微生物菌剂在农业废弃物堆肥腐熟过程中的应用及其田间试验效果

以农村生活垃圾中的可堆肥腐熟成分和蘑菇渣为堆肥原料,通过添加微生物菌剂进行堆肥试验,研究其在农业废弃物堆肥腐熟过程中的作用,并通过田间试验研究堆肥腐熟后肥料样品对黄瓜和青椒的增产效果,以验证其肥效。结果表明添加微生物菌剂有助于堆肥腐熟后样品的氮、磷、钾的保全和有机质的增加,促进养分均衡。添加微生物菌剂的堆肥腐熟肥料样品在田间试验中对黄瓜和青椒的增产效果最为显著,分别为22.21%和19.87%。     

残留地膜对番茄幼苗形态和生理特性的影响

采用盆栽试验的方法,研究了土壤中残留地膜对番茄(Lycopersicon esculentum L.)幼苗形态及生理特性的影响.结果表明,残留地膜使番茄幼苗的株高、茎粗、地上部和根系鲜重、根系活力及叶片氮代谢水平等降低;而且根系的IBA含量降低和ABA含量增加,抑制了根系的生长.同时地膜残留量越大,抑制的效果越显著.这...     

A Study of the Effect of Red Mud Amendments on the Growth of Cyanobacterial Species

Red mud is a bauxite residue, a by-product of the Bayer process for extraction of alumina from bauxite ore. It is highly alkaline in nature and contains heavy metal oxides and a variety of minor trace elements. Its disposal is the paramount environmental issue in alumina refining. Establishment of vegetation on red mud dumping sites is difficult because of alkaline pH and high concentrations of soluble ions and toxic compounds. The bioremediation of red mud seems to be a realistically convenient way for environmentally safe disposal of this industrial residue. The present study specifically deals with the utilization of cyanobacteria to bioremediate red mud. Being predominantly a nitrogen-fixing photosynthetic microorganism, it has considerable potential for bioremediation of bauxite residue. As a prelude step, four cyanobacterial species, viz. Oscillatoria sp., Lyngbya sp., Phormidium sp., and Microcystis sp. were selected to study their capability to grow on red mud–amended medium. The results indicate that Oscillatoria and Phormidium performed well on red mud–amended medium, followed by Lyngbya. Growth of Microcystis was inhibited significantly even at lower concentrations of red mud amendments. These findings point out the potential of these microorganisms, to be utilized as active biological agents for bioremediation of red mud.     

Indirect carbon dioxide emissions from producing bioenergy from forest harvest residues

Forest harvest residues are important raw materials for bioenergy in regions practicing forestry. Removing these residues from a harvest site reduces the carbon stock of the forest compared with conventional stem‐only harvest because less litter in left on the site. The indirect carbon dioxide (CO₂) emission from producing bioenergy occur when carbon in the logging residues is emitted into the atmosphere at once through combustion, instead of being released little by little as a result of decomposition at the harvest sites. In this study (1) we introduce an approach to calculate this indirect emission from using logging residues for bioenergy production, and (2) estimate this emission at a typical target of harvest residue removal, i.e. boreal Norway spruce forest in Finland. The removal of stumps caused a larger indirect emission per unit of energy produced than the removal of branches because of a lower decomposition rate of the stumps. The indirect emission per unit of energy produced decreased with time since starting to collect the harvest residues as a result of decomposition at older harvest sites. During the 100 years of conducting this practice, the indirect emission from average‐sized branches (diameter 2 cm) decreased from 340 to 70 kg CO₂ eq. MWh^?1 and that from stumps (diameter 26 cm) from 340 to 160 kg CO₂ eq. MWh^?1. These emissions are an order of magnitude larger than the other emissions (collecting, transporting, etc.) from the bioenergy production chain. When the bioenergy production was started, the total emissions were comparable to fossil fuels. The practice had to be carried out for 22 (stumps) or four (branches) years until the total emissions dropped below the emissions of natural gas. Our results emphasize the importance of accounting for land‐use‐related indirect emissions to correctly estimate the efficiency of bioenergy in reducing CO₂ emission into the atmosphere.     

The effect of long-range interactions on the secondary structure formation of proteins

The influence of long-range residue interactions on defining secondary structure in a protein has long been discussed and is often cited as the current limitation to accurate secondary structure prediction. There are several experimental examples where a local sequence alone is not sufficient to determine its secondary structure, but a comprehensive survey on a large data set has not yet been done. Interestingly, some earlier studies denied the negative effect of long-range interactions on secondary structure prediction accuracy. Here, we have introduced the residue contact order (RCO), which directly indicates the separation of contacting residues in terms of the position in the sequence, and examined the relationship between the RCO and the prediction accuracy. A large data set of 2777 nonhomologous proteins was used in our analysis. Unlike previous studies, we do find that prediction accuracy drops as residues have contacts with more distant residues. Moreover, this negative correlation between the RCO and the prediction accuracy was found not only for beta-strands, but also for alpha-helices. The prediction accuracy of beta-strands is lower if residues have a high RCO or a low RCO, which corresponds to the situation that a beta-sheet is formed by beta-strands from different chains in a protein complex. The reason why the current study draws the opposite conclusion from the previous studies is examined. The implication for protein folding is also discussed.     

Anchor profiles of HLA-specific peptides: analysis by a novel affinity scoring method and experimental validation

The study of intermolecular interactions is a fundamental research subject in biology. Here we report on the development of a quantitative structure-based affinity scoring method for peptide-protein complexes, named PepScope. The method operates on the basis of a highly specific force field function (CHARMM) that is applied to all-atom structural representations of peptide-receptor complexes. Peptide side-chain contributions to total affinity are scored after detailed rotameric sampling followed by controlled energy refinement. A de novo approach to estimate dehydration energies was developed, based on the simulation of individual amino acids in a solvent box filled with explicit water molecules. Transferability of the method was demonstrated by its application to the hydrophobic HLA-A2 and -A24 receptors, the polar HLA-A1, and the sterically ruled HLA-B7 receptor. A combined theoretical and experimental study on 39 anchor substitutions in FxSKQYMTx/HLA-A2 and -A24 complexes indicated a prediction accuracy of about two thirds of a log-unit in Kd. Analysis of free energy contributions identified a great role of desolvation and conformational strain effects in establishing a given specificity profile. Interestingly, the method rightly predicted that most anchor profiles are less specific than so far assumed. This suggests that many potential T-cell epitopes could be missed with current prediction methods. The results presented in this work may therefore significantly affect T-cell epitope discovery programs applied in the field of peptide vaccine development.     

Conformation of peptides constructed from achiral amino acid residues Aib and DeltaZPhe: computational study of the effect of L/D- Leu at terminal positions

Conformational studies of the peptides constructed from achiral amino acid residues Aib and Delta(Z)Phe (I) Ac-Aib-Delta(Z)Phe-NHMe (II), and Ac-(Aib-Delta(Z)Phe)(3)-NHMe; peptides III-VI having L-Leu or D-Leu at either the N- or the C-terminal position and of peptides VII-X having Leu residues in different enantiomeric combinations at both the N- and the C-terminal positions in peptide II have been studied to design the peptide with the required helical sense. Peptide II, as expected, adopts degenerate left- and right-handed helical structures. It has been shown that the peptides IV and VI having D-Leu at either the N or the C terminus can be realized in the right-handed helical structure with the phi,psi values of -20 degrees and -60 degrees for the Aib/Delta(Z)Phe residues. L-Leu and D- Leu at both the terminals in peptides VII and VIII, respectively, have hardly any effect as both the left- and the right-handed structures are found to be degenerate. Peptides III and IX can be realized in right- and left-handed helical structures, respectively, in solvents of low polarity whereas peptides V and X are predicted to be in the right-handed helical structures stabilized by carbonyl-carbonyl interactions without the formation of hydrogen bonds. The conformational states with the phi,psi values of 0 degrees and -85 degrees in peptide V are characterized by rise per residue of 2.03 A, rotation per residue of 117.5 degrees , and 3.06 residues per turn. In all peptides having Leu residue at the N terminus, the methyl moiety of the acetyl group is involved in the CH/pi interactions with the Cepsilon--Cdelta edge of the aromatic ring of Delta(Z)Phe (3) and the amino group NH of Delta(Z)Phe is involved in the NH/pi interactions with its own aromatic ring. The CH(3) groups of the Aib residues are also involved in CH/pi interactions with the i + 1th and i + 3th Delta(Z)Phe's aromatic side chains.     

Redox control of catalytic activities of membrane-associated protein tyrosine kinases

Protein tyrosine kinases (PTKs) play key roles in starting the signal transduction network for cellular development and functions. A number of both receptor-type and non-receptor-type PTKs, which are normally at a resting state, are initially activated in association with functions of the cell membrane and membrane rafts. Results of recent studies have suggested that these membrane-associated mechanisms for activation of PTKs consist of the two steps that are under redox control. The first step is activation of cell surface receptors through chemical crosslinkage or aggregation of receptors and membrane rafts, which leads to production of reactive oxygen species (ROS) as second messengers of intracellular signal transduction. The second step involves chemical modification of PTKs at the highly conserved cysteine in the MXXCW motif as a global switch for starting the tyrosine phosphorylation-dependent local switch for activation of the catalytic activity of the enzyme.     

Alkali‐based AFEX pretreatment for the conversion of sugarcane bagasse and cane leaf residues to ethanol

Sugarcane is one of the major agricultural crops cultivated in tropical climate regions of the world. Each tonne of raw cane production is associated with the generation of 130 kg dry weight of bagasse after juice extraction and 250 kg dry weight of cane leaf residue postharvest. The annual world production of sugarcane is ～1.6 billion tones, generating 279 MMT tones of biomass residues (bagasse and cane leaf matter) that would be available for cellulosic ethanol production. Here, we investigated the production of cellulosic ethanol from sugar cane bagasse and sugar cane leaf residue using an alkaline pretreatment: ammonia fiber expansion (AFEX). The AFEX pretreatment improved the accessibility of cellulose and hemicelluloses to enzymes during hydrolysis by breaking down the ester linkages and other lignin carbohydrate complex (LCC) bonds and the sugar produced by this process is found to be highly fermentable. The maximum glucan conversion of AFEX pretreated bagasse and cane leaf residue by cellulases was ～85%. Supplementation with hemicellulases during enzymatic hydrolysis improved the xylan conversion up to 95–98%. Xylanase supplementation also contributed to a marginal improvement in the glucan conversion. AFEX‐treated cane leaf residue was found to have a greater enzymatic digestibility compared to AFEX‐treated bagasse. Co‐fermentation of glucose and xylose, produced from high solid loading (6% glucan) hydrolysis of AFEX‐treated bagasse and cane leaf residue, using the recombinant Saccharomyces cerevisiae (424A LNH‐ST) produced 34–36 g/L of ethanol with 92% theoretical yield. These results demonstrate that AFEX pretreatment is a viable process for conversion of bagasse and cane leaf residue into cellulosic ethanol. Biotechnol. Bioeng. 2010;107: 441–450. © 2010 Wiley Periodicals, Inc.