Evaluation of cotton stalk hydrolysate for xylitol production

Cotton stalk is a widely distributed and abundant lignocellulosic waste found in Turkey. Because of its rich xylose content, it can be a promising source for the production of xylitol. Xylitol can be produced by chemical or biotechnological methods. Because the biotechnological method is a simple process with great substrate specificity and low energy requirements, it is more of an economic alternative for the xylitol production. This study aimed to use cotton stalk for the production of xylitol with Candida tropicalis Kuen 1022. For this purpose, the combined effects of different oxygen concentration, inoculum level and substrate concentration were investigated to obtain high xylitol yield and volumetric xylitol production rate. Candida tropicalis Kuen 1022 afforded different concentrations of xylitol depending on xylose concentration, inoculum level, and oxygen concentration. The optimum xylose, yeast concentration, and airflow rate for cotton stalk hydrolysate were found as 10.41 g L^?1, 0.99 g L^?1, and 1.02 vvm, respectively, and under these conditions, xylitol yield and volumetric xylitol production rate were obtained as 36% and 0.06 g L^?1 hr^?1, respectively. The results of this study show that cotton stalk can serve as a potential renewable source for the production of xylitol.     

Ex vivo protective effects of nicotinamide and 3‐aminobenzamide on rat synaptosomes treated with Aβ(1–42)

Alzheimer's disease (AD) is the most common form of dementia and is characterized by the presence of senile plaques and neurofibrillary tangles, along with synaptic loss. The underlying mechanisms of AD are not clarified yet, but oxidative stress and mitochondrial dysfunction are important factors. Overactivation of poly(adenosine diphosphate ribose) polymerase‐1 (PARP‐1) enzyme has been known to cause neuroinflammation and cell death in neurodegenerative processes. The aim of the present study was to investigate the protective effects of the PARP‐1 inhibitors, 3‐aminobenzamide (3‐AB) and nicotinamide (NA), against amyloid β peptide (1–42) (Aβ(1–42))‐induced oxidative damage and mitochondrial reduction capacity on isolated synaptosomes. Rats were injected intraperitoneally with 3‐AB (30–100 mg kg^?1), NA (100–500 mg kg^?1) or with saline for 7 days. Synaptosomes were incubated with 10–30 μM Aβ(1–42) or saline for 6 h at 37 °C. Ex vivo Aβ(1–42) treatment significantly induced oxidative stress and mitochondrial dysfunction in synaptosomes of the saline group, while synaptosomes of 3‐AB and NA groups showed significant decreases in lipid peroxidation, reactive oxygen species production and protein oxidation. Moreover, both NA and 3‐AB were able to improve the mitochondrial reduction capacity against Aβ(1–42). These data suggest that NA and 3‐AB may have protective effects in neurodegenerative processes because of the reduced levels of oxidative stress and the improvement of mitochondrial function. Copyright © 2014 John Wiley & Sons, Ltd.     

Synthesis and evaluation of stability of m3G-CAP analogues in serum-supplemented medium and cytosolic extract

Increased efficiency in splice-correction (splice-switching) has been shown by use of a synthetic RNA 5′-end nuclear localization signal composed of an m₃G-CAP. Use of the m₃G-CAP as an NLS signal for therapeutic compounds in vivo is likely to require additional stability towards enzymatic degradation. For this reason introduction of stabilizing modifications into the triphosphate bridge may be beneficial. Here we report on synthesis of three m₃G-CAP derivatives with a ‘native’ (m₃GpppA_OMe) as well as with a methylenephosphonate stabilized triphosphate bridge (m₃GpCH₂ppA_OMe, m₃GppCH₂pA_OMe) and the investigation of the enzymatic stability of these compounds in 10% (v/v) fetal bovine serum (FBS) and cytosolic extract from HeLa cells, thus mimicking in vivo conditions. Our results indicate that introduction of methylene group between the β and γ phosphates in m₃GpCH₂ppA_OMe improves to some extent stability of this analogue in 10% serum but does not prolong life of this compound in the cytosolic extract. In contrast the stabilization introduced between α and β phosphates in m₃GppCH₂pA_OMe offers threefold longer life in 10% serum and almost complete protection in cytosolic extract.     

Bone metabolism in ovariectomized rats with induced hyperthyroidism: the effect of estrogen replacement

We aimed to investigate whether or not the estrogen is playing any role in the effect of thyroid hormones on bone metabolism. The rats were divided into five groups. In the first group L-thyroxine-induced hyperthyroid rats were ovariectomized (OVX) while the OVX rats were administered L-thyroxine in the second group. 17beta-Estradiol (E2) was replaced in OVX rats in Group III. L-thyroxine and E2 were simultaneously administered to OVX rats in Group IV. The fifth group received sham operation. Blood samples taken from the tail vein of rats were analyzed for plasma T3, T4, TSH and serum interleukin (IL)-1beta, IL-6, tumor necrosis factor (TNF)alpha, calcium (Ca), phosphorous (P), parathyroid [corrected] hormone (PTH), alkaline phosphatase (t-ALP), bone-specific alkaline phosphatase (b-ALP) and E2. The levels of cytokines, t-ALP and b-ALP increased but PTH decreased, while there was no change in Ca and P levels in L-thyroxine-administrated rats. However, the levels of cytokines, Ca, P, PTH, t-ALP and b-ALP did not change in L-thyroxine-administered OVX rats. In OVX rats, the cytokines, t-ALP and b-ALP increased while Ca, P remained the same, but PTH decreased. L-thyroxine administration to OVX rats did not change the cytokines, Ca, P, PTH, t-ALP and b-ALP levels. The replacement of E2 in OVX rats decreased the cytokines, t-ALP and b-ALP values, increased PTH levels while there was no change in Ca and P. L-thyroxine and E2 administration to OVX rats increased the cytokines, t-ALP and b-ALP levels and decreased PTH, but Ca and P remained the same. In sham-operated rats, there was no change in all parameters compared to initial values. This study suggests that estrogen may play a role in the effects of thyroid hormones on bone metabolism.     

Fast pyrolysis of soybean cake: product yields and compositions

This study was an investigation of the role of important parameters influencing pyrolysis yields from soybean cake. Experiments were carried out at temperatures ranging from 400 to 700 degrees C, for various nitrogen flow rates, heating rates and particle sizes. The maximum liquid yield was 42.83% at a pyrolysis temperature of 550 degrees C with a sweeping gas rate of 200 cm3 min(-1) and heating rate of 700 degrees C min(-1) for a soybean cake sample having 0.425 < D(p) < 0.85 mm particle size. The various characteristics of liquid product were identified. Thus, the aliphatic sub-fraction of the bio-oil was analysed by GC-MS and further structural analyses of bio-oil and aromatic and polar sub-fractions were conducted using FT-IR and 1H-NMR. The H/C ratios and the structural analysis of the fractions obtained from the biocrudes showed that the fractions were quite similar to currently utilised transport fuels.     

Endosomal Deubiquitinating Enzymes Control Ubiquitination and Down-regulation of Protease-activated Receptor 2

The E3 ubiquitin ligase c-Cbl ubiquitinates the G protein-coupled receptor protease-activated receptor 2 (PAR₂), which is required for postendocytic sorting of activated receptors to lysosomes, where degradation terminates signaling. The mechanisms of PAR₂ deubiquitination and its importance in trafficking and signaling of endocytosed PAR₂ are unknown. We report that receptor deubiquitination occurs between early endosomes and lysosomes and involves the endosomal deubiquitinating proteases AMSH and UBPY. Expression of the catalytically inactive mutants, AMSH(D348A) and UBPY(C786S), caused an increase in PAR₂ ubiquitination and trapped the receptor in early endosomes, thereby preventing lysosomal trafficking and degradation. Small interfering RNA knockdown of AMSH or UBPY also impaired deubiquitination, lysosomal trafficking, and degradation of PAR₂. Trapping PAR₂ in endosomes through expression of AMSH(D348A) or UBPY(C786S) did not prolong the association of PAR₂ with β-arrestin2 or the duration of PAR₂-induced ERK2 activation. Thus, AMSH and UBPY are essential for trafficking and down-regulation of PAR₂ but not for regulating PAR₂ dissociation from β-arrestin2 or PAR₂-mediated ERK2 activation.Ubiquitination of certain G protein-coupled receptors (GPCRs)³ is an essential signal for their postendocytic trafficking to lysosomes, which prevents uncontrolled signaling during chronic stimulation. Agonists stimulate ubiquitination of the β₂-adrenergic receptor (β₂AR), chemokine (CXC motif) receptor 4, and protease-activated receptor 2 (PAR₂), and the E3 ubiquitin ligases that mediate ubiquitination of these GPCRs and associated proteins, such as β-arrestins, have been identified (1–3). Although ubiquitination of these receptors is not required for endocytosis, ubiquitin-resistant mutant receptors show diminished postendocytic sorting to lysosomes and impaired down-regulation. However, despite of the reversible nature of this post-translational modification, little is known about the role of deubiquitinating proteases (DUBs) in the postendocytic trafficking and signaling of GPCRs.Our understanding of the role of DUBs in postendocytic receptor trafficking mostly derives from studies of receptor tyrosine kinases, such as epidermal growth factor receptor (EGFR). Two endosomal DUBs, AMSH (associated molecule with the Src homology 3 domain of STAM (signal-transducing adapter molecule)) and UBPY (ubiquitin-specific protease Y) (also known as USP8), regulate deubiquitination and postendocytic trafficking of EGFR (4). AMSH belongs to the JAMM (JAB1/MPN/Mov34) family of metalloproteases and shows specificity for Lys⁶³- over Lys⁴⁸-linked ubiquitin chains (5, 6). UBPY is a cysteine protease of the ubiquitin-specific protease (USP) family and does not discriminate between Lys⁴⁸- and Lys⁶³-linked ubiquitin (7, 8). Activated EGFR recruits the E3 ligase c-Cbl, which ubiquitinates the receptor (9). Ubiquitinated EGFR then interacts with the Hrs (hepatocyte growth factor-regulated tyrosine kinase substrate)-STAM complex in early endosomes (10). Hrs-STAM forms part of the ESCRT (endosomal sorting complex required for transport)-I, -II, -III complex that sorts ubiquitinated receptors in multivesicular bodies (MVBs) to intralumenal vesicles that eventually fuse with lysosomes, where degradation occurs (11). Before receptors are incorporated into the intralumenal vesicles, they are deubiquitinated, which serves to maintain levels of free ubiquitin (11). AMSH and UBPY interact directly with STAM through a common binding site within its Src homology 3 domain (12–14). The balance of EGFR ubiquitination by c-Cbl and deubiquitination by AMSH and UBPY controls the postendocytic trafficking and down-regulation of the EGFR. c-Cbl promotes lysosomal degradation of the EGFR (9), AMSH opposes c-Cbl action and promotes EGFR recycling (5), and UBPY is required for lysosomal sorting and degradation of EGFR (8, 15–17). The role of AMSH and UBPY in regulating deubiquitination, trafficking, and signaling of GPCRs in endosomes is largely unknown. A recent study has shown, however, that AMSH and UBPY regulate the down-regulation of the δ-opioid receptor (DOR), a GPCR that is ubiquitinated and degraded following activation (18). Expression of catalytically inactive mutants of AMSH or UBPY or knockdown of AMSH or UBPY levels using siRNA inhibits down-regulation of DOR. Interestingly, the roles of AMSH and UBPY in DOR down-regulation appear to be nonredundant, since depletion of either DUB produced comparable effects, and simultaneous depletion of both DUBs did not have additional consequences (18). Different DUBs, USP20 and -33, have been recently shown to reverse agonist-induced ubiquitination of the β₂AR (19).We examined the roles of AMSH and UBPY in the ubiquitination, postendocytic trafficking, and lysosomal degradation of PAR₂. We also determined whether AMSH and UBPY regulate PAR₂ association with β-arrestins in endosomes and control β-arrestin-mediated extracellular signal-regulated kinase (ERK) activation. PAR₂ is a receptor for multiple serine proteases that are generated during injury and inflammation (20). Activated PAR₂ promotes inflammation and pain, and PAR₂ contributes to inflammatory diseases of the airway, joints, and intestine. PAR₂ levels are elevated during inflammation, due to increased mRNA expression or perhaps decreased receptor degradation, which amplifies the proinflammatory actions of proteases (21). Given the irreversible nature of proteolytic activation, and since the internalized receptor probably signals by the β-arrestin-dependent recruitment of mitogen-activated protein kinase (MAPK) to endosomes (22), termination of PAR₂ signaling requires receptor degradation in lysosomes, which in turn is ubiquitination-dependent (3, 23). It is therefore important to understand mechanisms of PAR₂ ubiquitination and lysosomal targeting and also how these processes can be reversed. We have reported that activated PAR₂ is monoubiquitinated at multiple sites by the E3 ligase c-Cbl and targeted to lysosomes by an Hrs-dependent pathway (3, 24). Nothing is known about the mechanism and function of PAR₂ deubiquitination. Herein, we examined the role of AMSH and UBPY in regulating the deubiquitination, lysosomal trafficking, and degradation of PAR₂, the interaction of PAR₂ with β-arrestin2, and β-arrestin-mediated ERK2 activation. We demonstrate that endosomal DUBs are key regulators of GPCR down-regulation.     

An Enhancing Effect of Exogenous Mannitol on the Antioxidant Enzyme Activities in Roots of Wheat Under Salt Stress

The role of mannitol as an osmoprotectant, a radical scavenger, a stabilizer of protein and membrane structure, and protector of photosynthesis under abiotic stress has already been well described. In this article we show that mannitol applied exogenously to salt-stressed wheat, which normally cannot synthesize mannitol, improved their salt tolerance by enhancing activities of antioxidant enzymes. Wheat seedlings (3 days old) grown in 100 mM mannitol (corresponding to −0.224 MPa) for 24 h were subjected to 100 mM NaCl treatment for 5 days. The effect of exogenously applied mannitol on the salt tolerance of plants in view of growth, lipid peroxidation levels, and activities of antioxidant enzymes in the roots of salt-sensitive wheat (Triticum aestivum L. cv. Kızıltan-91) plants with or without mannitol was studied. Although root growth decreased under salt stress, this effect could be alleviated by mannitol pretreatment. Peroxidase (POX) and ascorbate peroxidase (APX) activities increased, whereas superoxide dismutase (SOD), catalase (CAT), and glutathione reductase (GR) activities decreased in Kızıltan-91 under salt stress. However, activities of antioxidant enzymes such as SOD, POX, CAT, APX, and GR increased with mannitol pretreatment under salt stress. Although root tissue extracts of salt-stressed wheat plants exhibited only nine different SOD isozyme bands of which two were identified as Cu/Zn-SOD and Mn-SOD, mannitol treatment caused the appearance of 11 different SOD activity bands. On the other hand, five different POX isozyme bands were determined in all treatments. Enhanced peroxidation of lipid membranes under salt stress conditions was reduced by pretreatment with mannitol. We suggest that exogenous application of mannitol could alleviate salt-induced oxidative damage by enhancing antioxidant enzyme activities in the roots of salt-sensitive Kızıltan-91.     

Immobilization of α-galactosidase on galactose-containing polymeric beads

Industrial application of α-galactosidase requires efficient methods to immobilize the enzyme, yielding a biocatalyst with high activity and stability compared to free enzyme. An α-galactosidase from tomato fruit was immobilized on galactose-containing polymeric beads. The immobilized enzyme exhibited an activity of 0.62 U/g of support and activity yield of 46%. The optimum pH and temperature for the activity of both free and immobilized enzymes were found as pH 4.0 and 37 °C, respectively. Immobilized α-galactosidase was more stable than free enzyme in the range of pH 4.0–6.0 and more than 85% of the initial activity was recovered. The decrease in reaction rate of the immobilized enzyme at temperatures above 37 °C was much slower than that of the free counterpart. The immobilized enzyme shows 53% activity at 60 °C while free enzyme decreases 33% at the same temperature. The immobilized enzyme retained 50% of its initial activity after 17 cycles of reuse at 37 °C. Under same storage conditions, the free enzyme lost about 71% of its initial activity over a period of 7 months, whereas the immobilized enzyme lost about only 47% of its initial activity over the same period. Operational stability of the immobilized enzyme was also studied and the operational half-life (t_1/2 was determined as 6.72 h for p-nitrophenyl α-d-galactopyranoside (PNPG) as substrate. The kinetic parameters were determined by using PNPG as substrate. The K_m and V_max values were measured as 1.07 mM and 0.01 U/mg for free enzyme and 0.89 mM and 0.1 U/mg for immobilized enzyme, respectively. The synthesis of the galactose-containing polymeric beads and the enzyme immobilization procedure are very simple and also easy to carry out.     

Use of linear mixed models for genetic evaluation of gestation length and birth weight allowing for heavy-tailed residual effects

Background

The distribution of residual effects in linear mixed models in animal breeding applications is typically assumed normal, which makes inferences vulnerable to outlier observations. In order to mute the impact of outliers, one option is to fit models with residuals having a heavy-tailed distribution. Here, a Student''s-t model was considered for the distribution of the residuals with the degrees of freedom treated as unknown. Bayesian inference was used to investigate a bivariate Student''s-t (BSt) model using Markov chain Monte Carlo methods in a simulation study and analysing field data for gestation length and birth weight permitted to study the practical implications of fitting heavy-tailed distributions for residuals in linear mixed models.

Methods

In the simulation study, bivariate residuals were generated using Student''s-t distribution with 4 or 12 degrees of freedom, or a normal distribution. Sire models with bivariate Student''s-t or normal residuals were fitted to each simulated dataset using a hierarchical Bayesian approach. For the field data, consisting of gestation length and birth weight records on 7,883 Italian Piemontese cattle, a sire-maternal grandsire model including fixed effects of sex-age of dam and uncorrelated random herd-year-season effects were fitted using a hierarchical Bayesian approach. Residuals were defined to follow bivariate normal or Student''s-t distributions with unknown degrees of freedom.

Results

Posterior mean estimates of degrees of freedom parameters seemed to be accurate and unbiased in the simulation study. Estimates of sire and herd variances were similar, if not identical, across fitted models. In the field data, there was strong support based on predictive log-likelihood values for the Student''s-t error model. Most of the posterior density for degrees of freedom was below 4. Posterior means of direct and maternal heritabilities for birth weight were smaller in the Student''s-t model than those in the normal model. Re-rankings of sires were observed between heavy-tailed and normal models.

Conclusions

Reliable estimates of degrees of freedom were obtained in all simulated heavy-tailed and normal datasets. The predictive log-likelihood was able to distinguish the correct model among the models fitted to heavy-tailed datasets. There was no disadvantage of fitting a heavy-tailed model when the true model was normal. Predictive log-likelihood values indicated that heavy-tailed models with low degrees of freedom values fitted gestation length and birth weight data better than a model with normally distributed residuals.Heavy-tailed and normal models resulted in different estimates of direct and maternal heritabilities, and different sire rankings. Heavy-tailed models may be more appropriate for reliable estimation of genetic parameters from field data.