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A common feature of morphogenesis is the formation of three-dimensional structures from the folding of two-dimensional epithelial sheets, aided by cell shape changes at the cellular-level. Changes in cell shape must be studied in the context of cell-polarised biomechanical processes within the epithelial sheet. In epithelia with highly curved surfaces, finding single-cell alignment along a biological axis can be difficult to automate in silico. We present 'Origami', a MATLAB-based image analysis pipeline to compute direction-variant cell shape features along the epithelial apico-basal axis. Our automated method accurately computed direction vectors denoting the apico-basal axis in regions with opposing curvature in synthetic epithelia and fluorescence images of zebrafish embryos. As proof of concept, we identified different cell shape signatures in the developing zebrafish inner ear, where the epithelium deforms in opposite orientations to form different structures. Origami is designed to be user-friendly and is generally applicable to fluorescence images of curved epithelia. Author summary: During embryonic development, two-dimensional epithelial sheets bend and fold into complex three-dimensional structures–like paper in the origami art form. The genetic and biomechanical processes driving epithelial folding can be polarised in the epithelium, leading to asymmetric shape changes at the single cell level. Defects in such epithelial shaping have been linked to many developmental anomalies and diseases. It is, therefore, important not only to quantify shape change at the single cell level, but also to orientate these asymmetrical changes along an epithelial axis of polarity when studying morphogenetic processes. Origami is a MATLAB-based software that has been developed to automatically extract such single-cell asymmetrical shape features along the epithelial apico-basal axis from fluorescence microscopy images of folding epithelia. Origami provides a solution to computing directional vectors along the epithelial apico-basal axis followed by extracting direction-variant shape features of each segmented cell. It is generally applicable to epithelial structures regardless of complexity or direction of folding and is robust to imaging conditions. As proof of concept, Origami successfully differentiated between different cell shape signatures in highly curved structures at different developmental timepoints in the zebrafish inner ear. [ABSTRACT FROM AUTHOR]

Traditional methods of healing have been beneficial in many countries with or without access to conventional allopathic medicine. In the United States, these traditional practices are increasingly being sought after for illnesses that cannot be easily treated by allopathic medicine. More and more people are becoming interested in the knowledge maintained by traditional healers and in the diversity of medicinal plants that flourish in areas like Northern Peru. While scientific studies of medicinal plants are underway, concern has arisen over the preservation of both the large diversity of medicinal plants and the traditional knowledge of healing methods that accompanies them. To promote further conservation work, this study attempted to document the sources of the most popular and rarest medicinal plants sold in the markets of Trujillo (Mayorista and Hermelinda) and Chiclayo (Modelo and Moshoqueque), as well as to create an inventory of the plants sold in these markets, which will serve as a basis for comparison with future inventories. Individual markets and market stalls were subjected to cluster analysis based on the diversity of the medicinal plants they carry. The results show that markets were grouped based on the presence of: (1) common exotic medicinal plants; (2) plants used by laypeople for self-medication related to common ailments ("everyday remedies"); (3) specialized medicinal plants used by curanderos or traditional healers; and (4) highly "specialized" plants used for magical purposes. The plant trade in the study areas seems to correspond well with the specific health care demands from clientele in those areas. The specific market patterns of plant diversity observed in the present study represent a foundation for comparative market research in Peru and elsewhere. [ABSTRACT FROM AUTHOR]

Necrosis of infected macrophages constitutes a critical pathogenetic event in tuberculosis by releasing mycobacteria into the growth-permissive extracellular environment. In zebrafish infected with Mycobacterium marinum or Mycobacterium tuberculosis , excess tumor necrosis factor triggers programmed necrosis of infected macrophages through the production of mitochondrial reactive oxygen species (ROS) and the participation of cyclophilin D, a component of the mitochondrial permeability transition pore. Here, we show that this necrosis pathway is not mitochondrion-intrinsic but results from an inter-organellar circuit initiating and culminating in the mitochondrion. Mitochondrial ROS induce production of lysosomal ceramide that ultimately activates the cytosolic protein BAX. BAX promotes calcium flow from the endoplasmic reticulum into the mitochondrion through ryanodine receptors, and the resultant mitochondrial calcium overload triggers cyclophilin-D-mediated necrosis. We identify ryanodine receptors and plasma membrane L-type calcium channels as druggable targets to intercept mitochondrial calcium overload and necrosis of mycobacterium-infected zebrafish and human macrophages. • TNF induces mitochondrial ROS to cause necrosis of mycobacterium-infected macrophages • Mitochondrial ROS activate lysosomal enzymes that lead to BAX activation • BAX activates ER ryanodine receptors to cause Ca2+ flow into the mitochondrion • Drugs preventing mitochondrial Ca2+ overload prevent pathogenic macrophage necrosis in TB During TB infection, the necrosis of infected macrophages involves an inter organelle signaling relay involving druggable targets such as ryanodine receptors and plasma membrane L-type Ca2+ channels. [ABSTRACT FROM AUTHOR]