bluuebunny/crossref_metadata_2025 huggingface dataset:
FFA and OFA encode distinct types of face identity information
Authors: Tsantani Maria , Kriegeskorte Nikolaus , Storrs Katherine , Williams Adrian Lloyd , McGettigan Carolyn , Garrido Lúcia
Published: May 2020

Faces of different people elicit distinct functional MRI (fMRI) patterns in several face-selective brain regions. Here we used representational similarity analysis to investigate what type of identity-distinguishing information is encoded in three face-selective regions: fusiform face area (FFA), occipital face area (OFA), and posterior superior temporal sulcus (pSTS). We used fMRI to measure brain activity patterns elicited by naturalistic videos of famous face identities, and compared their representational distances in each region with models of the differences between identities. Models included low-level to high-level image-computable properties and complex human-rated properties. We found that the FFA representation reflected perceived face similarity, social traits, and gender, and was well accounted for by the OpenFace model (deep neural network, trained to cluster faces by identity). The OFA encoded low-level image-based properties (pixel-wise and Gabor-jet dissimilarities). Our results suggest that, although FFA and OFA can both discriminate between identities, the FFA representation is further removed from the image, encoding higher-level perceptual and social face information.
Complex small-world regulatory networks emerge from the 3D organisation of the human genome
Authors: Brackley C. A. , Gilbert N. , Michieletto D. , Papantonis A. , Pereira M. C. F. , Cook P. R. , Marenduzzo D.
Published: May 2020

The discovery that overexpressing one or a few critical transcription factors can switch cell state suggests that gene regulatory networks are relatively simple. In contrast, genome-wide association studies (GWAS) point to complex phenotypes being determined by hundreds of loci that rarely encode transcription factors and which individually have small effects. Here, we use computer simulations and a simple fitting-free polymer model of chromosomes to show that spatial correlations arising from 3D genome organisation naturally lead to stochastic and bursty transcription plus complex small-world regulatory networks (where the transcriptional activity of each genomic region subtly affects almost all others). These effects require factors to be present at sub-saturating levels; increasing levels dramatically simplifies networks as more transcription units are pressed into use. Consequently, results from GWAS can be reconciled with those involving overexpression. We apply this pan-genomic model to predict patterns of transcriptional activity in whole human chromosomes, and, as an example, the effects of the deletion causing the diGeorge syndrome.
Genome-wide analyses of transcription factors and co-regulators across seven cohorts identified reduced PPARGC1A expression as a driver of prostate cancer progression
Authors: Siddappa Manjunath , Wani Sajad A. , Long Mark D. , Leach Damien A , Mathé Ewy A. , Bevan Charlotte L. , Campbell Moray J.
Published: May 2020

Defining altered transcription factor (TF) and coregulators that are oncogenic drivers remains a challenge, in part because of the multitude of TFs and coregulators. We addressed this challenge by using bootstrap approaches to test how expression, copy number alterations or mutation of TFs (n = 2662), coactivators (COA; n= 766); corepressor (COR; n = 599); mixed function coregulators (MIXED; n = 511) varied across seven prostate cancer (PCa) cohorts (three of localized and four advanced disease). COAS, CORS, MIXED and TFs all displayed significant down-regulated expression (q.value < 0.1) and correlated with protein expression (ρ 0.4 to 0.55). Stringent expression filtering identified commonly altered TFs and coregulators including well-established (e.g. ERG) and underexplored (e.g.PPARGC1A, encodes PGC1α) in localized PCa. ReducedPPARGC1Aexpression significantly associated with worse disease-free survival in two cohorts of localized PCa. Stable PGC1α knockdown in LNCaP cells increased growth rates and invasiveness and RNA-Seq revealed a profound basal impact on gene expression (~2300 genes; FDR < 0.05, logFC > 1.5), but only modestly impacted PPARγ responses. GSEA analyses of the PGC1α transcriptome revealed that it significantly altered the AR-dependent transcriptome, and was enriched for epigenetic modifiers. PGC1α-dependent genes were overlapped with PGC1α-ChIP-Seq genes and significantly associated in TCGA with higher grade tumors and worse disease-free survival. Together these data demonstrate an approach to identify cancer-driver coregulators in cancer and that PGC1α expression is clinically significant yet underexplored coregulator in aggressive early stage PCa.
Performance and behavioral flexibility on a complex motor task depend on available sensory inputs in early blind and sighted short-tailed opossums
Authors: Englund Mackenzie , Faridjoo Samaan , Iyer Chris , Krubitzer Leah
Published: May 2020

The early loss of vision results in a reorganized visual cortex that processes tactile and auditory inputs. Recent studies in the short-tailed opossum (Monodelphis domestica)found that the connections and response properties of neurons in somatosensory cortex of early blind animals are also altered. While research in humans and other mammals shows that early vision loss leads to heightened abilities on discrimination tasks involving the spared senses, if and how this superior discrimination leads to adaptive sensorimotor behavior has yet to be determined. Moreover, little is known about the extent to which blind animals rely on the spared senses. Here, we tested early blind opossums on a sensorimotor task involving somatosensation and found that they had increased limb placement accuracy. However, increased reliance on tactile inputs in early blind animals resulted in greater deficits in limb placement and behavioral flexibility when the whiskers were trimmed.
Effects of High-Grain Diet with Buffering Agent on the Milk Protein Synthesis in Lactating Goats
Authors: He Meilin , Nie Xintian , Wang Huanhuan , Yan Shuping , Zhang Yuanshu
Published: May 2020

Feeding of straw as main roughage with numerous high-grain diets improves the performance of ruminants but it can easily lead to subacute ruminal acidosis. In recent years, buffering agent is applied to prevent the acid poisoning of ruminants and improve the production performance of ruminants in animal husbandry. it is necessary to understand feeding high-grain diet with buffering agent which transport carriers amino acids mainly take amino acids into the mammary gland and the signal mechanism of amino acids in the mammary gland synthesize milk proteins. To gain insight on the effects of a high-grain diet with buffering agent on the amino acids in the jugular blood, and the effects of amino acids on the synthesis of milk protein, commercial kit and high performance liquid chromatography (HPLC) were applied to determine the concentration of amino acids of jugular blood samples, quantitative real-time PCR, comparative proteomic approach and western blot were employed to investigate proteins differentially expressed in mammary tissues and the mechanism of amino acids on the synthesis of milk protein in mammary gland of lactating dairy goats fed high-grain diet with buffering agent or only high-grain diet.

Results showed that feeding high-grain diet with buffering agent to lactating dairy goats could outstanding increase amino acid content of jugular blood (p<0.05), and mRNA transcriptional level of amino acid transporters in the mammary gland were also increased; the CSN2 and LF protein expression level were significant higher by 2-DE technique, MALDI-TOF/TOF proteomics analyzer and western blot analysis further validated in mammary of lactating dairy goats compared with high-grain group; the research on the mechanism of milk protein synthesis increasing suggested that it was related to the activation of mTOR pathway signaling.

Feeding of high-grain diet with buffering agent promoted the jugular vein blood of amino acids concentration, and more amino acids flowed into the mammary. In addition, milk protein synthesis was increased and the increase of milk protein synthesis was related to the activation of mTOR pathway signalling.
A novel tool for standardizing clinical data in a realism-based common data model
Authors: Freedman Hayden G. , Williams Heather , Miller Mark A. , Birtwell David , Mowery Danielle L. , Stoeckert Christian J.
Published: May 2020

Standardizing clinical information in a common data model is important for promoting interoperability and facilitating high quality research. Semantic Web technologies such as Resource Description Framework can be utilized to their full potential when a clinical data model accurately reflects the reality of the clinical situation it describes. To this end, the Open Biomedical Ontologies Foundry provides a set of ontologies that conform to the principles of realism and can be used to create a realism-based clinical data model. However, the challenge of programmatically defining such a model and loading data from disparate sources into the model has not been addressed by pre-existing software solutions. The PennTURBO Semantic Engine is a tool developed at the University of Pennsylvania that works in conjunction with data aggregation software to transform source-specific RDF data into a source-independent, realism-based data model. This system sources classes from an application ontology and specifically defines how instances of those classes may relate to each other. Additionally, the system defines and executes RDF data transformations by launching dynamically generated SPARQL update statements. The Semantic Engine was designed as a generalizable RDF data standardization tool, and is able to work with various data models and incoming data sources. Its human-readable configuration files can easily be shared between institutions, providing the basis for collaboration on a standard realism-based clinical data model.
Cobalt(III) Schiff Base complexes stabilize non-fibrillar amyloid-β aggregates with reduced toxicity
Authors: Roberts K. F. , Brue C. R. , Preston A. , Baxter D. , Herzog E. , Varelas E. , Meade T. J.
Published: May 2020

The aggregation of Aβ is believed to be foundational to the pathogenesis of Alzheimer’s disease (AD).In vitroaggregation kinetics have been shown to correlate with rates of disease progression in both AD patients and animal models, thus proving to be a useful metric for testing Aβ-targeted therapeutics. Here we present evidence of Cobalt(III) Schiff base complex (Co(III)-sb) modulation of Aβ aggregation kinetics by a variety of complementary techniques. These include Thioflavin T (ThT) fluorescence, circular dichroism (CD) spectroscopy, transmission electron microscopy (TEM), and atomic force microscopy (AFM). Our data was fitted to kinetic rate laws using a mathematical model developed by Knowles et al. in order to extract mechanistic information about the effect of Co(III)-sb on aggregation kinetics. Our analysis revealed that Co(III)-sb significantly decreases the kinetic parameter k+,and significantly increases the polymerization rate kn, suggesting that Co(III)-sb causes Aβ to rapidly form stable oligomeric species that are unable to elongate into mature fibrils. This result was corroborated by TEM and AFM of Aβ aggregatesin vitro. We also demonstrate that Aβ aggregate mixtures produced in the presence of Co(III)-sb exhibit decreased cytotoxicity compared to untreated samples.

Statement of Significance

Amyloid-β is thought to be a key mediator in the pathology of Alzheimer’s disease, yet its precise mechanisms of toxicity are poorly understood. The interaction of Aβ with endogenous metal ions via its N terminal Histidine residues has been shown to alter the peptide’s aggregation and toxicity. As such, metal-based complexes have been developed both as therapeutic agents as well as tools for investigating the role of metal binding in the pathogenesis of AD. This work expands on our previous studies developing Cobalt(III) Schiff base complexes as amyloid inhibitors. Here we demonstrate effective inhibition of aggregation by various complementary modalities. Additionally we show that Co(III)-sb reduces the toxicity of Aβ aggregates to cells in culture.
Are mice born normally with an egg-only diet?
Authors: Isobe Ken-ichi , Sato Natsumi , Ono Karin , Fujita Haruka , kawamura Marin , Sasaki Harumi , Yamamoto Saori , Nishio Naomi
Published: May 2020

Chicken eggs (egg) contain high amounts of important proteins and fat with a very low amount of carbohydrates, and also contain all vitamins and minerals needed for the chick to develop. We mated 8-week-old mice consuming an egg-only diet, and examined whether mice got pregnant and mice gave birth. Then we continued to raise newborn mice only consuming an egg-only diet compared to normal chew diet. We found that the rate of pregnancy of the mice consuming an egg-only diet was not different from that of the mice consuming normal chew diet. Further, we found that the number of pupus born from the mother consuming only eggs was not different from that of the mother consuming normal chew diet. However, the newborn mice from the mother fed only eggs did not grow healthy when they consume egg-only diet. Only few mice were alive at one month after birth. Then we change the diet just before or just after birth from egg only diet to normal chew diet and we found that both group grew healthy more than one month. These results indicate that mice are born healthy only with egg only diet.
Effect of different derivatization protocols on the calculation of trophic position using amino acids compound-specific stable isotopes
Authors: Martinez Stephane , Lalzer Maya , Shemesh Eli , Einbinder Shai , Tchernov Beverly Goodman , Tchernov Dan
Published: May 2020

Amino acids compound-specific nitrogen stable isotope (AA-CSIA) is an emerging tool in ecology for understanding trophic system dynamics. While it has been successfully used for several independent studies across a range of environments and study locations, researchers have encountered calculation issues for determining trophic position values. Most studies introduce modifications to the constants of trophic position equation calculations, but then fail to account for the equation variations when comparing the results of separate research studies. The acceptance of this approach is related to the underlying presumption that no addition of the exogenous nitrogen atom occurs in the different methods and, therefore, such variations should not affect the outcome. In this paper, we evaluate the use of the EZfaast amino acid derivatization kit (chloroformate) and compare it to the isotopic results of two other derivatization methods. We highlight new considerations for working with AA-CSIA that might account for some of the variations in the results and lead researchers to modify constants in the equation. This likely requires developing the unique constants per derivatization method in order to be able to compare the trophic position results across different studies.
Thrombin-free polymerization leads to pure fibrin(ogen) materials with extended processing capacity
Authors: Rieu Clément , Mosser Gervaise , Haye Bernard , Sanson Nicolas , Coradin Thibaud , Trichet Léa
Published: May 2020

Fibrin is a key protein for various clinical applications such as tissue reconstruction. However, in contrast to type I collagen, fibrin shaping has so far faced major limitations related to the necessity to add thrombin enzyme to fibrinogen precursors to induce fibrin self-assembly. Here we report a thrombin-free gelation pathway of fibrinogen solutions by incubation at 37°C in mild acidic conditions. We unravel the biochemical mechanisms underlying the gelation process and draw comparison between fibrinogen and fibrin at both molecular and supramolecular levels in these conditions. The protocol enables to control the viscosity of fibrin(ogen) solutions, and to induce fibrin(ogen) gel formation by simple 37°C incubation, with a reinforcement effect at neutralization. It facilitates processing of fibrin(ogen) materials, for coating, molding and extrusion, and offers new possibilities such as 3D printing. This approach is further compatible with type I collagen processing and can provide advanced tissue engineering scaffolds with high bioactivity.
Seizures are a druggable mechanistic link between TBI and subsequent tauopathy
Authors: Alyenbaawi Hadeel , Kanyo Richard , Locskai Laszlo F. , Kamali-Jamil Razieh , DuVal Michèle G. , Bai Qing , Wille Holger , Burton Edward A. , Allison W. Ted
Published: May 2020

Traumatic brain injury (TBI) is a prominent risk factor for neurodegenerative diseases and dementias including chronic traumatic encephalopathy (CTE). TBI and CTE, like all tauopathies, are characterized by accumulation of Tau into aggregates that progressively spread to other brain regions in a prion-like manner. The mechanisms that promote spreading and cellular uptake of tau seeds after TBI are not fully understood, in part due to lack of tractable animal models. Here, we test the putative roles for excess neuronal activity and dynamin-dependent endocytosis in promoting thein vivospread of tauopathy. We introduce ‘tauopathy reporter’ zebrafish expressing a genetically-encoded fluorescent Tau biosensor that reliably reports accumulation of human tau species when seededviaintra-ventricular brain injections. Subjecting zebrafish larvae to a novel TBI paradigm produced various TBI symptoms including cell death, hemorrhage, blood flow abnormalities, post–traumatic seizures, and Tau inclusions. Bath application of anticonvulsant drugs rescued TBI-induced tauopathy and cell death; these benefits were attributable to inhibition of post-traumatic seizures because co-application of convulsants reversed these beneficial effects. However, one convulsant drug, 4-Aminopyridine, unexpectedly abrogated TBI-induced tauopathy - this was due to its inhibitory action on endocytosis as confirmed via additional dynamin inhibitors. These data suggest a role for seizure activity and dynamin-dependent endocytosis in the prion-like seeding and spreading of tauopathy following TBI. Further work is warranted regarding anti-convulsants that dampen post-traumatic seizures as a route to moderating subsequent tauopathy. Moreover, the data highlight the utility of deployingin vivoTau biosensor and TBI methods in larval zebrafish, especially regarding drug screening and intervention.

Graphical Abstract

Highlights

Introduces first Traumatic Brain Injury (TBI) model in larval zebrafish, and its easy

TBI induces clinically relevant cell death, haemorrhage & post-traumatic seizures

Ca2+imagingduringTBI reveals spike in brain activity concomitant with seizures

Tau-GFP Biosensor allows repeatedin vivomeasures of prion-like tau aggregation

post-TBI, anticonvulsants stop tauopathies akin to Chronic Traumatic Encephalopathy
Identification ofFusarium solanif. sp.pisi(Fsp) responsive genes inPisum sativum
Authors: Williamson-Benavides Bruce A. , Sharpe Richard , Nelson Grant , Bodah Eliane T. , Porter Lyndon D. , Dhingra Amit
Published: May 2020

Pisum sativum(pea) is rapidly emerging as an inexpensive and major contributor to the plant-derived protein market. Due to its nitrogen-fixation capability, short life cycle, and low water usage, pea is a useful cover-and-break crop that requires minimal external inputs. It is critical for sustainable agriculture and indispensable for future food security. Root rot in pea, caused by the fungal pathogenFusarium solanif. sp.pisi(Fsp), can result in a 15-60% reduction in yield. It is urgent to understand the molecular basis ofFspinteraction in pea to develop root rot tolerant cultivars. A complementary genetics and gene expression approach was undertaken in this study to identifyFsp-responsive genes in four tolerant and four susceptible pea genotypes. Time course RNAseq was performed on both sets of genotypes afterFspchallenge. Analysis of the transcriptome data resulted in the identification of 42,905 differentially expressed contigs (DECs). Interestingly, the vast majority of DECs were overexpressed in the susceptible genotypes at all sampling time points, rather than in the tolerant genotypes. Gene expression and GO enrichment analyses revealed genes coding for receptor-mediated endocytosis, sugar transporters, salicylic acid synthesis and signaling, and cell death were overexpressed in the susceptible genotypes. In the tolerant genotypes, genes involved in exocytosis, and secretion by cell, the anthocyanin synthesis pathway, as well as the DRR230 gene, a pathogenesis-related (PR) gene, were overexpressed. The complementary genetic and RNAseq approach has yielded a set of potential genes that could be targeted for improved tolerance against root rot inP. sativum. Fspchallenge produced a futile transcriptomic response in the susceptible genotypes. This type of response is hypothesized to be related to the speed at which the pathogen infestation advances in the susceptible genotypes, and the preexisting level of disease-preparedness in the tolerant genotypes.
A systematic dissection of human primary osteoblastsin vivoat single-cell resolution
Authors: Gong Yun , Yang Junxiao , Li Xiaohua , Zhou Cui , Chen Yu , Wang Zun , Qiu Xiang , Liu Ying , Zhang Huixi , Greenbaum Jonathan , Cheng Liang , Hu Yihe , Xie Jie , Yang Xuecheng , Li Yusheng , Bai Yuntong , Wang Yu-Ping , Chen Yiping , Tan Li-Jun , Shen Hui , Xiao Hong-Mei , Deng Hong-Wen
Published: May 2020

Osteoblasts are multifunctional bone cells, which play essential roles in bone formation, angiogenesis regulation, as well as maintenance of hematopoiesis. Although bothin vivoandin vitrostudies on mice have identified several potential osteoblast subtypes based on their different transition stages or biological responses to external stimuli, the categorization of primary osteoblast subtypesin vivoin humans has not yet been achieved. Here, we used single-cell RNA sequencing (scRNA-seq) to perform a systematic cellular taxonomy dissection of freshly isolated human osteoblasts. Based on the gene expression patterns and cell lineage reconstruction, we identified three distinct cell clusters including preosteoblasts, mature osteoblasts, and an undetermined rare osteoblast subpopulation. This novel subtype was mainly characterized by the nuclear receptor subfamily 4 group A member 1 and 2 (NR4A1 and NR4A2), and its existence was confirmed by immunofluorescence staining. Trajectory inference analysis suggested that the undetermined cluster, together with the preosteoblasts, are involved in the regulation of osteoblastogenesis and also give rise to mature osteoblasts. Investigation of the biological processes and signaling pathways enriched in each subpopulation revealed that in addition to bone formation, preosteoblasts and undetermined osteoblasts may also regulate both angiogenesis and hemopoiesis. Finally, we demonstrated that there are systematic differences between the transcriptional profiles of human osteoblastsin vivoand mouse osteoblasts bothin vivoandin vitro, highlighting the necessity for studying bone physiological processes in humans rather than solely relying on mouse models. Our findings provide novel insights into the cellular heterogeneity and potential biological functions of human primary osteoblasts at the single-cell level, which is an important and necessary step to further dissect the biological roles of osteoblasts in bone metabolism under various (patho-) physiological conditions.
De NovoAssembly of the Northern Cardinal (Cardinalis cardinalis) Genome Reveals Candidate Regulatory Regions for Sexually Dichromatic Red Plumage Coloration
Authors: Wa Sin Simon Yung , Lu Lily , Edwards Scott V.
Published: May 2020

Northern cardinals (Cardinalis cardinalis) are common, mid-sized passerines widely distributed in North America. As an iconic species with strong sexual dichromatism, it has been the focus of extensive ecological and evolutionary research, yet genomic studies investigating the evolution of genotype–phenotype association of plumage coloration and dichromatism are lacking. Here we present a new, highly contiguous assembly forC. cardinalis. We generated a 1.1 Gb assembly comprised of 4,762 scaffolds, with a scaffold N50 of 3.6 Mb, a contig N50 of 114.4 kb and a longest scaffold of 19.7 Mb. We identified 93.5% complete and single-copy orthologs from an Aves dataset using BUSCO, demonstrating high completeness of the genome assembly. We annotated the genomic region comprising the CYP2J19 gene, which plays a pivotal role in the red coloration in birds. Comparative analyses demonstrated non-exonic regions unique to the CYP2J19 gene in passerines and a long insertion upstream of the gene inC. cardinalis. Transcription factor binding motifs discovered in the unique insertion region inC. cardinalissuggest potential androgen-regulated mechanisms underlying sexual dichromatism. Pairwise Sequential Markovian Coalescent (PSMC) analysis of the genome reveals fluctuations in historic effective population size between 100,000–250,000 in the last 2 millions years, with declines concordant with the beginning of the Pleistocene epoch and Last Glacial Period. This draft genome ofC. cardinalisprovides an important resource for future studies of ecological, evolutionary, and functional genomics in cardinals and other birds.
Chromosome-level genome construction of a Japanese stickleback species using ultra-dense linkage analysis using single-cell sequencing of sperms
Authors: Yoshitake Kazutoshi , Ishikawa Asano , Yonezawa Ryo , Kinoshita Shigeharu , Kitano Jun , Asakawa Shuichi
Published: May 2020

The presence of high quality genomes at the chromosome level is very useful in the search for the causal genes of mutants and in genetic breeding. The advent of next-generation sequencers has made it easier to decode genomes, but it is still difficult to construct the genomes of higher organisms. In order to construct the genome of a higher organism, the genome sequence of the organism is extended to the length of the chromosome by linkage analysis after assembly and scaffolding. However, in the past linkage analysis, it was difficult to make a high-density linkage map, and it was not possible to analyze organisms without an established breeding system. As an innovative alternative to conventional linkage analysis, we devised a method for genotyping sperm using 10x single-cell genome (CNV) sequencing libraries to generate a linkage map without interbreeding individuals. The genome was constructed using sperm fromGasterosteus nipponicus, and single-cell genotyping yielded 1,864,430 very dense hetero-SNPs. The average coverage per sperm cell is 0.13x. The number of sperm used is 1,738, which is an order of magnitude higher than the number of sperm used for conventional linkage analysis. We have improved the linkage analysis tool SELDLA (Scaffold Extender with Low Depth Linkage Analysis) so that we can analyze the data in accordance with the characteristics of single-cell genotyping data. Finally, we were able to determine the location and orientation on the chromosome for 85.6% of the contigs in the 456 Mbase genome ofGasterosteus nipponicussequenced in nanopores. A total of 95.6% of the contigs in which a cross-reaction was detected within the contigs.
High concordance between hippocampal transcriptome of the intraamygdala kainic acid model and human temporal lobe epilepsy
Authors: Conte Giorgia , Parras Alberto , Alves Mariana , Ollà Ivana , de Diego-Garcia Laura , Beamer Edward , Alalqam Razi , Ocampo Alejandro , Mendez Raúl , Henshall David C. , Lucas José J. , Engel Tobias
Published: May 2020

Objective

Pharmacoresistance and the lack of disease-modifying actions of current anti-seizure drugs persist as major challenges in the treatment of epilepsy. Experimental models of chemoconvulsant-induced status epilepticus remain the models of choice to discover potential anti-epileptogenic drugs but doubts remain as to the extent to which they model human pathophysiology. The aim of the present study was to compare the molecular landscape of the intraamygdala kainic acid model of status epilepticus in mice with findings in resected brain tissue from patients with drug-resistant temporal lobe epilepsy (TLE).

Methods

Status epilepticus was induced via intraamygdala microinjection of kainic acid in C57BL/6 mice and gene expression analysed via microarrays in hippocampal tissue at acute and chronic time-points. Results were compared to reference datasets in the intraperitoneal pilocarpine and intrahippocampal kainic acid model and to human resected brain tissue (hippocampus and cortex) from patients with drug-resistant TLE.

Results

Intraamygdala kainic acid injection in mice triggered extensive dysregulation of gene expression which was ∼3-fold greater shortly after status epilepticus (2729 genes) when compared to epilepsy (412). Comparison to samples of patients with TLE revealed a particular high correlation of gene dysregulation during established epilepsy. Pathway analysis found suppression of calcium signalling to be highly conserved across different models of epilepsy and patients. CREB was predicted as one of the main up-stream transcription factors regulating gene expression during acute and chronic phases and inhibition of CREB reduced seizure severity in the intraamygdala kainic acid model.

Significance

Our findings suggest the intraamygdala kainic acid model faithfully replicates key molecular features of human drug-resistant temporal lobe epilepsy and provides potential rationale target approaches for disease-modification through new insights into the unique and shared gene expression landscape in experimental epilepsy.

Key point box

More genes show expression changes shortly following intraamygdala kainic acid-induced status epilepticus when compared to established epilepsy.

The intraamygdala kainic acid mouse model mimics closely the gene expression landscape in the brain of patients with temporal lobe epilepsy.

Supressed calcium signalling in the brain as common feature across experimental models of epilepsy and patients with temporal lobe epilepsy.

CREB is a major up-stream transcription factor during early changes following status epilepticus and once epilepsy is established.
Palmitic acid induces inflammation in placental trophoblasts and impairs their migration toward smooth muscle cells through plasminogen activator inhibitor-1
Authors: Rampersaud Amanda M. , Dunk Caroline E. , Lye Stephen J. , Renaud Stephen J.
Published: May 2020

A critical component of early human placental development includes migration of extravillous trophoblasts (EVTs) into the decidua. EVTs migrate toward, and displace vascular smooth muscle cells (SMCs) surrounding several uterine structures, including spiral arteries. Shallow trophoblast invasion features in several pregnancy complications including preeclampsia. Maternal obesity is a risk factor for placental dysfunction, suggesting that factors within an obese environment may impair early placental development. Herein, we tested the hypothesis that palmitic acid, a saturated fatty acid circulating at high levels in obese women, induces an inflammatory response in EVTs that hinders their capacity to migrate toward SMCs. We found that SMCs and SMC-conditioned media stimulated migration and invasion of an EVT-like cell line, HTR8/SVneo. Palmitic acid impaired EVT migration and invasion toward SMCs, and induced expression of several vasoactive and inflammatory mediators in EVTs, including endothelin, interleukin (IL)-6, IL8, and PAI1. PAI1 was increased in plasma of women with early-onset preeclampsia, and PAI1-deficient EVTs were protected from the anti-migratory effects of palmitic acid. Using first trimester placental explants, palmitic acid exposure decreased EVT invasion through Matrigel. Our findings reveal that palmitic acid induces an inflammatory response in EVTs and attenuates their migration through a mechanism involving PAI1. High levels of palmitic acid in pathophysiological situations like obesity may impair early placental development and predispose to placental dysfunction.
Phenotyping Root Architecture of Soil-Grown Rice: A Robust Protocol Combining Manual Practices with Image-based Analyses
Authors: De Bauw P. , Ramarolahy J. A. , Senthilkumar K. , Rakotoson T. , Merckx R. , Smolders E. , Van Houtvinck R. , Vandamme E.
Published: May 2020

Background

Breeding towards resilient rice varieties is often constrained by the limited data on root system architecture obtained from relevant agricultural environments. Knowledge on the genotypic differences and responses of root architecture to environmental factors is limited due the difficulty of analysing soil-grown rice roots. An improved method using imaging is thus needed, but the existing methods were never proven successful for rice. Here, we aimed to evaluate and improve a higher throughput method of image-based root phenotyping for rice grown under field conditions. Rice root systems from seven experiments were phenotyped based on the “shovelomics” method of root system excavation followed by manual root phenotyping and digital root analysis after root imaging. Analyzed traits were compared between manual and image-based root phenotyping systems using Spearman rank correlations to evaluate whether both methods similarly rank the phenotypes. For each trait, the relative phenotypic variation was calculated. A principal component analysis was then conducted to assess patterns in root architectural variation.

Results

Several manually collected and image-based root traits were identified as having a high potential of differentiating among contrasting phenotypes, while other traits are found to be inaccurate and thus unreliable for rice. The image-based traits projected area, root tip thickness, stem diameter, and root system depth successfully replace the manual determination of root characteristics, however attention should be paid to the lower accuracy of the image-based methodology, especially when working with older and larger root systems.

Conclusions

The challenges and opportunities of rice root phenotyping in field conditions are discussed for both methods. We therefore propose an integrated protocol adjusted to the complexity of the rice root structure combining image analysis in a water bath and the manual scoring of three traits (i.e. lateral density, secondary branching degree, and nodal root thickness at the root base). The proposed methodology ensures higher throughput and enhanced accuracy during root phenotyping of soil grown rice in fields or pots compared to manual scoring only, it is cheap to develop and operate, it is valid in remote environments, and it enables fast data extraction.
OpenStats: A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput Phenotypic Data
Authors: Haselimashhadi Hamed , Mason Jeremy C , Mallon Ann-Marie , Smedley Damian , Meehan Terrence F , Parkinson Helen
Published: May 2020

Reproducibility in the statistical analyses of data from high-throughput phenotyping screens requires a robust and reliable analysis foundation that allows modelling of different possible statistical scenarios. Regular challenges are scalability and extensibility of the analysis software. In this manuscript, we describe OpenStats, a freely available software package that addresses these challenges. We show the performance of the software in a high-throughput phenomic pipeline in the International Mouse Phenotyping Consortium (IMPC) and compare the agreement of the results with the most similar implementation in the literature. OpenStats has significant improvements in speed and scalability compared to existing software packages including a 13-fold improvement in computational time to the current production analysis pipeline in the IMPC. Reduced complexity also promotes FAIR data analysis by providing transparency and benefiting other groups in reproducing and re-usability of the statistical methods and results. OpenStats is freely available under a Creative Commons license atwww.bioconductor.org/packages/OpenStats.
Comparing orthology methods and their performance by recapitulating patterns of eukaryotic genome evolution
Authors: Deutekom Eva S. , Snel Berend , van Dam Teunis J.P.
Published: May 2020

Insights into the evolution of ancestral complexes and pathways are generally achieved through careful and time-intensive manual analysis often using phylogenetic profiles of the constituent proteins. This manual analysis limits the possibility of including more protein-complex components, repeating the analyses for updated genome sets, or expanding the analyses to larger scales. Automated orthology inference should allow such large scale analyses, but substantial differences between orthologous groups generated by different approaches are observed.

We evaluate orthology methods for their ability to recapitulate a number of observations that have been made with regards to genome evolution in eukaryotes. Specifically, we investigate phylogenetic profile similarity (co-occurrence of complexes), the Last Eukaryotic Common Ancestor’s gene content, pervasiveness of gene loss, and the overlap with manually determined orthologous groups. Moreover, we compare the inferred orthologies to each other.

We find that most orthology methods reconstruct a large Last Eukaryotic Common Ancestor, with substantial gene loss, and can predict interacting proteins reasonably well when applying phylogenetic co-occurrence. At the same time derived orthologous groups show imperfect overlap with manually curated orthologous groups. There is no strong indication of which orthology method performs better than another on individual or all of these aspects. Counterintuitively, despite the orthology methods behaving similarly regarding large scale evaluation, the obtained orthologous groups differ vastly from one another.

Availability and implementation

The data and code underlying this article are available in github and/or upon reasonable request to the corresponding author:https://github.com/ESDeutekom/ComparingOrthologies.

We compared multiple orthology inference methods by looking at how well they perform in recapitulating multiple observations made in eukaryotic genome evolution.

Co-occurrence of proteins is predicted fairly well by most methods and all show similar behaviour when looking at loss numbers and dynamics.

All the methods show imperfect overlap when compared to manually curated orthologous groups and when compared to orthologous groups of the other methods.

Differences are compared between methods by looking at how the inferred orthologies represent a high-quality set of manually curated orthologous groups.

We conclude that all methods behave similar when describing general patterns in eukaryotic genome evolution. However, there are large differences within the orthologies themselves, arising from how a method can differentiate between distant homology, recent duplications, or classifying orthologous groups.
Monocytes mediateSalmonellaTyphimurium-induced tumour growth inhibition
Authors: Johnson Síle A. , Ormsby Michael J. , Wessel Hannah M. , Hulme Heather E. , Bravo-Blas Alberto , McIntosh Anne , Mason Susan , Coffelt Seth B. , Tait Stephen W.G. , Mowat Allan McI. , Milling Simon W.F. , Blyth Karen , Wall Daniel M.
Published: May 2020

The use of bacteria as an alternative cancer therapy has been re-investigated in recent years. A number of bacterial strains for this purpose have been generated, one of which is SL7207: an auxotrophicSalmonella entericaserovar TyphimuriumaroAmutant with immune-stimulatory potential. Here we show that systemic administration of SL7207 induces melanoma tumour growth arrestin vivo, with greater survival of the SL7207-treated group compared to control PBS-treated mice. Administration of SL7207 is accompanied by a change in the immune phenotype of the tumour-infiltrating cells towards pro-inflammatory, with expression of the TH1 cytokines IFN-γ, TNF-α, and IL-12 significantly increased. Interestingly, Ly6C+MHCII+monocytes were recruited to the tumours following SL7207 treatment and were pro-inflammatory. Accordingly, the abrogation of these infiltrating monocytes using clodronate liposomes prevented SL7207-induced tumour growth inhibition. These data demonstrate a previously unappreciated role for infiltrating inflammatory monocytes underlying bacterial-mediated tumour growth inhibition. This information highlights a novel role for monocytes in controlling tumour growth, contributing to our understanding of the immune responses required for successful immunotherapy of cancer.
Sparse input neural networks to differentiate 32 primary cancer types based on somatic point mutations
Authors: Dikaios Nikolaos
Published: May 2020

This paper aims to differentiate cancer types from primary tumour samples based on somatic point mutations (SPM). Primary cancer site identification is necessary to perform site-specific and potentially targeted treatment. Current methods like histopathology/lab-tests cannot accurately determine cancers origin, which results in empirical patient treatment and poor survival rates. The availability of large deoxyribonucleic-acid sequencing datasets has allowed scientists to examine the ability of SPM to classify primary cancer sites. These datasets are highly sparse since most genes will not be mutated, have low signal-to-noise ratio and are imbalanced since rare cancers have less samples. To overcome these limitations a sparse-input neural network (spinn) is suggested that projects the input data in a lower dimensional space, where the more informative genes are used for learning. To train and evaluate spinn, an extensive dataset was collected from the cancer genome atlas containing 7624 samples spanning 32 cancer types. Different sampling strategies were performed to balance the dataset but have not benefited the classifiers performance except for removing Tomek-links. This is probably due to high amount of class overlapping. Spinn consistently outperformed algorithms like extreme gradient-boosting, deep neural networks and support-vector-machines, achieving an accuracy up to 73% on independent testing data.
SLE non-coding Genetic Risk Variant Determines the Epigenetic Dysfunction of an Immune Cell Specific Enhancer that Controls Disease-critical microRNA Expression
Authors: Hou Guojun , Harley Isaac T.W. , Lu Xiaoming , Zhou Tian , Xu Ning , Yao Chao , Qin Yuting , Ouyang Ye , Ma Jianyang , Zhu Xinyi , Yu Xiang , Xu Hong , Dai Dai , Ding Huihua , Tang Yuanjia , Namjou Bahram , Weirauch Matthew T. , Kottyan Leah C. , Harley John B. , Shen Nan
Published: May 2020

The human genome contains millions of putative regulatory elements, which regulate gene expression. We are just beginning to understand the functional consequences of genetic variation within these regulatory elements. Since the bulk of common genetic variation impacting polygenic disease phenotypes localizes to these non-coding regions of the genome, understanding the consequences will improve our understanding of the mechanisms mediating genetic risk in human disease. Here, we define the systemic lupus erythematosus (SLE) risk variant rs2431369 as likely causal for SLE and show that it is located in a functional regulatory element that modulates miR-146a expression. We use epigenomic analysis and genome-editing to show that the rs2431697-containing region is a distal enhancer that specifically regulates miR-146a expression in a cell-type dependent manner. 3D chromatin structure analysis demonstrates physical interaction between the rs2431697-containing region and the miR-146a promoter. Further, our data show that NF-kB binds the disease protective allele in a sequence-specific manner, leading to increased expression of this immunoregulatory microRNA. Our work provides a strategy for using disease-associated variants to define the functional regulatory elements of non-coding RNA molecules such as miR-146a and provides mechanistic links between autoimmune disease risk genetic variation and disease etiology.
An RNA dynamic ensemble at atomic resolution
Authors: Shi Honglue , Rangadurai Atul , Assi Hala Abou , Roy Rohit , Case David A. , Herschlag Daniel , Yesselman Joseph D. , Al-Hashimi Hashim M.
Published: May 2020

Biomolecules do not fold into a single 3D structure but rather form dynamic ensembles of many inter-converting conformations1. Knowledge of dynamic ensembles is key for understanding how biomolecules fold and function, and for rationally manipulating their activities in drug discovery and synthetic biology2–4. However, solving dynamic ensembles of biomolecules at atomic resolution is a major challenge in structural biology because the information required to specify the position of all atoms in thousands of conformations in an ensemble far exceeds the information content of experimental measurements. Here we addressed the data gap and dramatically simplified and accelerated RNA ensemble determination by using structure prediction tools that leverage the growing database of RNA structures to generate a conformational library. Library refinement with NMR residual dipolar couplings enabled determination of an atomic-resolution ensemble for HIV-1 TAR as confirmed by quantum-mechanical calculations of NMR chemical shifts, comparison to a crystal structure of a substate, and through the successful redistribution of the ensemble by design using atomic mutagenesis. The ensemble provides an unprecedented view of how bulge residues cooperatively flip out and undergo sugar repuckering to allow the adjoining helices to stack. The generality of this approach will make determination of atomic-resolution RNA ensembles routine.