bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: insights from a natural arms race
Authors: McKitterick Amelia C. , LeGault Kristen N. , Angermeyer Angus , Alam Munirul , Seed Kimberley D. 
Published: March 2019

CRISPR-Cas systems function as adaptive immune systems by acquiring nucleotide sequences called spacers that mediate sequence-specific defence against competitors. Uniquely, the phage ICP1 encodes a Type I-F CRISPR-Cas system that is deployed to target and overcome PLE, a mobile genetic element with anti-phage activity inVibrio cholerae. Here, we exploit the arms race between ICP1 and PLE to examine spacer acquisition and interference under laboratory conditions to reconcile findings from wild populations. Natural ICP1 isolates encode multiple spacers directed against PLE, but we find that single spacers do not interfere equally with PLE mobilization. High-throughput sequencing to assay spacer acquisition reveals that ICP1 can also acquire spacers that target theV. choleraechromosome. We find that targeting theV. choleraechromosome proximal to PLE is sufficient to block PLE and is dependent on Cas2-3 helicase activity. We propose a model in which indirect chromosomal spacers are able to circumvent PLE by Cas2-3-mediated processive degradation of theV. choleraechromosome before PLE mobilization. Generally, laboratory-acquired spacers are much more diverse than the subset of spacers maintained by ICP1 in nature, showing how evolutionary pressures can constrain CRISPR-Cas targeting in ways that are often not appreciated throughin vitroanalyses.This article is part of a discussion meeting issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
Aquaculture as a source of empirical evidence for coevolution between CRISPR-Cas and phage
Authors: Hoikkala Ville , Almeida Gabriel M. F. , Laanto Elina , Sundberg Lotta-Riina 
Published: March 2019

So far, studies on the bacterial immune system CRISPR-Cas and its ecological and evolutionary effects have been largely limited to laboratory conditions. While providing crucial information on the constituents of CRISPR-Cas, such studies may overlook fundamental components that affect bacterial immunity in natural habitats. Translating laboratory-derived predictions to nature is not a trivial task, owing partly to the instability of natural communities and difficulties in repeated sampling. To this end, we review how aquaculture, the farming of fishes and other aquatic species, may provide suitable semi-natural laboratories for examining the role of CRISPR-Cas in phage/bacterium coevolution. Existing data from disease surveillance conducted in aquaculture, coupled with growing interest towards phage therapy, may have already resulted in large collections of bacterium and phage isolates. These data, combined with premeditated efforts, can provide empirical evidence on phage–bacterium dynamics such as the bacteriophage adherence to mucus hypothesis, phage life cycles and their relationship with CRISPR-Cas and other immune defences. Typing of CRISPR spacer content in pathogenic bacteria can also provide practical information on diversity and origin of isolates during outbreaks. In addition to providing information of CRISPR functionality and phage–bacterium dynamics, aquaculture systems can significantly impact perspectives on design of phage-based disease treatment at the current era of increasing antibiotic resistance.This article is part of a discussion meeting issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
Editing the microbiome the CRISPR way
Authors: Ramachandran Gayetri , Bikard David 
Published: March 2019

Our bodies are colonized by a complex ecosystem of bacteria, unicellular eukaryotes and their viruses that together play a major role in our health. Over the past few years tools derived from the prokaryotic immune system known as CRISPR-Cas have empowered researchers to modify and study organisms with unprecedented ease and efficiency. Here we discuss how various types of CRISPR-Cas systems can be used to modify the genome of gut microorganisms and bacteriophages. CRISPR-Cas systems can also be delivered to bacterial population and programmed to specifically eliminate members of the microbiome. Finally, engineered CRISPR-Cas systems can be used to control gene expression and modulate the production of metabolites and proteins. Together these tools provide exciting opportunities to investigate the complex interplay between members of the microbiome and our bodies, and present new avenues for the development of drugs that target the microbiome.
This article is part of a discussion meeting issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
Mice Against Ticks: an experimental community-guided effort to prevent tick-borne disease by altering the shared environment
Authors: Buchthal Joanna , Evans Sam Weiss , Lunshof Jeantine , Telford Sam R. , Esvelt Kevin M. 
Published: March 2019

Mice Against Ticks is a community-guided ecological engineering project that aims to prevent tick-borne disease by using CRISPR-based genome editing to heritably immunize the white-footed mice (Peromyscus leucopus) responsible for infecting many ticks in eastern North America. Introducing antibody-encoding resistance alleles into the local mouse population is anticipated to disrupt the disease transmission cycle for decades. Technology development is shaped by engagement with community members and visitors to the islands of Nantucket and Martha's Vineyard, including decisions at project inception about which types of disease resistance to pursue. This engagement process has prompted the researchers to use only white-footed mouse DNA if possible, meaning the current project will not involve gene drive. Instead, engineered mice would be released in the spring when the natural population is low, a plan unlikely to increase total numbers above the normal maximum in autumn. Community members are continually asked to share their suggestions and concerns, a process that has already identified potential ecological consequences unanticipated by the research team that will likely affect implementation. As an early example of CRISPR-based ecological engineering, Mice Against Ticks aims to start small and simple by working with island communities whose mouse populations can be lastingly immunized without gene drive.This article is part of a discussion meeting issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
Have It, Know It, but Don’t Show It: Examining Physiological Arousal, Anxiety, and Facial Expressions over the Course of a Social Skills Intervention for Autistic Adolescents
Authors: Jain Niharika , Ahamed Sheikh Iqbal , Bozdag Serdar , Dolan Bridget K. , McVey Alana J. , Willar Kirsten S. , Pleiss Sheryl S. , Murphy Christina C. , Casnar Christina L. , Potts Stephanie , Cibich Daniel , Nelsen-Freund Kylie , Fernandez Dana , Hernandez Illeana , Van Hecke Amy Vaughan 
Published: March 2019

AbstractFacial expressions provide a nonverbal mechanism for social communication, a core challenge for autistic people. Little is known regarding the association between arousal, self-report of anxiety, and facial expressions among autistic adolescents. Therefore, this study investigated session-by-session facial expressions, self-report of anxiety, and physiological arousalviaElectrodermal Activity (EDA), of 12 autistic male adolescents in a didactic social skills intervention setting. The goals of this study were threefold: 1) identify physiological arousal levels (“have-it”), 2) examine if autistic adolescents’ facial expressions indicated arousal (“show-it”), and 3) determine whether autistic adolescents were self-aware of their anxiety (“know-it”). Our results showed that autistic adolescents’ self-rated anxiety was significantly associated with peaks in EDA. Both machine learning algorithms and human participant-based methods, however, had low accuracy in predicting autistic adolescents’ arousal state from facial expressions, suggesting that autistic adolescent’s facial expressions did not coincide with their arousal. Implications for understanding social communication difficulties among autistic adolescents, as well as future targets for intervention, are discussed. This project is registered with ClinicalTrials.gov, Identifier:NCT02680015.
Computational and experimental insights into the chemosensory navigation ofAedes aegyptimosquito larvae
Authors: Lutz Eleanor K. , Grewal Tjinder S. , Riffell Jeffrey A. 
Published: March 2019

AbstractMosquitoes are prolific disease vectors that affect public health around the world. Although many studies have investigated search strategies used by host-seeking adult mosquitoes, little is known about larval search behavior. Larval behavior affects adult body size and fecundity, and thus the capacity of individual mosquitoes to find hosts and transmit disease. Understanding vector survival at all life stages is crucial for improving disease control. In this study we use experimental and computational methods to investigate the chemical ecology and search behavior ofAedes aegyptimosquito larvae. We show that larvae do not respond to several olfactory cues used by adultAe. aegyptito assess larval habitat quality, but perceive microbial RNA as a potent foraging attractant. Second, we demonstrate thatAe. aegyptilarvae use a strategy consistent with chemokinesis, rather than chemotaxis, to navigate chemical gradients. Using computational modeling, we further show that chemokinesis is more efficient than chemotaxis for avoiding repellents in ecologically relevant larval habitat sizes. Finally, we use experimental observations and computational analyses to demonstrate that larvae respond to starvation pressure by optimizing exploration behavior. Our results identify key characteristics of foraging behavior in a disease vector mosquito, including the identification of a surprising foraging attractant and an unusual behavioral mechanism for chemosensory preference. In addition to implications for better understanding and control of disease vectors, this work establishes mosquito larvae as a tractable model for chemosensory behavior and navigation.
Extraordinary claims require extraordinary evidence in the case of asserted mtDNA biparental inheritance
Authors: Salas Antonio , Schönherr Sebastian , Bandelt Hans-Jürgen , Gómez-Carballa Alberto , Weissensteiner Hansi 
Published: March 2019

AbstractA breakthrough article published in PNAS by Luo et al. (2018) challenges a central dogma in biology which states that the mitochondrial DNA (mtDNA) is inherited exclusively from the mother. By sequencing the mitogenomes of several members of three independent families, the authors inferred an unprecedented pattern of biparental inheritance that requires the participation of an autosomal nuclear factor in the molecular process. However, a comprehensive analysis of their data reveals a number of issues that must be carefully addressed before challenging the current paradigm. Unfortunately, the methods section lacks any description of sample management, validation of their results in independent laboratories was deficient, and the reported findings have been observed at a frequency at complete variance with established evidence. Moreover, the remarkably high (and unusually homogeneous) levels of heteroplasmy reported can be readily detected using classical techniques for DNA sequencing. By reassessing the raw sequencing data with an alternative computational pipeline, we report strong correlation to the NextGENe results provided by the authors on a per sample base. However, the sequencing replicates from the same donors show aberrations in the variants detected that need further investigation to exclude contributions from other sources or methodological artifacts. Finally, applying the principle ofreductio ad absurdum, we demonstrate that the nuclear factor invoked by the authors would need to be extraordinarily complex and precise in order to preclude linear accumulation of mtDNA lineages across generations. We discuss alternate scenarios that explain findings of the same nature as reported by Luo et al., in the context ofin-vitrofertilization and therapeutic mtDNA replacement ooplasmic transplantation.
Carrion flies as sentinels for monitoring rabbit calicivirus activity in Australia
Authors: Hall Robyn N , Huang Nina , Roberts John , Strive Tanja 
Published: March 2019

SummaryRabbit caliciviruses are an essential tool for managing wild rabbit populations in Australia. Our understanding of rabbit calicivirus epidemiology in Australia currently depends on members of the public submitting liver samples from dead rabbits through a monitoring program called Rabbitscan. However, many wild rabbits die in inaccessible locations or are scavenged before sampling can occur, leading to considerable sampling bias. In this study we screened field-caught carrion flies for the presence of rabbit caliciviruses to monitor virus circulation patterns in the landscape, with an aim to establish a less biased epidemiological surveillance tool. Carrion flies were collected from two study sites over a 22 month period and these samples were used to optimise and validate molecular testing methods in this sample type for the currently circulating rabbit calicivirus variants. Virus was clearly detectable in field-caught carrion flies using optimised SYBR-green RT-qPCR and RT-PCR assays. However, variant identification was frequently hindered by the low virus loads present in carrion fly samples and spurious RT-PCR amplification. This was overcome by frequent sampling, which effectively acts as replicate sampling to verify inconclusive results. There was good correlation between virus detections in carrion flies and in samples recovered from wild rabbits, both temporally and for virus variant identification. The methods reported here provide a robust and efficient additional surveillance tool to monitor rabbit calicivirus activity at a landscape scale, which in turn can help to guide more effective rabbit management programs.
Codon Bias Confers Stability to mRNAs via ILF2 in Humans
Authors: Hia Fabian , Yang Sheng Fan , Shichino Yuichi , Yoshinaga Masanori , Murakawa Yasuhiro , Vandenbon Alexis , Fukao Akira , Fujiwara Toshinobu , Landthaler Markus , Natsume Tohru , Adachi Shungo , Iwasaki Shintaro , Takeuchi Osamu 
Published: March 2019

AbstractCodon bias has been implicated as one of the major factors contributing to mRNA stability in yeast. However, the effects of codon-bias on mRNA stability remain unclear in humans. Here we show that human cells possess a mechanism to modulate RNA stability through a unique codon bias different from that of yeast. Bioinformatics analysis showed that codons could be clustered into two distinct groups – codons with G or C at the third base position (GC3) and codons with either A or T at the third base position (AT3); the former stabilizing while the latter destabilizing mRNA. Quantification of codon bias showed that increased GC3 content entails proportionately higher GC content. Through bioinformatics, ribosome profiling andin vitroanalysis, we show that decoupling of the effects of codon bias reveals two modes of mRNA regulation, GC3- and GC-content dependent. Employing an immunoprecipitation-based strategy, we identified ILF2 as an RNA binding protein that differentially regulates global mRNA abundances based on codon bias. Our results demonstrate that codon bias is a two-pronged system that governs mRNA abundance.
Identifying suitableListeria innocuastrains as surrogates forListeria monocytogenesfor horticultural products
Authors: Mohan Vathsala , Wibisono Reginald , de Hoop Lana , Summers Graeme , Fletcher Graham C 
Published: March 2019

AbstractWe conducted a laboratory-based study testing nineListeria innocuastrains independently and a cocktail of 11Listeria monocytogenesstrains. The aim was to identify suitableL. innocuastrain(s) to modelL. monocytogenesin inactivation experiments. Three separate inactivation procedures and a hurdle combination of the three were employed: thermal inactivation (55°C), UV-C irradiation (245 nm) and chemical sanitiser (Tsunami™ 100, a mixture of acetic acid, peroxyacetic acid and hydrogen peroxide). The responses were strain dependent in the case ofL. innocuawith different strains responding differently to different regimes.L. innocuaisolates generally responded differently to theL. monocytogenescocktail and had different responses among themselves. In the thermal inactivation treatment, inactivation of all strains including theL. monocytogenescocktail plateaued after 120 minutes. Chemical sanitiser, inactivation could be achieved at concentrations of 10 and 20 ppm with inactivation increasing with contact time up to 8 minutes, beyond which there was no significant benefit. Although most of theL. innocuastrains in the study responded similarly toL. monocytogeneswhen subjected to a single inactivation treatment, when the treatments were applied as hurdle, allL. innocuastrains except PFR16D08 were more sensitive than theL. monocytogenescocktail. PFR16D08 almost matched the resistance of theL. monocytogenescocktail but was much more resistant to the individual treaments. A cocktail of twoL. innocuastrains (PFR 05A07 and PFR 05A10) had the closest responses to the hurdle treatment to those of theL. monocytogenescocktail and is therefore recommended for hurdle experiments.ImportanceOwing to researcher safety risks it is often difficult to use actual pathogens, such asListeria monocytogenes, to explore different inactivation procedures under field conditions. Organisms that are closely related to the pathogen but without its virulence are therefore used as surrogates for the actual pathogen. However, this assumes that the surrogate will behave in a similar manner to the pathogen and it is difficult to predict the responses of the surrogate compared to the actual pathogen. This study compares the responses of individual and combined “cocktails” of strains of non-pathogenicListeria innocuato different inactivation procedures when compared to the response of a cocktail ofL. monocytogenes. Our study highlights the importance of evaluating a number of strains when choosing surrogates.
First record of the endophytic bacteria ofDeschampsia antarcticaE. Desv. from two distant localities of the maritime Antarctica
Authors: Podolich O. , Parnikoza I. , Voznyuk T. , Zubova G. , Zaets I. , Miryuta N. , Myryuta G. , Poronnik O. , Kozeretska I. , Kunakh V. , Pirttila A.M. , Kozyrovska N. 
Published: March 2019

AbstractThe vascular plantDeschampsia antarcticasamples were collected for endophytic bacteria study from two regions in the maritime Antarctic 400 km distant from one another: Point Thomas oasis (King George Island) and Argentine Islands (Galindez Island). The endophytes were isolated from roots and leaves ofD. antarctica, cultivated and identified by using a partial sequencing of the 16S rRNA gene served as a phylomarker. Endophyte isolates from two sites of Galindez Island were represented mainly byPseudomonasspecies and byGammaproteobacteria, FirmicutesandActinobacteria. The vast majority of the isolates had specific for endophytes cellulase and pectinase activities, however,Bacillusspp. did not express both activities. A group-specific PCR screening at the four sites of Galindez Island and two sites of King George Island, indicatedAlphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, Cytophaga-FlavobacteriaandActinobacteria.Notably, the number of endophytic bacteria taxa was significantly larger in leaves than in roots of plants.
Meningitis pathogens evade immune responses by thermosensing
Authors: Eichner Hannes , Spelmink Laura , Pathak Anuj , Henriques-Normark Birgitta , Loh Edmund 
Published: March 2019

AbstractBacterial meningitis is a major cause of death and disability in children worldwide. Two human restricted pathogens, Streptococcus pneumoniae and Haemophilus influenzae, are the major causative agents of bacterial meningitis, attributing to 200,000 deaths annually. These pathogens are often part of the nasopharyngeal microflora of healthy carriers. However, what factors elicit them to disseminate and cause invasive diseases remain unknown. Elevated temperature and fever are hallmarks of inflammation triggered by infections and can act as warning signal to these pathogens. Here, we investigate whether these pathogens could sense environmental temperature to evade host complement-mediated killing. We show that expression of two vital virulence factors and vaccine components, the capsule and factor H binding proteins, are temperature dependent. We identify and characterize four novel RNA thermosensors in S. pneumoniae and H. influenzae within their 5′-untranslated regions of genes, responsible for capsular biosynthesis and production of factor H binding proteins. Our data further demonstrate that these pathogens have co-evolved thermosensing abilities independently with unique RNA sequences, but distinct secondary structures, to evade the human immune system.Author SummaryStreptococcus pneumoniae and Haemophilus influenzae are bacteria that reside in the upper respiratory tract. This harmless colonization may progress to severe and often lethal septicaemia and meningitis, but molecular mechanisms that control why these pathogens invade the circulatory system remain largely unknown. Here we show that both S. pneumoniae and H. influenzae can evade complement killing by sensing the temperature of the host. We identify and characterize four novel RNA thermosensors in S. pneumoniae and H. influenzae within their respective 5′-untranslated regions of genes, influencing capsular biosynthesis and production of factor H binding proteins. Moreover, we show that these RNA thermosensors evolved independently with exclusive unique RNA sequences to sense the temperature in the nasopharynx and in other body sites to avoid immune killing. Our finding that regulatory RNA senses temperatures and directly regulate expression of two important virulence factors and vaccine components of S. pneumoniae and H. influenzae, is most important for our understanding of bacterial pathogenesis and for vaccine development. Our work could pave the way for similar studies in other important bacterial pathogens and enables clinicians and microbiologists to adjust their diagnostic techniques, and treatments to best fit the condition of the patients.
Global biogeographical regions reveal a signal of past human impacts
Authors: Rueda Marta , González-Suárez Manuela , Revilla Eloy 
Published: March 2019

AbstractEcologists have long documented that the world’s biota is spatially organized in regions with boundaries shaped by processes acting on geological and evolutionary timescales. Although growing evidence suggests that human impact has been key in how biodiversity is currently assembled, its role as a driver of the geographical organization of biodiversity remains unclear. Here, we quantify the relative importance of human land use from ∼5000 years ago to predict the current assemblage of terrestrial mammals in biogeographical regions across the Earth. Results show that past anthropogenic land use has left an imprint on the taxonomic differentiation of some of the largest biogeographical realms, whereas land use at present stands out as a driver of the taxonomic differences between medium-sized subregions, i.e., within and among continents. Our findings highlight the far-reaching effect that past anthropogenic actions have had on the organization of biodiversity globally.