When peptides fly: Advances in Drosophila proteomics

In the past decade, improvements in genome annotation, protein fractionation methods and mass spectrometry instrumentation resulted in rapid growth of Drosophila proteomics. This review presents the current status of proteomics research in the fly. Areas that have seen major advances in recent years include efforts to map and catalog the Drosophila proteome and high-throughput as well as targeted studies to analyze protein–protein interactions and post-translational modifications. Stable isotope labeling of flies and other applications of quantitative proteomics have opened up new possibilities for functional analyses. It is clear that proteomics is becoming an indispensable tool in Drosophila systems biology research that adds a unique dimension to studying gene function.     

Chlamydomonas reinhardtii as a model system for pro-active herbicide resistance evolution research

Modern herbicides greatly contribute to world agricultural production but their sustainability is threatened by the widespread evolution of herbicide resistant weedy plant populations. Despite the commercial and scientific importance of resistance, there has not been an experimental model system for pro-actively evaluating the potential for herbicide resistance evolution. Here, utilizing the rapidly growing, unicellular photosynthetic microalgae Chlamydomona s reinhardtii (Dangeard), a ratchet protocol has been developed that solves the problem of maintaining both large populations and strong herbicide selection. The ratchet protocol is a progressive set of cycles, each cycle commencing with a population of approximately one million individuals apportioned amongst three herbicide doses for 14 days. Whenever the evolving population demonstrates growth across the three herbicide selection intensities, then the population ratchets to the next cycle of higher herbicide dose. Therefore, by always maintaining large populations under selection pressure, this system offers the opportunity for beneficial mutations to arise and be enriched. Using the well-characterized atrazine herbicide, the ratchet protocol resulted in rapid evolution of populations with different levels of resistance. This robust laboratory based Chlamydomonas system is proposed for application in establishing the respective propensity for resistance evolution to herbicides or other selecting agents.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 257–266.     

Metabolic model for acetate uptake by a mixed culture of phosphate- and glycogen-accumulating organisms under anaerobic conditions

This paper proposes a new metabolic model for acetate uptake by a mixed culture of phosphate- and glycogen-accumulating organisms (PAOs and GAOs) under anaerobic conditions. The model uses variable overall stoichiometry based on the assumption that PAOs may have the ability of using the glyoxylate pathway to produce the required reducing power for polyhydroxyalkonate (PHA) synthesis. The proposed model was tested and verified by experimental results. A sequencing batch reactor system was operated for enhanced biological phosphorus removal (EBPR) with acetate as the sole carbon source at different influent acetate/phosphate ratios. The resulting experimental data supported the validity of the proposed model, indicating the presence of GAOs for all tested HAc/P ratios, especially under P-limiting conditions. Strong agreement is observed between experimental values and model predictions for all model components, namely, PHB production, PHA composition, glycogen utilization, and P release.     

Composition and structure of aquatic organism communities in various water conditions of a paddy field

The purpose of this study was to clarify the differences of the community structure and the diversity of aquatic organisms (i) among sampling sites that the distances from inlets or outlets were different each other, and (ii) between the floodwater and the irrigation water during the crop season in a paddy field. The irrigation water was sampled from one inlet. The taxonomical groups and the number of aquatic organisms ranging in size from 30µm to 2cm in the floodwater and the irrigation water were surveyed approximately every 10days during the growth period of the rice plant. Aquatic organisms were classified mainly at the order level. Thirty-eight taxonomical groups of aquatic organisms were found in the floodwater, while 18 groups were found in the irrigation water. We were not able to find the differences of the community structure of aquatic organisms among the sites. In the floodwater, the number of taxonomical group increased and the community structure changed during the late flooding period (over 50days after the onset of flooding) at any site, while those in the irrigation water hardly changed. Although the community structure of aquatic organisms differed between the floodwater and the irrigation water throughout the flooding period, the differences became especially bigger during the late flooding period. Principal component analysis showed that three groups (Pennales, Dinoflagellida, Choreotrichida) characterized the community structure in the irrigation water. Their population densities tended to be the highest at the site near inlets and the lowest at the site far from inlets.     

海湾扇贝衣原体样生物超微结构观察

对海湾扇贝生长不同阶段的样品进行了透射电镜观察,在样品消化腺上皮细胞内发现类衣原体感染。该类衣原体具有原体、网状体和中间体等典型发育阶段,原体个体小而致密,网状体大而疏松,以等体积分裂进行繁殖。在细胞质内形成单层膜包被的包涵体,包涵体发育晚期破裂,宿主细胞崩解,衣原体逸出。衣原体感染可导致细胞核变形,染色质凝聚,内质网核糖体脱落,线粒体内嵴消失。     

Porphyra monospore system (Bangiales, Rhodophyta): A model for the developmental biology of marine plants

We have developed an experimental system of cohort monospores from clonal culture of leafy gametophytes in Porphyra yezoensis Ueda (strain TU-1). This system is quite different from traditional systems for algal protoplast experimentation, which require expensive enzymatic treatment and utilize an ineffective method of preservation. Cohort monospores were obtained by utilizing a mode of asexual reproduction in the culture strain (monospores) and artificial regulation (thallus length, temperature, light, etc.) of monospore release. When the leafy gametophytes that formed monospores were frozen at - 20°C in a cryoprotective solution composed of 5% DMSO and 5% dextran in 100% seawater, about 98% survived for 3 months. When stored at 5°C without cryoprotectants, these leafy gametophytes could be kept without monospore release for 1 week. Maximum monospore yield was about 3000 spores per 100 gametophytes, and germination rate was about 70%, This system will accelerate developmental biology studies in Porphyra.     

The morphology of cells and cell organelles in the anhydrobiotic tardigrade,Macrobiotus hufelandi

Summary Anhydrobiotic and active hydrated specimens of the tardigradeMacrobiotus hufelandi were investigated by electron microscopy, and the cellular fine structure of both stages was compared. Besides conventional preparation methods, totally anhydrous techniques were used to avoid hydration artefacts in the anhydrobiotic specimens. In the latter the cytoplasm was very electron dense and masked many cell constituents, however, membraneous structures, nuclei, mitochondria, microtubules, and myofilaments could be resolved in the micrographs. After substraction of all peculiarities caused by the preparation methods within the micrographs of cells from anhydrobiotic specimens, the comparison revealed that the basic morphology of the cells and their organelles is not changed in the anhydrobiotic specimens. Maintenance of the structural integrity of its cells is a basic ability of this organism to survive desiccation.This report is part of a doctoral dissertation submitted by the author to the Fakultät für Naturwissenschaften of the University of Heidelberg in 1976. The author would like to thank Prof. Dr. E.Schnepf who guided the dissertation. I would like to thank too the Studienstiftung des deutschen Volkes for general support by a Promotionsstipendium.     

Fine- and regional-scale genetic structure of the exotic ascidian Styela clava (Tunicata) in southwest England, 50 years after its introduction

Styela clava , an ascidian native to the northwest Pacific, was first recorded in the Atlantic at Plymouth, southwest England, in 1953. It now ranges in the northeast Atlantic from Portugal to northern Denmark, and has colonized the east coast of North America. Within the region of first introduction, we aimed to characterize current genetic diversity in the species, elucidate the respective roles of human-aided vs. natural dispersal, and assess the extent of larval dispersal by looking for genetic differentiation at very small scales. Eight sites, mostly marinas, were studied along c . 200 km of coast in southwest England encompassing Plymouth. Five microsatellite loci were genotyped in 303 individuals to analyse gene flow at regional (among sites) and fine (within sites) scales. F -statistics and assignment tests were used to investigate regional genetic structure. At the fine scale, deviation from mutation–drift equilibrium was tested, and isolation by distance and genetic clustering analyses were undertaken. Significant genetic differentiation existed between sites, unrelated to geographical separation; migration between geographically distant marinas was inferred, highlighting the likely importance of human-mediated dispersal in range expansion and occupancy by S. clava . Fine-scale population structure was present within at least four sites, which may be explained by the limited dispersal ability of this ascidian and recruitment from differentiated pools of larvae. Populations in enclosed marinas had higher self-recruitment rates than those in open sites. Some marinas might therefore function as reservoirs of propagules for subsequent spread, whereas others might be sinks for migrants.     

Validation of a cotton-specific gene, Sad1, used as an endogenous reference gene in qualitative and real-time quantitative PCR detection of transgenic cottons

Genetically modified (GM) cotton lines have been approved for commercialization and widely cultivated in many countries, especially in China. As a step towards the development of reliable qualitative and quantitative PCR methods for detecting GM cottons, we report here the validation of the cotton (Gossypium hirsutum) endogenous reference control gene, Sad1, using conventional and real-time (RT)-PCR methods. Both methods were tested on 15 different G. hirsutum cultivars, and identical amplicons were obtained with all of them. No amplicons were observed when DNA samples from three species of genus Gossypium, Arabidopsis thaliana, maize, and soybean and others were used as amplified templates, demonstrating that these two systems are specific for the identification and quantification of G. hirsutum. The results of Southern blot analysis also showed that the Sad1 gene was two copies in these 15 different G. hirsutum cultivars. Furthermore, one multiplex RT-quantitative PCR employing this gene as an endogenous reference gene was designed to quantify the Cry1A(c) gene modified from Bacillus thuringiensis (Bt) in the insect-resistant cottons, such as Mon531 and GK19. The quantification detection limit of the Cry1A(c) and Sad1 genes was as low as 10 pg of genomic DNA. These results indicat that the Sad1 gene can be used as an endogenous reference gene for both qualitative and quantitative PCR detection of GM cottons.