bluuebunny/crossref_metadata_2025 huggingface dataset:
Toxic stress-specific cytoprotective responses regulate learned behavioral decisions inC. elegans
Authors: Hajdú Gábor , Gecse Eszter , Taisz István , Móra István , Sőti Csaba
Published: February 2020

Background

Protection of organismal integrity involve physiological stress responses and behavioral defenses. Recent studies in the roundwormCaenorhabditis eleganshave shown that pathogen and toxin exposure simultaneously stimulate cellular stress and detoxification responses and aversive behavior. However, whether a coordinate regulation exists between cellular and neurobehavioral defenses remains unclear.

Results

Here we show that exposure ofC. elegansto high concentrations of naturally attractive food-derived odors, benzaldehyde and diacetyl, induces toxicity and aversive behavior. Benzaldehyde preconditioning activates systemic cytoprotective stress responses involving DAF-16/FOXO, SKN-1/Nrf and Hsp90 in somatic cells, which confer behavioral tolerance to benzaldehyde and cross-tolerance to the structurally similar methyl-salicylate, but not to the structurally unrelated diacetyl. In contrast, diacetyl preconditioning augments diacetyl avoidance and does not induce apparent molecular defenses. Reinforcement of the experiences using massed training forms relevant associative memories. Memory retrieval by the odor olfactory cues leads to avoidance of food contaminated by diacetyl and context-dependent behavioral decision to avoid benzaldehyde only if there is an alternative, food-indicative odor.

Conclusions

Our findings reveal a regulatory link between physiological stress responses and learned behavior which facilitates self-protection in real and anticipated stresses. The potential conservation of this somato-neuronal connection might have relevance in maladaptive avoidant human behaviors.
Interferon-induced Protein-44 and Interferon-induced Protein 44-like restrict replication of Respiratory Syncytial Virus
Authors: Busse D. C. , Habgood-Coote D. , Clare S. , Brandt C. , Bassano I. , Kaforou M. , Herberg J. , Levin M. , Eleouet Jean-Francois , Kellam P. , Tregoning J. S.
Published: February 2020

Cellular intrinsic immunity, mediated by the expression of an array of interferon-stimulated antiviral genes, is a vital part of host defence. We have previously used a bioinformatic screen to identify two interferon stimulated genes (ISG) with poorly characterised function, Interferon-induced protein 44 (IFI44) and interferon-induced protein 44-like (IFI44L), as potentially being important in Respiratory Syncytial Virus (RSV) infection. Using overexpression systems, CRISPR-Cas9-mediated knockout, and a knockout mouse model we investigated the antiviral capability of these genes in the control of RSV replication. Over-expression of IFI44 or IFI44L was sufficient to restrict RSV infection at an early time post infection. Knocking out these genes in mammalian airway epithelial cells increased levels of infection. Both genes express antiproliferative factors that have no effect on RSV attachment but reduce RSV replication in a minigenome assay. The loss ofIfi44was associated with a more severe infection phenotypein vivo. These studies demonstrate a function for IFI44 and IFI44L in controlling RSV infection.

Importance

RSV infects all children under two years of age, but only a subset of children get severe disease. We hypothesize that susceptibility to severe RSV necessitating hospitalization in children without pre-defined risk factors is in part mediated at the anti-viral gene level. But there is a large array of anti-viral genes, particularly in the ISG family about which the mechanism is poorly understood. Having observed significantly lower levels of IFI44 and IFI44L gene expression in hospitalized children with a confirmed diagnosis of RSV, we dissected the function of these two genes. Through a range of over-expression and knockout studies we show that the genes are anti-viral and anti-proliferative. This study is important because IFI44 and IFI44L are upregulated after a wide range of viral infections and IFI44L can serve as a diagnostic bio-marker of viral infection.
An Effective CTL Peptide Vaccine for Ebola Zaire Based on Survivors’ CD8+ Targeting of a Particular Nucleocapsid Protein Epitope with Potential Implications for COVID-19 Vaccine Design
Authors: Herst CV , Burkholz S , Sidney J , Sette A , Harris PE , Massey S , Brasel T , Cunha-Neto E , Rosa DS , Chao WCH , Carback R , Hodge T , Wang L , Ciotlos S , Lloyd P , Rubsamen R
Published: February 2020

The 2013-2016 West Africa EBOV epidemic was the biggest EBOV outbreak to date. An analysis of virus-specific CD8+ T-cell immunity in 30 survivors showed that 26 of those individuals had a CD8+ response to at least one EBOV protein. The dominant response (25/26 subjects) was specific to the EBOV nucleocapsid protein (NP). It has been suggested that epitopes on the EBOV NP could form an important part of an effective T-cell vaccine for Ebola Zaire. We show that a 9-amino-acid peptide NP44-52 (YQVNNLEEI) located in a conserved region of EBOV NP provides protection against morbidity and mortality after mouse adapted EBOV challenge. A single vaccination in a C57BL/6 mouse using an adjuvanted microsphere peptide vaccine formulation containing NP44-52 is enough to confer immunity in mice. Our work suggests that a peptide vaccine based on CD8+ T-cell immunity in EBOV survivors is conceptually sound and feasible. Nucleocapsid proteins within SARS-CoV-2 contain multiple class I epitopes with predicted HLA restrictions consistent with broad population coverage. A similar approach to a CTL vaccine design may be possible for that virus.
Epitope-based peptide vaccine design and target site characterization against novel coronavirus disease caused by SARS-CoV-2
Authors: Li Lin , Sun Ting , He Yufei , Li Wendong , Fan Yubo , Zhang Jing
Published: February 2020

The outbreak of the 2019 novel coronavirus (SARS-CoV-2) has infected thousands of people with a large number of deaths across 26 countries. The sudden appearance of the virus leads to the limited existing therapies for SARS-CoV-2. Therefore, vaccines and antiviral medicines are in desperate need. This study took immune-informatics approaches to identify B- and T-cell epitopes for surface glycoprotein (S) of SARS-CoV-2, followed by estimating their antigenicity and interactions with the human leukocyte antigen (HLA) alleles. We identified four B cell epitopes, two MHC class-I and nine MHC class-II binding T-cell epitopes, which showed highly antigenic features. Allergenicity, toxicity and physiochemical properties analysis confirmed the specificity and selectivity of epitopes. The stability and safety of epitopes were confirmed by digestion analysis. No mutations were observed in all the selected B- and T-cell epitopes across all isolates from different locations worldwide. Epitopes were thus identified and some of them can be potential candidates for vaccine development.
Genome editing human primary T cells with microfluidic vortex shedding & CRISPR Cas9
Authors: Jarrell Justin A. , Sytsma Brandon J. , Wilson Leah H. , Pan Fong L. , Lau Katherine H.W.J. , Kirby Giles T. S. , Lievano Adrian A. , Pawell Ryan S.
Published: February 2020

Microfluidic vortex shedding (μVS) can rapidly deliver mRNA to T cells with high yield. The mechanistic underpinning ofμVSintracellular delivery remains undefined andμVS-Cas9 genome editing requires further studies. Herein, we evaluated a series ofμVSdevices containing splitter plates to attenuate vortex shedding and understand the contribution of computed force and frequency on efficiency and viability. We then selected aμVSdesign to knockout the expression of the endogenous T cell receptor in primary human T cells via delivery of CRISPR-Cas9 ribonucleoprotein (RNP) with and without brief exposure to an electric field (eμVS).μVSalone resulted in an equivalent yield of genome-edited T cells relative to electroporation with improved cell quality. A 1.8-fold increase in editing efficiency was demonstrated witheμVSwith negligible impact on cell viability. Cumulatively, these results demonstrate the utility ofμVSandeμVSfor genome editing human primary T cells with Cas9 RNPs.
Using karyotyping and achene morphology to accurately identifySonchus oleraceus(Asteraceae) in the context of its biological control
Authors: Ollivier M. , Gauthier P. , Lesieur V. , Thomann T. , Jourdan M. , Bon M. C. , Sheppard A. , Raghu S. , Tixier M. S. , Martin J.-F.
Published: February 2020

In weed biocontrol, accurate identification of the target weed is essential to select effective and host-specific biocontrol agents. This study focuses on the biocontrol of an invasive weed species in Australia, native from Europe, the common sowthistle,Sonchus oleraceusL. (Asteraceae). During field surveys, the distinction betweenS. oleraceusand a morphologically related species (S. asperL.) was difficult because of specimens bearing intermediate morphological features. These observations raised questions about the reliability the morphological characters used for distinguishing between these species and the identity of the intermediate phenotypes. First, cytological analyses coupled with morphological comparisons were carried out on specimens collected in Europe and Australia. Results showed that specimens morphologically described asS. oleraceusandS. asperpossessed, in accordance with literature 32 and 18 chromosomes, respectively. Specimens with intermediate morphotypes had 32 chromosomes, showing that they belong toS. oleraceusspecies. The variability of characters used for diagnosis is discussed and for a particular feature, achene ornamentation, an inquiry among 30 people was carried out to determine how this character might be relevant for distinguishing the two species herein considered. The successful identification rate was 92.2% (SE ± 0.77) showing the practical interest of this feature for diagnosis.
Single cell transcriptomics reveals lineage trajectory of the retinal ganglion cells in wild-type andAtoh7-null retinas
Authors: Wu Fuguo , Bard Jonathan E. , Kann Julien , Yergeau Donald , Sapkota Darshan , Ge Yichen , Hu Zihua , Wang Jie , Liu Tao , Mu Xiuqian
Published: February 2020

Past studies concluded that Atoh7 is critical for the emergence of the retinal ganglion cell (RGC) lineage in the developing retina, whereas Pou4f2 and Isl1 function in RGC differentiation. Atoh7 is expressed in a subset of retinal progenitor cells (RPCs) and is considered a competence factor for the RGC fate, but the molecular properties of these RPCs have not been well characterized. In this study, we first used conventional RNA-seq to investigate transcriptomic changes inAtoh7-,Pou4f2-, andIsl1-null retinas at embryonic (E) day 14.5 and identified the differentially expressed genes (DEGs), which expanded our understanding of the scope of downstream events. We then performed single cell RNA-seq (scRNA-seq) on E13.5 and E17.5 wild-type andAtoh7-null retinal cells. Clustering analysis not only correctly identified known cell types at these developmental stages but also revealed a transitional cell state which was marked byAtoh7and genes for other lineages in a highly overlapping fashion and shared by all early developmental trajectories. Further, analysis of theAtoh7-null retina revealed that, unlike previously believed, the RGC lineage still progressed considerably and a substantial amount of RGC-specific gene expression still occurred. Thus, Atoh7 likely collaborates with other factors to shepherd the transitional RPCs to the RGC lineage by competing with other lineage factors and activating RGC-specific genes. This study thus provides significant insights into the nature of RPC competence for different retinal cell fates and revises our current view on the emergence of the RGC lineage.
Artesunate interacts with Vitamin D receptor to reverse mouse model of sepsis-induced immunosuppression via enhancing autophagy
Authors: Shang Shenglan , Wu Jiaqi , Li Xiaoli , Liu Xin , Li Pan , Zheng Chunli , Wang Yonghua , Liu Songqing , Zheng Jiang , Zhou Hong
Published: February 2020

Background and Purpose

Immunosuppression is the predominant cause of mortality for sepsis due to failure to eradicate invading pathogens. Unfortunately, no effective and specific drugs capable of reversing immunosuppression are available for clinical use. Increasing evidence implicates vitamin D receptor (VDR) involved in sepsis-induced immunosuppression. Herein, artesunate (AS) was discovered to reverse sepsis-induced immunosuppression and its molecular mechanism is investigated.

Experimental Approach

Effect of artesunate on sepsis-induced immunosuppression was investigated in mice andin vitro. VDR was predicted to be an interacted candidate of AS by bioinformatics predict, then identified using PCR and immunoblotting. VDR,ATG16L1and NF-κB p65 were modified to investigate the alteration of AS’s effect on pro-inflammatory cytokines release, bacteria clearance and autophagy activities in sepsis-induced immunosuppression.

Key Results

AS significantly reduced the mortality of cecal ligation and puncture (CLP)-induced sepsis immunosuppression mice challenged withPseudomonas Aeruginosa, and enhanced proinflammatory cytokines release and bacterial clearance to reverse sepsis-induced immunosuppressionin vivoandin vitro. Mechanically, AS interacted with VDR thereby inhibited the nuclear translocation of VDR, then influencingATG16L1transcription and subsequent autophagy activity. In addition, AS inhibited physical interaction between VDR and NF-κB p65 in LPS tolerance macrophages, then promoted nuclear translocation of NF-κB p65, which activated the transcription of NF-κB p65 target genes such as pro-inflammatory cytokines.

Conclusion and Implications

Our findings provide an evidence that AS interacted with VDR to reverse sepsis-induced immunosuppression in an autophagy and NF-κB dependent way, highlighting a novel approach for sepsis treatment and drug repurposing of AS in the future.
Stimulus transformation into motor action: dynamic graph analysis reveals a posterior-to-anterior shift in brain network communication of older subjects
Authors: Rosjat Nils , Wang Bin A. , Liu Liqing , Fink Gereon R. , Daun Silvia
Published: February 2020

Cognitive performance slows down with increasing age. This includes cognitive processes that are essential for the performance of a motor act, such as the slowing down in response to an external stimulus. The objective of this study was to identify aging-associated functional changes in the brain networks that are involved in the transformation of external stimuli into motor action. To investigate this topic, we employed dynamic graphs based on phase-locking of Electroencephalography signals recorded from healthy younger and older subjects while performing a simple visually-cued finger-tapping task. The network analysis yielded specific age-related network structures varying in time in the low frequencies (2-7 Hz), which are closely connected to stimulus processing, movement initiation and execution in both age groups. The networks in older subjects, however, contained several additional, particularly interhemispheric, connections and showed an overall increased coupling density. Cluster analyses revealed reduced variability of the subnetworks in older subjects, particularly during movement preparation. In younger subjects, occipital, parietal, sensorimotor and central regions were - temporally arranged in this order - heavily involved in hub nodes. Whereas in older subjects, a hub in frontal regions preceded the noticeably delayed occurrence of sensorimotor hubs, indicating different neural information processing in older subjects.

All observed changes in brain network organization, which are based on neural synchronization in the low frequencies, provide a possible neural mechanism underlying previous fMRI data, which report an overactivation, especially in the prefrontal and pre-motor areas, associated with a loss of hemispheric lateralization in older subjects.
Dissimilarity-Overlap Analysis of Replicate Enrichment Communities
Authors: Vila Jean C. C. , Liu Yang-Yu , Sanchez Alvaro
Published: February 2020

The taxonomic composition of microbial communities can vary substantially between individual hosts and within the same host over time. Efforts to build quantitative and predictive models of microbial population dynamics are underway, but fundamental questions remain. How different are population dynamics in different hosts? Do communities that share the same taxa also exhibit identical dynamics? In vitro communities can help establish baseline expectations that are critical towards resolving these questions in natural communities. Here, we applied a recently developed tool, Dissimilarity-Overlap Analysis (DOA), to a set of experimental in vitro communities that differed in nutrient composition. The Dissimilarity and Overlap of these communities are negatively correlated in replicate habitats, as one would expect if microbial population dynamics were on average strongly convergent (or “universal”) across these replicate habitats. However, the existence of such a negative correlation does not necessarily imply that population dynamics are always universal in all communities. Even in replicate, identical habitats, two different communities may contain the same set of taxa at different abundances in equilibrium. The formation of alternative states in community assembly is strongly associated with the presence of specific taxa in the communities. Our results benchmark DOA, providing support for some of its core assumptions, and suggest that communities sharing the same taxa and external abiotic factors generally (but not necessarily) have a negative correlation between Dissimilarity and Overlap.
Deciphering and modelling the TGF-β signalling interplays specifying the dorsal-ventral axis of the sea urchin embryo
Authors: Floc’hlay Swann , Molina Maria Dolores , Hernandez Céline , Haillot Emmanuel , Thomas-Chollier Morgane , Lepage Thierry , Thieffry Denis
Published: February 2020

During sea urchin development, secretion of Nodal and BMP2/4 ligands and their antagonists Lefty and Chordin from a ventral organizer region specifies the ventral and dorsal territories. This process relies on a complex interplay between the Nodal and BMP pathways through numerous regulatory circuits. To decipher the interplay between these pathways, we used a combination of treatments with recombinant Nodal and BMP2/4 proteins and a computational modelling approach. We assembled a logical model focusing on cell responses to signalling inputs along the dorsal-ventral axis, which was extended to cover ligand diffusion and enable multicellular simulations. Our model simulations accurately recapitulate gene expression in wild type embryos, accounting for the specification of ventral ectoderm, ciliary band and dorsal ectoderm. Our model simulations further recapitulate various morphant phenotypes, reveals a dominance of the BMP pathway over the Nodal pathway, and stresses the crucial impact of the rate of Smad activation in D/V patterning. These results emphasise the key role of the mutual antagonism between the Nodal and BMP2/4 pathways in driving early dorsal-ventral patterning of the sea urchin embryo.

Summary Statement

We propose a predictive computational model of the regulatory network controlling the dorsal-ventral axis specification in sea urchin embryos, and highlight key features of Nodal and BMP antagonism.
Myosin 1b Flattens and Prunes Branched Actin Filaments
Authors: Pernier Julien , Morchain Antoine , Caorsi Valentina , Bertin Aurélie , Bousquet Hugo , Bassereau Patricia , Coudrier Evelyne
Published: February 2020

Motile and morphological cellular processes require a spatially and temporally coordinated branched actin network that is controlled by the activity of various regulatory proteins including the Arp2/3 complex, profilin, cofilin and tropomyosin. We have previously reported that myosin 1b regulates the density of the actin network in the growth cone. Usingin vitroF-actin gliding assays and total internal reflection fluorescence (TIRF) microscopy we show in this report that this molecular motor flattens the Arp2/3-dependent actin branches up to breaking them and reduces the probability to form new branches. This experiment reveals that myosin 1b can produce force sufficient enough to break up the Arp2/3-mediated actin junction. Together with the formerin vivostudies, this work emphasizes the essential role played by myosins in the architecture and in the dynamics of actin networks in different cellular regions.

Short summary

Usingin vitroF-actin gliding assays and total internal reflection fluorescence (TIRF) microscopy we show that myosin flattens the Arp2/3-dependent actin branches up to breaking them and reduces the probability to form new branches
A systematic, label-free method for identifying RNA-associated proteinsin vivoprovides insights into vertebrate ciliary beating
Authors: Drew Kevin , Lee Chanjae , Cox Rachael M. , Dang Vy , Devitt Caitlin C. , Papoulas Ophelia , Huizar Ryan L. , Marcotte Edward M. , Wallingford John B.
Published: February 2020

Cell-type specific RNA-associated proteins (RAPs) are essential for development and homeostasis in animals. Despite a massive recent effort to systematically identify RAPs, we currently have few comprehensive rosters of cell-type specific RAPs in vertebrate tissues. Here, we demonstrate the feasibility of determining the RNA-interacting proteome of a defined vertebrate embryonic tissue using DIF-FRAC, a systematic and universal (i.e., label-free) method. Application of DIF-FRAC to cultured tissue explants ofXenopusmucociliary epithelium identified dozens of known RAPs as expected, but also several novel RAPs, including proteins related to assembly of the mitotic spindle and regulation of ciliary beating. In particular, we show that the inner dynein arm tether Cfap44 is an RNA-associated protein that localizes not only to axonemes, but also to liquid-like organelles in the cytoplasm called DynAPs. This result led us to discover that DynAPs are generally enriched for RNA. Together, these data provide a useful resource for a deeper understanding of mucociliary epithelia and demonstrate that DIF-FRAC will be broadly applicable for systematic identification of RAPs from embryonic tissues.
Identification of viruses from fungal transcriptomes
Authors: Jo Yeonhwa , Choi Hoseong , Chu Hyosub , Cho Won Kyong
Published: February 2020

Viruses infecting fungi are referred to as mycoviruses. Here, we carried outin silicomycovirome studies using public fungal transcriptomes. We identified 468 virus-associated contigs assigned to five orders, 21 families, 26 genera, and 88 species. We assembled 120 viral genomes with diverse RNA and DNA genomes. The phylogenetic tree and genome organization unveiled the possible host origin of mycovirus species and diversity of their genome structures. Most identified mycoviruses were originated from fungi; however, some mycoviruses had strong phylogenetic relationships with those from insects and plants. The viral abundance and mutation frequency of mycoviruses were very low; however, the compositions and populations of mycoviruses were very complex. Although coinfection of diverse mycoviruses in the fungi was common in our study, most mycoviromes had a dominant virus species. The compositions and populations of mycoviruses were more complex than we expected.Moniliniaviromes revealed that there were strong deviations in the composition of viruses and viral abundance among samples.Gigasporaviromes showed that the chemical strigolactone might promote virus replication and mutations, while symbiosis with endobacteria might suppress virus replication and mutations. This study revealed the diversity and host distribution of mycoviruses.
CRISPR Screen in Regulatory T Cells Reveals Ubiquitination Modulators of Foxp3
Authors: Cortez Jessica T. , Montauti Elena , Shifrut Eric , Zhang Yusi , Shaked Oren , Xu Yuanming , Roth Theodore L. , Simeonov Dimitre R. , Zhang Yana , Chen Siqi , Li Zhongmei , Vogel Ian A. , Prator Grace Y. , Zhang Bin , Lee Youjin , Sun Zhaolin , Ifergan Igal , Van Gool Frédéric , Bluestone Jeffrey A. , Marson Alexander , Fang Deyu
Published: February 2020

Regulatory T cells (Tregs) are required to control immune responses and maintain homeostasis but are a significant barrier to anti-tumor immunity1. Conversely, Treg instability, characterized by loss of the master transcription factor Foxp3 and acquisition of pro-inflammatory properties2, can promote autoimmunity and/or facilitate more effective tumor immunity3,4. A comprehensive understanding of the pathways that regulate Foxp3 could lead to more effective Treg therapies for autoimmune disease and cancer. Despite improved functional genetic tools that now allow for systematic interrogation, dissection of the gene regulatory programs that modulate Foxp3 expression has not yet been reported. In this study, we developed a CRISPR-based pooled screening platform for phenotypes in primary mouse Tregs and applied this technology to perform a targeted loss-of-function screen of ∼490 nuclear factors to identify gene regulatory programs that promote or disrupt Foxp3 expression. We discovered several novel modulators including ubiquitin-specific peptidase 22 (Usp22), Ataxin 7 like 3 (Atxn7l3) and ring finger protein 20 (Rnf20). Members of the deubiquitination module of the SAGA chromatin modifying complex, Usp22 and Atxn7l3, were discovered to be positive regulators that stabilized Foxp3 expression; whereas the screen suggested Rnf20, an E3 ubiquitin ligase, is a negative regulator of Foxp3. Treg-specific ablation of Usp22 in mice reduced Foxp3 protein and created defects in their suppressive function that led to spontaneous autoimmunity but protected against tumor growth in multiple cancer models. Foxp3 destabilization in Usp22-deficient Tregs could be rescued by ablation of Rnf20, revealing a reciprocal ubiquitin switch in Tregs. These results reveal novel modulators of Foxp3 and demonstrate a screening method that can be broadly applied to discover new targets for Treg immunotherapies for cancer and autoimmune disease.
Joint profiling of DNA and proteins in single cells to dissect genotype-phenotype associations in leukemia
Authors: Demaree Benjamin , Delley Cyrille L. , Vasudevan Harish N. , Peretz Cheryl A.C. , Ruff David , Smith Catherine C. , Abate Adam R.
Published: February 2020

Studies of acute myeloid leukemia rely on DNA sequencing and immunophenotyping by flow cytometry as primary tools for disease characterization. However, leukemia tumor heterogeneity complicates integration of DNA variants and immunophenotypes from separate measurements. Here we introduce DAb-seq, a novel technology for simultaneous capture of DNA genotype and cell surface phenotype from single cells at high throughput, enabling direct profiling of proteogenomic states in tens of thousands of cells. To demonstrate the approach, we analyze the disease of three patients with leukemia over multiple treatment timepoints and disease recurrences. We observe complex genotype-phenotype dynamics that illustrate the subtlety of the disease process and the degree of incongruity between blast cell genotype and phenotype in different clinical scenarios. Our results highlight the importance of combined single-cell DNA and protein measurements to fully characterize the heterogeneity of leukemia.
Integration of Mechanistic Immunological Knowledge into a Machine Learning Pipeline Increases Predictive Power
Authors: Culos Anthony , Tsai Amy S. , Stanley Natalie , Becker Martin , Ghaemi Mohammad S. , Mcilwain David R. , Fallahzadeh Ramin , Tanada Athena , Nassar Huda , Ganio Edward , Peterson Laura , Han Xiaoyuan , Stelzer ina , Ando Kazuo , Gaudilliere Dyani , Phongpreecha Thanaphong , Marić Ivana , Chang Alan L. , Shaw Gary M. , Stevenson David K. , Bendall Sean , Davis Kara L. , Fantl Wendy , Nolan Garry P. , Hastie Trevor , Tibshirani Robert , Angst Martin S. , Gaudilliere Brice , Aghaeepour Nima
Published: February 2020

The dense network of interconnected cellular signaling responses quantifiable in peripheral immune cells provide a wealth of actionable immunological insights. While high-throughput single-cell profiling techniques, including polychromatic flow and mass cytometry, have matured to a point that enables detailed immune profiling of patients in numerous clinical settings, limited cohort size together with the high dimensionality of data increases the possibility of false positive discoveries and model overfitting. We introduce a machine learning platform, the immunological Elastic-Net (iEN), which incorporates immunological knowledge directly into the predictive models. Importantly, the algorithm maintains the exploratory nature of the high-dimensional dataset, allowing for the inclusion of immune features with strong predictive power even if not consistent with prior knowledge. In three independent studies our method demonstrates improved predictive power for clinically-relevant outcomes from mass cytometry data generated from whole blood, as well as a large simulated dataset.
Quality control and processing of nascent RNA profiling data
Authors: Smith Jason P. , Dutta Arun B. , Sathyan Kizhakke Mattada , Guertin Michael J. , Sheffield Nathan C.
Published: February 2020

Nascent RNA profiling is growing in popularity; however, there is no standard analysis pipeline to uniformly process the data and assess quality. Here, we introduce PEPPRO, a comprehensive, scalable work-flow for GRO-seq, PRO-seq, and ChRO-seq data. PEPPRO produces uniformly processed output files for downstream analysis and assesses adapter abundance, RNA integrity, library complexity, nascent RNA purity, and run-on efficiency. PEPPRO is restartable and fault-tolerant, records copious logs, and provides a web-based project report. PEPPRO can be run locally or using cluster, providing a portable first step for genomic nascent RNA analysis.

Availability

BSD2-licensed code and documentation: https://peppro.databio.org.
Increasing proteome coverage using cysteine-specific DIA Mass spectrometry – Cys-DIA
Authors: Tahir Muhammad , Nawrocki Arkadiusz , Ditzel Henrik J. , Larsen Martin R.
Published: February 2020

We report a Data Independent Analysis (DIA) mass spectrometric method for quantitative proteomics based on cysteine-containing peptides derived by tryptic digestion from biological samples (termed Cys-DIA). This technology significantly increases the coverage of the identifiable and quantifiable proteome in DIA/SWATH analyses by >35% compared to the conventional DIA/SWATH methods. The strategy was applied here to illustrate the quantitative difference in the proteome between isogenic human cancer cell lines with different metastatic capabilities.
Brain disconnections link structural connectivity with function and behaviour
Authors: de Schotten Michel Thiebaut , Foulon Chris , Nachev Parashkev
Published: February 2020

Brain lesions do not just disable but also disconnect brain areas, which once deprived of their input or output, can no longer subserve behaviour and cognition. The role of white matter connections has remained an open question for the past 250 years. Based on 1333 stroke lesions we reveal the human Disconnectome and demonstrate its relationship to the functional segregation of the human brain. Results indicate that functional territories are not only defined by white matter connections, but also by the highly stereotyped spatial distribution of brain disconnections. While the former has granted us the possibility to map 590 functions on the white matter of the whole brain, the latter compels a revision of the taxonomy of brain functions. Overall, our freely available Functional Atlas of the White Matter will enable improved clinical-neuroanatomical predictions for brain lesion studies and provide a platform for novel explorations in the domain of cognition.
FreiPose: A Deep Learning Framework for Precise Animal Motion Capture in 3D Spaces
Authors: Zimmermann Christian , Schneider Artur , Alyahyay Mansour , Brox Thomas , Diester Ilka
Published: February 2020

The increasing awareness of the impact of spontaneous movements on neuronal activity has raised the need to track behavior. We present FreiPose, a versatile learning-based framework to directly capture 3D motion of freely definable points with high precision (median error < 3.5% body length, 41.9% improvement compared to state-of-the-art) and high reliability (82.8% keypoints within < 5% body length error boundary, 72.0% improvement). The versatility of FreiPose is demonstrated in two experiments: (1) By tracking freely moving rats with simultaneous electrophysiological recordings in motor cortex, we identified neuronal tuning to behavioral states and individual paw trajectories. (2) We inferred time points of optogenetic stimulation in rat motor cortex from the measured pose across individuals and attributed the stimulation effect automatically to body parts. The versatility and accuracy of FreiPose open up new possibilities for quantifying behavior of freely moving animals and may lead to new ways of setting up experiments.
A synthetic synaptic organizer protein restores glutamatergic neuronal circuits
Authors: Suzuki Kunimichi , Elegheert Jonathan , Song Inseon , Sasakura Hiroyuki , Senkov Oleg , Kakegawa Wataru , Clayton Amber J. , Chang Veronica T. , Ferrer-Ferrer Maura , Miura Eriko , Kaushik Rahul , Ikeno Masashi , Morioka Yuki , Takeuchi Yuka , Shimada Tatsuya , Otsuka Shintaro , Stoyanov Stoyan , Watanabe Masahiko , Takeuchi Kosei , Dityatev Alexander , Aricescu A. Radu , Yuzaki Michisuke
Published: February 2020

Neuronal synapses undergo structural and functional changes throughout life, essential for nervous system physiology. However, these changes may also perturb the excitatory/inhibitory neurotransmission balance and trigger neuropsychiatric and neurological disorders. Molecular tools to restore this balance are highly desirable. Here, we report the design and characterization of CPTX, a synthetic synaptic organizer combining structural elements from cerebellin-1 and neuronal pentraxin-1 to interact with presynaptic neurexins and postsynaptic AMPA-type ionotropic glutamate receptors. CPTX induced the formation of excitatory synapsesin vitroandin vivoand restored synaptic functions, motor coordination, spatial and contextual memories, and locomotion in mouse models for cerebellar ataxia, Alzheimer’s disease and spinal cord injury, respectively. Thus, CPTX represents a prototype for novel structure-guided biologics that can efficiently repair or remodel neuronal circuits.

One Sentence Summary

Structural biology information was used to design CPTX, a synthetic protein that induces functional excitatory synapses and restores normal behaviors in mouse models of neurological diseases.
Dose-dependent phorbol 12-myristate-13-acetate-mediated monocyte-to-macrophage differentiation induces unique proteomic signatures in THP-1 cells
Authors: Pinto Sneha M. , Kim Hera , Subbannayya Yashwanth , Giambelluca Miriam , Bösl Korbinian , Kandasamy Richard K.
Published: February 2020

Macrophages are sentinels of the innate immune system, and the human monocytic cell line THP-1 is one of the widely usedin vitromodels to study immune responses. Several monocyte-to-macrophage differentiation protocols exist, with phorbol 12-myristate-13-acetate (PMA) being the widely used and accepted method. However, the concentrations and duration of PMA treatment vary widely in the published literature and their effect on protein expression is not fully deciphered. In this study, we employed a dimethyl labeling-based quantitative proteomics approach to determine the changes in the protein repertoire of macrophage-like cells differentiated from THP-1 monocytes by three commonly used PMA-based differentiation protocols. Our analysis shows that variations in PMA concentration and duration of rest post-stimulation result in downstream differences in the protein expression and cellular processes. We demonstrate that these differences result in altered gene expression of cytokines upon stimulation with various TLR agonists. Together, these findings provide a valuable resource that significantly expands the knowledge of protein expression dynamics with one of the most commonin vitromodels for macrophages, which in turn has a profound impact on the immune responses being studied.
Subphase Material Stabilizes Films of Pulmonary Surfactant
Authors: Andreev K. , Martynowycz M. W. , Kuzmenko I. , Bu W. , Hall S. B. , Gidalevitz D.
Published: February 2020

When compressed by the shrinking alveolar surface area during exhalation, films of pulmonary surfactantin situreduce surface tension to levels, at which surfactant monolayers collapse from the surfacein vitro. Vesicles of pulmonary surfactant added below these monolayers slow collapse. X-ray scattering here determined the structural changes that improve stability. Grazing incidence X-ray diffraction on monolayers of extracted calf surfactant detected an ordered phase. Mixtures of dipalmitoyl phosphatidylcholine and cholesterol, but not the phospholipid alone, mimic that structure. At concentrations that stabilize the monolayers, vesicles in the subphase had no effect on the unit cell, and the film remained monomolecular. The added vesicles, however, produced a concentration-dependent increase in the diffracted intensity. These results suggest that the enhanced resistance to collapse results from components of an ordered interfacial phase which partition from subphase to the surface, increasing the area of the ordered structure.

SIGNIFICANCE

Low alveolar surface tensions are essential for maintaining the integrity of the pulmonary air-sacks during normal breathing. Films of pulmonary surfactant cause the low tensions. The interfacial structures required for the low surface tensions remain uncertain. These studies used X-ray scattering to determine the initial structure of pulmonary surfactant monolayers, and to establish how vesicles of pulmonary surfactant enhance the ability of those initial monolayers to sustain low tensions. The initial monolayers contained ordered structures that differ from the crystalline forms widely speculated to occur in alveolar films. The added vesicles had no effect on the local structure of the initial monolayer, but substantially increased the area of the ordered regions. This structural change reasonably explains the functional improvement.
Designing membrane-reshaping nanostructures through artificial evolution
Authors: Forster Joel C. , Krausser Johannes , Vuyyuru Manish R. , Baum Buzz , Šarić Anđela
Published: February 2020

In this paper we combine the rules of natural evolution with molecular dynamics simulations to design a nanostructure with a desired function. We apply this scheme to the case of a ligand-covered nanoparticle and evolve ligand patterns that promote efficient cell uptake. Surprisingly, we find that in the regime of low ligand number the fittest structures are characterised by ligands arranged into long one-dimensional chains that pattern the surface of the particle. We show that these chains of ligands provide particles with high rotational freedom and they lower the free energy barrier for membrane crossing. This demonstrates the efficacy of artificial evolution to identify non-intuitive design rules and reveals a new principle of design that can be used to inform artificial nanoparticle construction and the search for inhibitors of viral entry.
Genome wide-association study identifies novel loci in the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study
Authors: Gudiseva Harini V. , Verma Shefali Setia , Chavali Venkata R. M. , Salowe Rebecca J. , Lucas Anastasia , Collins David W. , Rathi Sonika , He Jie , Lee Roy , Merriam Sayaka , Bowman Anita S. , McHugh Caitlin P. , Zody Michael C. , Pistilli Maxwell , Khachataryan Naira , Daniel Ebenezer , Murphy Windell , Weiner Mark , Henderer Jeffrey , Ross Ahmara , Cui Qi N. , Addis Victoria , Lehman Amanda , Miller-Ellis Eydie , Sankar Prithvi S. , Varma Rohit , Williams Scott M. , Ying Gui-shuang , Moore Jason H. , Ritchie Marylyn D. , O’Brien Joan M.
Published: February 2020

Primary open-angle glaucoma (POAG), the leading cause of irreversible blindness worldwide, disproportionately affects African Americans. Large-scale POAG genetic studies have focused on individuals of European and Asian ancestry, limiting our understanding of disease biology. Here we report genetic analysis of the largest-ever deeply phenotyped African American population (n=5950), identifying a novel POAG-associated SNP on chromosome 11 near theTRIM66gene (rs112369934). POAG trait association also implicated SNPs in genes involved in trabecular meshwork homeostasis and retinal ganglion cell maintenance. These new loci deepen our understanding of the pathophysiology of POAG in African Americans.
Dynamic modulation of glucose utilisation by glucocorticoid rhythms in health and disease
Authors: Zavala Eder , Gil-Gómez Carlos A. , Wedgwood Kyle C. A. , Burgess Romana , Tsaneva-Atanasova Krasimira , Herrera-Valdez Marco A.
Published: February 2020

A systems level coordination of physiological rhythms is essential to sustain healthy states, especially in the face of stimuli that may disrupt such rhythms. The timing of meals, medication and chronic stress can profoundly influence metabolism, which depends on the dynamic interactions between glucose, insulin and cortisol. Although the metabolic and stress endocrine axes are simultaneously disrupted in many diseases, a theoretical framework to understand how chronodisruption leads to disease is lacking. By developing a mathematical model of glucose utilisation that accounts for the antagonism between insulin and cortisol, we investigate the dynamic effects of glucose boluses under normal and disrupted cortisol rhythms, including the effects of cortisol agonists and antagonists. We also predict how cortisol rhythms modulate circadian responses to oral glucose diagnostic tests, and analyse the disruptions caused by hypercortisolism. Finally, we predict the mechanisms leading to type 2 diabetes in patients with normal and excess cortisol.
Amalgams: data-driven amalgamation for the reference-free dimensionality reduction of zero-laden compositional data
Authors: Quinn Thomas P. , Erb Ionas
Published: February 2020

In the health sciences, many data sets produced by next-generation sequencing (NGS) only contain relative information because of biological and technical factors that limit the total number of nucleotides observed for a given sample. As mutually dependent elements, it is not possible to interpret any component in isolation, at least without normalization. The field of compositional data analysis (CoDA) has emerged with alternative methods for relative data based on log-ratio transforms. However, NGS data often contain many more features than samples, and thus require creative new ways to reduce the dimensionality of the data without sacrificing interpretability. The summation of parts, called amalgamation, is a practical way of reducing dimensionality, but can introduce a non-linear distortion to the data. We exploit this non-linearity to propose a powerful yet interpretable dimension reduction method. In this report, we present data-driven amalgamation as a new method and conceptual framework for reducing the dimensionality of compositional data. Unlike expert-driven amalgamation which requires prior domain knowledge, our data-driven amalgamation method uses a genetic algorithm to answer the question, “What is the best way to amalgamate the data to achieve the user-defined objective?”. We present a user-friendly R package, called amalgam, that can quickly find the optimal amalgamation to (a) preserve the distance between samples, or (b) classify samples as diseased or not. Our benchmark on 13 real data sets confirm that these amalgamations compete with the state-of-the-art unsupervised and supervised dimension reduction methods in terms of performance, but result in new variables that are much easier to understand: they are groups of features added together.
Prefrontal responses during proactive and reactive inhibition are differentially impacted by stress in anorexia and bulimia nervosa
Authors: Westwater Margaret L. , Mancini Flavia , Gorka Adam X. , Shapleske Jane , Serfontein Jaco , Grillon Christian , Ernst Monique , Ziauddeen Hisham , Fletcher Paul C.
Published: February 2020

Background

Binge-eating is a distressing, transdiagnostic eating disorder symptom associated with impulsivity, particularly in negative mood states. Neuroimaging studies of bulimia nervosa (BN) report reduced activity in fronto-striatal regions implicated in self-regulatory control. However, it remains unknown if negative affective states, including stress, impair self-regulation, and, if so, whether such self-regulatory deficits generalize to binge-eating in underweight individuals (i.e., the bingeing/purging subtype of anorexia nervosa; AN-BP).

Methods

We determined the effect of acute stress on inhibitory control in 85 women (33 BN, 22 AN-BP, 30 matched controls). Participants underwent repeated functional MRI scanning, during performance of the stop-signal anticipation task, a validated measure of proactive (i.e., anticipation of stopping) and reactive (outright stopping) inhibition. Neural and behavioral responses to induced, psychological stress and a control task were evaluated on two separate days.

Results

Women with BN had reduced proactive inhibition while prefrontal responses were increased in both AN-BP and BN. Reactive inhibition was neurally and behaviorally intact in both diagnostic groups. Both AN-BP and BN groups showed distinct, stress-induced changes in prefrontal activity during both proactive and reactive inhibition. However, task performance was not significantly affected by stress.

Conclusions

These findings offer novel evidence of reduced proactive inhibition in BN, yet inhibitory control deficits did not generalize to AN-BP. While both groups showed altered neural responses during inhibition following stress, neither group demonstrated stress-induced performance deficits. As such, our findings counsel against a simplistic, stress-induced failure of regulation as a holistic explanation for binge-eating in these conditions.
Microbiome shifts associated with the introduction of wild Atlantic horseshoe crabs (Limulus polyphemus) into a touch-tank exhibit
Authors: Friel Ariel D. , Neiswenter Sean A. , Seymour Cale O. , Bali Lauren Rose , McNamara Ginger , Leija Fabian , Jewell Jack , Hedlund Brian P.
Published: February 2020

The Atlantic horseshoe crab (Limulus polyphemus) is a common marine aquarium species and model organism for research. There is potential monetary and conservation value in developing a stable captive population of horseshoe crabs, however, one major impediment to achieving captivity is a lack of knowledge regarding captive diseases. We utilized 16S rRNA gene amplicon sequencing to track changes in the microbiomes of four body locations in three wild-caught (tracked over 14 months in captivity) and three tank-acclimated (>2 years in captivity) adultL. polyphemusin a touch tank at Shark Reef Aquarium at Mandalay Bay in Las Vegas, NV. The wild population hosted diverse and distinct microbiomes on the carapace (737 amplicon sequence variants or ASVs), cloaca (1078 ASVs), gills (941 ASVs), and oral cavity (1193 ASVs), which were dominated by classesGammaproteobacteria,Bacteroidia, andAlphaproteobacteria. A rapid decline in richness across all body locations was observed within 1 month of captivity, with tank-acclimated (>2 years) animals having <5% of the initial microbiome richness and a nearly completely restructured microbial community. The carapace, oral cavity, and gills of the tank-acclimated animals hosted abundant populations ofAeromonas(>60%) andPseudomonas(>20%), both of which are known opportunistic pathogens of aquatic animals and can express chitinases, providing a plausible mechanism for the development of the carapace lesion pathology observed in this and other studies. These results provide an important baseline on the microbiomes of both wild and tank-acclimated horseshoe crabs and underscore the need to continue to investigate how native microbial populations may protect animals from pathogens.