PlantDB – a versatile database for managing plant research

Background Research in plant science laboratories often involves usage of many different species, cultivars, ecotypes, mutants, alleles or transgenic lines. This creates a great challenge to keep track of the identity of experimental plants and stored samples or seeds. Results Here, we describe PlantDB – a Microsoft® Office Access database – with a user-friendly front-end for managing information relevant for experimental plants. PlantDB can hold information about plants of different species, cultivars or genetic composition. Introduction of a concise identifier system allows easy generation of pedigree trees. In addition, all information about any experimental plant – from growth conditions and dates over extracted samples such as RNA to files containing images of the plants – can be linked unequivocally. Conclusion We have been using PlantDB for several years in our laboratory and found that it greatly facilitates access to relevant information.ISSN:1746-481

Local stratopause temperature variabilities and their embedding in the global context

The stratopause is by definition the transition between the stratosphere and mesosphere. During winter the circulation at mid-latitudes and high latitudes in the stratosphere is mainly driven by quasi-stationary planetary waves (PWs), while the circulation in the mesosphere is mainly driven by gravity waves (GWs). The question arises of whether PWs or GWs dominate the variability of the stratopause. The most famous and dramatic variability of the middle atmosphere is a sudden stratospheric warming (SSW) generated by PWs interacting with the polar vortex. A similar phenomenon but smaller in magnitude and more regional is stratopause temperature enhancements (STEs) initially observed by local measurements and generated by breaking PWs. Thus it seems that PWs dominate the variability of the stratopause. In this study we want to quantify to which extent quasi-stationary PWs contribute to the stratopause variability. To do that we combine local lidar observations at Kühlungsborn (54∘ N, 11∘ E) and Andenes (69∘ N, 16∘ E) with global MERRA-2 reanalysis data bringing the local variability of the stratopause into the global context. Therefore we compare the temperature time series at Kühlungsborn and Andenes at 2 hPa, the altitude where STEs maximize, with characteristics (amplitude and phase) of PWs with wave numbers 1, 2 and 3. We found that for Kühlungsborn and Andenes 98 % of the local day-to-day variability of the stratopause can be explained by the variability of PWs with wave number 1, 2 and 3. Thus, the winter stratopause day-to-day variability is highly dominated by the variability of PWs

a versatile tool for the analysis and integrative visualization of DNA copy number variants

Background The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multidimensional data analysis and comparison of patient cohorts are needed to assist in the discrimination of clinically relevant CNVs from others. Results We developed GenomeCAT, a standalone Java application for the analysis and integrative visualization of CNVs. GenomeCAT is composed of three modules dedicated to the inspection of single cases, comparative analysis of multidimensional data and group comparisons aiming at the identification of recurrent aberrations in patients sharing the same phenotype, respectively. Its flexible import options ease the comparative analysis of own results derived from microarray or NGS platforms with data from literature or public depositories. Multidimensional data obtained from different experiment types can be merged into a common data matrix to enable common visualization and analysis. All results are stored in the integrated MySQL database, but can also be exported as tab delimited files for further statistical calculations in external programs. Conclusions GenomeCAT offers a broad spectrum of visualization and analysis tools that assist in the evaluation of CNVs in the context of other experiment data and annotations. The use of GenomeCAT does not require any specialized computer skills. The various R packages implemented for data analysis are fully integrated into GenomeCATs graphical user interface and the installation process is supported by a wizard. The flexibility in terms of data import and export in combination with the ability to create a common data matrix makes the program also well suited as an interface between genomic data from heterogeneous sources and external software tools. Due to the modular architecture the functionality of GenomeCAT can be easily extended by further R packages or customized plug-ins to meet future requirements

Podoplanin immunopositive lymphatic vessels at the implant interface in a rat model of osteoporotic fractures

Insertion of bone substitution materials accelerates healing of osteoporotic fractures. Biodegradable materials are preferred for application in osteoporotic patients to avoid a second surgery for implant replacement. Degraded implant fragments are often absorbed by macrophages that are removed from the fracture side via passage through veins or lymphatic vessels. We investigated if lymphatic vessels occur in osteoporotic bone defects and whether they are regulated by the use of different materials. To address this issue osteoporosis was induced in rats using the classical method of bilateral ovariectomy and additional calcium and vitamin deficient diet. In addition, wedge-shaped defects of 3, 4, or 5 mm were generated in the distal metaphyseal area of femur via osteotomy. The 4 mm defects were subsequently used for implantation studies where bone substitution materials of calcium phosphate cement, composites of collagen and silica, and iron foams with interconnecting pores were inserted. Different materials were partly additionally functionalized by strontium or bisphosphonate whose positive effects in osteoporosis treatment are well known. The lymphatic vessels were identified by immunohistochemistry using an antibody against podoplanin. Podoplanin immunopositive lymphatic vessels were detected in the granulation tissue filling the fracture gap, surrounding the implant and growing into the iron foam through its interconnected pores. Significant more lymphatic capillaries were counted at the implant interface of composite, strontium and bisphosphonate functionalized iron foam. A significant increase was also observed in the number of lymphatics situated in the pores of strontium coated iron foam. In conclusion, our results indicate the occurrence of lymphatic vessels in osteoporotic bone. Our results show that lymphatic vessels are localized at the implant interface and in the fracture gap where they might be involved in the removal of lymphocytes, macrophages, debris and the implants degradation products. Therefore the lymphatic vessels are involved in implant integration and fracture healing

Exceptionally strong summer-like zonal wind reversal in the upper mesosphere during winter 2015/16

The 2015/16 Northern Hemisphere winter season was marked by peculiarities in the circulation pattern in the high-latitude mesopause region. Wind measurements from the Andenes (69° N, 13° E) meteor radar show westward winds below 84 km and eastward winds above. This wind pattern in the zonal wind was observable between the end of December 2015 and the end of January 2016, i.e., conditions that are typical for the summer were found during winter. Additional meteor radar measurements at midlatitude stations did not show such a zonal wind reversal but indicate, together with the polar latitude stations, a reversal of the horizontal temperature gradient. This is confirmed by global satellite measurements. Therefore, it is plausible that the polar latitude summer-like zonal wind reversal in December–January is in accordance with the reversed horizontal temperature gradient assuming a thermal wind balance between mid- and polar latitudes. The reversed horizontal temperature gradient itself is induced by stationary planetary waves at lower and midlatitudes in the mesosphere, leading to a weakening of the residual circulation above the European sector

Exceptionally strong summer-like zonal wind reversal in the upper mesosphere during winter 2015/16

The 2015/16 Northern Hemisphere winter season was marked by peculiarities in the circulation pattern in the high-latitude mesopause region. Wind measurements from the Andenes (69° N, 13° E) meteor radar show westward winds below 84 km and eastward winds above. This wind pattern in the zonal wind was observable between the end of December 2015 and the end of January 2016, i.e., conditions that are typical for the summer were found during winter. Additional meteor radar measurements at midlatitude stations did not show such a zonal wind reversal but indicate, together with the polar latitude stations, a reversal of the horizontal temperature gradient. This is confirmed by global satellite measurements. Therefore, it is plausible that the polar latitude summer-like zonal wind reversal in December–January is in accordance with the reversed horizontal temperature gradient assuming a thermal wind balance between mid- and polar latitudes. The reversed horizontal temperature gradient itself is induced by stationary planetary waves at lower and midlatitudes in the mesosphere, leading to a weakening of the residual circulation above the European sector

Exceptionally strong summer-like zonal wind reversal in the upper mesosphere during winter 2015/16

The 2015/16 Northern Hemisphere winter season was marked by peculiarities in the circulation pattern in the high-latitude mesopause region. Wind measurements from the Andenes (69° N, 13° E) meteor radar show westward winds below 84 km and eastward winds above. This wind pattern in the zonal wind was observable between the end of December 2015 and the end of January 2016, i.e., conditions that are typical for the summer were found during winter. Additional meteor radar measurements at midlatitude stations did not show such a zonal wind reversal but indicate, together with the polar latitude stations, a reversal of the horizontal temperature gradient. This is confirmed by global satellite measurements. Therefore, it is plausible that the polar latitude summer-like zonal wind reversal in December–January is in accordance with the reversed horizontal temperature gradient assuming a thermal wind balance between mid- and polar latitudes. The reversed horizontal temperature gradient itself is induced by stationary planetary waves at lower and midlatitudes in the mesosphere, leading to a weakening of the residual circulation above the European sector

Brassinin Promotes the Degradation of Tie2 and FGFR1 in Endothelial Cells and Inhibits Triple-Negative Breast Cancer Angiogenesis

Brassinin, a phytoalexin derived from cruciferous vegetables, has been reported to exhibit anti-cancer activity in multiple cancer types. However, its effects on triple-negative breast cancer (TNBC) development and the underlying mechanisms have not been elucidated so far. In this study, we demonstrated in vitro that brassinin preferentially reduces the viability of endothelial cells (ECs) when compared to other cell types of the tumor microenvironment, including TNBC cells, pericytes, and fibroblasts. Moreover, brassinin at non-cytotoxic doses significantly suppressed the proliferation, migration, tube formation, and spheroid sprouting of ECs. It also efficiently inhibited angiogenesis in an ex-vivo aortic ring assay and an in-vivo Matrigel plug assay. Daily intraperitoneal injection of brassinin significantly reduced tumor size, microvessel density, as well as the perfusion of tumor microvessels in a dorsal skinfold chamber model of TNBC. Mechanistic analyses showed that brassinin selectively stimulates the degradation of Tie2 and fibroblast growth factor receptor 1 in ECs, leading to the down-regulation of the AKT and extracellular signal-regulated kinase pathways. These findings demonstrate a preferential and potent anti-angiogenic activity of brassinin, which may be the main mechanism of its anti-tumor action. Accordingly, this phytochemical represents a promising candidate for the future anti-angiogenic treatment of TNBC

Linalool inhibits the angiogenic activity of endothelial cells by downregulating intracellular ATP levels and activating TRPM8

Angiogenesis crucially contributes to various diseases, such as cancer and diabetic retinopathy. Hence, anti-angiogenic therapy is considered as a powerful strategy against these diseases. Previous studies reported that the acyclic monoterpene linalool exhibits anticancer, anti-inflammatory and anti-oxidative activity. However, the effects of linalool on angiogenesis still remain elusive. Therefore, we investigated the action of (3R)-(−)-linalool, a main enantiomer of linalool, on the angiogenic activity of human dermal microvascular endothelial cells (HDMECs) by a panel of angiogenesis assays. Non-cytotoxic doses of linalool significantly inhibited HDMEC proliferation, migration, tube formation and spheroid sprouting. Linalool also suppressed the vascular sprouting from rat aortic rings. In addition, Matrigel plugs containing linalool exhibited a significantly reduced microvessel density 7 days after implantation into BALB/c mice. Mechanistic analyses revealed that linalool promotes the phosphorylation of extracellular signal-regulated kinase (ERK), downregulates the intracellular level of adenosine triphosphate (ATP) and activates the transient receptor potential cation channel subfamily M (melastatin) member (TRPM)8 in HDMECs. Inhibition of ERK signaling, supplementation of ATP and blockade of TRPM8 significantly counteracted linalool-suppressed HDMEC spheroid sprouting. Moreover, ATP supplementation completely reversed linalool-induced ERK phosphorylation. In addition, linalool-induced ERK phosphorylation inhibited the expression of bone morphogenetic protein (BMP)-2 and linalool-induced TRPM8 activation caused the inhibition of β1 integrin/focal adhesion kinase (FAK) signaling. These findings indicate an anti-angiogenic effect of linalool, which is mediated by downregulating intracellular ATP levels and activating TRPM8