A convenient and efficient protocol for isolating high-quality RNA from latex of Hevea brasiliensis (para rubber tree)

Isolating high-quality RNA from latex of H. brasiliensis is a prerequisite to elucidating the molecular mechanisms of rubber biosynthesis and its regulation. Here, an improved protocol was developed for latex collection, transportation, storage, and RNA isolation. Compared with existing ones, our protocol eliminated liquid nitrogen for latex collection and subsequent low-temperature (-70 degrees C) condition for latex storage, making it more convenient and feasible when latex was collected in remote sampling sites, and latex storage and RNA isolation were conducted in poorly-equipped laboratories. Different methods (UV absorbance scans, denaturing gel electrophoresis, autoradiograph monitoring of cDNA synthesis) were used to confirm the high quality of the RNA prepared with this protocol, whose usefulness was further verified by several practical applications, including construction of one high-quality cDNA library, cloning of the full-length cDNAs of 3 novel Hevea sucrose transporter genes, and semi-quantitative RT-PCR analysis of two rubber-biosynthesis essential genes and one sucrose transporter gene.     

Effect of sucrose on dynamic mechanical characteristics of maize and potato starch films

The dynamic mechanical properties of prepared maize and potato starch films were evaluated for mixtures containing 0%, 10% and 15% (w/w) of sucrose at temperatures ranging from 40.0 to 140.0 °C. The spectra of storage modulus (G′), loss modulus (G″), and loss factor (tan δ) of starch films were acquired. Remarkable reduction in the glass transition temperature of maize and potato starch films was observed with the increasing sucrose content. The spectra of storage modulus (G′), loss modulus (G″), and loss factor (tan δ) were measured for the second and third time after two and seven days, respectively. The peaks of loss factor (tan δ) appeared at 59.81 ± 1.86 °C and 95.96 ± 1.67 °C after two-day-storage, but only one peak appeared at 85.46 ± 5.50 °C after seven days. A shifting trend from higher to lower temperature for loss factor was observed after seven days.     

Functional characterization of the sucrose isomerase responsible for trehalulose production in plant-associated Pectobacterium species

Fifty-three plant-associated microorganisms were investigated for their ability to convert sucrose to its isomers. These microorganisms included one Dickeya zeae isolate and 7 Enterobacter, 3 Pantoea, and 43 Pectobacterium species. Eleven out of the 53 strains (21%) showed the ability to transform sucrose to isomaltulose and trehalulose. Among those, Pectobacterium carotovorum KKH 3-1 showed the highest bioconversion yield (97.4%) from sucrose to its isomers. In this strain, the addition of up to 14% sucrose in the medium enhanced sucrose isomerase (SIase) production. The SIase activity at 14% sucrose (47.6 U/mg dcw) was about 3.6-fold higher than that of the negative control (13.3 U/mg dcw at 0% sucrose). The gene encoding SIase, which is comprised a 1776 bp open reading frame (ORF) encoding 591 amino acids, was cloned from P. carotovorum KKH 3-1 and expressed in Escherichia coli. The recombinant SIase (PCSI) was shown to have optimum activity at pH 6.0 and 40 °C. The reaction temperature significantly affected the ratio of sucrose isomers produced by PCSI. The amount of trehalulose increased from 47.5% to 79.1% as temperature was lowered from 50 °C to 30 °C, implying that SIase activity can be controlled by reaction temperature.     

Stability of oxidative stress biomarkers in flathead mullet,Mugil cephalus,serum during short-term storage

The production of reactive oxygen species (ROS) by aquatic organisms in response to stressful factor is a common feature in aquatic environment. Thus, the evaluation of parameters related to oxidative stress in fish, in first instance those showing the redox potential, is notable to characterize the environmental conditions.Short-term storage of samples is essential when blood must be transported from collection sites to laboratories. Therefore, excessive delays in processing might compromise the reliability of results. The aim of the present study was to assess the effect of short-term storage time at +4 °C on total oxidant status (TOS), total antioxidant capacity (TAC) and oxidative stress index (OSI) in flathead mullet (Mugil cephalus) serum. After blood collection, all sample were analyzed and the assays were repeated after 24, 48 and 72 h from sampling. results showed a significant effect of short-term storage on TOS and TAC (P ≤ 0.0001), while the statistical significance of the linear regression study for these parameters was reduced as consequence of storage. These results highlight that the activities of oxidants and antioxidants in flathead mullet serum change during short-term storage at 4 °C and should be assesses as soon as possible from collection.     

A rapid,efficient method for the mass production of pollen protoplasts from Pinus bungeana Zucc. ex Endl. and Picea wilsonii Mast.

An optimized protocol was established to isolate large numbers of mature living pollen protoplasts of Pinus bungeana Zucc. ex Endl. and Picea wilsonii Mast. Intact pollen grains of P. bungeana or pollen with short tubes were incubated with gentle agitation in a solution of 2% cellulase R-10, 1.5% macerozyme R-10, 15% sucrose, 0.01% H₃BO₃, and 0.01% CaCl₂. Intact pollen protoplasts with diameters of 40 μm were liberated, with an isolation rate of up to 70% after 6 h of enzymatic incubation. The optimal pH and temperature for the reaction were 5.8 and 24 °C, respectively, and the optimal enzymatic digestion conditions were 6 h of incubation in the above solution. The method for isolating pollen protoplasts from P. wilsonii was similar to that for P. bungeana, except that the incubation medium contained 12% rather than 15% sucrose and the optimal enzyme concentrations were 3% cellulase and 2% macerozyme. The isolated pollen protoplasts were demonstrated to be living by microscopy in a fluorochromatic reaction with fluorescein diacetate (FDA).     

Succinic acid production from sucrose and molasses by metabolically engineered E. coli using a cell surface display system

To achieve sucrose-metabolizing capability, different sucrose utilization operons have been introduced into E. coli that cannot utilize sucrose. However, these engineered strains still suffer from low growth rates and low sucrose uptake rates. In this study, cell surface display system was adopted in engineered E. coli AFP111 for succinic acid production from sucrose and molasses directly. Invertase (CscA) from E. coli W was successfully anchored to outer membrane by fusion with OmpC anchoring motif, and the displayed CscA showed high extracellular activity. Compared with the sucrose permease system, the cell surface display system consumed less ATP during sucrose metabolism. When less ATP was consumed by AFP111/pTrcC-cscA, the succinic acid productivity from sucrose was 23% higher than that by AFP111/pCR2.1-cscBKA that having the sucrose permease system. As a result, 41 g L⁻¹ and 36.3 g L⁻¹ succinic acid were produced by AFP111/pTrcC-cscA from sucrose and sugarcane molasses respectively at 34 h in 3-L fermentor during dual-phase fermentation. In addition, 79 g L⁻¹ succinic acid was accumulated with recovered AFP111/pTrcC-cscA cells at the end of dual-phase fermentation in 3-L fermentor, and the overall yield was 1.19 mol mol⁻¹ hexose.     

Diversity,complexity and transmission of double-stranded RNA elements in Chalara elegans (synanam. Thielaviopsis basicola)

Double-stranded (ds) RNA banding patterns were determined in 21 wild-type strains of the soilborne plant pathogen Chalara elegans originating from different geographic regions worldwide. Five strains, each with a unique dsRNA pattern, were selected for cDNA cloning, northern blot analysis and dsRNA transmission experiments. Four strains contained multiple (up to 6) dsRNA elements (2.0 kbp to 12 kbp in size) and one strain contained a single 2.8 kbp fragment. These five strains were distinguished from one another by their unique RAPD-PCR patterns. Seven partial cDNA clones were derived from the predominant 2.8, 5.3, and 12 kbp dsRNA elements. Nucleotide sequence analysis and northern blot hybridizations revealed a high degree of genetic dissimilarity among the different molecular-size dsRNA elements, even those found within a single strain. Four clones from the 5.3 kbp dsRNA fragment showed a 23-43 % amino acid identity to either the coat protein or RNA-dependent RNA polymerase regions of viruses in the Totiviridae. One clone from the 2.8 kbp dsRNA fragment had a 55-57 % amino acid identity to the RdRp region of viruses in the Narnaviridae. Two clones from the 12 kbp dsRNA fragment showed no significant homology to any known virus group. Colonies derived from 100 single-conidia isolates of C. elegans strains with the 2.8, 5.3 and 12 kbp elements all contained the corresponding dsRNA element, indicating that dsRNA transmission through conidia was highly efficient, regardless of molecular size. However, transmission of dsRNA between the mycelium of strains of C. elegans could not be achieved in this study. Genetically unique strains carrying diverse dsRNA elements appear to have evolved within populations of C. elegans. Based on our findings, there are at least 3 groups of viruses present in C. elegans.     

Production of di-d-fructofranosyl-2,6′:2′,6-anhydride (DFA IV) by recombinant Bacillus subtilis carrying heterogenous levan fructotransferase from Arthrobacter nicotinovorans GS-9

We developed di-d-fructofranosyl-2,6′:2′,6-anhydride (DFA IV) production system with single culture of Bacillus subtilis directly from sucrose. This system can avoid the purification procedure of levan which organic solvent was used for precipitation. The levan fructotransferase (LFTase) gene was cloned from Arthrobacter nicotinovorans GS-9 (AHU1840, FERM P-15285) and expressed in levan producing B. subtilis 168. LFTase activity was detected in the culture supernatant of the transformant with maximal activity of 0.062 U/ml after 15.5 h post induction. Then sucrose was added as substrate and incubated. About 78 h after addition of sucrose, 20.5 g/l of DFA IV was produced from 139.3 g/l of sucrose consumed. The yield of DFA IV from sucrose was 14.7 wt.%.     

Evaluation and comparison of four methods of ranking horses based on reactivity

Four methods of ranking horses on reactivity were evaluated and compared: isolation from conspecifics, presentation of a static novel stimulus, traversing a novel stimulus in a runway (isolation, novel stimulus and runway tests, respectively) and assigning subjective emotionality scores. In all tests, horses’ heart rates were recorded and behaviour was videotaped. To be considered a valid test of reactivity, at least one heart rate and one behavioural measurement in the test had to change significantly between treatments (tranquilizer administation versus sham tranquilizer administration), and behavioural measures had to be displayed in at least 75% of the trials. Forty horses performed each of the three tests daily on three different days in a switchback design. Horses were assigned randomly to a daily test sequence, which was maintained throughout the study. In the runway test, no significant difference in heart rate values in tranquilized and non-tranquilized horses was found, and no behavioural attribute was displayed in more than 52% of the trials; therefore it was rejected as a valid test of reactivity. Both isolation and novel stimulus tests produced valid measurements. Mean heart rate was the most precise physiological measure for these tests, and walking and defecation frequency were the most precise behavioural measures for novel stimulus and isolation tests, respectively. Mean heart rates on the novel stimulus and isolation tests were correlated (r_s = 0.79, P < 0.01) indicating that these tests produced similar rankings based on physiological responses. However, behavioural measures ranked horses differently (r_s = 0.27, P < 0.10) on the tests. Rank correlations between mean heart rates and behavioural measures were higher in the novel stimulus (r_s = 0.66, P < 0.01) than the isolation test (r_s = 0.55, P < 0.01), indicating that the novel stimulus test ranked horses based on either physiological or behavioural responses more similarly than did the isolation test. Therefore, the novel stimulus test was considered the more accurate evaluation of reactivity. Subjective emotionality scores were correlated moderately with mean heart rates (r_s > 0.33, P < 0.01) from the novel stimulus and isolation tests and with walking scores (r_s = 0.47, P < 0.01) from the novel stimulus test. Assignment of subjective emotionality scores was not as accurate as the novel stimulus or isolation tests in ranking horses for reactivity. Using physiological data alone, combining physiological and behavioural measurements or using more than one behavioural measurement in reactivity tests may reflect the reactivity of the horse better than a single behavioural measurement.     

Complete mitochondrial genome of Coelomactra antiquata (Mollusca: Bivalvia): The first representative from the family Mactridae with novel gene order and unusual tandem repeats

The complete mitochondrial genome plays an important role in the accurate inference of phylogenetic relationships among metazoans. Mactridae, also known as trough shells or duck clams, is an important family of marine bivalve clams in the order Veneroida. Here we present the complete mitochondrial genome sequence of the Xishishe Coelomactra antiquata (Mollusca: Bivalvia), which is the first representative from the family Mactridae. The mitochondrial genome of C. antiquata is of 17,384 bp in length, and encodes 35 genes, including 12 protein-coding, 21 transfer RNA, and 2 ribosomal RNA genes. Compared with the typical gene content of animal mitochondrial genomes, atp8 and tRNAS₂ are missing. Gene order of the mitochondrial genome of C. antiquata is unique compared with others from Veneroida. In the mitochondrial genome of the C. antiquata, a total of 2189 bp of non-coding nucleotides are scattered among 26 non-coding regions. The largest non-coding region contains one section of tandem repeats (99 bp × 11), which is the second largest tandem repeats found in the mitochondrial genomes from Veneroida. The phylogenetic trees based on mitochondrial genomes support the monophyly of Veneridae and Lucinidae, and the relationship at the family level: ((Veneridae + Mactridae) + (Cardiidae + Solecurtidae)) + Lucinidae. The phylogenetic result is consistent with the morphological classification. Meanwhile, bootstrap values are very high (BP = 94–100), suggesting that the evolutionary relationship based on mitochondrial genomes is very reliable.     

Differential expression of cytochrome oxidase and ALY-family genes in resistant and susceptible tomato cultivars (Solanum lycopersicum) inoculated with Tomato bushy stunt virus

Tomato cultivars (TY20, TY70/84 and TY70/70) were mechanically inoculated with purified virus preparations of Tomato bushy stunt virus (TBSV). Inoculated plant tissues were collected after 1 day, 1 week and 2 weeks post-inoculation. Messenger RNA of the inoculated and healthy plants was scanned using the differential display to discover the up- and down-regulated genes induced or suppressed in the infected plants. Three down-regulated and four up-regulated genes were observed in different molecular weights. Sequence analysis revealed that the 400 bp up-regulated gene of cultivars TY70/84 and TY70/70 was cytochrome oxidase gene. Expression of these genes was higher in the two resistant cultivars more than the control and the susceptible one (TY20). The other four genes belong to the ALY-gene family which possibly function as a chaperone to promote the interaction of DNA-binding proteins.     

Optimization of the cryopreservation of African clawed frog (Xenopus laevis) sperm

Cryopreservation of testicular sperm in the African clawed frog, Xenopus laevis, was tested using three penetrating cryoprotectants (DMSO, methanol, and glycerol) and three semen diluents (300 mmol/L glucose, 300 mmol/L sucrose, and a motility inhibiting saline [MIS] solution [150 mmol/L NaCl, 3 mmol/L KCL, 1 mmol/L Mg₂SO₄, 1 mmol/L CaCl₂, and 20 mmol/L Tris, pH 8.0]). Three freezing rates and four thawing rates were also tested, and the best freezing/thawing conditions have been determined. The responses of sperm motility, viability, and fertility were assessed. Incubation of the sperm macerates with penetrating cryoprotectants showed that DMSO was the least toxic and methanol the most toxic. Semen in cryodiluents frozen 10 cm above the surface of liquid nitrogen (freezing rate of 20 to 25 °C/min) and thawed at room temperature for 40 sec had significantly higher percentages of motile and viable sperm than that of semen frozen 5 cm or 8 cm above the surface of liquid nitrogen and thawed at 5, 25, or 30 °C for 10, 15, or 60 sec, respectively. Sperm frozen in MIS containing 5% DMSO had a higher hatching rate than that of sperm frozen in sucrose and glucose diluents containing 5% or 10% DMSO and in MIS containing 10% DMSO. Addition of 73 mmol/L sucrose to the sperm extender MIS + 5% DMSO could improve the postthaw sperm motility and fertility. In conclusion, dilution of collected sperm in MIS solution (to have a final concentration of 6.5 × 10⁶ to 8 × 10⁶/mL) containing 5% DMSO and 73 mmol/L sucrose, freezing in a vapor of liquid nitrogen at 10 cm above the surface, and thawing at room temperature for 40 sec was the best cryopreservation protocol. This protocol gave 70% hatching rate, 80% motility rate, and 75% viability rate of fresh hormonally induced sperm.     

Cloning of Wap65 in sea bass (Dicentrarchus labrax) and sea bream (Sparus aurata) and expression in sea bass tissues

The complementary DNA encoding WAP65 protein was cloned from the liver of two fish species sea bass (Dicentrarchus labrax) and sea bream (Sparus aurata). Full-length cDNA sequences were obtained from reverse transcribed total RNA, followed by 5′ and 3′ rapid amplification of cDNA end (RACE) experiments. The full-length cDNA sequence of D. labrax is 1709 bp and the coding sequence is flanked by a 67 bp 5′-UTR and a 358 bp 3′-UTR. The full-length cDNA sequence of S. aurata is 1599 bp, and the coding sequence is flanked by a 48 bp 5′-UTR and a 273 bp 3′-UTR. The deduced amino acid putative primary sequences are composed of 427 and 425 amino acid residues for D. labrax and S. aurata, respectively. They display high homologies with previously described fish WAP65 and other hemopexin-like proteins from rabbit (Oryctolagus cuniculus). Expression of Wap65 has proved to be a natural physiological adaptive answer of teleost fish to warm temperature acclimation. In all fish species studied to date, Wap65 was found expressed mainly by the liver, although other tissues seem able to express Wap65 in response to a warm temperature acclimation, in a specie specific manner. Here, we investigate the tissue specific expression of Wap65 in D. labrax and S. aurata in response to a warm temperature acclimation, by RT-PCR analysis.     

Slurry bioreactors with simultaneous electron acceptors for bioremediation of an agricultural soil polluted with lindane

The purpose of our study was 2-fold: (i) to evaluate the effect of dominant electron acceptor [either aerobic, methanogenic, or sulfate-reducing slurry bioreactor (SB)] and biostimulation with sucrose on lindane removal from heavy soil and (ii) to assess the effect of the type of combined environments [partially aerated methanogenic (PAM) and simultaneous methanogenic-sulfate reducing (M-SR)] and addition of silicone oil as solvent on lindane removal from a clayish agricultural soil with high levels of organic matter.In the first experiment, the main effect of electron acceptor was significant (p < 0.0001); lindane removals followed the order SR > A ? M SBs. On the other hand, co-substrate sucrose was not significant (p = 0.67). Yet, the interaction was moderately significant (p < 0.007); co-substrate influence was distinct depending on the type of electron acceptor. In our case, co-substrate slightly improved lindane removal in both anoxic SBs (SR and M units), whereas lindane removal in A-SB with sucrose was lower than A-SB without sucrose. Metabolites from lindane transformation in our single electron acceptor SBs were consistent with lindane metabolites reported in the literature for anaerobic and aerobic degradation of the insecticide.In the second experiment, both factors [simultaneous electron acceptor (SEA) combination and solvent addition] were significant (p < 0.0001). Removal of lindane in SEA-SBs, PAM and M-SR without silicone oil was low (～16%). On the other hand, the order of lindane removals in SBs with oil silicone M-SR SB was significantly superior (65%) to that of PAM SB (39%).Finally, in our work, SBs with SEA where one of the anaerobic metabolites is methanogenic were not as successful as SBs with single electron acceptors for removal of lindane from heavy soil.     

Unmarked insertional inactivation in the gfo gene improves growth and ethanol production by Zymomonas mobilis ZM4 in sucrose without formation of sorbitol as a by-product,but yields opposite effects in high glucose

Sorbitol, one of the main by-products of growth on high sucrose concentrations, is catalyzed by glucose-fructose oxidoreductase (GFOR, EC 1.1.99.28) in Zymomonas mobilis, which decreases the ethanol yield. In this study, an unmarked gfo mutant from Z. mobilis ZM4 was constructed using a site-specific FLP recombinase, and growth and ethanol production were evaluated with or without the addition of sorbitol to the media. The inactivation of gfo had contrasting effects in different substrates, especially at high concentrations. The maximum specific growth rate (μ_m) and theoretical ethanol yield value (Y_m) increased from 0.065 h⁻¹ and 60.56% to 0.094 h⁻¹ and 83.87% in 342 g/L sucrose, respectively. Conversely, in 200 g/L glucose, gfo inactivation decreased μ_m and Y_m from 0.15 h⁻¹ and 89.85% to 0.10 h⁻¹ and 67.59%, respectively, and prolonged the lag period from 16 h to 40 h. The addition of sorbitol slightly accelerated growth and sucrose hydrolysis by the gfo mutant in 342 g/L sucrose; however, addition of sorbitol restored the μ_m and Y_m of the gfo mutant in 200 g/L glucose to 0.14 h⁻¹ and 82.50%, respectively. Inactivation of gfo had a small effect on fructose utilization, and a positive one on mixture of glucose and fructose similar to that on sucrose. These results provide further understanding of the osmoregulation mechanisms in Z. mobilis and may help to exploit the biotechnological applications of this industrially important bacterium.     

Effect of deglycosylation on the properties of thermophilic invertase purified from the yeast Candida guilliermondii MpIIIa

Invertase from Candida guilliermondii MpIIIa was purified and biochemically characterized. The purified enzyme (INV3a-N) is a glycoprotein with a carbohydrate composition comprising nearly 74% of its total molecular weight (MW) and specific activity of 82,027 U/mg of protein. The enzyme displayed optimal activity at pH 5.0 and 65 ˚C. The Km and V_max values for INV3a-N were 0.104 mM and 10.9 μmol/min/mg of protein, respectively, using sucrose as the substrate. The enzyme retained 50% and 20% of its maximal activity after 168 h and 30 days, respectively, at 50 ˚C. INV3a-N was fully active at sucrose concentrations of 400 mM and the activity of the enzyme dropped slowly at higher substrate concentration. Interestingly, the deglycosylated form of INV3a-N (INV3a-D) displayed 76–92% lower thermostability than that of INV3a-N at all temperatures assayed (50–70 ˚C), and was inhibited at sucrose concentrations of 200 mM. Findings here indicate glycosylation plays an important role, not only in the thermostability of INV3a-N, but also in the inhibition of the enzyme by sucrose. Since the enzyme is active at high sucrose concentrations, INV3a-N may be considered a suitable candidate for numerous industrial applications involving substrates with high sugar content or for improvement of ethanol production from cane molasses.     

Production of isomaltulose using Erwinia sp. D12 cells: Culture medium optimization and cell immobilization in alginate

Isomaltulose is a structural isomer of sucrose commercially used in food industries. Glucosyltransferase produced by Erwinia sp. D12 catalyses an intramolecular transglucosylation of sucrose giving isomaltulose. An experimental Design and Response Surface Methodology were applied for the optimization of the nutrient concentration in the culture medium for enzyme production in shaken flasks at 200 rpm and 30 °C. A higher production of glucosyltransferase (7.47 Uml⁻¹) was observed in the culture medium containing sugar cane molasses (160 gl⁻¹), bacteriological peptone (20 gl⁻¹) and yeast extract Prodex Lac SD^® (15 gl⁻¹) after 8 h, at 30 °C. The highest production of glucosyltransferase in the 6.6-l bioreactor (14.6 Uml⁻¹) was obtained in the optimized culture medium after 10 h at 26 °C. When Erwinia sp. D12 cells were immobilized in sodium alginate, it was verified that sodium alginate solution A could be substituted by a cheaper one, sodium alginate solution B. Using a 40% cell suspension and 2% sodium alginate solution B for cell immobilization in a packed-bed reactor, 64.1% conversion of sucrose to isomaltulose was obtained. The packed-bed reactor with immobilized cells plus glutaraldehyde and polyethylenimine solutions remained in a pseudo-steady-state for 180 h.