Search

U-Net is a generic deep-learning solution for frequently occurring quantification tasks such as cell detection and shape measurements in biomedical image data. We present an ImageJ plugin that enables non-machine-learning experts to analyze their data with U-Net on either a local computer or a remote server/cloud service. The plugin comes with pretrained models for single-cell segmentation and allows for U-Net to be adapted to new tasks on the basis of a few annotated samples.

The Tertiary Lausitz Volcanic Field covers a broad area encompassing parts of Eastern Saxony (Germany), Lower Silesia (Poland) and North Bohemia (Czech Republic). Volcanism was predominantly controlled by the volcano-tectonic evolution of the Ohře Rift and culminated in the Lower Oligocene. This paper deals with the highest volcano of this area, the Lausche Hill (792.6 m a.s.l.) situated in the Lausitz Mountains. We offer a reconstruction of the volcanic edifice and its eruptive history. Its complex genesis is reflected by six different eruption styles and an associated petrographic variety. Furthermore, the Lausche Volcano provides valuable information concerning the morphological evolution of its broader environs. The remnant of an alluvial fan marking a Middle Paleocene–Lower Eocene (62–50 Ma) palaeo-surface is preserved at the base of the volcano. The deposition of this fan can be attributed to a period of erosion of its nearby source area, the Lausitz Block that has undergone intermittent uplift at the Lausitz Overthrust since the Upper Cretaceous. The Lausche Hill is one of at least six volcanoes in the Lausitz Mountains which show an eminent low level of erosion despite their Oligocene age and position on elevated terrain. These volcanoes are exposed in their superficial level which clearly contradicts their former interpretation as subvolcanoes. Among further indications, this implies that the final morphotectonic uplift of the Lausitz Mountains started in the upper Lower Pleistocene (~ 1.3 Ma) due to revived subsidence of the nearby Zittau Basin. It is likely that this neotectonic activity culminated between the Elsterian and Saalian Glaciation (~ 320 ka). The formation of the low mountain range was substantially controlled by the intersection of the Lausitz Overthrust and the Ohře Rift.

On the 24th January 2019 the former director of the Senckenberg Museum of Natural History Görlitz (formerly the Staatliches Museum für Naturkunde Görlitz) Prof. Dr. Wolfram Dunger passed away at the age of 89. The employees of the Museum, his colleagues and friends will always remember him as an international authority on soil zoology and as the ‘leader of the Museum’.

U-Net is a generic deep-learning solution for frequently occurring quantification tasks such as cell detection and shape measurements in biomedical image data. We present an ImageJ plugin that enables non-machine-learning experts to analyze their data with U-Net on either a local computer or a remote server/cloud service. The plugin comes with pretrained models for single-cell segmentation and allows for U-Net to be adapted to new tasks on the basis of a few annotated samples.

Climate change is known to affect the stability of agricultural production all over the world. One of the most important problems associated with agriculture is uptake of water and nutrients by plants. Plant roots are vital organs, which are involved in water and nutrient acquisition and gravitropic responses. This review describes the pivotal role of auxin in root growth, gravitropic and abiotic stress responses, focusing on the regulatory role of CDPK superfamily members in stress tolerance.

The gravitropic bending in plant roots is caused by asymmetric cell elongation. This requires an asymmetric increase in cell surface and therefore plasma membrane components such as lipids, sterols, and membrane proteins. We have identified an early gravity-regulated protein in Arabidopsis thaliana root apices that binds stigmasterol and phosphoethanolamines. This root-specific protein interacts with the membrane transport protein synaptotagmin-1 and was therefore named InteractoR Of SYnaptotagmin1 (ROSY1). While interactions between ML-domain proteins with membrane transport proteins and their impact have been reported from animal cell systems, this is the first report of such an interaction in a plant system. Homozygous mutants of ROSY1 exhibit decreased basipetal auxin transport, a faster root gravitropic response, and an increase in salt stress tolerance. Our results suggest that ROSY1 plays a role in root gravitropism, possibly by facilitating membrane trafficking and asymmetric cell elongation via its interaction with synaptotagmin-1.

Ground-based simulators of microgravity such as fast rotating 2-D clinostats are valuable tools to study gravity related processes. We describe here a versatile g-value-adjustable 2-D clinostat that is suitable for plant analysis. To avoid seedling adaptation to 1 g after clinorotation, we designed chambers that allow rapid fixation. A detailed protocol for fixation, RNA isolation and the analysis of selected genes is described. Using this clinostat we show that mRNA levels of LONG HYPOCOTYL 5 (HY5), MIZU-KUSSEI 1 (MIZ1) and microRNA MIR163 are down-regulated in 5-day-old Arabidopsis thaliana roots after 3 min and 6 min of clinorotation using a maximal reduced g-force of 0.02 g, hence demonstrating that this 2-D clinostat enables the characterization of early transcriptomic events during root response to microgravity. We further show that this 2-D clinostat is able to compensate the action of gravitational force as both gravitropic-dependent statolith sedimentation and subsequent auxin redistribution (monitoring D R5 r e v ::G F P reporter) are abolished when plants are clinorotated. Our results demonstrate that 2-D clinostats equipped with interchangeable growth chambers and tunable rotation velocity are suitable for studying how plants perceive and respond to simulated microgravity.

Three out of seven institutes belonging to the Senckenberg Gesellschaft fur Naturforschung (SGN) house considerable palaeontological collections: The Senckenberg Research Institute and Natural History Museum in Frankfurt on the Main including the Research Station on Quaternary Palaeontology in Weimar, the Senckenberg Naturhistorische Sammlungen Dresden and the Senckenberg Museum fur Naturkunde in Gorlitz. The palaeontological collections of the SGN comprise a total of more than two million specimens and series. Traditionally the different institutes have different stratigraphic and regional focal points, due to the long history of most collections. Frankfurt has a focus on the Palaeozoic (especially Devonian) of the Rhenish slate mountains and the Eocene of the Messel fossil pit (an UNESCO world-heritage site since 1995), Dresden has a focus on the Cretaceous of Saxony and the Tertiary of Central Germany, whereas the smaller collections in Gorlitz have a focus on Eastern Saxony and the Lausitz.

In the version of this paper originally published, one of the affiliations for Dominic Mai was incorrect: "Center for Biological Systems Analysis (ZBSA), Albert-Ludwigs-University, Freiburg, Germany" should have been "Life Imaging Center, Center for Biological Systems Analysis, Albert-Ludwigs-University, Freiburg, Germany." This change required some renumbering of subsequent author affiliations. These corrections have been made in the PDF and HTML versions of the article, as well as in any cover sheets for associated Supplementary Information.

Active polar transport establishes directional auxin flow and the generation of local auxin gradients implicated in plant responses and development. Auxin modulates gravitropism at the root tip and root hair morphogenesis at the differentiation zone. Genetic and biochemical analyses provide evidence for defective basipetal auxin transport in trh1 roots. The trh1, pin2, axr2 and aux1 mutants, and transgenic plants overexpressing PIN1, all showing impaired gravity response and root hair development, revealed ectopic PIN1 localization. The auxin antagonist hypaphorine blocked root hair elongation and caused moderate agravitropic root growth, also leading to PIN1 mislocalization. These results suggest that auxin imbalance leads to proximal and distal developmental defects in Arabidopsis root apex, associated with agravitropic root growth and root hair phenotype, respectively, providing evidence that these two auxin-regulated processes are coupled. Cell-specific subcellular localization of TRH1-YFP in stele and epidermis supports TRH1 engagement in auxin transport, and hence impaired function in trh1 causes dual defects of auxin imbalance. The interplay between intrinsic cues determining root epidermal cell fate through the TTG/GL2 pathway and environmental cues including abiotic stresses modulates root hair morphogenesis. As a consequence of auxin imbalance in Arabidopsis root apex, ectopic PIN1 mislocalization could be a risk aversion mechanism to trigger root developmental responses ensuring root growth plasticity.

Image quality in light-sheet fluorescence microscopy is strongly affected by the shape of the illuminating laser beam inside embryos, plants or tissue. While the phase of Gaussian or Bessel beams propagating through thousands of cells can be partly controlled holographically, the propagation of fluorescence light to the detector is difficult to control. With each scatter process a fluorescence photon loses information necessary for the image generation. Using Arabidopsis root tips we demonstrate that ballistic and diffusive fluorescence photons can be separated by analyzing the image spectra in each plane without a priori knowledge. We introduce a theoretical model allowing to extract typical scattering parameters of the biological material. This allows to attenuate image contributions from diffusive photons and to amplify the relevant image contributions from ballistic photons through a depth dependent deconvolution. In consequence, image contrast and resolution are significantly increased and scattering artefacts are minimized especially for Bessel beams with confocal line detection.

Remnants of numerous monogenetic volcanoes are preserved in the Central European Volcanic Province (CEVP). The Landeskrone Hill, a monogenetic scoria cone in the Lusatian Volcanic Field, is reconstructed here. This was done using measurements of the dip of columnar jointing of lava lake basalts and the detailed mapping of the volcaniclastic rocks. The reconstruction implies a large scoria cone and a lava lake; filling the crater with a thickness of more than 110 m. Volcanic activity was characterized by strombolian eruptions possibly after an opening phreatomagmatic phase. A scoria cone was developed in an initial maar-diatreme volcano. A late phreatomagmatic phase could explain the unusual modified crater of the scoria cone. The conduit was emptied and so the crater was widened in this late eruption stage. An increased magma flux probably induced a change in the eruptive style and, finally, the crater was filled in a single event by a lava lake. This effusive phase completed the multi-stage volcano development. The 34 Ma-old volcano is an excellent example for the persistence of relicts of monogenetic volcanoes over a long period of time. There are some other remnants of monogenetic scoria cones that survived degradation processes in the area. With respect to the present surface, the reconstruction of the paleosurface implies low uplift and erosion rates of about 3 mm/ka since the Oligocene. These denudation values support and expand on the previously published fission track data (prior to the Upper Cretaceous) and glacial-sedimentological data on neotectonic movements since the Middle Pleistocene. The erosion rate estimated by physical volcanological data implies stagnation of tectonic uplift from the Upper Paleogene to the Middle Neogene and a reactivation of tectonic movement for the Lusatian Massif in the Middle Pleistocene. Thus, the reconstructed edifice provides a powerful tool for the study of landscape evolution by clearly defining the characteristics of the paleosurfaces at certain times.

Plant roots show an impressive degree of plasticity in adapting their branching patterns to ever-changing growth conditions. An important mechanism underlying this adaptation ability is the interaction between hormonal and developmental signals. Here, we analyze the interaction of jasmonate with auxin to regulate lateral root (LR) formation through characterization of an Arabidopsis thaliana mutant, jasmonate-induced defective lateral root1 (jdl1/asa1-1). We demonstrate that, whereas exogenous jasmonate promotes LR formation in wild-type plants, it represses LR formation in jdl1/asa1-1. JDL1 encodes the auxin biosynthetic gene ANTHRANILATE SYNTHASE α1 (ASA1), which is required for jasmonate-induced auxin biosynthesis. Jasmonate elevates local auxin accumulation in the basal meristem of wild-type roots but reduces local auxin accumulation in the basal meristem of mutant roots, suggesting that, in addition to activating ASA1-dependent auxin biosynthesis, jasmonate also affects auxin transport. Indeed, jasmonate modifies the expression of auxin transport genes in an ASA1-dependent manner. We further provide evidence showing that the action mechanism of jasmonate to regulate LR formation through ASA1 differs from that of ethylene. Our results highlight the importance of ASA1 in jasmonate-induced auxin biosynthesis and reveal a role for jasmonate in the attenuation of auxin transport in the root and the fine-tuning of local auxin distribution in the root basal meristem.

Transformation of plant cells with T-DNA of virulent agrobacteria is one of the most extreme triggers of developmental changes in higher plants. For rapid growth and development of resulting tumors, specific changes in the gene expression profile and metabolic adaptations are required. Increased transport and metabolic fluxes are critical preconditions for growth and tumor development. A functional genomics approach, using the Affymetrix whole genome microarray (∼22,800 genes), was applied to measure changes in gene expression. The solute pattern of Arabidopsis thaliana tumors and uninfected plant tissues was compared with the respective gene expression profile. Increased levels of anions, sugars, and amino acids were correlated with changes in the gene expression of specific enzymes and solute transporters. The expression profile of genes pivotal for energy metabolism, such as those involved in photosynthesis, mitochondrial electron transport, and fermentation, suggested that tumors produce C and N compounds heterotrophically and gain energy mainly anaerobically. Thus, understanding of gene-to-metabolite networks in plant tumors promotes the identification of mechanisms that control tumor development.

In multicellular organisms, patterning is a process that generates axes in the primary body plan, creates domains upon organ formation, and finally leads to differentiation into tissues and cell types. We identified the Arabidopsis thaliana TORNADO1 (TRN1) and TRN2 genes and their role in leaf patterning processes such as lamina venation, symmetry, and lateral growth. In trn mutants, the leaf venation network had a severely reduced complexity: incomplete loops, no tertiary or quaternary veins, and vascular islands. The leaf laminas were asymmetric and narrow because of a severely reduced cell number. We postulate that the imbalance between cell proliferation and cell differentiation and the altered auxin distribution in both trn mutants cause asymmetric leaf growth and aberrant venation patterning. TRN1 and TRN2 were epistatic to ASYMMETRIC LEAVES1 with respect to leaf asymmetry, consistent with their expression in the shoot apical meristem and leaf primordia. TRN1 codes for a large plant-specific protein with conserved domains also found in a variety of signaling proteins, whereas TRN2 encodes a transmembrane protein of the tetraspanin family whose phylogenetic tree is presented. Double mutant analysis showed that TRN1 and TRN2 act in the same pathway.

Suspension cultures from Arabidopsis thaliana wild type and AtPIN1-deficient lines were initiated and maintained for more than 3 years. A protocol for efficient regeneration from long-term suspension cultures was established. Arabidopsis wild-type and respectively AtPIN1 mutant plants have been regenerated from these cultures and characterized. Additionally, transgenic suspension cultures expressing the uidA (β -glucuronidase) reporter gene under the control of AtPIN1 promoter have been used for morphogenic studies. Our studies suggest that a lack of AtPIN1 function affects shoot differentiation and development, but does not influence in vitro regeneration of plants.

We have isolated, cloned and characterized a cDNA from Zea mays L., denoted ZmAP1, coding for an anionic peroxidase. The open reading frame of ZmAP1 starting 72 residues from the 5' end of the cDNA predicts a 37,778 dalton protein of 356 amino acid residues. The protein has high similarity to other peroxidases and contains two peroxidase motifs that carry two highly conserved histidines in the active center. We expressed recombinant ZmAP1 protein in E. coli as a fusion with maltose-binding protein. The fusion protein was biochemically active after addition of hemin to the apoprotein. The maize peroxidase ZmAP1 has a pH optimum at pH 4.0 and a Km of 0.2 mM for the substrate 2,2'-azino-bis-(3-ethyl-benzothiazolin-6-sulfonic acid) at this pH. In maize seedlings the ZmAP1 gene is expressed predominantly in roots, the mesocotyl, the coleoptile and to a lower extent in the node, whereas no expression in the primary leaf was found. In situ hybridization shows that the expression of ZmAP1 in the young maize root is confined to the epidermis, hypodermis and the pericycle.

6 School of Biological Science and Technology, University of Jinan, 336, West Road of Nan Xinzhuang, Jinan 250022, China Wang et al.: 2-D Clinostat for Simulated Microgravity Experiments with Arabidopsis Seedlings Microgravity Sci. Technol. 28, 59–66 (2016). doi:10.1007/s12217-015-94781 was published in an earlier issue instead of being included in this “Topical issue on Ground-Based Facilities”.

After qualitative examination of the inclusion inventory of 80 zircon megacrysts from alluvial placers of the Cenozoic alkali basalt area of northern Bohemia and south-eastern Saxony, three representative megacrysts from the Podsedice deposit were selected for an in-depth study of inclusion minerals. Primary and secondary inclusions were distinguished and used as monitor for zircon-related syn- and epigenetic processes. The trace-element characteristics of the zircon hosts imply an alkali silicatic parental rock, probably nepheline syenites or fenites, which occur as enclaves in placer-near breccia fillings. The genetically most interesting inclusion species is “strontiopyrochlore”, for which its presence within areas of oscillatory zonation suggests a magmatic origin. This mode of origin contrasts to previous observations indicating formation of “strontiopyrochlore” as secondary mineral in altered carbonatite. The Sr concentration of “strontiopyrochlore” from Podsedice varies between 7.4 and 12 wt.% SrO, corresponding to a proportion of Sr of 29–48 at.% of the total A-site cations. The infiltration of late- or post-magmatic Fe-rich hydrothermal fluids along fractures crosscutting the zircon host caused a partial substitution of Nb5+ by Fe3+ in the B-site of the pyrochlore structure and the breakdown of primary fergusonite-like inclusions into undefined Nb–Y–REE–Fe oxide phases usually associated with goethite-like minerals. Thorite and related Y–REE–Th silicate phases are the most frequent secondary inclusions originated by dissolution−re-precipitation. Baddeleyite probably formed in response to desilicification that the zircon host has experienced during the contact with the SiO2-undersaturated alkali basalt melt.

Since the divergence of plants and animals about 1.5 billion yr ago, the signal transduction pathways in both kingdoms have been subjected to very different selection pressures. These fundamental differences have influenced the evolution of both the signaling molecules themselves and the mechanisms by which signals are relayed. Among these differences, a plant’s ability to continuously form new organs during its postembryonic development, the increased frequency of high degrees of both ploidy and gene duplication in many higher plants, and the multicellular haploid gametophytes of more primitive plants could be particularly significant. Particular developmental processes, such as totipotency (the ability of a plant to regenerate itself from vegetative tissue), have enabled plants to increase their reproductive potential and are consequences of the idiosyncrasies of a plant’s cellular signaling mechanisms.

Dark-grown Arabidopsis seedlings develop an apical hook by differential cell elongation and division, a process driven by cross-talk between multiple hormones. Auxins, ethylene and gibberellins interact in the formation of the apical hook. In the light, a similar complexity of hormonal regulation has been revealed at the level of hypocotyl elongation. Here, we describe the involvement of brassinosteroids (BRs) in auxin- and ethylene-controlled processes in the hypocotyls of both light- and dark-grown seedlings. We show that BR biosynthesis is necessary for the formation of an exaggerated apical hook and that either application of BRs or disruption of BR synthesis alters auxin response, presumably by affecting auxin transport, eventually resulting in the disappearance of the apical hook. Furthermore, we demonstrate that ethylene-stimulated hypocotyl elongation in the light is largely controlled by the same mechanisms as those governing formation of the apical hook in darkness. However, in the light, BRs appear to compensate for the insensitivity to ethylene in hls mutants, supporting a downstream action of BRs. Hence, our results indicate that HLS1, SUR1/HLS3/RTY1/ALF1 and AMP1/HPT/COP2/ HLS2/PT act on the auxin–ethylene interaction, rather than at the level of BRs. A model for the tripartite hormone interactions is presented.

Polar transport–dependent local accumulation of auxin provides positional cues for multiple plant patterning processes. This directional auxin flow depends on the polar subcellular localization of the PIN auxin efflux regulators. Overexpression of the PINOID protein kinase induces a basal-to-apical shift in PIN localization, resulting in the loss of auxin gradients and strong defects in embryo and seedling roots. Conversely, pid loss of function induces an apical-to-basal shift in PIN1 polar targeting at the inflorescence apex, accompanied by defective organogenesis. Our results show that a PINOID-dependent binary switch controls PIN polarity and mediates changes in auxin flow to create local gradients for patterning processes.

STYLOSA (STY) in Antirrhinum and LEUNIG(LUG) in Arabidopsis control the spatially correct expression of homeotic functions involved in the control of floral organ identity. We show here that the sty mutant also displays alteration in leaf venation patterns and hypersensitivity towards auxin and polar auxin transport inhibitors, demonstrating that STY has a more general role in plant development. STY and LUG are shown to be orthologues that encode proteins with structural relation to GRO/TUP1-like co-repressors. Using a yeast-based screen we found that STY interacts with several transcription factors, suggesting that STY, like GRO/TUP1, forms complexes in vivo. Proteins of the YABBY family, characterised by containing a partial HMG domain, represent a major group of such interactors. In vivo association of STY with one of the YABBY proteins, GRAMINIFOLIA (GRAM), is supported by enhanced phenotypic defects in sty gram double mutants,for instance in the control of phyllotaxis, floral homeotic functions and organ polarity. Accordingly, the STY and GRAM protein and mRNA expression patterns overlap in emerging lateral organ primordia. STY is expressed in all meristems and later becomes confined to the adaxial domain and (pro)vascular tissue. This pattern is similar to genes that promote adaxial identity, and, indeed, STY expression follows,although does not control, adaxial fate. We discuss the complex roles of STY and GRAM proteins in reproductive and vegetative development, performed in part in physical association but also independently.

Ethylene or its precursor 1-aminocyclopropane-1-carboxylic acid (ACC) can stimulate hypocotyl elongation in light-grown Arabidopsis seedlings. A mutant, designated ACC-related long hypocotyl 1 (alh1), that displayed a long hypocotyl in the light in the absence of the hormone was characterized. Etiolatedalh1 seedlings overproduced ethylene and had an exaggerated apical hook and a thicker hypocotyl, although no difference in hypocotyl length was observed when compared with wild type.Alh1 plants were less sensitive to ethylene, as reflected by reduction of ACC-mediated inhibition of hypocotyl growth in the dark and delay in flowering and leaf senescence.Alh1 also had an altered response to auxin, whereas auxin levels in whole alh1 seedlings remained unaffected. In contrast to wild type, alh1 seedlings showed a limited hypocotyl elongation when treated with indole-3-acetic acid. Alh1 roots had a faster response to gravity. Furthermore, the hypocotyl elongation of alh1 and of ACC-treated wild type was reverted by auxin transport inhibitors. In addition, auxin up-regulated genes were ectopically expressed in hypocotyls upon ACC treatment, suggesting that the ethylene response is mediated by auxins. Together, these data indicate thatalh1 is altered in the cross talk between ethylene and auxins, probably at the level of auxin transport.

The ca. 30 Ma Steinberg basanite occurs at the NE termination of the Eger (Ohře) Rift in the NW Bohemian Massif, Central Europe, and belongs to the Cenozoic alkaline Central European Volcanic Province. The basanite hosts a suite of mantle xenoliths, most of which are harzburgites containing relatively magnesian olivine (Fo 90.5–91.6) and Al-poor (0.04–0.13 a pfu) orthopyroxene (mg# 0.90–0.92). Some of these harzburgites also contain volumetrically minor clinopyroxene (mg# 0.92–0.95, Al 0.03–0.13 a pfu) and have U-shaped LREE-enriched REE patterns. The Steinberg harzburgites are typical for the Lower Silesian - Upper Lusatian domain of the European subcontinental lithospheric mantle. They represent residual mantle that has undergone extensive partial melting and was subsequently affected by mantle metasomatism by mixed carbonatite-silicate melts. The Steinberg xenolith suite comprises also dunitic xenoliths affected by metasomatism by melt similar to the host basanite, which lowered the Fo content in olivine to 87.6 %. This metasomatism happened shortly before xenolith entrainment in the erupting lava. One of the xenoliths is a wehrlite (olivine Fo 73 %, clinopyroxene mg# 0.83–0.85, subordinate orthopyroxene mg# 0.76–0.77). Its clinopyroxene REE pattern is flat and slightly LREE-depleted. This wehrlite is considered to be a tholeiitic cumulate. One of the studied harzburgites contains clinopyroxene with similar trace element contents to those in wehrlite. This type of clinopyroxene records percolation of tholeiitic melt through harzburgite. The tholeiitic melt might be similar to Cenozoic continental tholeiites occurring in the Central European Volcanic Province (e.g., Vogelsberg, Germany).