Two strings to the systems biology bow: co-extracting the metabolome and proteome of yeast

Experimental samples are valuable and can represent a significant investment in time and resources. It is highly desirable at times to obtain as much information as possible from a single sample. This is especially relevant for systems biology approaches in which several ‘omics platforms are studied simultaneously. Unfortunately, each platform has a particular extraction methodology which increases sample number and sample volume requirements when multiple ‘omics are analyzed. We evaluated the integration of a yeast extraction method; specifically we explored whether fractions from a single metabolite extraction could be apportioned to multiple downstream ‘omics analytical platforms. In addition, we examined how variations to a chloroform/methanol yeast metabolite extraction regime influence metabolite recoveries. We show that protein suitable for proteomic analysis can be recovered from a metabolite extraction and that recovery of lipids, while reproducible, are not wholly quantitative. Higher quenching solution temperatures (?30 °C) can be used without significant leakage of intracellular metabolites when lower fermentation temperatures (20 °C) are employed. However, extended residence time in quenching solution, in combination with vigorous washing of quenched cell pellets, leads to extensive leakage of intracellular metabolites. Finally, there is minimal difference in metabolite amounts obtained when metabolite extractions are performed at 4 °C compared to extractions at ?20 °C. The evaluated extraction method delivers material suitable for metabolomic and proteomic analyses from the same sample preparation.     

Synthesis and in vitro trypanocide activity of several polycyclic drimane-quinone derivatives

The Diels-Alder reaction between two polygodial-derived dienes and simple quinones to yield substituted naphtho- and anthraquinones, is described. The in vitro trypanocide activity for the series was determined. Two of the new compounds showed an activity ten and two times higher, respectively, than nifurtimox and benznidazole, the medicines of choice for the treatment of the acute Chagas' disease.     

Benzimidazole- and benzoxazole-based inhibitors of Rho kinase

Inhibitors of Rho kinase have been developed based on two distinct scaffolds, benzimidazoles, and benzoxazoles. SAR studies and efforts to optimize the initial lead compounds are described. Novel selective inhibitors of ROCK-II with excellent potency in both enzyme and cell-based assays were obtained. These inhibitors possess good microsomal stability, low cytochrome P-450 inhibitions and good oral bioavailability.     

Carpology,germination and seedling performance in Digitalis thapsi L. (Scrophulariaceae)

Summary

We analyse the fruiting phase of the life cycleof Digitalis thapsi L. We studied the production and size of seeds and capsules, and the interpopulational variability and inter-relationships of these parameters. The capsule volume, number of seeds per capsule, of seeds per individual, and of capsules per individual were inter-related and fairly affected by the medium, whereas seed weight was found to bea more independent character. A germination study showed that the species has agreat germinative capacity and has positive photoblasty. It is non-dormant especially if incubated under experimental conditions close to the climatic conditions of the site of provenance of the samples. An increase in temperature speeds up the process without increasing germinability. The morphological and biometric characteristics of the first stages of development of the species following germination were analysed. It was found that seed weight is not positively correlated with cotyledon length nor with any of the other parameters con-sidered, and that the length of the fifth leaf is a useful parameter to express inter-populational genetic variability. Seedling production in spring seems to be influenced more by physical than by chemical factors.     

SMN requirement for synaptic vesicle, active zone and microtubule postnatal organization in motor nerve terminals

Low levels of the Survival Motor Neuron (SMN) protein produce Spinal Muscular Atrophy (SMA), a severe monogenetic disease in infants characterized by muscle weakness and impaired synaptic transmission. We report here severe structural and functional alterations in the organization of the organelles and the cytoskeleton of motor nerve terminals in a mouse model of SMA. The decrease in SMN levels resulted in the clustering of synaptic vesicles (SVs) and Active Zones (AZs), reduction in the size of the readily releasable pool (RRP), and the recycling pool (RP) of synaptic vesicles, a decrease in active mitochondria and limiting of neurofilament and microtubule maturation. We propose that SMN is essential for the normal postnatal maturation of motor nerve terminals and that SMN deficiency disrupts the presynaptic organization leading to neurodegeneration.     

Ultrastructural Study of the Filum Terminate and Caudal Ampulla of the Spinal Cord of Amphioxus (Branchiostoma lanceolatum Pallas)

The filum terminale and caudal ampulla of amphioxus were studied by electron microscopy. The filum terminale consists of ependymal cells whose cilia are directed caudally. Remarkably, nerve fibres course through the filum terminale and caudal ampulla and end on the basal lamina forming neuro-connective structures. Moreover, these nerve boutons are divisible into several classes according to their vesicle content. Boutons containing large dense-cored vesicles are very similar in appearance to the neurosecretory terminals found in the caudal spinal cord of some vertebrates. These observations on nerve fibres suggest that a primitive neurosecretory system similar to the fish urophysis is present in the amphioxus.     

Cold storage to overcome dormancy affects the carbohydrate status and photosynthetic capacity of Rhododendron simsii

Global warming leads to increasing irregular and unexpected warm spells during autumn, and therefore natural chilling requirements to break dormancy are at risk. Controlled cold treatment can provide an answer to this problem. Nevertheless, artificial cold treatment will have consequences for carbon reserves and photosynthesis. In this paper, the effect of dark cold storage at 7 °C to break flower bud dormancy in the evergreen Rhododendron simsii was quantified. Carbohydrate and starch content in leaves and flower buds of an early (‘Nordlicht’), semi‐early (‘M. Marie’) and late (‘Mw. G. Kint’) flowering cultivar showed that carbon loss due to respiration was lowest in ‘M. Marie’, while ‘Mw. G. Kint’ was completely depleted of starch reserves at the end of cold treatment. Gene isolation resulted in a candidate gene for sucrose synthase (SUS) RsSus, which appears to be homologous to AtSus3 and had a clear increase in expression in leaves during cold treatment. Photosynthesis measurements on ‘Nordlicht’ and the late‐flowering cultivar ‘Thesla’ showed that during cold treatment, dark respiration decreased 58% and 63%, respectively. Immediately after cold treatment, dark respiration increased and stabilised after 3 days. The light compensation point followed the same trend as dark respiration. Quantum efficiency showed no significant changes during the first days after cold treatment, but was significantly higher than in plants with dormant flower buds at the start of cold treatment. In conclusion, photosynthesis stabilised 3 days after cold treatment and was improved compared to the level before cold treatment.     

In vitro parthenogenesis of mouse oocytes under several experimental conditions

Although the in vitro fertilisation index is a parameter commonly employed to investigate sperm functional activity, little attention has been given to the occurrence of parthenogenesis. The purpose of this study was to study at 6 h or 22 h incubation: (a) the cleavage-related events that occur in in vitro incubated mouse oocytes, in the absence (parthenogenesis) or presence of homologous spermatozoa; (b) the effect of mineral oil, commonly used in in vitro fertilisation assays; (c) the effect of piroxicam, a prostaglandin synthesis inhibitor, on the parthenogenetic rate; and (d) the influence on parthenogenesis of spontaneous loss of the cumulus oophorus coat during incubation. Under the experimental conditions employed, there was parthenogenetic activation and activation due to fertilisation. Both increased in a time-dependent manner. The mineral oil enhanced the parthenogenetic rate at 22 h incubation. However, it did not have any effect when the oocytes were inseminated. Since we can not discriminate how much of this activation was due to fertilisation and how much to parthenogenesis we must be very careful with this comparison. Piroxicam 10(-8) M did not show any effect on the mouse oocyte parthenogenetic rate at neither 6 h or 22 h incubation. Our results suggest that oocyte susceptibility to spontaneous parthenogenetic activation may be modified by the presence of the cumulus and corona radiata cells. In conclusion, we consider that further rigorous studies on these influences are necessary in order to confer more reliability on the results.