Gel‐free mass spectrometry analysis of Drosophila melanogaster heads

Membrane proteins play key roles in several fundamental biological processes such as cell signalling, energy metabolism and transport. Despite the significance, these still remain an under‐represented group in proteomics datasets. Herein, a bottom‐up approach to analyse an enriched membrane fraction from Drosophila melanogaster heads using multidimensional liquid chromatography (LC) coupled with tandem‐mass spectrometry (MS/MS) that relies on complete solubilisation and digestion of proteins, is reported. An enriched membrane fraction was prepared using equilibrium density centrifugation on a discontinuous sucrose gradient, followed by solubilisation using the filter‐aided sample preparation (FASP), tryptic and sequential chymotryptic digestion of proteins. Peptides were separated by reversed‐phase (RP) LC at high pH in the first dimension and acidic RP‐LC in the second dimension coupled directly to an Orbitrap Velos Pro mass spectrometer. A total number of 4812 proteins from 114 865 redundant and 38 179 distinct peptides corresponding to 4559 genes were identified in the enriched membrane fraction from fly heads. These included brain receptors, transporters and channels that are most important elements as drug targets or are linked to disease. Data are available via ProteomeXchange with identifier PXD001712 ( http://proteomecentral.proteomexchange.org/dataset/PXD001712 ).     

Resilience to changes in lake trophic state: Nutrient allocation into Daphnia resting eggs

During past decades, many lakes underwent drastic human‐caused changes in trophic state with strong implications for population dynamics and food web processes. We investigated the influence of trophic state on nutrient allocation into Daphnia resting eggs. The production of resting eggs is an important survival strategy, allowing Daphnia to cope with unfavorable environmental conditions. Allocation of essential nutrients into resting eggs may crucially influence embryonic development and offspring survival and thus is of great ecological and evolutionary interest. The capacity of Daphnia to adjust the allocation of nutrients into resting eggs may depend on the dietary nutrient supply, which may vary with trophic state‐related changes in the phytoplankton community composition. Resting eggs were isolated from sediment cores taken from Lake Constance, a large prealpine lake with a distinct eutrophication and reoligotrophication history, and analyzed for elemental (carbon, nitrogen, and phosphorus) and biochemical (sterols and fatty acids) nutrients. Carbon allocation into Daphnia resting eggs continuously decreased over time, irrespective of changes in trophic state. The allocation of nitrogen into Daphnia resting eggs followed the changes in trophic state, that is, nitrogen concentrations in resting eggs increased with eutrophication and decreased again with reoligotrophication. The allocation of phosphorus, sterols and long‐chain polyunsaturated fatty acids, such as eicosapentaenoic acid, into Daphnia resting eggs did not change significantly over time. Changes in trophic state strikingly influenced all trophic levels in Lake Constance. However, nutrient allocation into Daphnia resting eggs was mostly resilient to changes in lake trophic state.     

Assessing Impacts of Hydropattern Restoration of an Overdrained Wetland on Soil Nutrients, Vegetation and Fire

Restoring hydrology to overdrained wetlands can facilitate restoration of degraded ecosystems. In the northern Everglades, the Rotenberger Wildlife Management Area (RWMA) became a rain-driven system as historic overland inflows were redirected. Consequently, the soil experienced severe drying, resulting in frequent muck fires, oxidation and a shift in vegetation composition. In July 2001, the RWMA hydropattern restoration began utilizing discharge from Stormwater Treatment Area 5 (STA-5), a constructed wetland. As a result, predischarge hydroperiods averaging 124 days increased to an average of 183 days. Soil total phosphorus (TP) concentrations in the topsoil layer did not significantly change from predischarge (637 mg/kg) to postdischarge (633 mg/kg) concentrations. Muck fires appear to be the catalyst for rapid alterations in the bioavailability and solubility of P. Prior to muck fires, soil P pools were 88% organic P and 12% inorganic P, shifting to 49% organic P and 51% inorganic P measured after a muck fire. Sawgrass ( Cladium jamaicense , OBL) and Cattail ( Typha domingensis , OBL) cover approximately 75% of the RWMA area as dominant or codominant species. Predischarge vegetation community composition documented obligate (OBL) and facultative wetland (FACW) species, each composing 46% of all species surveyed. Postdischarge vegetation compositions shifted to 59% OBL and 39% FACW species. In addition, there were significant elevations in tissue nutrient concentrations, TP, and total nitrogen, between pre- and postdischarge samples. An adaptive management approach to inflow and outflow operations will be an important part of successful wetland restoration.     

Evidence that P36, a human sperm acrosomal antigen involved in the fertilization process is triosephosphate isomerase

P36 is one of the immunodominant sperm antigens identified by antibodies eluted from the spermatozoa of infertile men. In a previous study, we isolated and characterized this auto-antigen as a glycoprotein with several isoforms. Specific rabbit antibodies were produced to investigate sperm topography and the role of P36 in the fertilization process and we showed that P36 is present on the equatorial segment of acrosome-reacted spermatozoa and is involved in sperm-binding and the penetration of zona-free hamster oocytes. In the present study, we demonstrated, by means of immunofluorescence and electron microscopy, that P36 is present all over the acrosomal membranes of non-reacted spermatozoa. We also investigated the role of P36 in the acrosome reaction and sperm binding to the zona pellucida (ZP). The exposure of capacitated spermatozoa to rabbit anti-P36 antibodies had no effect on primary fixation to the ZP, but inhibited secondary binding to the ZP and the Ca2+ ionophore-induced acrosome reaction. These results suggest that P36, an acrosomal antigen, is involved in several steps of the fertilization process. On two-dimensional Western blots, human anti-sperm antibodies (ASA) and rabbit anti-P36 antibodies recognized five to six isoforms of P36, all 36/37 kDa in size, with a pI between 5.1 and 5.7. Two major spots were identified as human triosephosphate isomerase (TPI) by MALDI-TOF mass spectrometry. Anti-TPI antibodies were shown to react with the isoforms recognized by human and rabbit anti-P36 antibodies. We also demonstrated the presence of TPI in human sperm heads. Further studies are underway to establish whether there is a sperm-specific isoform of TPI and its role in sperm function.     

Expression of a cucumber class III chitinase and <Emphasis Type="Italic">Nicotiana plumbaginifolia</Emphasis>class I glucanase genes in transgenic potato plants

The genes encoding for a cucumber class III chitinase and Nicotiana plumbaginifolia class I glucanase were co-introduced into Slovak potato (Solanum tuberosum L.) breeding line 116/86 using Agrobacterium tumefaciens. For both transgenes the number of integrated copies and level of RNA expression were determined. These analyses demonstrated low variation and significant correlation in expression of the introduced transgenes. The effect of transgene expression on fungal susceptibility of transformants was evaluated in vitro. Hyphal extension assays revealed no obvious differences in the ability of extracts from transformants to inhibit growth of Rhizoctonia solani comparing to non-transformed potato.     

A mammalian ortholog of Saccharomyces cerevisiae Vac14 that associates with and up-regulates PIKfyve phosphoinositide 5-kinase activity

Multivesicular body morphology and size are controlled in part by PtdIns(3,5)P(2), produced in mammalian cells by PIKfyve-directed phosphorylation of PtdIns(3)P. Here we identify human Vac14 (hVac14), an evolutionarily conserved protein, present in all eukaryotes but studied principally in yeast thus far, as a novel positive regulator of PIKfyve enzymatic activity. In mammalian cells and tissues, Vac14 is a low-abundance 82-kDa protein, but its endogenous levels could be up-regulated upon ectopic expression of hVac14. PIKfyve and hVac14 largely cofractionated, populated similar intracellular locales, and physically associated. A small-interfering RNA-directed gene-silencing approach to selectively eliminate endogenous hVac14 rendered HEK293 cells susceptible to morphological alterations similar to those observed upon expression of PIKfyve mutants deficient in PtdIns(3,5)P(2) production. Largely decreased in vitro PIKfyve kinase activity and unaltered PIKfyve protein levels were detected under these conditions. Conversely, ectopic expression of hVac14 increased the intrinsic PIKfyve lipid kinase activity. Concordantly, intracellular PtdIns(3)P-to-PtdIns(3,5)P(2) conversion was perturbed by hVac14 depletion and was elevated upon ectopic expression of hVac14. These data demonstrate a major role of the PIKfyve-associated hVac14 protein in activating PIKfyve and thereby regulating PtdIns(3,5)P(2) synthesis and endomembrane homeostasis in mammalian cells.     

Mathematical model of real-time PCR kinetics

Several real-time PCR (rtPCR) quantification techniques are currently used to determine the expression levels of individual genes from rtPCR data in the form of fluorescence intensities. In most of these quantification techniques, it is assumed that the efficiency of rtPCR is constant. Our analysis of rtPCR data shows, however, that even during the exponential phase of rtPCR, the efficiency of the reaction is not constant, but is instead a function of cycle number. In order to understand better the mechanisms belying this behavior, we have developed a mathematical model of the annealing and extension phases of the PCR process. Using the model, we can simulate the PCR process over a series of reaction cycles. The model thus allows us to predict the efficiency of rtPCR at any cycle number, given a set of initial conditions and parameter values, which can mostly be estimated from biophysical data. The model predicts a precipitous decrease in cycle efficiency when the product concentration reaches a sufficient level for template-template re-annealing to compete with primer-template annealing; this behavior is consistent with available experimental data. The quantitative understanding of rtPCR provided by this model can allow us to develop more accurate methods to quantify gene expression levels from rtPCR data.     

Monovalent cation conductance in Xenopus laevis oocytes expressing hCAT-3

hCAT-3 (human cationic amino acid transporter type three) was investigated with both the two-electrode voltage clamp method and tracer experiments. Oocytes expressing hCAT-3 displayed less negative membrane potentials and larger voltage-dependent currents than native or water-injected oocytes did. Ion substitution experiments in hCAT-3-expressing oocytes revealed a large conductance for Na+ and K+. In the presence of L-Arg, voltage-dependent inward and outward currents were observed. At symmetrical (inside/outside) concentrations of L-Arg, the conductance of the transporter increased monoexponentially with the L-Arg concentrations; the calculated Vmax and KM values amounted to 8.3 microS and 0.36 mM, respectively. The time constants of influx and efflux of [3H]L-Arg, at symmetrically inside/outside L-Arg concentrations (1 mM), amounted to 79 and 77 min, respectively. The flux data and electrophysiological experiments suggest that the transport of L-Arg through hCAT-3 is symmetric, when the steady state of L-Arg flux has been reached. It is concluded that hCAT-3 is a passive transport system that conducts monovalent cations including L-Arg. The particular role of hCAT-3 in the diverse tissues remains to be elucidated.     

Ezrin controls the macromolecular complexes formed between an adapter protein Na+/H+ exchanger regulatory factor and the cystic fibrosis transmembrane conductance regulator

Na(+)/H(+) exchanger regulatory factor (NHERF) is an adapter protein that is responsible for organizing a number of cell receptors and channels. NHERF contains two amino-terminal PDZ (postsynaptic density 95/disk-large/zonula occluden-1) domains that bind to the cytoplasmic domains of a number of membrane channels or receptors. The carboxyl terminus of NHERF interacts with the FERM domain (a domain shared by protein 4.1, ezrin, radixin, and moesin) of a family of actin-binding proteins, ezrin-radixin-moesin. NHERF was shown previously to be capable of enhancing the channel activities of cystic fibrosis transmembrane conductance regulator (CFTR). Here we show that binding of the FERM domain of ezrin to NHERF regulates the cooperative binding of NHERF to bring two cytoplasmic tails of CFTR into spatial proximity to each other. We find that ezrin binding activates the second PDZ domain of NHERF to interact with the cytoplasmic tails of CFTR (C-CFTR), so as to form a specific 2:1:1 (C-CFTR)(2).NHERF.ezrin ternary complex. Without ezrin binding, the cytoplasmic tail of CFTR only interacts strongly with the first amino-terminal PDZ domain to form a 1:1 C-CFTR.NHERF complex. Immunoprecipitation and immunoblotting confirm the specific interactions of NHERF with the full-length CFTR and with ezrin in vivo. Because of the concentrated distribution of ezrin and NHERF in the apical membrane regions of epithelial cells and the diverse binding partners for the NHERF PDZ domains, the regulation of NHERF by ezrin may be employed as a general mechanism to assemble channels and receptors in the membrane cytoskeleton.