A Draft of the Human Septin Interactome

Background: Septins belong to the GTPase superclass of proteins and have been functionally implicated in cytokinesis and the maintenance of cellular morphology. They are found in all eukaryotes, except in plants. In mammals, 14 septins have been described that can be divided into four groups. It has been shown that mammalian septins can engage in homo- and heterooligomeric assemblies, in the form of filaments, which have as a basic unit a hetero-trimeric core. In addition, it has been speculated that the septin filaments may serve as scaffolds for the recruitment of additional proteins. Methodology/Principal Findings: Here, we performed yeast two-hybrid screens with human septins 1-10, which include representatives of all four septin groups. Among the interactors detected, we found predominantly other septins, confirming the tendency of septins to engage in the formation of homo- and heteropolymeric filaments. Conclusions/Significance: If we take as reference the reported arrangement of the septins 2, 6 and 7 within the heterofilament, (7-6-2-2-6-7), we note that the majority of the observed interactions respect the ""group rule"", i.e. members of the same group (e. g. 6, 8, 10 and 11) can replace each other in the specific position along the heterofilament. Septins of the SEPT6 group preferentially interacted with septins of the SEPT2 group (p<0.001), SEPT3 group (p<0.001) and SEPT7 group (p<0.001). SEPT2 type septins preferentially interacted with septins of the SEPT6 group (p<0.001) aside from being the only septin group which interacted with members of its own group. Finally, septins of the SEPT3 group interacted preferentially with septins of the SEPT7 group (p<0.001). Furthermore, we found non-septin interactors which can be functionally attributed to a variety of different cellular activities, including: ubiquitin/sumoylation cycles, microtubular transport and motor activities, cell division and the cell cycle, cell motility, protein phosphorylation/signaling, endocytosis, and apoptosis.

Gene Expression Complex Networks: Synthesis, Identification, and Analysis

Thanks to recent advances in molecular biology, allied to an ever increasing amount of experimental data, the functional state of thousands of genes can now be extracted simultaneously by using methods such as cDNA microarrays and RNA-Seq. Particularly important related investigations are the modeling and identification of gene regulatory networks from expression data sets. Such a knowledge is fundamental for many applications, such as disease treatment, therapeutic intervention strategies and drugs design, as well as for planning high-throughput new experiments. Methods have been developed for gene networks modeling and identification from expression profiles. However, an important open problem regards how to validate such approaches and its results. This work presents an objective approach for validation of gene network modeling and identification which comprises the following three main aspects: (1) Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data; (2) a computational method for gene network identification from the simulated data, which is founded on a feature selection approach where a target gene is fixed and the expression profile is observed for all other genes in order to identify a relevant subset of predictors; and (3) validation of the identified AGN-based network through comparison with the original network. The proposed framework allows several types of AGNs to be generated and used in order to simulate temporal expression data. The results of the network identification method can then be compared to the original network in order to estimate its properties and accuracy. Some of the most important theoretical models of complex networks have been assessed: the uniformly-random Erdos-Renyi (ER), the small-world Watts-Strogatz (WS), the scale-free Barabasi-Albert (BA), and geographical networks (GG). The experimental results indicate that the inference method was sensitive to average degree k variation, decreasing its network recovery rate with the increase of k. The signal size was important for the inference method to get better accuracy in the network identification rate, presenting very good results with small expression profiles. However, the adopted inference method was not sensible to recognize distinct structures of interaction among genes, presenting a similar behavior when applied to different network topologies. In summary, the proposed framework, though simple, was adequate for the validation of the inferred networks by identifying some properties of the evaluated method, which can be extended to other inference methods.

Environmental stresses inhibit splicing in the aquatic fungus Blastocladiella emersonii

Background: Exposure of cells to environmental stress conditions can lead to the interruption of several intracellular processes, in particular those performed by macromolecular complexes such as the spliceosome. Results: During nucleotide sequencing of cDNA libraries constructed using RNA isolated from B. emersonii cells submitted to heat shock and cadmium stress, a large number of ESTs with retained introns was observed. Among the 6,350 ESTs obtained through sequencing of stress cDNA libraries, 181 ESTs presented putative introns (2.9%), while sequencing of cDNA libraries from unstressed B. emersonii cells revealed only 0.2% of ESTs containing introns. These data indicate an enrichment of ESTs with introns in B. emersonii stress cDNA libraries. Among the 85 genes corresponding to the ESTs that retained introns, 19 showed more than one intron and three showed three introns, with intron length ranging from 55 to 333 nucleotides. Canonical splicing junctions were observed in most of these introns, junction sequences being very similar to those found in introns from genes previously characterized in B. emersonii, suggesting that inhibition of splicing during stress is apparently a random process. Confirming our observations, analyses of gpx3 and hsp70 mRNAs by Northern blot and S1 protection assays revealed a strong inhibition of intron splicing in cells submitted to cadmium stress. Conclusion: In conclusion, data indicate that environmental stresses, particularly cadmium treatment, inhibit intron processing in B. emersonii, revealing a new adaptive response to cellular exposure to this heavy metal.

A study of cell disruption of Candida mogii by glass bead mill for the recovery of xylose reductase

The release of xylose reductase (XR) from Candida mogii by cell disruption in a glass beads mill was studied using an experimental design. Statistical analysis of the results indicated that XR volumetric activity increases by using lower glass beads diameter and cell concentration, and by increasing the number of agitation pulses. Based on results attained in experimental design, assays were carried out aiming at the maximization of XR release. Under optimized conditions (300 mu m glass beads, 45 g/l of cell concentration and 50 pulses), the XR volumetric activity reach 0.683 U/ml. Disruption with glass beads showed to be the most efficient method for XR release when compared to sonication process. The highest specific activity (0.175 U/mg of protein) was found in extracts obtained by suspension freezing and thawing, which suggests that this method can be used as a selective process of cell disruption for XR release. (c) 2008 Elsevier B.V. All rights reserved.

Fermentation of cellulosic hydrolysates obtained by enzymatic saccharification of sugarcane bagasse pretreated by hydrothermal processing

This work aims to evaluate the fermentability of cellulosic hydrolysates obtained by enzymatic saccharification of sugarcane bagasse pretreated by hydrothermal processing using Candida guilliermondii FTI 20037 yeast. The inoculum was obtained from yeast culture in a medium containing glucose as a carbon source supplemented with rice bran extract, CaCl(2)center dot 2H(2)O and (NH(4))(2)SO(4) in 50 mL Erlenmeyer flasks, containing 20 mL of medium, initial 5.5 pH under agitation of an orbital shaker (200 rpm) at 30A degrees C for 24 h. The cellulosic hydrolysates, prior to being used as a fermentation medium, were autoclaved for 15 min at 0.5 atm and supplemented with the same nutrients employed for the inoculum, except the glucose, using the same conditions for the inoculum, but with a period of 48 h. Preliminary results showed the highest consumption of glucose (97%) for all the hydrolysates, at 28 h of fermentation. The highest concentration of ethanol (20.5 g/L) was found in the procedure of sugarcane bagasse pretreated by hydrothermal processing (195A degrees C/10 min in 20 L reactor) and delignificated with NaOH 1.0% (w/v), 100A degrees C, 1 h in 500 mL stainless steel ampoules immersed in an oil bath.

Effects of medium supplementation and pH control on lactic acid production from brewer`s spent grain

A cellulose pulp obtained by chemical pre-treatment of brewer`s spent grain was saccharified by a commercial cellulase preparation and the produced hydrolysate (50 g/l glucose) was fermented to lactic acid by Lactobacillus delbrueckii. The effects of pH control and nutrient supplementation of the hydrolysate on fermentation performance were investigated. Addition of 5g/l yeast extract enhanced the lactic acid volumetric productivity that attained 0.53 g/l h, value 18% higher than that obtained from non-supplemented hydrolysate. Addition of the MRS broth medium components (except the carbon source) was still better, providing a productivity of 0.79 g/l h. In all the cases, the lactic acid yield factor was of 0.7 g/g glucose consumed, but the fermentations stopped after 24 h due to the pH drop from 6.0 to 4.2, resulting in large amounts of residual glucose (38-41 g/l). Fermentation runs pH-controlled at 6.0 gave better results than those where the initial pH was not further controlled. The best result, 35.54 g/l lactic acid (0.99 g/g glucose consumed) was obtained during the pH-controlled fermentation of hydrolysate medium supplemented with MRS components. The volumetric productivity at the end of this fermentation was 0.59 g/l h, with a maximum of 0.82 g/l h during the first 12 h. (c) 2008 Elsevier B.V. All rights reserved.

Evaluation of hexose and pentose in pre-cultivation of Candida guilliermondii on the key enzymes for xylitol production in sugarcane hemicellulosic hydrolysate

The evaluation of hexose and pentose in pre-cultivation of Candida guilliermondii FTI 20037 yeast on xylose reductase (XR) and xylitol dehydrogenase (XDH) enzymes activities was performed during fermentation in sugarcane bagasse hemicellulosic hydrolysate. The xylitol production was evaluated by using cells previously growth in 30.0 gl(-1) xylose, 30.0 gl(-1) glucose and in both sugars mixture (30.0 gl(-1) xylose and 2.0 gl(-1) glucose). The vacuum evaporated hydrolysate (80 gl(-1)) was detoxificated by ion exchange resin (A-860S; A500PS and C-150-Purolite(A (R))). The total phenolic compounds and acetic acid were 93.0 and 64.9%, respectively, removed by the resin hydrolysate treatment. All experiments were carried out in Erlenmeyer flasks at 200 rpm, 30A degrees C. The maximum XR (0.618 Umg (Prot) (-1) ) and XDH (0.783 Umg (Prot) (-1) ) enzymes activities was obtained using inoculum previously growth in both sugars mixture. The highest cell concentration (10.6 gl(-1)) was obtained with inoculum pre-cultivated in the glucose. However, the xylitol yield and xylitol volumetric productivity were favored using the xylose as carbon source. In this case, it was observed maximum xylose (81%) and acetic acid (100%) consumption. It is very important to point out that maximum enzymatic activities were obtained when the mixture of sugars was used as carbon source of inoculum, while the highest fermentative parameters were obtained when xylose was used.

Establishment of the optimum initial xylose concentration and nutritional supplementation of brewer`s spent grain hydrolysate for xylitol production by Candida guilliermondii

The effects of initial xylose concentration and nutritional supplementation of brewer`s spent grain hydrolysate on xylitol production by Candida guilliermondii were evaluated using experimental design methodology. The hydrolysate containing 55, 75 or 95 g/l xylose, supplemented or not with nutrients (calcium chloride, ammonium sulfate and rice bran extract), was used as fermentation medium. The increase in xylitol yield and productivity was related to the increase of initial xylose concentration, but up to a certain limit. above of which the yeast performance was not improved. The hydrolysate supplementation with nutrients did not interfere with xylose-to-xylitol conversion. By using the statistic tool the best conditions for maximum xylitol production were found. which consisted in using the non-supplemented hydrolysate containing 70 g/l initial xylose concentration. Under these conditions, a xylitol yield of 0.78 g/g and productivity of 0.58 g/(l h) were achieved. (C) 2008 Elsevier Ltd. All rights reserved.

Fermentation kinetics for xylitol production by a Pichia stipitis D-Xylulokinase mutant previously grown in spent sulfite liquor

Spent sulfite pulping liquor (SSL) contains lignin, which is present as lignosulfonate, and hemicelluloses that are present as hydrolyzed carbohydrates. To reduce the biological oxygen demand of SSL associated with dissolved sugars, we studied the capacity of Pichia stipitis FPL-YS30 (xyl3 Delta) to convert these sugars into useful products. FPL-YS30 produces a negligible amount of ethanol while converting xylose into xylitol. This work describes the xylose fermentation kinetics of yeast strain P.stipitis FPL-YS30. Yeast was grown in rich medium supplemented with different carbon sources: glucose, xylose, or ammonia-base SSL. The SSL and glucose-acclimatized cells showed similar maximum specific growth rates (0.146 h(-1)). The highest xylose consumption at the beginning of the fermentation process occurred using cells precultivated in xylose, which showed relatively high specific activity of glucose-6-phosphate dehydrogenase (EC 1.1.1.49). However, the maximum specific rates of xylose consumption (0.19 g(xylose)/g(cel) h) and xylitol production (0.059 g(xylitol)/g(cel) h) were obtained with cells acclimatized in glucose, in which the ratio between xylose reductase (EC 1.1.1.21) and xylitol dehydrogenase (EC 1.1.1.9) was kept at higher level (0.82). In this case, xylitol production (31.6 g/l) was 19 and 8% higher than in SSL and xylose-acclimatized cells, respectively. Maximum glycerol (6.26 g/l) and arabitol (0.206 g/l) production were obtained using SSL and xylose-acclimatized cells, respectively. The medium composition used for the yeast precultivation directly reflected their xylose fermentation performance. The SSL could be used as a carbon source for cell production. However, the inoculum condition to obtain a high cell concentration in SSL needs to be optimized.

High gravity batch and continuous processes for beer production: Evaluation of fermentation performance and beer quality

This study deals with two innovative brewing processes, high gravity batch and complete continuous beer fermentation systems. The results show a significant influence of the variables such as concentration and temperature on the yield factor of the substrate into ethanol and consequently on the productivity of the high gravity batch process. The technological feasibility of continuous production of beer based on yeast immobilization on cheap alternative carriers was also demonstrated. The influence of process parameters on fermentation performance and quality of the obtained beers was studied by sensorial analysis. No significant difference in the degree of acceptance between the obtained products and some traditional market brands was found. (c) 2008 Institute of Chemistry, Slovak Academy of Sciences.

Inhibitory action of toxic compounds present in lignocellulosic hydrolysates on xylose to xylitol bioconversion by Candida guilliermondii

The inhibitory action of acetic acid, ferulic acid, and syringaldehyde on metabolism of Candida guilliermondii yeast during xylose to xylitol bioconversion was evaluated. Assays were performed in buffered and nonbuffered semidefined medium containing xylose as main sugar (80.0 g/l), supplemented or not with acetic acid (0.8-2.6 g/l), ferulic acid (0.2-0.6 g/l), and/or syringaldehyde (0.3-0.8 g/l), according to a 2(3) full factorial design. Since only individual effects of the variables were observed, assays were performed in a next step in semidefined medium containing different concentrations of each toxic compound individually, for better understanding of their maximum concentration that can be present in the fermentation medium without affecting yeast metabolism. It was concluded that acetic acid, ferulic acid, and syringaldehyde are compounds that may affect Candida guilliermondii metabolism (mainly cell growth) during bioconversion of xylose to xylitol. Such results are of interest and reveal that complete removal of toxic compounds from the fermentation medium is not necessary to obtain efficient conversion of xylose to xylitol by Candida guilliermondii. Fermentation in buffered medium was also considered as an alternative to overcome the inhibition caused by these toxic compounds, mainly by acetic acid.

Characterization of different fruit wines made from cacao, cupuassu, gabiroba, jaboticaba and umbu

The main aim of this work was to produce fruit wines from pulp of gabiroba, cacao, umbu, cupuassu and jaboticaba and characterize them using gas chromatography-mass spectrometry for determination of minor compounds and gas chromatography-flame ionization detection for major compounds. Ninety-nine compounds (C(6) compounds, alcohols, monoterpenic alcohols, monoterpenic oxides, ethyl esters, acetates, volatile phenols, acids, carbonyl compounds, sulfur compounds and sugars) were identified in fruit wines. The typical composition for each fruit wine was evidenced by principal component analysis and Tukey test. The yeast UFLA CA 1162 was efficient in the fermentation of the fruit pulp used in this work. The identification and quantification of the compounds allowed a good characterization of the fruit wines. With our results, we conclude that the use of tropical fruits in the production of fruit wines is a viable alternative that allows the use of harvest surpluses and other underused fruits, resulting in the introduction of new products into the market. (C) 2010 Elsevier Ltd. All rights reserved.

The Influence of Initial Xylose Concentration, Agitation, and Aeration on Ethanol Production by Pichia stipitis from Rice Straw Hemicellulosic Hydrolysate

Rice straw hemicellulosic hydrolysate was used as fermentation medium for ethanol production by Pichia stipitis NRRL Y-7124. Shaking bath experiments were initially performed aiming to establish the best initial xylose concentration to be used in this bioconversion process. In the sequence, assays were carried out under different agitation (100 to 200 rpm) and aeration ((V) under bar (flask)/V(medium) ratio varying from 2.5 to 5.0) conditions, and the influence of these variables on the fermentative parameters values (ethanol yield factor, Y(P/S); cell yield factor, Y(X/S); and ethanol volumetric productivity, Q(P)) was investigated through a 2(2) full-factorial design. Initial xylose concentration of about 50 g/l was the most suitable for the development of this process, since the yeast was able to convert substrate in product with high efficiency. The factorial design assays showed a strong influence of both process variables in all the evaluated responses. The agitation and aeration increase caused a deviation in the yeast metabolism from ethanol to biomass production. The best results (Y(P/S) = 0.37 g/g and Q(P) = 0.39 g/l. h) were found when the lowest aeration (2.5 V(flask)/V(medium) ratio) and highest agitation (200 rpm) levels were employed. Under this condition, a process efficiency of 72.5% was achieved. These results demonstrated that the establishment of adequate conditions of aeration is of great relevance to improve the ethanol production from xylose by Pichia stipitis, using rice straw hemicellulosic hydrolysate as fermentation medium.

Fermentative behavior of Saccharomyces strains during microvinification of raspberry juice (Rubus idaeus L.)

Sixteen different strains of Saccharomyces cerevisiae and Saccharomyces bayanus were evaluated in the production of raspberry fruit wine. Raspberry juice sugar concentrations were adjusted to 16 degrees Brix with a sucrose solution, and batch fermentations were performed at 22 degrees C. Various kinetic parameters, such as the conversion factors of the substrates into ethanol (Y(p/s)), biomass (Y(x/s)), glycerol (Y(g/s)) and acetic acid (Y(ac/s)), the volumetric productivity of ethanol (Q(p)), the biomass productivity (P(x)), and the fermentation efficiency (E(f)) were calculated. Volatile compounds (alcohols, ethyl esters, acetates of higher alcohols and volatile fatty acids) were determined by gas chromatography (GC-FID). The highest values for the E(f), Y(p/s), Y(g/s), and Y(x/s) parameters were obtained when strains commonly used in the fuel ethanol industry (S. cerevisiae PE-2, BG, SA, CAT-1, and VR-1) were used to ferment raspberry juice. S. cerevisiae strain UFLA FW 15, isolated from fruit, displayed similar results. Twenty-one volatile compounds were identified in raspberry wines. The highest concentrations of total volatile compounds were found in wines produced with S. cerevisiae strains UFLA FW 15 (87,435 mu g/L), CAT-1 (80,317.01 mu g/L), VR-1 (67,573.99 mu g/L) and S. bayanus CBS 1505 (71,660.32 mu g/L). The highest concentrations of ethyl esters were 454.33 mu g/L, 440.33 mu g/L and 438 mu g/L for S. cerevisiae strains UFLA FW 15, VR-1 and BG, respectively. Similar to concentrations of ethyl esters, the highest concentrations of acetates (1927.67 mu g/L) and higher alcohols (83,996.33 mu g/L) were produced in raspberry wine from S. cerevisiae UFLA FW 15. The maximum concentration of volatile fatty acids was found in raspberry wine produced by S. cerevisiae strain VR-1. We conclude that S. cerevisiae strain UFLA FW 15 fermented raspberry juice and produced a fruit wine with low concentrations of acids and high concentrations of acetates, higher alcohols and ethyl esters. (c) 2010 Elsevier B.V. All rights reserved.

Ethanol Production from Sugarcane Bagasse Hydrolysate Using Pichia stipitis

The objective of this study was to evaluate the ethanol production from the sugars contained in the sugarcane bagasse hemicellulosic hydrolysate with the yeast Pichia stipitis DSM 3651. The fermentations were carried out in 250-mL Erlenmeyers with 100 mL of medium incubated at 200 rpm and 30 A degrees C for 120 h. The medium was composed by raw (non-detoxified) hydrolysate or by hydrolysates detoxified by pH alteration followed by active charcoal adsorption or by adsorption into ion-exchange resins, all of them supplemented with yeast extract (3 g/L), malt extract (3 g/L), and peptone (5 g/L). The initial concentration of cells was 3 g/L. According to the results, the detoxification procedures removed inhibitory compounds from the hemicellulosic hydrolysate and, thus, improved the bioconversion of the sugars into ethanol. The fermentation using the non-detoxified hydrolysate led to 4.9 g/L ethanol in 120 h, with a yield of 0.20 g/g and a productivity of 0.04 g L(-1) h(-1). The detoxification by pH alteration and active charcoal adsorption led to 6.1 g/L ethanol in 48 h, with a yield of 0.30 g/g and a productivity of 0.13 g L(-1) h(-1). The detoxification by adsorption into ion-exchange resins, in turn, provided 7.5 g/L ethanol in 48 h, with a yield of 0.30 g/g and a productivity of 0.16 g L(-1) h(-1).