bluuebunny/crossref_metadata_2025 huggingface dataset:
Preparation and execution of voluntary action both contribute to awareness of intention
Authors: Schultze-Kraft Matthias , Parés-Pujolràs Elisabeth , Matić Karla , Haggard Patrick , Haynes John-Dylan
Published: March 2020

How and when motor intentions form has long been controversial. In particular, the extent to which motor preparation and action-related processes produce a conscious experience of intention remains unknown. Here, we used a brain–computer interface (BCI) while participants performed a self-paced movement task to trigger cues upon the detection of a readiness potential (a well-characterized brain signal that precedes movement) or in its absence. The BCI-triggered cues instructed participants either to move or not to move. Following this instruction, participants reported whether they felt they were about to move at the time the cue was presented. Participants were more likely to report an intention (i) when the cue was triggered by the presence of a readiness potential than when the same cue was triggered by its absence, and (ii) when they had just made an action than when they had not. We further describe a time-dependent integration of these two factors: the probability of reporting an intention was maximal when cues were triggered in the presence of a readiness potential, and when participants also executed an action shortly afterwards. Our results provide a first systematic investigation of how prospective and retrospective components are integrated in forming a conscious intention to move.
Listening to birdsong reveals basic features of rate perception and aesthetic judgements
Authors: Roeske Tina , Larrouy-Maestri Pauline , Sakamoto Yasuhiro , Poeppel David
Published: March 2020

The timing of acoustic events is central to human speech and music. Tempo tends to be slower in aesthetic contexts: rates in poetic speech and music are slower than non-poetic, running speech. We tested whether a general
aesthetic
preference for slower rates can account for this, using birdsong as a stimulus: it structurally resembles human sequences but is unbiased by their production or processing constraints. When listeners selected the birdsong playback tempo that was most pleasing, they showed no bias towards any range of note rates. However, upon hearing a novel stimulus, listeners rapidly formed a robust, implicit memory of its temporal properties, and developed a stimulus-specific preference for the memorized tempo. Interestingly,
tempo perception
in birdsong stimuli was strongly determined by individual, internal preferences for rates of 1–2 Hz. This suggests that processing complex sound sequences relies on a default time window, while aesthetic appreciation appears flexible, experience-based and not determined by absolute event rates.
Dynamic aqueous multiphase reaction system for simple, sensitive and quantitative one-pot CRISPR-Cas12a based molecular diagnosis
Authors: Yin Kun , Ding Xiong , Li Ziyue , Zhao Hui , Cooper Kumarasen , Liu Changchun
Published: March 2020

Recently, CRISPR-Cas technology has opened a new era of nucleic acid-based molecular diagnostics. However, current CRISPR-Cas-based nucleic acid biosensing has largely a lack of the quantitative detection ability and typically requires separate manual operations. Herein, we reported a dynamic aqueous multiphase reaction (DAMR) system for simple, sensitive and quantitative one-pot CRISPR-Cas12a based molecular diagnosis by taking advantage of density difference of sucrose concentration. In the DAMR system, recombinase polymerase amplification (RPA) and CRISPR-Cas12a derived fluorescent detection occurred in spatially separated but connected aqueous phases. Our DAMR system was utilized to quantitatively detect human papillomavirus (HPV) 16 and 18 DNAs with sensitivities of 10 and 100 copies within less than one hour. Multiplex detection of HPV16/18 in clinical human swab samples were successfully achieved in the DAMR system using 3D-printed microfluidic device. Furthermore, we demonstrated that target DNA in real human plasma samples can be directly amplified and detected in the DAMR system without complicated sample pre-treatment. As demonstrated, the DAMR system has shown great potential for development of next-generation point-of-care molecular diagnostics.
The O2-independent pathway of ubiquinone biosynthesis is essential for denitrification inPseudomonas aeruginosa
Authors: Vo Chau-Duy-Tam , Michaud Julie , Elsen Sylvie , Faivre Bruno , Bouveret Emmanuelle , Barras Frédéric , Fontecave Marc , Pierrel Fabien , Lombard Murielle , Pelosi Ludovic
Published: March 2020

Many proteobacteria, such asEscherichia coli, contain two main types of quinones, benzoquinones represented by ubiquinone (UQ) and naphthoquinones such as menaquinone (MK) and dimethyl-menaquinone (DMK). MK and DMK function predominantly in anaerobic respiratory chains, whereas UQ is the major electron carrier used for reduction of dioxygen. However, this division of labor is probably not so stric. Indeed, a pathway that produces UQ under anaerobic conditions in an UbiU-, UbiV- and UbiT-dependent manner has been recently discovered inE. coliwhile its physiological relevance is not yet understood because of the presence of MK and DMK in this bacterium. In the present study, we established that UQ9is the single quinone ofP. aeruginosaand that is required for growth under anaerobic respiration (denitrification). We demonstrated that ORFsPA3911, PA3912andPA3913, which are homologues to theE. coli ubiT, ubiVandubiUgenes, respectively, were essential for UQ9biosynthesis and thus for denitrification inP. aeruginosa. These three genes were hereafter calledubiTPa, ubiVPaandubiUPa. We showed that UbiVPaaccommodates a [4Fe-4S] cluster. Moreover, we demonstrated that UbiUPaand UbiTPawere able to bind UQ and that the isoprenoid tail of UQ was the structural determinant for the recognition by these Ubi proteins. Since the denitrification metabolism ofP. aeruginosais believed to be important for pathogenicity in cystic fibrosis patients, our results highlight the O2-independent UQ biosynthesis pathway as a new possible target to develop innovative antibiotics.
BCKDK regulates the TCA cycle through PDC to ensure embryonic development in the absence of PDK family
Authors: Heinemann-Yerushalmi Lia , Bentovim Lital , Felsenthal Neta , Vinestock Ron Carmel , Michaeli Nofar , Krief Sharon , Silberman Alon , Cohen Marina , Ben-Dor Shifra , Brenner Ori , Haffner-Krausz Rebecca , Itkin Maxim , Malitsky Sergey , Erez Ayelet , Zelzer Elazar
Published: March 2020

Pyruvate dehydrogenase kinases (PDK1-4) inhibit the TCA cycle by phosphorylating pyruvate dehydrogenase complex (PDC). Here, we show that the PDK family is dispensable for the survival of murine embryonic development and that BCKDK serves as a compensatory mechanism by inactivating PDC.

First, we knocked out all fourPdkgenes one by one. Surprisingly,Pdktotal KO embryos developed and were born in expected ratios, but died by postnatal day 4 due to hypoglycemia or ketoacidosis.

Finding that PDC was phosphorylated in these embryos suggested that another kinase compensates for the PDK family. Bioinformatic analysis implicated brunch chain ketoacid dehydrogenase kinase (Bckdk), a key regulator of branched chain amino acids (BCAA) catabolism. Indeed, knockout ofBckdkand thePdkfamily led to loss of PDC phosphorylation, increment in PDC activity, elevation of Pyruvate flux into the TCA and early embryonic lethality. These findings reveal a new regulatory crosstalk hardwiring BCAA and glucose catabolic pathways, which feed the TCA cycle.
Kappa but not delta or mu opioid receptors form homodimers at low membrane densities
Authors: Cechova Kristina , Lan Chenyang , Macik Matus , Barthes Nicolas P. F. , Jung Manfred , Ulbrich Maximilian H.
Published: March 2020

Opioid receptors (ORs) have been observed as homo- and heterodimers, but it is unclear if the dimers are stable under physiological conditions, and whether monomers or dimers comprise the predominant fraction in a cell. Here we use three live-cell imaging approaches to assess dimerization of ORs at different expression levels. At high membrane densities, a split GFP assay reveals that κOR dimerizes, while μOR and δOR stay monomeric. In contrast, single-molecule imaging showed no κOR dimers at low receptor densities. To reconcile our seemingly contradictory results, we used a high-density single-molecule assay to assess membrane protein interactions at densities up to 100x higher than conventional single-molecule imaging. We observe that κOR is monomeric at low densities and forms dimers at densities that are considered physiological. In contrast, μOR and δOR stay monomeric even at the highest densities covered by our approach. The observation of long-lasting κOR dimers but not higher-order aggregates suggests that ORs dimerize through a single, specific interface.
Three Essential Resources to Improve Differential Scanning Fluorimetry (DSF) Experiments
Authors: Wu Taia , Yu Joshua , Gale-Day Zachary , Woo Amanda , Suresh Arundhati , Hornsby Michael , Gestwicki Jason E.
Published: March 2020

Differential Scanning Fluorimetry (DSF) is a method that enables rapid determination of a protein’s apparent melting temperature (Tma). Owing to its high throughput, DSF has found widespread application in fields ranging from structural biology to chemical screening. Yet DSF has developed two opposing reputations: one as an indispensable laboratory tool to probe protein stability, another as a frustrating platform that often fails. Here, we aim to reconcile these disparate reputations and help users perform more successful DSF experiments with three resources: an updated, interactive theoretical framework, practical tips, and online data analysis. We anticipate that these resources, made available online at DSFworld (https://gestwickilab.shinyapps.io/dsfworld/), will broaden the utility of DSF.
The physiological adaptation for the “fore-mid” four-legged walking behavior of the pygmy mole cricketXya sichuanensis
Authors: Zhang Yi , Wang Shuying , Feng Zhu-Jun , Liu Tong-Xian , Cao Chengquan
Published: March 2020

Animals have developed numerous specialized biological characteristics due to selective pressure from the environment. The pygmy mole cricketXya sichuanensishas well-developed saltatorial hind legs for jumping and benefits for its survival, but these legs cannot be used for walking. Therefore, the typical tripedal gait used by most insects with six legs is not possible, andX. sichuanensiswalks exclusively using its fore and mid legs. In this study, we describe a “fore-mid” walking pattern inX. sichuanensis.Further, we sought to deepen our understanding of the biological and physiological adaptations of this “four-legged” insect. We found the positions of tarsi points relative to the ground, integrated hind leg-abdomen structure, thickened ventral cuticle, and leg movements during walking to all show a unique biological adaptation. Of interest,X. sichuanensiswas observed to demonstrate four-legged walking, underlining the general theme that insects have strong plasticity at both physiological and behavioral levels. We suggest that on an evolutionary timescale,X. sichuanensishas developed behavioral characteristics such as optimized jumping behavior and a unique walking pattern alongside specialized anatomical adaptations to enable survival in a competitive environment. This study could help explain biological and physiological adaptations for insects’ behaviors with important implications for the study of diversity in insect locomotion.
Deep Learning Enable Untargeted Metabolite Extraction from High Throughput Coverage Data-Independent Acquisition
Authors: Ji Hongchao , Lu Hongmei , Zhang Zhimin
Published: March 2020

The sequential window acquisition of all theoretical spectra (SWATH) technique is a specific variant of data-independent acquisition (DIA), which is supposed to increase the metabolite coverage and the reproducibility compared to data-dependent acquisition (DDA). However, SWATH technique lost the direct link between the precursor ion and the fragments. Here, we propose a deep-learning-based approach (DeepSWATH) to reconstruct the association between the MS/MS spectra and their precursors. Comparing with MS-DIAL, the proposed method can extract more accurate spectra with less noise to improve the identification accuracy of metabolites. Besides, DeepSWATH can also handle severe coelution conditions.
Comparative analysis of seven short-reads sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing
Authors: Kim Hak-Min , Jeon Sungwon , Chung Oksung , Jun Je Hoon , Kim Hui-Su , Blazyte Asta , Lee Hwang-Yeol , Yu Youngseok , Cho Yun Sung , Bolser Dan M. , Bhak Jong
Published: March 2020

Background

MGISEQ-T7 is a new whole-genome sequencer developed by Complete Genomics and MGI utilizing DNA nanoball and combinatorial probe anchor synthesis technologies for generating short reads at a very large scale – up to 60 human genomes per day. However, it has not been objectively and systematically compared against Illumina short-read sequencers.

Findings

By using the same KOREF sample, the Korean Reference Genome, we have compared seven sequencing platforms including BGISEQ-500, MGISEQ-T7, HiSeq2000, HiSeq2500, HiSeq4000, HiSeqX10, and NovaSeq6000. We measured sequencing quality by comparing sequencing statistics (base quality, duplication rate, and random error rate), mapping statistics (mapping rate, depth distribution, and %GC coverage), and variant statistics (transition/transversion ratio, dbSNP annotation rate, and concordance rate with SNP genotyping chip) across the seven sequencing platforms. We found that MGI platforms showed a higher concordance rate of SNP genotyping than HiSeq2000 and HiSeq4000. The similarity matrix of variant calls confirmed that the two MGI platforms have the most similar characteristics to the HiSeq2500 platform.

Conclusions

Overall, MGI and Illumina sequencing platforms showed comparable levels of sequencing quality, uniformity of coverage, %GC coverage, and variant accuracy, thus we conclude that the MGI platforms can be used for a wide range of genomics research fields at approximately half the cost of the Illumina platforms.
Evaluation of biodiversity in estuaries using environmental DNA metabarcoding
Authors: Ahn Hyojin , Kume Manabu , Terashima Yuki , Ye Feng , Kameyama Satoshi , Miya Masaki , Yamashita Yoh , Kasai Akihide
Published: March 2020

Biodiversity is an important parameter for the evaluation of the extant environmental conditions. Here, we used environmental DNA (eDNA) metabarcoding to investigate fish biodiversity in five different estuaries in Japan. Water samples for eDNA were collected from river mouths and adjacent coastal areas of two estuaries with high degrees of development (the Tama and Miya Rivers) and three estuaries with relatively low degrees of development (the Aka, Takatsu, and Sendai Rivers). A total of 182 fish species across 67 families were detected. Among them, 11 species occurred in all the rivers studied. Rare fishes including endangered species were successfully detected in rich natural rivers. Biodiversity was the highest in the Sendai River and lowest in the Tama River, reflecting the degree of human development along each river. Even though nutrient concentration was low in both the Aka and Sendai Rivers, the latter exhibited greater diversity, including many tropical or subtropical species, owing to its more southern location. Species composition detected by eDNA varied among rivers, reflecting the distribution and migration of fishes. Our results are in accordance with the ecology of each fish species and environmental conditions of each river, suggesting the potential of eDNA for non-invasive assessment of aquatic biodiversity.
Reconciling Qualitative, Abstract, and Scalable Modeling of Biological Networks
Authors: Paulevé Loïc , Kolčák Juraj , Chatain Thomas , Haar Stefan
Published: March 2020

Predicting the behaviors of complex biological systems, underpinning processes such as cellular differentiation, requires taking into account many molecular and genetic elements for which limited information is available past a global knowledge of their pairwise interactions. Logical modeling, notably with Boolean Networks (BNs), is a well-established approach which enables reasoning on the qualitative dynamics of networks accounting for many species. Several dynamical approaches have been proposed to interpret the logic of the regulations encoded by the BNs. The synchronous and (fully) asynchronous ones are the most prominent, where the value of either all or only one component can change at each step. Here we prove that, besides being costly to analyze, these usual interpretations are not adequate to represent quantitative systems, being able to both predict spurious behaviors and miss others. We introduce a new paradigm, the Most Permissive Boolean Networks (MPBNs), which offer the formal guarantee not to miss any behavior achievable by a quantitative model following the same logic. Moreover, MPBNs significantly reduce the complexity of dynamical analysis, enabling to model genome-scale networks.
Cooperative genetic networks drive a mammalian cell state transition
Authors: Lackner Andreas , Sehlke Robert , Garmhausen Marius , Stirparo Giuliano Giuseppe , Huth Michelle , Titz-Teixeira Fabian , van der Lelij Petra , Ramesmayer Julia , Thomas Henry Fabian , Ralser Meryem , Santini Laura , Sarov Mihail , Stewart A. Francis , Smith Austin , Beyer Andreas , Leeb Martin
Published: March 2020

In the mammalian embryo, epiblast cells must exit their naïve state and acquire formative pluripotency. This cell state transition is recapitulated by mouse embryonic stem cells (ESCs), which undergo pluripotency progression in defined conditionsin vitro. However, our understanding of the molecular cascades and gene-networks involved in the exit from naïve pluripotency remains fragmented. Here we employed a combination of genetic screens in haploid ESCs, CRISPR/Cas9 gene disruption, large-scale transcriptomics and computational systems-biology to delineate the regulatory circuits governing naïve state exit. Transcriptome profiles for 73 knockout ESC lines predominantly manifest delays on the trajectory from naive to formative epiblast. We find that gene networks operative in ESCs are active during transition from pre- to post-implantation epiblastin utero. We identified 374 naïve-associated genes tightly connected to epiblast state and largely conserved in human ESCs and primate embryos. Integrated analysis of mutant transcriptomes revealed funneling of multiple gene activities into discrete regulatory modules. Finally, we delineate how intersections with signaling pathways direct this pivotal mammalian cell state transition.
Screening for functional circular RNAs using the CRISPR-Cas13 system
Authors: Li Siqi , Li Xiang , Xue Wei , Zhang Lin , Cao Shi-Meng , Lei Yun-Ni , Yang Liang-Zhong , Guo Si-Kun , Zhang Jia-Lin , Gao Xiang , Wei Jia , Li Jinsong , Yang Li , Chen Ling-Ling
Published: March 2020

Circular RNAs (circRNAs) produced from back-spliced exons are widely expressed, but individual circRNA functions remain poorly understood due to inadequate methods, such as RNAi and genome engineering, in distinguishing overlapped exons in circRNAs from those in linear cognate mRNAs1,2. Here we report that the programable RNA-guided, RNA-targeting CRISPR-Cas13, RfxCas13d, effectively and specifically discriminates circRNAs from mRNAs, using guide (g)RNAs targeting sequences spanning the back-splicing junction (BSJ) sites featured in RNA circles. Using a lentiviral library that targets sequences across BSJ sites of highly expressed human circRNAs, we show that a group of circRNAs are important for cell growth mostly in a cell-type specific manner and that a common oncogenic circRNA,circFAM120A,promotes cell proliferationin vitroandin vivoby preventingFAM120AmRNA from binding the translation inhibitor IGF2BP2 for efficient translation. Application of RfxCas13d/BSJ-gRNA screening has also uncoveredcircMan1a2with regulatory potential in mouse embryo preimplantation development. Together, these results establish CRISPR-RfxCas13d as a useful tool for the discovery and functional study of circRNAs at both individual and large-scale levels.
Prioritized experience replays on a hippocampal predictive map for learning
Authors: Igata Hideyoshi , Ikegaya Yuji , Sasaki Takuya
Published: March 2020

Hippocampal cells are central to spatial and predictive representations, and experience replays by place cells are crucial for learning and memory. Nonetheless, how hippocampal replay patterns dynamically change during the learning process remains to be largely elucidated. We found that when rats updated their behavioral strategies in response to a novel salient location, place cells increased theta sequences and sharp wave ripple-associated synchronous spikes that preferentially replayed salient locations and reward-related contexts in reverse order. The directionality and contents of the replays progressively varied with learning, including an optimized path that had never been exploited by the animals. Realtime suppression of sharp wave ripples during learning inhibited the rapid stabilization of optimized behavior. Our results suggest that hippocampal replays prioritize salient experiences and support the reinforcement of new behavioral policies.

One-Sentence Summary

Neuronal network mechanisms to internally rehearse learned information for updating behavioral strategy are revealed
Finding associations in a heterogeneous setting: Statistical test for aberration enrichment
Authors: Mezlini Aziz M. , Das Sudeshna , Goldenberg Anna
Published: March 2020

Most two-group statistical tests are implicitly looking for a broad pattern such as an overall shift in mean, median or variance between the two groups. Therefore, they operate best in settings where the effect of interest is uniformly affecting everyone in one group versus the other. In real-world applications, there are many scenarios where the effect of interest is heterogeneous. For example, a drug that works very well on only a proportion of patients and is equivalent to a placebo on the remaining patients, or a disease associated gene expression dysregulation that only occurs in a proportion of cases whereas the remaining cases have expression levels indistinguishable from the controls for the considered gene. In these examples with heterogeneous effect, we believe that using classical two-group statistical tests may not be the most powerful way to detect the signal. In this paper, we developed a statistical test targeting heterogeneous effects and demonstrated its power in a controlled simulation setting compared to existing methods. We focused on the problem of finding meaningful associations in complex genetic diseases using omics data such as gene expression, miRNA expression, and DNA methylation. In simulated and real data, we showed that our test is complementary to the traditionally used statistical tests and is able to detect disease-relevant genes with heterogeneous effects which would not be detectable with previous approaches.
Whole genome bisulfite sequencing dataset of mycelium and spore of chalkbrood disease pathogenAscosphaera apis
Authors: Du Yu , Jiang Haibin , Chen Huazhi , Wang Jie , Fan Yuanchan , Fan Xiaoxue , Xiong Cuiling , Zheng Yanzhen , Chen Dafu , Guo Rui
Published: March 2020

Chalkbrood, a widespread fungal disease of bee larvae, is caused by the fungusAscosphaera apis. In this article, mecylia and spores ofA. apiswere respectively collected followed by DNA isolation, bisulfite conversion, cDNA library construction and next-generation sequencing. Using whole genome bisulfite sequencing (WGBS), 69,844,360 and 60,570,990 raw reads were yielded from Aam and Aas, and after quality control, 9,982,386,951 and 8,825,601,434 clean reads were obtained, respectively. In addition, 67,685,866 and 58,886,072 clean reads were mapped to the reference genome ofA. apis, including 37,643,592 and 31,568,442 unique mapped clean reads, and 49,686 and 13,348 multiple mapped clean reads. Furthermore, after bisulfite treatment, the conversion ratio of clean reads from Aam and Aas were 99.38% and 99.51%, respectively. The WGBS data ducumented here contributes to genome-wide identification of 5mC methylation sites inA. apisand comparison of methylomes between mycelium and spore.

Value of the data

This dataset can be used for genome-wide identification of 5mC methylation sites inA. apis.

The accessible data could be used to systematically compare methylomes between mycelium and spore ofA. apis.

Current data provides a useful resource for further study on DNA methylation-mediated mechanism underlying mycelium growth, spore germination and sexual reproduction of mycelium with the opposite sex.
Delineating the relationship between immune system aging and myogenesis in muscle repair
Authors: Tobin Stephanie W. , Alibhai Faisal J. , Wlodarek Lukasz , Yeganeh Azadeh , Millar Sean , Wu Jun , Li Shu-hong , Weisel Richard D. , Li Ren-Ke
Published: March 2020

How aging affects the communication between immune cells and myoblasts during myogenesis is unclear. We therefore investigated how aging impacts the cellular synchronization of these two processes after muscle injury. Muscles of old mice (20 months) had chronic inflammation and fewer satellite cells compared to young mice (3 months). After injury, young mice developed a robust, but transient inflammatory response and a stepwise myogenic gene expression program. These responses were impaired with age. Replacement of old bone marrow (BM) via heterochronic bone marrow transplantation (BMT) increased muscle mass and performance on locomotive and behavioural tests. After injury, Y-O BMT restored the immune cell and cytokine profiles to a young phenotype and enhanced satellite cell activity while O-O BMT amplified a late-onset proinflammatory response.In vitro,conditioned media from young or old macrophages had no effect or impaired myoblast proliferation, respectively. Thus, BM age negatively affects myogenesis by inhibiting myoblast proliferation.
The importance of species interactions in spatially explicit eco-evolutionary community dynamics under climate change
Authors: Åkesson Anna , Curtsdotter Alva , Eklöf Anna , Ebenman Bo , Norberg Jon , Barabás György
Published: March 2020

Eco-evolutionary dynamics are essential in shaping the biological response of communities to ongoing climate change. Here we develop a spatially explicit eco-evolutionary framework which integrates evolution, dispersal, and species interactions within and between trophic levels. This allows us to analyze how these processes interact to shape species- and community-level dynamics under climate change. Additionally, we incorporate the heretofore unexplored feature that species interactions themselves might change due to increasing temperatures and affect the impact of climate change on ecological communities. The new modeling framework captures previously reported ecological responses to climate change, and also reveals two new key results. First, interactions between trophic levels as well as temperature-dependent competition within a trophic level mitigate the negative impact of climate change on global biodiversity, emphasizing the importance of understanding biotic interactions in shaping climate change impact. Second, using a trait-based perspective, we found a strong negative relationship between the within-community variation in preferred temperatures and the capacity to respond to climate change. Communities resulting from different ecological interaction structures form distinct clusters along this relationship, but varying species’ abilities to disperse and adapt to new temperatures leave it unaffected.
N-glycosylation blocks and simultaneously fosters different receptor-ligand binding sites: the chameleonic CD44–hyaluronan interaction
Authors: Vuorio Joni , Škerlová Jana , Fábry Milan , Veverka Václav , Vattulainen Ilpo , Řezáčová Pavlína , Martinez-Seara Hector
Published: March 2020

While DNA encodes protein structure, glycans provide a complementary layer of information to protein function. As a prime example of the significance of glycans, the ability of the cell surface receptor CD44 to bind its ligand, hyaluronan, is modulated by N-glycosylation. However, the details of this modulation remain unclear. Based on atomistic simulations and NMR, we provide evidence that CD44 has multiple distinct binding sites for hyaluronan, and that N-glycosylation modulates their respective roles. We find that non-glycosylated CD44 favors the canonical sub-micromolar binding site, while glycosylated CD44 binds hyaluronan with an entirely different micromolar binding site. Our findings show (for the first time) how glycosylation can alter receptor affinity by shielding specific regions of the host protein, thereby promoting weaker binding modes. The mechanism revealed in this work emphasizes the importance of glycosylation in protein function and poses a challenge for protein structure determination where glycosylation is usually neglected.
Genetic and behavioral adaptation ofCandida parapsilosisto the microbiome of hospitalized infants revealed byin situgenomics, transcriptomics and proteomics
Authors: West Patrick T. , Peters Samantha L. , Olm Matthew R. , Yu Feiqiao B. , Lou Yue Clare , Firek Brian A. , Baker Robyn , Johnson Alexander D. , Morowitz Michael J. , Hettich Robert L. , Banfield Jillian F.
Published: March 2020

Candida parapsilosisis a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades.C. parapsilosishas been primarily studied in pure culture, leaving gaps in understanding of its function in microbiome context. Here, we reconstructed five uniqueC. parapsilosisgenomes from premature infant fecal samples and analyzed their genome structure, population diversity andin situactivity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructedC. parapsilosisgenomes have four to sixteen copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with aC. parapsilosisblood infection revealed highly variablein situexpression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressedin situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples,C. parapsilosiscoexisted withEnterococcus faecalisthat shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition. The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes.
Environmentally Induced Sperm RNAs Transmit Cancer Susceptibility to Offspring in a Mouse Model
Authors: da Cruz Raquel Santana , Dominguez Odalys , Chen Elaine , Gonsiewski Alexandra K. , Nasir Apsra , Cruz M. Idalia , Zou Xiaojun , Galli Susana , Makambi Kepher , McCoy Matthew , Schmidt Marcel O. , Jin Lu , Peran Ivana , de Assis Sonia
Published: March 2020

DNA sequence accounts for the majority of disease heritability, including cancer. Yet, not all familial cancer cases can be explained by genetic factors. It is becoming clear that environmentally induced epigenetic inheritance occurs and that the progeny’s traits can be shaped by parental environmental experiences. In humans, epidemiological studies have implicated environmental toxicants, such as the pesticide DDT, in intergenerational cancer development, including breast and childhood tumors. Here, we show that the female progeny of males exposed to DDT in the pre-conception period have higher susceptibility to developing aggressive tumors in mouse models of breast cancer. Sperm of DDT-exposed males exhibited distinct patterns of small non-coding RNAs, with an increase in miRNAs and a specific surge in miRNA-10b levels. Remarkably, embryonic injection of the entire sperm RNA load of DDT-exposed males, or synthetic miRNA-10b, recapitulated the tumor phenotypes observed in DDT offspring. Mechanistically, miR-10b injection altered the transcriptional profile in early embryos with enrichment of genes associated with cell differentiation, tissue and immune system development. In adult DDT-derived progeny, transcriptional and protein analysis of mammary tumors revealed alterations in stromal and in immune system compartments. Our findings reveal a causal role for sperm RNAs in environmentally induced inheritance of cancer predisposition and, if confirmed in humans, this could help partially explain some of the “missing heritability” of breast, and other, malignancies.
Direct evidence of abortive lytic infection-mediated establishment of Epstein-Barr virus latency during B-cell infection
Authors: Inagaki Tomoki , Sato Yoshitaka , Ito Jumpei , Takaki Mitsuaki , Okuno Yusuke , Yaguchi Masahiro , Al Masud H. M. Abdullah , Watanabe Takahiro , Sato Kei , Iwami Shingo , Murata Takayuki , Kimura Hiroshi
Published: March 2020

Viral infection induces dynamic changes in transcriptional profiles. Virus-induced and anti-viral responses are intertwined during the infection. Epstein-Barr virus (EBV) is a human gammaherpesvirus that provides a model of herpesvirus latency. To measure the transcriptome changes during the establishment of EBV latency, EBV-negative Akata cells were infected with EBV-EGFP and observed by transcriptome sequencing (RNA-seq) at 0, 2, 4, 7, 10, and 14 days after infection. We found transient downregulation of mitotic division-related genes, reflecting reprograming of cell growth by EBV. Moreover, a burst of viral lytic gene expression was detected in the early phase of infection. Experimental and mathematical investigations demonstrated that infectious virions were not produced in the pre-latent phase, suggesting the presence of an abortive lytic infection. Finally, we conducted fate mapping using recombinant EBV, enabling the noninvasive, continuous observation of infected cells during EBV infection. Our tracking analysis provided direct evidence that the abortive lytic infection in the pre-latent phase converges to latent infection during EBV infection of B-cells, shedding light on novel roles of viral lytic gene(s) in establishing latency.

Author summary

Viral infection is a complex process that activates both virus-triggered and host anti-viral responses. This process has classically been studied by snapshot analysis such as microarray and RNA-seq at discrete time points as population averages. Snapshot data lead to invaluable findings in host-pathogen interactions. However, these “snapshot” omics, even from a single cell, lack temporal resolution. Because the behavior of infected cells is highly dynamic and heterogenous, continuous analysis is required for deciphering the fate of infected cells during viral infection. Here, we exploited fate mapping techniques with recombinant Epstein-Barr virus (EBV) to track the infected cells and recorded a log of lytic gene expression during EBV infection. Our continuous observation of infected cells revealed that EBV established latency in B-cells via an abortive lytic infection in the pre-latent phase.
Atypical brain asymmetry in autism – a candidate for clinically meaningful stratification
Authors: Floris Dorothea L. , Wolfers Thomas , Zabihi Mariam , Holz Nathalie E. , Zwiers Marcel P. , Charman Tony , Tillmann Julian , Ecker Christine , Dell’Acqua Flavio , Banaschewski Tobias , Moessnang Carolin , Baron-Cohen Simon , Holt Rosemary , Durston Sarah , Loth Eva , Murphy Declan , Marquand Andre , Buitelaar Jan K. , Beckmann Christian F. ,   the EU-AIMS LEAP group
Published: March 2020

Background

Autism Spectrum Disorder (henceforth ‘autism’) is a highly heterogeneous neurodevelopmental condition with few effective treatments for core and associated features. To make progress we need to both identify and validate neural markers that help to parse heterogeneity to tailor therapies to specific neurobiological profiles. Atypical hemispheric lateralization is a stable feature across studies in autism, however its potential of lateralization as a neural stratification marker has not been widely examined.

Methods

In order to dissect heterogeneity in lateralization in autism, we used the large EU-AIMS Longitudinal European Autism Project dataset comprising 352 individuals with autism and 233 neurotypical (NT) controls as well as a replication dataset from ABIDE (513 autism, 691 NT) using a promising approach that moves beyond mean-group comparisons. We derived grey matter voxelwise laterality values for each subject and modelled individual deviations from the normative pattern of brain laterality across age using normative modeling.

Results

Results showed that individuals with autism had highly individualized patterns of both extreme right- and leftward deviations, particularly in language-, motor- and visuospatial regions, associated with symptom severity. Language delay (LD) explained most variance in extreme rightward patterns, whereas core autism symptom severity explained most variance in extreme leftward patterns. Follow-up analyses showed that a stepwise pattern emerged with individuals with autism with LD showing more pronounced rightward deviations than autism individuals without LD.

Conclusion

Our analyses corroborate the need for novel (dimensional) approaches to delineate the heterogeneous neuroanatomy in autism, and indicate atypical lateralization may constitute a neurophenotype for clinically meaningful stratification in autism.
Transcriptional network analysis of transcriptomic diversity in resident tissue macrophages and dendritic cells in the mouse mononuclear phagocyte system
Authors: Summers Kim M. , Bush Stephen J. , Hume David A.
Published: March 2020

The mononuclear phagocyte system (MPS) is a family of cells including progenitors, circulating blood monocytes, resident tissue macrophages and dendritic cells (DC) present in every tissue in the body. To test the relationships between markers and transcriptomic diversity in the MPS, we collected from NCBI-GEO >500 quality RNA-seq datasets generated from mouse MPS cells isolated from multiple tissues. The primary data were randomly down-sized to a depth of 10 million reads and requantified. The resulting dataset was clustered using the network analysis toolGraphia. A sample-to-sample matrix revealed that MPS populations could be separated based upon tissue of origin. Cells identified as classical DC subsets, cDC1 and cDC2, and lackingFcgr1(CD64), were centrally-located within the MPS cluster and no more distinct than other MPS cell types. A gene-to-gene correlation matrix identified large generic co-expression clusters associated with MPS maturation and innate immune function. Smaller co-expression gene clusters including the transcription factors that drive them showed higher expression within defined isolated cells, including macrophages and DC from specific tissues. They include a cluster containingLyve1that implies a function in endothelial cell homeostasis, a cluster of transcripts enriched in intestinal macrophages and a generic cDC cluster associated withCcr7. However, transcripts encoding many other putative MPS subset markers includingAdgre1, Itgax, Itgam, Clec9a, Cd163, Mertk, RetnlaandH2-a/e(class II MHC) clustered idiosyncratically and were not correlated with underlying functions. The data provide no support for the concept of markers of M2 polarization or the specific adaptation of DC to present antigen to T cells. Co-expression of immediate early genes (e.g.Egr1, Fos, Dusp1) and inflammatory cytokines and chemokines (Tnf, Il1b, Ccl3/4) indicated that all tissue disaggregation protocols activate MPS cells. Tissue-specific expression clusters indicated that all cell isolation procedures also co-purify other unrelated cell types that may interact with MPS cellsin vivo. Comparative analysis of public RNA-seq and single cell RNA-seq data from the same lung cell populations showed that the extensive heterogeneity implied by the global cluster analysis may be even greater at a single cell level with few markers strongly correlated with each other. This analysis highlights the power of large datasets to identify the diversity of MPS cellular phenotypes, and the limited predictive value of surface markers to define lineages, functions or subpopulations.
Genome-wide locus sequence typing (GLST) of eukaryotic pathogens
Authors: Schwabl Philipp , Sánchez Jalil Maiguashca , Costales Jaime A. , Ocaña Sofía , Segovia Maikell , Carrasco Hernán J. , Hernández Carolina , Ramírez Juan David , Lewis Michael D. , Grijalva Mario J. , Llewellyn Martin S.
Published: March 2020

Analysis of genetic polymorphism is a powerful tool for epidemiological surveillance and research. Powerful inference from pathogen genetic variation, however, is often restrained by limited access to representative target DNA, especially in the study of obligate parasitic species for whichex vivoculture is resource-intensive or bias-prone. Modern sequence capture methods enable pathogen genetic variation to be analyzed directly from vector/host material but are often too complex and expensive for resource-poor settings where infectious diseases prevail. This study proposes a simple, cost-effective ‘genome-wide locus sequence typing’ (GLST) tool based on massive parallel amplification of information hotspots throughout the target pathogen genome. The multiplexed polymerase chain reaction amplifies hundreds of different, user-defined genetic targets in a single reaction tube, and subsequent agarose gel-based clean-up and barcoding completes library preparation at under 4 USD per sample. Approximately 100 libraries can be sequenced together in one Illumina MiSeq run. Our study generates a flexible GLST primer panel design workflow forTrypanosoma cruzi, the parasitic agent of Chagas disease. We successfully apply our 203-target GLST panel to direct, culture-free metagenomic extracts from triatomine vectors containing a minimum of 3.69 pg/μlT. cruziDNA and further elaborate on method performance by sequencing GLST libraries fromT. cruzireference clones representing discrete typing units (DTUs) TcI, TcIII, TcIV, and TcVI. The 780 SNP sites we identify in the sample set repeatably distinguish parasites infecting sympatric vectors and detect correlations between genetic and geographic distances at regional (< 150 km) as well as continental scales. The markers also clearly separate DTUs. We discuss the advantages, limitations and prospects of our method across a spectrum of epidemiological research.
Endosomal free fatty acid receptor 2 signaling is essential for propionate-induced anorectic gut hormone release
Authors: Caengprasath Natarin , Gonzalez-Abuin Noemi , Shchepinova Maria , Ma Yue , Inoue Asuka , Tate Edward W. , Frost Gary , Hanyaloglu Aylin C.
Published: March 2020

The ability of propionate, a short chain fatty acid produced from the fermentation of non-digestible carbohydrates in the colon, to stimulate the release of anorectic gut hormones, such as glucagon like peptide-1 (GLP-1), is an attractive approach to enhance appetite regulation, weight management and glycaemic control. Propionate induces GLP-1 release via its G protein-coupled receptor (GPCR), free fatty acid receptor 2 (FFA2); a GPCR that activates Gαi and Gαq/11 pathways. However, how pleiotropic GPCR signaling mechanisms in the gut regulates appetite is poorly understood. Here, we identify propionate-mediated G protein signaling is spatially directed within the cell via the targeting of FFA2 to very early endosomes. Furthermore, propionate activates an endosomal Gαi/p38 signaling pathway, which is essential for propionate-induced GLP-1 release in enteroendocrine cells and colonic crypts. Our study reveals that intestinal metabolites can engage membrane trafficking pathways and endosomal signaling platforms to orchestrate complex GPCR pathways within the gut.
Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data
Authors: Xu Xiaofeng , Bei Jinlong , Xuan Yibo , Chen Jianyuan , Chen Defu , Barker Stephen C. , Kelava Samuel , He Bingjun , Gao Shan , Chen Ze
Published: March 2020

In 2014, A novel tick-borne virus of the genusFlaviviruswas first reported from the Mogiana region in Brazil. This virus was named the Mogiana tick virus (MGTV). Later, MGTV was also named as Jingmen tick virus (JMTV), Kindia tick virus (KDTV), Guangxi tick virus (GXTV) etc. In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and detected MGTV inAmblyomma testudinariumticks, which had been captured in Yunnan province of China in the year of 2016. The full-length genome sequence of a new MGTV strain Yunnan2016 (GenBank:MT080097,MT080098,MT080099andMT080100) was obtained and recommended to be included into the NCBI RefSeq database for the future studies of MGTV. Our phylogenetic analyses showed that viruses named MGTV, JMTV, KDTV and GXTV are monophyletic: the MGTV group (lineage) of viruses. We show, for the first time, that 5′ and 3′ sRNAs can be used to obtain full-length sequences of the 5’ and 3’ ends of, but not limited to genome sequences of RNA viruses. And we proved the feasibility of using the sRNA-seq based method for the detection of viruses in a sample containing miniscule RNA.