Resveratrol binds to the sulfonylurea receptor (SUR) and induces apoptosis in a SUR subtype-specific manner

Sulfonylurea receptors (SURs) constitute the regulatory subunits of ATP-sensitive K+ channels (K(ATP) channels). SUR binds nucleotides and synthetic K(ATP) channel modulators, e.g. the antidiabetic sulfonylurea glibenclamide, which acts as a channel blocker. However, knowledge about naturally occurring ligands of SUR is very limited. In this study, we show that the plant phenolic compound trans-resveratrol can bind to SUR and displace binding of glibenclamide. Electrophysiological measurements revealed that resveratrol is a blocker of pancreatic SUR1/K(IR)6.2 K(ATP) channels. We further demonstrate that, like glibenclamide, resveratrol induces enhanced apoptosis. This was shown by analyzing different apoptotic parameters (cell detachment, nuclear condensation and fragmentation, and activities of different caspase enzymes). The observed apoptotic effect was specific to cells expressing the SUR1 isoform and was not mediated by the electrical activity of K(ATP) channels, as it was observed in human embryonic kidney 293 cells expressing SUR1 alone. Enhanced susceptibility to resveratrol was not observed in pancreatic beta-cells from SUR1 knock-out mice or in cells expressing the isoform SUR2A or SUR2B or the mutant SUR1(M1289T). Resveratrol was much more potent than glibenclamide in inducing SUR1-specific apoptosis. Treatment with etoposide, a classical inducer of apoptosis, did not result in SUR isoform-specific apoptosis. In conclusion, resveratrol is a natural SUR ligand that can induce apoptosis in a SUR isoform-specific manner. Considering the tissue-specific expression patterns of SUR isoforms and the possible effects of SUR mutations on susceptibility to apoptosis, these observations could be important for diabetes and/or cancer research.     

A functional analysis of compound eye evolution

New data on the phylogenetic relationships of various arthropod groups have spurred interesting attempts to reconstruct the evolution of arthropod nervous and visual systems. Some of the relevant new data are cell identities and developmental processes in the nervous and sensory systems, which is particularly useful for reconstructing the evolution of these systems. Here, we focus on the structure of compound eye ommatidia, and make an evolutionary analysis with functional arguments. We investigate possible routes of evolution that can be understood in terms of selection for improved visual function, and arrive at a number of conclusions that are discussed in the light of recent phylogenetic hypotheses. On the basis of ommatidial focusing structures and the arrangement of receptor cells we show that the evolution of compound eyes proceeded largely independently along at least two lineages from very primitive ancestors. A common ancestor of insects and crustaceans is likely to have had ommatidia with focusing crystalline cones, and colour and/or polarization vision. In contrast, the compound eyes in myriapods and chelicerates are likely to date back to ancestors with corneal lenses and probably without the ability to discriminate colour and polarization.     

Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions

Initial environmental pyrosequencing studies suggested highly complex protistan communities with phylotype richness decisively higher than previously estimated. However, recent studies on individual bacteria or artificial bacterial communities evidenced that pyrosequencing errors may skew our view of the true complexity of microbial communities. We pyrosequenced two diversity markers (hypervariable regions V4 and V9 of the small-subunit rDNA) of an intertidal protistan model community, using the Roche GS-FLX and the most recent GS-FLX Titanium sequencing systems. After pyrosequencing 24 reference sequences we obtained up to 2039 unique tags (from 3879 V4 GS-FLX Titanium reads), 77% of which were singletons. Even binning sequences that share 97% similarity still emulated a pseudodiversity exceeding the true complexity of the model community up to three times (V9 GS-FLX). Pyrosequencing error rates were higher for V4 fragments compared with the V9 domain and for the GS-FLX Titanium compared with the GS-FLX system. Furthermore, this experiment revealed that error rates are taxon-specific. As an outcome of this study we suggest a fast and efficient strategy to discriminate pyrosequencing signals from noise in order to more realistically depict the structure of protistan communities using simple tools that are implemented in standard tag data-processing pipelines.     

Random generation of RNA secondary structures according to native distributions

Background

Random biological sequences are a topic of great interest in genome analysis since, according to a powerful paradigm, they represent the background noise from which the actual biological information must differentiate. Accordingly, the generation of random sequences has been investigated for a long time. Similarly, random object of a more complicated structure like RNA molecules or proteins are of interest.

Results

In this article, we present a new general framework for deriving algorithms for the non-uniform random generation of combinatorial objects according to the encoding and probability distribution implied by a stochastic context-free grammar. Briefly, the framework extends on the well-known recursive method for (uniform) random generation and uses the popular framework of admissible specifications of combinatorial classes, introducing weighted combinatorial classes to allow for the non-uniform generation by means of unranking. This framework is used to derive an algorithm for the generation of RNA secondary structures of a given fixed size. We address the random generation of these structures according to a realistic distribution obtained from real-life data by using a very detailed context-free grammar (that models the class of RNA secondary structures by distinguishing between all known motifs in RNA structure). Compared to well-known sampling approaches used in several structure prediction tools (such as SFold) ours has two major advantages: Firstly, after a preprocessing step in time for the computation of all weighted class sizes needed, with our approach a set of m random secondary structures of a given structure size n can be computed in worst-case time complexity while other algorithms typically have a runtime in . Secondly, our approach works with integer arithmetic only which is faster and saves us from all the discomforting details of using floating point arithmetic with logarithmized probabilities.

Conclusion

A number of experimental results shows that our random generation method produces realistic output, at least with respect to the appearance of the different structural motifs. The algorithm is available as a webservice at http://wwwagak.cs.uni-kl.de/NonUniRandGen and can be used for generating random secondary structures of any specified RNA type. A link to download an implementation of our method (in Wolfram Mathematica) can be found there, too.     

Comparison of three estrus detection systems during summer in a large commercial dairy herd

The objective of the study was to compare three systems for estrus detection and combinations of these systems on a large commercial dairy (1075 lactating cows) during stress of summer heat. At 37-45 days in milk (DIM), 255 cows were fitted with a HeatWatch device (HW; DDx Inc., Denver, CO), an activity sensor ALPRO (ALPRO; DeLaval Inc., Kansas City, MO), and visually observed (VO) three times daily. Pregnancy status was determined by uterine palpation per rectum 35-49 days following artificial insemination (AI). Effects of DIM, parity, standing events, inseminator, and interval between onset of estrus and AI on conception rates were determined using logistic regression. Efficiencies for detection of estrus, determined by comparing detected periods of estrus with a theoretical total of 570 periods, were 49.3% (VO), 37.2% (ALPRO), 48.0% (HW), and 80.2% for all three systems simultaneously. Conception rates (LSM+/-S.E.) for cows detected by one or more of the three systems were 6.2+/-3.9 for VO, 19.8+/-5.6 for ALPRO, 17.3+/-5.0 for HW, 22.8+/-7.0 for VO+ALPRO, 26.9+/-4.6 for VO+HW, 23.2+/-5.2 for ALPRO+HW, and 18.4+/-4.7 for VO+ALPRO+HW. Inseminations performed during no and mild heat stress (temperature-humidity index; THI< or =76) had greater conception rate (P<0.05; 38.8%) compared to AI performed during moderated heat stress conditions (THI>76; 17.6%). Number of mounts were higher for primiparous versus multiparous cows (P<0.05). Cows over 80 DIM during estrus exhibited fewer (P<0.05) standing events. The highest conception rate occurred with the combination of VO+HW, which confirms the premise that combination of multiple systems enhances both the efficiency and accuracy of estrus detection.     

Epitope down-modulation as a mechanism for the coexistence of competing T-cells

Efficient immune responses against pathogens are frequently characterized by the simultaneous targeting of multiple epitopes. However, it remains unclear how the targeting of multiple epitopes is maintained in the face of competition for antigenic stimulation. Here, we investigate this question by using mathematical models of the population dynamics of a viral pathogen, antigen presentation sites and T-cells. We first show that direct competition for access to antigen presenting sites and indirect competition through killing of the pathogen select for dominance of the T-cell response with the highest affinity for its epitope. We then incorporate in our model that epitopes can become down-modulated following interaction with epitope specific T-cells. We demonstrate that epitope down-modulation leads to differentiation of epitope presentation on antigen presenting sites. This differentiation promotes the coexistence of multiple epitope specific responses. Hence, we propose that the functional relevance of epitope down-modulation may be to enable the persistence of a broad immune response despite competition for antigenic stimulation.     

Xenopus cadherin-6 regulates growth and epithelial development of the retina

Cadherins are crucial for tissue cohesion, separation of cell layers and cell migration during embryogenesis. To investigate the role of classical type II Xcadherin-6 (Xcad-6), we performed loss-of-function studies by morpholino oligonucleotide injections. This resulted in severe eye defects which could be rescued with murine cadherin-6. In the absence of Xcadherin-6, morphological alterations and a decrease in cell proliferation were observed with eye cup formation. Eye field transplantations of Xcadherin-6 depleted donors yielded grafts that failed to form a proper neuroepithelium in a wildtype environment. At later developmental stages Xcadherin-6 deficient eyes showed lamination defects in the outer neural retina, a reduced thickness of the ganglion cell layer (GCL) and a fragmented retina pigment epithelium (RPE). Thus, Xcadherin-6 is essential early in eye development for structural organization and growth of the neuroepithelium before it differentiates into neural retina and RPE.