bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bottled aqua incognita: Microbiota assembly and dissolved organic matter diversity in natural mineral waters
Authors: Lesaulnier Celine C. , Herbold Craig W. , Pelikan Claus , Berry David , Gérard Cédric , Coz Xavier Le , Gagnot Sophie , Niggemann Jutta , Dittmar Thorsten , Singer Gabriel A. , Loy Alexander 
Published: June 2017

ABSTRACTBackgroundNon-carbonated natural mineral waters contain microorganisms that regularly grow after bottling despite low concentrations of dissolved organic matter (DOM). Yet, the compositions of bottled water microbiota and organic substrates that fuel microbial activity, and how both change after bottling, are still largely unknown.ResultsWe performed a multifaceted analysis of microbiota and DOM diversity in twelve natural mineral waters from six European countries. 16S rRNA gene-based analyses showed that less than ten species-level operational taxonomic units (OTUs) dominated the bacterial communities in the water phase and associated with the bottle wall after a short phase of post-bottling growth. Members of the betaproteobacterial generaCurvibacter,Aquabacterium, andPolaromonas(Comamonadaceae) grew in most waters and represent ubiquitous, mesophilic, heterotrophic aerobes in bottled waters. Ultrahigh-resolution mass spectrometry of DOM in bottled waters and their corresponding source waters identified thousands of molecular formulae characteristic of mostly refractory, soil-derived DOM.ConclusionsThe bottle environment, including source water physicochemistry, selected for growth of a similar low-diversity microbiota across various bottled waters. Relative abundance changes of hundreds of multi-carbon molecules were related to growth of less than ten abundant OTUs. We thus speculate that individual bacteria cope with oligotrophic conditions by simultaneously consuming diverse DOM molecules.
Hippo signaling restricts cells in the second heart field that differentiate into Islet-1-positive atrial cardiomyocytes
Authors: Fukui Hajime , Miyazaki Takahiro , Ishikawa Hiroyuki , Nakajima Hiroyuki , Mochizuki Naoki 
Published: June 2017

AbstractCardiac precursor cells (CPCs) in the first heart field (FHF) and the second heart field (SHF) present at both arterial and venous poles assemble to form a cardiac tube in zebrafish. Hippo kinase cascade is essential for proper heart formation; however, it remains elusive how Hippo signal contributes to early cardiac fate determination. We here demonstrate that mutants oflarge tumor suppressor kinase 1/2(lats1/2) exhibited an increase in a SHF marker, Islet1 (Isl1)-positive andhand2promoter-activated venous pole atrial cardiomyocytes (CMs) and that those showed expansion of the domain between between the anterior and the posterior lateral plate mesoderm. Consistently, TEAD-8 dependent transcription was activated in caudal region of the left ALPM cells that gave rise to the venous pole atrial CMs. Yap1/Wwtr1-promotedbmp2bexpression was essential for Smad-regulatedhand2expression in the left ALPM, indicating that Hippo signaling restricts the SHF cells originating from the left ALPM that move toward the venous pole.
The Molecular Genetic Basis of Herbivory between Butterflies and their Host-Plants
Authors: Nallu Sumitha , Hill Jason , Don Kristine , Sahagun Carlos , Zhang Wei , Meslin Camille , Snell-Rood Emilie , Clark Nathan L. , Morehouse Nathan I. , Bergelson Joy , Wheat Christopher W. , Kronforst Marcus R. 
Published: June 2017

AbstractInteractions between herbivorous insects and their host-plants are a central component of terrestrial food webs and a critical topic in agriculture, where a substantial fraction of potential crop yield is lost annually to pests. Important insights into plant-insect interactions have come from research on specific plant defenses and insect detoxification mechanisms. Yet, much remains unknown about the molecular mechanisms that mediate plant-insect interactions. Here we use multiple genome-wide approaches to map the molecular basis of herbivory from both plant and insect perspectives, focusing on butterflies and their larval host-plants. Parallel genome-wide association studies in the Cabbage White butterfly,Pieris rapae, and its host-plant,Arabidopsis thaliana, pinpointed a small number of butterfly and plant genes that influenced herbivory. These genes, along with much of the genome, were regulated in a dynamic way over the time course of the feeding interaction. Comparative analyses, including diverse butterfly/plant systems, showed a variety of genome-wide responses to herbivory, yet a core set of highly conserved genes in butterflies as well as their host-plants. These results greatly expand our understanding of the genomic causes and evolutionary consequences of ecological interactions across two of Nature’s most diverse taxa, butterflies and flowering plants.
Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy
Authors: Wu Yicong , Kumar Abhishek , Smith Corey , Ardiel Evan , Chandris Panagiotis , Christensen Ryan , Rey-Suarez Ivan , Guo Min , Vishwasrao Harshad D. , Chen Jiji , Tang Jianyong , Upadhyaya Arpita , Riviere Patrick J. La , Shroff Hari 
Published: June 2017

AbstractLight-sheet fluorescence microscopy (LSFM) enables high-speed, high-resolution, gentle imaging of live biological specimens over extended periods. Here we describe a technique that improves the spatiotemporal resolution and collection efficiency of LSFM without modifying the underlying microscope. By imaging samples on reflective coverslips, we enable simultaneous collection of multiple views, obtaining 4 complementary views in 250 ms, half the period it would otherwise take to collect only two views in symmetric dual-view selective plane illumination microscopy (diSPIM). We also report a modified deconvolution algorithm that removes the associated epifluorescence contamination and fuses all views for resolution recovery. Furthermore, we enhance spatial resolution (to < 300 nm in all three dimensions) by applying our method to a new asymmetric diSPIM, permitting simultaneous acquisition of two high-resolution views otherwise difficult to obtain due to steric constraints at high numerical aperture (NA). We demonstrate the broad applicability of our method in a variety of samples of moderate (< 50 μm) thickness, studying mitochondrial, membrane, Golgi, and microtubule dynamics in single cells and calcium activity in nematode embryos.
Analysis of Copy Number Loss of the ErbB4 Receptor Tyrosine Kinase in Glioblastoma
Authors: Jones DeAnalisa C. , Scanteianu Adriana , DiStefano Matthew , Bouhaddou Mehdi , Birtwistle Marc R. 
Published: June 2017

ABSTRACTCurrent treatments for glioblastoma multiforme (GBM)—an aggressive form of brain cancer—are minimally effective and yield a median survival of 14.6 months and a two-year survival rate of 30%. Given the severity of GBM and the limitations of its treatment, there is a need for the discovery of novel drug targets for GBM and more personalized treatment approaches based on the characteristics of an individual’s tumor. Most receptor tyrosine kinases—such as EGFR—act as oncogenes, but publicly available data from the Cancer Cell Line Encyclopedia (CCLE) indicates copy number loss in the ERBB4 RTK gene across dozens of GBM cell lines, suggesting a potential tumor suppressor role. This loss is mutually exclusive with loss of its cognate ligand NRG1 in CCLE as well, more strongly suggesting a functional role. The availability of higher resolution copy number data from clinical GBM patients in The Cancer Genome Atlas (TCGA) revealed that a region in Intron 1 of the ERBB4 gene was deleted in 69.1% of tumor samples harboring ERBB4 copy number loss; however, it was also found to be deleted in the matched normal tissue samples from these GBM patients (n = 81). Using the DECIPHER Genome Browser, we also discovered that this mutation occurs at approximately the same frequency in the general population as it does in the disease population. We conclude from these results that this loss in Intron 1 of the ERBB4 gene is neither ade novodriver mutation nor a predisposing factor to GBM, despite the indications from CCLE. A biological role of this significantly occurring genetic alteration is still unknown. While this is a negative result, the broader conclusion is that while copy number data from large cell line-based data repositories may yield compelling hypotheses, careful follow up with higher resolution copy number assays, patient data, and general population analyses are essential to codify initial hypotheses.
Dopamine neuron dependent behaviors mediated by glutamate cotransmission
Authors: Mingote Susana , Chuhma Nao , Kalmbach Abigail , Thomsen Gretchen M. , Wang Yvonne , Mihali Andra , Sferrazza Caroline , Zucker-Scharff Ilana , Siena Anna-Claire , Welch Martha G. , Lizardi-Ortiz José , Sulzer David , Moore Holly , Gaisler-Salomon Inna , Rayport Stephen 
Published: June 2017

ABSTRACTDopamine neurons in the ventral tegmental area use glutamate as a cotransmitter. To elucidate the behavioral role of the cotransmission, we targeted the glutamate-recycling enzyme glutaminase (geneGLS1). In mice with a DAT-driven conditional heterozygous (cHET) reduction of GLS1 in their dopamine neurons, dopamine neuron survival and transmission were unaffected, while glutamate cotransmission at phasic firing frequencies was reduced, enabling focusing the cotransmission. DAT GLS1 cHET mice showed normal emotional and motor behaviors, and an unaffected response to acute amphetamine. Strikingly, amphetamine sensitization was reduced and latent inhibition potentiated. These behavioral effects, also seen in global GLS1 HETs with a schizophrenia resilience phenotype, were not seen in mice with an Emx1-driven forebrain reduction affecting most brain glutamatergic neurons. Thus, a reduction in dopamine neuron glutamate cotransmission appears to mediate significant components of the GLS1 HET schizophrenia resilience phenotype, and glutamate cotransmission appears to be important in attribution of motivational salience.
Scaling of optogenetically evoked signaling in a higher-order corticocortical pathway in the anesthetized mouse
Authors: Li Xiaojian , Yamawaki Naoki , Barrett John M. , Körding Konrad P. , Shepherd Gordon M. G. 
Published: June 2017

ABSTRACTQuantitative analysis of corticocortical signaling is needed to understand and model information processing in cerebral networks. However, higher-order pathways, hodologically remote from sensory input, are not amenable to spatiotemporally precise activation by sensory stimuli. Here, we combined parametric channelrhodopsin-2 (ChR2) photostimulation with multi-unit electrophysiology to study corticocortical driving in a parietofrontal pathway from retrosplenial cortex (RSC) to posterior secondary motor cortex (M2) in micein vivo. Ketamine anesthesia was used both to eliminate complex activity associated with the awake state and to enable stable recordings of responses over a wide range of stimulus parameters. Photostimulation of ChR2-expressing neurons in RSC, the upstream area, produced local activity that decayed quickly. This activity in turn drove downstream activity in M2 that arrived rapidly (5-10 ms latencies), and scaled in amplitude across a wide range of stimulus parameters as an approximately constant fraction (~0.2) of the upstream activity. A model-based analysis could explain the corticocortically driven activity with exponentially decaying kernels (~20 ms time constant) and small delay. Reverse (antidromic) driving was similarly robust. The results show that corticocortical signaling in this pathway drives downstream activity rapidly and scalably, in a mostly linear manner. These properties, identified in anesthetized mice and represented in a simple model, suggest a robust basis for supporting complex non-linear dynamic activity in corticocortical circuits in the awake state.SIGNIFICANCE STATEMENTThe signaling properties of corticocortical connections are not well understood, particularly for higher-order inter-areal pathways. Here, we developed a paradigm based on parametric optogenetic photostimulation, linear-array electrophysiology, and mathematical modeling to characterize signaling along corticortical connections linking retrosplenial cortex to posterior secondary motor cortex (M2) in anesthetized mice. The results indicate that corticocortically driven activity in the downstream area followed the optogenetically evoked upstream activity in a rapid and scalable manner, and could be described with a simple linear integrator model. These findings suggest that this pathway, when activated selectively in the unconscious state, supports intrinsically linear inter-areal communication.
Neurodegeneration-associated mutant TREM2 proteins abortively cycle between the ER and ER–Golgi intermediate compartment
Authors: Sirkis Daniel W. , Aparicio Renan E. , Schekman Randy 
Published: June 2017

ABSTRACTTriggering receptor expressed on myeloid cells 2 (TREM2) is a transmembrane protein expressed on microglia within the brain. Several rare mutations inTREM2cause an early-onset form of neurodegeneration when inherited homozygously. Here we investigate how these mutations affect the intracellular transport of TREM2. We find that most pathogenic TREM2 mutant proteins fail to undergo normal maturation in the Golgi complex and show markedly reduced cell surface expression. Prior research has suggested that two such mutants are retained in the endoplasmic reticulum (ER), but we find, using a cell-free COPII vesicle budding reaction, that mutant TREM2 is exported efficiently from the ER. In addition, mutant TREM2 becomes sensitive to cleavage by endoglycosidase D under conditions that inhibit recycling to the ER, indicating that it normally reaches a post-ER compartment. Maturation-defective TREM2 mutants are also efficiently bound by a lectin that recognizesO-glycans added in the ER–Golgi intermediate compartment (ERGIC) andcisGolgi cisterna. Finally, mutant TREM2 accumulates in the ERGIC in cells depleted of COPI. These results indicate that efficient ER export is not sufficient to enable normal cell surface expression of TREM2. Moreover, our findings suggest that the ERGIC may play an underappreciated role as a quality-control center for mutant and/or malformed membrane proteins.
Acquired bilateral telangiectasia macularis eruptiva perstans: A unique clinical feature of photodamaging rather than a subtype of cutaneous mastocytosis
Authors: Moon Hye‐Rim , Kim Young Jae , Jung Joon Min , Won Chong Hyun , Lee Mi Woo , Choi Jee Ho , Chang Sung Eun 
Published: June 2017

AbstractTelangiectasia macularis eruptiva perstans (TMEP) is a rare subtype of cutaneous mastocytosis, characterized by telangiectatic tan to brown macules on the trunk and extremities. Although TMEP has been descried as an uncommon disease in the literature, we often encounter patients with TMEP lesions in the outpatient clinic. We aimed to assess the clinical and histopathological characteristics of acquired bilateral TMEP, and the pathophysiological mechanism of acquired bilateral TMEP among these patients. We retrospectively reviewed 30 patients (28 men and 2 women) with acquired bilateral TMEP; multiple telangiectatic dark red to brown macules that were symmetrically distributed. The clinical characteristics and general histopathological findings of lesional skin were investigated. The number of mast cells was evaluated using immunohistochemical analysis with an antibody directed against c‐kit (CD117). Acquired bilateral TMEP was predominantly localized on the sun‐exposed area: the upper arm in 30 patients (100%), forearm in 19 patients (63.3%) and anterior chest in 15 patients (50%). A total of 16 patients (53.3%) showed at least one aggravating factor, including UV irradiation, alcohol use and heat exposure. Compared with the mast cell numbers in 19 age‐ and biopsy site‐matched healthy controls (91 ± 29.0/mm2), the number of mast cells in the papillary dermal skin of acquired bilateral TMEP patients was significantly increased (159 ± 37.2/mm2, P < 0.01). In addition, a significant difference in vessel numbers in the papillary dermis was observed between acquired bilateral TMEP patients and healthy controls (10.5 ± 1.9 vs 5.4 ± 1.0/mm2, P < 0.01). Acquired bilateral TMEP is a relatively common disorder in middle‐aged Asian men. An increased number of mast cells and dilated vessels might be a photoaging‐related reactive process of chronic sun‐exposure, which consequently leads to the formation of characteristic telangiectatic hyperpigmentary macules through certain melanogenic mediators.
Field evidence for a rapid adaptive plastic response in morphology and growth of littoral and pelagic brook charr: A reciprocal transplant experiment
Authors: Pépino Marc , Magnan Pierre , Proulx Raphaël 
Published: June 2017

AbstractPhenotypic plasticity, a process by which individuals modify their morphology, physiology, or behaviour in response to environmental changes, can be seen as the first step in adaptive evolution. Phenotypic plasticity is adaptive if two conditions are met: (1) the phenotype is associated with an environment (plastic response) and (2) the phenotype–environment association increases individual fitness (adaptive response).Using a reciprocal transplant experiment, we tested the hypothesis that functional morphological responses are correlated with growth at two organizational levels (between and within ecotypes) in brook charr.Four‐month‐old individuals from four littoral and four pelagic families raised in the laboratory were transferred into eight littoral (3 m × 4 m × 1.5 m depth) and eight pelagic (3 m × 4 m × 6 m depth) lake enclosures for a period of 12 weeks.Fin length (the main discriminant trait of the littoral and pelagic ecotypes) was less plastic than body shape. Growth was higher in the pelagic than in the littoral habitat, but offspring from littoral and pelagic parental origins did not experience higher growth in their respective habitats (comparison between ecotypes). The body shape of most individuals transplanted to their reciprocal environment shifted toward the form expected in that environment. This plastic response in body shape was functionally correlated with growth within ecotypes, but only in the littoral habitat. Furthermore, the within‐ecotype variance of both morphological traits and growth were higher in the littoral than in the pelagic habitat.Small phenotypic differences could have direct consequences on fitness in the less favourable habitat, inducing higher inter‐individual variance in growth and stronger phenotype–growth associations. We suggest that phenotypic accommodation and cryptic genetic variation, two mechanisms previously proposed as mechanisms involved in distinct situations, could be simultaneously involved to hasten the process of adaptive evolution in an unfavourable environment.Aplain language summaryis available for this article.
Detecting elusive aspects of wildlife ecology using drones: New insights on the mating dynamics and operational sex ratios of sea turtles
Authors: Schofield Gail , Katselidis Kostas A. , Lilley Martin K. S. , Reina Richard D. , Hays Graeme C. 
Published: June 2017

Abstract

Offspring and breeding (operational) sex ratios (OSR) are a key component of demographic studies. While offspring sex ratios are often relatively easy to measure, measuring OSRs is often far more problematic. Yet, highly skewed OSRs, and a lack of male–female encounters, may be an important extinction driver.

Using loggerhead sea turtles (Caretta caretta) as a case study, we showed the utility of drones, i.e. unmanned aerial vehicles (UAVs), to distinguish adult males and females in a marine breeding area, using a combination of morphological characteristics (tail length) and behavioural differences (active mating, courting and searching by males versus resting by females). Through repeated surveys, we documented seasonal changes in the OSR.

While the number, and ratio, of males and females on the breeding grounds changed massively, the ratio of receptive females (derived from the rate of influx of new individuals to the area) to breeding males remained close to 1:1 for much of the period before nesting commenced. Hence, we show how large imbalances in the number of adult males and females may translate into relatively balanced OSRs.

Our results suggest that the departure of males from the breeding grounds is linked to a decline in female receptivity, with female sea turtles being known to store sperm to ensure high clutch fertility throughout the nesting season.

In conclusion, while we detected up to three times more females than males at the breeding ground, at present, OSRs appear stable. However, because most males breed annually (vs. biannually by females), there might only be c. 100 males in the adult population (i.e. adult sex ratio of 1:7.5), which might become further skewed under expected climate change scenarios; thus, we need to identify the minimum number of males required to prevent extinction. Finally, we highlight the use of UAVs for assessing the mating dynamics of other marine, terrestrial or avian species, in which adults might exhibit visually detectable differences, such as sexual dimorphism, external body characteristics or grouping tendencies.

A plain language summary is available for this article.
Detecting hybridization by likelihood calculation of gene tree extra lineages given explicit models
Authors: Olave Melisa , Avila Luciano J. , Sites Jack W. , Morando Mariana 
Published: June 2017

Abstract

Explanations for gene tree discordance with respect to a species tree are commonly attributed to deep coalescence (also known as incomplete lineage sorting [ILS]), as well as different evolutionary processes such as hybridization, horizontal gene transfer and gene duplication. Among these, deep coalescence is usually quantified as the number of extra linages and has been studied as the principal source of discordance among gene trees, while the other processes that could contribute to gene tree discordance have not been fully explored. This is an important issue for hybridization because interspecific gene flow is well documented and widespread across many plant and animal groups.
Here, we propose a new way to detect gene flow when ILS is present that evaluates the likelihood of different models with various levels of gene flow, by comparing the expected gene tree discordance, using the number of extra lineages. This approach consists of proposing a model, simulating a set of gene trees to infer a distribution of expected extra lineages given the model, and calculating a likelihood function by comparing the fit of the real gene trees to the simulated distribution. To count extra lineages, the gene tree is first reconciled within the species tree, and for a given species tree branch the number of gene lineages minus one is counted. We develop a set of r functions to parallelize software to allow simulations, and to compare hypotheses via a likelihood ratio test to evaluate the presence of gene flow when ILS is present, in a fast and simple way.
Our results show high accuracy under very challenging scenarios of high impact of ILS and low gene flow levels, even using a modest dataset of 5–10 loci and 5–10 individuals per species.
We present a powerful and fast method to detect hybridization in the presence of ILS. We discuss its advantage with large dataset (such as genomic scale), and also identifies possible issues that should be explored with more complex models in future studies.