A Rab8-specific GDP/GTP exchange factor is involved in actin remodeling and polarized membrane transport

The mechanisms mediating polarized delivery of vesicles to cell surface domains are poorly understood in animal cells. We have previously shown that expression of Rab8 promotes the formation of new cell surface domains through reorganization of actin and microtubules. To unravel the function of Rab8, we used the yeast two-hybrid system to search for potential Rab8-specific activators. We identified a coil-coiled protein (Rabin8), homologous to the rat Rabin3 that stimulated nucleotide exchange on Rab8 but not on Rab3A and Rab5. Furthermore, we show that rat Rabin3 has exchange activity on Rab8 but not on Rab3A, supporting the view that rat Rabin3 is the rat equivalent of human Rabin8. Rabin8 localized to the cortical actin and expression of Rabin8 resulted in remodeling of actin and the formation of polarized cell surface domains. Activation of PKC by phorbol esters enhanced translocation of both Rabin8 and Rab8-specific vesicles to the outer edge of lamellipodial structures. Moreover, coexpression of Rabin8 with dominant negative Rab8 (T22N) redistributes Rabin8 from cortical actin to Rab8-specific vesicles and promotes their polarized transport to cell protrusions. The C-terminal region of Rabin8 plays an essential role in this transport. We propose that Rabin8 is a Rab8-specific activator that is connected to processes that mediate polarized membrane traffic to dynamic cell surface structures.     

Mapping the genome of Miscanthus sinensis for QTL associated with biomass productivity

In light of rising energy costs, lignocellulosic ethanol has been identified as a renewable alternative to petroleum-based transportation fuels. In an attempt to reach government mandated ethanol production levels, potential plant biofeedstock candidates have been investigated, and cold-tolerant, perennial accessions within the C₄ grass genus Miscanthus have been identified as leading contenders in the Midwestern US. To facilitate the development of improved cultivars through marker-assisted breeding, a quantitative trait locus (QTL) study was conducted on a full-sib, F₁ mapping population segregating for flowering time, height, leaf width, and yield using a genetic map consisting of 846 segregating SNP and SSR markers. This was a 3 year study investigating the genetic architecture underlying traits important to biomass production in a population of 221 progeny from a cross between M. sinensis ‘Grosse Fountaine’ and M. sinensis ‘Undine’ established in the spring of 2010; 72 QTLs with LOD scores above the genome-wide, permuted threshold equivalent to a P-value of 0.05 were identified across 13 traits. Of the 36 QTLs identified in 2011, 22 were detected again the following year. Both the use of spring emergence and vigor rating as a covariate to account for variation related to differences in establishment increased the power to detect QTLs in the 2 year establishment period. Finally, a dry period in the middle of the 2012 growing season suggested that yield declines were due to a decrease in tiller diameter.     

2‐photon excitation fluorescence microscopy enables deeper high‐resolution imaging of voltage and Ca2+ in intact mice,rat, and rabbit hearts

We describe a novel two‐photon (2P) laser scanning microscopy (2PLSM) protocol that provides ratiometric transmural measurements of membrane voltage (V_m) via Di‐4‐ANEPPS in intact mouse, rat and rabbit hearts with subcellular resolution. The same cells were then imaged with Fura‐2/AM for intracellular Ca²⁺ recordings. Action potentials (APs) were accurately characterized by 2PLSM vs. microelectrodes, albeit fast events (<1 ms) were sub‐optimally acquired by 2PLSM due to limited sampling frequencies (2.6 kHz). The slower Ca²⁺ transient (CaT) time course (>1ms) could be accurately described by 2PLSM. In conclusion, V_m ‐ and Ca²⁺‐sensitive dyes can be 2P excited within the cardiac muscle wall to provide AP and Ca²⁺ signals to ～400 µm. (© 2013 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

Population-based cervical screening with a 5-year interval in The Netherlands. Stabilization of the incidence of squamous cell carcinoma and its precursor lesions in the screened population

OBJECTIVE: To evaluate the outcome of population-based cervical screening at 5-year intervals. STUDY DESIGN: Results from the west region of the Netherlands (population 2 million) were used. The 1995-2000 round was compared with the first 2 years of the second (2001-2002). All results were prospectively collected in a central database. Positive cytologies and histoscores per 1,000 screened for preinvasive squamous cervical intraepithelial neoplasia (CIN) lesions and invasive squamous cell carcinoma were calculated. RESULTS: In the first round, 378,081 women were screened; in the second round, 100,561 women were screened. In both rounds the youngest screenees had the highest cytoscores. Cytoscores in the first round did not differ significantly from those in the second. The histoscore for CIN 1 and 2 was 1.42 per 1,000 in the first round and 1.18 per 1,000 (NS, P < .01) in the second. The histoscore for CIN 3 was 2.07 per 1,000 in the first round and 2.13 per 1,000 (NS, P < .01) in the second. Histoscores for invasive squamous cell carcinoma remained virtually the same (0.16 per 1,000 in the first, 0.14 per 1,000 in the second round). CONCLUSION: Population-based screening at 5-year intervals in the Netherlands may result in stabilization of positive cytology and of the incidence of CIN and (histologic) invasive squamous cell carcinoma. The program seems more cost effective than that of 2 decades ago, with a screening interval of 3 years.     

Loss of the Plasma Membrane-Bound Protein Gas1p in Saccharomyces cerevisiae Results in the Release of β1,3-Glucan into the Medium and Induces a Compensation Mechanism To Ensure Cell Wall Integrity

Deletion of GAS1/GGP1/CWH52 results in a lower β-glucan content of the cell wall and swollen, more spherical cells (L. Popolo, M. Vai, E. Gatti, S. Porello, P. Bonfante, R. Balestrini, and L. Alberghina, J. Bacteriol. 175:1879–1885, 1993; A. F. J. Ram, S. S. C. Brekelmans, L. J. W. M. Oehlen, and F. M. Klis, FEBS Lett. 358:165–170, 1995). We show here that gas1Δ cells release β1,3-glucan into the medium. Western analysis of the medium proteins with β1,3-glucan- and β1,6-glucan-specific antibodies showed further that at least some of the released β1,3-glucan was linked to protein as part of a β1,3-glucan–β1,6-glucan–protein complex. These data indicate that Gas1p might play a role in the retention of β1,3-glucan and/or β-glucosylated proteins. Interestingly, the defective incorporation of β1,3-glucan in the cell wall was accompanied by an increase in chitin and mannan content in the cell wall, an enhanced expression of cell wall protein 1 (Cwp1p), and an increase in β1,3-glucan synthase activity, probably caused by the induced expression of Fks2p. It is proposed that the cell wall weakening caused by the loss of Gas1p induces a set of compensatory reactions to ensure cell integrity.     

Identifying and correcting spatial bias in opportunistic citizen science data for wild ungulates in Norway

Many publications make use of opportunistic data, such as citizen science observation data, to infer large‐scale properties of species’ distributions. However, the few publications that use opportunistic citizen science data to study animal ecology at a habitat level do so without accounting for spatial biases in opportunistic records or using methods that are difficult to generalize. In this study, we explore the biases that exist in opportunistic observations and suggest an approach to correct for them. We first examined the extent of the biases in opportunistic citizen science observations of three wild ungulate species in Norway by comparing them to data from GPS telemetry. We then quantified the extent of the biases by specifying a model of the biases. From the bias model, we sampled available locations within the species’ home range. Along with opportunistic observations, we used the corrected availability locations to estimate a resource selection function (RSF). We tested this method with simulations and empirical datasets for the three species. We compared the results of our correction method to RSFs obtained using opportunistic observations without correction and to RSFs using GPS‐telemetry data. Finally, we compared habitat suitability maps obtained using each of these models. Opportunistic observations are more affected by human access and visibility than locations derived from GPS telemetry. This has consequences for drawing inferences about species’ ecology. Models naïvely using opportunistic observations in habitat‐use studies can result in spurious inferences. However, sampling availability locations based on the spatial biases in opportunistic data improves the estimation of the species’ RSFs and predicted habitat suitability maps in some cases. This study highlights the challenges and opportunities of using opportunistic observations in habitat‐use studies. While our method is not foolproof it is a first step toward unlocking the potential of opportunistic citizen science data for habitat‐use studies.     

Settling cyanobacterial blooms do not improve growth conditions for soft bottom meiofauna

Summer blooms of the toxin-producing cyanobacteria Nodularia spumigena are frequent in the Baltic Sea and recent findings suggest that they may be an important food source for the benthos below the euphotic zone. To investigate the effects of settling spring and summer phytoplankton blooms on meiofaunal growth, we assayed concentrations of nucleic acids in three ostracod species (Candona neglecta; Heterocyprideis sorbyana and Paracyprideis fennica) and one genus of nematodes (Paracanthonchus spp.) after incubation in sediments with the one of the following food additions: (1) diatoms, (2) the cyanobacterium Nodularia spumigena, (3) Tetraphyll® as a known high-quality food source, (4) lignin as a refractory artificial food, and (5) control (no added organic matter). The ribosomal ribonucleic acid (RNA) content and RNA:DNA ratios of the tested organisms were lower in the cyanobacteria treatment than in the diatom treatment, with the difference in RNA:DNA ratios being statistically significant for all species except C. neglecta. Moreover, individuals incubated with N. spumigena showed RNA:DNA levels similar to those found in the lignin and control treatments. Furthermore, N. spumigena had lower concentrations of both enzymatically hydrolysable amino acids (EHAA) and eicosapentaenoic acid (EPA) than diatoms suggesting lower nutritional quality for consumers. These results indicate that recently settled summer blooms of N. spumigena are nutritionally poor and do not improve conditions for meiofaunal growth in Baltic sediments. In contrast, input of diatoms to the sediments during spring is crucial for meiofaunal growth.     

Local polarity and hydrogen bonding inside the Sec14p phospholipid-binding cavity: high-field multi-frequency electron paramagnetic resonance studies

Sec14p promotes the energy-independent transfer of either phosphatidylinositol (PtdIns) or phosphatidylcholine (PtdCho) between lipid bilayers in vitro and represents the major PtdIns/PtdCho transfer protein in the budding yeast Saccharomyces cerevisiae. Herein, we employ multi-frequency high-field electron paramagnetic resonance (EPR) to analyze the electrostatic and hydrogen-bonding microenvironments for series of doxyl-labeled PtdCho molecules bound by Sec14p in a soluble protein-PtdCho complex. A structurally similar compound, 5-doxyl stearic acid dissolved in a series of solvents, was used for experimental calibration. The experiments yielded two-component rigid limit 130- and 220-GHz EPR spectra with excellent resolution in the gx region. Those components were assigned to hydrogen-bonded and nonhydrogen-bonded nitroxide species. Partially resolved 130-GHz EPR spectra from n-doxyl-PtdCho bound to Sec14p were analyzed using this two-component model and allowed quantification of two parameters. First, the fraction of hydrogen-bonded nitroxide species for each n-doxyl-PtdCho was calculated. Second, the proticity profile along the phospholipid-binding cavity of Sec14p was characterized. The data suggest the polarity gradient inside the Sec14p cavity is a significant contributor to the driving molecular forces for extracting a phospholipid from the bilayer. Finally, the enhanced g-factor resolution of EPR at 130 and 220 GHz provides researchers with a spectroscopic tool to deconvolute two major contributions to the x-component of the nitroxide g-matrix: hydrogen-bond formation and local electrostatic effects.     

IL‐1α and IL‐1β have different effects on formation and activity of large osteoclasts

Interleukin 1 (IL‐1) is a proinflammatory cytokine upregulated in conditions such as rheumatoid arthritis and periodontal disease. Both isoforms, IL‐1α and IL‐1β, have been shown to activate osteoclasts (OCs), the cells responsible for resorbing bone. Inflammatory conditions are also characterized by increased bone loss and by the presence of large OCs (10+ nuclei). We and others have previously shown that large OCs are more likely to be resorbing compared to small OCs (2–5 nuclei). Moreover, large OCs express higher levels of the IL‐1 activating receptor IL‐1RI, integrins αv and β3, RANK, and TNFR1, while small OCs have higher levels of the decoy receptor IL‐1RII. We hypothesized that IL‐1 would have different effects on large and small OCs due to these distinct receptor expression patterns. To test this hypothesis, RAW 264.7 cells were differentiated into populations of small and large OCs and treated with IL‐1α or IL‐1β (1 and 10 ng/ml). In the presence of sRANKL, both IL‐1α and IL‐1β increased total OC number and resorptive activity of large OCs. IL‐1α stimulated formation of large OCs and increased the number of resorption pits, while IL‐1β changed the morphology of large OCs and integrin‐β3 phosphorylation. No effects were seen in small OCs in response to either IL‐1 isoform. These results demonstrate that IL‐1 predominantly affects large OCs. The dissimilarity of responses to IL‐1α and IL‐1β suggests that these isoforms activate different signaling pathways within the two OC populations. J. Cell. Biochem. 109: 975–982, 2010. © 2010 Wiley‐Liss, Inc.     

Lipogenesis Is Decreased by Grape Seed Proanthocyanidins According to Liver Proteomics of Rats Fed a High Fat Diet

Bioactive proanthocyanidins have been reported to have several beneficial effects on health in relation to metabolic syndrome, type 2 diabetes, and cardiovascular disease. We studied the effect of grape seed proanthocyanidin extract (GSPE) in rats fed a high fat diet (HFD). This is the first study of the effects of flavonoids on the liver proteome of rats suffering from metabolic syndrome. Three groups of rats were fed over a period of 13 weeks either a chow diet (control), an HFD, or a high fat diet supplemented for the last 10 days with GSPE (HFD + GSPE). The liver proteome was fractionated, using a Triton X-114-based two-phase separation, into soluble and membrane protein fractions so that total proteome coverage was considerably improved. The data from isobaric tag for relative and absolute quantitation (iTRAQ)-based nano-LC-MS/MS analysis revealed 90 proteins with a significant (p < 0.05) minimal expression difference of 20% due to metabolic syndrome (HFD versus control) and 75 proteins due to GSPE treatment (HFD + GSPE versus HFD). The same animals have previously been studied (Quesada, H., del Bas, J. M., Pajuelo, D., Díaz, S., Fernandez-Larrea, J., Pinent, M., Arola, L., Salvadó, M. J., and Bladé, C. (2009) Grape seed proanthocyanidins correct dyslipidemia associated with a high-fat diet in rats and repress genes controlling lipogenesis and VLDL assembling in liver. Int. J. Obes. 33, 1007–1012), and GSPE was shown to correct dyslipidemia observed in HFD-fed rats probably through the repression of hepatic lipogenesis. Our data corroborate those findings with an extensive list of proteins describing the induction of hepatic glycogenesis, glycolysis, and fatty acid and triglyceride synthesis in HFD, whereas the opposite pattern was observed to a large extent in GSPE-treated animals. GSPE was shown to have a wider effect than previously thought, and putative targets of GSPE involved in the reversal of the symptoms of metabolic syndrome were revealed. Some of these novel candidate proteins such as GFPT1, CD36, PLAA (phospholipase A₂-activating protein), METTL7B, SLC30A1, several G signaling proteins, and the sulfide-metabolizing ETHE1 and SQRDL (sulfide-quinone reductase-like) might be considered as drug targets for the treatment of metabolic syndrome.An increase in high calorie diets and a sedentary lifestyle are considered the key factors in explaining the epidemic rise in obesity in developed countries (1). Obese patients, especially those with abdominal obesity due to visceral adipose tissue accumulation, run a higher risk of impaired glucose tolerance, which frequently evolves into insulin resistance (2). Obesity and insulin resistance are frequently associated with hypertension, proatherogenic dyslipidemia, chronic inflammation, a prothrombotic state, and recently also fatty liver (3), conditions that together make up what is known as metabolic syndrome and lead to an increased risk of developing cardiovascular disease (CVD)¹ and type 2 diabetes (4). Conversely, some dietary patterns and specific food components have been associated with a lower prevalence of obesity, type 2 diabetes, and CVD. In this sense, the traditional Mediterranean diet (characterized by a high fiber content, low glycemic index carbohydrates, unsaturated fats, vitamins, and antioxidant polyphenols) has been linked to a lower incidence of CVD, obesity, and type 2 diabetes (5–8). Moreover, the French population presents a very low prevalence of death due to CVD despite consuming a diet rich in saturated fats and cholesterol. This phenomenon, known as “the French paradox” (9), has been ascribed to the moderate consumption of red wine and specifically to its content of polyphenols (10–12).Polyphenols include flavonoids of which flavan-3-ols and their oligomeric forms (proanthocyanidins) have been reported to exhibit several beneficial health effects by acting as antioxidant, anticarcinogen, cardioprotective, antimicrobial, antiviral, and neuroprotective agents (for a review, see Ref. 13). Specifically, grape and wine proanthocyanidins have a cardioprotective effect through increasing plasma high density lipoprotein cholesterol, decreasing low density lipoprotein-derived atherosclerotic foam cell lesions, attenuating oxidant formation by quenching harmful radicals, increasing endothelium-dependent vasorelaxation, etc. (13). In this context, our group has been working for years on the effect of a grape seed proanthocyanidin extract (GSPE) (containing monomers and oligomers of flavan-3-ols) in relation to metabolic syndrome. In previous works, we have found that GSPE prevents oxidative injury (14), has an insulinomimetic effect on adipocytes and adipose tissue (15), modulates glucose homeostasis (16), decreases plasma levels of triglycerides (TGs) and apolipoprotein B in normolipidemic rats (17), and acts as an in vitro (18, 19) and in vivo (20) anti-inflammatory. We have also shown that GSPE decreases postprandial plasma TG and apolipoprotein B in mice through a hepatic induction of a farnesoid X receptor (FXR) and the small heterodimer partner (SHP) that in turn down-regulates SREBP1c and other lipogenic genes in the liver (21, 22). Furthermore, we have demonstrated that the molecules responsible for the reduced TG synthesis in HepG2 cells treated with GSPE are the sum of a proanthocyanidins trimer and a dimer gallate because they reproduce the GSPE effect (23).The effect of GSPE on metabolic syndrome has been studied in our laboratory by feeding rats a “cafeteria diet.” This diet is an experimental model of a western high sugar and high fat diet extensively used to produce obesity in rats because its palatability induces the animals to increase their energy intake (24). In a recent study conducted by our group (25) as well as this study, the rats were fed a high fat diet (HFD) (cafeteria diet) for 13 weeks, and one group of the animals was treated with a daily dose of GSPE (25 mg/kg of body weight) for the last 10 days (HFD + GSPE). In that study, HFD was shown to cause the animals to be overweight and to suffer from fatty liver, dyslipidemia, and hepatic overexpression of key genes involved in lipogenesis and VLDL assembly, whereas GSPE treatment corrected dyslipidemia and down-regulated some of the genes up-regulated by HFD (25).To better investigate the mechanism behind the changes observed in HFD- and HFD + GSPE-fed rats, we analyzed protein expression in the liver. Because GSPE treatment and obesity have multiple effects, a proteome-wide approach is needed to map proteins from different pathways. Proteomics studies related to obesity, metabolic syndrome, fatty liver, or insulin resistance have previously been performed on the liver (26–32). Two such studies looked into the effects of flavonoids in mouse livers (33, 34), but to our knowledge, this is the first hepatic proteome analysis of the effect of flavonoids in rats suffering from metabolic syndrome. To improve the proteome coverage of the complex liver samples, we performed a proteome fractionation according to protein solubility using a two-phase detergent protocol (35). This strategy was advantageous because it captured membrane proteins that otherwise would have been difficult to detect. The resulting soluble and membrane protein fractions were digested, iTRAQ-labeled, fractionated according to isoelectric point, and analyzed by nano-LC-MS/MS. The proteomics study presented here reports a differential expression due to HFD or HFD + GSPE for approximately 140 proteins, indicating that both conditions were potent modifiers of the liver proteome. We have focused on the sugar and lipid metabolism data, which confirmed the repression of hepatic lipogenesis in HFD + GSPE rats. Additionally, new proteins have been revealed as putative GSPE targets.