bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Glycolytic Protein Phosphofructokinase Dynamically Relocalizes into Subcellular Compartments with Liquid-like Properties in vivo
Authors: Jang SoRi , Xuan Zhao , Lagoy Ross C. , Jawerth Louise M. , Gonzalez Ian , Singh Milind , Prashad Shavanie , Kim Hee Soo , Patel Avinash , Albrecht Dirk R. , Hyman Anthony A. , Colón-Ramos Daniel A. 
Published: May 2019

AbstractWhile much is known about the biochemical regulation of glycolytic enzymes, less is understood about how they are organized inside cells. Here we built a hybrid microfluidic-hydrogel device for use in Caenorhabditis elegans to systematically examine and quantify the dynamic subcellular localization of the rate-limiting enzyme of glycolysis, phosphofructokinase-1/PFK-1.1. We determine that endogenous PFK-1.1 localizes to distinct, tissue-specific subcellular compartments in vivo. In neurons, PFK-1.1 is diffusely localized in the cytosol, but capable of dynamically forming phase-separated condensates near synapses in response to energy stress from transient hypoxia. Restoring animals to normoxic conditions results in the dispersion of PFK-1.1 in the cytosol, indicating that PFK-1.1 reversibly organizes into biomolecular condensates in response to cues within the cellular environment. PFK-1.1 condensates exhibit liquid-like properties, including spheroid shapes due to surface tension, fluidity due to deformations, and fast internal molecular rearrangements. Prolonged conditions of energy stress during sustained hypoxia alter the biophysical properties of PFK-1.1 in vivo, affecting its viscosity and mobility within phase-separated condensates. PFK-1.1’s ability to form tetramers is critical for its capacity to form condensates in vivo, and heterologous self-association domain such as cryptochrome 2 (CRY2) is sufficient to constitutively induce the formation of PFK-1.1 condensates. PFK-1.1 condensates do not correspond to stress granules and might represent novel metabolic subcompartments. Our studies indicate that glycolytic protein PFK-1.1 can dynamically compartmentalize in vivo to specific subcellular compartments in response to acute energy stress via multivalency as phase-separated condensates.
Defining the root endosphere and rhizosphere microbiomes from the World Olive Germplasm Collection
Authors: Fernández-González Antonio J. , Villadas Pablo J. , Cabanás Carmen Gómez-Lama , Valverde-Corredor Antonio , Belaj Angjelina , Mercado-Blanco Jesús , Fernández-López Manuel 
Published: May 2019

ABSTRACTUp to date, the bacterial and fungal microbial communities from the olive (Olea europaeaL.) root systems have not been simultaneously studied. In this work, we show that microbial communities from the olive root endosphere are less diverse than those from the rhizosphere. But more relevant was to unveil that olive belowground communities are mainly shaped by the genotype of the cultivar when growing under the same environmental, pedological and agronomic conditions. Furthermore,Actinophytocola,StreptomycesandPseudonocardiaare the most abundant bacterial genera in the olive root endosphere,Actinophytocolabeing the most prevalent genus by far. In contrast,Gp6,Gp4,RhizobiumandSphingomonasare the main genera in the olive rhizosphere.Canalisporium,Aspergillus,MinimelanolocusandMacrophominaare the main fungal genera present in the olive root system. Interestingly enough, a high proportion of so far unclassified fungal sequences at class level were detected in the rhizosphere. From the belowground microbial profiles here reported, it can be concluded that the genusActinophytocolamay play an important role in olive adaptation to environmental stresses. Moreover, the huge unknown fungal diversity suggests that there are still some fungi with important ecological and biotechnological implications that have yet to be discovered.
Evolution-driven attenuation of alphaviruses highlights key glycoprotein determinants regulating viral infectivity and dissemination
Authors: Noval Maria G. , Rodriguez-Rodriguez Bruno A. , Rangel Margarita , Stapleford Kenneth A. 
Published: May 2019

SUMMARYUnderstanding the fundamental mechanisms of arbovirus transmission and pathogenesis is essential to develop new strategies for treatment and prevention. We previously took anin vivoevolution-based approach and identified the chikungunya virus E1 glycoprotein residue 80 to play a critical role in viral transmission and pathogenesis. In this study, we address the genetic robustness and function of position 80 and demonstrate that this highly conserved residue is a key determinant in alphavirus infectivity and dissemination through modulation of viral fusion and cholesterol dependence. In addition, in studying the evolution of position 80, we identified a network of glycoprotein residues, including epidemic determinants, that regulate virus dissemination and infectivity. These studies underscore the importance of taking evolution-based approaches to not only identify key viral determinants driving arbovirus transmission and pathogenesis but also to uncover fundamental aspects of arbovirus biology.
Hypermutation inCryptococcusreveals a novel pathway to 5-fluorocytosine (5FC) resistance
Authors: Billmyre R. Blake , Clancey Shelly Applen , Li Lucy X. , Doering Tamara L. , Heitman Joseph 
Published: May 2019

AbstractDrug resistance is a critical challenge in treating infectious disease. For fungal infections, this issue is exacerbated by the limited number of available and effective antifungal agents. Patients infected with the fungal pathogenCryptococcusare most effectively treated with a combination of amphotericin B and 5-fluorocytosine (5FC). Isolates causing infections frequently develop resistance to 5FC although the mechanism of this resistance is poorly understood. Here we show that resistance is acquired more frequently in isolates with defects in DNA mismatch repair that confer an elevated mutation rate. Natural isolates ofCryptococcuswith mismatch repair defects have recently been described and defective mismatch repair has been reported in other pathogenic fungi. In addition, whole genome sequencing was utilized to identify mutations associated with 5FC resistancein vitro. Using a combination of candidate-based Sanger and whole genome Illumina sequencing, the presumptive genetic basis of resistance in 16 independent isolates was identified, including mutations in the known resistance genesFUR1andFCY2, as well as a novel gene,UXS1. Mutations inUXS1lead to accumulation of a metabolic intermediate that appears to suppress toxicity of both 5FC and its toxic derivative 5FU. Interestingly, while aUXS1ortholog has not been identified in other fungi likeSaccharomyces cerevisiae, where the mechanisms underlying 5FC and 5FU resistance were elucidated, aUXS1ortholog is found in humans, suggesting that mutations inUXS1in cancer cells may also play a role in resistance to 5FU when used during cancer chemotherapy in humans.
Aβ42 oligomers trigger synaptic loss through CAMKK2-AMPK-dependent effectors coordinating mitochondrial fission and mitophagy
Authors: Lee Annie , Kondapalli Chandana , Virga Daniel M. , Lewis Tommy L. , Koo So Yeon , Ashok Archana , Mairet-Coello Georges , Herzig Sebastien , Shaw Reuben , Sproul Andrew , Polleux Franck 
Published: May 2019

AbstractDuring the early stages of Alzheimer’s disease (AD) in both mouse models and human patients, soluble forms of Amyloid-β1-42 oligomers (Aβ42o) trigger loss of excitatory synapses (synaptotoxicity) in cortical and hippocampal pyramidal neurons (PNs) prior to the formation of insoluble Aβ plaques. We observed a spatially restricted structural remodeling of mitochondria in the apical tufts of CA1 PNs dendrites in the hAPPSWE,IND transgenic AD mouse model (J20), corresponding to the dendritic domain receiving presynaptic inputs from the entorhinal cortex and where the earliest synaptic loss is detected in vivo. We also observed significant loss of mitochondrial biomass in human neurons derived from a new model of human ES cells where CRISPR-Cas9-mediated genome engineering was used to introduce the ‘Swedish’ mutation bi-allelically (APPSWE/SWE). Recent work uncovered that Aβ42o mediates synaptic loss by over-activating the CAMKK2-AMPK kinase dyad, and that AMPK is a central regulator of mitochondria homeostasis in non-neuronal cells. Here, we demonstrate that Aβ42o-dependent over-activation of CAMKK2-AMPK mediates synaptic loss through coordinated MFF-dependent mitochondrial fission and ULK2-dependent mitophagy in dendrites of PNs. We also found that the ability of Aβ42o-dependent mitochondrial remodeling to trigger synaptic loss requires the ability of AMPK to phosphorylate Tau on Serine 262. Our results uncover a unifying stress-response pathway triggered by Aβo and causally linking structural remodeling of dendritic mitochondria to synaptic loss.
Proxies of CRISPR-Cas9 activity to aid in the identification of mutagenized Arabidopsis plants
Authors: Li Renyu , Vavrik Charles , Danna Cristian H. 
Published: May 2019

AbstractCRISPR-Cas9 has become the preferred gene editing technology to obtain loss-of-function mutants in plants, and hence a valuable tool to study gene function. This is mainly due to the easy reprograming of Cas9 specificity using customizable small non-coding RNAs, and to the ability to target several independent genes simultaneously. Despite these advances, the identification of CRISPR-edited plants remains time and resource consuming. Here, based on the premise that one editing event in one locus is a good predictor of editing event/s in other locus/loci, we developed a CRISPR co-editing selection strategy that greatly facilitates the identification of CRISPR-mutagenized Arabidopsis plants. This strategy is based on targeting the gene/s of interest simultaneously with a proxy of CRISPR-Cas9-directed mutagenesis. The proxy is an endogenous gene whose loss-of-function mutation produces an easy-to-detect visible phenotype that is unrelated to the expected phenotype of the gene/s under study. We tested this strategy via assessing the frequency of co-editing of three functionally unrelated proxies. We found all three proxies predicted the occurrence of mutations in either or both of the other two proxies with efficiencies ranging from 40% to 100%, dramatically reducing the number of plants that need to be screened to identify CRISPR mutants. This selection strategy provides a framework to facilitate gene function studies of gene families as well as the function of single copy genes in polyploid plant species where the identification of multiplex mutants remains challenging.
Low additive genetic variation in a trait under selection in domesticated rice
Authors: Karavolias Nicholas G. , Greenberg Anthony J. , Barrero Luz S. , Maron Lyza G. , Shi Yuxin , Monteverde Eliana , Piñeros Miguel A. , McCouch Susan R. 
Published: May 2019

AbstractQuantitative traits are important targets of both natural and artificial selection. The genetic architecture of these traits and its change during the adaptive process is thus of fundamental interest. The fate of the additive effects of variants underlying a trait receives particular attention because they constitute the genetic variation component that is transferred from parents to offspring and thus governs the response to selection. While estimation of this component of phenotypic variation is challenging, the increasing availability of dense molecular markers puts it within reach. Inbred plant species offer an additional advantage because phenotypes of genetically identical individuals can be measured in replicate. This makes it possible to estimate marker effects separately from the contribution of the genetic background. We focused on root growth in domesticated rice,Oryza sativa, under normal and aluminum (Al) stress conditions, a trait under recent selection because it correlates with survival under drought. A dense single nucleotide polymorphism (SNP) map is available for all accessions studied. Taking advantage of this map and a set of Bayesian models, we assessed additive marker effects. While total genetic variation accounted for a large proportion of phenotypic variance, marker effects contributed little information, particularly in the Al-toleranttropical japonicapopulation of rice. We were unable to identify any loci associated with root growth in this population. Models estimating the aggregate effects of all measured genotypes like-wise produced low estimates of marker heritability and were unable to predict total genetic values accurately. Our results support the long-standing conjecture that additive genetic variation is depleted in traits under selection. We further provide evidence that this depletion is due to the prevalence of low-frequency alleles that underlie the trait.
Reduced Cognitive Performance in Aged Rats Correlates with Increased Excitation/Inhibition Ratio in the Dentate Gyrus in Response to Lateral Entorhinal Input
Authors: Tran Trinh , Bridi Michelle , Koh Ming Teng , Gallagher Michela , Kirkwood Alfredo 
Published: May 2019

ABSTRACTAging often impairs cognitive functions associated with the medial temporal lobe (MTL). Anatomical studies identified the layer II pyramidal cells of the lateral entorhinal cortex (LEC) as one of the most vulnerable elements within the MTL. These cells provide a major excitatory input to the dentate gyrus hippocampal subfield by synapsing onto granule cells and onto local inhibitory interneurons, and a fraction of these contacts are lost in aged individuals with impaired learning. Using optogenetics we evaluated the functional status of the remaining inputs in an outbred rat model of aging that distinguishes between learning impaired and learning unimpaired individuals. We found that aging affects the pre- and postsynaptic strength of the LEC inputs onto granule cells. However, the magnitude these changes was similar in impaired and un-impaired rats. In contrast, the recruitment of inhibition by LEC activation was selectively reduced in the aged impaired subjects. These findings are consistent with the notion that the preservation of an adequate balance of excitation and inhibition is crucial for maintain proficient memory performance during aging.
A zero-inflated gamma model for post-deconvolved calcium imaging traces
Authors: Wei Xue-Xin , Zhou Ding , Grosmark Andres , Ajabi Zaki , Sparks Fraser , Zhou Pengcheng , Brandon Mark , Losonczy Attila , Paninski Liam 
Published: May 2019

AbstractCalcium imaging is a critical tool for measuring the activity of large neural populations. Much effort has been devoted to developing “pre-processing” tools applied to calcium video data, addressing the important issues of e.g., motion correction, denoising, compression, demixing, and deconvolution. However, computational modeling of deconvolved calcium signals (i.e., the estimated activity extracted by a pre-processing pipeline) is just as critical for interpreting calcium measurements. Surprisingly, these issues have to date received significantly less attention. To fill this gap, we examine the statistical properties of the deconvolved activity estimates, and propose several density models for these random signals. These models include a zero-inflated gamma (ZIG) model, which characterizes the calcium responses as a mixture of a gamma distribution and a point mass which serves to model zero responses. We apply the resulting models to neural encoding and decoding problems. We find that the ZIG model out-performs simpler models (e.g., Poisson or Bernoulli models) in the context of both simulated and real neural data, and can therefore play a useful role in bridging calcium imaging analysis methods with tools for analyzing activity in large neural populations.
Machine learning to detect Alzheimer’s disease from circulating non-coding RNAs
Authors: Ludwig Nicole , Fehlmann Tobias , Gogol Manfred , Maetzler Walter , Deutscher Stephanie , Gurlit Simone , Schulte Claudia , von Thaler Anna-Katharina , Deuschle Christian , Metzger Florian , Berg Daniela , Suenkel Ulrike , Keller Verena , Backes Christina , Lenhof Hans-Peter , Meese Eckart , Keller Andreas 
Published: May 2019

AbstractBackgroundTo develop therapeutics for Alzheimer’s disease, early detection of patients awakes new hope. Circulating small non-coding RNAs are among the prominent candidates for a blood-based diagnosis, requiring however growing cohort sizes.MethodsWe determined abundance levels of 21 known circulating microRNAs in 465 individuals encompassing Alzheimer’s patients and controls recruited in US and Germany. We computed models to assess the relation between microRNA-expression and phenotypes, gender, age and disease severity (Mini-Mental State Examination MMSE).Results20 of 21 miRNAs were consistently dys-regulated in the US and Germany. 18 were significantly correlated to neurodegeneration (adjusted p<0.05) with highest significance for miR-532-5p (adjusted p=4.8×10−30). Ten miRNAs were significantly correlated with MMSE, in particular miR-26a/26b-5p (adjusted p=0.0002). Machine learning models reached an AUC value of 87.6% in differentiating AD patients from controls.ConclusionsOur data provide strong evidence for the relevance of circulating non-coding RNAs to detect Alzheimer’s from a blood sample.
Quantification of DNA damage induced γH2AX focus formation via super-resolution dSTORM localization microscopy
Authors: Varga Dániel , Majoros Hajnalka , Újfaludi Zsuzsanna , Erdélyi Miklós , Pankotai Tibor 
Published: May 2019

SUMMARYIn eukaryotic cells, each process, in which DNA is involved, should take place in the context of chromatin structure. DNA double-strand breaks (DSBs) are one of the most deleterious damages often leading to chromosomal rearrangement. In response to environmental stresses, cells have developed repair mechanisms to eliminate the DSBs. Upon DSB induction, several factors play roles in chromatin relaxation by catalysing the appropriate histone posttranslational modification (PTM) steps, therefore promoting the access of the repair factors to the DSBs. Among these PTMs, the phosphorylation of the histone variant H2AX at its Ser139 residue (also known as γH2AX) could be observed at the break sites. The structure of γH2AX focus has to be organized during the repair as it contributes to accessibility of specific repair proteins to the damaged site. Our aim was to develop a quantitative approach to analyse the morphology of individual repair foci by super-resolution dSTORM microscopy to gain insight into genome organization in DNA repair. We have established a specific dSTORM measurement process by developing a new analytical algorithm for gaining quantitative information about chromatin morphology and repair foci topology at individual γH2AX enriched repair focus. By this method we quantified unique repair foci to show the average distribution of γH2AX clusters. By monitoring γH2AX signal, we could reach 20 nm spatial resolution and resolve a single DNA damage spot, which allow us to identify different chromatin sub-clusters around the break site. Additionally, based on our new analysis method, we were able to show the number of nucleosomes in each sub-cluster that could allow us to define the possible chromatin structure and the nucleosome density around the break sites. This method is the first demonstration of a single-cell based quantitative measurement of a discrete repair focus, which could provide new opportunities to categorize spatial organization of dot patterns by parametric determination of topological similarity.
Discovery, Expression, Cellular Localization, and Molecular Properties of a Novel, Alternative Spliced HP1γ Isoform, Lacking the Chromoshadow Domain
Authors: Mathison Angela , De Assuncao Thiago Milech , Dsouza Nikita R. , Williams Monique , Zimmermann Michael T. , Lomberk Gwen , Urrutia Raul 
Published: May 2019

AbstractBy reading the H3K9Me3 mark through their N-terminal chromodomain (CD), HP1 proteins play a significant role in cancer-associated processes, including cell proliferation, differentiation, chromosomal stability, and DNA repair. Here, we used a combination of bioinformatics-based methodologies, as well as experimentally-derived datasets, that reveal the existence of a novel short HP1γ (CBX3) isoform, named here sHP1γ, generated by alternative splicing of the CBX3 locus. The sHP1γ mRNA encodes a protein composed of 101 residues and lacks the C-terminal chromoshadow domain (CSD) that is required for dimerization and heterodimerization in the previously described 183 a. a HP1γ protein. Fold recognition, order-to-disorder calculations, threading, homology-based molecular modeling, docking, and molecular dynamic simulations show that the sHP1γ is comprised of a CD flanked by intrinsically disordered regions (IDRs) with an IDR-CD-IDR domain organization and likely retains the ability to bind to the H3K9Me3. Both qPCR analyses and mRNA-seq data derived from large-scale studies confirmed that sHP1γ mRNA is expressed in the majority of human tissues at approximately constant ratios with the chromoshadow domain containing isoform. However, sHP1γ mRNA levels appear to be dysregulated in different cancer types. Thus, our data supports the notion that, due to the existence of functionally different isoforms, the regulation of HP1γ-mediated functions is more complex than previously anticipated.