bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neurocognitive mechanisms of social inferences in typical and autistic adolescents
Authors: Rosenblau Gabriela , Korn Christoph W. , Dutton Abigail , Lee Daeyeol , Pelphrey Kevin A. 
Published: November 2019

AbstractBackgroundMany of our efforts in social interactions are dedicated to learning about others. Adolescents with autism have core deficits in social learning, but a mechanistic understanding of these deficits and how they relate to neural development is lacking. The current study aimed to specify how adolescents with and with autism represent and acquire social knowledge and how these processes are implemented in neural activity.MethodsTypically developing (TD) adolescents (N=26) and adolescents with autism (N=20) rated in the MR scanner how much three peers liked a variety of items and received trial-by-trial feedback about the peer’s actual preference ratings. In a separate study, we established the preferences of a new sample of adolescents (N=99), used to examine population preference structures. Using computational models, we tested whether participants in the MR study relied on preference structures during learning and how model predictions were implemented in brain activity.ResultsTD adolescents relied on average population preferences and prediction error (PE) updating. Importantly, PE updating was scaled by the similarity between items. In contrast, preferences of adolescents with autism were best described by a No-learning model that relied only on participants own preferences for each item. Model predictions were encoded in neural activity. TD adolescents encoded PEs in the putamen and adolescents with autism showed greater encoding of own preferences in the angular gyrus.ConclusionsWe specified how adolescents represent and update social knowledge during learning. Our findings indicate that adolescents with ASD rely only on their own preferences when making social inferences.
Designing combination therapies using multiple optimal controls
Authors: Sharp Jesse A , Browning Alexander P , Mapder Tarunendu , Baker Christopher M , Burrage Kevin , Simpson Matthew J 
Published: November 2019

AbstractStrategic management of populations of interacting biological species routinely requires interventions combining multiple treatments or therapies. This is important in key research areas such as ecology, epidemiology, wound healing and oncology. Despite the well developed theory and techniques for determining single optimal controls, there is limited practical guidance supporting implementation of combination therapies. In this work we use optimal control theory to calculate optimal strategies for applying combination therapies to a model of acute myeloid leukaemia. We consider various combinations of continuous and bang-bang (discrete) controls, and we investigate how the control dynamics interact and respond to changes in the weighting and form of the pay-off characterising optimality. We demonstrate that the optimal controls respond non-linearly to treatment strength and control parameters, due to the interactions between species. We discuss challenges in appropriately characterising optimality in a multiple control setting and provide practical guidance for applying multiple optimal controls. Code used in this work to implement multiple optimal controls is available on GitHub.
The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification
Authors: Pilosof Shai , Alcalá-Corona Sergio A. , Wang Tong , Kim Ted , Maslov Sergei , Whitaker Rachel , Pascual Mercedes 
Published: November 2019

AbstractAs a heritable sequence-specific adaptive immune system, CRISPR-Cas is a powerful force shaping strain diversity in host-virus systems. While the diversity of CRISPR alleles has been explored, the associated structure and dynamics of host-virus interactions have not. We explore the role of CRISPR in mediating the interplay between host-virus interaction structure and eco-evolutionary dynamics in a computational model and compare results with three empirical datasets from natural systems. We show that the structure of the networks describing who infects whom and the degree to which strains are immune, are respectively modular (containing groups of hosts and viruses that interact strongly) and weighted-nested (specialist hosts are more susceptible to subsets of viruses that in turn also infect the more generalist hosts with many spacers matching many viruses). The dynamic interplay between these networks influences transitions between dynamical regimes of virus diversification and host control. The three empirical systems exhibit weighted-nested protection networks, a pattern our theory shows is indicative of hosts able to suppress virus diversification. Previously missing from studies of microbial host-pathogen systems, the protection network plays a key role in the coevolutionary dynamics.
Uncoupling splicing from transcription using antisense oligonucleotides reveals a dual role for I exon donor splice sites in antibody class switching
Authors: Marchalot Anne , Ashi Mohamad Omar , Lambert Jean-Marie , Srour Nivine , Delpy Laurent , Le Pennec Soazig 
Published: November 2019

ABSTRACTClass switch recombination (CSR) changes antibody isotype by replacing Cμ constant exons with different constant exons located downstream on the immunoglobulin heavy (IgH) locus. During CSR, transcription through specific switch (S) regions and processing of noncoding germline transcripts (GLTs) are essential for the targeting of Activation-Induced cytidine Deaminase (AID). While CSR to IgG1 is abolished in mice lacking Iγ1 exon donor splice site (dss), many questions remain regarding the importance of I exon dss recognition in CSR. To further clarify the role of I exon dss in CSR, we first evaluated RNA polymerase II (RNA pol II) loading and chromatin accessibility in S regions after activation of mouse B cells lacking Iγ1 dss. We found that deletion of Iγ1 dss markedly reduced RNA pol II pausing and active chromatin marks in the Sγ1 region. We then challenged the post-transcriptional function of I exon dss in CSR by using antisense oligonucleotides (ASO) masking I exon dss on GLTs. Treatment of stimulated B cells with an ASO targeting Iγ1 dss, in the acceptor Sγ1 region, or Iμ dss, in the donor Sμ region, did not decrease germline transcription but strongly inhibited constitutive splicing and CSR to IgG1. Altogether, this study reveals that the recognition of I exon dss first supports RNA pol II pausing and the opening of chromatin in targeted S regions and that GLTs splicing events using constitutive I exon dss appear mandatory for the later steps of CSR, most likely by guiding AID to S regions.
Colony volatiles and substrate-borne vibrations entrain circadian rhythms and are potential mediators of social synchronization in honey bee colonies
Authors: Siehler Oliver , Bloch Guy 
Published: November 2019

AbstractInternal circadian clocks organize animal behavior and physiology and are entrained by ecologically-relevant external time-givers such as light and temperature cycles. In the highly social honey bee, social time-givers are important and can override photic entrainment, but the cues mediating social synchronization are unknown. Here we tested whether substrate-borne vibrations and hive volatiles can mediate social synchronization in honey bees. We first placed newly-emerged worker bees on the same or on a different substrate on which we placed cages with foragers entrained to ambient day- night cycles, while minimizing transfer of volatiles between cages. In the second experiment, we exposed young bees to constant airflow coming from either a free-foraging colony or a similar size control hive containing only empty combs, while minimizing transfer of substrate-borne vibrations between cages. After five days, we individually isolated each focal bee in an individual cage in an environmental chamber, and monitored locomotor activity. We repeated each experiment five times, each trail with bees from a different source colony, monitoring a total of more than 1000 bees representing diverse genotypes. We found that bees placed on the same substrate as foragers showed a stronger phase coherence; and in 3 of 5 trials their phase was more similar to that of foragers, compared to bees placed on a different substrate. In the second experiment, bees exposed to air from a colony showed a stronger phase coherence, and in 4 out of 5 trial their phase was more similar to that of foragers, compared to control bees exposed to air from an empty hive. These findings lend credence to the hypothesis that surrogates of activity such as substrate-borne vibrations, and volatile cues entrain circadian rhythms in natural free-foraging honey bee colonies.
AURKA destruction is decoupled from its activity at mitotic exit but suppresses interphase activity
Authors: Abdelbaki Ahmed , Akman H. Begum , Poteau Marion , Grant Rhys , Gavet Olivier , Guarguaglini Giulia , Lindon Catherine 
Published: November 2019

AbstractActivity of AURKA is controlled through multiple mechanisms including phosphorylation, ubiquitin-mediated degradation, and allosteric interaction with TPX2. Activity peaks at mitosis before AURKA is degraded during mitotic exit in a process strictly dependent on APC/C coactivator FZR1. We used FZR1 knockout cells (FZR1KO) and a novel FRET-based AURKA biosensor to investigate how activity is regulated in absence of destruction. We found that AURKA activity in FZR1KO cells dropped at mitotic exit as rapidly as in parental cells, despite absence of destruction. Unexpectedly, TPX2 was degraded normally in FZR1KO cells. Overexpression of an N-terminal TPX2 fragment sufficient for AURKA binding, but not degraded at mitotic exit, caused delay in AURKA inactivation. We conclude that AURKA inactivation in mitotic exit is determined not by its own degradation but by degradation of TPX2 and therefore dependent on CDC20 rather than FZR1. The biosensor revealed that FZR1 instead suppresses AURKA activity in interphase and is critically required for assembly of the interphase mitochondrial network after mitosis.
A high-quality genome assembly of the North American Song Sparrow, Melospiza melodia
Authors: Louha Swarnali , Ray David A. , Winker Kevin , Glenn Travis 
Published: November 2019

AbstractThe song sparrow, Melospiza melodia, is one of the most widely distributed species of songbirds found in North America. It has been used in a wide range of behavioral and ecological studies. This species’ pronounced morphological and behavioral diversity across populations makes it a favorable candidate in several areas of biomedical research. We have generated a high-quality de novo genome assembly of M. melodia using Illumina short read sequences from genomic and in vitro proximity-ligation libraries. The assembled genome is 978.3 Mb, with a coverage of 24.9×, N50 scaffold size of 5.6 Mb and N50 contig size of 31.7 Kb. Genes within our genome assembly are largely complete, with 87.5% full-length genes present out of a set of 4,915 universal single-copy orthologs present in most avian genomes. We annotated our genome assembly and constructed 15,086 gene models, a majority of which have high homology to related birds, Taeniopygia guttata and Junco hyemalis. In total, 83% of the annotated genes are assigned with putative functions. Furthermore, only ~7% of the genome is found to be repetitive; these regions and other non-coding functional regions are also identified. The high-quality M. melodia genome assembly and annotations we report will serve as a valuable resource for facilitating studies on genome structure and evolution that can contribute to biomedical research and serve as a reference in population genomic and comparative genomic studies of closely related species.
Semaphorin 3A binding to chondroitin sulfate E enhances the biological activity of the protein, and cross-links and rigidifies glycosaminoglycan matrices
Authors: Djerbal Lynda , Vivès Romain R. , Lopin-Bon Chrystel , Richter Ralf P. , Kwok Jessica C.F. , Lortat-Jacob Hugues 
Published: November 2019

ABSTRACTSemaphorin 3A (Sema3A) is a secreted protein that signals to cells through binding to neuropilin and plexin receptors and provides neurons with guidance cues key for axon pathfinding, and also controls cell migration in several other biological systems. Sema3A interacts with glycosaminoglycans (GAGs), an interaction that could localize the protein within tissues and involves the C-terminal domain of the protein. This domain comprises several furin cleavage sites that are processed during secretion and in previous works have hampered recombinant production of full-length wild type Sema3A, and the biochemical analysis of Sema3A interaction with GAGs. In this work, we have developed a strategy to purify the full-length protein in high yield and identified two sequences in the C-terminal domain, KRDRKQRRQR and KKGRNRR, which confer to the protein sub nM affinity for chondroitin sulfate and heparan sulfate polysaccharides. Using chemically defined oligosaccharides and solid phase binding assays, we report that Sema3A recognizes a (GlcA-GalNAc4S6S)2motif but not a (GlcA2S-GalNAc6S)2motif and is thus highly specific for type E chondroitin sulfate. Functionally, we found that Sema3A rigidified CS-E films that mimic the GAG presentation within extracellular matrices (ECMs), suggesting that Sema3A may have a previously unidentified function to cross-link and thus stabilize GAG-rich ECMs. Finally, we demonstrated that the full-length Sema3A is more potent at inhibiting neurite outgrowth than the truncated or mutant forms that were previously purified and that the GAG binding sites are required to achieve full activity. The results suggest that Sema3A can rigidify and cross-link GAG matrices, implicating Sema3A could function as an extracellular matrix organizer in addition to binding to and signaling through its cognate cell surface receptors.
On the inference of a southern origin of the North American fireflyPhotinus pyralis
Authors: Catalán Ana , Höhna Sebastian , Lower Sarah E. , Duchen Pablo 
Published: November 2019

AbstractThe fireflyPhotinus pyralisinhabits a wide range of latitudinal and ecological niches, with populations living from temperate to tropical habitats. Its ample geographic distribution makes this species an ideal system for the study of local adaptation and demographic inference of wild populations. Therefore, in this study we modelled and inferred different demographic scenarios for North American populations ofP. pyralis, collected from Texas to New Jersey. To do this, we used a combination of ABC techniques (for multi-population/colonization analyses), and likelihood inference (dadi) for single-population demographic inference, which proved useful with our RAD data.We uncovered that the most ancestral North American population lays in Texas, which further colonized the Central region of the US and more recently the North Eastern coast. Our study confidently rejects a demographic scenario where the North Eastern populations colonized more southern populations until reaching Texas. Our results suggest thatP. pyralisoriginated in Central- or South America, followed by migration events that populated northern latitudes. Finally, modelling the demographic history of North AmericanP. pyralisserves as a null model of nucleotide diversity patterns, which will inform future studies of adaptation, not only inP. pyralis, but also in other North American taxa.
Neolithic genomes reveal a distinct ancient HLA allele pool and population transformation in Europe
Authors: Immel Alexander , Rinne Christoph , Meadows John , Barquera Rodrigo , Szolek András , Pierini Federica , Susat Julian , Böhme Lisa , Dose Janina , Bonczarowska Joanna , Drummer Clara , Fuchs Katharina , Ellinghaus David , Kässens Jan Christian , Furholt Martin , Kohlbacher Oliver , Schade-Lindig Sabine , Mathieson Iain , Franke Andre , Krause Johannes , Müller Johannes , Lenz Tobias L. , Nebel Almut , Krause-Kyora Ben 
Published: November 2019

AbstractThe Wartberg culture (WBC, 3,500-2,800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We perform a genome-wide analysis of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3,300-3,200 cal. BCE). Our results highlight that the Niedertiefenbach population indeed emerged at the beginning of the WBC. This farming community was genetically heterogeneous and carried a surprisingly large hunter-gatherer ancestry component (40%). We detect considerable differences in the human leukocyte antigen gene pool between contemporary Europeans and the Niedertiefenbach individuals whose immune response was primarily geared towards defending viral infections.
Balancing cell populations endowed with a synthetic toggle switch via adaptive pulsatile feedback control
Authors: Guarino A. , Fiore D. , Salzano D. , di Bernardo M. 
Published: November 2019

AbstractControlling cells endowed with the genetic toggle switch has been suggested as a benchmark problem in synthetic biology. It has been shown that a carefully selected periodic forcing can balance a population of such cells in an undifferentiated state. The effectiveness of these control strategies, however, can be mined by the presence of stochastic perturbations and uncertainties typically observed in biological systems and is therefore not robust. Here, we propose the use of feedback control strategies to enhance robustness and performance of the balancing action by selecting in real-time both the amplitude and the duty-cycle of the inducer molecular signals affecting the toggle switch behavior. We show, via in-silico experiments and realistic agent-based simulations, the effectiveness of the proposed strategies even in presence of uncertainties and stochastic effects. In so doing, we confirm previous observations made in the literature about coherence of the population when pulsatile forcing inputs are used but, contrary to what proposed in the past, we leverage feedback control techniques to endow the balancing strategy with unprecedented robustness and stability properties. We compare via in-silico experiments different control solutions and show their advantages and limitations from an in-vivo implementation viewpoint.
Existence and functions of hypothalamic kisspeptin neuropeptide signaling system in a non-chordate deuterostome species
Authors: Wang Tianming , Cao Zheng , Shen Zhangfei , Yang Jingwen , Chen Xu , Yang Zhen , Xu Ke , Xiang Xiaowei , Yu Qiuhan , Song Yimin , Wang Weiwei , Tian Yanan , Sun Lina , Zhang Libin , tGuo Su , Zhou Naiming 
Published: November 2019

AbstractThe kisspeptin (Kp) system is a central modulator of the hypothalamic-pituitary-gonadal axis in vertebrates. Its existence outside the vertebrate lineage remains largely unknown. Here we report the identification and characterization of Kp system in the sea cucumber Apostichopus japonicus. The gene encoding the Kp precursor, generates two mature neuropeptides, AjKiss1a and AjKiss1b. The Kp receptors, AjKissR1 and AjKissR2, are strongly activated by synthetic A. japonicus and vertebrate Kps, triggering a rapid intracellular mobilization of Ca2+, followed by receptor internalization. AjKissR1 and AjKissR2 share similar intracellular signaling pathways via Gαq/PLC/PKC/MAPK cascade, when activated by C-terminal decapeptide (AjKiss1b-10). The A. japonicus Kp system functions in mutiple tissues which are closely related to reproduction and metabolism. Overall, our findings uncover for the first time, to our knowledge, the existence and function of the Kp system in a non-chordate species and provide new evidence to support the ancient origin of the hypothalamic neurosecretory system.
Transcriptional activation of cyclin D1 via HER2/HER3 contributes to cell survival and EGFR tyrosine kinase inhibitor resistance in non-small cell lung carcinoma
Authors: Liu Bin , Chen Deng , Chen Shipeng , Saber Ali , Haisma Hidde 
Published: November 2019

AbstractSeveral different mechanisms are implicated in the resistance of lung cancer cells to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), and only few have been functionally investigated. Here, using genetically knocked out EGFR and TKI-resistant lung cancer cells, we show that loss of wild-type EGFR attenuates cell proliferation, migration and 3D-spherid formation, whereas loss of mutant EGFR or resistance to TKIs reinforces those processes. Consistently, disruption of wild-type EGFR leads to suppression of HER2/HER3, while mutant EGFR ablation or resistance to TKIs increases HER2/HER3 expression, compensating for EGFR loss. Furthermore, HER2/HER3 nuclear translocation mediates overexpression of cyclin D1, leading to tumor cell survival and drug resistance. Cyclin D1/CDK4/6 inhibition resensitizes erlotinib-resistant (ER) cells to erlotinib. Analysis of cyclin D1 expression in patients with non-small cell lung carcinoma (NSCLC) showed that its expression is negatively associated with overall survival and disease-free survival. Our results provide biological and mechanistic insights into targeting EGFR and TKI resistance.
Bulk and single-molecule analysis of a novel DNA2-like helicase-nuclease reveals a single-stranded DNA looping motor
Authors: Wilkinson O.J. , Carrasco C. , Aicart-Ramos C. , Moreno-Herrero F. , Dillingham M.S. 
Published: November 2019

ABSTRACTDNA2 is an essential enzyme involved in DNA replication and repair in eukaryotes. In a search for homologues of this protein, we identified and characterisedGeobacillus stearothermophilusBad, a novel bacterial DNA helicase-nuclease with similarity to human DNA2. We show that Bad contains an Fe-S cluster and identify four cysteine residues that are likely to co-ordinate the cluster by analogy to DNA2. The purified enzyme specifically recognises ss-dsDNA junctions and possesses ssDNA-dependent ATPase, ssDNA binding, ssDNA endonuclease, 5’ to 3’ ssDNA translocase and 5’ to 3’ helicase activity. Single molecule analysis reveals that Bad is a highly processive DNA motor capable of moving along DNA for distances of more than 4 kbp at a rate of ∼200 base pairs per second at room temperature. Interestingly, as reported for the homologous human and yeast DNA2 proteins, the DNA unwinding activity of Bad is cryptic and can be unmasked by inactivating the intrinsic nuclease activity. Strikingly, our experiments also show that the enzyme loops DNA while translocating, which is an emerging feature of highly processive DNA unwinding enzymes. The bacterial Bad enzymes will provide an excellent model system for understanding the biochemical properties of DNA2-like helicase-nucleases and DNA looping motor proteins in general.