Proteomic analysis of the microenvironment of developing oocytes

We utilized a setup based on extensive pre-fractionation of proteolytic peptides and nanoflow reversed-phase LC-MS/MS to identify the (sub)proteome of human follicular fluid (FF). In this in-depth screen, 246 specific proteins were identified, the majority of which are involved in coagulation- and immune-response pathways. Our aim is to define a set of FF protein markers, which could predict oocyte quality.     

The Use of Cystometry in Small Rodents: A Study of Bladder Chemosensation

The lower urinary tract (LUT) functions as a dynamic reservoir that is able to store urine and to efficiently expel it at a convenient time. While storing urine, however, the bladder is exposed for prolonged periods to waste products. By acting as a tight barrier, the epithelial lining of the LUT, the urothelium, avoids re-absorption of harmful substances. Moreover, noxious chemicals stimulate the bladder''s nociceptive innervation and initiate voiding contractions that expel the bladder''s contents. Interestingly, the bladder''s sensitivity to noxious chemicals has been used successfully in clinical practice, by intravesically infusing the TRPV1 agonist capsaicin to treat neurogenic bladder overactivity¹. This underscores the advantage of viewing the bladder as a chemosensory organ and prompts for further clinical research. However, ethical issues severely limit the possibilities to perform, in human subjects, the invasive measurements that are necessary to unravel the molecular bases of LUT clinical pharmacology. A way to overcome this limitation is the use of several animal models². Here we describe the implementation of cystometry in mice and rats, a technique that allows measuring the intravesical pressure in conditions of controlled bladder perfusion.After laparotomy, a catheter is implanted in the bladder dome and tunneled subcutaneously to the interscapular region. Then the bladder can be filled at a controlled rate, while the urethra is left free for micturition. During the repetitive cycles of filling and voiding, intravesical pressure can be measured via the implanted catheter. As such, the pressure changes can be quantified and analyzed. Moreover, simultaneous measurement of the voided volume allows distinguishing voiding contractions from non-voiding contractions³.Importantly, due to the differences in micturition control between rodents and humans, cystometric measurements in these animals have only limited translational value⁴. Nevertheless, they are quite instrumental in the study of bladder pathophysiology and pharmacology in experimental pre-clinical settings. Recent research using this technique has revealed the key role of novel molecular players in the mechano- and chemo-sensory properties of the bladder.     

Perapion connexum (Schilsky, 1902) (Coleoptera, Apionidae) in Central Europe, a case of plant expansion chase

Perapion connexum (Schilsky) is recorded for the first time from Hungary and Kyrgyzstan, and new distribution data from Ukraine and Russia are provided. Preliminary placements of this weevil in faunal checklists for Poland and Slovakia are here documented with detailed data. Its occurrence in Austria based on older evidence, is discussed. The neophytic and invasive in Central Europe sorrel Rumex confertus Willd. is confirmed to be its unique host plant in Poland. Morphology of the newcoming weevil is described and illustrated, and the key to all Central European species of Perapion is presented.     

Photochemical probing of the B--a conformational transition in a linearized pUC19 DNA and its polylinker region

We induced the B-to-A conformational transition by ethanol in a linearized pUC19 DNA. A primer extension method was used in combination with UV light irradiation to follow the transition, based on pausing of DNA synthesis due to the presence of damaged bases in the template. Primer extension data highly correlated with the results of another method monitoring the B-A transition, i.e. inhibition of restriction endonuclease cleavage of UV light-irradiated DNA. Primer extension enabled us to locate damaged nucleotides within the region of interest. Most damaged nucleotides were located in B-form trimers, exclusively containing both pyrimidine bases (TTC, TCT, CTC, and CTT), and in a cytosine tetramer. The amount of damaged bases decreased in the course of B-A transition. Some of the damage even disappeared in the A-form, which mainly concerns the C(4) and C(3) blocks. The cleavage was nearly restored in the A-form within this region (Eco88I). On the contrary the decrease of damage was less significant with thymine dimers, only dropping to 50-60% of the B-form level. Consequently, the cleavage with EcoRI and HindIII remained mostly as before the transition (75% and 60% of uncleaved DNA preserved). We found significant differences in the B- and A-form pattern of UV light-damaged bases within the same region (polylinker) of DNA embedded within long (plasmid) or short (127 bp fragment) DNA molecules. The B-A transition of the fragment was found less cooperative than with linearized plasmid, which was confirmed by both CD spectroscopy and restriction cleavage inhibition.     

Alga-derived substrates select for distinct Betaproteobacterial lineages and contribute to niche separation in Limnohabitans strains

We examined the proportions of major Betaproteobacteria subgroups within bacterial communities in diverse nonaxenic, monospecific cultures of algae or cyanobacteria: four species of cryptophyta (genera Cryptomonas and Rhodomonas), four species of chlorophyta (genera Pediastrum, Staurastrum, and Chlamydomonas), and two species of cyanobacteria (genera Dolichospermum and Aphanizomenon). In the cryptophyta cultures, Betaproteobacteria represented 48 to 71% of total bacteria, the genus Limnohabitans represented 18 to 26%, and the Polynucleobacter B subcluster represented 5 to 16%. In the taxonomically diverse chlorophyta group, the genus Limnohabitans accounted for 7 to 45% of total bacteria. In contrast, cyanobacterial cultures contained significantly lower proportions of the Limnohabitans bacteria (1 to 3% of the total) than the cryptophyta and chlorophyta cultures. Notably, largely absent in all of the cultures was Polynucleobacter necessarius (Polynucleobacter C subcluster). Subsequently, we examined the growth of Limnohabitans strains in the presence of different algae or their extracellular products (EPP). Two strains, affiliated with Limnohabitans planktonicus and Limnohabitans parvus, were separately inoculated into axenic cultures of three algal species growing in an inorganic medium: Cryptomonas sp., Chlamydomonas noctigama, and Pediastrum boryanum. The Limnohabitans strains cocultured with these algae or inoculated into their EPP consistently showed (i) pronounced population growth compared to the control without the algae or EPP and (ii) stronger growth stimulation of L. planktonicus than of L. parvus. Overall, growth responses of the Limnohabitans strains cultured with algae were highly species specific, which suggests a pronounced niche separation between two closely related Limnohabitans species likely mediated by different abilities to utilize the substrates produced by different algal species.     

Reproductive responses of temperate and boreal Tengmalm's Owl Aegolius funereus populations to spatial and temporal variation in prey availability

Environmental variation across space and time can strongly influence life‐history strategies in vertebrates. It has been shown that the reproductive success of birds of prey is closely related to food availability. However, relatively little is known about intraspecific differences in reproductive success of birds in relation to varying ecological conditions across environmental gradients. We investigated the reproductive performance of Tengmalm's Owls Aegolius funereus in a temperate (Czech Republic, 50°N) and a boreal (Finland, 63°N) population in relation to long‐term variations in the abundance of their main prey (small rodents). Prey densities at the northern site were much higher, but there were also large inter‐annual fluctuations and years with steep summer declines of vole densities. Northern owls laid larger clutches but offspring production per nest was similar at both study sites. This resulted from higher nestling mortality in the northern population, especially in nests established later in the season. Despite much greater nesting losses due to predation by Pine Martens Martes martes, productivity at the population level was about four times greater at the temperate site, mainly due to the much higher breeding densities compared with Finland. Tengmalm's Owls at the temperate study site may benefit from relatively stable prey abundance, a more diverse prey community that offers alternative prey during vole scarcity, longer nights in summer that allow more time for foraging, and a lower level of interspecific competition with other vole‐specialized predators.     

Factors Affecting Vocalization in Tengmalm’s Owl (Aegolius funereus) Fledglings during Post-Fledging Dependence Period: Scramble Competition or Honest Signalling of Need?

Begging behaviour of nestlings has been intensively studied for several decades as a key component of parent-offspring conflict. There are essentially two main theories to account for intensity of food solicitation among offspring: that intensity of begging is related to some form of scramble competition between nest mates or that it offers honest signalling of need to parents. The vast majority of studies which have addressed begging behaviour have been based on observations of, and experiments on, nestlings and have not considered begging behaviour, during the post-fledging period. Begging vocalizations in this post-fledging phase of dependence have rarely been studied, despite the importance of vocalizations as a communication method between offspring and parents, particularly for nocturnal species. We radiotracked 39 fledglings of the Tengmalm’s owl (Aegolius funereus) in two years with different availability of prey: 2010 (n = 29 fledglings) and 2011 (n = 10 fledglings) and made 1320 nightly localizations in which we recorded presence or absence of begging calls. Within years, the most important measures related to the probability of vocalization were body condition at fledging, time of night, number of surviving siblings, age and weather conditions. Begging intensity increased with age in both years; however, in the year with low prey availability fledglings vocalized significantly more often. The main factor causing these differences between years was probably the different availability of prey, affecting breeding success, post-fledging behaviour, and thus also both short- and long-term needs of offspring. We believe that our results suggest honest signalling of their fledgling’s need.     

Methodology for systematic analysis and improvement of manufacturing unit process life cycle inventory (UPLCI) CO2PE! initiative (cooperative effort on process emissions in manufacturing). Part 2: case studies

Purpose  

This report presents two case studies, one for both the screening approach and the in-depth approach, demonstrating the application of the life cycle assessment-oriented methodology for systematic inventory analysis of the machine tool use phase of manufacturing unit processes, which has been developed in the framework of the CO₂PE! collaborative research programme (CO₂PE! 2011) and is described in part 1 of this paper (Kellens et al. 2011).     

Atomic Scissors: A New Method of Tracking the 5-Bromo-2′-Deoxyuridine-Labeled DNA In Situ

A new method of the light microscopy detection of BrdU-labeled DNA in situ is described. It is based on the oxidative attack at the deoxyribose moiety by copper(I) in the presence of oxygen, which leads to the abstraction of hydrogen atom from deoxyribose culminating in the elimination of the nucleobase, scission of the nucleic-acid strand and formation of frequent gaps. The gaps allow the reaction of the antibodies with the commonly used markers of replication (e.g. 5-bromo-2′-deoxyuridine), which are otherwise masked. The method developed makes it possible to detect nuclear and mitochondrial DNA replication efficiently. In most cases, it does not inhibit effective protein detections and in addition enables simultaneous localization of newly-synthesized RNA. The alternative presently-used methods result in protein denaturation and/or extensive DNA cleavage followed by the DNA-bound proteins peeling off.     

Most Anti-BrdU Antibodies React with 2′-Deoxy-5-Ethynyluridine — The Method for the Effective Suppression of This Cross-Reactivity

5-Bromo-2′-deoxyuridine (BrdU) and 2′-deoxy-5-ethynyluridine (EdU) are widely used as markers of replicated DNA. While BrdU is detected using antibodies, the click reaction typically with fluorescent azido-dyes is used for EdU localisation. We have performed an analysis of ten samples of antibodies against BrdU with respect to their reactivity with EdU. Except for one sample all the others evinced reactivity with EdU. A high level of EdU persists in nuclear DNA even after the reaction of EdU with fluorescent azido-dyes if the common concentration of dye is used. Although a ten-time increase of azido-dye concentration resulted in a decrease of the signal provided by anti-BrdU antibodies, it also resulted in a substantial increase of the non-specific signal. We have shown that this unwanted reactivity is effectively suppressed by non-fluorescent azido molecules. In this respect, we have tested two protocols of the simultaneous localisation of incorporated BrdU and EdU. They differ in the mechanism of the revelation of incorporated BrdU for the reaction with antibodies. The first one was based on the use of hydrochloric acid, the second one on the incubation of samples with copper(I) ions. The use of hydrochloric acid resulted in a significant increase of the non-specific signal. In the case of the second method, no such effect was observed.