bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternative transcription cycle for bacterial RNA polymerase
Authors: Harden Timothy T. , Herlambang Karina S. , Chamberlain Mathew , Lalanne Jean-Benoît , Wells Christopher D. , Li Gene-Wei , Landick Robert , Hochschild Ann , Kondev Jane , Gelles Jeff 
Published: June 2019

SummaryRNA polymerases (RNAPs) transcribe genes through a cycle of recruitment to promoter DNA, initiation, elongation, and termination. After termination, RNAP is thought to initiate the next round of transcription by detaching from DNA and rebinding a new promoter. We used single-molecule fluorescence microscopy to observe individual RNAP molecules after transcript release at a terminator. Following termination, RNAP almost always remained bound to DNA and sometimes exhibited one-dimensional sliding over thousands of basepairs. Unexpectedly, the DNA-bound RNAP often restarted transcription, usually in reverse direction, thus producing an antisense transcript. Furthermore, we report evidence of this “secondary initiation” in live cells, using genome-wide RNA sequencing. These findings reveal an alternative transcription cycle that allows RNAP to reinitiate without dissociating from DNA, which is likely to have important implications for gene regulation.
The impact of CO2/HCO3-availability on anaplerotic flux in PDHC-deficientCorynebacterium glutamicumstrains
Authors: Krüger Aileen , Wiechert Johanna , Gätgens Cornelia , Polen Tino , Mahr Regina , Frunzke Julia 
Published: June 2019

AbstractThe pyruvate dehydrogenase complex (PDHC) catalyzes the oxidative decarboxylation of pyruvate yielding acetyl-CoA and CO2. The PDHC-deficientCorynebacterium glutamicumstrain ΔaceEis therefore lacking an important decarboxylation step in central metabolism. Additional inactivation ofpyc, encoding pyruvate carboxylase, resulted in a >15 hour lag phase in the presence of glucose, while no growth defect was observed on gluconeogenetic substrates like acetate. Growth was successfully restored by deletion ofptsGencoding the glucose-specific permease of the PTS system, thereby linking the observed phenotype to the increased sensitivity of strain ΔaceEΔpycto glucose catabolism. In the following, strain ΔaceEΔpycwas used to systematically study the impact of perturbations of the intracellular CO2/HCO3-pool on growth and anaplerotic flux. Remarkably, all measures leading to enhanced CO2/HCO3-levels, such as external addition of HCO3-, increasing the pH, or rerouting metabolic flux via pentose phosphate pathway, at least partially eliminated the lag phase of strain ΔaceEΔpycon glucose medium. In accordance, inactivation of the urease enzyme, lowering the intracellular CO2/HCO3-pool, led to an even longer lag phase accompanied with the excretion of L-valine and L-alanine. Transcriptome analysis as well as an adaptive laboratory evolution experiment of strain ΔaceEΔpycrevealed the reduction of glucose uptake as a key adaptive measure to enhance growth on glucose/acetate mixtures. Altogether, our results highlight the significant impact of the intracellular CO2/HCO3-pool on metabolic flux distribution, which becomes especially evident in engineered strains suffering from low endogenous CO2production rates as exemplified by PDHC-deficient strains.ImportanceCO2is a ubiquitous product of cellular metabolism and an essential substrate for carboxylation reactions. The pyruvate dehydrogenase complex (PDHC) catalyzes a central metabolic reaction contributing to the intracellular CO2/HCO3-pool in many organisms. In this study, we used a PDHC-deficient strain ofCorynebacterium glutamicum, which was additionally lacking pyruvate carboxylase (ΔaceEΔpyc). This strain featured a >15 h lag phase during growth on glucose-acetate mixtures. We used this strain to systematically assess the impact of alterations in the intracellular CO2/HCO3-pool on growth on glucose-containing medium. Remarkably, all measures enhancing the CO2/HCO3-levels successfully restored growth emphasizing the strong impact of the intracellular CO2/HCO3-pool on metabolic flux especially in strains suffering from low endogenous CO2production rates.
Characteristics and Evolutionary analysis of Photosynthetic Gene Clusters on Extrachromosomal Replicons: from streamlined plasmids to chromids
Authors: Liu Yanting , Zheng Qiang , Lin Wenxin , Jiao Nianzhi 
Published: June 2019

AbstractAerobic anoxygenic photoheterotrophic bacteria (AAPB) represent intermediates in the evolution from photoautotrophic to heterotrophic metabolisms. Substantial evidence indicates that highly conserved photosynthetic gene clusters (PGCs) of AAPB can be transferred between species, genera, and even phyla. Furthermore, analysis of recently discovered PGCs carried by extrachromosomal replicons (exPGCs) suggests that extrachromosomal replicons (ECRs) play an important role in the transfer of PGCs. In the present study, thirteenRoseobacterclade genomes from seven genera that harbored exPGCs were used to analyze characteristics and evolution of PGCs. The identification of plasmid-like and chromid-like ECRs from PGC-containing ECRs revealed two different functions: the spread of PGCs among strains and the maintenance of PGCs within genomes. Phylogenetic analyses indicated two independent origins of exPGCs, corresponding to PufC-containing and PufX-containing photosynthetic reaction complexes. Furthermore, the two different types of complexes were observed within different strains of the sameTateyamariaandJannaschiagenera. The two different complexes were also differentially carried by chromosomes and ECRs in the strains, respectively, which provided clear evidence for ECR-mediated PGC transfer. Multiple recombination events of exPGCs were also observed, wherein the majority of exPGCs were inserted by replication modules at the same genomic positions. However, the exPGCs of theJannaschiastrains comprised superoperons without evidence of insertion, and therefore likely represent an initial evolutionary stage where the PGC was translocated from chromosomes to ECRs without further combinations. Lastly, a scenario of PGC gain and loss is proposed that specifically focuses on ECR-mediated exPGC transfer to explain the evolution and patchy distribution of AAPB within theRoseobacterclade.ImportanceThe evolution of photosynthesis was a significant event during the diversification of biological life. Aerobic anoxygenic heterotrophic bacteria (AAPB) share physiological characteristics with both photoautotrophs and heterotrophs and are therefore suggested to be evolutionary intermediates between the two lifestyles. Here, characterization and evolutionary analyses were conducted for thirteen bacterial strains that contained photosynthetic gene clusters (PGCs) carried by extrachromosomal replicons (ECRs) to shed light on the evolution of photosynthesis in bacteria. Specifically, these analyses improved the “Think Pink” scenario of PGC transfer that is mediated by ECRs inRoseobacterclade strains. This study advances our understanding of the importance of ECRs in the transfer of PGCs within marine photoheterotrophic bacteria.
The Cellular Immunity Agent Based Model (CIABM): Replicating the cellular immune response to viral respiratory infection
Authors: Becker Andrew , An Gary , Cockrell Chase 
Published: June 2019

AbstractViral respiratory infections, such as influenza, result in over 1 million deaths worldwide each year. To date, there are few therapeutic interventions able to affect the course of the disease once acquired, a deficit with stark consequences that were readily evident in the current COVID-19 pandemic. We present the Cellular Immune Agent Based Model (CIABM) as a flexible framework for modeling acute viral infection and cellular immune memory development. The mechanism/rule-based nature of the CIABM allows for interrogation of the complex dynamics of the human immune system during various types of viral infections. The CIABM is an extension of a prior agent-based model of the innate immune response, incorporating additional cellular types and mediators involved in the response to viral infection. The CIABM simulates the dynamics of viral respiratory infection in terms of epithelial invasion, immune cellular population changes and cytokine measurements. Validation of the CIABM involved effectively replicating in vivo measurements of circulating mediator levels from a clinical cohort of influenza patients. The general purpose nature of the CIABM allows for both the representation of various types of known viral infections and facilitates the exploration of hypothetical, novel viral pathogens.
Links between central CB1-receptor availability and peripheral endocannabinoids in patients with first episode psychosis
Authors: Dickens Alex M. , Borgan Faith , Laurikainen Heikki , Lamichhane Santosh , Marques Tiago , Rönkkö Tuukka , Veronese Mattia , Lindeman Tuomas ,   METSY Investigators, Hyötyläinen Tuulia , Howes Oliver , Hietala Jarmo , Orešič Matej 
Published: June 2019

AbstractThere is an established, albeit poorly-understood link between psychosis and metabolic abnormalities such as altered glucose metabolism and dyslipidemia, which often precede the initiation of antipsychotic treatment. It is known that obesity-associated metabolic disorders are promoted by peripheral activation of the endocannabinoid system (ECS). Our recent data suggest that ECS dysregulation may also play a role in psychosis. With the aim of characterizing the involvement of the central and peripheral ECSs and their mutual associations, here we performed a combined neuroimaging and metabolomic study in patients with first-episode psychosis (FEP) and healthy controls (HC). Regional brain cannabinoid receptor type 1 (CB1R) availability was quantified in two, independent samples of patients with FEP (n=20 and n=8) and HC (n=20 and n=10), by applying 3D positron emission tomography (PET), using two radiotracers, [11C]MePPEP and [18F]FMPEP-d2. Ten endogenous endocannabinoids or related metabolites were quantified in serum, drawn from these individuals during the same imaging session. Circulating levels of arachidonic acid and oleyl ethanolamide were reduced in FEP individuals, but not in those who were predominantly medication-free. In HC, there was an inverse association between levels of circulating arachidonoyl glycerol, anandamide, oleyl ethanolamide and palmitoyl ethanolamide, and CB1R availability in the posterior cingulate cortex. This phenomenon was, however, not observed in FEP patients. Our data thus provide evidence of cross-talk and dysregulation between peripheral endocannabinoids and central CB1R availability in FEP.
Nanopore device-based fingerprinting of RNA oligos and microRNAs enhanced with an Osmium tag
Authors: Sultan Madiha , Kanavarioti Anastassia 
Published: June 2019

Nanopores, both protein and solid-state, are explored as single molecule analytical tools, but using an experimental platform is challenging. Here we show that a commercially available nanopore device, MinION from Oxford Nanopore Technologies (ONT), successfully accomplishes a task challenging for a conventional analytical tool. Specifically the MinION discriminates among 31 nucleotide (nt) long oligoriboadenylates with a single pyrimidine (Py) substitution, when this pyrimidine is tagged/labeled with a bulky group (Osmium tetroxide 2,2’-bipyridine or OsBp). This platform also discriminates between an osmylated Py (Py-OsBp) followed by a purine (Pu) and a Py-OsBp followed by a second Py-OsBp, leading to the conjecture that the bulky tag enables sensing of a two-nucleotide sequence. Two-nucleotide sensing could greatly improve base-calling accuracy in motor enzyme-assisted nanopore sequencing.We attribute the observed discrimination neither to the specific pore protein nor to OsBp, but to the tag’s bulkiness, that leads to markedly slower translocation and “touching” proximity at the pore’s constriction zone, that forces desolvation and reorganization, and enables strong interactions among the nanopore, the tagged pyrimidine, and the adjacent nucleobase. These results constitute proof-of-principle that size-suitable nanopores may be superior to traditional analytical tools, for the characterization of RNA oligos and microRNAs enhanced by selective labelling.
Magainin 2 and PGLa in Bacterial Membrane Mimics I: Peptide-Peptide and Lipid-Peptide Interactions
Authors: Pachler Michael , Kabelka Ivo , Appavou Marie-Sousai , Lohner Karl , Vácha Robert , Pabst Georg 
Published: June 2019

ABSTRACTWe addressed the onset of synergistic activity of the two well-studied antimicrobial peptides magainin 2 (MG2a) and PGLa using lipid-only mimics of Gram-negative cytoplasmic membranes. Specifically, we coupled a joint analysis of small-angle X-ray and neutron scattering experiments on fully hydrated lipid vesicles in the presence of MG2a and L18W-PGLa to all-atom and coarse-grained molecular dynamics simulations. In agreement with previous studies both peptides, as well as their equimolar mixture, were found to remain in a surface-aligned topology upon membrane insertion and to induce significant membrane perturbation as evidenced by membrane thinning and hydrocarbon order parameter changes in the vicinity of the inserted peptide. These effects were particularly pronounced for the so called synergistic mixture of 1:1 (mol/mol) L18W-PGLa/MG2a and cannot be accounted for by a linear combination of the membrane perturbations of two peptides individually. Our data are consistent with parallel heterodimers forming at much lower concentrations than previously considered, but which do not induce a synergistic leakage of dyes. Our simulations further show that the heterodimers interact via salt bridges and hydrophobic forces, which apparently makes them more stable than putatively formed antiparallel L18W-PGLa and MG2a homodimers. Moreover, dimerization of L18W-PGLa and MG2a leads to a relocation of the peptides within the lipid headgroup regime as compared to the individual peptides. The early onset of dimerization of L18W-PGLa and MG2a at low peptide concentrations consequently appears to be key to their synergistic dye-releasing activity from lipid vesicles at high concentrations.STATEMENT OF SIGNIFICANCEWe demonstrate that specific interactions of the antimicrobial peptides MG2a and PGLa with each other in POPE/POPG bilayers lead to the formation of surface-aligned parallel dimers, which provide already at low peptide concentrations the nucleus for the peptides’ well-known synergistic activity.
Differential turnover of Nup188 controls its levels at centrosomes and role in centriole duplication
Authors: Vishnoi Nidhi , Dhanasekeran Karthigeyan , Chalfant Madeleine , Surovstev Ivan , Khokha Mustafa K. , Lusk C. Patrick 
Published: June 2019

AbstractNUP188 encodes a scaffold component of the nuclear pore complex (NPC) and has been implicated as a congenital heart disease gene through an ill-defined function at centrioles. Here, we explore the mechanisms that physically and functionally segregate Nup188 between the pericentriolar material (PCM) and NPCs throughout the cell cycle. Pulse-chase fluorescent labeling approaches indicate that Nup188 populates centrosomes with newly synthesized protein that does not exchange with NPCs even after mitotic NPC breakdown. In addition, the steady-state level of Nup188 at centrosomes is controlled by the sensitivity of the PCM pool, but not the NPC pool, to proteasomal degradation. Proximity-labeling and super-resolution microscopy supports that Nup188 interacts with components of PCM including Cep192 and the centriolar satellite component, PCM1. Consistent with this, Nup188 plays a role in centriole duplication at or upstream of Sas6 loading. Together, our data establish Nup188 as a functional component of PCM and potentially provides insight into the pathogenesis of congenital heart disease.
A robust benchmark for germline structural variant detection
Authors: Zook Justin M. , Hansen Nancy F. , Olson Nathan D. , Chapman Lesley M. , Mullikin James C. , Xiao Chunlin , Sherry Stephen , Koren Sergey , Phillippy Adam M. , Boutros Paul C. , Sahraeian Sayed Mohammad E. , Huang Vincent , Rouette Alexandre , Alexander Noah , Mason Christopher E. , Hajirasouliha Iman , Ricketts Camir , Lee Joyce , Tearle Rick , Fiddes Ian T. , Barrio Alvaro Martinez , Wala Jeremiah , Carroll Andrew , Ghaffari Noushin , Rodriguez Oscar L. , Bashir Ali , Jackman Shaun , Farrell John J , Wenger Aaron M , Alkan Can , Soylev Arda , Schatz Michael C. , Garg Shilpa , Church George , Marschall Tobias , Chen Ken , Fan Xian , English Adam C. , Rosenfeld Jeffrey A. , Zhou Weichen , Mills Ryan E. , Sage Jay M. , Davis Jennifer R. , Kaiser Michael D. , Oliver John S. , Catalano Anthony P. , Chaisson Mark JP , Spies Noah , Sedlazeck Fritz J. , Salit Marc ,   the Genome in a Bottle Consortium
Published: June 2019

AbstractNew technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution, and comprehensiveness. Translating these methods to routine research and clinical practice requires robust benchmark sets. We developed the first benchmark set for identification of both false negative and false positive germline SVs, which complements recent efforts emphasizing increasingly comprehensive characterization of SVs. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle (GIAB) Consortium integrated 19 sequence-resolved variant calling methods, both alignment- and de novo assembly-based, from short-, linked-, and long-read sequencing, as well as optical and electronic mapping. The final benchmark set contains 12745 isolated, sequence-resolved insertion and deletion calls ≥50 base pairs (bp) discovered by at least 2 technologies or 5 callsets, genotyped as heterozygous or homozygous variants by long reads. The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.66 Gbp and 9641 SVs supported by at least one diploid assembly. Support for SVs was assessed using svviz with short-, linked-, and long-read sequence data. In general, there was strong support from multiple technologies for the benchmark SVs, with 90 % of the Tier 1 SVs having support in reads from more than one technology. The Mendelian genotype error rate was 0.3 %, and genotype concordance with manual curation was >98.7 %. We demonstrate the utility of the benchmark set by showing it reliably identifies both false negatives and false positives in high-quality SV callsets from short-, linked-, and long-read sequencing and optical mapping.
Modeling microbial metabolic trade-offs in a chemostat
Authors: Li Zhiyuan , Liu Bo , Li Sophia Hsin-Jung , King Christopher G. , Gitai Zemer , Wingreen Ned S. 
Published: June 2019

ABSTRACTMicrobes face intense competition in the natural world, and so need to wisely allocate their resources to multiple functions, in particular to metabolism. Understanding competition among metabolic strategies that are subject to trade-offs is therefore crucial for deeper insight into the competition, cooperation, and community assembly of microorganisms. In this work, we evaluate competing metabolic strategies within an ecological context by considering not only how the environment influences cell growth, but also how microbes shape their chemical environment. Utilizing chemostat-based resource-competition models, we exhibit a set of intuitive and general procedures for assessing metabolic strategies. Using this framework, we are able to relate and unify multiple metabolic models, and to demonstrate how the fitness landscape of strategies becomes intrinsically dynamic due to species-environment feedback. Such dynamic fitness landscapes produce rich behaviors, and prove to be crucial for ecological and evolutionary stable coexistence in all the models we examined.
Rhizosphere metagenomics of mine tailings colonizing plants: assembling and selecting synthetic bacterial communities to enhance in situ bioremediation
Authors: Romero Miguel , Gallego Diana , Blaz Jazmin , Lechuga Arely , Martínez José F. , Barajas Hugo R. , Hayano-Kanashiro Corina , Peimbert Mariana , Cruz-Ortega Rocío , Molina-Freaner Francisco E. , Alcaraz Luis D. 
Published: June 2019

AbstractMine tailings phytostabilization has been proposed as a bioremediation strategy to constrain the contaminants dispersion using plants to limit the effects of erosion. Rhizospheric bacteria impact plant health and facilitate plant establishment through their metabolic functions, which could be relevant in bioremediation strategies. We studied both culturable and metagenomic diversity or rhizospheric bacteria of mine tailings colonizing plants of an abandoned mine operation in Nacozari de García, Sonora, Mexico. Diversity was described through amplification of the 16S rRNA gene and whole metagenome shotgun sequencing of both environmental and cultured rhizosphere associated microbes. The culturable bacteria were assembled in a synthetic community (SC; 235 bacteria genera). Subsequently, we performed an experimental evolution setup with the SC, selecting for heavy metal resistance, microbial competition, and the ability for growing in plant-derived nutrient sources. The selection experiment show that bacteria diversity decreases from the environmental culture-free microbiomes to the mine tailings rhizospheres and the experimental evolution outcome: the synthetic community (FSC; 43 bacteria genera). The rhizosphere communities shifted from the dominance of Actinobacteria in their environment to Proteobacteria in the cultivated consortia and the synthetic communities. Both environmental and cultured metagenomes contained plant-growth promotion, heavy-metal homeostasis, and antibiotic resistance predicted genes. The FSC included predicted proteins related to plant-growth promotion such as siderophore production and plant hormone regulation proteins. We reconstructed a metagenome assembled genomic sequence named Enterobacter sp., Nacozari. The recovered Enterobacter sp. Nacozari, have predicted coding genes for direct and indirect plant growth promotion along with adhesion and oxidative stress-related proteins. The metabolic potential of the FSC presents promising features that might make it useful for plant-growth promotion in tailored phytostabilization strategies for the abandoned mine-tailings of Nacozari.
A high-content in vivo screen to identify microRNA epistasis in the repopulating mouse liver
Authors: Zahm Adam M. , Wang Amber W. , Wang Yue J. , Schug Jonathan , Wangensteen Kirk J. , Kaestner Klaus H. 
Published: June 2019

ABSTRACTLiver regeneration is impaired in mice with hepatocyte-specific deficiencies in microRNA (miRNA) processing; yet the roles of individual miRNAs or their combinatorial effects in this process are largely unknown. In this study, we sought to identify miRNAs that regulate hepatocyte repopulation following toxic liver injury in a high-throughput manner using the Fah−/− mouse. We constructed plasmid pools encoding over 30,000 tough decoy (TuD) miRNA inhibitors designed to target hepatocyte miRNAs in a pairwise manner. Plasmid libraries were delivered to hepatocytes of Fah−/− mice at the time of liver injury via hydrodynamic tail vein injection and integrated transgene-containing transposons were quantified following repopulation via high-throughput sequencing. Changes in polysome-bound transcripts following miRNA inhibition were determined using translating ribosome affinity purification followed by high-throughput sequencing. Analysis of TuD abundance in hepatocyte genomic DNA and input plasmid pools identified several thousand miRNA inhibitors that were significantly altered following repopulation. We classified a subset of miRNA-binding sites (MBSs) as having strong effect on liver repopulation, thus implicating the targeted hepatocyte miRNAs as regulators of this process. Furthermore, we generated a high-content map of pairwise interactions between 171 MBSs and identified both synergistic and redundant effects. Our study highlights the power of higher-order screens to uncover miRNA functions that would go undetected by individual miRNA perturbations, and provides a new paradigm for the study of epistasis of miRNA activities.