bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circadian diversity in SwedishArabidopsisaccessions is associated with naturally occurring genetic variation inCOR28
Authors: Rees Hannah , Joynson Ryan , Brown James K.M. , Hall Anthony 
Published: June 2019

AbstractCircadian clocks have evolved to resonate with external day and night cycles. However, these entrainment signals are not consistent everywhere and vary with latitude, climate and seasonality. This leads to divergent selection for clocks which are locally adapted. To investigate the genetic basis for this, we used a Delayed Fluorescence (DF) imaging assay to screen 191 naturally occurring SwedishArabidopsisaccessions for their circadian phenotypes. We demonstrate period variation with both latitude and sub-population. Several candidate loci linked to period, phase and Relative Amplitude Error (RAE) were revealed by genome-wide association mapping and candidate genes were investigated using TDNA mutants. We show that natural variation in a single non-synonymous substitution withinCOR28is associated with a long-period and late-flowering phenotype similar to that seen in TDNA knock-out mutants.COR28is a known coordinator of flowering time, freezing tolerance and the circadian clock; all of which may form selective pressure gradients across Sweden. Finally, we tested circadian variation under reduced temperatures and show that fast and slow period phenotypic tails remain diverged and follow a distinctive ‘arrow-shaped’ trend indicative of selection for a cold-biased temperature compensation response.
Auto-regressive modeling and diagnostics for qPCR amplification
Authors: Hsu Benjamin , Sherina Valeriia , McCall Matthew N. 
Published: June 2019

AbstractCurrent methods used to analyze real-time quantitative polymerase chain reaction (qPCR) data exhibit systematic deviations from the assumed model over the progression of the reaction. Slight variations in the amount of the initial target molecule or in early amplifications are likely responsible for these deviations. Commonly-used 4- and 5-parameter sigmoidal models appear to be particularly susceptible to this issue, often displaying patterns of autocorrelation in the residuals. The presence of this phenomenon, even for technical replicates, suggests that these parametric models may be misspecified. Specifically, they do not account for the sequential dependent nature of qPCR fluorescence measurements. We demonstrate that a Smooth Transition Autoregressive (STAR) model addresses this limitation by explicitly modeling the dependence between cycles and the gradual transition between amplification regimes. In summary, application of a STAR model to qPCR amplification data improves model fit and reduces autocorrelation in the residuals.
Beyond redistribution: In-stream habitat restoration increases capacity for young-of-the-year Chinook salmon and steelhead in the Entiat River, WA
Authors: Polivka Carlos M. , Claeson Shannon M. 
Published: June 2019

AbstractWe conducted snorkel surveys for juvenile salmonids in reaches of the Entiat River (Washington, USA) treated with engineered log jams (ELJs), and in reaches without treatments, to determine if habitat-unit-scale observations can identify whether restoration has increased the habitat capacity of a reach. The conceptual basis and field methodology emphasize fish density data (fish/habitat area in m2) from unrestored habitat within a reach treated with ELJs compared to surveys in 1) unrestored habitat in untreated reaches and 2) restored habitat in treated reaches. A Bayesian generalized linear model enabled us to quantify density differences among habitat types using advanced computational statistics. Modal density of young-of-the-year Chinook salmon (Oncorhynchus tschawytscha) and steelhead (O. mykiss) was at least 3.1-fold and 2.7-fold greater, respectively, in restored habitat compared with unrestored habitat for all treated reaches examined. To distinguish the density differences in those reaches as capacity increases rather than redistribution from poor habitat to good habitat, we compared density in unrestored habitat in both treated and untreated reaches. Here we found no differences for either species, confirming that the increased density in restored habitat units did not come from depletion of unrestored habitat in the same reach. We thus concluded that restoration increased the habitat capacity of the reach at the scale of pools created by ELJs.
A blueprint of seed desiccation sensitivity in the genome ofCastanospermum australe
Authors: Marques Alexandre , Costa Maria-Cecília D. , Chathuri Udisha , Jonkheer Eef , Zhao Tao , Schijlen Elio , Derks Martijn , Nijveen Harm , Marcet-Houben Marina , Julca Irene , Delahaie Julien , Schranz M. Eric , Gabaldon Toni , Pelletier Sandra , Leprince Olivier , Ligterink Wilco , Buitink Julia , Hilhorst Henk W.M. , Farrant Jill M. 
Published: June 2019

SummaryMost angiosperms produce seeds that are desiccated on dispersal with the ability to retain viability in storage facilities for prolonged periods. However, some species produce desiccation sensitive seeds which rapidly lose viability in storage, precludingex situconservation. Current consensus is that desiccation sensitive seeds either lack or do not express mechanisms necessary for the acquisition of desiccation tolerance.We sequenced the genome ofCastanospermum australe, a legume species producing desiccation sensitive seeds, and characterized its seed developmental physiology and - transcriptomes.C. australehas a low rate of evolution, likely due to its perennial life-cycle and long generation times. The genome is syntenic with itself, with several orthologs of genes from desiccation tolerant legume seeds, from gamma whole-genome duplication events being retained. Changes in gene expression during development ofC. australeseeds, as compared to desiccation tolerantMedicago truncatulaseeds, suggest they remain metabolically active, prepared for immediate germination.Our data indicates that the phenotype ofC. australeseeds arose through few changes in specific signalling pathways, precluding or bypassing activation of mechanisms necessary for acquisition of desiccation tolerance. Such changes have been perpetuated as the habitat in which dispersal occurs is favourable for prompt germination.
Thalamic-medial temporal lobe connectivity underpins familiarity memory
Authors: Kafkas Alex , Mayes Andrew R. , Montaldi Daniela 
Published: June 2019

AbstractThe neural basis of memory is highly distributed, but the thalamus is known to play a particularly critical role. However, exactly how the different thalamic nuclei contribute to different kinds of memory is unclear. Moreover, whether thalamic connectivity with the medial temporal lobe (MTL), arguably the most fundamental memory structure, is critical for memory, remains unknown. We explore these questions using an fMRI recognition memory paradigm that taps familiarity and recollection (i.e., the two types of memory that support recognition) for objects, faces and scenes. We show that the mediodorsal thalamus (MDt) plays a material-general role in familiarity, while the anterior thalamus plays a material-general role in recollection. Material-specific regions were found for scene familiarity (ventral posteromedial and pulvinar thalamic nuclei) and face familiarity (left ventrolateral thalamus). Critically, increased functional connectivity between the MDt and the parahippocampal (PHC) and perirhinal cortices (PRC) of the MTL underpinned increases in reported familiarity confidence. These findings suggest that familiarity signals are generated through the dynamic interaction of functionally connected MTL-thalamic structures.
Using low-cost alcohol sensors to monitor real-time olfactory information during odor-guided navigation
Authors: Tariq Mohammad F. , Lewis Suzanne M. , Lowell Aliena , Perkel David J. , Gire David H. 
Published: June 2019

AbstractOlfaction — an evolutionarily conserved chemosensory modality — guides navigation and decision-making in organisms from multiple phyla within the animal kingdom. However, using olfactory cues to guide navigation is a complicated problem. This is because the spread of odor molecules from the source is governed by turbulent and chaotic air currents, resulting in intermittent and spatiotemporally varying sensory cues as odor plumes. Precisely correlating olfactory information with behavior and neurophysiology from freely behaving animals has thus been a challenging avenue due to the dynamic nature of the odor plumes. Current technologies for chemical quantification are cumbersome and not feasible for monitoring the olfactory information at the temporal and spatial scales relevant for plume and odor tracking in animals. Here we present an alternate method for real-time monitoring of olfactory information using low-cost, lightweight sensors that robustly detect common solvent molecules, like alcohols. Paired recordings were made from these ethanol sensors with a Photoionization detector (PID) to precisely controlled ethanol stimuli. The ethanol sensor recordings were then deconvolved using a double exponential kernel, showing robust correlations with the PID recordings at behaviorally relevant time, frequency and spatial scales. Furthermore, the light weight of these sensors allows us to mount them on the heads of freely behaving rodents engaged in odor-guided navigation. Our preliminary experiments in mice show robust behavioral and neurophysiological responses correlated with ethanol plume contacts detected by these sensors.
Immunoglobulin heavy chains are sufficient to determine most B cell clonal relationships1
Authors: Zhou Julian Q. , Kleinstein Steven H. 
Published: June 2019

AbstractB cell clonal expansion is vital for adaptive immunity. High-throughput B cell receptor (BCR) sequencing enables investigating this process, but requires computational inference to identify clonal relationships. This inference usually relies on only the BCR heavy chain, as most current protocols do not preserve heavy:light chain pairing. The extent to which paired light chains aids inference is unknown. Using human single-cell paired BCR datasets, we assessed the ability of heavy chain-based clonal clustering to identify clones. Of the expanded clones identified, <20% grouped cells expressing inconsistent light chains. Heavy chains from these misclustered clones contained more distant junction sequences and shared fewer V segment mutations than the accurate clones. This suggests that additional heavy chain information could be leveraged to refine clonal relationships. Conversely, light chains were insufficient to refine heavy chain-based clonal clusters. Overall, the BCR heavy chain alone is sufficient to identify clonal relationships with confidence.
An assessment of land use land cover change in Central Highland of Deccan Peninsula and Semi-Arid tracts of India
Authors: Mondal Tamali , Basu Parabita , Qureshi Qamar , Jhala Yadvendradev 
Published: June 2019

AbstractHuman consumption and management of land, i.e., how people transmit to a landscape as a source of livelihood, shelter, recreation, or industry, are powerful forces shaping patterns and dynamics in human-occupied landscapes. Understanding and managing landscape change, therefore, requires a thorough knowledge of the developmental processes the area is undergoing, causing the change in the land use pattern over time. In this study land use/cover dynamics of the Central Highland of Deccan Peninsula and Semi-Arid zone of Gujarat Rajputana bio-geographic regions of India was assessed using a combination of hybrid classification, markov analysis approach within the time frame of 2000-2013. In this time frame, major changes have been identified in dense forest, open forest, cropland, fallow land and in the barren landforms. The landscape has witnessed a substantial increase in built-up areas from 31317 sq. km. in 2000 to 52338 sq. km in 2013. The scrubland has largely declined from 35713.06 sq. km in 2000 to 23003.88 sq.km in 2013; it might have resulted from the transition of scrubland to the fallow land which was predicted as more than 70% in the first phase and more than 30% in the later phase. The area under dense forest constantly decreased in the studied time (84027 sq. km to 71225.37 sq. km). The Markov analysis estimated a probability of changing of open forest types to fallow land (36% in 2000-2006 and 20% in 2006-2013). As the environmental damage is irreversible due to industrialization, therefore a sound strategy needs to be implemented for sustainable use of natural resources that can go hand in hand.
The Arabidopsis Diacylglycerol Kinase 4 is involved in nitric oxide-dependent pollen tube guidance and fertilization
Authors: Wong Aloysius , Donaldson Lara , Portes Maria Teresa , Eppinger Jörg , Feijó José , Gehring Christoph 
Published: June 2019

SummaryNitric oxide (NO) is a key signaling molecule that regulates diverse biological processes in both animals and plants. In animals, NO regulates vascular wall tone, neurotransmission and immune response while in plants, NO is essential for development and responses to biotic and abiotic stresses [1–3]. Interestingly, NO is involved in the sexual reproduction of both animals and plants mediating physiological events related to the male gamete [2, 4]. In animals, NO stimulates sperm motility [4] and binding to the plasma membrane of oocytes [5] while in plants, NO mediates pollen-stigma interactions and pollen tube guidance [6, 7]. NO generation in pollen tubes (PTs) has been demonstrated [8] and intracellular responses to NO include cytosolic Ca2+ elevation, actin organization, vesicle trafficking and cell wall deposition [7, 9]. However, the NO-responsive proteins that mediate these responses are still elusive. Here we show that PTs of Arabidopsis lacking the pollen-specific Diacylglycerol Kinase 4 (DGK4) grow slower and become insensitive to NO-dependent growth inhibition and re-orientation responses. Recombinant DGK4 protein yields NO-responsive spectral and catalytic changes in vitro which are compatible with a role in NO perception and signaling in PTs. NO is a fast, diffusible gas and, based on our results, we hypothesize it could serve in long range signaling and/or rapid cell-cell communication functions mediated by DGK4 downstream signaling during the progamic phase of angiosperm reproduction.
A systematic comparison of chloroplast genome assembly tools
Authors: Freudenthal Jan A , Pfaff Simon , Terhoeven Niklas , Korte Arthur , Ankenbrand Markus J , Förster Frank 
Published: June 2019

AbstractBackgroundChloroplasts are intracellular organelles that enable plants to conduct photosynthesis. They arose through the symbiotic integration of a prokaryotic cell into an eukaryotic host cell and still contain their own genomes with distinct genomic information. Plastid genomes accommodate essential genes and are regularly utilized in biotechnology or phylogenetics. Different assemblers that are able to assess the plastid genome have been developed. These assemblers often use data of whole genome sequencing experiments, which usually contain reads from the complete chloroplast genome.ResultsThe performance of different assembly tools has never been systematically compared. Here we present a benchmark of seven chloroplast assembly tools, capable of succeeding in more than 60% of known real data sets. Our results show significant differences between the tested assemblers in terms of generating whole chloroplast genome sequences and computational requirements. The examination of 105 data sets from species with unknown plastid genomes leads to the assembly of 20 novel chloroplast genomes.ConclusionsWe create docker images for each tested tool that are freely available for the scientific community and ensure reproducibility of the analyses. These containers allow the analysis and screening of data sets for chloroplast genomes using standard computational infrastructure. Thus, large scale screening for chloroplasts within genomic sequencing data is feasible.
A Novel Tmem119-tdTomato Reporter Mouse Model for Studying Microglia in the Central Nervous System
Authors: Ruan Chunsheng , Sun Linlin , Kroshilina Alexandra , Beckers Lien , De Jager Philip L. , Bradshaw Elizabeth M. , Hasson Samuel , Yang Guang , Elyaman Wassim 
Published: June 2019

AbstractMicroglia are resident immune cells of the central nervous system (CNS). The exact role of microglia in the physiopathology of CNS disorders is not clear due to lack of tools to discriminate between CNS resident and infiltrated innate immune cells. Here, we present a novel reporter mouse model targeting a microglia-specific marker (TMEM119) for studying the function of microglia in health and disease. By placing a reporter cassette (GSG-3xFlag-P2A-tdTomato) between the coding sequence of exon 2 and 3’UTR of the Tmem119 gene using CRISPR/Cas9 technology, we generated a Tmem119-tdTomato knock-in mouse strain. Gene expression assay showed no difference of endogenous Tmem119 mRNA level in the CNS of Tmem119tdTomato/+ relative to control Wild-type mice. The cells expressing tdTomato-were recognized by immunofluorescence staining using commercially available anti-TMEM119 antibodies. Using immunofluorescence and flow cytometry techniques, tdTomato+ cells were detected throughout the CNS, but not in peripheral tissues of adult Tmem119tdTomato/+ mice. In addition, aging does not seem to influence TMEM119 expression as tdTomato+ cells were detectable in the CNS of older mice (300 and 540 days old). Further immunofluorescence characterization shows that the tdTomato+ cells were highly colocalized with Iba1+ cells (microglia and macrophages) in the brain, but not with NeuN- (neurons), GFAP- (astrocytes) or Olig2- (oligodendrocytes) labeled cells. Moreover, flow cytometry analysis of brain tissues of adult mice demonstrates that the majority of microglial CD45lowCD11b+ cells (96.6%) are tdTomato positive. Functionally, using a laser-induced injury model, we measured time-lapse activation of tdTomato-labeled microglia by transcranial two-photon microscopy in live Tmem119tdTomato/+ mice. Taken together, the Tmem119-tdTomato reporter mouse model will serve as a valuable tool to specifically study the role of microglia in health and disease.
Laboratory evolution ofEscherichia colienables life based on fluorinated amino acids
Authors: Agostini Federica , Sinn Ludwig , Petras Daniel , Schipp Christian J. , Kubyshkin Vladimir , Berger Allison Ann , Dorrestein Pieter C. , Rappsilber Juri , Budisa Nediljko , Koksch Beate 
Published: June 2019

AbstractOrganofluorine compounds are toxic to various living beings in different habitats. On the other hand, fluorine incorporation into single proteins via related amino acid analogues has become common practice in protein engineering. Thus, an essential question remains: can fluorinated amino acids generally be used as xeno-nutrients to build up biomass, or do large amounts of fluorine in the cells render them nonviable? To gain information about the effect of long-term exposure of a cellular proteome to fluorinated organic compounds, we constructed an experiment based on bacterial adaptation in artificial fluorinated habitats. We propagatedEscherichia coli(E. coli) in the presence of either 4- or 5-fluoroindole as essential precursors for the in situ synthesis of tryptophan (Trp) analogues. We found that full adaptation requires astonishingly few genetic mutations but is accompanied by large rearrangements in regulatory networks, membrane integrity and quality control of protein folding. These findings highlight the cellular mechanisms of the evolutionary adaption process to unnatural amino acids and provide the molecular foundation for novel and innovative bioengineering of microbial strains with potential for biotechnological applications.One Sentence SummaryLaboratory evolution enabled for the first timeEscherichia colito use fluorinated indoles as essential precursors for protein synthesis by introducing few genetic mutations but large rearrangements in regulatory networks, membrane integrity and quality control of protein folding.
Circadian modulation of neurons and astrocytes controls synaptic plasticity in hippocampal area CA1
Authors: McCauley John P. , Petroccione Maurice A. , D’Brant Lianna Y. , Todd Gabrielle C. , Affinnih Nurat , Wisnoski Justin J. , Zahid Shergil , Shree Swasti , Sousa Alioscka A. , De Guzman Rose M. , Migliore Rosanna , Brazhe Alexey , Leapman Richard D. , Khmaladze Alexander , Semyanov Alexey , Zuloaga Damian G. , Migliore Michele , Scimemi Annalisa 
Published: June 2019

SummaryMost animal species operate according to a 24-hour period set by the suprachiasmatic nucleus (SCN) of the hypothalamus. The rhythmic activity of the SCN is known to modulate hippocampal-dependent memory processes, but the molecular and cellular mechanisms that account for this effect remain largely unknown. Here, we show that there are cell-type specific structural and functional changes that occur with circadian rhythmicity in neurons and astrocytes in hippocampal area CA1. Pyramidal neurons change the surface expression of NMDA receptors, whereas astrocytes change their proximity to synapses. Together, these phenomena alter glutamate clearance, receptor activation and integration of temporally clustered excitatory synaptic inputs, ultimately shaping hippocampal-dependent learningin vivo. We identify corticosterone as a key contributor to changes in synaptic strength. These findings identify important mechanisms through which neurons and astrocytes modify the molecular composition and structure of the synaptic environment, contribute to the local storage of information in the hippocampus and alter the temporal dynamics of cognitive processing.
An Optimization framework for Nonspiking Neuronal Networks and Aided Discovery of a Model for the Elementary Motion Detector
Authors: Banerjee Arunava 
Published: June 2019

AbstractWe present a general optimization procedure that given a parameterized network of nonspiking conductance based compartmentally modeled neurons, tunes the parameters to elicit a desired network behavior. Armed with this tool, we address the elementary motion detector problem. Central to established theoretical models, the Hassenstein-Reichardt and Barlow-Levick detectors, are delay lines whose outputs from spatially separated locations are prescribed to be nonlinearly integrated with the direct outputs to engender direction selectivity. The neural implementation of the delays—which are substantial as stipulated by interomatidial angles—has remained elusive although there is consensus regarding the neurons that constitute the network. Assisted by the optimization procedure, we identify parameter settings consistent with the connectivity architecture and physiology of the Drosophila optic lobe, that demonstrates that the requisite delay and the concomitant direction selectivity can emerge from the nonlinear dynamics of small recurrent networks of neurons with simple tonically active synapses. Additionally, although the temporally extended responses of the neurons permit simple synaptic integration of their signals to be sufficient to induce direction selectivity, both preferred direction enhancement and null direction suppression is necessary to abridge the overall response. Finally, the characteristics of the response to drifting sinusoidal gratings are readily explained by the charging-up of the recurrent networks and their low-pass nature.