Systematic significance of achene morphology in Soroseris,Syncalathium and Parasyncalathium (Asteraceae: Cichorieae)

The systematic significance of the morphological structure of achenes in the Himalayan–Tibetan Plateau endemic genera Soroseris, Syncalathium and Parasyncalathium is described and discussed. The achene surface sculpturing of 15 samples representing 13 species of the three genera was investigated using scanning electronic microscopy (SEM) to evaluate inter‐ and intrageneric relationships of the three genera. Characters such as cell arrangement, shape of the epidermis, type of ornamentation of the outer cell wall and degree of wax development are described. The results show that characters such as the shape of the epidermis and the type of ornamentation of the outer cell wall are distinct between the three genera and useful for species‐level classification. Parasyncalathium souliei differs from Syncalathium, in which it has traditionally been placed, in the short, stout beak of the achene and especially in the obscure outline of the epidermal cells and their long acuminate, steeple‐like, end walls. Combined with karyological and molecular data, the differences in achene morphology and sculpturing further support our recognition of Parasyncalathium as distinct from Syncalathium. The achene characters are not only useful for assessing relationships, but are also useful for delimiting species. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 476–486.     

Synthesis and biological evaluation of novel 4β-(1,3,4-oxadiazole-2-amino)-podophyllotoxin derivatives

A series of new 4β-(1,3,4-oxadiazole-2-amino)-podophyllotoxin derivatives were designed and synthesized. Their cytotoxicity in vitro against six tumor cell lines (DU-145, SGC-7901, A549, SH-SY5Y, HepG2 and HeLa) were evaluated by standard MTT assay. The pharmacological results showed that most of the newly synthesized podophyllotoxin derivatives displayed potent cytotoxicity against at least one of the tested tumor cells; and among the new derivatives, 11b was more potent than podophyllotoxin against HepG2 and Hela cell lines. Furthermore, 11b exhibited much better selectivity toward the normal cell lines L929 and Vero than etoposide, 5-Fu and podophyllotoxin. The possible antitumor mechanism of 11b is to inhibit the activity of DNA topoisomerase II, result in the S-phase arrest, and then cause apoptotic cell death.     

Large scale maximum average power multiple inference on time-course count data with application to RNA-seq analysis

Experiments that longitudinally collect RNA sequencing (RNA-seq) data can provide transformative insights in biology research by revealing the dynamic patterns of genes. Such experiments create a great demand for new analytic approaches to identify differentially expressed (DE) genes based on large-scale time-course count data. Existing methods, however, are suboptimal with respect to power and may lack theoretical justification. Furthermore, most existing tests are designed to distinguish among conditions based on overall differential patterns across time, though in practice, a variety of composite hypotheses are of more scientific interest. Finally, some current methods may fail to control the false discovery rate. In this paper, we propose a new model and testing procedure to address the above issues simultaneously. Specifically, conditional on a latent Gaussian mixture with evolving means, we model the data by negative binomial distributions. Motivated by Storey (2007) and Hwang and Liu (2010), we introduce a general testing framework based on the proposed model and show that the proposed test enjoys the optimality property of maximum average power. The test allows not only identification of traditional DE genes but also testing of a variety of composite hypotheses of biological interest. We establish the identifiability of the proposed model, implement the proposed method via efficient algorithms, and demonstrate its good performance via simulation studies. The procedure reveals interesting biological insights, when applied to data from an experiment that examines the effect of varying light environments on the fundamental physiology of the marine diatom Phaeodactylum tricornutum.     

A simple and modified manometric method for measuring oxygen uptake rate of plant cells in flask cultures

Summary A simple and convenient technique was developed based on the principle of Warburg manometric method to measure O₂ uptake rate (OUR) and CO₂ evolution rate (CER) of suspended cells in a shake flask culture. It was successfully applied to suspension cultures of rice (Oryza sativa) and Panax notoginseng cells, and some important bioprocess parameters, such as OUR, CER, respiratory quotient (RQ), specific OUR (SOUR) and specific CER (SCER), were quantitatively obtained. The measuring system is easy to operate, able to treat many samples simultaneously and is economical.     

High auxin stimulates callus through SDG8-mediated histone H3K36 methylation in Arabidopsis

Callus induction,which results in fate transition in plant cells,is considered as the first and key step for plant regeneration.This process can be stimulated in different tissues by a callus-inducing medium(CIM),which contains a high concentration of phytohormone auxin.Although a few key regulators for callus induction have been identified,the multiple aspects of the regulatory mechanism driven by high levels of auxin still need further investigation.Here,we find that high auxin induces callus ...     

Spatiotemporal cytokinin response imaging and ISOPENTENYLTRANSFERASE 3 function in Medicago nodule development

Most legumes can establish a symbiotic association with soil rhizobia that trigger the development of root nodules. These nodules host the rhizobia and allow them to fix nitrogen efficiently. The perception of bacterial lipo-chitooligosaccharides (LCOs) in the epidermis initiates a signaling cascade that allows rhizobial intracellular infection in the root and de-differentiation and activation of cell division that gives rise to the nodule. Thus, nodule organogenesis and rhizobial infection need to be coupled in space and time for successful nodulation. The plant hormone cytokinin (CK) contributes to the coordination of this process, acting as an essential positive regulator of nodule organogenesis. However, the temporal regulation of tissue-specific CK signaling and biosynthesis in response to LCOs or Sinorhizobium meliloti inoculation in Medicago truncatula remains poorly understood. In this study, using a fluorescence-based CK sensor (pTCSn::nls:tGFP), we performed a high-resolution tissue-specific temporal characterization of the sequential activation of CK response during root infection and nodule development in M. truncatula after inoculation with S. meliloti. Loss-of-function mutants of the CK-biosynthetic gene ISOPENTENYLTRANSFERASE 3 (IPT3) showed impairment of nodulation, suggesting that IPT3 is required for nodule development in M. truncatula. Simultaneous live imaging of pIPT3::nls:tdTOMATO and the CK sensor showed that IPT3 induction in the pericycle at the base of nodule primordium contributes to CK biosynthesis, which in turn promotes expression of positive regulators of nodule organogenesis in M. truncatula.

Precise spatial and temporal characterization of cytokinin (CK) responses reveals the function of the CK biosynthesis gene ISOPENTENYLTRANSFERASE 3 during nodule development in Medicago truncatula.     

Laplacian normalization and bi-random walks on heterogeneous networks for predicting lncRNA-disease associations

Background

Evidences have increasingly indicated that lncRNAs (long non-coding RNAs) are deeply involved in important biological regulation processes leading to various human complex diseases. Experimental investigations of these disease associated lncRNAs are slow with high costs. Computational methods to infer potential associations between lncRNAs and diseases have become an effective prior-pinpointing approach to the experimental verification.

Results

In this study, we develop a novel method for the prediction of lncRNA-disease associations using bi-random walks on a network merging the similarities of lncRNAs and diseases. Particularly, this method applies a Laplacian technique to normalize the lncRNA similarity matrix and the disease similarity matrix before the construction of the lncRNA similarity network and disease similarity network. The two networks are then connected via existing lncRNA-disease associations. After that, bi-random walks are applied on the heterogeneous network to predict the potential associations between the lncRNAs and the diseases. Experimental results demonstrate that the performance of our method is highly comparable to or better than the state-of-the-art methods for predicting lncRNA-disease associations. Our analyses on three cancer data sets (breast cancer, lung cancer, and liver cancer) also indicate the usefulness of our method in practical applications.

Conclusions

Our proposed method, including the construction of the lncRNA similarity network and disease similarity network and the bi-random walks algorithm on the heterogeneous network, could be used for prediction of potential associations between the lncRNAs and the diseases.

     

Solving post-prandial reduction in performance by adaptive regurgitation in a freshwater fish

Foraging animals must balance benefits of food acquisition with costs induced by a post-prandial reduction in performance. Eating to satiation can lead to a reduction in locomotor and escape performance, which increases risk should a threat subsequently arises, but limiting feeding behaviour may be maladaptive if food intake is unnecessarily reduced in the prediction of threats that do not arise. The efficacy of the trade-off between continued and interrupted feeding therefore relies on information about the future risk, which is imperfect. Here, we find that black carp (Mylopharyngodon piceus) can balance this trade-off using an a posteriori strategy; by eating to satiation but regurgitating already ingested food when a threat arises. While degrees of satiation (DS) equal to or greater than 60% reduce elements of escape performance (turning angle, angular velocity, distance moved, linear velocity), at 40% DS or lower, performance in these tasks approaches levels comparable to that at 0% satiation. After experiencing a chasing event, we find that fish are able to regurgitate already ingested food, thereby changing the amount of food in their gastrointestinal tract to consistent levels that maintain high escape performance. Remarkably, regurgitation results in degrees of satiation between 40 and 60% DS, regardless of whether they had previously fed to 40, 60 or 100% DS. Using this response, fish are able to maximize food intake, but regurgitate extra food to maintain escape performance when they encounter a threat. This novel strategy may be effective for continual grazers and species with imperfect information about the level of threat in their environment.