bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial neuronal synchronization and the waveform of oscillations: implications for EEG and MEG
Authors: Schaworonkow Natalie , Nikulin Vadim V. 
Published: August 2018

AbstractNeuronal oscillations are ubiquitous in the human brain and are implicated in virtually all brain functions. Often they are referred to by their frequency content, i.e., α-, β-, γ-oscillations. Although they indeed can be described by a prominent peak in the power spectrum, their waveform is not necessarily sinusoidal and shows a rather complex morphology which needs to be captured with multiple spectral harmonics. Both frequency and temporal descriptions of such non-sinusoidal neuronal oscillations can be utilized. However, in non-invasive EEG/MEG recordings the waveform of oscillations often takes a sinusoidal shape which in turn leads to a rather oversimplified view on oscillatory processes.In this study, we show in simulations how spatial synchronization can mask non-sinusoidal features of the underlying rhythmic neuronal processes. Consequently, the degree of non-sinusoidality can serve as a measure of spatial synchronization. To confirm this empirically, we show that a mixture of EEG components is indeed associated with more sinusoidal oscillations compared to the waveform of oscillations in each constituent component. Using simulations, we also show that the spatial mixing of the non-sinusoidal neuronal signals strongly affects the amplitude ratio of the spectral harmonics constituting the waveform. This in turn has high relevance for the interpretation of the relative strength of spectral peaks, which is commonly used for inferring neuronal signatures corresponding to specific behavioral states.Moreover, our simulations show how spatial mixing can affect the strength and even the direction of the amplitude coupling between constituent neuronal harmonics. Consistently with these simulations, we also demonstrate these effects in real EEG recordings. Our findings have far reaching implications for the neu-rophysiological interpretation of neuronal oscillations and cross-frequency interactions, as well as for the unequivocal determination of oscillatory phase.
Interferometric scattering microscopy reveals microsecond nanoscopic protein motion on a live cell membrane
Authors: Taylor Richard W. , Mahmoodabadi Reza Gholami , Rauschenberger Verena , Giessl Andreas , Schambony Alexandra , Sandoghdar Vahid 
Published: August 2018

AbstractMuch of the biological functions of a cell are dictated by the intricate motion of proteins within its membrane over a spatial range of nanometers to tens of micrometers and time intervals of microseconds to minutes. While this rich parameter space is not accessible to fluorescence microscopy, it can be within reach of interferometric scattering (iSCAT) particle tracking. Being sensitive even to single unlabeled proteins, however, iSCAT is easily accompanied by a large speckle-like background, which poses a substantial challenge for its application to cellular imaging. Here, we show that these difficulties can be overcome and demonstrate tracking of transmembrane epidermal growth factor receptors (EGFR) with nanometer precision in all three dimensions at up to microsecond speeds and tens of minutes duration. We provide unprecedented examples of nanoscale motion and confinement in ubiquitous processes such as diffusion in the plasma membrane, transport on filopodia, and endocytosis.
The context-dependent nature of the neural implementation of intentions
Authors: Uithol Sebo , Görgen Kai , Pischedda Doris , Toni Ivan , Haynes John-Dylan 
Published: August 2018

AbstractMany studies have identified networks in parietal and prefrontal cortex that are involved in intentional action. Yet, knowledge about what these networks exactly encoded is still scarce. In this study we look into the content of those processes. We ask whether the neural representations of intentions are context- and reason-invariant, or whether these processes depend on the context we are in, and the reasons we have for choosing an action. We use a combination of functional magnetic resonance imaging and multivariate decoding to directly assess the context- and reason-dependency of the processes underlying intentional action. We were able to decode action decisions in the same context and for the same reasons from the fMRI data, in line with previous decoding studies. Furthermore, we could decode action decisions across different reasons for choosing an action. Importantly, though, decoding decisions across different contexts was at chance level. These results suggest that for voluntary action, there is considerable context-dependency in intention representations. This suggests that established invariance in neural processes may not reflect an essential feature of a certain process, but that this stable character could be dependent on invariance in the experimental setup, in line with predictions from situated cognition theory.
Fungal growth is affected by and affects pH and redox potential (Eh) of the growth medium
Authors: Bousset L. , Ermel M. , Soglonou B. , Husson O. 
Published: August 2018

AbstractFungal plant pathogens live in the specific environment of plants. Understanding of the interaction between pathogens and their host plants might open new ways to control plant diseases. Yet, the specificities of the plant environment and its effects on fungal growth are not yet fully explored. Both pH and Eh play a key role during the interaction between the fungus and its host plants, but often studied independently or at different scales. To decipher the interrelation between plant growth and their soil environment, recent theoretical and methodological advances have been made through the joint characterization of the pH and Eh. This opens the prospect to develop similar methods for fungi. The aim of our study was to investigate whether the methods developed for soil could be transposed to fungi. We first worked on artificial media, assessing the impact of fungal growth on the media in cultures. The growth of all 16 species tested significantly altered either Eh, pH or both in agar media. Measuring Eh reveals that even the species not modifying pH can have an impact on the surrounding environment. Reciprocally, altered media were used to characterize sensitivity of fungal growth to both pH and Eh parameters. The response of the six fungi tested to the modified media was quantitative with a decrease in colony diameter. In addition, colony aspect was repeatedly and thoroughly modified. As a first step towards the same studies in conditions matching the natural environment of fungal pathogens, we tested how the measurement can be performed with fungi growing on oilseed rape plants. In infected plant stems, pH and Eh were significantly altered, in opposite directions for L. maculans and S. sclerotiorum. The observed alcalinisation or acidification correlates with canker length. Our series of experiments indicate that the procedure published for Eh and pH in soil can be extended for measurement in agar media and in infected plants. Further, the joint characterization of both parameters opens the way to a more precise understanding of the impact of fungi on their environment, and conversely, of the environment on fungal growth. The availability of methods for measurement opens the prospect to study combinations of stresses, either on agar media or in plants, and get an understanding of the involvement of pH and Eh modifications in these interactions.
Microsatellite primer development for invasive perennial herb,Gypsophila paniculata(Caryophyllaceae)
Authors: Leimbach-Maus Hailee B. , Parks Syndell R. , Partridge Charlyn G. 
Published: August 2018

ABSTRACTPremise of the study: Gypsophila paniculataL. (baby’s breath) is an herbaceous perennial that has invaded much of northern and western United States and Canada, outcompeting and crowding out native and endemic species. Microsatellite primers were developed to analyze the genetic structure of invasive populations.Methods and Results:We have identified 16 polymorphic nuclear microsatellite loci forG. paniculataout of 73 loci that successfully amplified from a primer library created using Illumina sequencing technology. The developed primers amplified microsatellite loci in 3 invasive populations in Michigan. Primers amplified di-, tri-, and tetra-nucleotide repeats.Conclusions:These markers will be useful in characterizing the genetic structure of invasive populations throughout North America to aid targeted management efforts, and in native Eurasian populations to better understand invasion history. Five of these developed primers also amplified inG. elegans.
CLIP-Seq and massively parallel functional analysis of the CELF6 RNA binding protein reveals a role in destabilizing synaptic gene mRNAs through interaction with 3’UTR elements in vivo
Authors: Rieger Michael A. , King Dana M. , Cohen Barak A. , Dougherty Joseph D. 
Published: August 2018

AbstractCELF6 is a RNA-binding protein in a family of proteins with roles in human health and disease, however little is known about the mRNA targets or in vivo function of this protein. We utilized CLIP-Seq to identify, for the first time, in vivo targets of CELF6 and identify hundreds of transcripts bound by CELF6 in the brain. We found these are disproportionately mRNAs coding for synaptic proteins. We then conducted functional validation of these targets, testing greater than 400 CELF6 bound sequence elements for their activity, applying a massively parallel reporter assay framework to evaluation of the CLIP data. We also mutated potential binding motifs within these elements and tested their impact. This comprehensive analysis led us to ascribe a previously unknown function to CELF6: we found bound elements were generally repressive of translation, that CELF6 further enhances this repression via decreasing RNA abundance, and this process was dependent on UGU-rich sequence motifs. This greatly extends the known role for CELF6, which had previously been defined only as a splicing factor. We further extend these findings by demonstrating the same function for CELF3, CELF4, and CELF5. Finally, we demonstrate that the CELF6 targets are derepressed in CELF6 mutant mice in vivo, confirming this new role in the brain. Thus, our study demonstrates that CELF6 and other sub-family members are repressive CNS RNA-binding proteins, and CELF6 downregulates specific mRNAs in vivo.
Computational Analysis of Dynamical Fluctuations of Oncoprotein E7 (HPV) for the Hot Spot Residue Identification Using Elastic Network Model
Authors: Malik R. M. , Nazir F. , Fazal S. , Bhatti A. , Ullah M. , Malik S. I. , Kanwal A. , Aziz S. E. , Azam S. 
Published: August 2018

AbstractVirus proteins after invading human body alter host protein-protein interaction networks, resulting in the creation of new interactions, along with destroying or modifying other interactions or proteins. Topological features of new or modified networks compromise the host system causing increased production of viral particles. The molecular basis for this alteration of proteins interactivity is short linear peptide motifs similar in both virus and humans. These motifs are identified by modular domains, which are the subunits of a protein, in the human body, resulting in stabilization or moderation of these protein interactions Protein molecules can be modeled by elastic network models showing the fluctuations of residues when they are biologically active. We focused our computational study on the binding and competing interactions of the E7 protein of HPV with Rb protein. Our study was based on analysis of dynamic fluctuations of E7 in host cell and correlation analysis of specific residue found in motif of LxCxE, that is the key region in stabilizing interaction between E7 and Rb. Hot spot residue of E7 were also identified which could provide platform for drug prediction in future. Nevertheless, our study validates the role of linear binding motifs LxCxE of E7 of HPV in interacting with Rb as an important event in propagation of HPV in human cells and transformation of infection into cervical cancer.
Dot6 is a major regulator of cell size and a transcriptional activator of ribosome biogenesis in the opportunistic yeast Candida albicans
Authors: Chaillot Julien , Malick Jaideep , Sellam Adnane 
Published: August 2018

AbstractIn most species, size homeostasis appears to be exerted in late G1 phase as cells commit to division, called Start in yeast and the Restriction Point in metazoans. This size threshold couples cell growth to division and thereby establishes long-term size homeostasis. Our former investigations have shown that hundreds of genes markedly altered cell size under homeostatic growth conditions in the opportunistic yeast Candida albicans, but surprisingly only few of these overlapped with size control genes in the budding yeast Saccharomyces cerevisiae. Here, we investigated one of the divergent potent size regulators in C. albicans, the Myb-like HTH transcription factor Dot6. Our data demonstrated that Dot6 is a negative regulator of Start and also acts as a transcriptional activator of ribosome biogenesis (Ribi) genes. Genetic epistasis uncovered that Dot6 interacted with the master transcriptional regulator of the G1 machinery, SBF complex, but not with the Ribi and cell size regulators Sch9, Sfp1 and p38/Hog1. Dot6 was required for carbon-source modulation of cell size and it is regulated at the level of nuclear localization by TOR pathway. Our findings support a model where Dot6 acts as a hub that integrate directly growth cues via the TOR pathway to control the commitment to mitotic division at G1.
Ventral tegmental area astrocytes orchestrate avoidance and approach behavior
Authors: Gomez J. A. , Perkins J. M. , Beaudoin G. M. , Cook N. B. , Quraishi S. A. , Szoeke Erin A , Thangamani K. , Tschumi C. W. , Wanat M. J. , Maroof A. M. , Beckstead M. J. , Rosenberg P. A. , Paladini C. A. 
Published: August 2018

AbstractThe ventral tegmental area (VTA) is a heterogeneous midbrain structure, containing neurons and astrocytes, that coordinates approach and avoidance behaviors by integrating activity from numerous afferents. Within neuron-astrocyte networks, astrocytes control signals from distinct afferents in a circuit-specific manner, but whether this capacity scales up to drive motivated behavior has been undetermined. Using genetic and optical dissection strategies in vitro and during behavior we report that VTA astrocytes tune glutamatergic signaling selectively on local inhibitory neurons to drive a functional circuit for learned avoidance. In this circuit, VTA astrocytes facilitate excitation of local GABA neurons to increase inhibition of dopamine neurons. The increased inhibition of dopamine neurons elicits real-time and learned avoidance behavior that is sufficient to impede expression of learned preference for reward. Despite the large number of functions performed by astrocytes, loss of one glutamate transporter (GLT-1) from VTA astrocytes selectively blocks these avoidance behaviors and spares preference for reward. Thus, VTA astrocytes selectively regulate excitation of local GABA neurons to drive a distinct learned avoidance circuit that opposes learned approach behavior.
Progression of recent Mycobacterium tuberculosis exposure to active tuberculosis is a highly heritable complex trait driven by 3q23 in Peruvians
Authors: Luo Yang , Suliman Sara , Asgari Samira , Amariuta Tiffany , Calderon Roger , Lecca Leonid , León Segundo R. , Jimenez Judith , Yataco Rosa , Contreras Carmen , Galea Jerome T. , Becerra Mercedes , Nejentsev Sergey , Martínez-Bonet Marta , Nigrovic Peter A. , Moody D. Branch , Murray Megan B , Raychaudhuri Soumya 
Published: August 2018

AbstractAmong 1.8 billion people worldwide infected with Mycobacterium tuberculosis, 5-15% are expected to develop active tuberculosis (TB). Approximately half of these will progress to active TB within the first 18 months after infection, presumably because they fail to mount the initial immune response that contains the local bacterial spread. The other half will reactivate their latent infection later in life, likely triggered by a loss of immune competence due to factors such as HIV-associated immunosuppression or ageing. This natural history suggests that undiscovered host genetic factors may control early progression to active TB. Here, we report results from a large genome-wide genetic study of early TB progression. We genotyped a total of 4,002 active TB cases and their household contacts in Peru and quantified genetic heritability of early TB progression to be 21.2% under the liability scale. Compared to the reported of genome-wide TB susceptibility (15.5%), this result indicates early TB progression has a stronger genetic basis than population-wide TB susceptibility. We identified a novel association between early TB progression and variants located in an enhancer region on chromosome 3q23 (rs73226617, OR=1.19; P < 5×10−8). We used in silico and in vitro analyses to identify likely functional variants and target genes, highlighting new candidate mechanisms of host response in early TB progression.
Genomic data provides new insights on the demographic history and the extent of recent material transfers in Norway spruce
Authors: Chen Jun , li Lili , Milesi Pascal , Jansson Gunnar , Berlin Mats , Karlsson Bo , Aleksic Jelena , Vendramin Giovanni G. , Lascoux Martin 
Published: August 2018

AbstractPrimeval forests are today exceedingly rare in Europe and transfer of forest reproductive material for afforestation and improvement have been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce and estimate the amount of recent introduction used to establish the Norway spruce breeding program in Southern Sweden. Most of these trees belong to P. abies and originate from the base population of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, i.e. a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain, and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya) and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genome-wide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.
In SilicoIdentification of Three Types of Integrative and Conjugative Elements (ICEs) inElizabethkingia anophelisStrains Isolated from Around the World
Authors: Xu Jiannong , Pei Dong , Nicholson Ainsley , Lan Yuhao , Xia Qing 
Published: August 2018

ABSTRACTElizabethkingia anophelisis an emerging global multidrug-resistant opportunistic pathogen. We assessed the diversity among 13 complete genomes and 23 draft genomes ofE. anophelisderived from various environmental settings and human infections from different geographic regions around the world over past decades from 1950s. Thirty-one of these 36 strains harbor integrative and conjugative elements (ICEs). A total of 52 ICEs were identified, and categorized into three ICE types based on the architecture of signature genes in the conjugation module. The type II and III ICEs were found to integrate into regions adjacent to tRNA genes, while type I ICEs used a variety of integration sites, inserting into intergenic regions or even directly into a gene, sometimes disrupting gene function. Integrases such as tyrosine recombinases, serine recombinases and DDE transposases were found in most ICEs. The ICEs carry various cargo genes including transcription regulators and those involved in antibiotic resistance. The CRISPR-Cas system was found in nine strains, including four strains in which CRISPR-Cas machinery and ICEs co-exist. ICE distribution in the strains showed no geographic or temporal patterns. The ICEs inE. anophelisdiffer in gene structure and sequence from CTnDOT, a well-studied ICE prevalent inBacteroidesspp. This is the first set of ICEs identified in the family Flavobacteriaceae. As a prevalent type of mobile genetic elements in various strains ofE. anophelisaround the world, the categorization of ICEs will facilitate further investigations such as virulence, genome epidemiology and adaptation genomics ofE. anophelis.ImportanceElizabethkingia anophelisis an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. The Integrative Conjugative Element (ICE), found in many bacterial species, contains genes for transfer via conjugation and integration into the chromosome, along with various cargo genes. ICEs are identified in 31 of 36 strains and categorized into three types based on architecture of modular genes, integrases, and integration sites. ICE distribution in different strains displays no spatial and temporal patterns. Several ICE-containing strains also possessed CRISPR-Cas units, considered to be the bacterial adaptive immune system providing protection against phage and predatory mobile genetic elements. This co-existence suggests that ICEs are beneficial or at least not harmful to the bacterial cells they inhabit. ICEs as a component of the mobile genetic repertoire enable recipients to resist antibiotics, survive disinfecting agents, and adapt to various ecological niches.