bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct roles for dopamine clearance mechanisms in regulating behavioral flexibility
Authors: Korn Clio , Akam Thomas , Jensen Kristian HR , Vagnoni Cristiana , Huber Anna , Tunbridge Elizabeth M , Walton Mark E 
Published: October 2019

AbstractDopamine plays a crucial role in adaptive behavior, and dysfunctional dopamine is implicated in multiple psychiatric conditions characterized by inflexible or inconsistent choices. However, the precise relationship between dopamine and flexible decision making remains unclear. One reason is that, while many studies have focused on the activity of dopamine neurons, efficient dopamine signaling also relies on clearance mechanisms, notably the dopamine transporter (DAT), which predominates in striatum, and catechol-O-methyltransferase (COMT), which predominates in cortex. The exact locus, extent, and timescale of the effects of DAT and COMT are uncertain. Moreover, there is limited data on how acute disruption of either mechanism affects flexible decision making strategies mediated by cortico-striatal networks. To address these issues, we combined pharmacological modulation of DAT and COMT with electrochemistry and behavior in mice. DAT blockade, but not COMT inhibition, regulated sub-second dopamine release in the nucleus accumbens core, but surprisingly neither clearance mechanism affected evoked release in prelimbic cortex. This was not due to a lack of sensitivity, as both amphetamine and atomoxetine changed the kinetics of sub-second release. In a multi-step decision making task where mice had to respond to reversals in either reward probabilities or the choice sequence to reach the goal, DAT blockade selectively impaired, and COMT inhibition improved, performance after reward reversals, but neither manipulation affected the adaptation of choices after actionstate transition reversals. Together, our data suggest that DAT and COMT shape specific aspects of behavioral flexibility by regulating striatal and cortical dopamine, respectively, at fast and slow timescales.
Messenger RNAs with large numbers of upstream ORFs are translated via leaky scanning and reinitiation in the asexual stages ofPlasmodium falciparum
Authors: Kaur Chhaminder , Kumar Mayank , Patankar Swati 
Published: October 2019

AbstractThe genome ofPlasmodium falciparumhas one of the most skewed base pair compositions of any eukaryote, with an AT content of 80-90%. As start and stop codons are AT-rich, the probability of finding upstream open reading frames (uORFs) in messenger RNAs (mRNAs) is high and parasite mRNAs have an average of 10 uORFs in their leader sequences. Similar to other eukaryotes, uORFs repress the translation of the downstream gene (dORF) inP. falciparum, yet the parasite translation machinery is able to bypass these uORFs and reach the dORF to initiate translation. This can happen by leaky scanning and/or reinitiation.In this report, we assessed leaky scanning and reinitiation by studying the effect of uORFs on the translation of a dORF, in this case the luciferase reporter gene, and showed that both mechanisms are employed in the asexual blood stages ofP. falciparum. Furthermore, in addition to codon usage of the uORF, translation of the dORF is governed by the Kozak sequence and length of the uORF, and inter-cistronic distance between the uORF and dORF. Based on these features whole genome data was analyzed to uncover classes of genes that might be regulated by uORFs. This study indicates that leaky scanning and reinitiation appear to be widespread in asexual stages ofP. falciparum, which may require modifications of existing factors that are involved in translation initiation in addition to novel, parasite-specific proteins.
Tumor neoantigen heterogeneity thresholds provide a time window for combination immunotherapy
Authors: Aguadé-Gorgorió Guim , Solé Ricard 
Published: October 2019

Following the advent of immunotherapy as a possible cure for cancer, remarkable insight has been gained on the role of mutational load and neoantigens as key ingredients in T cell recognition of malignancies. However, not all highly mutational tumors react to immune therapies, and even initial success is often followed by eventual relapse. Recent research points out that high heterogeneity in the neoantigen landscape of a tumor might be key in understanding the failure of immune surveillance. In this work we present a mathematical framework able to describe how neoantigen distributions shape the immune response. Modeling T cell reactivity as a function of antigen dominancy and distribution across a tumor indicates the existence of a diversity threshold beyond which T cells fail at controling heterogeneous cancer growth. Furthemore, an analytical estimate for the evolution of average antigen clonality indicates rapid increases in epitope heterogeneity in early malignancy growth. In this scenario, we propose that therapies targeting the tumor prior to immunotherapy can reduce neoantigen heterogeneity, and postulate the existence of a time window, before tumor relapse due to de novo resistance, rendering immunotherapy more effective.Major FindingsGenetic heterogeneity affects the immune response to an evolving tumor by shaping the neoantigen landscape of the cancer cells, and highly heterogeneous tumors seem to escape T cell recognition. Mathematical modeling predicts the existence of a well defined neoantigen diversity threshold, beyond which lymphocites are not able to counteract the growth of a population of highly heterogeneous subclones. Furthermore, evolutionary dynamics predict a fast decay of neoantigen clonality, rendering advanced tumors hard to attack at the time of immunotherapy. Within this mathematical framework we propose that targeted therapy forcing a selective pressure for resistance might as well increase neoantigen homogeneity, providing a novel possibility for combination therapy.
Interconversion between Anticipatory and Active GID E3 Ubiquitin Ligase Conformations via Metabolically Driven Substrate Receptor Assembly
Authors: Qiao Shuai , Langlois Christine R. , Chrustowicz Jakub , Sherpa Dawafuti , Karayel Ozge , Hansen Fynn M. , Beier Viola , von Gronau Susanne , Bollschweiler Daniel , Schäfer Tillman , Alpi Arno F. , Mann Matthias , Prabu J. Rajan , Schulman Brenda A. 
Published: October 2019

SUMMARYCells respond to environmental changes by toggling metabolic pathways, preparing for homeostasis, and anticipating future stresses. For example, inSaccharomyces cerevisiae, carbon stress-induced gluconeogenesis is terminated upon glucose availability, a process that involves the multiprotein E3 ligase, GIDSR4, recruiting N-termini and catalyzing ubiquitylation of gluconeogenic enzymes. Here, genetics, biochemistry, and cryo electron microscopy define molecular underpinnings ofglucose-induceddegradation. Unexpectedly, carbon stress induces an inactive anticipatory complex (GIDAnt), which awaits a glucose-induced substrate receptor to form the active GIDSR4. Meanwhile, other environmental perturbations elicit production of an alternative substrate receptor assembling into a related E3 ligase complex. The intricate structure of GIDAntenables anticipating and ultimately binding various N-degron targeting (i.e. “N-end rule”) substrate receptors, while the GIDSR4E3 forms a clamp-like structure juxtaposing substrate lysines with the ubiquitylation active site. The data reveal evolutionarily conserved GID complexes as a family of multisubunit E3 ubiquitin ligases responsive to extracellular stimuli.
SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences from Reference Genomes
Authors: Xing Yue , Dabney Alan R. , Li Xiao , Wang Guosong , Gill Clare A. , Casola Claudio 
Published: October 2019

AbstractCopy number variants are insertions and deletions of 1 kb or larger in a genome that play an important role in phenotypic changes and human disease. Many software applications have been developed to detect copy number variants using either whole-genome sequencing or whole-exome sequencing data. However, there is poor agreement in the results from these applications. Simulated datasets containing copy number variants allow comprehensive comparisons of the operating characteristics of existing and novel copy number variant detection methods. Several software applications have been developed to simulate copy number variants and other structural variants in whole-genome sequencing data. However, none of the applications reliably simulate copy number variants in whole-exome sequencing data. We have developed and tested SECNVs (Simulator of Exome Copy Number Variants), a fast, robust and customizable software application for simulating copy number variants and whole-exome sequences from a reference genome. SECNVs is easy to install, implements a wide range of commands to customize simulations, can output multiple samples at once, and incorporates a pipeline to output rearranged genomes, short reads and BAM files in a single command. Variants generated by SECNVs are detected with high sensitivity and precision by tools commonly used to detect copy number variants. SECNVs is publicly available at https://github.com/YJulyXing/SECNVs.
Annual Cycle Dampening and the Decrease Predictability of Water Level Fluctuations in a Dam-Regulated Neotropical Floodplain
Authors: Zanon Jaques Everton 
Published: October 2019

AbstractThe flood pulse concept refers to seasonal variations in river water level and is the driving force in river-floodplain systems that ‘responsible for the existence, productivity and interactions’ of these system’s biota. This seasonal variation is inherent to river-floodplain systems and establishes a natural pattern of these ecosystems that has frequently been observed in nature. One particular river-floodplain system of interest is the Upper Parana River and its floodplain, whose upstream contains a reservoir cascade that caused profound alterations on its flooding regime by having diminished flood magnitude, but increased its frequency. In this study, I sought to explore the flood pulse condition in the Upper Paraná River Floodplain by using a set of state-of-the-art spectral and non-linear analyses and a time series of water level fluctuations (1968-2017) from this system. I divided the data into four periods: i) natural regime period, ii) transitional period, iii) dam cascade period, and iv) Primavera’s dam period. Spectral analysis demonstrated a decrease in the annual cycle amplitude, reflected in its power spectrum, which means a weakening in the difference between flood and drought events. Additionally, nonlinear dynamical analysis revealed a less deterministic and predicable behavior leading to more erratic fluctuations jeopardizing the temporal heterogeneity of that system.
Study on the efficacy of dsRNAs with increasing length in RNAi-based silencing of the Fusarium CYP51 genes
Authors: Höfle L , Shrestha A , Werner B , Jelonek L , Koch A 
Published: October 2019

AbstractPreviously, we have demonstrated that transgenic Arabidopsis and barley plants, expressing a 791 nucleotide (nt) dsRNA (CYP3RNA) that targets all three CYP51 genes (FgCYP51A, FgCYP51B, FgCYP51C) in Fusarium graminearum (Fg), inhibited fungal infection via a process designated as host-induced gene silencing (HIGS). More recently, we have shown that spray applications of CYP3RNA also protect barley from fungal infection via a process termed spray-induced gene silencing (SIGS). Thus, RNAi technology may have the potential to revolutionize plant protection in agriculture. Therefore, successful field application will require optimization of RNAi design necessary to maximize the efficacy of the RNA silencing construct for making RNAi-based strategies a realistic and sustainable approach.Previous studies indicate that silencing is correlated with the number of siRNAs generated from a dsRNA precursor. To prove the hypothesis that silencing efficiency is correlated with the number of siRNAs processed out of the dsRNA precursor, we tested in a HIGS and SIGS approach dsRNA precursors of increasing length ranging from 400 nt to 1500 nt to assess gene silencing efficiency of individual FgCYP51 genes. Concerning HIGS-mediated disease control, we found that there is no significant correlation between the length of the dsRNA precursor and the reduction of Fg infection on CYP51-dsRNA expressing Arabidopsis plants. Importantly and in clear contrast to HIGS, we measured a decrease in SIGS-mediated Fg disease resistance that significantly correlates with the length of the dsRNA construct that was sprayed, indicating that the size of the dsRNA interferes with a sufficient uptake of dsRNAs by the fungus.
A High-throughput Screening Method to Identify Proteins Involved in Unfolded Protein Response Signaling in Plants
Authors: Alcântara André , Seitner Denise , Navarrete Fernando , Djamei Armin 
Published: October 2019

AbstractBackgroundThe unfolded protein response (UPR) is a highly conserved process in eukaryotic organisms that plays a crucial role in adaptation and development. While the most ubiquitous components of this pathway have been characterized, current efforts are focused on identifying and characterizing other UPR factors that play a role in specific conditions, such as developmental changes, abiotic cues, and biotic interactions. Considering the central role of protein secretion in plant pathogen interactions, there has also been a recent focus on understanding how pathogens manipulate their host’s UPR to facilitate infection.ResultsWe developed a high-throughput screening assay to identify proteins that interfere with UPR signalingin planta. A set of 35 genes from a library of secreted proteins from the maize pathogenUstilago maydiswere transiently co-expressed with a reporter construct that upregulates enhanced yellow fluorescent protein (eYFP) expression upon UPR stress inNicotiana benthamianaplants. After UPR stress induction, leaf discs were placed in 96 well plates and eYFP expression was measured. This allowed us to identify a previously undescribed fungal protein that inhibits plant UPR signaling, which was then confirmed using the classical but more laborious qRT-PCR method.ConclusionsWe have established a rapid and reliable fluorescence-based method to identify heterologously expressed proteins involved in UPR stress in plants. This system can be used for initial screens with libraries of proteins and potentially other molecules to identify candidates for further validation and characterization.
Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases
Authors: Hu Zheng , Li Zan , Ma Zhicheng , Curtis Christina 
Published: October 2019

AbstractMetastasis is the primary cause of cancer-related deaths, but the natural history, clonal evolution and impact of treatment are poorly understood. We analyzed exome sequencing data from 457 paired primary tumor and metastatic samples from 136 breast, colorectal and lung cancer patients, including untreated (n=99) and treated (n=100) metastatic tumors. Treated metastases often harbored private ‘driver’ mutations whereas untreated metastases did not, suggesting that treatment promotes clonal evolution. Polyclonal seeding was common in untreated lymph node metastases (n=17/29, 59%) and distant metastases (n=20/70, 29%), but less frequent in treated distant metastases (n=9/94, 10%). The low number of metastasis-private clonal mutations is consistent with early metastatic seeding, which we estimated commonly occurred 2-4 years prior to diagnosis across these cancers. Further, these data suggest that the natural course of metastasis is selectively relaxed relative to early tumor development and that metastasis-private mutations are not drivers of cancer spread but instead associated with drug resistance.
Modular protein-oligonucleotide signal exchange
Authors: Agrawal Deepak K. 
Published: October 2019

ABSTRACTThe ability to detect a protein selectively and produce a predicted signal in real time is a long-lasting engineering challenge in the field of biochemistry. Such a mechanism typically requires a sensing module to recognize the input protein and a translation module to produce a programmable output signal that reflects the concentration of the input. Here we present a generic biomolecular reaction process that exchanges the concentration of an input protein with a DNA oligonucleotide. This approach uses the unique characteristic of DNA oligonucleotide aptamer that can either bind to a specific protein or to a complementary DNA oligonucleotide reversibly. We then pass the information of the protein concentration to the output signal through DNA strand displacement reactions. Using this strategy, we design and characterize four different exchange processes that can produce modular DNA oligonucleotides in response to different proteins such as clinically important human α-thrombin and vascular endothelial growth factor (VEGF). These exchange processes are capable of real time sensing and are modular such that they can be used for concurrent detection of different proteins with well-defined input-output characteristics. The novelty and simplicity of our approach encourage to develop advanced biochemical systems for point-of-care testing of infectious diseases and treatments.
Wolbachiamanipulates host pre-imaginal learning in a parasitoid wasp
Authors: Abroon Pouria , Ashori Ahmad , Duplouy Anne , Farahani Hossein Kishani 
Published: October 2019

AbstractThe Hopkin’s host-selection principle (HHSP) suggests that organisms at higher trophic levels demonstrate a preference for the host species on which they developed during larval stage. Although investigated in many herbivorous and predatory insects, the HHSP has, to our knowledge, never been tested in the context of insects hosting selfish endosymbiotic passengers such as the maternally inherited bacteriumWolbachia pipientis. Here, we investigate the effect ofWolbachiainfection on host pre-imaginal learning in the parasitoid waspTrichogramma brassicae(Hymenoptera: Trichogrammatidae). We compare host-choice inWolbachia-infected and uninfected adult female parasitoids after rearing them on two different Lepidopteran hosts, namely the flour mothEphestia kuehniellaZeller (Lepidoptera: Pyralidae) or the grain mothSitotroga cerealella(Lep.: Gelechiidae). We show that inT. brassicae, Wolbachiaaffect the pre-imaginal learning ability of female wasps.Wolbachiainfected wasps do not show any host preference and easily switch hosts in the laboratory, while uninfected wasps significantly prefer to lay eggs on the host species they developed on. We discuss how the facilitation of a generalist strategy byWolbachiamay allowT. brassicaeto escape intraspecific competition with their uninfected counterparts, and may have important evolutionary consequences for the host and its symbionts.
Intrinsic Buffer Hydroxyl Radical Dosimetry Using Tris(Hydroxymethyl)Aminomethane
Authors: Roush Addison E. , Riaz Mohammad , Misra Sandeep K. , Weinberger Scot R. , Sharp Joshua S. 
Published: October 2019

AbstractFast Photochemical Oxidation of Proteins (FPOP) is a powerful covalent labeling tool that uses hydroxyl radicals generated by laser flash photolysis of hydrogen peroxide to footprint protein surfaces. Because radical production varies with many experimental parameters, hydroxyl radical dosimeters have been introduced to track the effective radical dosage experienced by the protein analyte. FPOP experiments performed using adenine optical radical dosimetry containing protein in Tris buffer demonstrated unusual dosimetry behavior. We have investigated the behavior of Tris under oxidative conditions in detail. We find that Tris can act as a novel gain-of-signal optical hydroxyl radical dosimeter in FPOP experiments. This new dosimeter is also amenable to inline real-time monitoring thereby allowing real-time adjustments to compensate for differences in samples for their quenching ability.
Role of the central junction in folding topology of the protein-free human U2-U6 snRNA complex analyzed by time-resolved FRET
Authors: Chu Huong , Greenbaum Nancy L. 
Published: October 2019

ABSTRACTIntron removal during splicing of precursor pre-mRNA requires assembly of spliceosomal small nuclear (sn)RNAs into catalytically competent conformations to promote two transesterification reactions. U2 and U6 snRNA are the only snRNAs directly implicated in pre-mRNA splicing catalysis, but rearrangement and remodeling steps prior to catalysis require numerous proteins. Previous studies have shown that the protein-free U2-U6 snRNA complex adopts two conformations characterized by four and three helices surrounding a central junction in equilibrium. To analyze the role of the central junction in positioning the two helices critical for formation of the active site, we used ensemble time-resolved fluorescence resonance energy transfer to measure distances between fluorophores at selected locations in constructs representing the protein-free human U2-U6 snRNA complex. Data describing four angles in the four-helix conformer suggest the complex adopts a tetrahedral geometry; addition of Mg2+results in shortening of the distances between neighboring helices, indicating compaction of the complex around the junction. In contrast, the three-helix conformer shows a closer approach between the two helices bearing critical elements, but addition of Mg2+widens the distance between these stems. Presence of Mg2+also enhances the steady state fraction of the three-helix conformer found to be active in spliceosomes. Although the central junction assumes a significant role in orienting helices, in neither conformer, with or without Mg2+, are the critical helices positioned sufficiently close to favor interaction, implying that a major role of spliceosomal remodeling proteins is to overcome such distances to create and stabilize a catalytically active fold.
Topology of the U12-U6atac snRNA complex of the minor spliceosome and binding by NTC-related protein RBM22
Authors: Ciavarella Joanna , Perea William , Greenbaum Nancy L. 
Published: October 2019

ABSTRACTSplicing of precursor messenger RNA is catalyzed by the spliceosome, a dynamic ribonucleoprotein assembly composed of five small nuclear (sn)RNAs and >100 proteins. RNA components catalyze the two transesterification reactions, but proteins perform critical roles in assembly and rearrangement. The catalytic core comprises a paired complex involving U2 and U6 snRNAs for the major form of the spliceosome and U12 and U6atac snRNAs for the minor variant (~0.3% of all spliceosomes in higher eukaryotes); the latter performs identical chemistry, despite limited sequence conservation outside key catalytic elements, and lack of the multi-stem central junction found in the U2-U6 snRNA complex. Here we use solution NMR techniques to show that base pairing patterns of the U12-U6atac snRNA complex of both human and Arabidopsis share key elements with the major spliceosome’s U2-U6 snRNA complex; probing of the single-stranded segment opposing termini of the snRNAs indicates elongation in this region in place of the stacked base pairs at the base of the U6 intramolecular stem loop in the U2-U6 snRNA complex. Binding affinity of RBM22, a protein implicated in remodeling human U2-U6 snRNA prior to catalysis, to U12-U6atac was analyzed by electrophoretic mobility shift assays in which we monitored migration of both protein and RNA components in the same gel. Results indicate that RBM22 binds the U2-U6 and U12-U6atac snRNA complexes specifically and with Kd = 3.5 µM and 8.2 µM, respectively. Similar affinity between RBM22 and each RNA complex suggests that the protein performs the same role in both spliceosomes.