North American bison (Bison bison) are becoming increasingly important to both grassland management and commercial ranching. However, a lack of quantitative data on their diet constrains conservation ...efforts and the ability to predict bison effects on grasslands. In particular, we know little about the seasonality of the bison diet, the degree to which bison supplement their diet with eudicots, and how changes in diet influence gut microbial communities, all of which play important roles in ungulate performance. To address these knowledge gaps, we quantified seasonal patterns in bison diet and gut microbial community composition for a bison herd in Kansas using DNA sequencing-based analyses of both chloroplast and microbial DNA contained in fecal matter. Across the 11 sampling dates that spanned 166 days, we found that diet shifted continuously over the growing season, allowing bison to take advantage of the seasonal availability of high-protein plant species. Bison consumed more woody shrubs in spring and fall than in summer, when forb and grass intake predominated. In examining gut microbiota, the bacterial phylum Tenericutes shifted significantly in relative abundance over the growing season. This work suggests that North American bison can continuously adjust their diet with a high reliance on non-grasses throughout the year. In addition, we find evidence for seasonal patterns in gut community composition that are likely driven by the observed dietary changes.
Broad (∼10,000 km s−1), double-peaked emission-line profiles of Balmer lines emitted by active galactic nuclei (AGN) are thought to originate in the outer parts of an accretion disk surrounding a ...nuclear supermassive black hole (SMBH), at ∼1000 gravitational radii, and are most frequently observed in the nuclear spectra of low-luminosity AGN (LLAGN) and radio galaxies. In the present paper we argue that broad double-peaked profiles are present also in the spectra of other type 1 AGN, such as Seyfert 1 galaxies, suggesting that the inner part of the broad-line region (BLR) is also the outer part of the accretion disk. We use the Palomar spectral survey of nearby galaxies to show that the only difference between Seyfert 1 BLR line profiles and "bona fide" double-peakers is that, in most cases, besides a disk component, we need an additional Gaussian component attributed to nondisk clouds. The recognition that the inner and most variable part of the BLR has a disk geometry suggests that the factor f in the expression to obtain the SMBH mass in type 1 AGN, , is for the disk-dominated sources. Our median i = 27° implies f = 4.5, very close to the most recent value of f = 4.3 1.05, obtained from independent studies. We derive a relation between f and the FWHM of the broad profile that may help to reduce the uncertainties in the SMBH mass determinations of AGN.
Frequency tagging has been widely used to study the role of visual selective attention. Presenting a visual stimulus flickering at a specific frequency generates so-called steady-state visually ...evoked responses. However, frequency tagging is mostly done at lower frequencies (<30 Hz). This produces a visible flicker, potentially interfering with both perception and neuronal oscillations in the theta, alpha and beta band. To overcome these problems, we used a newly developed projector with a 1440 Hz refresh rate allowing for frequency tagging at higher frequencies. We asked participants to perform a cued spatial attention task in which imperative pictorial stimuli were presented at 63 Hz or 78 Hz while measuring whole-head magnetoencephalography (MEG). We found posterior sensors to show a strong response at the tagged frequency. Importantly, this response was enhanced by spatial attention. Furthermore, we reproduced the typical modulations of alpha band oscillations, i.e., decrease in the alpha power contralateral to the attentional cue. The decrease in alpha power and increase in frequency tagged signal with attention correlated over subjects. We hereby provide proof-of-principle for the use of high-frequency tagging to study sensory processing and neuronal excitability associated with attention.
ABSTRACT
We report on the determination of electron densities, and their impact on the outflow masses and rates, measured in the central few hundred parsecs of 11 local luminous active galaxies. We ...show that the peak of the integrated line emission in the active galactic nuclei (AGN) is significantly offset from the systemic velocity as traced by the stellar absorption features, indicating that the profiles are dominated by outflow. In contrast, matched inactive galaxies are characterized by a systemic peak and weaker outflow wing. We present three independent estimates of the electron density in these AGN, discussing the merits of the different methods. The electron density derived from the S ii doublet is significantly lower than that found with a method developed in the last decade using auroral and transauroral lines, as well as a recently introduced method based on the ionization parameter. The reason is that, for gas photoionized by an AGN, much of the S ii emission arises in an extended partially ionized zone where the implicit assumption that the electron density traces the hydrogen density is invalid. We propose ways to deal with this situation and we derive the associated outflow rates for ionized gas, which are in the range 0.001–0.5 M⊙ yr−1 for our AGN sample. We compare these outflow rates to the relation between $\dot{M}_{\rm out}$ and LAGN in the literature, and argue that it may need to be modified and rescaled towards lower mass outflow rates.
Diversity and composition of microbial communities was compared across the 13 major sections of the digestive tract (esophagus, reticulum, rumen, omasum, abomasum, duodenum, jejunum, ileum, cecum, ...ascending colon, transverse colon, descending colon, and rectum) in two captive populations of American bison (Bison bison), one of which was finished on forage, the other on grain.
Microbial diversity fell to its lowest levels in the small intestine, with Bacteroidetes reaching their lowest relative abundance in that region, while Firmicutes and Euryarchaeota attained their highest relative abundances there. Gammaproteobacteria were most abundant in the esophagus, small intestine, and colon. The forage-finished bison population exhibited higher overall levels of diversity, as well as a higher relative abundance of Bacteroidetes in most gut sections. The grain-finished bison population exhibited elevated levels of Firmicutes and Gammaproteobacteria. Within each population, different sections of the digestive tract exhibited divergent microbial community composition, although it was essentially the same among sections within a given region of the digestive tract. Shannon diversity was lowest in the midgut. For each section of the digestive tract, the two bison populations differed significantly in microbial community composition.
Similarities among sections indicate that the esophagus, reticulum, rumen, omasum, and abomasum may all be considered to house the foregut microbiota; the duodenum, jejunum, and ileum may all be considered to house the small intestine or midgut microbiota; and the cecum, ascending colon, transverse colon, descending colon, and rectum may all be considered to house the hindgut microbiota. Acid from the stomach, bile from the gall bladder, digestive enzymes from the pancreas, and the relatively low retention time of the small intestine may have caused the midgut's low microbial diversity. Differences in microbial community composition between populations may have been most strongly influenced by differences in diet (forage or grain). The clinical condition of the animals used in the present study was not evaluated, so further research is needed to establish whether the microbial profiles of some bison in this study are indeed indicative of dysbiosis, a predisposing factor to ruminal acidosis and its sequelae.
ABSTRACT
We analyse optical data cubes of the inner kiloparsec of 30 local (z ≤ 0.02) active galactic nucleus (AGN) hosts that our research group, AGNIFS, has collected over the past decade via ...observations with the integral field units of the Gemini Multi-Object Spectrographs. Spatial resolutions range between 50 and 300 pc and spectral coverage is from 4800 or 5600 to 7000 Å, at velocity resolutions of ≈50 $\rm ~km~s^{-1}$. We derive maps of the gas excitation and kinematics, and determine the AGN ionization axis – which has random orientation relative to the galaxy – and the kinematic major axes of the emitting gas.
We find that rotation dominates the gas kinematics in most cases, but is disturbed by the presence of inflows and outflows. Outflows have been found in 21 nuclei, usually along the ionization axis. The gas velocity dispersion is traced by W80 (velocity width encompassing 80 per cent of the line flux), adopted as a tracer of outflows. In seven sources, W80 is enhanced perpendicularly to the ionization axis, indicating lateral expansion of the outflow. We have estimated mass-outflow rates $\dot{M}$ and powers $\dot{E}$, finding median values of $\log \, \dot{M}/({\rm \, M_\odot \, yr^{-1}})=-2.1_{-1.0}^{+1.6}$ and $\log \, \dot{E}/({\rm \, erg\, s^{-1}})=38.5_{-0.9}^{+1.8}$, respectively. Both quantities show a mild correlation with the AGN luminosity (LAGN). $\dot{E}$ is of the order of 0.01 LAGN for four sources, but much lower for the majority (nine) of the sources, with a median value of $\log \, \dot{E}/L_{\rm AGN} =-5.34_{-0.9}^{+3.2}$, indicating that typical outflows in the local Universe are unlikely to significantly impact their host galaxy evolution.
Verrucomicrobia are ubiquitous in soil, but members of this bacterial phylum are thought to be present at low frequency in soil, with few studies focusing specifically on verrucomicrobial abundance, ...diversity, and distribution. Here we used barcoded pyrosequencing to analyze verrucomicrobial communities in surface soils collected across a range of biomes in Antarctica, Europe, and the Americas (112 samples), as well as soils collected from pits dug in a montane coniferous forest (69 samples). Data collected from surface horizons indicate that Verrucomicrobia average 23% of bacterial sequences, making them far more abundant than had been estimated. We show that this underestimation is likely due to primer bias, as many of the commonly used PCR primers appear to exclude verrucomicrobial 16S rRNA genes during amplification. Verrucomicrobia were detected in 180 out of 181 soils examined, with members of the class Spartobacteria dominating verrucomicrobial communities in nearly all biomes and soil depths. The relative abundance of Verrucomicrobia was highest in grasslands and in subsurface soil horizons, where they were often the dominant bacterial phylum. Although their ecology remains poorly understood, Verrucomicrobia appear to be dominant in many soil bacterial communities across the globe, making additional research on their ecology clearly necessary.
► A total of 181 soils from Antarctica, Europe, and the Americas were analyzed via pyrosequencing. ► Verrucomicrobia was found to be a dominant phylum in soil, averaging 23% of bacterial 16S rRNA gene sequences. ► Relative abundance of Verrucomicrobia was highest in grasslands and some subsurface soils, where >50% of bacterial 16S rRNA gene sequences were verrucomicrobial. ► Abundance of Verrucomicrobia has been underestimated, probably due to primer bias. ► Class Spartobacteria was dominant within phylum Verrucomicrobia.
Lysosomal degradative compartments hydrolyze macromolecules to generate basic building blocks that fuel metabolic pathways in our cells. They also remove misfolded proteins and control size, ...function, and number of cytoplasmic organelles via constitutive and regulated autophagy. These catabolic processes attract interest because their defective functioning is linked to human disease and their molecular components are promising pharmacologic targets. The capacity to quantitatively assess them is highly sought-after. Here we present a tandem-fluorescent reporter consisting of a HaloTag-GFP chimera appended at the C- or at the N-terminus of select polypeptides to monitor protein and organelle delivery to the lysosomal compartment. The Halo-GFP changes color on fluorescent pulse with cell-permeable HaloTag ligands and, again, on delivery to acidic, degradative lysosomal compartments, where the fluorescent ligand-associated HaloTag is relatively stable, whereas the GFP portion is not, as testified by loss of the green fluorescence and generation of a protease-resistant, fluorescent HaloTag fragment. The Halo-GFP tandem fluorescent reporter presented in our study allows quantitative and, crucially, time-resolved analyses of protein and organelle transport to the lysosomal compartment by high resolution confocal laser scanning microscopy, antibody-free electrophoretic techniques and flow cytometry.
•Reviews current features of COPASI – a software for modeling biological processes.•Shows usage of the software COPASI.•Represents use cases of COPASI when applied in biotechnology.
COPASI is ...software used for the creation, modification, simulation and computational analysis of kinetic models in various fields. It is open-source, available for all major platforms and provides a user-friendly graphical user interface, but is also controllable via the command line and scripting languages. These are likely reasons for its wide acceptance. We begin this review with a short introduction describing the general approaches and techniques used in computational modeling in the biosciences. Next we introduce the COPASI package, and its capabilities, before looking at typical applications of COPASI in biotechnology.
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