bluuebunny/crossref_metadata_2025 huggingface dataset:
Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis
Authors: Seirup Morten , Chu Li-Fang , Sengupta Srikumar , Leng Ning , Browder Hadley , Kapadia Kevin , Shafer Christina M. , Duffin Bret , Elwell Angela L. , Bolin Jennifer M. , Swanson Scott , Stewart Ron , Kendziorski Christina , Thomson James A. , Bacher Rhonda
Published: September 2019

As newer single-cell protocols generate increasingly more cells at reduced sequencing depths, the value of a higher read depth may be overlooked. Using data from three different single-cell RNA-seq protocols that lend themselves to having either higher read depth (Smart-seq) or many cells (MARS-seq and 10X), we evaluate their ability to recapitulate biological signals in the context of pseudo-spatial reconstruction. Overall, we find gene expression profiles after spatial-reconstruction analysis are highly reproducible between datasets despite being generated by different protocols and using different computational algorithms. While UMI based protocols such as 10X and MARS-seq allow for capturing more cells, Smart-seq’s higher sensitivity and read-depth allows for analysis of lower expressed genes and isoforms. Additionally, we evaluate trade-offs for each protocol by performing subsampling analyses, and find that optimizing the balance between sequencing depth and number of cells within a protocol is important for efficient use of resources. Our analysis emphasizes the importance of selecting a protocol based on the biological questions and features of interest.
DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis
Authors: Hong Ping , Jiang Hao , Xu Weize , Lin Da , Xu Qian , Cao Gang , Li Guoliang
Published: September 2019

Background

It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (Chromosome Conformation Capture) and its derived methods are now widely applied to investigate genome organizations and gene regulation. Digestion-Ligation-Only Hi-C (DLO Hi-C) is a new technology with high efficiency and effective cost for whole-genome chromosome conformation capture.

Results

Here, we introduce DLO Hi-C Tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering. We applied DLO Hi-C Tool to different DLO Hi-C datasets, and demonstrated its ability of processing large data in multi-threading.

Conclusions

DLO Hi-C Tool is suitable for processing DLO Hi-C and in situ DLO Hi-C datasets. It is convenient and efficient for DLO Hi-C data processing.
Evaluation of High-Pressure Processing in Inactivation of the Hepatitis E Virus
Authors: Nasheri Neda , Doctor Tanushka , Chen Angela , Harlow Jennifer , Gill Alexander
Published: September 2019

Hepatitis E virus (HEV) causes acute hepatitis with approximately 20 million cases per year globally. While HEV is endemic in certain regions of Asia, Africa and South America, it is considered an emerging foodborne pathogen in developed countries. Based on genetic diversity, HEV is classified into different genotypes, with genotype 3 (HEV-3) being most prevalent in Europe and North America. The transmission of HEV-3 has been shown to be zoonotic and mainly associated with the consumption of raw or undercooked pork products. Herein, we investigated the efficacy of high-pressure processing (HPP) in the inactivation of HEV-3 using a cell culture system. HPP has been indicated as a promising nonthermal pathogen inactivation strategy for treatment of certain high-risk food commodities, without any noticeable changes in their nature. For this purpose, we treated HEV-3 in media as well as in artificially inoculated pork pâté, with different conditions of HPP: 400 MPa for 1 and 5 minutes, as well as 600 MPa for 1 and 5 minutes, at ambient temperature. In general, we observed approximately a 2-log reduction in HEV load by HPP treatments in media; however, similar treatment in the pork pâté resulted in a much lower reduction in viral load. Therefore, the efficacy of HPP treatment in the inactivation of HEV-3 is matrix-dependent.
Native plasmid-encoded mercury resistance genes are functional and demonstrate natural transformation in environmental bacterial isolates
Authors: Kothari Ankita , Soneja Drishti , Tang Albert , Carlson Hans , Deutschbauer Adam M. , Mukhopadhyay Aindrila
Published: September 2019

Plasmid-mediated horizontal gene transfer (HGT) is a major driver of genetic diversity in bacteria. We experimentally validated the function of a putative mercury resistance operon present on an abundant 8 kilobase pair native plasmid found in groundwater samples without detectable levels of mercury. Phylogenetic analyses of the plasmid-encoded mercury reductases from the studied groundwater site show them to be distinct from those reported in proximal metal-contaminated sites. We synthesized the entire native plasmid and demonstrated that the plasmid was sufficient to confer functional mercury resistance inEscherichia coli. Given the possibility that natural transformation is a prevalent HGT mechanism in the low cell density environments of groundwaters, we also assayed bacterial strains from this environment for competence. We used the native plasmid-encoded metal resistance to design a screen and identified 17 strains positive for natural transformation. We selected 2 of the positive strains along with a model bacterium to fully confirm HGT via natural transformation. From an ecological perspective, the role of the native plasmid population in providing advantageous traits combined with the microbiome’s capacity to take up environmental DNA enables rapid adaptation to environmental stresses.

Importance

Horizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identify seventeen strains including Gram-positive and Gram-negative bacteria to be naturally competent. These strains were able to successfully take up the plasmid DNA and obtain a clear growth advantage in the presence of mercury. Our study provides important insights into gene dissemination via natural transformation enabling rapid adaptation to dynamic stresses in groundwater environments.
SpineJ : A software tool for quantitative analysis of nanoscale spine morphology
Authors: Levet Florian , Tønnesen Jan , Nägerl Valentin , Sibarita Jean-Baptiste
Published: September 2019

Super-resolution microscopy provides diffraction-unlimited optical access to the intricate morphology of neurons in living brain tissue, resolving their finest structural details, which are critical for neuronal function. However, as existing image analysis software tools have been developed for diffraction-limited images, they are generally not well suited for quantifying nanoscale structures like dendritic spines. We present SpineJ, a semi-automatic ImageJ plugin that is specifically designed for this purpose. SpineJ comes with an intuitive and user-friendly graphical user interface, facilitating fast, accurate, and unbiased analysis of spine morphology.
Cell cycle-balanced expression of pluripotency regulators via cyclin-dependent kinase 1
Authors: Kasvandik Sergo , Schilf Reelika , Saarma Merilin , Loog Mart , Jääger Kersti
Published: September 2019

Embryonic stem cells (ESCs) have a unique ability to remain pluripotent while undergoing rapid rounds of cell division required for self-renewal. However, it is not known how cell cycle and pluripotency regulatory networks co-operate in ESCs. Here, we used stable isotope labeling with amino acids in cell culture (SILAC) combined with mass spectrometry to determine pluripotency proteome dynamics during cell cycle in mouse ESCs. We found the S/G2M-fluctuating pluripotency transcription factors (ESRRB, REST), chromatin regulators (JARID2, TRIM24) and proteins with E3 ligase activity (NEDD4L, PIAS2) to peak in S phase. This expression balance was disrupted upon inhibition of cyclin-dependent kinase 1 (CDK1) activity resulting in the shift of the expression peak from S to G2M. Our results demonstrate that mouse ESCs require CDK1 activity to maintain high S to G2M ratio of pluripotency regulators revealing critical role of cell cycle dynamics in balancing ESC identity.
Genome-wide changes in genetic diversity in a population ofMyotis lucifugusaffected by white-nose syndrome
Authors: Lilley Thomas M. , Wilson Ian W. , Field Kenneth A. , Reeder DeeAnn M. , Vodzak Megan E. , Turner Gregory G. , Kurta Allen , Blomberg Anna S. , Hoff Samantha , Herzog Carl J. , Sewall Brent J. , Paterson Steve
Published: September 2019

Novel pathogens can cause massive declines in populations, and even extirpation of hosts. But disease can also act as a selective pressure on survivors, driving the evolution of resistance or tolerance. Bat white-nose syndrome (WNS) is a rapidly spreading wildlife disease in North America. The fungus causing the disease invades skin tissues of hibernating bats, resulting in disruption of hibernation behavior, premature energy depletion, and subsequent death. We used whole-genome sequencing to investigate changes in allele frequencies within a population ofMyotis lucifugusin eastern North America to search for genetic resistance to WNS. Our results show low FSTvalues within the population across time, i.e. prior to WNS (Pre-WNS) compared to the population that has survived WNS (Post-WNS). However, when dividing the population with a geographical cut-off between the states of Pennsylvania and New York, a sharp increase in values on scaffold GL429776 is evident in the Post-WNS samples. Genes present in the diverged area are associated with thermoregulation and promotion of brown fat production. Thus, although WNS may not have subjected the entireM. lucifuguspopulation to selective pressure, it may have selected for specific alleles in Pennsylvania through decreased gene flow within the population. However, the persistence of remnant sub-populations in the aftermath of WNS is likely due to multiple factors in bat life history.
Topoisomerase II inhibitors induce cGAS-STING dependent inflammation resulting in cytokine induction and immune checkpoint activation
Authors: Wilkinson R. D. A , McCabe N. , Parkes E. E. , Barros E.M. , Johnston D. I. , Ali R.M.M , Lappin K. , Greenberg R.A. , Harkin D. P. , McIntosh S. A. , Kennedy R. D. , Savage K. I.
Published: September 2019

Tumours with genomic instability demonstrate enhanced immunogenicity and potential for response to immune checkpoint blockade (ICB). We previously demonstrated activation of the cGAS-STING pathway following loss of DNA repair, resulting in cytokine induction, lymphocytic infiltration and immune checkpoint activation. Here we explore the role of chemotherapies in inducing this innate immune response, identifying topoisomerase II (topo-II) inhibitors, particularly doxorubicin and epirubicin, as potent inducers of a cGAS-STING dependent interferon response. Mechanistically, topo-II inhibition resulted in significant induction of cytoplasmic DNA and subsequent micronuclei formation, a requirement for efficient cGAS-STING activation and consequent cytokine and immune checkpoint gene induction. Importantly, increased cytokine and immune checkpoint gene expression, as well as increased immune cell infiltration, was also observed in patient derived breast tumour biopsies following topo-II inhibitor-based treatment. Taken together, this study indicates topo-II inhibitors such as doxorubicin, may be best placed to induce immunogenic inflammation, and thereby increase responses to ICB therapies.

Significance

This work demonstrates how topo-II inhibitors induce STING-pathway activation, cytokine induction and immune checkpoint protein upregulation in cancer cells and provides a rationale for combining topo-II inhibitors with ICB therapy in early breast cancer.
A new high-throughput tool to screen mosquito-borne viruses in Zika virus endemic/epidemic areas
Authors: Moutailler Sara , Yousfi Lena , Mousson Laurence , Devillers Elodie , Vazeille Marie , Vega-Rúa Anubis , Perrin Yvon , Jourdain Frédéric , Chandre Fabrice , Cannet Arnaud , Chantilly Sandrine , Restrepo Johana , Guidez Amandine , Dusfour Isabelle , Santos de Abreu Filipe Vieira , Pereira dos Santos Taissa , Jiolle Davy , Visser Tessa M. , Koenraadt Constantianus J.M. , Wongsokarijo Merril , Diallo Mawlouth , Diallo Diawo , Gaye Alioune , Boyer Sébastien , Duong Veasna , Piorkowski Géraldine , Paupy Christophe , de Oliveira Ricardo Lourenco , de Lamballerie Xavier , Failloux Anna-Bella
Published: September 2019

Mosquitoes are vectors of arboviruses affecting animal and human health. Arboviruses circulate primarily within an enzootic cycle and recurrent spillovers contribute to the emergence of human-adapted viruses able to initiate an urban cycle involving anthropophilic mosquitoes. The increasing volume of travel and trade offers multiple opportunities for arbovirus introduction in new regions. This scenario has been exemplified recently with the Zika pandemic. To incriminate a mosquito as vector of a pathogen, several criteria are required such as the detection of natural infections in mosquitoes. In this study, we used a high-throughput chip based on the BioMarkTM Dynamic arrays system capable of detecting 64 arboviruses in a single experiment. A total of 17,958 mosquitoes collected in Zika-endemic/epidemic countries (Brazil, French Guiana, Guadeloupe, Suriname, Senegal, and Cambodia) were analyzed. Here we show that this new tool can detect endemic and epidemic viruses in different mosquito species in an epidemic context. Thus, this fast and low-cost method can be suggested as a novel epidemiological surveillance tool to identify circulating arboviruses.
Hispanic/Latino gastric adenocarcinoma patients have distinct molecular profiles including a high rate of germline CDH1 mutations
Authors: Wang Sam C. , Yeu Yunku , Hammer Suntrea T.G. , Xiao Shu , Zhu Min , Hong Changjin , Yoon Lynn Y. , Nassour Ibrahim , Shen Jeanne , Agarwal Deepak , Reznik Scott I. , Mansour John C. , Yopp Adam C. , Zhu Hao , Hwang Tae Hyun , Porembka Matthew R.
Published: September 2019

Hispanic/Latino patients have a higher incidence of gastric cancer and worse cancer-related outcomes as compared to patients of other backgrounds. Whether there is a molecular basis for these disparities is unknown, as very few Hispanic/Latino patients were included in previous studies. We performed a large, integrated genomic analysis of gastric cancer samples from Hispanic/Latino patients. Whole-exome sequencing (WES) and RNA sequencing were performed on 57 Hispanic/Latino gastric cancer patient samples. Germline analysis was conducted on 83 patients. Functional testing of CDH1 germline mutations was performed in Chinese hamster ovary cells. Tumors from Hispanic/Latino patients were significantly enriched for the genomically-stable subtype (as defined by The Cancer Genome Atlas), compared to Asians and Whites (65% vs 21% vs 20%, P < 0.001). Transcriptomic analysis identified molecular signatures that were prognostic. Of the 43 Hispanic/Latino patients with diffuse-type gastric cancer, 7 (16%) had germline mutations in CDH1. Mutation carriers were significantly younger than non-carriers (41 vs 50 years, P < 0.05). E-cadherin expression was reduced in 5 of 6 mutation carrier tumor samples available for analysis. In silico algorithms predicted 5 variants were deleterious. For the two variants that were predicted to be benign, we demonstrated that the mutations conferred increased migratory capability, suggesting pathogenicity. Hispanic/Latino gastric cancer patients possess unique genomic landscapes. This includes a high rate of CDH1 germline mutations that may partially explain their aggressive clinical phenotypes. Individualized screening, genetic counseling, and treatment protocols based on patient ethnicity and race may be necessary.
Animacy modulates gender agreement computation in Hindi: An ERP study
Authors: Bhattamishra Shikha , Muralikrishnan R. , Choudhary Kamal Kumar
Published: September 2019

Gender has been investigated in psycholinguistics research both with respect to how it is retrieved when a noun is encountered and the computation of its agreement dependencies between different elements in a sentence. The literature is abound with differences as to the processing of gender agreement computations across languages and constructs. Similarly, neurophysiological evidence with respect to gender retrieval mechanisms differ wherein languages differ in the way the gender feature is retrieved when a noun is encountered based on different properties. The present study aims to scrutinize gender agreement computations in verb-agreement relations in Hindi and to ascertain if the intrinsic property (i.e. the animacy) of a noun participating in the relation plays a role in processing agreement dependencies. In addition, it also looks into the issue of whether the gender retrieval mechanism in the language influences agreement comprehension. Results revealed a positivity for the animate subject agreement and a negativity for the inanimate subject agreement violations at the position of the verb respectively. The results are suggestive of distinct processing mechanisms underlying semantic and syntactic gender. Further, the results also suggest that gender agreement computation in Hindi is modulated by the way gender is retrieved at the position of the noun.
Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains
Authors: Khrameeva Ekaterina , Kurochkin Ilia , Han Dingding , Guijarro Patricia , Kanton Sabina , Santel Malgorzata , Qian Zhengzong , Rong Shen , Mazin Pavel , Bulat Matvei , Efimova Olga , Tkachev Anna , Guo Song , Sherwood Chet C. , Camp J. Gray , Paabo Svante , Treutlein Barbara , Khaitovich Philipp
Published: September 2019

Identification of gene expression traits unique to the human brain sheds light on the mechanisms of human cognition. Here we searched for gene expression traits separating humans from other primates by analyzing 88,047 cell nuclei and 422 tissue samples representing 33 brain regions of humans, chimpanzees, bonobos, and macaques. We show that gene expression evolves rapidly within cell types, with more than two-thirds of cell type-specific differences not detected using conventional RNA sequencing of tissue samples. Neurons tend to evolve faster in all hominids, but non-neuronal cell types, such as astrocytes and oligodendrocyte progenitors, show more differences on the human lineage, including alterations of spatial distribution across neocortical layers.
GLUT1 inhibition blocks growth of RB1-positive Triple Negative Breast Cancer
Authors: Wu Qin , ba-alawi Wail , Deblois Genevieve , Cruickshank Jennifer , Duan Shili , Lima-Fernandes Evelyne , Haight Jillian , Tonekaboni Seyed Ali Madani , Fortier Anne-Marie , Kuasne Hellen , McKee Trevor D. , Mahmoud Hassan , Cameron Sarina , Dogan-Artun Nergiz , Chen WenJun , Vellanki Ravi N. , Zhou Stanley , Done Susan J. , Park Morag , Cescon David W. , Haibe-Kains Benjamin , Lupien Mathieu , Arrowsmith Cheryl H.
Published: September 2019

Triple negative breast cancer (TNBC) is a deadly form of breast cancer due to the development of resistance to chemotherapy affecting over 30% of patients. New therapeutics and companion biomarkers are urgently needed. Recognizing the elevated expression of glucose transporter 1 (GLUT1, encoded by SLC2A1) and associated metabolic dependencies in TNBC, we investigated the vulnerability of TNBC cell lines and patient-derived samples to GLUT1 inhibition. We report that genetic or pharmacological inhibition of GLUT1 with BAY-876 impairs the growth of a subset of TNBC cells displaying high glycolytic and lower oxidative phosphorylation (OXPHOS) rates. Pathway enrichment analysis of gene expression data implicates E2F Targets pathway activity as a surrogate of OXPHOS activity. Furthermore, the protein levels of retinoblastoma tumor suppressor (RB1) are strongly correlated with the degree of sensitivity to GLUT1 inhibition in TNBC, where RB1-negative cells are insensitive to GLUT1 inhibition. Collectively, our results highlight a strong and targetable RB1-GLUT1 metabolic axis in TNBC and warrant clinical evaluation of GLUT1 inhibition in TNBC patients stratified according to RB1 protein expression levels.
Learning action-oriented models through active inference
Authors: Tschantz Alexander , Seth Anil K. , Buckley Christopher L.
Published: September 2019

Converging theories suggest that organisms learn and exploit probabilistic models of their environment. However, it remains unclear how such models can be learned in practice. The open-ended complexity of natural environments means that it is generally infeasible for organisms to model their environment comprehensively. Alternatively, action-oriented models attempt to encode a parsimonious representation of adaptive agent-environment interactions. One approach to learning action-oriented models is to learn online in the presence of goal-directed behaviours. This constrains an agent to behaviourally relevant trajectories, reducing the diversity of the data a model need account for. Unfortunately, this approach can cause models to prematurely converge to sub-optimal solutions, through a process we refer to as a bad-bootstrap. Here, we exploit the normative framework of active inference to show that efficient action-oriented models can be learned by balancing goal-oriented and epistemic (information-seeking) behaviours in a principled manner. We illustrate our approach using a simple agent-based model of bacterial chemotaxis. We first demonstrate that learning via goal-directed behaviour indeed constrains models to behaviorally relevant aspects of the environment, but that this approach is prone to sub-optimal convergence. We then demonstrate that epistemic behaviours facilitate the construction of accurate and comprehensive models, but that these models are not tailored to any specific behavioural niche and are therefore less efficient in their use of data. Finally, we show that active inference agents learn models that are parsimonious, tailored to action, and which avoid bad bootstraps and sub-optimal convergence. Critically, our results indicate that models learned through active inference can support adaptive behaviour in spite of, and indeed because of, their departure from veridical representations of the environment. Our approach provides a principled method for learning adaptive models from limited interactions with an environment, highlighting a route to sample efficient learning algorithms.
Disruption of NOX2-dependent Oxidative Injury with a Targeted Gene-Therapy Approach Prevents Atrial Fibrillation in a Canine Model
Authors: Yoo Shin , Pfenniger Anna , Hoffman Jacob , Zhang Wenwei , Ng Jason , Burrell Amy , Johnson David A. , Gussak Georg , Waugh Trent , Bull Suzanne , Benefield Brandon , Knight Bradley P. , Passman Rod , Wasserstrom J. Andrew , Aistrup Gary L. , Arora Rishi
Published: September 2019

Atrial fibrillation is the most common heart rhythm disorder in adults and a major cause of stroke. Unfortunately, current treatments of AF are suboptimal as they are not targeted to the molecular mechanisms underlying AF. In this study, we demonstrated using a novel gene-based strategy in a clinically relevant large animal of AF that oxidative injury is a key mechanism underlying the onset and perpetuation of AF. First, we demonstrated that generation of oxidative injury in atrial myocytes is a frequency-dependent process, with rapid pacing in canine atrial myocytes inducing oxidative injury through induction of NADPH oxidase 2 (NOX2) and generation of mitochondrial reactive oxygen species. We show that oxidative injury likely contributes to electrical remodeling in AF by upregulating a constitutively active form of acetylcholine-dependent K+current (IKACh) – calledIKH- by a mechanism involving frequency-dependent activation of protein kinase C epsilon (PKCε). To understand the mechanism by which oxidative injury promotes the genesis and/or maintenance of AF, we performed targeted injection of NOX2 shRNA in atria of normal dogs followed by rapid atrial pacing. The time to onset of non-sustained AF increased by more than 5-fold in NOX2 shRNA treated dogs. Furthermore, animals treated with NOX2 shRNA did not develop sustained AF for up to 12 weeks. The electrophysiological mechanism underlying AF prevention was prolongation of atrial effective refractory periods, with attenuated activation of PKCε, a likely molecular mechanism underlying this beneficial electrophysiological remodeling. Future optimization of this approach may lead to a novel, mechanism-guided therapy for AF.

One Sentence Summary

Targeted disruption of NOX2-dependent oxidative injury with a novel gene therapy approach prevents onset as well as perpetuation of atrial fibrillation.
cAb-Rep: A Database of Curated Antibody Repertoires for Exploring antibody diversity and Predicting Antibody Prevalence
Authors: Guo Yicheng , Chen Kevin , Kwong Peter D. , Shapiro Lawrence , Sheng Zizhang
Published: September 2019

The diversity of B cell receptors provides a basis for recognizing numerous pathogens. Antibody repertoire sequencing has revealed relationships between B cell receptor sequences, their diversity, and their function in infection, vaccination, and disease. However, many repertoire datasets have been deposited without annotation or quality control, limiting their utility. To accelerate investigations of B cell immunoglobulin sequence repertoires and to facilitate development of algorithms for their analysis, we constructed a comprehensive public database of curated human B cell immunoglobulin sequence repertoires, cAb-Rep (https://cab-rep.c2b2.columbia.edu), which currently includes 306 immunoglobulin repertoires from 121 human donors, who were healthy, vaccinated, or had autoimmune disease. The database contains a total of 267.9 million V(D)J heavy chain and 72.9 million VJ light chain transcripts. These transcripts are full-length or near full-length, have been annotated with gene origin, antibody isotype, somatic hypermutations, and other biological characteristics, and are stored in FASTA format to facilitate their direct use by most current repertoire-analysis programs. We describe a website to search cAb-Rep for similar antibodies along with methods for analysis of the prevalence of antibodies with specific genetic signatures, for estimation of reproducibility of somatic hypermutation patterns of interest, and for delineating frequencies of somatically introducedN-glycosylation. cAb-Rep should be useful for investigating attributes of B cell sequence repertoires, for understanding characteristics of affinity maturation, and for identifying potential barriers to the elicitation of effective neutralizing antibodies in infection or by vaccination.
Fast and slow cortical high frequency oscillations for cortico-cortical and cortico-hippocampal network consolidation during NonREM sleep
Authors: Aleman-Zapata Adrian , Morris Richard GM , Genzel Lisa
Published: September 2019

Memory reactivation during NonREM-ripples is thought to communicate new information to a systems-wide network. Cortical high frequency events have also been described that co-occur with ripples. Focusing on NonREM sleep after different behaviors, both hippocampal ripples and parietal high frequency oscillations were detected. A bimodal frequency distribution was observed in the parietal high frequency events, faster and slower, with increases in prefrontal directionality measured by Granger causality analysis specifically seen during the fast parietal oscillations. Furthermore, fast events activated prefrontal-parietal cortex whereas slow events activated hippocampal-parietal areas. Finally, there was a learning-induced increase in both number and size of fast high frequency events. These patterns were not seen after novelty exposure or foraging, but occurred after the learning of a new goal location in a maze. Disruption of either sleep or hippocampal ripples impaired long-term memory consistent with these having a role in memory consolidation.
Dynamic arousal signals construct memories of time and events
Authors: Clewett David , Gasser Camille , Davachi Lila
Published: September 2019

Everyday life unfolds continuously, yet we tend to remember past experiences as discrete event sequences or episodes. Although this phenomenon has been well documented, the brain mechanisms that support the transformation of continuous experience into memorable episodes remain unknown. Here we show that a sudden change in context, or ‘event boundary’, elicits a burst of autonomic arousal, as indexed by pupil dilation. These boundaries during dynamic experience also led to the segmentation of adjacent episodes in later memory, evidenced by changes in memory for the timing, order, and perceptual details of recent event sequences. Critically, we find that distinct cognitive components of this pupil response were associated with both subjective (temporal distance judgements) and objective (temporal order discrimination) measures of episodic memory, suggesting that multiple arousal-mediated cognitive processes help construct meaningful mnemonic events. Together, these findings reveal that arousal processes may play a fundamental role in everyday memory organization.
The cryptic plastid of Euglena longa defines a new type of non-photosynthetic plastid organelles
Authors: Füssy Zoltán , Záhonová Kristína , Tomčala Aleš , Krajčovič Juraj , Yurchenko Vyacheslav , Oborník Miroslav , Eliáš Marek
Published: September 2019

Most secondarily non-photosynthetic eukaryotes have retained residual plastids whose physiological role is often still unknown. One such example is Euglena longa, a close non-photosynthetic relative of Euglena gracilis harbouring a plastid organelle of enigmatic function. By mining transcriptome data from E. longa we finally provide an overview of metabolic processes localized to its elusive plastid. The organelle plays no role in biosynthesis of isoprenoid precursors and fatty acids, and has a very limited repertoire of pathways concerning nitrogen-containing metabolites. In contrast, the synthesis of phospholipids and glycolipids has been preserved, curiously with the last step of sulfoquinovosyldiacylglycerol synthesis being catalysed by the SqdX form of the enzyme so far known only from bacteria. Notably, we show that the E. longa plastid synthesizes tocopherols and a phylloquinone derivative, the first such report for non-photosynthetic plastids studied so far. The most striking attribute of the organelle is the presence of a linearized Calvin-Benson (CB) pathway including RuBisCO yet lacking the gluconeogenetic part of the standard cycle, together with ferredoxin-NADP+ reductase (FNR) and the ferredoxin/thioredoxin systems. We hypothesize that FNR passes electrons to the ferredoxin/thioredoxin systems from NADPH to activate the linear CB pathway in response to the redox status of the E. longa cell. In effect, the pathway may function as a redox valve bypassing the glycolytic oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate. Altogether, the E. longa plastid defines a new class of relic plastids that is drastically different from the best studied organelle of this category, the apicoplast.

Importance

Colourless plastids incapable of photosynthesis evolved in many plant and algal groups, but what functions they perform is still unknown in many cases. Here we study the elusive plastid of Euglena longa, a non-photosynthetic cousin of the familiar green flagellate Euglena gracilis. We document an unprecedented combination of metabolic functions that the E. longa plastid exhibits in comparison with previously characterized non-photosynthetic plastids. For example, and truly surprisingly, it has retained the synthesis of tocopherols (vitamin E) and a phylloquinone (vitamin K) derivative. In addition, we offer a possible solution of the long-standing conundrum of the presence of the CO2-fixing enzyme RuBisCO in E. longa. Our work provides a detailed account on a unique variant of relic plastids, the first among non-photosynthetic plastids that evolved by secondary endosymbiosis from a green algal ancestor, and suggests that it has persisted for reasons not previously considered in relation to non-photosynthetic plastids.
A Virtual Nodule Environment (ViNE) for modelling the inter-kingdom metabolic integration during symbiotic nitrogen fixation
Authors: diCenzo George C , Tesi Michelangelo , Pfau Thomas , Mengoni Alessio , Fondi Marco
Published: September 2019

Biological associations are often premised upon metabolic cross-talk between the organisms, with the N2-fixing endosymbiotic relationship between rhizobia and leguminous plants being a prime example. Here, we report thein silicoreconstruction of a metabolic network of aMedicago truncatulaplant nodulated by the bacteriumSinorhizobium meliloti. The nodule tissue of the model contains five spatially distinct developmental zones and encompasses the metabolism of both the plant and the bacterium. Flux balance analysis (FBA) suggested that the majority of the metabolic costs associated with symbiotic nitrogen fixation are directly related to supporting nitrogenase activity, while a minority is related to the formation and maintenance of nodule and bacteroid tissue. Interestingly, FBA simulations suggested there was a non-linear relationship between the rate of N2-fixation per gram of nodule and the rate of plant growth; increasing the N2-fixation efficiency was associated with diminishing returns in terms of plant growth. Evaluating the metabolic exchange between the symbiotic partners provided support for: i) differentiating bacteroids having access to sugars (e.g., sucrose) as a major carbon source, ii) ammonium being the major nitrogen export product of N2-fixing bacteria, and iii) N2-fixation being dependent on the transfer of protons from the plant cytoplasm to the bacteria through acidification of the peribacteroid space. Our simulations further suggested that the use of C4-dicarboxylates by N2-fixing bacteroids may be, in part, a consequence of the low concentration of free oxygen in the nodule limiting the activity of the plant mitochondria. These results demonstrate the power of this integrated model to advance our understanding of the functioning of legume nodules, and its potential for hypothesis generation to guide experimental studies and engineering of symbiotic nitrogen fixation.
Approaches for integrating heterogeneous RNA-seq data reveals cross-talk between microbes and genes in asthmatic patients
Authors: Spakowicz Daniel , Lou Shaoke , Barron Brian , Li Tianxiao , Gomez Jose L , Liu Qing , Grant Nicole , Yan Xiting , Weinstock George , Chupp Geoffrey L , Gerstein Mark
Published: September 2019

Sputum induction is a non-invasive method to evaluate the airway environment, particularly for asthma. RNA sequencing (RNAseq) can be used on sputum, but it can be challenging to interpret because sputum contains a complex and heterogeneous mixture of human cells and exogenous (microbial) material. In this study, we developed a methodology that integrates dimensionality reduction and statistical modeling to grapple with the heterogeneity. We use this to relate bulk RNAseq data from 115 asthmatic patients with clinical information, microscope images, and single-cell profiles. First, we mapped sputum RNAseq to human and exogenous sources. Next, we decomposed the human reads into cell-expression signatures and fractions of these in each sample; we validated the decomposition using targeted single-cell RNAseq and microscopy. We observed enrichment of immune-system cells (neutrophils, eosinophils, and mast cells) in severe asthmatics. Second, we inferred microbial abundances from the exogenous reads and then associated these with clinical variables -- e.g.,Haemophiluswas associated with increased white blood cell count andCandida,with worse lung function. Third, we applied a generative model, Latent Dirichlet allocation (LDA), to identify patterns of gene expression and microbial abundances and relate them to clinical data. Based on this, we developed a method called LDA-link that connects microbes to genes using reduced-dimensionality LDA topics. We found a number of known connections, e.g. betweenHaemophilusand the gene IL1B, which is highly expressed by mast cells. In addition, we identified novel connections, includingCandidaand the calcium-signaling gene CACNA1E, which is highly expressed by eosinophils. These results speak to the mechanism by which gene-microbe interactions contribute to asthma and define a strategy for making inferences in heterogeneous and noisy RNAseq datasets.
Leveraging Distributed Biomedical Knowledge Sources to Discover Novel Uses for Known Drugs
Authors: Womack Finn , McClelland Jason , Koslicki David
Published: September 2019

Abstract

Computational drug repurposing, also called drug repositioning, is a low cost, promising tool for finding new uses for existing drugs. With the continued growth of repositories of biomedical data and knowledge, increasingly varied kinds of information are available to train machine learning approaches to drug repurposing. However, existing efforts to integrate a diversity of data sources have been limited to only a small selection of data types, typically gene expression data, drug structural information, and protein interaction networks. In this study, we leverage a graph-based approach to integrate biological knowledge from 20 publicly accessible repositories to represent information involving 11 distinct bioentity types. We then employ a graph node embedding scheme and use utilize a random forest model to make novel predictions about which drugs can be used to treat certain diseases. Utilizing this approach, we find a performance improvement over existing computational drug repurposing approaches and find promising drug repositioning targets, including drug and disease pairs currently in clinical trials.
Type I interferon responses to ischemic injury begin in the bone marrow of mice and humans and depend on Tet2, Nrf2, and Irf3
Authors: Calcagno David M. , Ng Richard P. , Toomu Avinash , Zhang Claire , Huang Kenneth , Aguirre Aaron D. , Weissleder Ralph , Daniels Lori B. , Fu Zhenxing , King Kevin R.
Published: September 2019

Sterile tissue injury locally activates innate immune responses via interactions with damage associated molecular patterns (DAMPs). Here, by analyzing ∼120K single cell transcriptomes after myocardial infarction (MI) in mice and humans, we show neutrophil and monocyte subsets induce type I interferon (IFN) stimulated genes (ISGs) in myeloid progenitors of the bone marrow, far from the site of injury. In patients with acute MI, peripheral blood neutrophils and monocytes express ISGs at levels far beyond healthy individuals and comparable to patients with lupus. In the bone marrow of Tet2-/-mice, ISGs are spontaneously induced in myeloid progenitors and their progeny. In the heart, IFN responses are negatively regulated by Ccr2- resident macrophages in a Nrf2-dependent fashion. Our results show post-MI IFN signaling begins in the bone marrow, implicate multiple transcription factors in its regulation (Tet2, Irf3, Nrf2), and provide a clinical biomarker (ISG score) for studying post-MI IFN signaling in patients.
Links between autobiographical memory richness and temporal discounting in older adults
Authors: Lempert Karolina M. , MacNear Kameron A. , Wolk David A. , Kable Joseph W.
Published: September 2019

When making choices between smaller, sooner rewards and larger, later ones, people tend to discount or devalue future outcomes. This propensity can be maladaptive, especially as individuals age and their decisions about health, investments, and relationships become increasingly consequential. Individual differences in temporal discounting in older adults have been associated with episodic memory abilities, as well as with cortical thickness in the entorhinal cortex. The mechanism by which better memory might lead to more future-oriented choice remains unclear, however. Here we used a fine-grained measure of autobiographical memory richness (Autobiographical Interview scoring protocol) to examine which categories of episodic details are associated with temporal discounting in cognitively normal older adults. We also examined whether recalling autobiographical memories prior to choice can alter temporal discounting in this group. Time, place, and perceptual details, but not event or emotion/thought details, were associated with temporal discounting. Furthermore, time, place, and perceptual details and temporal discount rates were associated with entorhinal cortical thickness. Retrieving autobiographical memories prior to choice did not affect temporal discounting overall, but the extent to which the memories were rich in event and time details predicted whether they would reduce discounting after they were recalled. Thus, more future-oriented decision-makers may have more contextual (i.e., time, place, and perceptual) details in their recollections overall, and retrieving central event details at the time of choice may shift decisions toward being more patient. These findings will help with the development of interventions to nudge intertemporal choices, especially in older adults with memory decline.
Spatial and phylogenetic structure of Alpine stonefly community assemblages across seven habitats using DNA-species
Authors: Gamboa Maribet , Serrana Joeselle , Takemon Yasuhiro , Monaghan Michael T. , Watanabe Kozo
Published: September 2019

Stream ecosystems are spatially heterogeneous, with many different habitat patches distributed within a small area. The influence of this heterogeneity on the biodiversity of benthic insect communities is well documented; however, studies of the role of habitat heterogeneity in species coexistence and community assembly remain limited. Here, we investigated how habitat heterogeneity influences spatial structure (beta biodiversity) and phylogenetic structure (evolutionary processes) of benthic stonefly (Plecoptera, Insecta) communities.

We sampled 20 sites along two Alpine rivers, including seven habitats in four different reaches (headwaters, meandering, bar-braided floodplain, and lowland spring-fed). We identified 21 morphological species and delineated 52 DNA-species based on sequences from mitochondrialcox1and nuclear ITS markers. Using DNA-species, we first analysed the patterns of variation in richness, diversity, and community composition by quantifing the contribution of each of the four reaches and seven habitats to the overall DNA-species diversity using an additive partition of species diversity analysis and distance-based redundancy analysis. Using gene-tree phylogenies, we assessed whether environmental filtering led to the co-occurrence of DNA-species using a two-step analysis to find a phylogenetic signal.

The four reaches significantly contributed to DNA-species richness; with the meandering section having the highest contribution. However, we found that habitats had an effect on DNA-species diversity, where glide, riffle and, pool influenced the spatial structure of stonefly communities possibly due to a high species turnover.

Among the habitats, the pool showed significant phylogenetic clustering, suggesting high levels of evolutionary adaptation and strong habitat filtering. This community structure may be caused by long-term stability of the habitat and the similar requirements for co-occurring species.

Our study shows the importance of different habitats on the spatial and phylogenetic structure of stonefly community assemblies and sheds light on the habitat-specific diversity that may help improve conservation practices.
Acute myocardial injury in mdx hearts ameliorated by ARB but not ACE inhibitor treatment
Authors: Meyers Tatyana A. , Heitzman Jackie A. , Townsend DeWayne
Published: September 2019

Duchenne muscular dystrophy (DMD) is a devastating muscle disease that afflicts males due to the loss of the protein dystrophin, resulting in muscle deterioration and cardiomyopathy. Dystrophin’s absence causes increased membrane fragility, myocyte death, and tissue remodeling. Inhibition of angiotensin signaling with ACE inhibitors or angiotensin receptor blockers (ARBs) is a mainstay of DMD therapy, with clinical guidelines recommending starting one of these therapies by the age of 10 to address cardiomyopathy.

Using the mdx mouse model of DMD, we previously showed that isoproterenol causes extensive damage in dystrophic hearts, and treatment with the ARB losartan starting only 1 hour before isoproterenol dramatically reduced this myocardial injury. In the present study, we probed whether ACE inhibitors, which are more frequently prescribed, can deliver similar protection. Surprisingly, lisinopril treatment initiated 1 hour before isoproterenol failed to demonstrate any effect on injury in mdx hearts. Further, with a 2-week pretreatment, only losartan significantly lowered mdx cardiac injury, without any benefit associated with lisinopril treatment. These results confirm the ability of ARBs, but not ACE inhibitors, to prevent acute injury in mouse hearts, and prompt the question whether ARBs should be more frequently used for DMD cardiomyopathy because of these potential protective actions.
How neurons move during action potentials
Authors: Ling Tong , Boyle Kevin C. , Zuckerman Valentina , Flores Thomas , Ramakrishnan Charu , Deisseroth Karl , Palanker Daniel
Published: September 2019

Neurons undergo nanometer-scale deformations during action potentials, and the underlying mechanism has been actively debated for decades. Previous observations were limited to a single spot or the cell boundary, while movement across the entire neuron during the action potential remained unclear.

We report full-field imaging of cellular deformations accompanying the action potential in mammalian neuron somas (−1.8nm~1.3nm) and neurites (−0.7nm~0.9nm), using fast quantitative phase imaging with a temporal resolution of 0.1ms and an optical pathlength sensitivity of <4pm per pixel. Spike-triggered average, synchronized to electrical recording, demonstrates that the time course of the optical phase changes matches the dynamics of the electrical signal, with the optical signal revealing the intracellular potential rather than its time derivative detected via extracellular electrodes. Using 3D cellular morphology extracted via confocal microscopy, we demonstrate that the voltage-dependent changes in the membrane tension induced by ionic repulsion can explain the magnitude, time course and spatial features of the phase imaging. Our full-field observations of the spike-induced deformations in mammalian neurons opens the door to non-invasive label-free imaging of neural signaling.
Species better track the shifting isotherms in the oceans than on lands
Authors: Lenoir J. , Bertrand R. , Comte L. , Bourgeaud L. , Hattab T. , Murienne J. , Grenouillet G.
Published: September 2019

Despite mounting evidence of species redistribution as climate warms, our knowledge of the coupling between species range shifts and isotherm shifts is limited. Compiling a global geo-database of 30,534 range shifts from 12,415 taxa, we show that only marine taxa closely track the shifting isotherms. In the oceans, the velocity of isotherm shifts interacts synergistically with anthropogenic disturbances and baseline temperatures such that isotherm tracking by marine life happens either in warm and undisturbed waters (e.g. Central Pacific Basin) or in colder waters where human activities are more pronounced (e.g. North Sea). On lands, increasing anthropogenic activities and temperatures negatively impact the capacity of terrestrial taxa to track isotherm shifts in latitude and elevation, respectively. This suggests that terrestrial taxa are lagging behind the shifting isotherms, most likely due to their wider thermal safety margin, more constrained physical environment for dispersal and higher availability of thermal microrefugia at shorter distances.