bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractNatural 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 statementNew 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

AbstractCultivation-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

ABSTRACTObjectiveTo evaluate native RNA sequencing for sequencing HIV-1 viral genomesMethodsFifteen 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.ResultsWe 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.ConclusionsONT 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

SummaryThe 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

AbstractThe 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

AbstractIntracellular 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

AbstractArterial 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.
Programmable CRISPR interference for gene silencing using Cas13a in mosquitoes
Authors: Kulkarni Aditi , Yu Wanqin , Moon Alex , Pandey Ashmita , Hanley Kathryn A. , Xu Jiannong 
Published: November 2019

AbstractIn the CRISPR-Cas systems, Cas13a is an RNA-guided RNA nuclease specifically targeting single strand RNA. We developed a Cas13a mediated CRISPR interference tool to target mRNA for gene silencing in mosquitoes. The machinery was tested in two mosquito species. A Cas13a expressing plasmid was delivered to mosquitoes by intrathoracic injection, and Cas13a transcripts were detectable at least10 days post-delivery. In Anopheles gambiae, vitellogenin gene was silenced by Vg-crRNA injection two hours post-blood meal, which was accompanied by a significant reduction in egg production. In Aedes aegypti, the α- and δ-subunits of COPI genes were silenced by a post-blood meal crRNA injection, which resulted in mortality and fragile midguts, reproducing a phenotype reported previously. Co-silencing genes simultaneously is achievable when a cocktail of target crRNAs is given. No detectable collateral cleavages of non-target transcripts were observed in the study. This study adds a programmable CRISPR tool to manipulate RNA in mosquitoes.
Therapeutic efficacy of an immune stimulatory gene therapy strategy in a mouse model of high grade brainstem glioma
Authors: Mendez Flor M. , Kadiyala Padma , Nunez Felipe J. , Carney Stephen , Nunez Fernando , Gauss Jessica C. , Ravindran Ramya , Pawar Sheeba , Edwards Marta , Lowenstein Pedro R. , Castro Maria G. 
Published: November 2019

AbstractPurposeDiffuse intrinsic pontine glioma (DIPG) bears a dismal prognosis. A genetically engineered brainstem glioma model harboring the recurrent DIPG mutation, ACVR1-G328V (mACVR1), was developed for testing an immune-stimulatory gene therapy.Experimental DesignWe utilized the Sleeping Beauty transposase system to generate an endogenous mouse model of mACVR1 brainstem glioma. Histology was used to characterize and validate the model. We performed RNAseq analysis on neurospheres (NS) harboring mACVR1. mACVR1 NS were implanted into the pons of immune competent mice to test the therapeutic efficacy and toxicity of immune stimulatory gene therapy using adenoviruses expressing thymidine kinase (TK) and fms-like tyrosine kinase 3 ligand (Flt3L). mACVR1 NS expressing the surrogate tumor antigen ovalbumin were generated to investigate if TK/Flt3L treatment induces the recruitment of tumor-antigen specific T cells.ResultsHistological analysis of mACVR1 tumors indicates that they are localized in the brainstem and have increased downstream signaling of bone morphogenetic pathway as demonstrated by increased phospho-smad1/5 and Id1 levels. Transcriptome analysis of mACVR1 NS identified an increase in the transforming growth factor beta (TGF-β) signaling pathway and the regulation of cell differentiation. Adenoviral delivery of TK/Flt3L in mice bearing brainstem gliomas resulted in anti-tumor immunity, recruitment of anti-tumor specific T cells and increased median survival.ConclusionsThis study provides insights into the phenotype and function of the tumor immune microenvironment in a mouse model of brainstem glioma harboring mACVR1. Immune stimulatory gene therapy targeting the hosts’ anti-tumor immune response inhibits tumor progression and increases median survival of mice bearing mACVR1 tumors.Translational RelevanceThe therapeutic efficacy of anti-DIPG immune responses is limited due to a low number of immune cells in the tumor microenvironment. We have uncovered a novel treatment strategy that utilizes adenoviral delivery of therapeutic genes, thymidine kinase (TK) and fms tyrosine kinase 3 ligand (Flt3L) into the tumor, eliciting a reprograming of the host’s own immune system to recognize and kill tumor cells. We demonstrate that TK/Flt3L therapy generates an effective anti-tumor response and can be safely delivered into the brainstem. This treatment approach could provide a novel translational approach towards potentiating an anti-DIPG immune response to overcome the current limitations in the treatment of patients with DIPG.
The extended recovery ring stage survival assay provides superior prediction of patient clearance half life and increases throughput
Authors: Davis Sage Z. , Singh Puspendra P. , Vendrely Katelyn M. , Shoue Douglas A. , Checkley Lisa A. , McDew-White Marina , Button-Simons Katrina A. , Cassady Zione , Sievert Mackenzie A.C. , Foster Gabriel J. , Nosten François H. , Anderson Timothy J.C. , Ferdig Michael T. 
Published: November 2019

AbstractBackgroundTracking and understanding artemisinin resistance is key for preventing global setbacks in malaria eradication efforts. The ring-stage survival assay (RSA) is the current gold standard for in vitro artemisinin resistance phenotyping. However, the RSA has several drawbacks: it is relatively low throughput, has high variance due to microscopy readout, and correlates poorly with the current benchmark for in vivo resistance, patient clearance half-life post-artemisinin treatment. Here a modified RSA is presented, the extended Recovery Ring-stage Survival Assay (eRRSA), using 15 cloned patient isolates from Southeast Asia with a range of patient clearance half-lives, including parasite isolates with and without kelch13 mutations.MethodsP. falciparum cultures were synchronized with single layer Percoll during the schizont stage of the erythrocytic cycle. Cultures were left to reinvade to early ring-stage and parasitemia was quantified using flow cytometry. Cultures were diluted to 2% hematocrit and 0.5% parasitemia in a 96-well plate to start the assay, allowing for increased throughput and decreased variability between biological replicates. Parasites were treated with 700nM of dihydroartemisinin or an equivalent amount of dimethyl sulfoxide (DMSO) for 6 h, washed three times in drug-free media, and incubated for 66 or 114 h, when samples were collected and frozen for PCR amplification. A SYBR Green-based quantitative PCR method was used to quantify the fold-change between treated and untreated samples.Results15 cloned patient isolates from Southeast Asia with a range of patient clearance half-lives were assayed using the eRRSA. Due to the large number of pyknotic and dying parasites at 66 h post-exposure (72 h sample), parasites were grown for an additional cell cycle (114 h post-exposure, 120 h sample), which drastically improved correlation with patient clearance half-life compared to the 66 h post-exposure sample. A Spearman correlation of 0.8393 between fold change and patient clearance half-life was identified in these 15 isolates from Southeast Asia, which is the strongest correlation reported to date.ConclusionseRRSA drastically increases the efficiency and accuracy of in vitro artemisinin resistance phenotyping compared to the traditional RSA, which paves the way for extensive in vitro phenotyping of hundreds of artemisinin resistant parasites.
Unveiling the physiological mechanisms that drive the emergence of antibiotic resisters from antibiotic persister population of mycobacteria
Authors: Jakkala Kishor , Sharan Deepti , Nair Rashmi Ravindran , Paul Avraneel , Pradhan Atul , Ajitkumar Parthasarathi 
Published: November 2019

AbstractThe physiological mechanisms behind the emergence of antibiotic-resistant bacteria from their antibiotic-persister population are beginning to be explored. Here we delineate the sequential physiological events that drive the emergence of rifampin-resistantrpoBmutants from rifampin-persister population of mycobacteria during prolonged exposure. The rifampin-persister population generated elevated levels of hydroxyl radical, which inflicted mutations, enabling regrowth of the persister cells to form multi-septated, multi-nucleated elongated cells. These cells, through multiple divisions, produced multiple sister-daughter cells, causing an abrupt, unexpectedly high increase of rifampin-resistant colonies. Similar response was observed against moxifloxacin also. Earlier studies on the rifampin/moxifloxacin-exposed laboratory/clinicalM. tuberculosisstrains fromin-vitrocultures and infected mouse-lung also showed cfu spurt, but went unnoticed/unreported. It is likely that these sequential physiological events may be driving the emergence of antibiotic-resistant tubercle bacilli in TB patients also.Escherichia colialso has been found to respond similarly against subminimal inhibitory concentrations of ciprofloxacin. Thus, the present findings attain broad significance as a general physiological mechanism used by diverse bacterial genera to emerge as drug-resistant strains against antibiotics.
bsAS, an antisense long non-coding RNA, controls cell fate through regulation ofblistered/DSRFisoform expression
Authors: Pérez-Lluch Sílvia , Breschi Alessandra , Klein Cecilia C. , Ruiz-Romero Marina , Abad Amaya , Palumbo Emilio , Bekish Lyazzat , Arnan Carme , Guigó Roderic 
Published: November 2019

SummaryNatural Antisense Transcripts (NATs) are long non-coding RNAs (lncRNAs) that overlap coding genes in the opposite strand. NATs roles have been related to gene regulation through different mechanisms, including post-transcriptional RNA processing. With the aim to identify NATs with potential regulatory function during fly development, we generated RNA-Seq data in eye-antenna, leg, and wing at third instar larvae. Among the candidate NATs, we foundbsAS, antisense tobs/DSRF, a gene involved in wing development and neural processes. Through the analysis of the RNA-Seq data, we found that these two different functions are carried out by the two different protein isoforms encoded in thebsgene. We also found that the usage of these isoforms is regulated bybsAS. This regulation is essential for the correct determination of cell fate duringDrosophiladevelopment, asbsASknockouts show highly aberrant phenotypes.bsregulation bybsASis mediated by the specific physical interaction of thebsASpromoter with the promoters ofbs, and it likely involves a mechanism, where expression ofbsASleads to the collision of RNA polymerases acting in opposite directions, preventing the elongation of the longer isoforms ofbs, the ones carrying the neural related functions. Evolutionary analysis suggests that thebsASNAT emerged simultaneously to the long-short isoform structure ofbs, preceding the emergence of wings in insects, and maybe related to regulation of neural differentiation.