bluuebunny/crossref_metadata_2025_split huggingface dataset:
Songs in the understory and colors in the canopy: habitat structure leads to different avian communication strategies in a tropical montane forest
Authors: Laverde-R Oscar , Cadena Carlos Daniel 
Published: August 2018

AbstractBirds inhabit a variety of habitats and they communicate using primarily visual and acoustic signals; two central hypotheses have been postulated to study the evolution of such a signals. The sensory drive hypothesis posits that variation in the physical properties of habitats leads to variation in natural selection pressures by affecting the ease with which different types of signals are perceived. Assuming that resources are limited for animals, the transfer hypothesis predicts a negative relationship between the investments in different types of signals. We evaluated these two hypotheses in a tropical montane forest bird assemblage. We also postulate a possible interaction between these two hypotheses: we predicted that the negative relationships between signals should be observed only when jointly considering birds from different environments (e.g. understory and canopy) due to the expected differences in communication strategies between habitats. The sensory drive hypothesis was supported by the differences we found between strata in vocal output, patch contrast to background and color conspicuousness, but not for the variables associated to song elaboration and hue disparity. We found support for the transfer hypothesis: birds with colors contrasting less against the background sing more frequently and birds with lower diversity of colors produce longer songs, understory birds showed also a negative relationship between signals, but only when accounting for phylogeny. We found partial support for the interaction between the sensory drive and the transfer hypotheses: hue disparity and vocal output were negatively related only when analyzing together birds from the canopy and the understory, but not when analyzing them separately. We conclude that the study of the evolution of communication signals needs to consider more than one channel and the functional interactions between them. The results of the interaction of optimal signaling strategies in two communication channels in the local habitats where animals signaling, are the patterns of colors and songs we revealed in a tropical montane forest bird assemblage.
TheRhizoctonia solaniRsLysM and RsRlpA effector proteins contribute to virulence by suppressing chitin-triggered immunity and hypersensitive response
Authors: Dölfors Fredrik , Holmquist Louise , Moschou Panagiotis N. , Dixelius Christina , Tzelepis Georgios 
Published: August 2018

AbstractRhizoctonia(in Greek “root-killer”) species and particularlyR. solaniattacks a broad range of plant species and crops. It belongs to Basidiomycota and is a soil-borne pathogen causing mainly damping-off diseases of seedlings and root rot, although it can infect plants in any stage. Despite the severity of this disease, many aspects inR. solaniinfection biology still remain to be elucidated. Here we investigated the role of two effector candidates, predicted from the genome of aR. solaniAG2-2IIIB strain that uses sugar beet as a host. Gene expression analysis showed that genes encoding for a LysM effector and a rare lipoprotein-A-like protein (RsRlpA) were induced upon early infection stages. When heterologous expressed inCercospora beticolathe two genes contributed to virulence. The RsLysM effector showed chitin‐ binding affinity and suppression of chitin-triggered immunity but could not protect hyphae from hydrolysis. The RsRlpA effector suppressed hypersensitive response inNicotiana benthamianaleaves. Overall, this study provides us with valuable information onR. solaniinfection biology, implying that this organism relies on mechanisms similar to hemibiotrophic pathogens in order to establish a successful infection.
Performance evaluation of inverse methods for identification and characterization of oscillatory brain sources: Ground truth validation & empirical evidences
Authors: Halder Tamesh , Talwar Siddharth , Jaiswal Amit Kumar , Banerjee Arpan 
Published: August 2018

AbstractOscillatory brain electromagnetic activity is an established tool to study neurophysiological mechanisms of human behavior using electro-encephalogram (EEG) and magneto-encephalogram (MEG) techniques. Often, to extract source level information in the cortex, researchers have to rely on inverse techniques that generate probabilistic estimation of the cortical activation underlying EEG/ MEG data from sensors located outside the body. State of the art source localization methods using current density estimates such as exact low resolution electromagnetic tomography (eLORETA) and minimum norm estimates (MNE) as well as beamformers such as Dynamic Imaging of Coherent Sources (DICS) and Linearly Constrained Minimum Variance (LCMV) have over the years been established as the prominent techniques of choice. However, these algorithms produce a distributed map of brain activity underlying sustained and transient responses during neuroimaging studies of behavior. Furthermore, the volume conduction effects, phase lags between sources and noise of the environment play a considerable role in adding uncertainty to source localization. There are very few comparative analyses that evaluates the “ground truth detection” capabilities of these methods and evaluates their efficacies based on sources in temporal cortex relevant for auditory processing as well as mesial temporal lobe epilepsies. In this Methods article, we compare the aforementioned techniques to estimate sources of spectral event generators in the cortex using a two-pronged approach. First, we simulated EEG data with point dipole (single and two-point), as well as, distributed dipole modelling techniques to validate the accuracy and sensitivity of each one of these methods of source localization. The abilities of the techniques were tested by comparing the localization error, focal width, false positive ratios while detecting already known location of neural activity generators under varying signal to noise ratios and depths of sources from cortical surface. Secondly, we performed source localization on empricial EEG data collected from human participants while they listened to rhythmic tone stimuli binaurally. Importantly, we found a less-distributed activation map is generated by LCMV and DICS when compared to eLORETA. However, control of false positives is much superior in eLORETA especially while using realistic distributed dipole scenarios. We also highlight the strengths and drawbacks of eLORETA, LCMV and DICS following a comprehensive analysis of simulated and empirical EEG data.
Xenopus hybrids provide insight into cell and organism size control
Authors: Gibeaux Romain , Miller Kelly , Acker Rachael , Kwon Taejoon , Heald Rebecca 
Published: August 2018

AbstractDetermining how size is controlled is a fundamental question in biology that is poorly understood at the organismal, cellular and subcellular levels. The Xenopus species, X. laevis and X. tropicalis differ in size at all three of these levels. Despite these differences, fertilization of X. laevis eggs with X. tropicalis sperm gives rise to viable hybrid animals that are intermediate in size. We observed that although hybrid and X. laevis embryogenesis initiates from the same sized zygote and proceeds synchronously through development, hybrid animals were smaller by the tailbud stage, and a change in the ratio of nuclear size to cell size was observed shortly after zygotic genome activation (ZGA), suggesting that differential gene expression contributes to size differences. Transcriptome analysis at the onset of ZGA identified twelve transcription factors paternally expressed in hybrids. A screen of these X. tropicalis factors by expression in X. laevis embryos revealed that Hes7 and Ventx2 significantly reduced X. laevis body length size by the tailbud stage, although nuclear to cell size scaling relationships were not affected as in the hybrid. Together, these results suggest that transcriptional regulation contributes to biological size control in Xenopus.
Computations performed by shadow enhancers and enhancer duplications vary across the Drosophila embryo
Authors: Scholes Clarissa , Biette Kelly M. , Harden Timothy T. , DePace Angela H. 
Published: August 2018

SUMMARYTranscription of developmental genes is controlled by multiple enhancers. Frequently, more than one enhancer can activate transcription from the same promoter in the same cells. In these cases, how is regulatory information from multiple enhancers combined to determine the overall expression output of their shared promoter? To investigate this question, we quantified nascent transcription driven by a pair shadow enhancers, each individual of the pair, and their duplications inDrosophilaembryos using live imaging. This set of constructs allows us to quantify the “computation” made by the pairs of enhancers: their combined output expression as a function of the expression that they drive separately. We show that the computation performed by these shadow enhancers and duplications varies across the expression pattern, implying that how their activities are combined depends on the transcriptional regulators bound to the enhancers in different parts of the embryo. Characterizing the computation made by multiple enhancers is a critical first step in developing conceptual and computational models of gene expression at the locus level, where multiple enhancers collaborate.
An Automated Behavioral Apparatus to Assess Distal Forelimb Function in Non-Human Primates
Authors: Totten Douglas , Novik Lisa , Christe Kari , Lemoy Marie-Josee , Roberts Jeffrey , Carmena Jose , Morecraft Robert , Ganguly Karunesh 
Published: August 2018

ABSTRACTBackgroundPrimate distal forelimb behaviors are commonly assessed using reach-to-grasp tasks. While these tasks are widely recognized as sensitive assays for forelimb function, they often require experimenter input, lack precise temporal cues for physiological monitoring, and can be expensive.New MethodUsing components developed by open-source electronics platforms, we have designed and tested a low-cost system to measure distal forelimb function in non-human primates. Our system is inexpensive; it is made primarily of acrylic and 3D printed plastic parts. Our control software, developed in MATLAB, was also used to control two cameras in order to capture and process video during behavior. The system was equipped with sensors, motors and microcontrollers to control the timing of the task and facilitate synchronization between behavior and neurophysiology with high temporal precision.ResultsWe demonstrate that this system can be used to monitor motor recovery after stroke and investigate neurophysiological correlates of motor control.Comparison with Existing MethodsCompared to a previous version of this task, our setup reduces experimenter input while providing unbiased delivery of behavioral cues and behavioral measurements with the temporal precision necessary for electrophysiological studies.ConclusionsIn summary, our system will allow unbiased monitoring of forelimb function in both healthy and injured animals that is compatible with electrophysiological studies.
Speaker-normalized vowel representations in the human auditory cortex
Authors: Sjerps Matthias J. , Fox Neal P. , Johnson Keith , Chang Edward F. 
Published: August 2018

AbstractHumans identify speech sounds, the fundamental building blocks of spoken language, using the same cues, or acoustic dimensions, as those that differentiate the voices of different speakers. The correct interpretation of speech cues is hence uncertain, and requires normalizing to the specific speaker. Here we assess how the human brain uses speaker-related contextual information to constrain the processing of speech cues. Using high-density electrocorticography, we recorded local neural activity from the cortical surface of participants who were engaged in a speech sound identification task. The speech sounds were preceded by speech from different speakers whose voices differed along the same acoustic dimension that differentiated the target speech sounds (the first formant; the lowest resonance frequency of the vocal tract). We found that the same acoustic speech sound tokens were perceived differently, and evoked different neural responses in auditory cortex, when they were heard in the context of different speakers. Such normalization involved the rescaling of acoustic-phonetic representations of speech, demonstrating a form of recoding before the signal is mapped onto phonemes or higher level linguistic units. This process is the result of auditory cortex’ sensitivity to the contrast between the dominant frequencies in speech sounds and those in their just preceding context. These findings provide important insights into the mechanistic implementation of normalization in human listeners. Moreover, they provide the first direct evidence of speaker-normalized speech sound representations in human parabelt auditory cortex, highlighting its critical role in resolving variability in sensory signals.
A large scale systemic RNAi screen in the red flour beetleTribolium castaneumidentifies novel genes involved in insect muscle development
Authors: Schultheis Dorothea , Weißkopf Matthias , Schaub Christoph , Ansari Salim , Dao Van Anh , Grossmann Daniela , Majumdar Upalparna , Hakeemi Muhammad Salim , Troelenberg Nicole , Richter Tobias , Schmitt-Engel Christian , Schwirz Jonas , Ströhlein Nadi , Teuscher Matthias , Bucher Gregor , Frasch Manfred 
Published: August 2018

AbstractAlthough muscle development has been widely studied inDrosophila melanogasterthere are still many gaps in our knowledge, and it is not known to which extent this knowledge can be transferred to other insects. To help in closing these gaps we participated in a large-scale RNAi screen that used the red flour beetle,Tribolium castaneum, as a screening platform. The effects of systemic RNAi were screened upon double-stranded RNA injections into appropriate muscle-EGFP tester strains. Injections into pupae were followed by the analysis of the late embryonic/early larval muscle patterns, and injections into larvae by the analysis of the adult thoracic muscle patterns. Herein we describe the results of the first-pass screens with pupal and larval injections, which covered ~8,500 and ~5,000 genes, respectively, of a total of ~16,500 genes of theTriboliumgenome. Apart from many genes known fromDrosophilaas regulators of muscle development, a collection of genes previously unconnected to muscle development yielded phenotypes in larval body wall and leg muscles as well as in indirect flight muscles. We then present the main candidates from the pupal injection screen that remained after being processed through a series of verification and selection steps. Further, we discuss why distinct though overlapping sets of genes are revealed by theDrosophilaandTriboliumscreening approaches.
Positive human health effects of sea spray aerosols: molecular evidence from exposed lung cell lines
Authors: Asselman Jana , Acker Emmanuel Van , Rijcke Maarten De , Tilleman Laurentijn , Nieuwerburgh Filip Van , Mees Jan , De Schamphelaere Karel A.C. , Janssen Colin R. 
Published: August 2018

AbstractSea spray aerosols (SSAs) have profound effects on climate and ecosystems. Furthermore, the presence of microbiota and biogenic molecules, produced by among others marine phytoplankton, in SSAs could lead to potential human health effects. Yet the exposure and effects of SSAs on human health remain poorly studied. Here, we exposed human epithelial lung cells to different concentrations of extracts of a natural sea spray aerosol (SSA), a laboratory-generated SSA, the marine algal toxin homoyessotoxin and a chemical mTOR inhibitor. The mTOR inhibitor was included as it has been hypothesized that natural SSAs may influence the mTOR cell signaling pathway. We observed significant effects on the mTOR pathway and PCSK9 in all exposures. Based on these expression patterns, a clear dose response relationship was observed. Our results indicate a potential for positive health effects when lung cells are exposed to environmentally relevant concentrations of natural SSAs, whereas potential negative effects were observed at high levels of the laboratory SSA and the marine algal toxin. Overall, these results provide a substantial molecular evidence base for potential positive health effects of SSAs at environmentally relevant concentrations through the mTOR pathway. The results provided here suggest that SSAs contain biomolecules with significant pharmaceutical potential in targeting PCSK9.
A Multiplexed DNA FISH strategy for Assessing Genome Architecture inC. elegans
Authors: Fields Brandon , Nguyen Son C. , Nir Guy , Kennedy Scott 
Published: August 2018

AbstractEukaryotic DNA is highly organized within nuclei and this genomic organization is important for genome function. Fluorescentin situhybridization (FISH) approaches allow the 3D architecture of genomes to be visualized. Scalable FISH technologies, which can be applied to whole animals, are needed to help unravel how genomic architecture regulates, or is regulated by, development, growth, reproduction, and aging. Here, we describe a multiplexed DNA FISH Oligopaint library that targets the entireC. elegansgenome at chromosome, three megabase, and 500 kb scales. We describe a hybridization strategy that provides flexibility to DNA FISH experiments by coupling a single primary probe synthesis reaction to dye conjugated detection oligos via bridge oligos, eliminating the time and cost typically associated with labeling probe sets for individual DNA FISH experiments. The approach allows visualization of genome organization at varying scales in all/most cells across all stages of development in an intact animal model system.
A divergent kinase lacking the glycine-rich loop regulates membrane ultrastructure of theToxoplasmaparasitophorous vacuole
Authors: Beraki Tsebaot , Xiaoyu Hu , Broncel Malgorzata , Young Joanna C. , O’Shaughnessy William J. , Borek Dominika M. , Treeck Moritz , Reese Michael L. 
Published: August 2018

AbstractApicomplexan parasites replicate within a protective organelle called the parasitophorous vacuole (PV). TheToxoplasma gondiiPV is filled with a network of tubulated membranes, which are thought to facilitate trafficking of effectors and nutrients. Despite being critical to parasite virulence, there is scant mechanistic understanding of the network’s functions. Here, we identify the parasite secreted kinase WNG1 as a critical regulator of tubular membrane biogenesis. WNG1 family members adopt an atypical protein kinase fold lacking the glycine rich ATP-binding loop that is required for catalysis in canonical kinases. Unexpectedly, we find that WNG1 is an active protein kinase that localizes to the PV lumen and phosphorylates PV-resident proteins, several of which are essential for the formation of a functional intravacuolar network. Moreover, we show that WNG1-dependent phosphorylation of these proteins is required for their membrane association, and thus their ability to tubulate membranes. Consequently, WNG1 knockout parasites have an aberrant PV membrane ultrastructure. Collectively, our results describe a unique family ofToxoplasmakinases and implicate phosphorylation of secreted proteins as a mechanism of regulating PV formation during parasite infection.
Revealing evolutionary constraints on proteins through sequence analysis
Authors: Wang Shou-Wen , Bitbol Anne-Florence , Wingreen Ned S. 
Published: August 2018

AbstractStatistical analysis of alignments of large numbers of protein sequences has revealed “sectors” of collectively coevolving amino acids in several protein families. Here, we show that selection acting on any functional property of a protein, represented by an additive trait, can give rise to such a sector. As an illustration of a selected trait, we consider the elastic energy of an important conformational change within an elastic network model, and we show that selection acting on this energy leads to correlations among residues. For this concrete example and more generally, we demonstrate that the main signature of functional sectors lies in the small-eigenvalue modes of the covariance matrix of the selected sequences. However, secondary signatures of these functional sectors also exist in the extensively-studied large-eigenvalue modes. Our simple, general model leads us to propose a principled method to identify functional sectors, along with the magnitudes of mutational effects, from sequence data. We further demonstrate the robustness of these functional sectors to various forms of selection, and the robustness of our approach to the identification of multiple selected traits.Author summaryProteins play crucial parts in all cellular processes, and their functions are encoded in their amino-acid sequences. Recently, statistical analyses of protein sequence alignments have demonstrated the existence of “sectors” of collectively correlated amino acids. What is the origin of these sectors? Here, we propose a simple underlying origin of protein sectors: they can arise from selection acting on any collective protein property. We find that the main signature of these functional sectors lies in the low-eigenvalue modes of the covariance matrix of the selected sequences. A better understanding of protein sectors will make it possible to discern collective protein properties directly from sequences, as well as to design new functional sequences, with far-reaching applications in synthetic biology.
Arnav: Site specific error models to identify variants in RNA
Authors: Ramu Avinash , Conrad Donald F. 
Published: August 2018

AbstractSummaryWe present Arnav (Analysis of RNA variants) a lightweight and easy-to-use statistical method for detecting mutations from RNA sequencing data. Site-specific error models allow Arnav to call variants with high specificity when the true variant allele fraction is unknown. We show the utility of Arnav by identifying variants using RNA sequencing data from the GTEx project.Availability and ImplementationArnav is implemented in C++ and is distributed under the GPL license at https://github.com/gatoravi/arnav.Contactaramu@wustl.edu
Optic Nerve Tortuosity and Globe Proptosis in Normal and Glaucoma Subjects
Authors: Wang Xiaofei , Rumpel Helmut , Baskaran Mani , Tun Tin A , Strouthidis Nicholas , Perera Shamira A , Nongpiur Monisha E , Hoe Lim Winston Eng , Aung Tin , Milea Dan , Girard Michaël J. A. 
Published: August 2018

AbstractPurposeTo assess the difference in optic nerve tortuosity during eye movements and globe proptosis between primary open angle glaucoma and normal subjects using orbital magnetic resonance imaging.Methods10 Chinese subjects matched for age, ethnicity and refractive errors were recruited, including five normal controls and five patients with primary open angle glaucoma. All subjects underwent magnetic resonance imaging to assess their optic nerves and globes for three eye positions: primary gaze, adduction and abduction. Optic nerve tortuosity (optic nerve length divided by the distance between two ends) and globe proptosis (maximum distance between cornea and interzygomatic line) were measured from magnetic resonance imaging images.ResultsIn adduction, the tortuosity of normal eyes was significantly larger than that of the glaucomatous eyes. Optic nerve tortuosity in adduction in the control and glaucoma groups were 1.004±0.003 (mean ± standard deviation) and 1.001±0.001, respectively (p=0.037). Globe proptosis (primary gaze) in glaucoma subjects (19.14±2.11 mm) was significantly higher than that in control subjects (15.32±2.79 mm; p = 0.046).ConclusionsIn this sample, subjects with glaucoma exhibited more taut optic nerves and more protruding eye globes compared to normal eyes. This may impact optic nerve head deformations in anatomically predisposed patients.PrécisEyes with glaucoma have tauter optic nerves compared with normal eyes, which may exert more force on the optic nerve head tissues during eye movements.