bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inter-decadal variability of phytoplankton biomass along the coastal West Antarctic Peninsula
Authors: Kim Hyewon , Ducklow Hugh W. , Abele Doris , Ruiz Barlett Eduardo M. , Buma Anita G. J. , Meredith Michael P. , Rozema Patrick D. , Schofield Oscar M. , Venables Hugh J. , Schloss Irene R. 
Published: May 2018

The West Antarctic Peninsula (WAP) is a climatically sensitive region where periods of strong warming have caused significant changes in the marine ecosystem and food-web processes. Tight coupling between phytoplankton and higher trophic levels implies that the coastal WAP is a bottom-up controlled system, where changes in phytoplankton dynamics may largely impact other food-web components. Here, we analysed the inter-decadal time series of year-round chlorophyll-a(Chl) collected from three stations along the coastal WAP: Carlini Station at Potter Cove (PC) on King George Island, Palmer Station on Anvers Island and Rothera Station on Adelaide Island. There were trends towards increased phytoplankton biomass at Carlini Station (PC) and Palmer Station, while phytoplankton biomass declined significantly at Rothera Station over the studied period. The impacts of two relevant climate modes to the WAP, the El Niño-Southern Oscillation and the Southern Annular Mode, on winter and spring phytoplankton biomass appear to be different among the three sampling stations, suggesting an important role of local-scale forcing than large-scale forcing on phytoplankton dynamics at each station. The inter-annual variability of seasonal bloom progression derived from considering all three stations together captured ecologically meaningful, seasonally co-occurring bloom patterns which were primarily constrained by water-column stability strength. Our findings highlight a coupled link between phytoplankton and physical and climate dynamics along the coastal WAP, which may improve our understanding of overall WAP food-web responses to climate change and variability.This article is part of the theme issue ‘The marine system of the West Antarctic Peninsula: status and strategy for progress in a region of rapid change’.
Spring–summer net community production, new production, particle export and related water column biogeochemical processes in the marginal sea ice zone of the Western Antarctic Peninsula 2012–2014
Authors: Ducklow Hugh W. , Stukel Michael R. , Eveleth Rachel , Doney Scott C. , Jickells Tim , Schofield Oscar , Baker Alex R. , Brindle John , Chance Rosie , Cassar Nicolas 
Published: May 2018

New production (New P, the rate of net primary production (NPP) supported by exogenously supplied limiting nutrients) and net community production (NCP, gross primary production not consumed by community respiration) are closely related but mechanistically distinct processes. They set the carbon balance in the upper ocean and define an upper limit for export from the system. The relationships, relative magnitudes and variability of New P (from
15
NO
3
–
uptake), O
2
: argon-based NCP and sinking particle export (based on the
238
U :
234
Th disequilibrium) are increasingly well documented but still not clearly understood. This is especially true in remote regions such as polar marginal ice zones. Here we present a 3-year dataset of simultaneous measurements made at approximately 50 stations along the Western Antarctic Peninsula (WAP) continental shelf in midsummer (January) 2012–2014. Net seasonal-scale changes in water column inventories (0–150 m) of nitrate and iodide were also estimated at the same stations. The average daily rates based on inventory changes exceeded the shorter-term rate measurements. A major uncertainty in the relative magnitude of the inventory estimates is specifying the start of the growing season following sea-ice retreat. New P and NCP(O
2
) did not differ significantly. New P and NCP(O
2
) were significantly greater than sinking particle export from thorium-234. We suggest this is a persistent and systematic imbalance and that other processes such as vertical mixing and advection of suspended particles are important export pathways.

This article is part of the theme issue ‘The marine system of the west Antarctic Peninsula: status and strategy for progress in a region of rapid change’.
Flow modification associated with reduced genetic health of a river-breeding frog,Rana boylii
Authors: Peek Ryan A. , O’Rourke Sean M. , Miller Michael R. 
Published: May 2018

AbstractRiver regulation or flow modification—the hydrological alteration of flow by dams and diversions—has been implicated as a cause of fundamental change to downstream aquatic ecosystems. Flow modification changes the patterns and functionality of the natural flow regime, and has the potential to restrict population connectivity and gene flow in river-dependent organisms. Since population connectivity and the maintenance of genetic diversity are fundamental drivers of long-term persistence, understanding the extent flow modification impacts these critical attributes of genetic health is an important goal for long-term conservation. Foothill yellow-legged frogs (Rana boylii) were historically abundant throughout many western rivers but have declined since the onset of regulation. However, the extent to whichR. boyliipopulations in rivers with altered flow regimes are maintaining connectivity and genetic diversity is unknown. Here we use genetic methods to investigate the impacts of flow alteration onR. boyliito explore their potential for long-term persistence under continued flow modification. We foundR. boyliiin rivers with flow modification showed striking patterns of isolation and trajectories of genetic diversity loss relative to unregulated rivers. For example, flow modification explained the greatest amount of variance in population genetic differentiation compared with other covariates including geographic distance. Importantly, patterns of connectivity and genetic diversity loss were observed regardless of flow alteration level but were most prominent in locations with the greatest flow modification intensity. Although our results do not bode well for long-term persistence ofR. boyliipopulations under current flow regulation regimes, they do highlight the power of genetic monitoring for assessing population health in aquatic organisms.
Brief Freezing Steps Lead to Robust Immunofluorescence in Drosophila Larval Brains
Authors: Buckley Dominic , Thapa Ada , Nguyen Minh Q. , Blankinship Essence , Williamson Diana , Cloud Veronica , Mohan Ryan D. 
Published: May 2018

AbstractDrosophila melanogaster possess complex neuronal networks regulating sophisticated behavioral outputs that aid in studying the molecular mechanisms of neuronal function and neurodegenerative disease. Immunofluorescence (IF) techniques provide a way to visualize the spatiotemporal organization of these networks, permitting observation of their development, functional location, remodeling, and eventually - degradation. However, general immunostaining techniques do not always result in sufficient antibody penetration through the brain, and techniques used to enhance permeability can compromise structural integrity. We have found that freezing larval brains facilitates permeability with no apparent loss of antibody specificity or structural integrity. To demonstrate the advantage of this freezing technique, we compared results to two commonly used permeation methods: Detergent alone (Basic) and proteolytic degradation (Collagenase) techniques.SummaryHere we compare four different immunofluorescence techniques demonstrating that freezing Drosophila brains results in robust staining of small neurons in the larval brain without compromising structural integrity.
Automating multimodal microscopy with NanoJ-Fluidics
Authors: Almada Pedro , Pereira Pedro M. , Culley Siân , Caillol Ghislaine , Boroni-Rueda Fanny , Dix Christina L. , Laine Romain F. , Charras Guillaume , Baum Buzz , Leterrier Christophe , Henriques Ricardo 
Published: May 2018

AbstractFluorescence microscopy can reveal all aspects of cellular mechanisms, from molecular details to dynamics, thanks to approaches such as super-resolution and live-cell imaging. Each of its modalities requires specific sample preparation and imaging conditions to obtain high-quality, artefact-free images, ultimately providing complementary information. Combining and multiplexing microscopy approaches is crucial to understand cellular events, but requires elaborate workflows involving multiple sample preparation steps. We present a robust fluidics approach to automate complex sequences of treatment, labelling and imaging of live and fixed cells. Our open-source NanoJ-Fluidics system is based on low-cost LEGO hardware controlled by ImageJ-based software and can be directly adapted to any microscope, providing easy-to-implement high-content, multimodal imaging with high reproducibility. We demonstrate its capacity to carry out complex sequences of experiments such as super-resolved live-to-fixed imaging to study actin dynamics; highly-multiplexed STORM and DNA-PAINT acquisitions of multiple targets; and event-driven fixation microscopy to study the role of adhesion contacts in mitosis.
Temperature response of Rubisco kinetics in Arabidopsis thaliana: thermal breakpoints and implications for reaction mechanisms
Authors: Boyd Ryan A. , Cavanagh Amanda P. , Kubien David S. , Cousins Asaph B. 
Published: May 2018

ABSTRACTOptimization of Rubisco kinetics could improve photosynthetic efficiency, ultimatly resulting in increased crop yield. However, imprecise knowledge of the reaction mechanism and the individual rate constants limit our ability to optimize the enzyme. Membrane inlet mass spectrometery (MIMS) may offer benefits over traditional methods for determining individual rate constants of the Rubisco reaction mechanism, as it can directly monitor concentration changes in CO2, O2, and their isotopologs during assays. However, a direct comparsion of MIMS to the traditional Radiolabel method of determining Rubisco kinetic parameters has not been made. Here, the temperature responses of Rubisco kinetic parameters from Arabidopsis thaliana were measured using the Radiolabel and MIMS methods. The two methods provided comparable parameters above 25 °C, but temperature responses deviated at low temperature as MIMS derived catalytic rates of carboxylation, oxygenation, and CO2/O2 specificity showed thermal breakpoints. Here we discuss the variability and uncertainty surrounding breakpoints in the Rubisco temperature response and relavance of individual rate constants of the reaction mechanisms to potential breakpoints.
Guppies prefer to follow large (robot) leaders irrespective of own size
Authors: Bierbach David , Mönck Hauke J. , Lukas Juliane , Habedank Marie , Romanczuk Pawel , Landgraf Tim , Krause Jens 
Published: May 2018

AbstractBody size is often assumed to determine how successful an individual can lead others with larger individuals being more likely to lead than smaller ones. However, direct evidence for such a relation is scarce. Furthermore, even if larger individuals are more likely to lead, body size correlates often with specific behavioral patterns (e.g., swimming capacity) and it is thus unclear whether larger individuals are more often followed than smaller ones because they are larger or because they behave in a certain way. To control for behavioral differences among differentially-sized leaders, we used biomimetic robotic fish – Robofish – of different sizes. Robofish is accepted as a conspecific by live guppies (Poecilia reticulata) and provides standardized behaviors irrespective of its size. We specifically asked whether larger leaders are preferentially followed when behavior is controlled for and whether the preferences of followers depend on their own body size or their risk taking behavior (‘boldness’). We found that live guppies followed larger Robofish leaders closer than smaller ones and this pattern was independent of the followers’ own body size as well as risk-taking behavior. This is the first study that shows a ‘bigger is better’ pattern in leadership in shoaling fish that is fully independent of behavioral differences between differentially-sized leaders and followers’ own size and personality.
Inositol 1,4,5-trisphosphate receptor type2-independent Ca2+ release from the endoplasmic reticulum in astrocytes
Authors: Okubo Yohei , Kanemaru Kazunori , Suzuki Junji , Kobayashi Kenta , Hirose Kenzo , Iino Masamitsu 
Published: May 2018

AbstractAccumulating evidence indicates that astrocytes are actively involved in the physiological and pathophysiological functions of the brain. Intracellular Ca2+ signaling, especially Ca2+ release from the endoplasmic reticulum (ER), is considered to be crucial for the regulation of astrocytic functions. Mice with genetic deletion of inositol 1,4,5-trisphosphate receptor type 2 (IP3R2) are reportedly devoid of astrocytic Ca2+ signaling, and thus widely used to explore the roles of Ca2+ signaling in astrocytic functions. While functional deficits in IP3R2-knockout (KO) mice have been found in some reports, no functional deficit was observed in others. Thus, there remains a controversy regarding the functional significance of astrocytic Ca2+ signaling. To address this controversy, we re-evaluated the assumption that Ca2+ release from the ER is abolished in IP3R2-KO astrocytes using a highly sensitive imaging technique. We expressed the ER luminal Ca2+ indicator G-CEPIA1er in cortical and hippocampal astrocytes to directly visualize spontaneous and stimulus-induced Ca2+ release from the ER. We found attenuated but significant Ca2+ release in response to application of norepinephrine to IP3R2-KO astrocytes. This IP3R2-independent Ca2+ release induced only minimal cytosolic Ca2+ transients but induced robust Ca2+ increases in mitochondria that are frequently in close contact with the ER. These results indicate that ER Ca2+ release is retained and is sufficient to increase the Ca2+ concentration in close proximity to the ER in IP3R2-KO astrocytes.
Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia
Authors: Minuesa Gerard , Albanese Steven K. , Chow Arthur , Schurer Alexandra , Park Sun-Mi , Rotsides Christina Z. , Taggart James , Rizzi Andrea , Naden Levi N. , Chou Timothy , Gourkanti Saroj , Cappel Daniel , Passarelli Maria C. , Fairchild Lauren , Adura Carolina , Glickman J Fraser , Schulman Jessica , Famulare Christopher , Patel Minal , Eibl Joseph K. , Ross Gregory M. , Tan Derek , Leslie Christina , Beuming Thijs , Goldgur Yehuda , Chodera John D. , Kharas Michael G. 
Published: May 2018

SUMMARYThe MUSASHI family of RNA binding proteins (MSI1 and MSI2) contribute to a wide spectrum of cancers including acute myeloid leukemia. We found that the small molecule Ro 08–2750 (Ro) directly binds to MSI2 and competes for its RNA binding in biochemical assays. Ro treatment in mouse and human myeloid leukemia cells resulted in an increase in differentiation and apoptosis, inhibition of known MSI-targets, and a shared global gene expression signature similar to shRNA depletion of MSI2. Ro demonstrated in vivo inhibition of c-MYC and reduced disease burden in a murine AML leukemia model. Thus, we have identified a small molecule that targets MSI’s oncogenic activity. Our study provides a framework for targeting RNA binding proteins in cancer.
Nuclear Respiratory Factor 1 (NRF-1) Controls the Activity Dependent Transcription of the GABA-A Receptor Beta 1 Subunit Gene in Neurons
Authors: Li Zhuting , Cogswell Meaghan , Hixson Kathryn , Brooks-Kayal Amy R. , Russek Shelley J. 
Published: May 2018

ABSTRACTWhile the exact role of β1 subunit-containing GABA-A receptors (GABARs) in brain function is not well understood, altered expression of the β1 subunit gene (GABRB1) is associated with neurological and neuropsychiatric disorders. In particular, down-regulation of β1 subunit levels is observed in brains of patients with epilepsy, autism, bipolar disorder, and schizophrenia. A pathophysiological feature of these disease states is imbalance in energy metabolism and mitochondrial dysfunction. The transcription factor, nuclear respiratory factor 1 (NRF-1), has been shown to be a key mediator of genes involved in oxidative phosphorylation and mitochondrial biogenesis. Using a variety of molecular approaches (including mobility shift, promoter/reporter assays, and overexpression of dominant negative NRF-1), we now report that NRF-1 regulates transcription of GABRB1 and that its core promoter contains a conserved canonical NRF-1 element responsible for sequence specific binding and transcriptional activation. Our identification of GABRB1 as a new target for NRF-1 in neurons suggests that genes coding for inhibitory neurotransmission may be coupled to cellular metabolism. This is especially meaningful as binding of NRF-1 to its element is sensitive to the kind of epigenetic changes that occur in multiple disorders associated with altered brain inhibition.
Long-distance communication in synthetic bacterial consortia through active signal propagation
Authors: Parkin James M. , Murray Richard M. 
Published: May 2018

AbstractA synthetic cell-cell signaling circuit should ideally be (1) metabolically lightweight, (2) insulated from endogenous gene networks, and (3) excitable rather than oscillatory or bistable. To accomplish these three features, we propose a synchronized pulse-generating circuit based on the design of published synchronized oscillators. This communication module employs a pulse generator built using Lux-type quorum sensing components and an IFFL transcriptional circuit. Both the input and output of this module are AHLs, the quorum sensing signaling molecule. Cells bearing this module therefore act as an excitable medium, producing a pulse of AHL when stimulated by exogenous AHL. Using simulation and microscopy, we demonstrate how this circuit enables traveling pulses of AHL production through microcolonies growing in two dimensions. Traveling pulses achieve cell-cell communication at longer distances than can be achieved by diffusion of signal from sender to receiver cells and may permit more sophisticated coordination in synthetic consortia.
A graph-based algorithm for RNA-seq data normalization
Authors: Tran Diem-Trang T. , Bhaskara Aditya , Might Matthew , Kuberan Balagurunathan 
Published: May 2018

AbstractThe use of RNA-sequencing has garnered much attention in the recent years for characterizing and understanding various biological systems. However, it remains a major challenge to gain insights from a large number of RNA-seq experiments collectively, due to the normalization problem. Current normalization methods are based on assumptions that fail to hold when RNA-seq profiles become more abundant and heterogeneous. We present a normalization procedure that does not rely on these assumptions, or on prior knowledge about the reference transcripts in those conditions. This algorithm is based on a graph constructed from intrinsic correlations among RNA-seq transcripts and seeks to identify a set of densely connected vertices as references. Application of this algorithm on our benchmark data showed that it can recover the reference transcripts with high precision, thus resulting in high-quality normalization. As demonstrated on a real data set, this algorithm gives good results and is efficient enough to be applicable to real-life data.2012 ACM Subject ClassificationApplied computing → Computational transcriptomics, Applied computing → BioinformaticsDigital Object Identifier10.4230/LIPIcs.WABI.2018.xxxFundingThis material was based on research supported by the National Heart, Lung, and Blood Institute (NHLBI)–NIH sponsored Programs of Excellence in Glycosciences [grant number HL107152 to B.K.], and partially by NSF [CAREER grant 1350344 to M.M.]. The U.S. Government is authorized to reproduce and distribute reprints for Governmental purposes notwithstanding any copyright notation thereon.
Recurrent connections between CA2 pyramidal cells
Authors: Okamoto Kazuki , Ikegaya Yuji 
Published: May 2018

AbstractRecurrent excitatory synapses are shown theoretically to play roles in memory storage and associative learning, and such recurrent synapses are well described to occur in the CA3 region of the hippocampus. Here, we report that the CA2 region also contains recurrent excitatory monosynaptic couplings. Using dual whole-cell patch-clamp recordings from CA2 pyramidal cells in mouse hippocampal slices under differential interference contrast microscopic controls, we evaluated monosynaptic excitatory connections. Unitary excitatory postsynaptic potentials occurred in 1.4% of 502 cell pairs. These connected pairs were located preferentially in the superficial layer and proximal part (CA2b) of the CA2 region. These results indicate that recurrent excitatory circuits are dense in the CA2 region as well as in the CA3 region.
Dopamine D1 receptor availability is not associated with delusional ideation measures of psychosis proneness
Authors: Matheson Granville James , Plavén-Sigray Pontus , Louzolo Anaïs , Borg Jacqueline , Farde Lars , Petrovic Predrag , Cervenka Simon 
Published: May 2018

AbstractThe dopamine D1 receptor (D1R) is thought to play a role in psychosis and schizophrenia, however the exact nature of this involvement is not clear. Positron emission tomography studies comparing D1R between patients and control subjects have produced inconsistent results. An important confounding factor in most clinical studies is previous exposure to antipsychotic treatment, which is thought to influence the density of D1R. To circumvent some of the limitations of clinical studies, an alternative approach for studying the relationship between D1R and psychosis is to examine individuals at increased risk for psychotic disorders, or variation in subclinical psychotic symptoms such as delusional ideation within the general population, referred to as psychosis proneness traits. In this study, we investigated whether D1R availability is associated with delusional ideation in healthy controls using data from 76 individuals measured with PET using [11C]SCH23390 and 217 individuals who completed delusional ideation questionnaires, belonging to three different study cohorts. We first performed exploratory, hypothesis-generating, analyses by creating and evaluating a new measure of delusional ideation (n=132 and n=27), which was then found to show a negative association with D1R availability (n=24). Next, we performed confirmatory analyses using Bayesian statistical modelling, in which we first attempted to replicate this result (n=20), and then evaluated the association of Peters Delusion Inventory scores with D1R availability in two independent cohorts (n=41 and 20). Collectively, we found strong evidence that there is little to no linear association between delusional ideation and D1R availability in healthy controls. If differences in D1R can be confirmed in drug-naive schizophrenia patients compared to controls, further studies are needed to ascertain whether these changes occur at the onset of psychotic symptoms or if they are associated with specific behavioural or genetic aspects of psychosis proneness other than delusional ideation.