bluuebunny/crossref_metadata_2025_split huggingface dataset:
The application of the CRISPR–Cas9 system in Pseudomonas syringae pv. actinidiae
Authors: Ho Joycelyn , Zhao Min , Wojcik Samuel , Taiaroa George , Butler Margi , Poulter Russell 
Published: January 2020

Introduction.Pseudomonas syringaepv. actinidiae (Psa) has emerged as a major bacterial pathogen of kiwifruit cultivation throughout the world.Aim.We aim to introduce a CRISPR–Cas9 system, a commonly used genome editing tool, into Psa. The protocols may also be useful in otherPseudomonasspecies.Methodology.Using standard molecular biology techniques, we modified plasmid pCas9, which carries the CRISPR–Cas9 sequences fromStreptococcus pyogenes,for use in Psa. The final plasmid, pJH1, was produced in a series of steps and is maintained with selection in bothEscherichia coliand Psa.Results.We have constructed plasmids carrying a CRISPR–Cas9 system based on that ofS. pyogenes, which can be maintained, under selection, in Psa. We have shown that the gene targeting capacity of the CRISPR–Cas9 system is active and that the Cas9 protein is able to cleave the targeted sites. The Cas9 was directed to several different sites in theP. syringaegenome. Using Cas9 we have generated Psa transformants that no longer carry the native plasmid present in Psa, and other transformants that lack the integrative, conjugative element, Pac_ICE1. Targeting of a specific gene, a chromosomal non-ribosomal peptide synthetase, led to gene knockouts with the transformants having deletions encompassing the target site.Conclusion.We have constructed shuttle plasmids carrying a CRISPR–Cas9 system that are maintained in bothE. coliandP. syringaepv. actinidiae. We have used this gene editing system to eliminate features of the accessory genome (plasmids or ICEs) from Psa and to target a single chromosomal gene.
Differences in Plasma Metabolites Related to Alzheimer’s Disease, APOE-ε4 status and Ethnicity
Authors: Vardarajan Badri , Kalia Vrinda , Manly Jennifer , Brickman Adam , Reyes-Dumeyer Dolly , Lantigua Rafael , Ionita-Laza Iuliana , Jones Dean P. , Miller Gary W. , Mayeux Richard 
Published: January 2020

AbstractINTRODUCTIONWe investigated metabolites in plasma to capture systemic biochemical changes associated with Alzheimer’s disease (AD).METHODSMetabolites in plasma were measured in 59 AD cases and 60 healthy participants of African American (AA), Caribbean Hispanic (CH) and non-Hispanic white (NHW) ancestry using untargeted liquid-chromatography based ultra-high resolution mass spectrometry. Metabolite differences between AD and healthy, ethnic groups and APOEε4 status were analyzed. Untargeted network analysis identified pathways enriched in AD-associated metabolites.RESULTS5,929 annotated metabolites were measured. PLS-DA analysis inferred that AD clustered separately from healthy controls (AUC=0.9816); discriminating pathways included glycerophospholipid, sphingolipid and non-essential amino acid (alanine, aspartate, glutamate) metabolism. Metabolic features in AA clustered differently from CH and NHW (AUC=0.9275), and differed betweenAPOEε4-carriers and non-carriers (AUC=0.9972).DISCUSSIONMetabolites, specifically lipids, were associated with AD,APOEε4 and ethnic group. Metabolite profiling could identify perturbed AD pathways, but genetic and ancestral background need to be considered.
Scaling of information in large neural populations reveals signatures of information-limiting correlations
Authors: Kafashan MohammadMehdi , Jaffe Anna , Chettih Selmaan N. , Nogueira Ramon , Arandia-Romero Iñigo , Harvey Christopher D. , Moreno-Bote Rubén , Drugowitsch Jan 
Published: January 2020

AbstractHow is information distributed across large neuronal populations within a given brain area? One possibility is that information is distributed roughly evenly across neurons, so that total information scales linearly with the number of recorded neurons. Alternatively, the neural code might be highly redundant, meaning that total information saturates. Here we investigated how information about the direction of a moving visual stimulus is distributed across hundreds of simultaneously recorded neurons in mouse primary visual cortex (V1). We found that information scales sublinearly, due to the presence of correlated noise in these populations. Using recent theoretical advances, we compartmentalized noise correlations into information-limiting and nonlimiting components, and then extrapolated to predict how information grows when neural populations are even larger. We predict that tens of thousands of neurons are required to encode 95% of the information about visual stimulus direction, a number much smaller than the number of neurons in V1. Overall, these findings suggest that the brain uses a widely distributed, but nonetheless redundant code that supports recovering most information from smaller subpopulations.
Engram reactivation during memory retrieval predicts long-term memory performance in aged mice
Authors: Karaca Kubra Gulmez , Brito David V.C. , Kupke Janina , Zeuch Benjamin , Oliveira Ana M.M. 
Published: January 2020

AbstractAge-related cognitive decline preferentially targets long-lasting episodic memories that require intact hippocampal function. Memory traces (or engrams) are believed to be encoded within the neurons activated during learning (neuronal ensembles), and recalled by reactivation of the same population. However, whether engram reactivation dictates memory performance late in life is not known. Here, we labelled neuronal ensembles formed during object location recognition learning in the dentate gyrus, and analyzed the reactivation of this population by long-term memory recall in young adult, cognitively impaired-and unimpaired-aged mice. We found that reactivation of memory-encoding neuronal ensembles at long-term memory recall was disrupted in impaired but not unimpaired-aged mice. Furthermore, we showed that the memory performance in the aged population correlated with the degree of engram reactivation at long-term memory recall. Overall, our data implicates recall-induced engram reactivation as a prediction factor of memory performance in aging. Moreover, our findings suggest impairments in neuronal ensemble stabilization and/or reactivation as an underlying mechanism in age-dependent cognitive decline.
The evolution of human SIRT1 for multi-specificity is enabled by active-site adaptation
Authors: Hendler Adi , Akiva Eyal , Sandhu Mahakaran , Goldberg Dana , Arbely Eyal , Jackson Colin J. , Aharoni Amir 
Published: January 2020

AbstractMany enzymes that catalyze protein post-translational modifications (PTM) can specifically modify multiple target proteins. However, little is known regarding the molecular basis and evolution of multi-specificity in these enzymes. Here, we used bioinformatics and experimental approaches to investigate the molecular basis and evolution of multi-specificity in the sirtuin-1 (SIRT1) deacetylase. Guided by bioinformatics analysis of SIRT1 orthologues and substrates, we identified and examined key mutations that have occurred during the evolution of human SIRT1. We found that while these mutants maintain high activity toward conserved histone substrates they exhibit a dramatic loss of activity toward acetylated p53 protein that appeared only in Metazoa. These results demonstrate that active site substitutions in SIRT1 are essential to enable the inclusion of p53 substrate. Our results are consistent with a model in which promiscuous ancestral activity can provide an evolutionary starting point from which multispecificity toward a number of cellular substrates can develop.
Periprotein membrane lipidomics and the role of lipids in transporter function in yeast
Authors: van ‘t Klooster Joury S , Cheng Tan-Yun , Sikkema Hendrik R , Jeucken Aike , Moody D. Branch , Poolman Bert 
Published: January 2020

AbstractThe yeast plasma membrane is segregated into domains: the Micro-Compartment-of-Can1 (MCC) and Pma1 (MCP) have a different protein composition, but their lipid composition is largely unknown. We extracted proteins residing in these microdomains via stoichiometric capture of lipids and proteins in styrene-maleic-acid-lipid-particles (SMALPs). We purified SMALPs by affinity chromatography and quantitatively analyzed the lipids by mass spectrometry and their role in transporter function. We found that phospholipid and sterol concentrations are similar for MCC and MCP, but sphingolipids are enriched in MCP. Ergosterol is depleted from the periprotein lipidome, whereas phosphatidylserine is enriched relative to the bulk of the plasma membrane. Phosphatidylserine, non-bilayer lipids and ergosterol are essential for activity of Lyp1; the transporter also requires a balance of saturated/unsaturated fatty acids. We propose that proteins can function in the yeast plasma membrane by the disordered state of surrounded lipids and diffuse slowly in domains of high lipid order.Impact statementMembrane protein-specific lipidomics provides information on the organization of the yeast plasma membrane and the functioning of solute transporters
Cortical source imaging of resting-state MEG with a high resolution atlas: An evaluation of methods
Authors: Tait Luke , Özkan Ayşegül , Szul Maciej J , Zhang Jiaxiang 
Published: January 2020

AbstractNon-invasive functional neuroimaging of the human brain at rest can give crucial insight into the mechanisms that underpin healthy cognition and neurological disorders. Magnetoencephalography (MEG) measures extracranial magnetic fields originating from neuronal activity with very high temporal resolution, but requires source reconstruction to make neuroanatomical inferences from these signals. Many source reconstruction algorithms for task-based MEG data are available. However, no consensus yet exists on the optimum algorithm for resting-state data.Here, we evaluated the performance of six commonly-used source reconstruction algorithms based on minimum-norm and beamforming estimates. In the context of human resting-state MEG, we compared the algorithms using quantitative metrics, including resolution properties of inverse solutions and explained variance in sensor-level data. Next, we proposed a data-driven approach to reduce the atlas from the Human Connectome Project’s multimodal parcellation of the human cortex. This procedure produced a reduced cortical atlas with 250 regions, optimized to match the spatial resolution and the rank of MEG data from the current generation of MEG scanners.For both voxel-wise and parcellated source reconstructions, we showed that the eLORETA inverse algorithm had zero localization error, high spatial resolution, and superior performance in predicting sensor-level activity. Our comprehensive comparisons and recommandations can serve as a guide for choosing appropriate methodologies in future studies of resting-state MEG.
The fate of standing variation and new mutation under climate change
Authors: Lu Cheng-Yueh , Lee Cheng-Ruei 
Published: January 2020

AbstractMany species face existence threat under anthropogenic climate change, and standing genetic variation was proposed as a way for sessile species to adapt to novel environments. However, it is still unknown whether standing genetic variants, being adaptive to current environmental variability, are sufficient to guarantee future survival. Here we investigate the relative importance of standing variation versus new mutations from the past to infer their future fate in nature. In the wild banana speciesMusa itineranswhere the Taiwanese populations were ancient immigrants from the Chinese populations, new mutations exert larger effect size in precipitation-related variables, where Taiwan contains extreme environments beyond the ancestral climatic range, and new alleles have stronger association with novel environments. For temperature-related variables where Taiwan is within the ancestral climatic range, standing variants are more important than new mutations. The effect sizes of adaptive variants therefore differ under distinct environmental pressures, supporting theoretical predictions that natural selection favors new mutations with larger effect sizes in novel environments where the population is far from the adaptive peak. Despite their importance, large-effect variants also have higher mismatch and may be more vulnerable to future environmental perturbation, leaving minor-effect variants the main source of adaptive response to rapid anthropogenic climate change. Our work provides a support in natural environment to the previous conclusions from theoretical modeling and microbial experiments in well-controlled lab conditions.
A Paradigm for Measuring Resting State Functional Connectivity in Young Children Using fNIRS and Freeplay
Authors: Kim Jaeah , Ruesch Alexander , Kang Nin Rebecca , Huppert Theodore J. , Kainerstorfer Jana , Thiessen Erik D. , Fisher Anna V. 
Published: January 2020

AbstractResting state functional connectivity (RSFC) reflects the organization of functional networks in the brain. Functional networks measured during “resting”, or task-absent, state are correlated with cognitive function, and much development of these networks occurs between infancy and adulthood. However, RSFC research in the intermediate years (especially between ages 3 and 5 years) has been limited, mainly due to a paucity of child-appropriate neural measures and behavioral paradigms. This paper presents a new paradigm to measure RSFC in young children, utilizing functional near-infrared spectroscopy (fNIRS) and Freeplay, a simple behavioral setup designed to approximate resting state in children. In Experiment 1, we recorded fNIRS data from children aged 3-8 years and adults aged 18-21 years and examined feasibility and validity of our measure of RSFC, and compared measures across the two groups. In Experiment 2, we recorded longitudinal data at two points (approximately 3 months apart) from children aged 3-5 years, and examined reliability under a variety of measures. In both experiments, all children were able to complete testing and provide usable data, a significant improvement over fMRI-based RSFC measurement in children. Results suggest this paradigm is practical and has good construct validity and test-retest reliability, and may contribute towards increasing the availability of reliable data on resting state networks in early childhood. In particular, these are some of the first positive results on the feasibility of reliably measuring functional connectivity in children aged 3-5 years.
Comparative primary paediatric nasal epithelial cell culture differentiation and RSV-induced cytopathogenesis following culture in two commercial media
Authors: Broadbent Lindsay , Manzoor Sheerien , Zarcone Maria , Barabas Judit , Shields Mike , Saglani Sejal , Lloyd Claire M. , Bush Andrew , Custovic Adnan , Ghazal Peter , Gore Mindy , Marsland Ben , Roberts Graham , Schwarze Jurgen , Turner Steve , Power Ultan F. 
Published: January 2020

AbstractThe culture of differentiated human airway epithelial cells allows the study of pathogen-host interactions and innate immune responses in a physiologically relevantin vitromodel. As the use of primary cell culture has gained popularity the availability of the reagents needed to generate these cultures has increased. In this study we assessed two different media, Promocell and PneumaCult, during the differentiation and maintenance of well-differentiated primary nasal epithelial cell cultures (WD-PNECs). We compared and contrasted the consequences of these media on WD-PNEC morphological and physiological characteristics and their responses to respiratory syncytial virus (RSV) infection. We found that cultures generated using PneumaCult resulted in greater total numbers of smaller, tightly packed, pseudostratified cells. However, cultures from both media resulted in similar proportions of ciliated and goblet cells. There were no differences in RSV growth kinetics, although more ciliated cells were infected in the PneumaCult cultures. There was also significantly more IL-29/IFNλ1 secreted from PneumaCult compared to Promocell cultures. In conclusion, the type of medium used for the differentiation of primary human airway epithelial cells impacts experimental results.
Providing new insights on the byphasic lifestyle of the predatory bacteriumBdellovibrio bacteriovorusthrough genome-scale metabolic modeling
Authors: Herencias C , Prieto MA , Nogales J 
Published: January 2020

ABSTRACTIn this study we analyze the growth-phase dependent metabolic states ofBdellovibrio bacteriovorusby constructing a fully compartmented, mass and charge-balanced genome-scale metabolic model of this predatory bacterium (iCH457). Considering the differences between life cycle phases driving the growth of this predator, growth-phase condition-specific models have been generated allowing the systematic study of its metabolic capabilities. Using these unprecedented computational tools, we have been able to analyze, from a system level, the dynamic metabolism of the predatory bacteria as the life cycle progresses. We provide solid computational evidences supporting potential axenic growth ofB. bacteriovorus’s in a rich medium based its encoded metabolic capabilities. Our systems-level analysis confirms the presence of “energy-saving” mechanisms in this predator as well as an abrupt metabolic shift between the attack and intraperiplasmic growth phases. Our results strongly suggest that predatory bacteria’s metabolic networks have low robustness, likely hampering their ability to tackle drastic environmental fluctuations, thus being confined to stable and predictable habitats. Overall, we present here a valuable computational testbed based on predatory bacteria activity for rational design of novel and controlled biocatalysts in biotechnological/clinical applications.AUTHOR SUMMARYBacterial predation is an interspecific relationship widely extended in nature. Among other predators,Bdellovibrioand like organism (BALOs) have received recently a great attention due to the high potential applications such as biocontrol agent in medicine, agriculture, aquaculture and water treatment. Despite the increasing interest in of this predatory bacterium its complex lifestyle and growth conditions hamper the full exploitation of their biotechnological properties. In order to overcome these important shortcomings, we provide here the first genome-scale model of a predator bacterium constructed so far. By using the model as a computational testbed, we provide solid evidences of the metabolic autonomy of this interesting bacterium in term of growth, as well as its dynamic metabolism powering the biphasic life style of this predator. We found a low metabolic robustness thus suggesting that Bdellovibrio is more niche-specific than previously thought and that the environmental conditions governing predation may be relatively uniform. Overall, we provide here a valuable computational tool largely facilitating rational design of novel and controlled predator-based biocatalysts in biotechnological/clinical applications.
In SilicoIdentification, Characterization and Diversity Analysis of RNAi Genes and their Associated Regulatory Elements in Sweet Orange (Citrus sinensis L)
Authors: Mosharaf Md. Parvez , Ahsan Md. Asif , Rahman Hafizur , Akond Zobaer , Ahmed Fee Faysal , Islam Md. Mazharul , Moni Mohammad Ali , Mollah Md. Nurul Haque 
Published: January 2020

AbstractRNA interference (RNAi) plays key roles in post-transcriptional and chromatin modification levels as well as regulates various eukaryotic gene expressions which involved in stress responses, development and maintenance of genome integrity during developmental stages. The whole mechanism of RNAi pathway is directly involved with the gene-silencing process by the interaction of Dicer-Like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) gene families. However, the genes of these three RNAi families are largely unknown yet in sweet orange (Citrus sinensis), though it is an economically important fruit plant all over the world. Therefore, a comprehensive investigation for genome-wide identification, characterization and diversity analysis of RNA silencing genes inC. sinensiswas conducted and identified 4 CsDCL, 8 CsAGO and 4 CsRDR as RNAi genes. To characterize and validate the predicted genes of RNAi families, various bioinformatics analysis was conducted. Phylogenetic analysis clustered the predicted CsDCLs, CsAGOs and CsRDRs genes into four, six and four subgroups with the relevant genes of Arabidopsis respectively. The domain and motif composition analysis, the gene structure for all three-gene families exhibited almost homogeneity within the same group members while showed significant differences in between groups. The GO enrichment analysis results clearly indicated that the predicted genes have direct involvement into the RNAi process as expected inC. sinensis. Moreover,Cis-regulatory elements and regulatory transcription factor analysis of the reported RNAi genes demonstrated the diverse connection to the huge biological functions and regulatory pathways. The expressed sequence tag (EST) analysis showed that these genes are highly expressed in fruit and leaves which indicate that these reported genes have great involvement inC. sinensisfood, flowering and fruit production. The expression analysis of the reported RNAi genes might be more useful to explore the most effective RNAi genes inC. sinensisfor further biotechnological application.
A high-affinity antibody against the CSP N-terminal domain lacksPlasmodium falciparuminhibitory activity
Authors: Thai Elaine , Costa Giulia , Weyrich Anna , Murugan Rajagopal , Oyen David , Prieto Katherine , Bosch Alexandre , Valleriani Angelo , Wu Nicholas C. , Pholcharee Tossapol , Scally Stephen W. , Wilson Ian A. , Wardemann Hedda , Julien Jean-Philippe , Levashina Elena A. 
Published: January 2020

AbstractMalaria is a global health concern and research efforts are ongoing to develop a superior vaccine to RTS,S/AS01. To guide immunogen design, we seek a comprehensive understanding of the protective humoral response againstPlasmodium falciparumcircumsporozoite protein (PfCSP). In contrast to the well-studied responses to the repeat region and the C-terminus, the antibody response against the N-terminal domain of PfCSP (N-CSP) remains obscure. Here, we characterized the molecular recognition and functional efficacy of the N-CSP-specific monoclonal antibody 5D5. The crystal structure at 1.85 Å resolution revealed that 5D5 binds anα-helical epitope in N-CSP with high affinity through extensive shape and charge complementarity, and the unusual utilization of an N-linked glycan. Nevertheless, functional studies indicated low 5D5 binding to live Pf sporozoites, and lack of sporozoite inhibitionin vitroand in mosquitoes. Overall, our data on low recognition and inhibition of sporozoites do not support the inclusion of the 5D5 epitope into the next generation of CSP-based vaccines.Summary StatementThePlasmodium falciparumsporozoite surface protein, PfCSP, is an attractive vaccine target, but the antibody response against the CSP N-terminal domain has remained understudied. Here, to guide immunogen design, Thai et al. provide insights into the binding motif and functional efficacy of the N-terminal domain-specific monoclonal antibody, 5D5.