FoCo: a simple and robust quantification algorithm of nuclear foci.

BACKGROUND: The number of γH2AX foci per nucleus is an accepted measure of the number of DNA double-strand breaks in single cells. One of the experimental techniques for γH2AX detection in cultured cells is immunofluorescent labelling of γH2AX and nuclei followed by microscopy imaging and analysis. RESULTS: In this study, we present the algorithm FoCo for reliable and robust automatic nuclear foci counting in single cell images. FoCo has the following advantages with respect to other software packages: i) the ability to reliably quantify even densely distributed foci, e.g., on images of cells subjected to radiation doses up to 10 Gy, ii) robustness of foci quantification in the sense of suppressing out-of-focus background signal, and iii) its simplicity. FoCo requires only 5 parameters that have to be adjusted by the user. CONCLUSIONS: FoCo is an open-source user-friendly software with GUI for individual foci counting, which is able to produce reliable and robust foci quantifications even for low signal/noise ratios and densely distributed foci.

Cytokinins enhance the metabolic activity of in vitro-grown catmint (Nepeta nuda L.).

The phytohormones cytokinins are essential mediators of developmental and environmental signaling, primarily during cell division and endophytic interactions, among other processes. Considering the limited understanding of the regulatory mechanisms that affect the growth and bioactivity of the medicinal plant Nepeta nuda (Lamiaceae), our study aimed to explore how cytokinins influence the plant's metabolic status. Exogenous administration of active cytokinin forms on in vitro N. nuda internodes stimulated intensive callus formation and de novo shoot regeneration, leading to a marked increase in biomass. This process involved an accumulation of oxidants, which were scavenged by peroxidases using phenolics as substrates. The callus tissue formed upon the addition of the cytokinin 6-benzylaminopurine (BAP) acted as a sink for sugars and phenolics during the allocation of nutrients between the culture medium and regenerated plants. In accordance, the cytokinin significantly enhanced the content of polar metabolites and their respective in vitro biological activities compared to untreated in vitro and wild-grown plants. The BAP-mediated accumulation of major phenolic metabolites, rosmarinic acid (RA) and caffeic acid (CA), corresponded with variations in the expression levels of genes involved in their biosynthesis. In contrast, the accumulation of iridoids and the expression of corresponding biosynthetic genes were not significantly affected. In conclusion, our study elucidated the mechanism of cytokinin action in N. nuda in vitro culture and demonstrated its potential in stimulating the production of bioactive compounds. This knowledge could serve as a basis for further investigations of the environmental impact on plant productivity.

Catmint (Nepeta nuda L.) Phylogenetics and Metabolic Responses in Variable Growth Conditions.

Nepeta nuda (catmint; Lamiaceae) is a perennial medicinal plant with a wide geographic distribution in Europe and Asia. This study first characterized the taxonomic position of N. nuda using DNA barcoding technology. Since medicinal plants are rich in secondary metabolites contributing to their adaptive immune response, we explored the N. nuda metabolic adjustment operating under variable environments. Through comparative analysis of wild-grown and in vitro cultivated plants, we assessed the change in phenolic and iridoid compounds, and the associated immune activities. The wild-grown plants from different Bulgarian locations contained variable amounts of phenolic compounds manifested by a general increase in flowers, as compared to leaves, while a strong reduction was observed in the in vitro plants. A similar trend was noted for the antioxidant and anti-herpesvirus activity of the extracts. The antimicrobial potential, however, was very similar, regardless the growth conditions. Analysis of the N. nuda extracts led to identification of 63 compounds including phenolic acids and derivatives, flavonoids, and iridoids. Quantification of the content of 21 target compounds indicated their general reduction in the extracts from in vitro plants, and only the ferulic acid (FA) was specifically increased. Cultivation of in vitro plants under different light quality and intensity indicated that these variable light conditions altered the content of bioactive compounds, such as aesculin, FA, rosmarinic acid, cirsimaritin, naringenin, rutin, isoquercetin, epideoxyloganic acid, chlorogenic acid. Thus, this study generated novel information on the regulation of N. nuda productivity using light and other cultivation conditions, which could be exploited for biotechnological purposes.

Automated three-dimensional tracking of living cells by digital holographic microscopy.

Digital holographic microscopy (DHM) enables a quantitative multifocus phase contrast imaging that has been found suitable for technical inspection and quantitative live cell imaging. The combination of DHM with fast and robust autofocus algorithms enables subsequent automated focus realignment by numerical propagation of the digital holographically reconstructed object wave. In combination with a calibrated optical imaging system, the obtained propagation data quantify axial displacements of the investigated sample. The evaluation of quantitative DHM phase contrast images also enables an effective determination of lateral cell displacements. Thus, 3-D displacement data are provided. Results from investigations on sedimenting red blood cells and HT-1080 fibrosarcoma cells in a collagen tissue model demonstrate that DHM enables marker-free automated quantitative dynamic 3-D cell tracking without mechanical focus adjustment.

Nongenomic effect of aldosterone on ion transport pathways of red blood cells.

The direct influence of aldosterone on the human and avian red blood cell (RBC) transport systems, Na(+)/K(+) pump, Na(+),K(+),2Cl(-) symporter, and K(+) (Na(+))/H(+) exchanger, was investigated with tracer kinetics. The present work proved that aldosterone has no significant effect on these transport pathways. However, in young human RBCs containing reticulocytes aldosterone showed a significant inhibition of the Na(+),K(+),2Cl(-) symporter. Investigations of the Li(+) efflux via the Na(+)/Li(+) exchanger using atom absorption spectroscopy revealed that aldosterone has no effect on this transporter. Studies of the effect of aldosterone on the Ca(2+) content and the intracellular pH (pH(i)) were carried out on single RBCs with a fluorescence imaging system. Both parameters are affected by aldosterone. The Ca(2+) uptake in the presence of aldosterone, under conditions where the Ca(2+) pump is inhibited, showed marked differences from the control. Since the effect is nifedipine-sensitive, it seems that aldosterone affects a Ca(2+) channel. In addition, aldosterone leads to an acidification of the intracellular medium after an initial alkalisation due to an effect on the Na(+)/H(+) exchanger.

Application of digital holographic microscopy to investigate the sedimentation of intact red blood cells and their interaction with artificial surfaces.

Red blood cells are able to undergo shape change from the "normal" discocyte to either echinocytes or stomatocytes depending on a large variety of membrane and cytoplasmic parameters. Such shape changes can be relatively fast (within seconds) during the sedimentation of the cells in suspension or after the cells are getting in contact with artificial surfaces. High resolution digital holographic microscopy has been applied to study these processes. This method represents a new set-up allowing a contact-less and marker-free quantitative phase-contrast imaging of living cells under conventional laboratory conditions. With the applied technique we were able to detect and analyse fast shape changes of red blood cells.

Changes in the intracellular Ca2+ content in human red blood cells in the presence of glycerol.

Changes of the intracellular Ca2+ content in human red blood cells (RBCs) in glycerol-containing solutions and after freeze-thawing the cells with glycerol and subsequent deglycerolization were investigated with the Ca2+-sensitive fluorescent dye fluo-4 using fluorescence microscopy. In the glycerol-containing solutions the Ca2+ content increased when compared with a physiological medium (Hepes buffered saline solution (HBSS)). This effect was most likely a result of an inhibition of the Ca2+ pump. After inhibiting the Ca2+ pump using o-vanadate, the Ca2+ uptake was not significantly different in the cells in glycerol-containing and physiological medium. Freeze-thawing and deglycerolization of RBCs resulted in a more pronounced increase in the Ca2+ content. Also in this case, the Ca2+ pump seemed to play a major role.

To senesce or not to senesce: how primary human fibroblasts decide their cell fate after DNA damage.

Excessive DNA damage can induce an irreversible cell cycle arrest, called senescence, which is generally perceived as an important tumour-suppressor mechanism. However, it is unclear how cells decide whether to senesce or not after DNA damage. By combining experimental data with a parameterized mathematical model we elucidate this cell fate decision at the G1-S transition. Our model provides a quantitative and conceptually new understanding of how human fibroblasts decide whether DNA damage is beyond repair and senesce. Model and data imply that the G1-S transition is regulated by a bistable hysteresis switch with respect to Cdk2 activity, which in turn is controlled by the Cdk2/p21 ratio rather than cyclin abundance. We experimentally confirm the resulting predictions that to induce senescence i) in healthy cells both high initial and elevated background DNA damage are necessary and sufficient, and ii) in already damaged cells much lower additional DNA damage is sufficient. Our study provides a mechanistic explanation of a) how noise in protein abundances allows cells to overcome the G1-S arrest even with substantial DNA damage, potentially leading to neoplasia, and b) how accumulating DNA damage with age increasingly sensitizes cells for senescence.