In the ten years since the initial publication of the RenSeq protocol, the method has proved to be a powerful tool for studying disease resistance in plants and providing target genes for breeding ...programmes. Since the initial publication of the methodology, it has continued to be developed as new technologies have become available and the increased availability of computing power has made new bioinformatic approaches possible. Most recently, this has included the development of a k-mer based association genetics approach, the use of PacBio HiFi data, and graphical genotyping with diagnostic RenSeq. However, there is not yet a unified workflow available and researchers must instead configure approaches from various sources themselves. This makes reproducibility and version control a challenge and limits the ability to perform these analyses to those with bioinformatics expertise.
Here we present HISS, consisting of three workflows which take a user from raw RenSeq reads to the identification of candidates for disease resistance genes. These workflows conduct the assembly of enriched HiFi reads from an accession with the resistance phenotype of interest. A panel of accessions both possessing and lacking the resistance are then used in an association genetics approach (AgRenSeq) to identify contigs positively associated with the resistance phenotype. Candidate genes are then identified on these contigs and assessed for their presence or absence in the panel with a graphical genotyping approach that uses dRenSeq. These workflows are implemented via Snakemake, a python-based workflow manager. Software dependencies are either shipped with the release or handled with conda. All code is freely available and is distributed under the GNU GPL-3.0 license.
HISS provides a user-friendly, portable, and easily customised approach for identifying novel disease resistance genes in plants. It is easily installed with all dependencies handled internally or shipped with the release and represents a significant improvement in the ease of use of these bioinformatics analyses.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The coordination of multiple metabolic activities in plants relies on an interorganelle communication network established through membrane contact sites (MCS). The MCS are maintained in transient or ...durable configurations by tethering structures which keep the two membranes in close proximity, and create chemical microdomains that allow localized and targeted exchange of small molecules and possibly proteins. The past few years have witnessed a dramatic increase in our understanding of the structural and molecular organization of plant interorganelle MCS, and their crucial roles in plant specialized functions including stress responses, cell to cell communication, and lipid transport. In this review we summarize recent advances in understanding the molecular components, structural organization, and functions of different plant-specific MCS architectures.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
This paper presents five different statistical methods for ground scene prediction (GSP) in wavelength-resolution synthetic aperture radar (SAR) images. The GSP image can be used as a reference image ...in a change detection algorithm yielding a high probability of detection and low false alarm rate. The predictions are based on image stacks, which are composed of images from the same scene acquired at different instants with the same flight geometry. The considered methods for obtaining the ground scene prediction include (i) autoregressive models; (ii) trimmed mean; (iii) median; (iv) intensity mean; and (v) mean. It is expected that the predicted image presents the true ground scene without change and preserves the ground backscattering pattern. The study indicates that the the median method provided the most accurate representation of the true ground. To show the applicability of the GSP, a change detection algorithm was considered using the median ground scene as a reference image. As a result, the median method displayed the probability of detection of 97 % and a false alarm rate of 0 . 11 / km 2 , when considering military vehicles concealed in a forest.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Strong coupling between light and the fundamental excitations of a two-dimensional electron gas (2DEG) is of foundational importance both to pure physics and to the understanding and development of ...future photonic nanotechnologies1–7. Here we study the relationship between spin polarization of a 2DEG in a monolayer semiconductor, MoSe2, and light–matter interactions modified by a zero-dimensional optical microcavity. We find pronounced spin-susceptibility of the 2DEG to simultaneously enhance and suppress trion-polariton formation in opposite photon helicities. This leads to observation of a giant effective valley Zeeman splitting for trion-polaritons (g-factor of >20), exceeding the purely trionic splitting by over five times. Going further, we observe clear effective optical nonlinearity arising from the highly nonlinear behaviour of the valley-specific strong light–matter coupling regime, and allowing all-optical tuning of the polaritonic Zeeman splitting from 4 meV to >10 meV. Our experiments lay the groundwork for engineering topological phases with true unidirectionality in monolayer semiconductors, accompanied by giant effective photonic nonlinearities rooted in many-body exciton–electron correlations.Researchers show spin-susceptibility in monolayer MoSe2 and demonstrate giant effective valley Zeeman splitting and nonlinearity for trion-polaritons.
The midbrain dopamine neurons are hypothesized to provide a physiological correlate of the reward prediction error signal required by current models of reinforcement learning. We examined the ...activity of single dopamine neurons during a task in which subjects learned by trial and error when to make an eye movement for a juice reward. We found that these neurons encoded the difference between the current reward and a weighted average of previous rewards, a reward prediction error, but only for outcomes that were better than expected. Thus, the firing rate of midbrain dopamine neurons is quantitatively predicted by theoretical descriptions of the reward prediction error signal used in reinforcement learning models for circumstances in which this signal has a positive value. We also found that the dopamine system continued to compute the reward prediction error even when the behavioral policy of the animal was only weakly influenced by this computation.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
•We extracted barley β-glucans by a wet method.•The extraction of barley β-glucans was influenced by temperature.•The extracted fraction of β-glucans had a concentration of 53%.•The extracted ...fraction of β-glucans showed impurities such as starch and proteins.•Characterization of extracted β-glucans was similar to that commercial β-glucans.
Barley is rarely used in the food industry, even though it is a main source of β-glucans, which have important health benefits and a technological role in food. This work evaluated the humid extraction of barley β-glucans and partially characterized them. The extraction was studied using surface response methodology with both temperature and pH as variables. The extracted β-glucans were characterized by chemical and rheological analysis, infrared spectroscopy and scanning electron microscopy. The effect on extraction of linear and quadratic terms of pH and temperature corresponding to the regression model was significant, and we obtained a maximum concentration of 53.4% at pH 7.56 and temperature 45.5°C, with protein and mainly starch contamination. The extracted β-glucans presented a higher apparent viscosity than the commercial ones, the behavior of the commercial and extracted samples can be described as Newtonian and pseudoplastic, respectively. The results of infrared spectroscopy and scanning electron microscopy were characteristic of commercial β-glucans, indicating that this method is efficient for extracting β-glucans.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
The plant hormone auxin mediates developmental patterning by a mechanism that is based on active transport. In the shoot apical meristem, auxin gradients are thought to be set up through a feedback ...loop between auxin and the activity and polar localization of its transporter, the PIN1 protein. Two distinct molecular mechanisms for the subcellular polarization of PIN1 have been proposed. For leaf positioning (phyllotaxis), an "up-the-gradient" PIN1 polarization mechanism has been proposed, whereas the formation of vascular strands is thought to proceed by "with-the-flux" PIN1 polarization. These patterning mechanisms intersect during the initiation of the midvein, which raises the question of how two different PIN1 polarization mechanisms may work together. Our detailed analysis of PIN1 polarization during midvein initiation suggests that both mechanisms for PIN1 polarization operate simultaneously. Computer simulations of the resulting dual polarization model are able to reproduce the dynamics of observed PIN1 localization. In addition, the appearance of high auxin concentration in our simulations throughout the initiation of the midvein is consistent with experimental observation and offers an explanation for a long-standing criticism of the canalization hypothesis; namely, how both high flux and high concentration can occur simultaneously in emerging veins.
We show that the magnetization of a thin ferromagnetic (Ga,Mn)As layer can be modulated by picosecond acoustic pulses. In this approach a picosecond strain pulse injected into the structure induces a ...tilt of the magnetization vector M, followed by the precession of M around its equilibrium orientation. This effect can be understood in terms of changes in magnetocrystalline anisotropy induced by the pulse. A model where only one anisotropy constant is affected by the strain pulse provides a good description of the observed time-dependent response.
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CMK, CTK, FMFMET, IJS, NUK, PNG, UM
Magneto-optical phenomena such as the Faraday and Kerr effects play a central role in controlling the polarization and intensity of optical fields propagating through a medium. Intensity effects in ...which the direction of light emission depends on the orientation of the external magnetic field are of particular interest, as they can be harnessed for routing light. Effects known so far for accomplishing such routing all control light emission along the axis parallel to the magnetic field. Here we report a new class of emission phenomena where directionality is established perpendicular to the externally applied magnetic field for light sources located in the vicinity of a surface. As a proof of principle for this effect, which we call transverse magnetic routing of light emission, we demonstrate the routing of emission for excitons in a diluted-magnetic-semiconductor quantum well. In hybrid plasmonic semiconductor structures, we observe significantly enhanced directionality of up to 60%.
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IJS, NUK, SBMB, UL, UM, UPUK
Brassinosteroids (BRs) are steroidal phytohormones that are essential for plant growth, development and adaptation to environmental stresses. BRs act in a dose-dependent manner and do not travel over ...long distances; hence, BR homeostasis maintenance is critical for their function. Biosynthesis of bioactive BRs relies on the cell-to-cell movement of hormone precursors. However, the mechanism of the short-distance BR transport is unknown, and its contribution to the control of endogenous BR levels remains unexplored. Here we demonstrate that plasmodesmata (PD) mediate the passage of BRs between neighboring cells. Intracellular BR content, in turn, is capable of modulating PD permeability to optimize its own mobility, thereby manipulating BR biosynthesis and signaling. Our work uncovers a thus far unknown mode of steroid transport in eukaryotes and exposes an additional layer of BR homeostasis regulation in plants.
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GEOZS, IJS, IMTLJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZAGLJ
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