bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cellular Dynamics and Genomic Identity of Centromeres in the Cereal Blast Fungus
Authors: Yadav Vikas , Yang Fan , Reza Md. Hashim , Liu Sanzhen , Valent Barbara , Sanyal Kaustuv , Naqvi Naweed I. 
Published: November 2018

AbstractA series of well-synchronized events mediated by kinetochore-microtubule interactions ensure faithful chromosome segregation in eukaryotes. Centromeres scaffold kinetochore assembly and are among the fastest evolving chromosomal loci in terms of the DNA sequence, length, and organization of intrinsic elements. Neither the centromere structure nor the kinetochore dynamics is well studied in plant pathogenic fungi. Here, we sought to understand the process of chromosome segregation in the rice blast fungus,Magnaporthe oryzae. High-resolution confocal imaging of GFP-tagged inner kinetochore proteins, CenpA and CenpC, revealed an unusual albeit transient declustering of centromeres just before anaphase separation inM. oryzae. Strikingly, the declustered centromeres positioned randomly at the spindle midzone without an apparent metaphase plateper se. Using chromatin immunoprecipitation followed by deep sequencing, all seven centromeres were identified as CenpA-rich regions in the wild-type Guy11 strain ofM. oryzae. The centromeres inM. oryzaeare regional and span 57 to 109 kb transcriptionally poor regions. No centromere-specific DNA sequence motif or repetitive elements could be identified in these regions suggesting an epigenetic specification of centromere function inM. oryzae. Highly AT-rich and heavily methylated DNA sequences were the only common defining features of all the centromeres in rice blast fungus. PacBio genome assemblies and synteny analyses facilitated comparison of the centromere regions in distinct isolate(s) of rice blast, wheat blast, and inM. poae.Overall, this study identified unusual centromere dynamics and precisely mapped the centromere DNA sequences in the top model fungal pathogens that belong to theMagnaporthalesand cause severe losses to global production of food crops and turf grasses.Author summaryMagnaporthe oryzaeis an important fungal pathogen that causes an annual loss of 10-30% of the rice crop due to the devastating blast disease. In most organisms, kinetochores are arranged either in the metaphase plate or are clustered together to facilitate synchronized anaphase separation of chromosomes. In this study, we show that the initially clustered kinetochores separate and position randomly prior to anaphase inM. oryzae. Centromeres, identified as the site of kinetochore assembly, are regional type without any shared sequence motifs inM. oryzae. Together, this study reveals atypical kinetochore dynamics and identifies functional centromeres inM. oryzae, thus paving the way to define heterochromatin boundaries and understand the process of kinetochore assembly on epigenetically specified centromere loci in the economically important cereal blast and summer patch pathogens. This study paves the way for understanding the contribution of heterochromatin in genome stability and virulence of the blast fungus.
Excess light priming in Arabidopsis thaliana genotypes with altered DNA methylomes
Authors: Ganguly Diep R. , Stone Bethany A. B. , Bowerman Andrew F. , Eichten Steven R. , Pogson Barry J. 
Published: November 2018

AbstractPlants must continuously react to the ever-fluctuating nature of their environment. Repeated exposure to stressful conditions can lead to priming, whereby prior encounters heighten a plant’s ability to respond to future events. A clear example of priming is provided by the model plant Arabidopsis thaliana (Arabidopsis), in which photosynthetic and photoprotective responses are enhanced following recurring light stress. While there are various post-translational mechanisms underpinning photoprotection, an unresolved question is the relative importance of transcriptional changes towards stress priming and, consequently, the potential contribution from DNA methylation – a heritable chemical modification of DNA capable of influencing gene expression. Here, we systematically investigate the potential molecular underpinnings of physiological priming against recurring excess-light (EL), specifically DNA methylation and transcriptional regulation: the latter having not been examined with respect to EL priming. The capacity for physiological priming of photosynthetic and photoprotective parameters following a recurring EL treatment was not impaired in Arabidopsis mutants with perturbed establishment, maintenance, or removal of DNA methylation. Importantly, no differences in development or basal photoprotective capacity were identified in the mutants that may confound the above result. Little evidence for a causal transcriptional component of physiological priming was identified; in fact, most alterations in primed plants presented as a transcriptional ‘dampening’ in response to an additional EL exposure, likely a consequence of physiological priming. However, a set of transcripts uniquely regulated in primed plants provide preliminary evidence for a novel transcriptional component of recurring EL priming, independent of physiological changes. Thus, we propose that physiological priming of recurring EL in Arabidopsis occurs independently of DNA methylation; and that the majority of the associated transcriptional alterations are a consequence, not cause, of this physiological priming.One sentence summaryPhotoprotection and priming against recurring excess light is functional despite impaired maintenance of the DNA methylome.
Reversing an extracellular electron transfer pathway for electrode-driven NADH generation
Authors: Tefft Nicholas M. , TerAvest Michaela A. 
Published: November 2018

AbstractMicrobial electrosynthesis is an emerging technology with the potential to simultaneously store renewably generated energy, fix carbon dioxide, and produce high-value organic compounds. However, limited understanding of the route of electrons into the cell remains an obstacle to developing a robust microbial electrosynthesis platform. To address this challenge, we engineered an inward electron transfer pathway inShewanella oneidensisMR-1. The pathway uses native Mtr proteins to transfer electrons from an electrode to the inner membrane quinone pool. Subsequently, electrons are transferred from quinones to NAD+by native NADH dehydrogenases. This reverse functioning of NADH dehydrogenases is thermodynamically unfavorable, therefore we have added a light-driven proton pump (proteorhodopsin) to generate proton-motive force to drive this activity. Finally, we use reduction of acetoin to 2,3-butanediol via a heterologous butanediol dehydrogenase (Bdh) as an electron sink. Bdh is an NADH-dependent enzyme, therefore, observation of acetoin reduction supports our hypothesis that cathodic electrons are transferred to intracellular NAD+. Multiple lines of evidence indicate proper functioning of the engineered electrosynthesis system: electron flux from the cathode is influenced by both light and acetoin availability; and 2,3-butanediol production is highest when both light and a poised electrode are present. Using a hydrogenase-deficientS. oneidensisbackground strain resulted in a stronger correlation between electron transfer and 2,3-butanediol production, suggesting that hydrogen production is an off-target electron sink in the wild-type background. This system represents a promising genetically engineered microbial electrosynthesis platform and will enable a new focus on synthesis of specific compounds using electrical energy.
Visual field advantage: Redefined by training?
Authors: Stone Scott A. , Baker Jared , Olsen Rob , Gibb Robbin , Doan Jon , Hoetmer Joshua , Gonzalez Claudia L.R. 
Published: November 2018

AbstractIn 1990, Fred Previc postulated that most peri-personal space interactions occurred in the lower visual field (LVF), leading to an advantage when compared to the upper visual field (UVF). It is not clear if extensive practice can affect the difference between interactions in the LVF/UVF. We tested male and female basketball varsity athletes and non-athletes on a DynaVision D2 visuomotor reaction task. We recruited basketball players because in their training they spend significant amount of time processing upper visual field information. We found a lower visual field advantage in all participants, but this advantage was significantly reduced in the athletes. The results suggest that training can be a powerful modulator of visuomotor function.
Convolutional Sparse Coded Dynamic Brain Functional Connectivity
Authors: Yan Jin , Zhu Yingying 
Published: November 2018

AbstractFunctional brain network has been widely studied in many previous work for brain disorder diagnosis and brain network analysis. However, most previous work focus on static dynamic brain network research. Lots of recent work reveals that the brain shows dynamic activity even in resting state. Such dynamic brain functional connectivity reveals discriminative patterns for identifying many brain disorders. Current sliding window based dynamic brain connectivity framework are not easy to be applied to real clinical applications due to many issues: First, how to set up the optimal sliding window size and how to determine the threshold for the brain connectivity patterns. Secondly, how to represent the high dimensional dynamic brain connectivity pattern in a low dimensional representations for diagnosis purpose. Last, how to deal with the different length dynamic brain network patterns especially when the raw data are of different length. In order to address all those above issues, we proposed a new framework, which employs multiple scale sliding windows and automatically learns a sparse and low ran dynamic brain functional connectivity patterns from raw fMRI data. Furthermore, we are able to measure different length dynamic brain functional connectivity patterns in an equal space by learning a sparse coded convolutional filters. We have evaluated our method with state of the art dynamic brain network methods and the results demonstrated the strong potential of our methods for brain disorder diagnosis in real clinical applications.
Agreement between 18F-Florbetapir PET imaging and cerebrospinal fluid Aβ1-42, Aβ1-40, tTau and pTau measured on the LUMIPULSE G fully automated platform
Authors: Alcolea Daniel , Pegueroles Jordi , Muñoz Laia , Camacho Valle , López-Mora Diego , Fernández-León Alejandro , Bastard Nathalie Le , Huyck Els , Nadal Alicia , Olmedo Verónica , Montal Victor , Vilaplana Eduard , Clarimón Jordi , Blesa Rafael , Fortea Juan , Lleó Alberto 
Published: November 2018

AbstractINTRODUCTIONThe development of fully automated immunoassay platforms has improved the technical reliability of cerebrospinal fluid (CSF) biomarkers for Alzheimer’s disease.METHODSWe quantified Aβ1-42, Aβ1-40, tTau and pTau levels using the Lumipulse G System in 94 CSF samples from participants of the SPIN cohort with available 18F-Florbetapir imaging. Amyloid scans were assessed visually and through automated quantification. We determined the cutoffs of CSF biomarkers that optimized their agreement with 18F-Florbetapir PET and evaluated concordance between markers of the amyloid category.RESULTSAβ1-42, tTau and pTau (but not Aβ1-40) and the ratios with Aβ1-42 had good diagnostic agreement with 18F-Florbetapir PET. As a marker of amyloid pathology, the Aβ1-42/Aβ1-40 ratio had higher agreement and better correlation with amyloid PET than Aβ1-42 alone.DISCUSSIONCSF biomarkers measured with the Lumipulse G System show good agreement with amyloid imaging. Combination of Aβ1-42 with Aβ1-40 increases the agreement between markers of amyloid pathology.
Regulation of eIF6 through multisite and sequential phosphorylation by GSK3β
Authors: Jungers Courtney F. , Elliff Jonah M. , Masson-Meyers Daniela S. , Phiel Christopher J. , Origanti Sofia 
Published: November 2018

AbstractEukaryotic translation initiation factor 6 is essential for the synthesis of 60S ribosomal subunits and for regulating the association of 60S and 40S subunits. A mechanistic understanding of how eIF6 modulates translation in response to stress, specifically starvation-induced stress, is lacking. Our studies have uncovered a novel mode of eIF6 regulation by GSK3 that is predominantly active in response to serum starvation. Human eIF6 is phosphorylated by GSK3β at a multisite motif in the C-terminus. Sequential phosphorylation by GSK3β requires phosphorylation at a priming site. In response to serum starvation, eIF6 accumulates in the cytoplasm and this altered localization is dependent on GSK3. Disruption of eIF6 phosphorylation enhances translation inhibition and markedly sensitizes the cells to serum starvation. These results suggest that eIF6 regulation by GSK3β contributes to the attenuation of global protein synthesis that is critical for adaptation to starvation-induced stress.
Population genome sequencing of the scab fungal speciesVenturia inaequalis,Venturia pirina,Venturia aucupariaeandVenturia asperata
Authors: Cam Bruno Le , Sargent Dan , Gouzy Jérôme , Amselem Joëlle , Bellanger Marie-Noëlle , Bouchez Olivier , Brown Spencer , Caffier Valérie , Gracia Marie De , Debuchy Robert , Duvaux Ludovic , Payen Thibaut , Sannier Mélanie , Shiller Jason , Collemare Jérôme , Lemaire Christophe 
Published: November 2018

AbstractTheVenturiagenus comprises fungal species that are pathogens onRosaceaehost plants, includingV. inaequalisandV. asperataon apple,V. aucupariaeon sorbus andV. pirinaon pear. Although the genetic structure ofV. inaequalispopulations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87Venturiastrains that represent each species and each population withinV. inaequalis. We present a PacBio genome assembly for theV. inaequalisEU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies ofV. inaequalisandV. aucupariaecontain a high content of transposable elements (TEs), most of which belong to the Gypsy or Copia LTR superfamilies and have been inactivated by Repeat-Induced Point mutations. The reference assembly ofV. inaequalispresents a mosaic structure of GC-equilibrated regions that mainly contain predicted genes and AT-rich regions, mainly composed of TEs. Six pairs of strains were identified as clones. Single-Nucleotide Polymorphism (SNP) analysis between these clones revealed a high number of SNPs that are mostly located in AT-rich regions due to misalignments and allowed determining a false discovery rate. The availability of these genome sequences is expected to stimulate genetics and population genomics research ofVenturiapathogens. Especially, it will help understanding the evolutionary history ofVenturiaspecies that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.
Women in neotropical science: Gender parity in the 21st century and prospects for a post-war Colombia
Authors: López-Aguirre Camilo 
Published: November 2018

AbstractAn increasing amount of research has focused on studying the drivers shaping demographics in science. As a result, we now have a better idea of the current state of gender disparity in science, which remains widespread worldwide. However, fewer studies and limited data have restricted our understanding of this phenomenon in the Neotropics, a highly important region in terms of cultural and biological diversity. Despite a civil war that lasted more than five decades and produced eight million victims (half of them women), Colombia is the fifth country with the highest scientific production in Latin America and the Caribbean, as well as the second most biodiverse country in the world. In order to evaluate the status of gender parity in science in Colombia throughout the 21st century, data of science demographics was gathered covering the 2000-2017 time period. Percentage of women in science was decomposed by research area, researcher rank level and education level. Gender disparity was also estimated for changes in average age, access to scholarships for postgraduate studies, and number of doctoral graduates. Finally, using logistic function modelling, temporal projections into the future were performed, in order to estimate how long could it take to reach gender parity. Of six research fields, medical and health science is the only one to have reached gender parity (55.99%), although it is also the only one showing a steady decrease in women representation across time. On the other hand, engineering, humanities and natural sciences had the lowest percentages of female representation (19.89%, 30.02%, and 30.21%, respectively). Female researchers were on average younger than male researchers, and they also showed a decreasing presence as they move upward to more senior levels, exemplifying the ‘leaky-pipeline phenomenon’ common in science. More men were observed both as scholarship awardees for doctoral studies, and as doctoral graduates, indicating that obtaining a doctoral degree could be a major limiting factor for women in science. Possible drivers of these results are analysed, suggesting that a combination of lack of research funding, insufficient legal framework, pre-existing biases, and poor protection of women’s rights inhibits female participation in science. Based on logistic function modelling it is estimated that, without any action to change current trends, it could take between 10 (humanities) and 175 (engineering) years to reach gender parity across all research areas.
Combining predictive coding with neural oscillations optimizes on-line speech processing
Authors: Hovsepyan Sevada , Olasagasti Itsaso , Giraud Anne-Lise 
Published: November 2018

ABSTRACTSpeech comprehension requires segmenting continuous speech to connect iton-linewith discrete linguistic neural representations. This process relies on theta-gamma oscillation coupling, which tracks syllables and encodes them in decipherable neural activity. Speech comprehension also strongly depends on contextual cues predicting speech structure and content. To explore the effects of theta-gamma coupling on bottom-up/top-down dynamics during on-line speech perception, we designed a generative model that can recognize syllable sequences in continuous speech. The model uses theta oscillations to detect syllable onsets and align both gamma-rate encoding activity with syllable boundaries and predictions with speech input. We observed that the model performed best when theta oscillations were used to align gamma units with input syllables, i.e. when bidirectional information flows were coordinated, and internal timing knowledge was exploited. This work demonstrates that notions of predictive coding and neural oscillations can usefully be brought together to account for dynamicon-linesensory processing.
Long-term balancing selection drives evolution of immunity genes inCapsella
Authors: Koenig Daniel , Hagmann Jörg , Li Rachel , Bemm Felix , Slotte Tanja , Neuffer Barbara , Wright Stephen I. , Weigel Detlef 
Published: November 2018

ABSTRACTGenetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genusCapsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. Our data point to long term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.
The crystal structure and localization ofTrypanosoma bruceiinvariant surface glycoproteins suggest a more permissive VSG coat in the tsetse-transmitted metacyclic stage
Authors: Casas-Sánchez Aitor , Perally Samïrah , Ramaswamy Raghavendran , Haines Lee R. , Rose Clair , Yunta Cristina , Aguilera-Flores Marcela , Lehane Michael J. , Almeida Igor C. , Boulanger Martin J. , Acosta-Serrano Alvaro 
Published: November 2018

AbstractTrypanosoma bruceispp. develop into mammalian-infectious metacyclic trypomastigotes inside the tsetse salivary glands. Besides acquiring a variant surface glycoprotein (VSG) coat, nothing is known about expression of invariant surface antigens by the metacyclic stage. Proteomic analysis of saliva fromT. brucei-infected flies revealed a novel family of hypothetical GPI-anchored surface proteins herein named Metacyclic Invariant Surface Proteins (MISP). MISP are encoded by five homolog genes and share ~80% protein identity. The crystal structure of MISP N-terminus at 1.82 Å resolution revealed a triple helical bundle that shares key features with other trypanosome surface proteins. However, molecular modelling combined with live fluorescent microscopy suggest that MISP N-termini are extended above the metacyclic VSG coat, exposing immunogenic epitopes. Collectively, we suggest that the metacyclic cell surface architecture appears more permissive than bloodstream forms in terms of expression of invariant GPI-anchored glycoproteins, which could be exploited for the development of novel vaccines against African trypanosomiases.
The (p)ppGpp-binding GTPase Era promotes rRNA processing and cold shock survival inStaphylococcus aureus
Authors: Wood Alison , Irving Sophie E. , Bennison Daniel J. , Corrigan Rebecca M. 
Published: November 2018

AbstractRibosome assembly cofactors are widely conserved across all domains of life. One such group, the ribosome-associated GTPases (RA-GTPase), act as molecular switches to coordinate ribosome assembly. We previously identified theStaphylococcus aureusRA-GTPase Era as a target for the stringent response alarmone (p)ppGpp, although the function of Era in ribosome assembly is unclear. Era is highly conserved throughout the bacterial kingdom and is essential in many species. Here we show that Era is not essential inS. aureusbut is important for 30S ribosomal subunit assembly. Protein interaction studies reveal that Era interacts with the endonuclease YbeY and the DEAD-box RNA helicase CshA. We determine that both Era and CshA are required for growth at suboptimal temperatures, virulence and 16S rRNA processing. Era and CshA also form direct interactions with the (p)ppGpp synthetase RelSA, with RelSA positively impacting the GTPase activity of Era. We propose that Era acts to direct enzymes involved in rRNA maturation and ribosome subunit assembly to their site of action, an activity that is regulated by components of the stringent response.Author summaryThe bacterial ribosome is an essential cellular component and as such is the target for a number of currently used antimicrobials. Correct assembly of this complex macromolecule requires a number of accessory enzymes, the functions of which are poorly characterised. Here we examine the function of Era, a GTPase enzyme involved in 30S ribosomal subunit biogenesis in the important human pathogenS. aureus. We uncover that Era is not an essential enzyme inS. aureus, as it is in many other species, but is important for correct ribosome assembly. In a bid to uncover the cellular function of this enzyme, we identify a number of protein interaction partners with roles in ribosomal RNA maturation and degradation, supporting the idea that Era acts as an intermediary protein facilitating ribosomal biogenesis. We also uncover a link between Era and the (p)ppGpp synthetase RelSA, revealing an additional level of control of rRNA levels by the stringent response. With this study we elaborate on the functions of GTPases in ribosomal assembly, processes that are controlled at multiple points by the stringent response.