bluuebunny/crossref_metadata_2025 huggingface dataset:
MARCH8 targets cytoplasmic lysine residues of various viral envelope glycoproteins
Authors: Zhang Yanzhao , Ozono Seiya , Tada Takuya , Tobiume Minoru , Kameoka Masanori , Kishigami Satoshi , Fujita Hideaki , Tokunaga Kenzo
Published: April 2021

The host transmembrane protein MARCH8 is a RING finger E3 ubiquitin ligase that downregulates various host transmembrane proteins, such as MHC-II. We have recently reported that MARCH8 expression in virus-producing cells impairs viral infectivity by reducing virion incorporation of not only HIV-1 envelope glycoproteins but also vesicular stomatitis virus G-glycoprotein through two different pathways. However, the MARCH8 inhibition spectrum remains largely unknown. Here, we investigate the antiviral spectrum of MARCH8 using HIV-1 pseudotyped with a variety of viral envelope glycoproteins. Pseudotyping experiments revealed that viral envelopes derived from the rhabdovirus, arenavirus, coronavirus, and togavirus (alphavirus) families were sensitive to MARCH8-mediated inhibition. Lysine mutations at the cytoplasmic tails of rabies virus-G, lymphocytic choriomeningitis virus glycoproteins, SARS-CoV and SARS-CoV-2 spike proteins, and Chikungunya virus and Ross River virus E2 proteins conferred resistance to MARCH8. Immunofluorescence showed impaired downregulation of the mutants of these viral envelopes by MARCH8, followed by lysosomal degradation, suggesting that MARCH8-mediated ubiquitination leads to intracellular degradation of these envelopes. Indeed, rabies virus-G and Chikungunya virus E2 proteins proved to be clearly ubiquitinated. We conclude that MARCH8 has inhibitory activity on a variety of viral envelope glycoproteins whose cytoplasmic lysine residues are targeted by this antiviral factor.
Wasl is crucial to maintain microglial core activities during glioblastoma initiation stages
Authors: Mazzolini Julie , Clerc Sigrid Le , Morisse Gregoire , Coulonges Cédric , Zagury Jean-François , Sieger Dirk
Published: April 2021

Microglia actively promote the growth of high-grade gliomas. Within the glioma microenvironment an activated (amoeboid) microglial morphology has been observed, however the underlying causes and the related impact on microglia functions and their tumour promoting activities is unclear. Using the advantages of the larval zebrafish model, we demonstrate that pre-neoplastic glioma cells have an immediate impact on microglial morphology and functions. Overexpression of human HRasV12 in proliferating domains of the larval brain induces an amoeboid morphology of microglia, increases microglial numbers and decreases their motility and phagocytic activity. RNA sequencing analysis revealed lower expression levels of the actin nucleation promoting factorwaslain microglia. Importantly, a microglia specific rescue ofwaslaexpression restores microglial morphology and functions. This results in increased phagocytosis of pre-neoplastic cells and slows down tumour progression. In conclusion, we identified a mechanism that de-activates core microglial functions within the emerging glioma microenvironment.
Reference genome-independent taxonomic profiling of microbiomes with mOTUs3
Authors: Ruscheweyh Hans-Joachim , Milanese Alessio , Paoli Lucas , Karcher Nicolai , Clayssen Quentin , Metzger Marisa Isabell , Wirbel Jakob , Bork Peer , Mende Daniel R. , Zeller Georg , Sunagawa Shinichi
Published: April 2021

Background

Taxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify the relative abundance of microorganisms in biological samples. Available methods using shotgun metagenomic data generally depend on the availability of sequenced and taxonomically annotated reference genomes. However, the majority of microorganisms have not been cultured yet and lack such reference genomes. Thus, a substantial fraction of microbial community members remains unaccounted for during taxonomic profiling of metagenomes, particularly in samples from underexplored environments. To address this issue, we have developed the mOTU profiler, a tool that enables reference genome-independent species-level profiling of metagenomes. As such, it supports the identification and quantification of both “known” and “unknown” species based on a set of select marker genes.

Results

Here, we present mOTUs3, a command line tool that enables the profiling of metagenomes for >33,000 species-level operational taxonomic units. To achieve this, we leveraged the reconstruction and analysis of >600,000 draft genomes, most of which are metagenome assembled genomes (MAGs), from diverse microbiomes, including soil, freshwater systems, and the gastrointestinal tract of ruminants and other animals, which we found to be greatly underrepresented by reference genomes. Overall, two-thirds of all species-level taxa lacked a reference genome. The cumulative relative abundance of these newly included taxa was low in well-studied microbiomes, such as the human body sites (6-11%). By contrast, they accounted for substantial proportions (ocean, freshwater, soil: 43-63%) or even the vast majority (pig, fish, cattle: 60-80%) of the relative abundance across diverse non-human-associated microbiomes. Using community-developed benchmarks and datasets, we found mOTUs3 to be more accurate than other methods and to be more congruent with 16S rRNA gene-based methods for taxonomic profiling. Furthermore, we demonstrate that mOTUs3 greatly increases the resolution of well-known microbial groups into species-level taxa and helps identify new differentially abundant taxa in comparative metagenomic studies.

Conclusions

We developed mOTUs3 to enable accurate species-level profiling of metagenomes. Compared to other methods, it provides a more comprehensive view of prokaryotic community diversity, in particular for currently underexplored microbiomes. To facilitate comparative analyses by the research community, it is released with >11,000 precomputed profiles for publicly available metagenomes and is freely available at:https://github.com/motu-tool/mOTUs.
The effective population size modulates the strength of GC biased gene conversion in two passerines
Authors: Barton Henry J , Zeng Kai
Published: April 2021

Understanding the determinants of genomic base composition is fundamental to understanding genome evolution. GC biased gene conversion (gBGC) is a key driving force behind genomic GC content, through the preferential incorporation of GC alleles over AT alleles during recombination, driving them towards fixation. The majority of work on gBGC has focussed on its role in coding regions, largely to address how it confounds estimates of selection. Non-coding regions have received less attention, particularly in regard to the interaction of gBGC and the effective population size (Ne) within and between species. To address this, we investigate how the strength of gBGC (B= 4Neb, wherebis the conversion bias) varies within the non-coding genome of two wild passerines. We use a dataset of published high coverage genomes (10 great tits and 10 zebra finches) to estimateB, nucleotide diversity, changes inNe, and crossover rates from linkage maps, in 1Mb homologous windows in each species. We demonstrate remarkable conservation of bothBand crossover rate between species. We show that the mean strength of gBGC in the zebra finch is more than double that in the great tit, consistent with its twofold greater effective population size.Balso correlates with both crossover rate and nucleotide diversity in each species. Finally, we estimate equilibrium GC content from both divergence and polymorphism data, which indicates thatBhas been increasing in both species, and provide support for population expansion explaining a large proportion of this increase in the zebra finch.

Significance statement

Understanding the forces that change the nucleotide base composition of genomes is central to understanding their evolution. One such force is GC biased gene conversion, a process that during recombination converts some heterozygous base positions to homozygous. This process is more likely to convert adenine and thymine bases to guanine and cytosine bases than the other way around, hence is GC biased. This increases the frequency of GC alleles in a way similar to positive selection. This process has largely been studied within protein coding regions, and not often compared between species. We measure its strength in the non-coding areas of the genomes of two bird species, showing it to be stronger in the species with the larger population size.
Epitranscriptome changes triggered by ammonium nutrition regulate the proteome response of maritime pine roots
Authors: Ortigosa Francisco , Lobato-Fernández César , Pérez-Claros Juan Antonio , Cantón Francisco R. , Ávila Concepción , Cánovas Francisco M. , Cañas Rafael A.
Published: April 2021

Epitranscriptomic modifications constitute a gene expression checkpoint in all living organisms. As nitrogen is an essential element for plant growth and development, a reasonable hypothesis is that changes in the epitranscriptome may regulate nitrogen acquisition and metabolism. In this study, epitranscriptomic modifications caused by ammonium nutrition were monitored in maritime pine roots through direct RNA sequencing using Oxford Nanopore Technology. Transcriptomic responses mainly affected transcripts involved in nitrogen and carbon metabolism, defense, hormone synthesis/signaling, and translation. Global detection of epitranscriptomic marks was performed to evaluate this posttranscriptional mechanism in untreated and ammonium-treated seedlings. Increased m6A deposition in the 3’-UTR was observed in response to ammonium, which seems to be correlated with poly(A) lengths and changes in the relative abundance of the corresponding proteins. The results showed that m6A deposition and its dynamics seem to be important regulators of translation under ammonium nutrition. These findings suggest that protein translation is finely regulated through epitranscriptomic marks likely by changes in mRNA poly(A) length, transcript abundance and ribosome protein composition. An integration of multiomics data suggests that the epitranscriptome modulates responses to developmental and environmental changes, including ammonium nutrition, through buffering, filtering, and focusing the final products of gene expression.
GPT-2’s activations predict the degree of semantic comprehension in the human brain
Authors: Caucheteux Charlotte , Gramfort Alexandre , King Jean-Rémi
Published: April 2021

Language transformers, like GPT-2, have demonstrated remarkable abilities to process text, and now constitute the backbone of deep translation, summarization and dialogue algorithms. However, whether these models encode information that relates to human comprehension remains controversial. Here, we show that the representations of GPT-2 not only map onto the brain responses to spoken stories, but also predict the extent to which subjects understand narratives. To this end, we analyze 101 subjects recorded with functional Magnetic Resonance Imaging while listening to 70 min of short stories. We then fit a linear model to predict brain activity from GPT-2’s activations, and correlate this mapping with subjects’ comprehension scores as assessed for each story. The results show that GPT-2’s brain predictions significantly correlate with semantic comprehension. These effects are bilaterally distributed in the language network and peak with a correlation of R=0.50 in the angular gyrus. Overall, this study paves the way to model narrative comprehension in the brain through the lens of modern language algorithms.
Commensal rodent habitat expansion enhances arthropod disease vectors on a tropical volcanic island
Authors: Wu De-Lun , Shih Han-Chun , Wang Jen-Kai , Teng Hwa-Jen , Kuo Chi-Chien
Published: April 2021

Release from predators and competitors on volcanic islands can lead to increased body size and population density, as well as expanded habitat usage of introduced animals relative to their mainland counterparts. Such alterations might help the spread of diseases on islands when these exotic animals also carry pathogenic agents, but is rarely investigated. The commensal Asian house rat (Rattus tanezumi) is confined to human residential surroundings in Taiwan mainland but can be observed in the primary forests of the nearby Orchid Island, a tropical volcanic island. Orchid Island is also a hotspot of scrub typhus, a lethal febrile disease transmitted by larval trombiculid mites (chiggers) infective of the rickettsiaOrientia tsutsugamushi(OT). We predicted an increase in chigger abundance when rodents, the primary host of chiggers, invade forests from human settlements as soils are largely devoid of in the latter habitat but is necessary for the survival of nymphal and adult mites. A trimonthly rodent survey in ten sites of three habitats (human resident, grassland, and forest) found onlyR. tanezumiand showed moreR. tanezumiand chiggers in forest than in human residential sites. There was a positive association between rodent and chigger abundance, as well between rodent body weight and load of chiggers. Lastly, >95% of chiggers wereLeptotrombidium delienseand their OT infection rates were similar among the habitats. Our study demonstrated potentially elevated risks of scrub typhus when the commensal rat is allowed to invade natural habitats on islands. In addition, while the success of invasive species can be ascribed to their parasites being left behind, island invaders might instead attain more parasites when the parasite requires only a single host (e.g. trombiculid mite), is a host generalist (L. deliense), and is transferred from unsuitable to suitable habitats (human settlement on mainland to forest on island).
Locating Macromolecular Assemblies in Cells by 2D Template Matching withcisTEM
Authors: Lucas Bronwyn A. , Himes Benjamin A. , Xue Liang , Grant Timothy , Mahamid Julia , Grigorieff Nikolaus
Published: April 2021

Over the last decade, single-particle electron cryo-microscopy has become one of the main techniques contributing to the growing library of high-resolution structures of macromolecules and their assemblies. For a full understanding of molecular mechanisms, however, it is important to place them into the broader context of a cell. Traditionally, this context can be visualized in 3D by electron cryo-tomography, and more recently, has also been studied by template matching of 2D images of cells and viruses. A current limitation of the latter approach is the high computational cost that limits the throughput and widespread adoption of this method. We describe here a GPU-accelerated implementation of 2D template matching in the image processing softwarecisTEM that allows for easy scaling and improves the accessibility of this approach. We apply 2D template matching to identify ribosomes in images of frozen-hydratedMycoplasma pneumoniaecells and demonstrate that it can function as a versatile tool forin situvisual proteomics andin situstructure determination. We compare the results with 3D template matching of tomograms acquired on identical sample locations. We identify strengths and weaknesses of both techniques which offer complementary information about target localization and identity.
Molecular features of exceptional response to neoadjuvant anti-androgen therapy in high-risk localized prostate cancer
Authors: Tewari Alok K. , Cheung Alexander T.M. , Crowdis Jett , Conway Jake R. , Camp Sabrina Y. , Wankowicz Stephanie A. , Livitz Dimitri G. , Park Jihye , Lis Rosina T. , Boosma-Moody Alice , He Meng Xiao , AlDubayan Saud H. , Zhang Zhenwei , McKay Rana R. , Leshchiner Ignaty , Brown Myles , Balk Steve , Getz Gad , Taplin Mary-Ellen , Van Allen Eliezer M.
Published: April 2021

High-risk localized prostate cancer (HRLPC) is associated with a substantial risk of recurrence and prostate cancer-specific mortality1. Recent clinical trials have shown that intensifying anti-androgen therapies administered prior to prostatectomy can induce pathologic complete responses (pCR) or minimal residual disease (MRD) (<5 mm), together termed exceptional response, although the molecular determinants of these clinical outcomes are largely unknown. Here, we performed whole exome (WES) and whole transcriptome sequencing (RNA-seq) on pre-treatment multi-regional tumor biopsies from exceptional responders (ER: pCR and MRD patients) and non-responders (NR: pathologic T3 or lymph node positive disease) treated with intensive anti-androgen therapies prior to prostatectomy. SPOP mutation and SPOPL copy number loss were exclusively observed in ER, while TP53 mutation and PTEN copy number loss were exclusively observed in NR. These alterations were clonal in all tumor phylogenies per patient. Additionally, transcriptional programs involving androgen signaling and TGFβ signaling were enriched in ER and NR, respectively. The presence of these alterations in routine biopsies from patients with HRLPC may inform the prospective identification of responders to neoadjuvant anti-androgen therapies to improve clinical outcomes and stratify other patients to alternative biologically informed treatment strategies.
A push-pull system of repressors matches levels of glucose transporters to extracellular glucose in budding yeast
Authors: Montaño-Gutierrez Luis Fernando , Sturrock Marc , Farquhar Iseabail , Correia Kevin , Shahrezaei Vahid , Swain Peter S.
Published: April 2021

A common cellular task is to match gene expression dynamically to a range of concentrations of a regulatory molecule. Studying glucose transport in budding yeast, we determine mechanistically how such matching occurs for seven hexose transporters. By combining time-lapse microscopy with mathematical modelling, we find that levels of transporters are history-dependent and are regulated by a push-pull system comprising two types of repressors. Repression by these two types varies with glucose in opposite ways, and not only matches the expression of transporters by their affinity to a range of glucose concentrations, but also the expression of some to how glucose is changing. We argue that matching is favoured by a rate-affinity trade-off and that the regulatory system allows yeast to import glucose rapidly enough to starve competitors. Matching expression to a pattern of input is fundamental, and we believe that push-pull repression is widespread.
Genome annotation with long RNA reads reveals new patterns of gene expression in an ant brain
Authors: Shields Emily J. , Sorida Masato , Sheng Lihong , Sieriebriennikov Bogdan , Ding Long , Bonasio Roberto
Published: April 2021

Functional genomic analyses rely on high-quality genome assemblies and annotations. Highly contiguous genome assemblies have become available for a variety of species, but accurate and complete annotation of gene models, inclusive of alternative splice isoforms and transcription start and termination sites remains difficult with traditional approaches. Here, we utilized full-length isoform sequencing (Iso-Seq), a long-read RNA sequencing technology, to obtain a comprehensive annotation of the transcriptome of the antHarpegnathos saltator. The improved genome annotations include additional splice isoforms and extended 3’ untranslated regions for more than 4,000 genes. Reanalysis of RNA-seq experiments using these annotations revealed several genes with caste-specific differential expression and tissue-or caste-specific splicing patterns that were missed in previous analyses. The extended 3’ untranslated regions afforded great improvements in the analysis of existing single-cell RNA-seq data, resulting in the recovery of the transcriptomes of 18% more cells. The deeper single-cell transcriptomes obtained with these new annotations allowed us to identify additional markers for several cell types in the ant brain, as well as genes differentially expressed across castes in specific cell types. Our results demonstrate that Iso-Seq is an efficient and effective approach to improve genome annotations and maximize the amount of information that can be obtained from existing and future genomic datasets inHarpegnathosand other organisms.
Exploring Extreme Signaling Failures in Intracellular Molecular Networks
Authors: Ozen Mustafa , Emamian Effat S. , Abdi Ali
Published: April 2021

Developing novel methods for the analysis of intracellular signaling networks is essential for understanding interconnected biological processes that underlie complex human disorders. A fundamental goal of this research is to quantify the vulnerability of a signaling network to the dysfunction of one or multiple molecules, when the dysfunction is defined as an incorrect response to the input signals. In this study, we propose an efficient algorithm to identify the extreme signaling failures that can induce the most detrimental impact on the physiological function of a molecular network. The algorithm basically finds the molecules, or groups of molecules, with the maximum vulnerability, i.e., the highest probability of causing the network failure, when they are dysfunctional. We propose another algorithm that efficiently accounts for signaling feedbacks in this analysis. The algorithms are tested on two experimentally verified ERBB and T cell signaling networks. Surprisingly, results reveal that as the number of concurrently dysfunctional molecules increases, the maximum vulnerability values quickly reach to a plateau following an initial increase. This suggests the specificity of vulnerable molecule (s) involved, as a specific number of faulty molecules cause the most detrimental damage to the function of the network. Increasing a random number of simultaneously faulty molecules does not further deteriorate the function of the network. Such a group of specific molecules whose dysfunction causes the extreme signaling failures can better elucidate the molecular mechanisms underlying the pathogenesis of complex trait disorders, and can offer new insights for the development of novel therapeutics.
Chemogenetic stimulation of a retinal circuit activates brain noradrenergic neurons, prevents apoptosis and suppresses depression-like behaviors
Authors: Bowrey Hannah E , James Morgan H , Omrani Mohsen , Mohammadkhani Aida , Aston-Jones G
Published: April 2021

A chronically dysregulated locus coeruleus (LC) system gives rise to mood disorders. In particular, prolonged LC hyperactivity often underlies stress disorders, whereas chronically reduced function often underlies symptoms of depression. Owing to its location deep in the brainstem, LC is difficult to access which limits translational approaches that involve manipulating these neurons. Here, we circumvent this problem by utilizing the retina as a chemogenetic target for commandeering a multsynaptic circuit to LC. We show that activation of this pathway can prevent depression-like behavior and associated pathology of the LC-noradrenergic (NA) system caused by light deprivation. Additionally, we show that melanopsin-containing intrinsically photosensitive retinal ganglion cells (ipRGCs) are the likely cell type responsible for initiating activity in this pathway. By capitalizing on this ocular route of designer receptor delivery, we demonstrate a novel, minimally-invasive method for manipulating this deep-brain circuit that is relevant to a wide array of neuropsychiatric disorders.
Taste Bud Connectome: Implications for Taste Information Processing
Authors: Wilson Courtney E. , Lasher Robert S. , Yang Ruibiao , Dzowo Yannick , Kinnamon John C. , Finger Thomas E.
Published: April 2021

Taste buds contain 3 types of morphologically identifiable mature cells, 2 of which mediate transduction of specific taste qualities: Type III cells transduce sour while Type II cells transduce either sweet, bitter or umami. A long-standing controversy is whether the nerve fibers innervating these cells are wired specifically, in a labeled-line fashion, or non-specifically, leading to broad responsiveness across taste qualities, the so-called across-fiber system of encoding. Using serial blockface scanning electron microscopy through 5 circumvallate mouse taste buds, we reconstructed the patterns of connectivity of nerve fibers as well as the degree of potential interaction between the two types of taste transducing cells. Type II and Type III cells share few points of contact with one another, and display no morphologically identifiable synapses, suggesting limited direct interaction between these cell types. Of the 127 nerve fibers that make synaptic contacts with taste cells in the sampling volume, about 70% (n=91) synapse with only one taste cell. Of the remaining 36 fibers, 4 synapse with both Type II and Type III cells, the remainder synapsing exclusively with multiple Type II taste cells or multiple Type III cells. Since Type II and Type III cells transduce different taste qualities, the few mixed fibers do not follow a labeled-line organization according to taste quality information and show that connectional specificity in taste buds is not absolute.

Significance Statement

Taste buds, the sensory end organs for the sense of taste, contain multiple types of sensory cells, with each responding to one of the primary tastes: salt, sweet, sour, bitter and umami. A long-standing question is whether each type of taste cell is wired specifically to a unique set of nerve fibers conveying a “labeled-line” message to the brain. Using serial sections, we determined the neural connectivity in mouse circumvallate taste buds. The majority of individual nerve fibers connect to a single type of taste cell, but 3.1% of the fibers branch to receive input from taste cells known to have different specificities. Thus taste cannot entirely be carried along nerve fibers dedicated to single taste qualities.
The genetics of assisted gene flow: immediate costs and long-term benefits
Authors: Grummer Jared A. , Booker Tom R. , Matthey-Doret Remi , Nietlisbach Pirmin , Thomaz Andréa T. , Whitlock Michael C.
Published: April 2021

Plant and animal populations are facing several novel risks such as human-mediated habitat fragmentation and climate change that threaten their long-term productivity and persistence. With the genetic health of many populations deteriorating due to climate change outpacing physiological adaptation, human interventions in the form of assisted gene flow (AGF) may provide genetic variation to adapt populations to predicted climate change scenarios and result in more robust and productive populations. We ran genetic simulations to mimic a variety of AGF scenarios and measured their outcomes on population-level fitness to answer the question: in which circumstances is it worthwhile to perform AGF? Based on the parameters we explored, AGF may be harmful in certain situations over the short term (e.g., the first ∼10-20 generations), due to outbreeding depression and introducing deleterious genetic variation. Moreover, under many parameter sets, the benefits of AGF were relatively weak or took many generations to accrue. In general, when the adaptive trait is controlled by many loci of small effect, the benefits of assisted gene flow take much longer to realize–potentially too long for most climate-related management decisions. We also show that when translocation effort is divided across several generations and outbreeding depression is strong, the recipient population experiences a smaller decrease in fitness as compared to moving all individuals in a single effort. Importantly, in most cases, we show that the genomic integrity of the recipient population remains relatively intact following AGF; the amount of genetic material from the donor population typically ends up constituting no more of the recipient population’s genome than the fraction introduced. Our results will be useful for conservation practitioners and silviculturists, for instance, aiming to intervene and adaptively manage so that populations maintain a robust genetic health and maintain productivity into the future given anthropogenic climate change.
The Backbone Network of Dynamic Functional Connectivity
Authors: Asadi Nima , Olson Ingrid R. , Obradovic Zoran
Published: April 2021

1.

Temporal networks have become increasingly pervasive in many real-world applications, including the functional connectivity analysis of spatially separated regions of the brain. A major challenge in analysis of such networks is the identification of noise confounds, which introduce temporal ties that are non-essential, or links that are formed by chance due to local properties of the nodes. Several approaches have been suggested in the past for static networks or temporal networks with binary weights for extracting significant ties whose likelihood cannot be reduced to the local properties of the nodes. In this work, we propose a data-driven procedure to reveal the irreducible ties in dynamic functional connectivity of resting state fRMI data with continuous weights. This framework includes a null model that estimates the latent characteristics of the distributions of temporal links through optimization, followed by a statistical test to filter the links whose formation can be reduced to the activities and local properties of their interacting nodes. We demonstrate the benefits of this approach by applying it to a resting state fMRI dataset, and provide further discussion on various aspects and advantages of it.
Estimating parameters of a stochastic cell invasion model with fluorescent cell cycle labelling using Approximate Bayesian Computation
Authors: Carr Michael J , Simpson Matthew J , Drovandi Christopher
Published: April 2021

We develop a parameter estimation method based on approximate Bayesian computation (ABC) for a stochastic cell invasion model using fluorescent cell cycle labeling with proliferation, migration, and crowding effects. Previously, inference has been performed on a deterministic version of the model fitted to cell density data, and not all the parameters were identifiable. Considering the stochastic model allows us to harness more features of experimental data, including cell trajectories and cell count data, which we show overcomes the parameter identifiability problem. We demonstrate that, whilst difficult to collect, cell trajectory data can provide more information about the parameters of the cell invasion model. To handle the intractability of the likelihood function of the stochastic model, we use an efficient ABC algorithm based on sequential Monte Carlo. Rcpp and MATLAB implementations of the simulation model and ABC algorithm used in this study are available athttps://github.com/michaelcarr-stats/FUCCI.
Forecasting the effects of water regulation on the population viability of a threatened amphibian
Authors: Mathwin Rupert , Wassens Skye , Gibbs Matthew S. , Young Jeanne , Ye Qifeng , Saltré Frédérik , Bradshaw Corey J.A.
Published: April 2021

The regulation of river systems alters hydrodynamics and often reduces lateral connectivity between river channels and floodplains. For taxa such as frogs that rely on floodplain wetlands to complete their lifecycle, decreasing inundation frequency can reduce recruitment and increase the probability of local extinction. We virtually reconstructed the inundation patterns of wetlands under natural and regulated flow conditions and built stochastic population models to quantify the probability of local extinction under different inundation scenarios. Specifically, we explored the interplay of habitat size, inundation frequency, and successive dry years on the local extinction probability of the threatened southern bell frogLitoria raniformisin the Murray River floodplains of South Australia. We hypothesised that the changes to wetland inundation resulting from river regulation are a principal driver ofL. raniformisdeclines in this semi-arid system.

Regulation has reduced the inundation frequency of essential habitats below critical thresholds for the persistence of many fresh water-dependent species. Successive dry years raise the probability of local extinction, and these effects are strongest in smaller wetlands. Larger wetlands and those with more frequent average inundation are less susceptible to these effects.

Elucidating these trends informs the prioritisation of treatment sites and the frequency of conservation interventions. Environmental water provision (through pumping or the operation of flow-regulating structures) is a promising tool to reduce the probability of breeding failure and local extinction. Our modelling approach can be used to prioritise the delivery of environmental water toL. raniformisand potentially many other frog species.
Daily rhythms in the transcriptomes of the human parasite Schistosoma mansoni
Authors: Rawlinson Kate A. , Reid Adam J. , Lu Zhigang , Driguez Patrick , Wawer Anna , Coghlan Avril , Sankaranarayanan Geetha , Buddenborg Sarah Kay , Soria Carmen Diaz , McCarthy Catherine , Holroyd Nancy , Sanders Mandy , Hoffmann Karl , Wilcockson David , Rinaldi Gabriel , Berriman Matt
Published: April 2021

Background

The consequences of the earth’s daily rotation have led to 24-hour biological rhythms in most organisms. Even parasites have daily rhythms, which, when in synchrony with host rhythms, optimize their fitness. Understanding these rhythms may enable development of novel control strategies that take advantage of rhythmic vulnerabilities. Recent work on blood-dwelling protozoan parasites has revealed daily rhythms in gene expression, physiology, drug sensitivity and the presence of an intrinsic circadian clock. However, similar studies on metazoan parasites are lacking. The aims of this study were to investigate if a metazoan parasite has daily molecular oscillations, whether they give us insight into how these longer-lived organisms can survive host daily cycles over a life-span of many years and to determine whether canonical metazoan circadian clock genes are present and rhythmic. We addressed these questions using the human blood fluke Schistosoma mansoni, that lives in the vasculature for decades and causes the serious neglected tropical disease schistosomiasis.

Results

Using round-the-clock transcriptomics of male and female adult worms we discovered that ∼2% of its genes followed a daily pattern of expression. Rhythmic processes included a night-time stress response and a day-time metabolic ‘rush hour’. Transcriptional profiles in the female reproductive system were mirrored by daily patterns in egg laying (eggs are the main drivers of the host pathology). Genes cycling with the highest amplitudes include drug targets and a vaccine candidate. These 24hr rhythms may be driven by host rhythms and/or generated by a circadian clock. However, core clock genes are missing and orthologues of secondary clock genes show no 24hr rhythmicity in transcript abundance.

Conclusions

The daily rhythms identified here reveal temporally compartmentalised internal processes and host interactions over the daily cycle, including processes relevant to within-host survival and between-host transmission. Our findings suggest that if these daily rhythms are generated by an intrinsic circadian clock then the oscillatory mechanism must be distinct from that in other Metazoa. Most importantly, knowing which gene transcripts oscillate at this temporal scale is relevant to functional genomic studies that will lead to the development and delivery of therapeutics against schistosomiasis.
Musical experience partially counteracts temporal speech processing deficits in mild cognitive impairment
Authors: Price Caitlin N. , Bidelman Gavin M.
Published: April 2021

Mild cognitive impairment (MCI) commonly impacts older adults resulting in more rapid cognitive and behavioral declines than typical aging. Individuals with MCI can exhibit impaired receptive speech abilities that may reflect neurophysiological changes in auditory-sensory processing prior to usual cognitive deficits. Benefits from current interventions targeting communication difficulties in MCI are limited. Yet, neuroplasticity associated with musical experience has been implicated in improving neural representations of speech and offsetting age-related declines in perception. Here, we asked whether these experience-dependent effects of musicianship might extend to aberrant aging and offer some degree of cognitive protection against MCI. During a vowel categorization task, we recorded single-channel EEGs in older adults with putative MCI to evaluate speech encoding across subcortical and cortical levels of the auditory system. Critically, listeners varied in their duration of formal musical training experience (0-21 years). Older musicians exhibited sharpened temporal precision in auditory cortical responses suggesting musical experience produces more efficient processing of acoustic features by offsetting age-related neural delays. Additionally, we found robustness of brainstem responses predicted severity of cognitive decline suggesting early speech representations are sensitive to pre-clinical stages of cognitive impairment. Our preliminary results extend prior studies by demonstrating positive benefits of musical experience in older adults with emergent cognitive impairments.
The ß-catenin-target Fascin-1, altering hepatocyte differentiation, is a new marker of immature cells in hepatoblastomas
Authors: Gest Caroline , Sena Sandra , Neaud Véronique , Loesch Robin , Dugot-Senant Nathalie , Paysan Lisa , Piquet Léo , Robbe Terezinha , Allain Nathalie , Dembele Doulaye , Guettier Catherine , Bioulac-Sage Paulette , Bail Brigitte Le , Grosset Christophe F. , Saltel Frédéric , Lagrée Valérie , Colnot Sabine , Moreau Violaine
Published: April 2021

BACKGROUND & AIMS

ß-catenin is a well-known effector of the Wnt pathway and a key player in cadherin-mediated cell adhesion. Oncogenic mutations of ß-catenin are highly frequent in pediatric liver primary tumors. Those mutations are mostly heterozygous allowing the co-expression of wild-type (WT) and mutated ß-catenins in tumor cells. We investigated the interplay between WT and mutated ß-catenins in liver tumor cells, and searched for new actors of the ß-catenin pathway.

METHODS

Using an RNAi strategy in ß-catenin-mutated hepatoblastoma (HB) cells, we dissociated the structural and transcriptional activities of β-catenin, carried mainly by, respectively, WT and mutated proteins. Their impact was characterized using transcriptomic and functional analyses. We studied mice that develop liver tumors upon activation of ß-catenin in hepatocytes (APCKOand ß-cateninΔexon3mice). We made use of transcriptomic data from mouse and human HB specimens and analyzed samples by immunohistochemistry.

RESULTS

We highlighted an antagonist role of WT and mutated ß-catenins on hepatocyte differentiation as attested by alteration of hepatocyte markers expression and bile canaliculi formation. We characterized Fascin-1 as a target of ß-catenin involved in hepatocyte differentiation. Using mouse models that allow the formation of two phenotypically distinct tumors (differentiated or undifferentiated), we found that Fascin-1 expression is higher in undifferentiated tumors. Finally, we found that Fascin-1 is a specific marker of the embryonal component in human HBs.

CONCLUSIONS

In mice and human, Fascin-1 expression is linked to loss of differentiation and polarity of hepatocytes. Thus, we highlighted Fascin-1 as a new player in the modulation of hepatocyte differentiation associated to ß-catenin pathway alteration in the liver.

Data Transparency Statement

study materials will be made available to other researchers upon request.
Cas9-mediated gene disruption in tetraploidGiardia intestinalis
Authors: Horáčková Vendula , Voleman Luboš , Hagen Kari D. , Petrů Markéta , Vinopalová Martina , Weisz Filip , Janowicz Natalia , Marková Lenka , Motyčková Alžběta , Tůmová Pavla , Dawson Scott C. , Doležal Pavel
Published: April 2021

CRISPR/Cas9 system is an extremely powerful technique that is extensively used for various genome modifications in different organisms including parasitic protists.Giardia intestinalis, a protist parasite infecting about 280 million people around the world each year, has been eluding the routine use of CRISPR/Cas9 for generating knock-out cell lines due to the presence of four copies of each gene in its two nuclei. Apart from single exception employing rather laborious Cre/loxP system, no full knock-out cell line has been established yet. In this work, we show the ability ofin-vitroassembled CRISPR/Cas9 components to successfully edit the genome ofG. intestinalis. We further established a cell line stably expressing Cas9 in bothG. intestinalisnuclei. Subsequent introduction of a template for homologous recombination containing the transcription units for the resistance marker and gRNA resulted in the removal of all gene copies at once for three independent experimental genes,mem, cwp1andmlf1. The method was also applicable for the incomplete disruption of an essential gene, as documented by markedly decreased expression oftom40. Finally, testing the efficiency of Cas9-induced recombination revealed that homologous arms as short as 150 bp can be sufficient to establish a full knock-out cell line inG. intestinalis.
Evolution under low antibiotic concentrations: a risk for the selection ofPseudomonas aeruginosamultidrug resistant mutants in nature
Authors: Sanz-García Fernando , Hernando-Amado Sara , Martínez José Luis
Published: April 2021

BACKGROUND

Antibiotic pollution of non-clinical environments might have a relevant impact on human health if resistant pathogens are selected. However, this potential risk is often overlooked, since drug concentrations in nature are usually below their minimal inhibitory concentrations (MICs). Albeit, antibiotic resistant bacteria can be selected even at sub-MIC concentrations, in a range that is dubbed the sub-MIC selective window, which depends on both the antibiotic and the pathogen.

OBJECTIVES

Determine the sub-MIC selective windows of seven antibiotics of clinical relevance in the opportunistic pathogenPseudomonas aeruginosaand evaluate the risk for selecting resistant mutants in nature, based on published data about the amount of antimicrobials detected in natural environments.

METHODS

We conducted evolution experiments ofP. aeruginosaPA14 in presence of sub-MIC concentrations of ceftazidime, amikacin, levofloxacin, ciprofloxacin, tetracycline, polymyxin B or imipenem, and measured drug susceptibility of the evolved populations.

RESULTS

Sub-MIC selective window of quinolones was the largest, and the ones of polymyxin B and imipenem, the narrowest. Clinically relevant multidrug resistant (MDR) mutants (presenting MICs above EUCAST clinical breakpoints) arose within the sub-MIC selective windows of the majority of antibiotics tested, being these phenotypes probably mediated by efflux pumps′ activity.

DISCUSSION

Our data show that the concentration of antibiotics reported in aquatic ecosystems -colonizable byP. aeruginosa- are, in occasions, higher than the ones able to select MDR mutants. This finding has implications for understanding the role of different ecosystems and conditions in the emergence of antibiotic resistance from a One-Health point of view. Further, it highlights the importance of delineating the sub-MIC selective windows for drugs of clinical value in pathogens with environmental niches, in order to evaluate the health risks due to antibiotic pollution of natural ecosystems and ultimately tackle antibiotic resistance.
Climate-induced forest dieback drives compositional change in insect communities that is concentrated amongst rare species
Authors: Sire Lucas , Yáñez Paul Schmidt , Wang Cai , Bézier Annie , Courtial Béatrice , Cours Jérémy , Fontaneto Diego , Larrieu Laurent , Bouget Christophe , Thorn Simon , Müller Jörg , Yu Douglas W. , Monaghan Michael T. , Herniou Elisabeth A. , Lopez-Vaamonde Carlos
Published: April 2021

Marked decline in insect species richness, abundance and biomass have recently been quantified in Europe. We metabarcoded 224 Malaise-trap samples to investigate whether drought-induced forest dieback and subsequent salvage logging have an impact on flying insects (ca. 3000 insect species) in silver fir Pyrenean forests. We found no evidence that climate-induced forest dieback impacted species richness of flying insects but revealed compositional turnover patterns consistent with those seen during natural forest succession, given that the key covariates explaining compositional variation were canopy openness versus microhabitat diversity and deadwood amount at local and landscape scales, respectively. Importantly, most change was driven by rare species. In contrast, observed levels of salvage logging did not explain change in species richness or composition. Hence, although forest dieback appears to cause changes in species assemblages mimicking natural forest succession, it also increases the risk of catastrophic loss of rare species through homogenization of environmental conditions.
FMRP DIRECTLY INTERACTS WITH R-LOOP AND SHOWS COMPLEX INTERPLAY WITH THE DHX9 HELICASE
Authors: Chakraborty Arijita , Dutta Arijit , Dettori Leonardo G. , Li Jing , Gonzalez Leticia , Xue Xiaoyu , Hehnly Heidi , Sung Patrick , Bah Alaji , Feng Wenyi
Published: April 2021

Mutations in, or deficiency of, FMRP is responsible for the Fragile X syndrome (FXS), the most common cause for inherited intellectual disability. FMRP is a nucleocytoplasmic protein, primarily characterized as a translation repressor with poorly understood nuclear function(s). We recently uncovered a genome protective role of FMRP. We reported that FXS patient-derived cells lacking FMRP sustain higher level of DNA double-strand breaks than normal cells, a phenotype further exacerbated by DNA replication stress. The stress-induced DSBs occur at sequences prone to form R-loops, which are co-transcriptional RNA:DNA hybrids that have been associated with genome instability. Concordantly, we showed that FXS cells accumulate R-loops under replication stress. Moreover, expression of FMRP and not a mutant deficient in binding nucleic acids and known to cause FXS, FMRPI304N, reduced R-loop-associated DSBs. These observations demonstrated that FMRP promotes genome integrity by preventing R-loop accumulation and chromosome breakage. Here, we explore the mechanism through which FMRP prevents R-loop accumulation in an isogenically controlled CRISPR KO ofFMR1(gene encoding for FMRP) in HEK293T cells. We demonstrate for the first time that FMRP directly binds R-loops. We show that FMRP interacts with DHX9, an RNA helicase that unwinds both double strand RNA and RNA:DNA hybrids and regulates R-loop formation through modulating these activities. This interaction is reduced with FMRPI304N, suggesting that FMRP regulation of R-loop is mediated through DHX9. Interestingly, we show that FMRP inhibits DHX9 helicase activity on RNA:DNA hybrids. Moreover, DHX9 binds chromatin containing R-loops more efficiently in the absence of a functional FMRP. These results suggest an antagonistic relationship between FMRP and DHX9 at the chromatin, where FMRP prevents R-loop formation by suppressing DHX9. Our study sheds new light on our understanding of the genome functions of FMRP.