bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brooding brittle-star is a global hybrid polyploid swarm
Authors: Hugall Andrew F. , Byrne Maria , O’Hara Timothy D. 
Published: July 2023

AbstractThe widespread and abundant brooding brittle-star (Amphipholis squamata) is a simultaneous hermaphrodite with a complex mitochondrial phylogeography of multiple divergent overlapping mtDNA lineages and can exhibit high levels of inbreeding or clonality and unusual sperm morphology. We use exon-capture and transcriptome data to show that the nuclear genome comprises multiple (>3) divergent (π > 6%) expressed components spread across the mitochondrial lineages, and encompassing several other genera, including diploid dioecious dimorphic species. We also report a massive sperm genome size inA. squamata, an order of magnitude larger than in the sperm of other brittle-star species, consistent with our genetic measures of elevated and variable ploidy (>6). We propose thatA. squamata(and related taxa) is a hybrid polyploid complex with many independent hybrid origins, variable ploidy, and complex patterns of parental subgenomes. We hypothesize thatA. squamatahas facultative sperm-dependent asexual reproduction, where sperm is required for embryogenesis but the egg and sperm only occasionally undergo fertilisation, a process that has been associated with the formation of polyploid hybrid swarms in other taxa [1]. Unique amongst known marine allopolyploids, theA. squamatacomplex inhabits an extensive bathymetric as well as geographic range. A. squamata is a much-studied animal amenable to laboratory culture: appreciating it as a hybrid polyploid complex makes it even more interesting to the study of evolutionary biology.
SPPUSM: An MS/MS spectra merging strategy for improved low-input and single-cell proteome identification
Authors: Chen Yongle , Du Zhuokun , Zhao Hongxian , Fang Wei , Liu Tong , Zhang Yangjun , Zhang Wanjun , Qin Weijie 
Published: July 2023

AbstractSingle and rare cell analysis provides unique insights into the investigation of biological processes and disease progress by resolving the cellular heterogeneity that is masked by bulk measurements. Although many efforts have been made, the techniques used to measure the proteome in trace amounts of samples or in single cells still lag behind those for DNA and RNA due to the inherent non-amplifiable nature of proteins and the sensitivity limitation of current mass spectrometry. Here, we report an MS/MS spectra merging strategy termed SPPUSM (same precursor-produced unidentified spectra merging) for improved low-input and single-cell proteome data analysis. In this method, all the unidentified MS/MS spectra from multiple test files are first extracted. Then, the corresponding MS/MS spectra produced by the same precursor ion from different files are matched according to their precursor mass and retention time (RT) and are merged into one new spectrum. The newly merged spectra with more fragment ions are next searched against the database to increase the MS/MS spectra identification and proteome coverage. Further improvement can be achieved by increasing the number of test files and spectra to be merged. Up to 18.2% improvement in protein identification was achieved for 1 ng HeLa peptides by SPPUSM. Reliability evaluation by the “entrapment database” strategy using merged spectra from human andE. colirevealed a marginal error rate for the proposed method. For application in single cell proteome (SCP) study, identification enhancement of 28%-61% was achieved for proteins for different SCP data. Furthermore, a lower abundance was found for the SPPUSM-identified peptides, indicating its potential for more sensitive low sample input and SCP studies.
Tuberculosis susceptibility in genetically diverse mice reveals functional diversity of neutrophils
Authors: Ravesloot-Chávez Mariëtta M. , Van Dis Erik , Fox Douglas , Anaya Sanchez Andrea , Espich Scott , Nguyenla Xammy H. , Rawal Sagar L. , Samani Helia , Ballinger Mallory A. , Thomas Henry , Kotov Dmitri , Vance Russell , Nachman Michael W. , Stanley Sarah A. 
Published: July 2023

AbstractTuberculosis (TB) is a heterogenous disease in humans with individuals exhibiting a wide range of susceptibility. This heterogeneity is not captured by standard laboratory mouse lines. We used a new collection of 19 wild-derived inbred mouse lines collected from diverse geographic sites to identify novel phenotypes duringMycobacterium tuberculosis(Mtb) infection. Wild derived mice have heterogenous immune responses to infection that result in differential ability to control disease at early timepoints. Correlation analysis with multiple parameters including sex, weight, and cellular immune responses in the lungs revealed that enhanced control of infection is associated with increased numbers of CD4 T cells, CD8 T cells and B cells. Surprisingly, we did not observe strong correlations between IFN-γ production and control of infection. Although in most lines high neutrophils were associated with susceptibility, we identified a mouse line that harbors high neutrophils numbers yet controls infection. Using single-cell RNA sequencing, we identified a novel neutrophil signature associated with failure to control infection.
Projecting COVID-19 intensive care admissions in the Netherlands for policy advice: February 2020 to January 2021
Authors: Klinkenberg Don , Backer Jantien A. , de Keizer Nicolette F. , Wallinga Jacco 
Published: July 2023

0.AbstractIntroductionModel projections of COVID-19 incidence into the future help policy makers about decisions to implement or lift control measures. During 2020, policy makers in the Netherlands were informed on a weekly basis with short-term projections of COVID-19 intensive care unit (ICU) admissions. Here we present the model and the procedure by which it was updated.Methodsthe projections were produced using an age-structured transmission model. A consistent, incremental update procedure that integrated all new surveillance and hospital data was conducted weekly. First, up-to-date estimates for most parameter values were obtained through re-analysis of all data sources. Then, estimates were made for changes in the age-specific contact rates in response to policy changes. Finally, a piecewise constant transmission rate was estimated by fitting the model to reported daily ICU admissions, with a change point analysis guided by Akaike’s Information Criterion.ResultsThe model and update procedure allowed us to make mostly accurate weekly projections, accounting for recent and future policy changes, and to adapt the estimated effectiveness of the policy changes based only on the natural accumulation of incoming data.DiscussionThe model incorporates basic epidemiological principles and most model parameters were estimated per data source. Therefore, it had potential to be adapted to a more complex epidemiological situation, as it would develop after 2020.
Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
Authors: Sandoval-Velasco Marcela , Dudchenko Olga , Rodríguez Juan Antonio , Estrada Cynthia Pérez , Dehasque Marianne , Fontsere Claudia , Mak Sarah S.T. , Plotnikov Valerii , Khan Ruqayya , Weisz David , Contessoto Vinícius G. , Oliveira Junior Antonio B. , Kalluchi Achyuth , Omer Arina D. , Batra Sanjit S. , Shamim Muhammad S. , Durand Neva C. , O’Connell Brendan , Roca Alfred L. , Gnirke Andreas , Garcia-Treviño Isabel , Coke Rob , Flanagan Joseph P. , Pletch Kelcie , Ruiz-Herrera Aurora , Lander Eric S. , Rowley M. Jordan , Onuchic José N. , Dalén Love , Marti-Renom Marc A. , Gilbert M. Thomas P. , Aiden Erez Lieberman 
Published: July 2023

AbstractAncient DNA (aDNA) sequencing analysis typically involves alignment to a modern reference genome assembly from a related species. Since aDNA molecules are fragmentary, these alignments yield information about small-scale differences, but provide no information about larger features such as the chromosome structure of ancient species. We report the genome assembly of a female Late Pleistocene woolly mammoth (Mammuthus primigenius) with twenty-eight chromosome-length scaffolds, generated using mammoth skin preserved in permafrost for roughly 52,000 years. We began by creating a modified Hi-C protocol, dubbed PaleoHi-C, optimized for ancient samples, and using it to map chromatin contacts in a woolly mammoth. Next, we developed “reference-assisted 3D genome assembly,” which begins with a reference genome assembly from a related species, and uses Hi-C and DNA-Seq data from a target species to split, order, orient, and correct sequences on the basis of their 3D proximity, yielding accurate chromosome-length scaffolds for the target species. By means of this reference-assisted 3D genome assembly, PaleoHi-C data reveals the 3D architecture of a woolly mammoth genome, including chromosome territories, compartments, domains, and loops. The active (A) and inactive (B) genome compartments in mammoth skin more closely resemble those observed in Asian elephant skin than the compartmentalization patterns seen in other Asian elephant tissues. Differences in compartmentalization between these skin samples reveal sequences whose transcription was potentially altered in mammoth. We observe a tetradic structure for the inactive X chromosome in mammoth, distinct from the bipartite architecture seen in human and mouse. Generating chromosome-length genome assemblies for two other elephantids (Asian and African elephant), we find that the overall karyotype, and this tetradic Xi structure, are conserved throughout the clade. These results illustrate that cell-type specific epigenetic information can be preserved in ancient samples, in the form of DNA geometry, and that it may be feasible to perform de novo genome assembly of some extinct species.
Selective consistency of recurrent neural networks induced by plasticity as a mechanism of unsupervised perceptual learning
Authors: Goto Yujin , Kitajo Keiichi 
Published: July 2023

AbstractUnderstanding the mechanism by which the brain overcomes its inherent inconsistency in activity to achieve consistent information processing is one of the major challenges in neuroscience. Recently, it has been reported that the consistency of neural responses to stimuli that are presented repeatedly is enhanced implicitly in an unsupervised way, and results in improved perceptual consistency. Here, we propose the term "selective consistency" to describe this input-dependent consistency and hypothesize that it will be acquired in a self-organizing manner by plasticity within the neural system. To test this, we investigated whether a reservoir-based plastic model could acquire selective consistency to repeated stimuli. We used white noise sequences randomly generated in each trial and referenced white noise sequences presented multiple times. The results showed that the plastic network was capable of acquiring selective consistency rapidly, with as little as five exposures to stimuli, even for white noise. The acquisition of selective consistency could occur independently of performance optimization, as the network’s time-series prediction accuracy for referenced stimuli did not improve with repeated exposure and optimization. Furthermore, the network could only achieve selective consistency when in the region between order and chaos. These findings suggest that the neural system can acquire selective consistency in a self-organizing manner and that this may serve as a mechanism for certain types of learning.
Cue- versus reward-encoding basolateral amygdala projections to nucleus accumbens
Authors: He Yi , Huang Yanhua H. , Schlüter Oliver M. , Dong Yan 
Published: July 2023

SummaryIn substance use disorders, drug use as unconditioned stimulus (US) reinforces drug taking. Meanwhile, drug-associated cues (conditioned stimulus, CS) also gain incentive salience to promote drug seeking. The basolateral amygdala (BLA) is implicated in both US- and CS-mediated responses. Here, we show that two genetically distinct BLA neuronal types, expressing Rspo2 versus Ppp1r1b, respectively, project to the nucleus accumbens (NAc) and form monosynaptic connections with both dopamine D1 and D2 receptor-expressing neurons. While intra-NAc stimulation of Rspo2 or Ppp1r1b presynaptic terminals establishes intracranial self-stimulation (ICSS), only Ppp1r1b-stimulated mice exhibit cue-induced ICSS seeking. Furthermore, increasing versus decreasing the Ppp1r1b-to-NAc, but not Rspo2-to-NAc, subprojection increases versus decreases cue-induced cocaine seeking after cocaine withdrawal. Thus, while both BLA- to-NAc subprojections contribute to US-mediated responses, the Ppp1r1b subprojection selectively encodes CS-mediated reward and drug reinforcement. Such differential circuit representations may provide insights into precise understanding and manipulation of drug-versus cue-induced drug seeking and relapse.TeaserTwo subprojections from the amygdala to nucleus accumbens differentially encode cue-vs reward-mediated reinforcement.
Labile assembly of a tardigrade protein induces biostasis
Authors: Sanchez-Martinez S. , Nguyen K. , Biswas S. , Nicholson V. , Romanyuk A.V. , Ramirez J. , KC S. , Akter A. , Childs C. , Usher E.T. , Ginell G.M. , Yu F. , Gollub E. , Malferrari M. , Francia F. , Venturoli G. , Martin E.W. , Caporaletti F. , Giubertoni G. , Woutersen S. , Sukenik S. , Woolfson D.N. , Holehouse A.S. , Boothby T.C. 
Published: July 2023

AbstractTardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins that form gels. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of gelation for CAHS D similar to that of intermediate filaments. We show that gelation restricts molecular motion, immobilizing and protecting labile material from the harmful effects of drying.In vivo, we observe that CAHS D forms fiber-like condensates during osmotic stress. Condensation of CAHS D improves survival of osmotically shocked cells through at least two mechanisms: reduction of cell volume change and reduction of metabolic activity. Importantly, condensation of CAHS D is reversible and metabolic rates return to control levels after CAHS condensates are resolved. This work provides insights into how tardigrades induce biostasis through the self-assembly of CAHS gels.
Inference for entomological semi-field experiments: Fitting a mathematical model assessing personal and community protection of vector-control interventions
Authors: Fairbanks Emma L , Saeung Manop , Pongsiri Arissara , Vajda Elodie , Wang Yuqian , McIver David J , Tatarsky Allison , Lobo Neil F , Moore Sarah J , Ponlawat Alongkot , Chareonviriyaphap Theeraphap , Ross Amanda , Chitnis Nakul 
Published: July 2023

AbstractThe effectiveness of vector-control tools is often assessed by experiments as a reduction in mosquito landings using human landing catches (HLCs). However, HLCs alone only quantify a single characteristic and therefore do not provide information on the overall impacts of the intervention product. Using data from a recent semi-field study which used time-stratified HLCs, aspiration of non-landing mosquitoes, and blood feeding, we suggest a Bayesian inference approach for fitting such data to a stochastic model. This model considers both personal protection, through a reduction in biting, and community protection, from mosquito mortality and disarming (prolonged inhibition of blood feeding). Parameter estimates are then used to predict the reduction of vectorial capacity induced by etofenpox-treated clothing, picaridin topical repellents, transfluthrin spatial repellents and metofluthrin spatial repellents, as well as combined interventions forPlasmodium falciparummalaria inAnopleles minimus. Overall, all interventions had both personal and community effects, preventing biting and killing or disarming mosquitoes. This led to large estimated reductions in the vectorial capacity, with substantial impact even at low coverage. As the interventions aged, fewer mosquitoes were killed; however the impact of some interventions changed from killing to disarming mosquitoes. Overall, this inference method allows for additional modes of action, rather than just reduction in biting, to be parameterised and highlights the tools assessed as promising malaria interventions.
The auditory P2 evoked by speech sounds consists of two separate subcomponents
Authors: Steinmetzger Kurt , Rupp André 
Published: July 2023

ABSTRACTThe P2 component of the auditory evoked potential is commonly thought to reflect acoustic stimulus properties as well as prior exposure to the materials, rather than change-related cortical activity. Here, we challenge this view by showing that the P2 is strongly increased in response to voice pitch changes with a stepwise pattern compared to changes in dynamic pitch contours typical for natural speech, and also reflects the magnitude of these pitch changes. Furthermore, it is demonstrated that neither the P2 nor any other component are affected by the harmonicity of the materials. Despite no prior exposure, artificially created inharmonic versions of the speech materials elicited similar activity throughout auditory cortex. This suggests that so-called harmonic template neurons observed in animal studies are either absent or do not exist in sufficient number in human auditory cortex to detect their activity extracranially. Crucially, both morphology and source reconstructions of the EEG data showed that the P2 appears to consist of two separate subcomponents. Whereas source activity for the “P2a” was strongest in right auditory cortex, the subsequent “P2b” included generators spread across auditory cortex and association areas, bilaterally. The two subcomponents thus likely reflect processing at different stages of the auditory pathway.
Spinal facilitation of descending motor input
Authors: Taccola Giuliano , Kissane Roger , Culaclii Stanislav , Apicella Rosamaria , Liu Wentai , Gad Parag , Ichiyama Ronaldo M. , Chakrabarty Samit , Edgerton V. Reggie 
Published: July 2023

AbstractHighly varying patterns of electrostimulation (Dynamic Stimulation, DS) delivered to the dorsal cord through an epidural array with 18 independent electrodes transiently facilitate corticospinal motor responses, even after spinal injury. To partly unravel how corticospinal input are affected by DS, we introduced a corticospinal platform that allows selective cortical stimulation during the multisite acquisition of cord dorsum potentials (CDPs) and the simultaneous supply of DS. Firstly, the epidural interface was validated by the acquisition of the classical multisite distribution of CDPs on the dorsal cord and their input-output profile elicited by pulses delivered to peripheral nerves. Apart from increased EMGs, DS selectively increased excitability of the spinal interneurons that first process corticospinal input, without changing the magnitude of commands descending from the motor cortex, suggesting a novel correlation between muscle recruitment and components of cortically-evoked CDPs. Finally, DS increases excitability of post-synaptic spinal interneurons at the stimulation site and their responsiveness to any residual supraspinal control, thus supporting the use of electrical neuromodulation whenever the motor output is jeopardized by a weak volitional input, due to a partial disconnection from supraspinal structures and/or neuronal brain dysfunctions.
Glycine fermentation byC. difficilepromotes virulence, spore formation, and is induced by host cathelicidin
Authors: Rizvi Arshad , Vargas-Cuebas Germán , Edwards Adrianne N. , DiCandia Michael A. , Carter Zavier A. , Lee Cheyenne D. , Monteiro Marcos P. , McBride Shonna M. 
Published: July 2023

SUMMARYThe amino acid glycine is enriched in the dysbiotic gut and is suspected to contribute toClostridioides difficileinfection. We hypothesized that the use of glycine as an energy source contributes to colonization of the intestine and pathogenesis ofC. difficile. To test this hypothesis, we deleted the glycine reductase genesgrdAB, renderingC. difficileunable to ferment glycine, and investigated the impact on growth and pathogenesis. We found that thegrdpathway promoted growth, toxin production, sporulation, and pathogenesis ofC. difficilein the hamster model of disease. Further, we determined that thegrdlocus is regulated by host cathelicidin (LL-37) and the cathelicidin-responsive regulator, ClnR, indicating that the host peptide signals to control glycine catabolism. The induction of glycine fermentation by LL-37 demonstrates a direct link between the host immune response and the bacterial reactions of toxin production and spore formation.
Plant Cellulose as a Substrate for 3D Neural Stem Cell Culture
Authors: Couvrette Lauren J. , Walker Krystal L. A. , Bui Tuan V. , Pelling Andrew E. 
Published: July 2023

AbstractNeural stem cell (NSC) based therapies are at the forefront of regenerative medicine strategies for various neural defects and injuries such as stroke, traumatic brain injury and spinal cord injury. For several clinical applications, NSC therapies require biocompatible scaffolds to support cell survival and to direct differentiation. Here, we investigate decellularized plant tissue as a novel scaffold for three-dimensional (3D)in vitroculture of NSCs. Plant cellulose scaffolds were shown to support attachment and proliferation of adult rat hippocampal neural stem cells (NSCs). Further, NSCs differentiated on the cellulose scaffold had significant increases in their expression of neuron-specific beta-III tubulin and glial fibrillary acidic protein compared to 2D culture on a polystyrene plate, indicating that the scaffold may enhance differentiation of NSCs towards astrocytic and neuronal lineages. Our findings suggest that plant-derived cellulose scaffolds have the potential to be used in neural tissue engineering and can be harnessed to direct differentiation of NSCs.
A CRISPR-based strategy for targeted sequencing in biodiversity science
Authors: Littleford-Colquhoun Bethan , Kartzinel Tyler R. 
Published: July 2023

AbstractMany applications in molecular ecology require the ability to match specific DNA sequences from single- or mixed-species samples to a diagnostic reference library. Widely used methods for DNA barcoding and metabarcoding require PCR and amplicon sequencing to identify taxa based on target sequences, but the target-specific enrichment capabilities of CRISPR-Cas systems may offer advantages in some applications. We identified 54,837 CRISPR-Cas guide RNAs that may be useful for enriching chloroplast DNA across phylogenetically diverse plant species. We then tested a subset of 17 guide RNAsin vitroto enrich and sequence plant DNA strands ranging in size from diagnostic DNA barcodes of 1,428 bp to entire chloroplast genomes of 121,284 bp. We used an Oxford Nanopore sequencer to evaluate sequencing success based on both single- and mixed-species samples, which yielded mean on-target chloroplast sequence lengths of 5,755-11,367 bp, depending on the experiment. Single-species experiments yielded more on-target sequence reads and greater accuracy, but mixed-species experiments yielded superior coverage. Comparing CRISPR-based strategies to a widely used protocol for plant DNA metabarcoding with the chloroplasttrnL-P6 marker, we obtained a 66-fold increase in sequence length and markedly better estimates of relative abundance for a commercially prepared mixture of plant species. Future work would benefit from developing bothin vitroandin silicomethods for analyses of mixed-species samples, especially when the appropriate reference genomes for contig assembly cannot be knowna priori. Prior work developed CRISPR-based enrichment protocols for long-read sequencing and our experiments pioneered its use for plant DNA barcoding and chromosome assemblies that may have advantages over workflows that require PCR and short-read sequencing.