FRET efficiency values constitute the fingerprint for a protein. To evaluate the feasibility of this approach, we simulated fingerprints for hundreds of proteins using a coarse-grained lattice model and experimentally demonstrated FRET X fingerprinting on a system of model peptides. Measured fingerprints are in agreement with our simulations, corroborating the validity of our modeling approach. In a simulated complex mixture of >300 human proteins of which only cysteines, lysines and arginines were labeled, a support vector machine was able to identify constituents with 95% accuracy. We anticipate that our FRET X fingerprinting approach will form the basis of an analysis tool for targeted proteomics.
Electrical synapse asymmetry results from, and masks, neuronal heterogeneity
Authors: Mendoza Austin , Haas Julie S. 
Published: July 2021

ABSTRACTElectrical synapses couple inhibitory neurons across the brain, underlying a variety of functions that are modifiable by activity. Despite recent advances, many basic functions and contributions of electrical synapses within neural circuitry remain underappreciated. Among these is the source and impact of electrical synapse asymmetry. Using multi-compartmental models of neurons coupled through dendritic electrical synapses, we investigated intrinsic factors that contribute to synaptic asymmetry and that result in modulation of spike time between coupled cells. We show that electrical synapse location along a dendrite, input resistance, internal dendritic resistance, or directional conduction of the electrical synapse itself each alter asymmetry as measured by coupling between cell somas. Conversely, true synapse asymmetry can be masked by each of these properties. Furthermore, we show that asymmetry alters the spiking timing and latency of coupled cells by up to tens of milliseconds, depending on direction of conduction or dendritic location of the electrical synapse. These simulations illustrate that causes of asymmetry are multifactorial, may not be apparent in somatic measurements of electrical coupling, influence dendritic processing, and produce a variety of outcomes on spike timing of coupled cells. Our findings highlight aspects of electrical synapses that should be considered in experimental demonstrations of coupling, and when assembling networks containing electrical synapses.
Characterization of the Brassica napus flavonol synthase gene family reveals bifunctional flavonol synthases
Authors: Schilbert Hanna Marie , Schöne Maximilian , Baier Thomas , Busche Mareike , Viehöver Prisca , Weisshaar Bernd , Holtgräwe Daniela 
Published: July 2021

AbstractFlavonol synthase (FLS) is a key enzyme for the formation of flavonols, which are a subclass of the flavonoids. FLS catalyses the conversion of dihydroflavonols to flavonols. The enzyme belongs to the 2-oxoglutarate-dependent dioxygenases (2-ODD) superfamily. We characterized the FLS gene family of Brassica napus that covers 13 genes, based on the genome sequence of the B. napus cultivar Express 617. The goal was to unravel which BnaFLS genes are relevant for seed flavonol accumulation in the amphidiploid species B. napus. Two BnaFLS1 homeologs were identified and shown to encode bifunctional enzymes. Both exhibit FLS activity as well as flavanone 3-hydroxylase (F3H) activity, which was demonstrated in vivo and in planta. BnaFLS1-1 and -2 are capable of converting flavanones into dihydroflavonols and further into flavonols. Analysis of spatio-temporal transcription patterns revealed similar expression profiles of BnaFLS1 genes. Both are mainly expressed in reproductive organs and co-expressed with the genes encoding early steps of flavonoid biosynthesis. Our results provide novel insights into flavonol biosynthesis in B. napus and contribute information for breeding targets with the aim to modify the flavonol content in rapeseed.
Intratumoral Heterogeneity Promotes Collective Cancer Invasion Through NOTCH1 Variation
Authors: Torab Peter , Yan Yue , Ahmed Mona , Yamashita Hironobu , Warrick Joshua I. , Raman Jay D. , DeGraff David J. , Wong Pak Kin 
Published: July 2021

AbstractCellular and molecular heterogeneity within tumors has long been associated with the progression of cancer to an aggressive phenotype and a poor prognosis. However, how such intratumoral heterogeneity contributes to the invasiveness of cancer is largely unknown. Here, using a multidisciplinary approach, we investigate the interaction between molecular subtypes within bladder microtumors and the corresponding effects on their invasiveness. Our results reveal heterogeneous microtumors formed by multiple molecular subtypes possess enhanced invasiveness compared to individual cells, even when both cells are not invasive individually. To examine the molecular mechanism of intratumoral heterogeneity mediated invasiveness, live single cell biosensing, RNA interference, and CRISPR-Cas9 gene editing approaches were applied to investigate and control the composition of the microtumors. An agent-based computational model was also developed to evaluate the influence of NOTCH1 variation on DLL4 expression within a microtumor. The data indicate that variation in NOTCH1 expression can lead to upregulation of DLL4 expression within the microtumor and enhancement of microtumor invasiveness. Overall, our results reveal a novel mechanism of heterogeneity mediated invasiveness through intratumoral variation of gene expression.Summary statementThis study reveals a mechanism that Notch1 variation, instead of the average value, promotes the invasiveness of microtumor, providing a link between intratumoral heterogeneity and collective cancer invasion.
The development of ovine gastric and intestinal organoids for studying ruminant host-pathogen interactions
Authors: Smith David , Price Daniel R. G. , Burrells Alison , Faber Marc N. , Hildersley Katie A. , Chintoan-Uta Cosmin , Chapuis Ambre F. , Stevens Mark , Stevenson Karen , Burgess Stewart T. G. , Innes Elisabeth A. , Nisbet Alasdair J. , McNeilly Tom N. 
Published: July 2021

AbstractGastrointestinal (GI) infections in sheep have significant implications for animal health, welfare and productivity, as well as being a source of zoonotic pathogens. Interactions between pathogens and epithelial cells at the mucosal surface play a key role in determining the outcome of GI infections; however, the inaccessibility of the GI tract in vivo significantly limits the ability to study such interactions in detail. We therefore developed ovine epithelial organoids representing physiologically important gastric and intestinal sites of infection, specifically the abomasum (analogous to the stomach in monogastrics) and ileum. We show that both abomasal and ileal organoids form self-organising three-dimensional structures with a single epithelial layer and a central lumen that are stable in culture over serial passage. We performed RNA-seq analysis on abomasal and ileal tissue from multiple animals and on organoids across multiple passages and show the transcript profile of both abomasal and ileal organoids cultured under identical conditions are reflective of the tissue from which they were derived and that the transcript profile in organoids is stable over at least five serial passages. In addition, we demonstrate that the organoids can be successfully cryopreserved and resuscitated, allowing long-term storage of organoid lines, thereby reducing the number of animals required as a source of tissue. We also report the first published observations of a helminth infecting gastric and intestinal organoids by challenge with the sheep parasitic nematode Teladorsagia circumcincta, demonstrating the utility of these organoids for pathogen co-culture experiments. Finally, the polarity in the abomasal and ileal organoids can be inverted to make the apical surface directly accessible to pathogens or their products, here shown by infection of apical-out organoids with the zoonotic enteric bacterial pathogen Salmonella enterica serovar Typhimurium. In summary, we report a simple and reliable in vitro culture system for generation and maintenance of small ruminant intestinal and gastric organoids. In line with 3Rs principals, use of such organoids will reduce and replace animals in host-pathogen research.
Bayesian calibration, process modeling and uncertainty quantification in biotechnology
Authors: Helleckes Laura Marie , Osthege Michael , Wiechert Wolfgang , von Lieres Eric , Oldiges Marco 
Published: July 2021

AbstractHigh-throughput experimentation has revolutionized data-driven experimental sciences and opened the door to the application of machine learning techniques. Nevertheless, the quality of any data analysis strongly depends on the quality of the data and specifically the degree to which random effects in the experimental data-generating process are quantified and accounted for. Accordingly calibration, i.e. the quantitative association between observed quantities with measurement responses, is a core element of many workflows in experimental sciences. Particularly in life sciences, univariate calibration, often involving non-linear saturation effects, must be performed to extract quantitative information from measured data. At the same time, the estimation of uncertainty is inseparably connected to quantitative experimentation. Adequate calibration models that describe not only the input/output relationship in a measurement system, but also its inherent measurement noise are required. Due to its mathematical nature, statistically robust calibration modeling remains a challenge for many practitioners, at the same time being extremely beneficial for machine learning applications. In this work, we present a bottom-up conceptual and computational approach that solves many problems of understanding and implementing non-linear, empirical calibration modeling for quantification of analytes and process modeling. The methodology is first applied to the optical measurement of biomass concentrations in a high-throughput cultivation system, then to the quantification of glucose by an automated enzymatic assay. We implemented the conceptual framework in two Python packages, with which we demonstrate how it makes uncertainty quantification for various calibration tasks more accessible. Our software packages enable more reproducible and automatable data analysis routines compared to commonly observed workflows in life sciences. Subsequently, we combine the previously established calibration models with a hierarchical Monod-like differential equation model of microbial growth to describe multiple replicates of Corynebacterium glutamicum batch microbioreactor cultures. Key process model parameters are learned by both maximum likelihood estimation and Bayesian inference, highlighting the flexibility of the statistical and computational framework.
Quantitative modeling of regular retinal microglia distribution
Authors: Endo Yoshie , Asanuma Daisuke , Namiki Shigeyuki , Hirose Kenzo , Uemura Akiyoshi , Kubota Yoshiaki , Miura Takashi 
Published: July 2021

1AbstractMicroglia are resident immune cells in the central nervous system (CNS), showing a regular distribution. Advancing microscopy and image processing techniques have contributed to elucidating microglia’s morphology, dynamics, and distribution. However, the mechanism underlying the regular distribution of microglia remains to be elucidated.First, we quantitatively confirmed the regularity of the distribution pattern of microglial soma. Second, we formulated a mathematical model that includes factors that may influence regular distribution. Next, we experimentally quantified the model parameters (cell movement, process formation, and ATP dynamics). The resulting model simulation from the measured parameters showed that direct cell-cell contact is most important in generating regular cell spacing. Finally, we tried to specify the molecular pathway responsible for the repulsion between neighboring microglia.Author summaryMicroglia are resident immune cells in the central nervous system. It is known that the microglia cells show a regular distribution, but the mechanism underlying the regular distribution remains to be elucidated. In the present study, we quantitatively assayed the regularity of the microglia soma distribution using the image processing technique. Next, we formulated a mathematical model of cell distribution that includes factors that may influence regular distribution. Next, we experimentally quantified the model parameters using organ culture. As a result, we obtained parameters for cell migration, cell process dynamics, and extracellular ATP dynamics. Then we undertook numerical simulation of the mathematical model using the parameters obtained by the experiments. The resulting model simulations showed that direct cell-cell contact is the most important factor in generating regular spacing. Finally, we screened possible molecular pathways involved in the regular spacing of microglia, which confirmed the validity of the model.
Mechanistic model-driven exometabolomic characterisation of human dopaminergic neuronal metabolism
Authors: Preciat German , Wegrzyn Agnieszka B. , Moreno Edinson Lucumi , Willacey Cornelius C.W. , Modamio Jennifer , Monteiro Fatima L. , El Assal Diana , Schurink Alissa , Oliveira Miguel A.P. , Zhang Zhi , Cousins Ben , Haraldsdóttir Hulda S. , Hachi Siham , Zach Susanne , Leparc German , Lee Yin Tat , Hengerer Bastian , Vempala Santosh , Saunders Michael A. , Harms Amy , Glaab Enrico , Schwamborn Jens C. , Thiele Ines , Hankemeier Thomas , Fleming Ronan M.T. 
Published: July 2021

AbstractStarting with a comprehensive generic reconstruction of human metabolism, we generated high-quality, constraint-based, genome-scale, cell-type and condition specific models of metabolism in human dopaminergic neurons, the cell type most vulnerable to degeneration in Parkinson’s disease. They are a synthesis of extensive manual curation of the biochemical literature on neuronal metabolism, together with novel, quantitative, transcriptomic and targeted exometabolomic data from human stem cell-derived, midbrainspecific, dopaminergic neuronsin vitro. Thermodynamic constraint-based modelling enabled qualitatively accurate and moderately quantitatively accurate prediction of dopaminergic neuronal metabolite exchange fluxes, including predicting the consequences of metabolic perturbations in a manner also consistent with literature on monogenic mitochondrial Parkinson’s disease. These dopaminergic neurons models provide a foundation for a quantitative systems biochemistry approach to metabolic dysfunction in Parkinson’s disease. Moreover, the plethora of novel mathematical and computational approaches required to develop them are generalisable to study any other disease associated with metabolic dysfunction.
Evolution of a minimal cell
Authors: Moger-Reischer RZ , Glass JI , Wise KS , Sun L , Bittencourt D , Lynch M , Lennon JT 
Published: July 2021

ABSTRACTPossessing only essential genes, a minimal cell can reveal mechanisms and processes that are critical for the persistence and stability of life. Here, we report on how a synthetically constructed minimal cell contends with the forces of evolution compared to a non-minimized cell from which it was derived. Genome streamlining was costly, but 80% of fitness was regained in 2000 generations. Although selection acted upon divergent sets of mutations, the rates of adaptation in the minimal and non-minimal cell were equivalent. The only apparent constraint of minimization involved epistatic interactions that inhibited the evolution of cell size. Together, our findings demonstrate the power of natural selection to rapidly optimize fitness in the simplest autonomous organism, with implications for the evolution of cellular complexity.