bluuebunny/crossref_metadata_2025_split huggingface dataset:
ICEs are the main reservoirs of the ciprofloxacin-modifyingcrpPgene inPseudomonas aeruginosa
Authors: Botelho João , Grosso Filipa , Peixe Luísa 
Published: March 2020

AbstractThe ciprofloxacin-modifyingcrpPgene was recently identified in a plasmid isolated from a clinicalPseudomonas aeruginosaclinical isolate. Homologues of this gene were also identified inEscherichia coli, Klebsiella pneumoniaeandAcinetobacter baumannii. We set out to explore the mobile genetic elements involved in the acquisition and spread of this gene in publicly available and complete genomes ofPseudomonas. ThecrpPgene was identified only inP. aeruginosa, in more than half of the complete chromosomes (61.9%, n=133/215) belonging to 52 sequence types, of which the high-risk clone ST111 was the most frequent. We identified 136crpP-harboring ICEs, with 93.4% belonging to the mating-pair formation G (MPFG) family. The ICEs were integrated at the end of a tRNALysgene and were all flanked by highly conserved 45-bp direct repeats. The core ICEome contains 26 genes (2.2% of all genes), which are present in 99% or more of thecrpP-harboring ICEs. The most frequently encoded traits on these ICEs include replication, transcription, intracellular trafficking and cell motility. Our work reveals that ICEs are the main vectors promoting the dissemination of the ciprofloxacin-modifyingcrpPgene inP. aeruginosa.Author NotesAll supporting data has been provided within the article or through supplementary data files. Supplementary material is available with the online version of this article.Impact StatementA high proportion ofPseudomonas aeruginosaclinical isolates are resistant to ciprofloxacin. Resistance to this antibiotic is often mediated by chromosomal mutations, but recently horizontally transferred genes have been identified. We assessed the repartition of the ciprofloxacin-modifyingcrpPgene amongPseudomonasgenomes and we characterized the mobile elements associated with its acquisition. We found that this gene is prevalent inP. aeruginosaand frequently associated with integrative and conjugative elements (ICEs). Importantly, we also identified highly conserved direct repeats that can be used to accurately delimitcrpP-carrying ICEs inP. aeruginosagenomes.Data SummaryAll the bacterial genomes scanned in this study have been deposited previously in the National Center for Biotechnology Information genome database and are listed on the supplementary tables. The newick files used to create the trees in Figures 1 and 4 are deposited on figshare athttps://figshare.com/projects/ICEs_are_the_main_reservoirs_of_the_ciprofloxacin-modifying_crpP_gene_in_Pseudomonas_aeruginosa/79308.
Measuring site-specific glycosylation similarity between influenza A virus variants with statistical certainty
Authors: Chang Deborah , Hackett William E. , Zhong Lei , Wan Xiu-Feng , Zaia Joseph 
Published: March 2020

AbstractInfluenza A virus (IAV) mutates rapidly, resulting in antigenic drift and poor year-to-year vaccine effectiveness. One challenge in designing effective vaccines is that genetic mutations frequently cause amino acid variations in IAV envelope protein hemagglutinin (HA) that create newN-glycosylation sequons; resultingN-glycans cause antigenic shielding, allowing viral escape from adaptive immune responses. Vaccine candidate strain selection currently involves correlating antigenicity with HA protein sequence among circulating strains, but quantitative comparison of site-specific glycosylation information may likely improve the ability to design vaccines with broader effectiveness against evolving strains. However, there is poor understanding of the influence of glycosylation on immunodominance, antigenicity, and immunogenicity of HA, and there are no well-tested methods for comparing glycosylation similarity among virus samples. Here, we present a method for statistically rigorous quantification of similarity between two related virus strains that considers the presence and abundance of glycopeptide glycoforms. We demonstrate the strength of our approach by determining that there was a quantifiable difference in glycosylation at the protein level between wild-type IAV HA from A/Switzerland/9715293/2013 (SWZ13) and a mutant strain of SWZ13, even though noN-glycosylation sequons were changed. We determined site-specifically that WT and mutant HA have varying similarity at the glycosylation sites of the head domain, reflecting competing pressures to evade host immune response while retaining viral fitness. To our knowledge, our results are the first to quantify changes in glycosylation state that occur in related proteins of considerable glycan heterogeneity. Our results provide a method for understanding how changes in glycosylation state are correlated with variations in protein sequence, which is necessary for improving IAV vaccine strain selection. Understanding glycosylation will be especially important as we find new expression vectors for vaccine production, as glycosylation state depends greatly on the host species.
Caenorhabditis elegansnematodes are not attracted to the terrestrial isopodPorcellio scaber
Authors: Archer Heather , Deiparine Selina , Andersen Erik C. 
Published: March 2020

ABSTRACTPhoresy is a behavior in which an organism, the phoront, travels from one location to another by ‘hitching a ride’ on the body of a host as it disperses. Some phoronts are generalists, taking advantage of any available host. Others are specialists and travel only when specific hosts are located using chemical cues to identify and move (chemotax) toward the preferred host. Free-living nematodes, likeCaenorhabditis elegans, are often found in natural environments that contain terrestrial isopods and other invertebrates. Additionally, theC. eleganswild strain PB306 was isolated associated with the isopodPorcellio scaber. However, it is currently unclear ifC. elegansis a phoront of terrestrial isopods, and if so, whether it is a specialist, generalist, or developmental stage-specific combination of both strategies. Because the relevant chemical stimuli might be secreted compounds or volatile odorants, we used different types of chemotaxis assays across diverse extractions of compounds or odorants to test whetherC. elegansis attracted toP. scaber. We show that two different strains – the wild isolate PB306 and the laboratory-adapted strain N2 – are not attracted toP. scaberduring either the dauer or adult life stages. Our results indicate thatC. eleganswas not attracted to chemical compounds or volatile odorants fromP. scaber, providing valuable empirical evidence to suggest that any associations between these two species are likely opportunistic rather than specific phoresy.
Injectable Nanoelectrodes Enable Wireless Deep Brain Stimulation of Native Tissue in Freely Moving Mice
Authors: Kozielski Kristen L. , Jahanshahi Ali , Gilbert Hunter B. , Yu Yan , Erin Önder , Francisco David , Alosaimi Faisal , Temel Yasin , Sitti Metin 
Published: March 2020

AbstractDevices that electrically modulate the central nervous system have enabled important breakthroughs in the management of neurological and psychiatric disorders. Such devices typically have centimeter-scale dimensions, requiring surgical implantation and wired-in powering. Using smaller, remotely powered materials could lead to less invasive neuromodulation. Herein, we present injectable magnetoelectric nanoelectrodes that wirelessly transmit electrical signals to the brain in response to an external magnetic field. Importantly, this mechanism of modulation requires no genetic modification of the brain, and allows animals to freely move during stimulation. Using these nanoelectrodes, we demonstrate neuronal modulationin vitroand in deep brain targetsin vivo. We also show that local thalamic modulation promotes modulation in other regions connected via basal ganglia circuitry, leading to behavioral changes in mice. Magnetoelectric materials present a versatile platform technology for less invasive, deep brain neuromodulation.
Assessment of mapping strategies for determining the 5□-end of mRNAs and long-noncoding RNAs with short read sequences
Authors: Noguchi Shuhei , Kawaji Hideya , Kasukawa Takeya 
Published: March 2020

AbstractBackgroundGenome mapping is an essential step in data processing for transcriptome analysis, and many previous studies have evaluated various methods and strategies for mapping RNA-seq data. Cap Analysis of Gene Expression (CAGE) is a sequencing-based protocol particularly designed to capture the 5□-ends of transcripts for quantitatively measuring the expression levels of transcription start sites genome-wide. Because CAGE analysis can also predict the activities of promoters and enhancers, this protocol has been an essential tool in studies of transcriptional regulation. Typically, the same mapping software is used to align both RNA-seq data and CAGE reads to a reference genome, but which mapping software and options are most appropriate for mapping the 5□-end sequence reads obtained through CAGE has not previously been evaluated systematically.ResultsHere we assessed various strategies for aligning CAGE reads, particularly ∼50-bp sequences, with the human genome by using the HISAT2, LAST, and STAR programs both with and without a reference transcriptome. One of the major inconsistencies among the tested strategies involves alignments to pseudogenes and parent genes: some of the strategies prioritized alignments with pseudogenes even when the read could be aligned with coding genes with fewer mismatches. Another inconsistency concerned the detection of exon-exon junctions. These preferences depended on the program applied and whether a reference transcriptome was included. Overall, the choice of strategy yielded different mapping results for approximately 2% of all promoters.ConclusionsAlthough the various alignment strategies produced very similar results overall, we noted several important and measurable differences. In particular, using the reference transcriptome in STAR yielded alignments with the fewest mismatches. In addition, the inconsistencies among the strategies were especially noticeable regarding alignments to pseudogenes and novel splice junctions. Our results indicate that the choice of alignment strategy is important because it might affect the biological interpretation of the data.
Expression of FoxP2 in the Basal Ganglia Regulates Vocal Motor Sequences in the Adult Songbird
Authors: Xiao Lei , Merullo Devin P. , Cao Mou , Co Marissa , Kulkarni Ashwinikumar , Konopka Genevieve , Roberts Todd F. 
Published: March 2020

SUMMARYDisruption of the transcription factor FoxP2, which is enriched in the basal ganglia, impair vocal development in humans and songbirds. The basal ganglia are essential for the selection and sequencing of motor actions, but the circuit mechanisms governing accurate sequencing of learned vocalizations are unknown. Here, we show expression of FoxP2 in the basal ganglia is vital for the fluent initiation and termination of birdsong, and the maintenance of song syllable sequencing in adulthood. Knockdown of FoxP2 imbalances dopamine receptor expression across striatal direct-like and indirect-like pathways, suggesting a role of dopaminergic signaling in regulating vocal-motor sequencing. Confirming this prediction, we show that phasic dopamine activation, and not inhibition, during singing drives repetition of song syllables, thus also impairing fluent initiation and termination of birdsong. These findings demonstrate discrete circuit origins for the dysfluent repetition of vocal elements, a phenotype commonly observed in speech disorders.
Human dorsal anterior cingulate neurons signal conflict by amplifying task-relevant information
Authors: Ebitz R. Becket , Smith Elliot H. , Horga Guillermo , Schevon Catherine A. , Yates Mark J. , McKhann Guy M. , Botvinick Matthew M. , Sheth Sameer A. , Hayden Benjamin Y. 
Published: March 2020

SUMMARYHemodynamic activity in dorsal anterior cingulate cortex (dACC) correlates with conflict, suggesting it contributes to conflict processing. This correlation could be explained by multiple neural processes that can be disambiguated by population firing rates patterns. We usedtargeted dimensionality reductionto characterize activity of populations of single dACC neurons as humans performed a task that manipulates two forms of conflict. Although conflict enhanced firing rates, this enhancement did not come from a discrete population of domain-general conflict-encoding neurons, nor from a distinct conflict-encoding response axis. Nor was it the epiphenomenal consequence of simultaneous coactivation of action plans. Instead, conflict amplified the task-relevant information encoded across the neuronal population. Effects of conflict were weaker and more heterogeneous in the dorsolateral prefrontal cortex (dlPFC), suggesting that dACC’s role in conflict processing may be somewhat specialized. Overall, these results support the theory that conflict biases competition between sensorimotor transformation processes occurring in dACC.
Development of A Novel Highly Selective TLR8 Agonist for Cancer Immunotherapy
Authors: Wang Yuxun , Yang Heping , Li Huanping , Zhao Shuda , Zeng Yikun , Zhang Panpan , Lin Xiaoqin , Sun Xiaoxiang , Wang Longsheng , Fu Guangliang , Gao Yaqiao , Wang Pei , Gao Daxin 
Published: March 2020

ABSTRACTToll-like receptors (TLRs) are a family of proteins that recognize pathogen associated molecular patterns (PAMPs). Their primary function is to activate innate immune responses while also involved in facilitating adaptive immune responses. Different TLRs exert distinct functions by activating varied immune cascades. Several TLRs are being pursued as cancer drug targets. We discovered a novel, highly potent and selective small molecule TLR8 agonist DN052. DN052 exhibited strong in vitro cellular activity with EC50 at 6.7 nM and was highly selective for TLR8 over other TLRs including TLR4, 7 and 9. The selectivity profile distinguished DN052 from all other TLR agonists currently in clinical development. DN052 displayed excellent in vitro ADMET and in vivo PK profiles. DN052 potently inhibited tumor growth as a single agent. Moreover, combination of DN052 with the immune checkpoint inhibitor, selected targeted therapeutics or chemotherapeutic drugs further enhanced efficacy of single agents. Mechanistically, treatment with DN052 resulted in strong induction of pro-inflammatory cytokines in ex vivo human PBMC assay and in vivo monkey study. GLP toxicity studies in rats and monkeys demonstrated favorable safety profile. This led to the advancement of DN052 into phase I clinical trials.
Lipid availability influences the metabolic maturation of human pluripotent stem cell-derived cardiomyocytes
Authors: Zhang Hui , Badur Mehmet G. , Spiering Sean , Divakaruni Ajit , Meurs Noah E. , Yu Michael S. , Colas Alexandre R. , Murphy Anne N. , Mercola Mark , Metallo Christian M. 
Published: March 2020

AbstractObjectivesPluripotent stem cell-derived cardiomyocytes are phenotypically immature, which limits their utility in downstream applications. Metabolism is dramatically reprogramed during cardiac maturationin vivoand presents a potential avenue to drivein vitromaturation. We aimed to identify and address metabolic bottlenecks in the generation of human pluripotent stem cell (hPSC)-derived cardiomyocytes.MethodshPSCs were differentiated into cardiomyocytes using an established, chemically-defined differentiation protocol. We applied 13C metabolic flux analysis (MFA) and targeted transcriptomics to characterize cardiomyocyte metabolism in during differentiation in the presence or absence of exogenous lipids.ResultshPSC-derived cardiomyocytes induced some cardiometabolic pathways (i.e. ketone body and branched-chain amino acid oxidation) but failed to effectively activate fatty acid oxidation. MFA studies indicated that lipid availability in cultures became limited during differentiation, suggesting potential issues with nutrient availability. Exogenous supplementation of lipids improved cardiomyocyte morphology, mitochondrial function, and promoted increased fatty acid oxidation in hPSC-derivatives.ConclusionhPSC-derived cardiomyocytes are dependent upon exogenous sources of lipids for metabolic maturation. Proper supplementation removes a potential roadblock in the generation of metabolically mature cardiomyocytes. These studies further highlight the importance of considering and exploiting metabolic phenotypes in thein vitroproduction and utilization of functional hPSC-derivatives.
Biochemical computation underlying behavioral decision-making
Authors: Thornquist Stephen C. , Pitsch Maximilian J. , Auth Charlotte S. , Crickmore Michael A. 
Published: March 2020

AbstractComputations in the brain are broadly assumed to emerge from patterns of fast electrical activity. Challenging this view, we show that a male fly’s decision to persist in mating, even through a potentially lethal threat, hinges on biochemical computations that enable processing over minutes to hours. Each neuron in a recurrent network measuring time into mating contains slightly different internal molecular estimates of elapsed time. Protein Kinase A (PKA) activity contrasts this internal measurement with input from the other neurons to represent evidence that the network’s goal has been achieved. When consensus is reached, PKA pushes the network toward a large-scale and synchronized burst of calcium influx, which we call an eruption. The eruption functions like an action potential at the level of the network, transforming deliberation within the network into an all-or-nothing output, after which the male will no longer sacrifice his life to continue mating. We detail the continuous transformation between interwoven molecular and electrical information over long timescales in this system, showing how biochemical activity, invisible to most large scale recording techniques, is the key computational currency directing a life-or-death decision.
RRE-Finder: A Genome-Mining Tool for Class-Independent RiPP Discovery
Authors: Kloosterman Alexander M. , Shelton Kyle E. , van Wezel Gilles P. , Medema Marnix H. , Mitchell Douglas A. 
Published: March 2020

AbstractNearly half of the classes of natural products known as ribosomally synthesized and post-translationally modified peptides (RiPPs) are reliant on a protein domain called the RiPP recognition element (RRE) for peptide maturation. The RRE binds specifically to a linear precursor peptide and directs the post-translational modification enzymes to their substrate. Given its prevalence across various types of RiPP biosynthetic gene clusters (BGCs), the RRE could theoretically be used as a bioinformatic handle to identify novel classes of RiPPs. In addition, due to the high affinity and specificity of most RRE:precursor peptide complexes, a thorough understanding of the RRE domain could be exploited for biotechnological applications. However, sequence divergence of the RRE domain across RiPP classes has precluded automated identification of RREs based solely on sequence similarity. Here, we introduce RRE-Finder, a novel tool for identifying RRE domains with high sensitivity. RRE-Finder can be used in “precision” mode to confidently identify RREs in a class-specific manner or in “exploratory” mode, which was designed to assist in the discovery of novel RiPP classes. RRE-Finder operating in precision mode on the UniProtKB protein database retrieved over 30,000 high-confidence RREs spanning all characterized RRE-dependent RiPP classes, as well as several yet-uncharacterized RiPP, putatively novel gene cluster architectures that will require future experimental work. Finally, RRE-Finder was used in precision mode to explore a possible evolutionary origin of the RRE domain. Altogether, RRE-Finder provides a powerful new method to probe RiPP biosynthetic diversity and delivers a rich dataset of RRE sequences that will provide a foundation for deeper biochemical studies into this intriguing and versatile protein domain.
Learning to Control the Brain through Adaptive Closed-Loop Patterned Stimulation
Authors: Tafazoli Sina , MacDowell Camden J. , Che Zongda , Letai Katherine C. , Steinhardt Cynthia , Buschman Timothy J. 
Published: March 2020

AbstractStimulation of neural activity is an important scientific and clinical tool, causally testing hypotheses and treating neurodegenerative and neuropsychiatric diseases. However, current stimulation approaches cannot flexibly control the pattern of activity in populations of neurons. To address this, we developed an adaptive, closed-loop stimulation (ACLS) system that uses patterned, multi-site electrical stimulation to control the pattern of activity in a population of neurons. Importantly, ACLS is a learning system; it monitors the response to stimulation and iteratively updates the stimulation pattern to produce a specific neural response.In silicoandin vivoexperiments showed ACLS quickly learns to produce specific patterns of neural activity (∼15 minutes) and was robust to noise and drift in neural responses. In visual cortex of awake mice, ACLS learned electrical stimulation patterns that produced responses similar to the natural response evoked by visual stimuli. Similar to how repetition of a visual stimulus causes an adaptation in the neural response, the response to electrical stimulation was adapted when it was preceded by the associated visual stimulus. Altogether, our results show ACLS can learn, in real-time, to generate specific patterns of neural activity, providing a framework for using closed-loop learning to control neural activity.
Unbiased homeologous recombination during pneumococcal transformation allows for multiple chromosomal integration events
Authors: Kurushima Jun , Campo Nathalie , van Raaphorst Renske , Cerckel Guillaume , Polard Patrice , Veening Jan-Willem 
Published: March 2020

AbstractThe rapid spread of antimicrobial resistance and vaccine escape in the opportunistic human pathogenStreptococcus pneumoniaecan be largely attributed to competence-induced transformation. To better understand the dynamics of competence-induced transformation, we studied this process at the single-cell level. We show that within isogenic populations, all cells become naturally competent and bind exogenous DNA. In addition, we find that transformation is highly efficient and that the chromosomal location of the integration site or whether the transformed gene is encoded on the leading or lagging strand has limited influence on recombination efficiency. Indeed, we have observed multiple recombination events in single recipients in real-time. However, because of saturation of the DNA uptake and integration machinery and because a single stranded donor DNA replaces the original allele, we find that transformation efficiency has an upper threshold of approximately 50% of the population. Counterintuitively, in the presence of multiple transforming DNAs, the fraction of untransformed cells increases to more than 50%. The fixed mechanism of transformation results in a fail-safe strategy for the population as half of the population generally keeps an intact copy of the original genome. Together, this work advances our understanding of pneumococcal genome plasticity.