Alkali treatment and fermentation of straw for animal feed

The feed value of annual ryegrass straw was improved by treatment with various concentrations of NaOH or NH₃ followed by fermentation of the treated straw with a mixed culture of Cellulomonas sp. and Alcaligenes faecalis. Laboratory feeding trials with voles showed that NaOH or NH₃ treatment considerably increased the feed efficiency of straw, but apparently gave a poorly palatable product. Fermentation tended to decrease the in vitro rumen digestibility (IVRD) of alkali-treated straw. The fermentations were carried out aerobically on a semisolid straw matrix having 11–86% moisture. Treatment by both NaOH and NH₃ increased the IVRD of straw. NH₃ also increased the nitrogen content in straw. The optimum condition for alkaline treatment of the straw was 4–6% NaOH for 1 hr or with 3% NH₃ for four weeks at room temperature. A minimum of 63% moisture was needed for significant fermentation of the straw. The combined effects of NaOH treatment and fermentation more than doubled crude protein, doubled crude fat, and increased IVRD by 75%. The NH₃ plus fermentation treatment tripled crude protein, doubled crude fat, and increased IVRD by 60%. Acetic acid was the main volatile fatty acid in the fermented straw.     

Extraction of hemicellulose from ryegrass straw for the production of glucose isomerase and use of the resulting straw residue for animal feed

The hemicellulose fraction of ryegrass straw was extracted with NaOH and used for the production of glucose isomerase by Streptomyces flavogriseus. The level of hemicellulose extracted increased proportionately with increasing NaOH concentration up to about 4%, then the rate of increase slowed down. Hemicellulose extraction was facilitated by the combined application of heat and NaOH. Approximately 15% hemicellulose (12% as pentosan) could be obtained by treating straw with 4% NaOH for either 3 hr at 90°C or 24 hr at room temperature. The highest level (3.04 units/ml culture) of intracellular glucose isomerase was obtained when the organism was grown at 30°C for two days on 2% straw hemicellulose. The organism also produced a high yield of glucose isomerase on xylose or xylan. The NaOH-treated straw residue, after removal of hemicellulose, had approximately 75% higher digestibility and 20% higher feed efficiency for weanling meadow voles than untreated straw. Thus, the residue could be used as animal feed. A process for the production of glucose isomerase and animal feed from ryegrass straw was also proposed.     

Focusing modelling on the tracheid development period – An alternative method for treatment of xylogenesis intra-annual data

Intra-annual repeated micro-sampling of the developing tree ring is getting more and more applied in xylogenesis studies. Variability in growth magnitude, notably due to different sampling positions on the stem, encouraged application of standardization and modelling techniques. Among these, methods using Gompertz equation had become widely spread, but tests made with black spruce revealed a frequent occurrence of crossovers between the cumulative number of cells in enlargement and the cumulative number of cells in wall thickening. This was due to a localized problem in the fitting for values close to the asymptote and was a major problem for estimating the timing of each individual cell development phases, which is an interesting application of these data. In this paper, a new method, based on a different approach, has been developed in order to avoid that problem and applied to intra-annual growth curves from four sites in Quebec (Canada). Since tracheid development analysis allows discriminating between active and inactive period of a phase, modelling can be restricted on the active period alone. The new method did not cause crossovers between the fitted curves. Therefore, it has been considered appropriate for estimating the timing for each individual cell in the whole range of data. Since resulting functions are polynomials from degree 1 to 3, possible studies concerning general tendency should be easy to lead. Also, the method has been tested with different sampling frequencies. To do this, number of observations from weekly samplings has been halved to simulate a semi-monthly sampling frequency and a comparison of the results from the new method applied on each version of the datasets has been tested. Generally, the simulated semi-monthly sampled dataset did not give significantly different results from the original weekly sampled dataset, in terms of general tendency and predicted intercept time in the extremities of the data range. This is very encouraging for situations when only semi-monthly sampling is available.     

SnTox5–Snn5: a novel Stagonospora nodorum effector–wheat gene interaction and its relationship with the SnToxA–Tsn1 and SnTox3–Snn3–B1 interactions

The Stagonospora nodorum–wheat interaction involves multiple pathogen‐produced necrotrophic effectors that interact directly or indirectly with specific host gene products to induce the disease Stagonospora nodorum blotch (SNB). Here, we used a tetraploid wheat mapping population to identify and characterize a sixth effector–host gene interaction in the wheat–S. nodorum system. Initial characterization of the effector SnTox5 indicated that it is a proteinaceous necrotrophic effector that induces necrosis on host lines harbouring the Snn5 sensitivity gene, which was mapped to the long arm of wheat chromosome 4B. On the basis of ultrafiltration, SnTox5 is probably in the size range 10–30 kDa. Analysis of SNB development in the mapping population indicated that the SnTox5–Snn5 interaction explains 37%–63% of the variation, demonstrating that this interaction plays a significant role in disease development. When the SnTox5–Snn5 and SnToxA–Tsn1 interactions occurred together, the level of SNB was increased significantly. Similar to several other interactions in this system, the SnTox5–Snn5 interaction is light dependent, suggesting that multiple interactions may exploit the same pathways to cause disease.     

Dendritic cells in the skin – potential use for melanoma treatment

Melanoma is an aggressive malignancy with poor prognosis. Eradication of tumor cells requires an effective interaction between melanoma cells and different players of the immune system. As the most potent professional antigen‐presenting cells, dendritic cells (DCs) play a pivotal role in mounting a specific immune response where their intratumoral and peritumoral density as well as their functional status are correlated with clinical staging of the disease and with patients’ survival. Under steady‐state conditions, internalization of apoptotic cells by immature DCs designates a state of tolerance to self‐antigens. Nevertheless, pathogens and necrotic cells interacting with pattern recognition receptors trigger downstream signaling pathways that evoke maturation of DCs, leading to the production of pro‐inflammatory cytokines. These mature DCs are essential for T‐cell priming and subsequent development of a specific immune response. Altered functions of DCs have an impact on the development of various disorders including autoimmune diseases and cancers. Herein, we focus on the checkpoints created throughout DCs antigen capturing and presentation to T cells, with subsequent development of either tolerance or immune response, with an emphasis on the role played by DCs in melanoma tumorigenesis and their therapeutic potential.     

Acid-mechanical,alkaline and enzymatic treatment of agricultural wastes to obtain substrate for microbiological conversion

The present paper deals with almost wasteless technologies of pretreatment and obtaining of sugars and biomass from straw and potato tops. Several variants ensure a 1 t of straw per hour productivity using original auger reactors 290 and 150 mm in diameter. The authors have studied the submerged and solid state cultivation of various microorganisms applying the obtained substrates.     

Screening of white‐rot fungi for bioprocessing of wheat straw into ruminant feed

Aim

In this study, the biological variation for improvement of the nutritive value of wheat straw by 12 Ceriporiopsis subvermispora, 10 Pleurotus eryngii and 10 Lentinula edodes strains was assessed. Screening of the best performing strains within each species was made based on the in vitro degradability of fungal‐treated wheat straw.

Methods and Results

Wheat straw was inoculated with each strain for 7 weeks of solid state fermentation. Weekly samples were evaluated for in vitro gas production (IVGP) in buffered rumen fluid for 72 h. Out of the 32 fungal strains studied, 17 strains showed a significantly higher (P < 0·05) IVGP compared to the control after 7 weeks (227·7 ml g^?1 OM). The three best Ceriporiopsis subvermispora strains showed a mean IVGP of 297·0 ml g^?1 OM, while the three best P. eryngii and L. edodes strains showed a mean IVGP of 257·8 and 291·5 ml g^?1 OM, respectively.

Conclusion

Ceriporiopsis subvermispora strains show an overall high potential to improve the ruminal degradability of wheat straw, followed by L. edodes and P. eryngii strains.

Significance and Impact of the Study

Large variation exists within and among different fungal species in the valorization of wheat straw, which offers opportunities to improve the fungal genotype by breeding.     

Structure of the Atg12–Atg5 conjugate reveals a platform for stimulating Atg8–PE conjugation

Atg12 is conjugated to Atg5 through enzymatic reactions similar to ubiquitination. The Atg12–Atg5 conjugate functions as an E3‐like enzyme to promote lipidation of Atg8, whereas lipidated Atg8 has essential roles in both autophagosome formation and selective cargo recognition during autophagy. However, the molecular role of Atg12 modification in these processes has remained elusive. Here, we report the crystal structure of the Atg12–Atg5 conjugate. In addition to the isopeptide linkage, Atg12 forms hydrophobic and hydrophilic interactions with Atg5, thereby fixing its position on Atg5. Structural comparison with unmodified Atg5 and mutational analyses showed that Atg12 modification neither induces a conformational change in Atg5 nor creates a functionally important architecture. Rather, Atg12 functions as a binding module for Atg3, the E2 enzyme for Atg8, thus endowing Atg5 with the ability to interact with Atg3 to facilitate Atg8 lipidation.     

Adapter-tagged competitive PCR (ATAC-PCR) – a high-throughput quantitative PCR method for microarray validation

Adapter-tagged competitive PCR (ATAC-PCR) is an advanced version of competitive quantitative PCR that is characterized by the addition of unique adapters to cDNA derived from each sample RNA. Using multiple adapters, we can accurately measure the relative expression ratios of many samples, with a calibration curve obtained from internal standards included in the same reaction. ATAC-PCR can identify differences in gene expression as small as twofold, even from very small amounts of sample RNA. This technique is suitable for confirming results obtained with cDNA microarrays or differential display, and it can process more than a thousand of genes per day when used in conjunction with a capillary DNA sequencer.     

Characterization of a self-splicing mini-intein and its conversion into autocatalytic N- and C-terminal cleavage elements: facile production of protein building blocks for protein ligation

The determinants governing the self-catalyzed splicing and cleavage events by a mini-intein of 154 amino acids, derived from the dnaB gene of Synechocystis sp. were investigated. The residues at the splice junctions have a profound effect on splicing and peptide bond cleavage at either the N- or C-terminus of the intein. Mutation of the native Gly residue preceding the intein blocked splicing and cleavage at the N-terminal splice junction, while substitution of the intein C-terminal Asn154 resulted in the modulation of N-terminal cleavage activity. Controlled cleavage at the C-terminal splice junction involving cyclization of Asn154 was achieved by substitution of the intein N-terminal cysteine residue with alanine and mutation of the native C-extein residues. The C-terminal cleavage reaction was found to be pH-dependent, with an optimum between pH6.0 and 7.5. These findings allowed the development of single junction cleavage vectors for the facile production of proteins as well as protein building blocks with complementary reactive groups. A protein sequence was fused to either the N-terminus or C-terminus of the intein, which was fused to a chitin binding domain. The N-terminal cleavage reaction was induced by 2-mercaptoethanesulfonic acid and released the 43kDa maltose binding protein with an active C-terminal thioester. The 58kDa T4 DNA ligase possessing an N-terminal cysteine was generated by a C-terminal cleavage reaction induced by pH and temperature shifts. The intein-generated proteins were joined together through a native peptide bond. This intein-mediated protein ligation approach opens up novel routes in protein engineering.     

Optimisation of a microwave pretreatment of wheat straw for methane production

This study aims at the optimisation of a microwave pretreatment for wheat straw solubilisation and anaerobic biodegradability. The maximum yield of methane production was obtained at 150 °C with an improvement of 28% compared to an untreated sample. In addition, at this temperature, the time to reach 80% of the methane volume obtained from untreated straw was about 35%. The study of ramp time and holding time at targeted temperature showed that they had no improvement effect. Thus, the best conditions are the highest heating rate for a final temperature 150 °C without any holding time. The reading of energy consumed by pretreatment and energy overproduced by pretreated samples showed that increasing tVS amount and heating rate led to a saving of energy consumption. Nevertheless, to obtain a positive energy balance, a microwave device should consume less than 2.65 kJ/g_tVS.     

FERM – a decision support system for fermentation processes

For recombinant DNA product fermentations in the laboratory and pilot scale as well as for antibiotic fermentations at the industrial scale decision support program systems for personal computers were developed. It assists the operator to solve control and decision tasks. Applying this program the data and knowledge bases increase, which include measured and derived process data, parameters and comments of previous fermentation runs as well as algorithmic and declarative rules.     

Protists – A textbook example for a paraphyletic taxon

Protists constitute a paraphyletic taxon since the latter is based on the plesiomorphic character of unicellularity and does not contain all descendants of the stem species. Multicellularity evolved several times independently in metazoans, higher fungi, heterokonts, red and green algae. Various hypotheses have been developed on the evolution and nature of the eukaryotic cell, considering the accumulating data on the chimeric nature of the eukaryote genome. Subsequent evolution of the protists was further complicated by primary, secondary, and even tertiary intertaxonic recombinations. However, multi-gene sequence comparisons and structural data point to a managable number of such events. Several putative monophyletic lineages and a gross picture of eukaryote phylogeny are emerging on the basis of those data. The Chromalveolata comprise Chromista and Alveolata (Dinoflagellata, Apicomplexa, Ciliophora, Perkinsozoa, and Haplospora). Major lineages of the former ‘amoebae’ group within the Heterolobosa, Cercozoa, and Amoebozoa. Cercozoa, including filose testate amoebae, chlorarachnids, and plasmodiophoreans seem to be affiliated with foraminiferans. Amoebozoa consistently form the sister group of the Opisthokonta (including fungi, and with choanoflagellates as sister group of metazoans). A clade of ‘plants’ comprises glaucocystophytes, red algae, green algae, and land vascular plants. The controversial debate on the root of the eukaryote tree has been accelerated by the interpretation of gene fusions as apomorphic characters. In the more traditional view, based on sequence comparisons using archaebacteria as outgroup representatives, parabasaleans and diplomonads branch off first, rendering the biflagellate eukaryotes paraphyletic. In sharp contrast, the root is placed between Bikonta and Opisthokonta plus Amoebozoa on the argument of a single enzyme gene fusion which is postulated to have occurred in the stem species of the Bikonta, and of a double enzyme gene fusion weighed as a synapomorphy of the Opisthokonta and Amoebozoa. We conclude that the paraphyletic taxon ‘protists’ may be maintained for practical reasons. However, introduction of new, clearly recognizable paraphyletic taxa should be avoided.     

Threshold criteria for conversion of probability of species presence to either–or presence–absence

For many applications the continuous prediction afforded by species distribution modeling must be converted to a map of presence or absence, so a threshold probability indicative of species presence must be fixed. Because of the bias in probability outputs due to frequency of presences (prevalence), a fixed threshold value, such as 0.5, does not usually correspond to the threshold above which the species is more likely to be present. In this paper four threshold criteria are compared for a wide range of sample sizes and prevalences, modeling a virtual species in order to avoid the omnipresent error sources that the use of real species data implies. In general, sensitivity–specificity difference minimizer and sensitivity–specificity sum maximizer criteria produced the most accurate predictions. The widely-used 0.5 fixed threshold and Kappa-maximizer criteria are the worst ones in almost all situations. Nevertheless, whatever the criteria used, the threshold value chosen and the research goals that determined its choice must be stated.     

Studies of visible oscillating chemiluminescence with a luminol–H2O2–KSCN–CuSO4–NaOH system in batch reactor

Oscillating chemical reactions are complex systems involving a large number of chemical species. In oscillating chemical reactions some species, usually reaction intermediates, exhibit fluctuation in concentration. Visible oscillating chemiluminescence, produced by the addition of luminol (3‐aminophthalhydrazide) to the oscillating system H₂O₂–KSCN–CuSO₄–NaOH, was investigated. In this study the effect of varying the concentration of H₂O₂, KSCN, CuSO₄, NaOH and luminol was investigated in a batch reactor. We showed that the concentration of all components involved in the oscillating chemilumenscent reaction influenced the light intensity and the oscillation period. Copyright © 2002 John Wiley & Sons, Ltd.