Enucleation: a possible mechanism of cancer cell death

There are few major morphologies of cell death that have been described so far: apoptosis (type I), cell death associated with autophagy (type II), necrosis (type III) and anchorage‐dependent mechanisms—anoikis. Here, we show for the first time a possibly novel mechanism inducing tumour cell death under in vitro conditions—enucleation. We pursued the influence of colloidal suspensions of Fe₃O₄ nanoparticles on tumour cell lines (SK‐BR‐3 and MCF‐7 breast cancer cell lines) grown according to standard cell culture protocols. Magnetite nanoparticles were prepared by combustion synthesis and double layer coated with oleic acid. Scanning and transmission electron microscopy revealed that tumour cells developed a network of intracytoplasmic stress fibres, which induce extrusion of nuclei, and enucleated cells die. Normal adult mesenchymal stem cells, used as control, did not exhibit the same behaviour. Intact nuclei were found in culture supernatant of tumour cells, and were visualized by immunofluorescence. Enucleation as a potential mechanism of tumour cell death might open new horizons in cancer biology research and development of therapeutic agents capable of exploiting this behaviour.     

Estimation of effective connectivity using multi-layer perceptron artificial neural network

Studies on interactions between brain regions estimate effective connectivity, (usually) based on the causality inferences made on the basis of temporal precedence. In this study, the causal relationship is modeled by a multi-layer perceptron feed-forward artificial neural network, because of the ANN’s ability to generate appropriate input–output mapping and to learn from training examples without the need of detailed knowledge of the underlying system. At any time instant, the past samples of data are placed in the network input, and the subsequent values are predicted at its output. To estimate the strength of interactions, the measure of “Causality coefficient” is defined based on the network structure, the connecting weights and the parameters of hidden layer activation function. Simulation analysis demonstrates that the method, called “CREANN” (Causal Relationship Estimation by Artificial Neural Network), can estimate time-invariant and time-varying effective connectivity in terms of MVAR coefficients. The method shows robustness with respect to noise level of data. Furthermore, the estimations are not significantly influenced by the model order (considered time-lag), and the different initial conditions (initial random weights and parameters of the network). CREANN is also applied to EEG data collected during a memory recognition task. The results implicate that it can show changes in the information flow between brain regions, involving in the episodic memory retrieval process. These convincing results emphasize that CREANN can be used as an appropriate method to estimate the causal relationship among brain signals.     

Intraspecific killing among Leopards (Panthera pardus) in Iran (Mammalia: Felidae)

Intraspecific aggression is one of the most common causes of death in leopards. Here, we report four cases of intraspecific killing amongst Persian Leopards (Panthera pardus saxicolor) in Iran. A young male leopard was found on 7 June 2008 which, according to camera trap images, had been killed by an adult male over a Red Deer (Cervus elaphus) kill, with trauma to his neck in Dorfak No-Hunting Area. A young female that had been fitted with a satellite GPS collar on 6 December 2015 in Tandoureh National Park died on 29 January 2016 at a site where an Urial Sheep (Ovis orientalis) ram had been freshly killed. Necropsy results, footprints at the scene of death and camera trap footage all supported the deduction that the animal was killed by a larger female leopard at the kill site. On 13 January 2017, a young, partially eaten female leopard was found with double puncture on the side of her throat. Finally, a rehabilitated adult female fitted with a satellite GPS collar found on 19 December 2017 with a double puncture on her head with several trauma and haemorrhages on her back. These instances seem to be the first documented reports of intraspecific killing among free-ranging leopards in Asia.     

Seasonal patterns of egg parasitism and natural biological control of rice brown planthopper in Indonesia

1 Egg mortality is known to be an important factor in brown planthopper (BPH) (Nilaparvata lugens) population dynamics in tropical Asia, but few quantitative data are available on the role of egg parasitoids. 2 Field studies are reported at two sites in Java, Indonesia, over a period of 4 years in both wet and dry seasons, where no chemical pesticides were used. Rice plants previously infested in the laboratory with BPH eggs were exposed to natural parasitism and predation in experimental fields for periods of 5 days. 3 Egg batches were dissected from both experimental and control plants after field exposure at seven fortnightly intervals through the rice growing season and BPH nymphs and adult parasitoids were allowed to emerge. 4 Parasitism by species of Oligosita (Hymenopera, Trichogrammatidae) and Anagrus (Hym., Mymaridae) varied between 18% and 61% in dry, and from 1% to 65% in wet, seasons. There was generally a trend from low to higher rates through wet seasons, contrasting with more uniform higher levels through dry seasons. 5 Reduction in BPH survival as a result of egg parasitism varied between 29% and 91%. Generally parasitism was density independent. 6 It is suggested that lower initial levels of parasitism in dry seasons may be due to the longer fallow period between dry and wet, than between wet and dry, resulting in lower local populations of appropriate natural enemies. 7 Unlike previous studies in Asia, little evidence was found for egg predation as an important mortality factor. 8 The conservation of egg parasitoids should form part of any rice pest management programmes in tropical Asia.     

A convenient protocol for extraction and purification of DNA from Fragaria

Summary In this paper we describe a simple and efficient DNA extraction protocol for Fragaria species, a highly recalcitrant genus due to the large amount of polyphenols and polymeric carbohydrates present in strawberry tissues. The protocol yields a high quality DNA that can be amplified by polymerase chain reaction and digested with restriction endonucleases.     

Evaluation of known and novel inhibitors of Orai1-mediated store operated Ca2+ entry in MDA-MB-231 breast cancer cells using a Fluorescence Imaging Plate Reader assay

The Orai1 Ca²⁺ permeable ion channel is an important component of store operated Ca²⁺ entry (SOCE) in cells. It’s over-expression in basal molecular subtype breast cancers has been linked with poor prognosis, making it a potential target for drug development. We pharmacologically characterised a number of reported inhibitors of SOCE in MDA-MB-231 breast cancer cells using a convenient Fluorescence Imaging Plate Reader (FLIPR) assay, and show that the rank order of their potencies in this assay is the same as those reported in a wide range of published assays. The assay was also used in a screening project seeking novel inhibitors. Following a broad literature survey of classes of calcium channel inhibitors we used simplified ligand structures to query the ZINC on-line database, and following two iterations of refinement selected a novel Orai1-selective dichlorophenyltriazole hit compound. Analogues of this were synthesized and evaluated in the FLIPR assay to develop structure–activity relationships (SAR) for the three domains of the hit; triazole (head), dichlorophenyl (body) and substituted phenyl (tail). For this series, the results suggested the need for a lipophilic tail domain and an out-of-plane twist between the body and tail domains.     

Biomolecular network motif counting and discovery by color coding

Protein-protein interaction (PPI) networks of many organisms share global topological features such as degree distribution, k-hop reachability, betweenness and closeness. Yet, some of these networks can differ significantly from the others in terms of local structures: e.g. the number of specific network motifs can vary significantly among PPI networks. Counting the number of network motifs provides a major challenge to compare biomolecular networks. Recently developed algorithms have been able to count the number of induced occurrences of subgraphs with k < or = 7 vertices. Yet no practical algorithm exists for counting non-induced occurrences, or counting subgraphs with k > or = 8 vertices. Counting non-induced occurrences of network motifs is not only challenging but also quite desirable as available PPI networks include several false interactions and miss many others. In this article, we show how to apply the 'color coding' technique for counting non-induced occurrences of subgraph topologies in the form of trees and bounded treewidth subgraphs. Our algorithm can count all occurrences of motif G' with k vertices in a network G with n vertices in time polynomial with n, provided k = O(log n). We use our algorithm to obtain 'treelet' distributions for k < or = 10 of available PPI networks of unicellular organisms (Saccharomyces cerevisiae Escherichia coli and Helicobacter Pyloris), which are all quite similar, and a multicellular organism (Caenorhabditis elegans) which is significantly different. Furthermore, the treelet distribution of the unicellular organisms are similar to that obtained by the 'duplication model' but are quite different from that of the 'preferential attachment model'. The treelet distribution is robust w.r.t. sparsification with bait/edge coverage of 70% but differences can be observed when bait/edge coverage drops to 50%.