bluuebunny/crossref_metadata_2025 huggingface dataset:
Insulin signaling gates long-term memory formation in Drosophila larvae
Authors: Eschment Melanie , Franz Hanna R. , Güllü Nazlı , Hölscher Luis G. , Huh Ko-Eun , Widmann Annekathrin
Published: November 2019

The ability to learn new skills and to store them as memory entities is one of the most impressive features of higher evolved organisms. However, not all memories are created equal; some are short-lived forms, and some are longer lasting. Formation of the latter is energetically costly and by the reason of restricted availability of food or fluctuations in energy expanses, efficient metabolic homeostasis modulating different needs like survival, growth, reproduction, or investment in longer lasting memories is crucial. Whilst equipped with cellular and molecular pre-requisites for formation of a protein synthesis dependent long-term memory (LTM), its existence in the larval stage of Drosophila remains elusive. Considering it from the viewpoint that larval brain structures are completely rebuilt during metamorphosis, and that this process depends completely on accumulated energy stores formed during the larval stage, investing in LTM represents an unnecessary expenditure. However, as an alternative, Drosophila larvae are equipped with the capacity to form a protein synthesis independent so-called larval anaesthesia resistant memory (lARM), which is consolidated in terms of being insensitive to cold-shock treatments. Motivated by the fact that LTM formation causes an increase in energy uptake in Drosophila adults, we tested the idea of whether an energy surplus can induce the formation of LTM in the larval stage. Indeed, increasing the metabolic state by feeding Drosophila larvae the disaccharide sucrose directly before aversive olfactory conditioning led to the formation of a larval LTM (lLTM). Moreover, we show that the metabolic state acts as a binary switch between the formation of lARM and lLTM. Based on this finding, we determined that it is the insulin receptor (InR) expressed in the mushroom body Kenyon cells (MB KCs) that mediates this switch to favor the formation of lLTM under energy-rich circumstances and lARM under energy-poor circumstances.
Associations between aversive learning processes and transdiagnostic psychiatric symptoms revealed by large-scale phenotyping
Authors: Wise Toby , Dolan Raymond J
Published: November 2019

Background

Symptom expression in a range of psychiatric conditions is linked to altered threat perception, manifesting particularly in uncertain environments. How precise computational mechanisms that support aversive learning, and uncertainty estimation, relate to the presence of specific psychiatric symptoms remains undetermined. 400 subjects completed an online game-based aversive learning task, requiring avoidance of negative outcomes, in conjunction with completing measures of common psychiatric symptoms. We used a probabilistic computational model to measure distinct processes involved in learning, in addition to inferred estimates of safety likelihood and uncertainty, and tested for associations between these variables and traditional psychiatric constructs alongside transdiagnostic dimensions. We used partial least squares regression to identify components of psychopathology grounded in both aversive learning behaviour and symptom self-report. We show that state anxiety and a transdiagnostic compulsivity-related factor are associated with enhanced learning from safety, and data-driven analysis indicated the presence of two separable components across our behavioural and questionnaire data: one linked enhanced safety learning and lower estimated uncertainty to physiological anxiety, compulsivity, and impulsivity; the other linked enhanced threat learning, and heightened uncertainty estimation, to symptoms of depression and social anxiety. Our findings implicate distinct aversive learning processes in the expression of psychiatric symptoms that transcend traditional diagnostic boundaries.
A sectioning and database enrichment approach for improved peptide spectrum matching in large, genome-guided protein sequence databases
Authors: Kumar Praveen , Johnson James E. , Easterly Caleb , Mehta Subina , Sajulga Ray , Nunn Brook , Jagtap Pratik D. , Griffin Timothy J.
Published: November 2019

Multi-omics approaches focused on mass-spectrometry (MS)-based data, such as metaproteomics, utilize genomic and/or transcriptomic sequencing data to generate a comprehensive protein sequence database. These databases can be very large, containing millions of sequences, which reduces the sensitivity of matching tandem mass spectrometry (MS/MS) data to sequences to generate peptide spectrum matches (PSMs). Here, we describe a sectioning method for generating an enriched database for those protein sequences that are most likely present in the sample. Our evaluation demonstrates how this method helps to increase the sensitivity of PSMs while maintaining acceptable false discovery rate statistics. We demonstrate increased true positive PSM identifications using the sectioning method when compared to the traditional large database searching method, whereas it helped in reducing the false PSM identifications when compared to a previously described two-step method for reducing database size. The sectioning method for large sequence databases enables generation of an enriched protein sequence database and promotes increased sensitivity in identifying PSMs, while maintaining acceptable and manageable FDR. Furthermore, implementation in the Galaxy platform provides access to a usable and automated workflow for carrying out the method. Our results show the utility of this methodology for a wide-range of applications where genome-guided, large sequence databases are required for MS-based proteomics data analysis.
Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers
Authors: He Bing , Gao Peng , Ding Yang-Yang , Chen Chia-Hui , Chen Gregory , Chen Changya , Kim Hannah , Tasian Sarah K. , Hunger Stephen P. , Tan Kai
Published: November 2019

Interpreting the function of noncoding mutations in cancer genomes remains a major challenge. Here we developed a computational framework to identify risk noncoding mutations of all classes by joint analysis of mutation and gene expression data. We identified thousands of SNVs/small indels and structural variants as candidate risk mutations in five major pediatric cancers. We experimentally validated the oncogenic role of CHD4 overexpression via enhancer hijacking in B-ALL. We observed a general exclusivity of coding and noncoding mutations affecting the same genes and pathways. We showed that integrated mutation signatures can help define novel patient subtypes with different clinical outcomes. Our study introduces a general strategy to systematically identify and characterize the full spectrum of noncoding mutations in cancers.
RNA modifications detection by comparative Nanopore direct RNA sequencing
Authors: Leger Adrien , Amaral Paulo P. , Pandolfini Luca , Capitanchik Charlotte , Capraro Federica , Barbieri Isaia , Migliori Valentina , Luscombe Nicholas M. , Enright Anton J , Tzelepis Konstantinos , Ule Jernej , Fitzgerald Tomas , Birney Ewan , Leonardi Tommaso , Kouzarides Tony
Published: November 2019

RNA molecules undergo a vast array of chemical post-transcriptional modifications (PTMs) that can affect their structure and interaction properties. To date, over 150 naturally occurring PTMs have been identified, however the overwhelming majority of their functions remain elusive. In recent years, a small number of PTMs have been successfully mapped to the transcriptome using experimental approaches relying on high-throughput sequencing. Oxford Nanopore direct-RNA sequencing (DRS) technology has been shown to be sensitive to RNA modifications. We developed and validated Nanocompore, a robust analytical framework to evaluate the presence of modifications in DRS data. To do so, we compare an RNA sample of interest against a non-modified control sample. Our strategy does not require a training set and allows the use of replicates to model biological variability. Here, we demonstrate the ability of Nanocompore to detect RNA modifications at single-molecule resolution in human polyA+ RNAs, as well as in targeted non-coding RNAs. Our results correlate well with orthogonal methods, confirm previous observations on the distribution of N6-methyladenosine sites and provide novel insights into the distribution of RNA modifications in the coding and non-coding transcriptomes. The latest version of Nanocompore can be obtained at https://github.com/tleonardi/nanocompore.
Genome-wide profiling of druggable active tumor defense mechanisms to enhance cancer immunotherapy
Authors: Kishton Rigel J. , Patel Shashank J. , Vodnala Suman K. , Decker Amy E. , Patel Yogin , Sukumar Madhusudhanan , Yamamoto Tori N. , Yu Zhiya , Ji Michelle , Henning Amanda N. , Gurusamy Devikala , Palmer Douglas C. , Lo Winifred , Pasetto Anna , Malekzadeh Parisa , Deniger Drew C. , Wood Kris C. , Sanjana Neville E. , Restifo Nicholas P.
Published: November 2019

All current highly effective anti-tumor immunotherapeutics depend on the activity of T cells, but tumor cells can escape immune recognition by several mechanisms including loss of function in antigen presentation and inflammatory response genes, expression of immunomodulatory proteins and an immunosuppressive tumor microenvironment. In contrast, the comprehensive identification of strategies that sensitize tumor cells to immunotherapy in vivo has remained challenging. Here, we combine a two-cell type (2CT) whole-genome CRISPR-Cas9 screen with dynamic transcriptional analysis (DTA) of tumor upon T cell encounter to identify a set of genes that tumor cells express as an active defense against T cell-mediated killing. We then employed small molecule and biologic screens designed to antagonize gene products employed by tumor cells to actively defend against T cell-mediated tumor destruction and found that the inhibition of BIRC2, ITGAV or DNPEP enhanced tumor cell destruction by T cells. Mechanistically, we found that BIRC2 promoted immunotherapy resistance through inhibiting non-canonical NF-κB signaling and limiting inflammatory chemokine production. These findings show the path forward to improving T cell-mediated tumor destruction in the clinic.
XenoCP: Cloud-based BAM cleansing tool for RNA and DNA from Xenograft
Authors: Rusch Michael , Ding Liang , Arunachalam Sasi , Thrasher Andrew , Jin Hongjian , Macias Michael , Kasper Lawryn , Silveira Andre , Dyer Michael A. , Baker Suzanne J. , Zhang Jinghui
Published: November 2019

Xenografts are important models for cancer research and the presence of mouse reads in xenograft next generation sequencing data can potentially confound interpretation of experimental results. We present an efficient, cloud-based BAM-to-BAM cleaning tool called XenoCP to remove mouse reads from xenograft BAM files. We show application of XenoCP in obtaining accurate gene expression quantification in RNA-seq and tumor heterogeneity in WGS of xenografts derived from brain and solid tumors.

Availability and Implementation

St. Jude Cloud (https://pecan.stjude.cloud/permalink/xenocp) and St. Jude Github (https://github.com/stjude/XenoCP)
Role of a versatile peptide motif in controlling Hox nuclear export and autophagy in theDrosophilafat body
Authors: Duffraisse Marilyne , Paul Rachel , Hudry Bruno , Carnesecchi Julie , Banretti Agnes , Reboulet Jonathan , Ajuria Leiore , Lohmann Ingrid , Merabet Samir
Published: November 2019

Hox proteins are major regulators of embryonic development, acting in the nucleus to regulate the expression of their numerous downstream target genes. By analyzing deleted forms of theDrosophilaHox protein Ultrabithorax (Ubx), we revealed the presence of an unconventional Nuclear Export Signal (NES) that overlaps with the highly conserved hexapeptide (HX) motif. This short linear motif was originally described as mediating the interaction with the PBC proteins, a generic and crucial class of Hox transcriptional cofactors in development and cancer. Here we show that the HX motif is involved in the interaction with the major CRM1/Embargoed exportin protein. This novel role was found in severalDrosophilaand human Hox proteins. We provide evidence that HX-dependent Hox nuclear export is tightly regulated in theDrosophilafat body to control the onset of autophagy. Our results underline the high molecular versatility of a unique short peptide motif for controlling context-dependent activity of Hox proteins at both transcriptional and non-transcriptional levels.
Cerebrovascular reactivity assessment with O2-CO2 exchange ratio under brief breath hold challenge
Authors: Chan Suk Tak , Evans Karleyton C. , Song Tian Yue , Selb Juliett , van der Kouwe Andre , Rosen Bruce R. , Zheng Yong Ping , Ahn Andrew , Kwong Kenneth K.
Published: November 2019

Hypercapnia during breath holding is believed to be the dominant driver behind the modulation of cerebral blood flow (CBF). Here we showed that the cerebrovascular responses to brief breath hold epochs were coupled not only with increased partial pressure of carbon dioxide (PCO2), but also with a decrease in partial pressure of oxygen (PO2). We used transcranial Doppler ultrasound to evaluate the CBF changes during breath holding by measuring the cerebral blood flow velocity (CBFv) in the middle cerebral arteries, a pair of cerebral arteries that supply most parts of the brain. The regional CBF changes during breath hold epochs were mapped with blood oxygenation level dependent (BOLD) signal changes as surrogate of CBF changes using functional magnetic resonance imaging (fMRI) technique. Given the interdependence of the dynamic changes between PCO2 and PO2, we found that the breath-by-breath O2-CO2 exchange ratio (bER), namely the ratio of changes in PO2 (ΔPO2) to changes in PCO2 (ΔPCO2) between end inspiration and end expiration, was superior to either ΔPO2 or ΔPCO2 alone in coupling with the changes of CBFv and BOLD signals under breath hold challenge. The regional cerebrovascular reactivity (CVR) results derived by regressing BOLD signal changes on bER under breath hold challenge resembled those derived by regressing BOLD signal changes on end-tidal partial pressure of CO2 (PETCO2) under exogenous CO2 challenge. Our findings provide a novel insight on the potential of using bER to better quantify CVR changes under breath hold challenge, although the physiological mechanisms of cerebrovascular changes underlying breath hold and exogenous CO2 challenges are potentially different.
Multiple routes to interspecific territoriality in sister species of North American perching birds
Authors: Cowen Madeline C. , Drury Jonathan P. , Grether Gregory F.
Published: November 2019

Behavioral interference between species can influence a wide range of ecological and evolutionary processes. Here we test foundational hypotheses regarding the origins and maintenance of interspecific territoriality, and evaluate the role of interspecific territoriality and hybridization in shaping species distributions and transitions from parapatry to sympatry in sister species of North American perching birds (Passeriformes). We found that interspecific territoriality is pervasive among sympatric sister species pairs, and that interspecifically territorial species pairs have diverged more recently than sympatric non-interspecifically territorial pairs. None of the foundational hypotheses alone explain the observed patterns of interspecific territoriality, but our results support the idea that some cases of interspecific territoriality arise from misdirected intraspecific aggression while others are evolved responses to resource competition. The combination of interspecific territoriality and hybridization appears to be an unstable state associated with parapatry, while species that are interspecifically territorial and do not hybridize are able to achieve extensive fine- and coarse-scale breeding range overlap. In sum, these results suggest that interspecific territoriality has multiple origins and that interspecific territoriality and hybridization together can have striking impacts on species ranges.
Integrating multi-OMICS data through sparse Canonical Correlation Analysis for predicting complex traits: A comparative study
Authors: Rodosthenous Theodoulos , Shahrezaei Vahid , Evangelou Marina
Published: November 2019

Motivation

Recent developments in technology have enabled researchers to collect multiple OMICS datasets for the same individuals. The conventional approach for understanding the relationships between the collected datasets and the complex trait of interest would be through the analysis of each OMIC dataset separately from the rest, or to test for associations between the OMICS datasets. In this work we show that by integrating multiple OMICS datasets together, instead of analysing them separately, improves our understanding of their in-between relationships as well as the predictive accuracy for the tested trait. As OMICS datasets are heterogeneous and high-dimensional (p >> n) integrating them can be done through Sparse Canonical Correlation Analysis (sCCA) that penalises the canonical variables for producing sparse latent variables while achieving maximal correlation between the datasets. Over the last years, a number of approaches for implementing sCCA have been proposed, where they differ on their objective functions, iterative algorithm for obtaining the sparse latent variables and make different assumptions about the original datasets.

Results

Through a comparative study we have explored the performance of the conventional CCA proposed by Parkhomenko et al. [2009], penalised matrix decomposition CCA proposed by Witten and Tibshirani [2009] and its extension proposed by Suo et al. [2017]. The aferomentioned methods were modified to allow for different penalty functions. Although sCCA is an unsupervised learning approach for understanding of the in-between relationships, we have twisted the problem as a supervised learning one and investigated how the computed latent variables can be used for predicting complex traits. The approaches were extended to allow for multiple (more than two) datasets where the trait was included as one of the input datasets. Both ways have shown improvement over conventional predictive models that include one or multiple datasets.

Contact

tr1915@ic.ac.uk
Natural diversity in the predatory behavior facilitates the establishment of a new robust model strain for nematode-trapping fungi
Authors: Yang Ching-Ting , de Ulzurrun Guillermo Vidal-Diez , Pedro Gonçalves A. , Lin Hung-Che , Chang Ching-Wen , Huang Tsung-Yu , Chen Sheng-An , Lai Cheng-Kuo , Tsai Isheng J. , Schroeder Frank C. , Stajich Jason E. , Hsueh Yen-Ping
Published: November 2019

Nematode-trapping fungi (NTF) are a group of specialized microbial predators that consume nematodes when food sources are limited. Predation is initiated when conserved nematode ascaroside pheromones are sensed, followed by the development of complex trapping devices. To gain insights into the co-evolution of this inter-kingdom predator-prey relationship, we investigated natural populations of nematodes and NTF, that we found to be ubiquitous in soils.Arthrobotrysspecies were sympatric with various nematode species and behaved as generalist predators. The ability to sense prey amongst wild isolates ofA. oligosporavaried greatly, as determined by the number of traps after exposure toCaenorhabditis elegans. While some strains were highly sensitive toC. elegansand the nematode pheromone ascarosides, others responded only weakly. Furthermore, strains that were highly sensitive to the nematode prey also developed traps faster. The polymorphic nature of trap formation correlated with competency in prey killing, as well as with the phylogeny ofA. oligosporanatural strains, calculated after assembly and annotation of the genomes of twenty isolates. A chromosome level genome assembly and annotation was established for one of the most sensitive wild isolate, and deletion of the only G proteinβsubunit-encoding gene ofA. oligosporanearly abolished trap formation, implicating G protein signaling in predation. In summary, our study establishes a highly responsiveA. oligosporawild isolate as a novel model strain for the study of fungal-nematode interactions and demonstrates that trap formation is a fitness character in generalist predators of the NTF family.

Significance statement

Nematode-trapping fungi (NTF) are carnivorous microbes that hold potential to be used as biological control agents due to their ability to consume nematodes. In this work we show that NTF are ubiquitous generalist predators found in sympatry with their prey in soil samples. Wild isolates of NTF displayed a naturally diverse ability to execute their predatory lifestyle. We generated a large whole genome sequencing dataset for many of the fungal isolates that will serve as the basis of future projects isolates. In particular, we establish TWF154, a highly responsive strain ofArthrobotrys oligospora, as a model strain to study the genetics of NTF. Lastly, we provide evidence that G-protein signaling is necessary for trap induction in NTF.
Pericyte-Like Cells Undergo Transcriptional Reprogramming and Distinct Functional Adaptations in Acute Lung Injury
Authors: Hung CF , Holton S , Chow YH , Liles WC , Gharib SA , Altemeier WA
Published: November 2019

Background

We previously reported on the role of pericyte-like cells as functional sentinel immune cells in lung injury. However, much about the biological role of pericytes in lung injury remains unknown. Lung pericyte-like cells are well-positioned to sense disruption to the epithelial barrier and coordinate local inflammatory responses due to their anatomic niche within the alveoli. In this report, we characterized transcriptional responses and functional changes in pericyte-like cells following activation by alveolar components from injured and uninjured lungs in a mouse model of acute lung injury (ALI).

Methods

We purified pericyte-like cells from lung digests using PDGFRβ as a selection marker and expanded them in culture as previously described (1). We induced sterile acute lung injury in mice with recombinant human Fas ligand (rhFasL) instillation followed by mechanical ventilation (1). We then collected bronchoalveolar lavage fluid (BALF) from injured and uninjured mice. Purified pericyte-like cells in culture were exposed to growth media only (control), BALF from uninjured mice, and BALF from injured mice for 6 and 24 h. RNA collected from these treatment conditions were processed for RNAseq. Targets of interest identified by pathway analysis were validated using in vitro and in vivo assays.

Results

We observed robust global transcriptional changes in pericyte-like cells following treatment with uninjured and injured BALF at 6 h, but this response persisted for 24 h only after exposure to injured BALF. Functional enrichment analysis of pericytes treated with injured BALF revealed activation of immuno-inflammatory, cell migration and angiogenesis-related pathways, whereas processes associated with tissue development and remodeling were down-regulated. We validated select targets in the inflammatory, angiogenesis-related, and cell migratory pathways using functional biological assays in vitro and in vivo.

Conclusion

Lung pericyte-like cells are highly responsive to alveolar compartment content from both uninjured and injured lungs, but injured BALF elicits a more sustained response. The inflammatory, angiogenic, and migratory changes exhibited by activated pericyte-like cells underscore the phenotypic plasticity of these specialized stromal cells in the setting of acute lung injury.
Mechanistic origin of drug interactions between translation-inhibiting antibiotics
Authors: Kavčič Bor , Tkačik Gašper , Bollenbach Tobias
Published: November 2019

Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we demonstrate that these interactions can be accounted for by “translation bottlenecks”: points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generated translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimicked antibiotic action and their interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further showed that the kinetics of drug uptake and binding together with growth laws allows direct prediction of a large fraction of observed interactions, yet fails for suppression. Simultaneously varying two translation bottlenecks in the same cell revealed how the dense traffic of ribosomes and competition for translation factors results in previously unexplained suppression. This result highlights the importance of “continuous epistasis” in bacterial physiology.
Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets
Authors: Pont Frédéric , Tosolini Marie , Gao Qing , Perrier Marion , Madrid-Mencía Miguel , Huang Tse Shun , Neuvial Pierre , Ayyoub Maha , Nazor Kristopher , Fournié Jean Jacques
Published: November 2019

The development of single cell transcriptomic technologies yields large datasets comprising multimodal informations such as transcriptomes and immunophenotypes. Currently however, there is no software to easily and simultaneously analyze both types of data. Here, we introduce Single-Cell Virtual Cytometer, an open-source software for flow cytometry-like visualization and exploration of multi-omics single cell datasets. Using an original CITE-seq dataset of PBMC from an healthy donor, we illustrate its use for the integrated analysis of transcriptomes and phenotypes of functional maturation in peripheral T lymphocytes from healthy donors. So this free and open-source algorithm constitutes a unique resource for biologists seeking for a user-friendly analytic tool for multimodal single cell datasets.
In situ cryo-electron tomography reveals filamentous actin within the microtubule lumen
Authors: Paul Danielle M , Mantell Judith , Borucu Ufuk , Coombs Jennifer , Surridge Katherine J , Squire John , Verkade Paul , Dodding Mark P
Published: November 2019

Microtubules and filamentous (F-) actin engage in complex interactions to drive many cellular processes from subcellular organisation to cell division and migration. This is thought to be largely controlled by proteins that interface between the two structurally distinct cytoskeletal components. Here, we use cryo-electron tomography to demonstrate that the microtubule lumen can be occupied by extended segments of F-actin in small-molecule induced, microtubule-based cellular projections. We uncover an unexpected versatility in cytoskeletal form that may prompt a significant development of our current models of cellular architecture and offer a new experimental approach for the in-situ study of microtubule structure and contents.
MyD88-Syk axis is a critical determinant for inflammatory response in macrophages
Authors: Yi Young-Su , Kim Ji Hye , Yang Woo Seok , Kim Eunji , Jeong Deok , Park Jae Gwang , Aziz Nur , Kim Suk , Parameswaran Narayanan , Cho Jae Youl
Published: November 2019

Inhibition of Syk or MyD88 decreased generation of reactive oxygen species (ROS)/reactive nitrogen species (RNS) and consequent ROS/RNS-induced phagocytic activity in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. Syk inhibition downregulated expression of ROS/RNS-generating enzymes by inhibiting the nuclear factor-kappa B (NF-kappa?B) signaling pathway and phagocytic activity by suppressing suppressor of cytokine signaling 1 (SOCS1) via its nitration in the LPS-stimulated RAW264.7 cells. Inhibition of ROS/RNS generation suppressed SOCS1 nitration, leading to a decrease in the phagocytic activity. Syk was activated by the interaction with MyD88, and the tyrosine 58 residue (Y58) in the hemi-immunoreceptor tyrosine-based activation motif (ITAM) of MyD88 was critical for interaction and consequent activation of Syk in macrophages. Src activated MyD88 by phosphorylation at Y58 via the Src kinase domain. Moreover, LPS-induced formation of filamentous actin (F-actin) and Ras-related C3 botulinum toxin substrate 1 (Rac1) activation induced Src activation. Conclusivley, these results suggest that the MyD88-Syk axis plays a pivotal role in macrophage-mediated inflammatory responses by inducing ROS/RNS generation and phagocytic activity via activation of Src and its upstream stimulators, F-actin and Rac1.
Magnetic-Alignment of Polymer Nanodiscs Probed by Solid-State NMR Spectroscopy
Authors: Ravula Thirupathi , Kim JaeWoong , Lee Dong-Kuk , Ramamoorthy Ayyalusamy
Published: November 2019

The ability of amphipathic polymers to self-assemble with lipids and form nanodiscs has been a boon for the field of functional reconstitution of membrane proteins. In a field dominated by detergent micelles, a unique feature of polymer nanodiscs is their much-desired ability to align in the presence of an external magnetic field. Magnetic alignment facilitates the application of solid-state NMR spectroscopy and aids in the measurement of residual dipolar couplings (RDCs) via well-established solution NMR spectroscopy. In this study, we comprehensively investigate the magnetic-alignment properties of SMA-QA polymer based nanodiscs by using 31P and 14N solid-state NMR experiments under static conditions. The results reported herein demonstrate the spontaneous magnetic-alignment of large-size (≥ 20 nm diameter) SMA-QA nanodiscs (also called as macro-nanodiscs) with the lipid-bilayer-normal perpendicular to the magnetic field direction. Consequently, the orientation of macro-nanodiscs are further shown to flip their alignment axis parallel to the magnetic field direction upon the addition of a paramagnetic lanthanide salt. These results demonstrate the use of SMA-QA polymer nanodiscs for solid-state NMR applications including structural studies on membrane proteins.
Dual oxidase geneDuoxand Toll-like receptor 3 geneTLR3in the Toll pathway suppress zoonotic pathogens through regulating the intestinal bacterial community homeostasis inHermetia illucensL.
Authors: Huang Yaqing , Yu Yongqiang , Zhan Shuai , Tomberlin Jeffery K. , Huang Dian , Cai Minmin , Zheng Longyu , Yu Ziniu , Zhang Jibin
Published: November 2019

Black soldier fly (BSF;Hermetia illucensL.) larvae can convert fresh pig manure into protein and fat-rich biomass, which can then be used as livestock feed. Currently, it is the only insect approved for such purposes in Europe, Canada, and the USA. Pig manure is rich in zoonotic pathogens (e.g.,Staphylococcus aureusandSalmonellaspp.). BSF larvae inhibit these zoonotic pathogens; however, the mechanism is unclear. We employed RNAi, qRT-PCR, and Illumina MiSeq bacterial 16S rDNA high-throughput sequencing molecular techniques to study the interaction between the two immune genes (Duoxin Duox-reactive oxygen species [ROS] immune system andTLR3in the Toll signaling pathway) and zoonotic pathogens to determine the mechanisms resulting in pathogen suppression.

Results indicated thatBsf Duox-TLR3RNAi increased bacterial load but decreased the relative abundance ofProvidenciaandDysgonomonasintestinal symbionts. Concurrently,Bsf Duox-TLR3RNAi inactivated the NF-κ B signaling pathway, downregulated the expression of antimicrobial peptides, and diminished inhibitory effects on zoonotic pathogen. The resulting dysbiosis stimulated an immune response by activatingBsfDuoxand promoting ROS, which regulated the composition and structure of the gut bacterial community.

Thus,BsfDuoxandBsfTLR3are important factors in regulating the gut key bacteriaProvidenciaandDysgonomonashomeostasis while inhibiting target zoonotic pathogens.
BlobToolKit – Interactive quality assessment of genome assemblies
Authors: Challis Richard , Richards Edward , Rajan Jeena , Cochrane Guy , Blaxter Mark
Published: November 2019

Reconstruction of target genomes from sequence data produced by instruments that are agnostic as to the species-of-origin may be confounded by contaminant DNA. Whether introduced during sample processing or through co-extraction alongside the target DNA, if insufficient care is taken during the assembly process, the final assembled genome may be a mixture of data from several species. Such assemblies can confound sequence-based biological inference and, when deposited in public databases, may be included in downstream analyses by users unaware of underlying problems.

We present BlobToolKit, a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. BlobToolKit can be used to process assembly, read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility.

We have been running an automated BlobToolKit pipeline on eukaryotic assemblies publicly available in the International Nucleotide Sequence Data Collaboration and are making the results available through a public instance of the Viewer at https://blobtoolkit.genomehubs.org/view. We aim to complete analysis of all publicly available genomes and then maintain currency with the flow of new genomes. We have worked to embed these views into the presentation of genome assemblies at the European Nucleotide Archive, providing an indication of assembly quality alongside the public record with links out to allow full exploration in the Viewer.
Including Data Analytical Stability in Cluster-based Inference
Authors: Roels Sanne P. , Loeys Tom , Moerkerke Beatrijs
Published: November 2019

In the statistical analysis of functional Magnetic Resonance Imaging (fMRI) brain data it remains a challenge to account for simultaneously testing activation in over 100.000 volume units or voxels. A popular method that reduces the dimensionality of this test problem is cluster-based inference. We propose a new testing procedure that allows to control the family-wise error (FWE) rate at the cluster level but improves cluster-based test decisions in two ways by (1) taking into account a measure for data analytical stability and (2) allowing a more voxel-based interpretation of the results. For each voxel, we define the re-selection rate conditional on a given FWE-corrected threshold and use this rate, which is a measure of stability, into the selection process. In our procedure, we set a more liberal and a more conservative FWE controlling threshold. Clusters that survive the liberal but not the conservative threshold are retained if sufficient evidence for voxelwise stability is available. Cluster that survive the conservative threshold are retained anyhow, and clusters that do not survive the liberal threshold are not further considered. Using the Human Connectome Project Data (Van Essen et al., 2012), we demonstrate how in a group analysis our method results not only in a higher number of selected voxels but also in a larger overlap between different test images. Additionally, we demonstrate the ability of our procedure to control the FWE, also in relatively small sample sizes.
Adaptive divergence in shoot gravitropism creates hybrid sterility in an Australian wildflower
Authors: Wilkinson Melanie J. , Roda Federico , Walter Greg M. , James Maddie E. , Nipper Rick , Walsh Jessica , Allen Scott L. , North Henry L. , Beveridge Christine A. , Ortiz-Barrientos Daniel
Published: November 2019

Natural selection is a significant driver of speciation. Yet it remains largely unknown whether local adaptation can drive speciation through the evolution of hybrid sterility between populations. Here, we show that adaptive divergence in shoot gravitropism, the ability of a plant’s shoot to bend upwards in response to the downward pull of gravity, contributes to the evolution of hybrid sterility in an Australian wildflower, Senecio lautus. We find that shoot gravitropism has evolved multiple times in association with plant height between adjacent populations inhabiting contrasting environments, suggesting that these traits have evolved by natural selection. We directly tested this prediction using a hybrid population subjected to eight rounds of recombination and three rounds of selection in the field. It revealed that shoot gravitropism responds to natural selection in the expected direction of the locally adapted population. This provided an ideal platform to test whether genetic differences in gravitropism contribute to hybrid sterility in S. lautus. Using this advanced hybrid population, we discovered that crossing individuals with extreme differences in gravitropism reduce their ability to produce seed by 21%, providing strong evidence that this adaptive trait is genetically correlated with hybrid sterility. Our results suggest that natural selection can drive the evolution of locally adaptive traits that also create hybrid sterility, thus indicating an evolutionary connection between local adaptation and the origin of new species.

Significance statement

New species originate as populations become reproductively isolated from one another. Despite recent progress in uncovering the genetic basis of reproductive isolation, it remains unclear whether intrinsic reproductive barriers, such as hybrid sterility, evolve as a by-product of local adaptation to contrasting environments or evolve through non-ecological processes, such as meiotic drive. Here, we show that differences in a plant’s response to the pull of gravity have repeatedly evolved amongst coastal populations of an Australian wildflower, thus implicating a role of natural selection in their evolution. We found a strong genetic correlation between variation in this adaptive trait and hybrid sterility, suggesting that intrinsic reproductive barriers contribute to the origin of new species as populations adapt to heterogeneous environments.
A comparative and functional genomics analysis of the genusRomboutsiaprovides insight into adaptation to an intestinal lifestyle
Authors: Gerritsen Jacoline , Hornung Bastian , Ritari Jarmo , Paulin Lars , Rijkers Ger T. , Schaap Peter J. , de Vos Willem M. , Smidt Hauke
Published: November 2019

Cultivation-independent surveys have shown that the recently described genusRomboutsiawithin the familyPeptostreptococcaceaeis more diverse than previously acknowledged. The majority ofRomboutsia-associated 16S rRNA gene sequences have an intestinal origin, but the specific roles thatRomboutsiaspecies play in the digestive tract are largely unknown. The complete genomes of the human intestinal isolateRomboutsia hominisFRIFIT(DSM 28814) and the soil isolateRomboutsia lituseburensisA25KT(DSM 797) were sequenced. An evaluation of the common traits of this recently defined genus was done based on comparative genome analysis of the two strains together with the previously elucidated genome of the type speciesRomboutsia ilealisCRIBT. These analyses showed that the genusRomboutsiacovers a broad range of metabolic capabilities with respect to carbohydrate utilization, fermentation of single amino acids, anaerobic respiration and metabolic end products. Main differences between strains were found in their abilities to utilize specific carbohydrates, to synthesize vitamins and other cofactors, and their nitrogen assimilation capabilities. In addition, differences were found with respect to bile metabolism and motility-related gene clusters.
Full-coverage native RNA sequencing of HIV-1 viruses
Authors: Gener Alejandro R. , Kimata Jason T.
Published: November 2019

Objective

To evaluate native RNA sequencing for sequencing HIV-1 viral genomes

Methods

Fifteen HIV-1 strains were processed with Direct RNA Sequencing (SQK-RNA002) library kits and sequenced on MinION Mk1B devices with RevD flow cells (Oxford Nanopore Technologies (ONT), Oxford, UK). Raw reads were converted to FASTQ, aligned to reference sequences, and assembled into contigs. Multi-sequence alignments of the contigs were generated and used for cladistics analysis.

Results

We sequenced full-length HIV-1 from the transcriptional start site to 3’ LTR (100% virion genome) in 3 out of 15 isolates (89.6, NLAD8, AD17), achieving majority coverage (defined as > 50%) in another 7 out of 15 isolates. Inspection of NLAD8 sequence alignments revealed splicing or deletion signatures. Despite the strong 3’ bias, read coverage was sufficient to evaluate single-nucleotide variants (SNVs), insertions and deletions in 9 isolates, and to assemble HIV-1 genomes directly from viral RNA, achieving a maximum of 94% assembly coverage for NLAD8. Phylogenetic relationships were maintained at the level of contigs, as well as individual reads.

Conclusions

ONT native RNA sequencing performed as expected, covering full-length HIV-1 RNA without PCR or cDNA sequencing. Native single-molecule RNA sequencing supported previous models of HIV-1 replication, and samples exhibited strain-specific transcriptional signals. We propose Context Dependency Variant Classification to describe variants occurring in information-dense regions of HIV. These data provide rich resources for emerging RNA modification detection schemes. Future work will expand HIV-1 transcript profiling to infection models and clinical samples.
Evaluation of Connectivity Map shows limited reproducibility in drug repositioning
Authors: Lim Nathaniel , Pavlidis Paul
Published: November 2019

The Connectivity Map (CMap) is a popular resource designed for data-driven drug repositioning using a large transcriptomic compendium. However, evaluations of its performance are limited. We used two iterations of CMap (CMap 1 and 2) to assess their comparability and reliability. We queried CMap 2 with CMap 1-derived signatures, expecting CMap 2 would highly prioritize the queried compounds; success rate was 17%. Analysis of previously published prioritizations yielded similar results. Low recall is caused by low differential expression (DE) reproducibility both between CMaps and within each CMap. DE strength was predictive of reproducibility, and is influenced by compound concentration and cell-line responsiveness. Reproducibility of CMap 2 sample expression levels was also lower than expected. We attempted to identify the “better” CMap by comparison with a third dataset, but they were mutually discordant. Our findings have implications for CMap usage and we suggest steps for investigators to limit false positives.
Quantum and Quantum-inspired Methods forde novoDiscovery of Altered Cancer Pathways
Authors: Alghassi Hedayat , Dridi Raouf , Robertson A. Gordon , Tayur Sridhar
Published: November 2019

The combinatorial calculations forde novodiscovery of altered pathways in cancer cohorts involve both coverage (i.e. recurrence) and mutual exclusivity, and solving mutual exclusivity problems is NP-hard for classical computers. Advances in quantum computing systems and our classical, quantum-inspired algorithm GAMA (Graver Aug-mented Multi-seed Algorithm) motivated us to revisit methods for identifying altered pathways. Using different types of quantum and classical algorithms, we report novel formulations of the problem that are tailored to these new computational models. Our formulations require fewer binary variables than available methods, and offer a tuning parameter that allows a trade-off between coverage and exclusivity; varying this parameter returns a variety of solutions. We illustrate our formulations and methods with TCGA mutation data for Acute Myeloid Leukemia (AML). Both the D-Wave quantum annealing solver and the classical GAMA solver returned altered pathways that are known to be important in AML, with different tuning parameter values returning alternative altered pathways. Our reduced-variable algorithm and QUBO problem for-mulations demonstrate how quantum annealing-based binary optimization solvers can be used now in cancer genomics.
Robust lysosomal rewiring in Mtb infected macrophages mediated by Mtb lipids restricts the intracellular bacterial survival
Authors: Sachdeva Kuldeep , Goel Manisha , Sudhakar Malvika , Mehta Mansi , Raju Rajmani , Raman Karthik , Singh Amit , Sundaramurthy Varadharajan
Published: November 2019

Intracellular pathogens commonly manipulate the host lysosomal system for their survival, however whether this affects the organization and functioning of the lysosomal system itself is not known. Here, we show usingin vitroandin vivoinfections that the lysosomal content and activity is globally elevated inM. tuberculosisinfected macrophages. The enhanced lysosomal state is sustained over time and defines an adaptive homeostasis of the infected cell. Lysosomal alterations are caused by mycobacterial surface components, notably the cell wall lipid SL-1, which functions through the mTORC1-TFEB axis. Mtb mutant defective for SL-1 levels shows reduced lysosomal content and activity compared to wild type. Importantly, this phenotype is conserved duringin vivoinfection. The alteration in lysosomal phenotype in mutant Mtb lead to decreased lysosomal delivery of Mtb, and importantly, increased survival of intracellular Mtb. These results define the global alterations in the host lysosomal system as a crucial distinguishing feature of Mtb infected macrophages that is host protective and contribute to the containment of the pathogen.
ExploreASL: an image processing pipeline for multi-center ASL perfusion MRI studies
Authors: Mutsaerts Henri , Petr Jan , Groot Paul , Vandemaele Pieter , Ingala Silvia , Robertson Andrew D , Václavů Lena , Groote Inge , Kuijf Hugo , Zelaya Fernando , O’Daly Owen , Hilal Saima , Wink Alle Meije , Kant Ilse , Caan Matthan W.A. , Morgan Catherine , de Bresser Jeroen , Lysvik Elisabeth , Schrantee Anouk , Bjørnebekk Astrid , Clement Patricia , Shirzadi Zahra , Kuijer Joost P.A. , Anazodo Udunna C. , Pajkrt Dasja , Richard Edo , Bokkers Reinoud P.H. , Reneman Liesbeth , Masellis Mario , Günther Matthias , MacIntosh Bradley J. , Achten Eric , Chappell Michael A. , van Osch Matthias J.P. , Golay Xavier , Thomas David L. , de Vita Enrico , Bjørnerud Atle , Nederveen Aart , Hendrikse Jeroen , Asllani Iris , Barkhof Frederik
Published: November 2019

Arterial spin labeling (ASL) has undergone significant development since its inception, with a focus on improving standardization and reproducibility of its acquisition and quantification. In a community-wide effort towards robust and reproducible clinical ASL image processing, we developed the software package ExploreASL, allowing standardized analyses across centers and scanners.

The procedures used in ExploreASL capitalize on published image processing advancements and address the challenges of multi-center datasets with scanner-specific processing and artifact reduction to limit patient exclusion. ExploreASL is self-contained, written in MATLAB and based on Statistical Parameter Mapping (SPM) and runs on multiple operating systems. The toolbox adheres to previously defined international standards for data structure, provenance, and best analysis practice.

ExploreASL was iteratively refined and tested in the analysis of >10,000 ASL scans using different pulse-sequences in a variety of clinical populations, resulting in four processing modules: Import, Structural, ASL, and Population that perform tasks, respectively, for data curation, structural and ASL image processing and quality control, and finally preparing the results for statistical analyses on both single-subject and group level. We illustrate ExploreASL processing results from three cohorts: perinatally HIV-infected children, healthy adults, and elderly at risk for neurodegenerative disease. We show the reproducibility for each cohort when processed at different centers with different operating systems and MATLAB versions, and its effects on the quantification of gray matter cerebral blood flow.

ExploreASL facilitates the standardization of image processing and quality control, allowing the pooling of cohorts to increase statistical power and discover between-group perfusion differences. Ultimately, this workflow may advance ASL for wider adoption in clinical studies, trials, and practice.