Complete genome sequence of Pseudomonas frederiksbergensis ERDD5:01 revealed genetic bases for survivability at high altitude ecosystem and bioprospection potential

Pseudomonas frederiksbergensis ERDD5:01 is a psychrotrophic bacteria isolated from the glacial stream flowing from East Rathong glacier in Sikkim Himalaya. The strain showed survivability at high altitude stress conditions like freezing, frequent freeze-thaw cycles, and UV-C radiations. The complete genome of 5,746,824 bp circular chromosome and a plasmid of 371,027 bp was sequenced to understand the genetic basis of its survival strategy. Multiple copies of cold-associated genes encoding cold active chaperons, general stress response, osmotic stress, oxidative stress, membrane/cell wall alteration, carbon storage/starvation and, DNA repair mechanisms supported its survivability at extreme cold and radiations corroborating with the bacterial physiological findings. The molecular cold adaptation analysis in comparison with the genome of 15 mesophilic Pseudomonas species revealed functional insight into the strategies of cold adaptation. The genomic data also revealed the presence of industrially important enzymes.     

Genome-wide analysis of long non-coding RNAs in Pichia pastoris during stress by RNA sequencing

Long non-coding RNAs play significant roles in many biological processes. The roles of lncRNAs in Pichia pastoris remain unclear. In this work, we focused on the identification of lncRNAs in P. pastoris and exploration of their potential roles in stress response to PLA₂ overexpression and methanol induction. By strand specific RNA sequencing, 208 novel long non-coding RNAs were identified and analyzed. Bioinformatic analysis showed potential trans-target genes and cis-regulated genes of 39 differential lncRNAs. Functional annotation and sequence motif analysis indicated that lncRNAs participate in pathways related to methanol degradation and production of the recombinant protein. The differential expression of lncRNAs was validated by qRT-PCR. Lastly, the potential functions of three lncRNAs were evaluated by knockdown of their expression and analysis of the expression levels of target genes. Our study identifies novel lncRNAs in P. pastoris induced during use as a bioreactor, facilitating future functional research.     

中国产业共生发展模式的国际比较及对策

产业共生和生态工业园区已经成为世界范围内产业生态化转型的重要手段之一。在厘清产业共生发展模式内涵的基础上,借鉴商业模式的划分准则辨识了世界范围内6种产业共生模式:丹麦卡伦堡模式、美国模式、英国模式、日本模式、韩国模式和中国模式。从关键参与者、核心能力以及资金流3个维度对这些模式进行了辨识,重点比较了我国产业共生与其他模式的差别。研究表明,我国产业共生实践数量众多,在关键参与主体、核心能力培育和资金流等方面存在丰富的多样化,虽然形成了一定的中国特色,但并没有形成固定的"中国模式"。可以说,我国的产业共生实践还停留在初级阶段,下一步可持续的发展必须要建立合理的管制架构、形成稳定的资金支持机制和培育核心竞争能力。初级提出了我国产业共生和生态工业园区建设的政策建议。     

Microbial xylanases: Engineering, production and industrial applications

Enzymatic depolymerization of hemicellulose to monomer sugars needs the synergistic action of multiple enzymes, among them endo-xylanases (EC 3.2.1.8) and β-xylosidases (EC 3.2.1.37) (collectively xylanases) play a vital role in depolymerizing xylan, the major component of hemicellulose. Recent developments in recombinant protein engineering have paved the way for engineering and expressing xylanases in both heterologous and homologous hosts. Functional expression of endo-xylanases has been successful in many hosts including bacteria, yeasts, fungi and plants with yeasts being the most promising expression systems. Functional expression of β-xylosidases is more challenging possibly due to their more complicated structures. The structures of endo-xylanases of glycoside hydrolase families 10 and 11 have been well elucidated. Family F/10 endo-xylanases are composed of a cellulose-binding domain and a catalytic domain connected by a linker peptide with a (β/α)(8) fold TIM barrel. Family G/11 endo-xylanases have a β-jelly roll structure and are thought to be able to pass through the pores of hemicellulose network owing to their smaller molecular sizes. The structure of a β-d-xylosidase belonging to family 39 glycoside hydrolase has been elucidated as a tetramer with each monomer being composed of three distinct regions: a catalytic domain of the canonical (β/α)(8) - TIM barrel fold, a β-sandwich domain and a small α-helical domain with the enzyme active site that binds to d-xylooligomers being present on the upper side of the barrel. Glycosylation is generally considered as one of the most important post-translational modifications of xylanases, but a few examples showed functional expression of eukaryotic xylanases in bacteria. The optimal ratio of these synergistic enzymes is very important in improving hydrolysis efficiency and reducing enzyme dosage but has hardly been addressed in literature. Xylanases have been used in traditional fields such as food, feed and paper industries for a longer time but more and more attention has been paid to using them in producing sugars and other chemicals from lignocelluloses in recent years. Mining new genes from nature, rational engineering of known genes and directed evolution of these genes are required to get tailor-made xylanases for various industrial applications.     

城市小区环境生物剂气溶胶的扩散模拟研究

目的:研究城市小区中生物剂气溶胶的扩散模拟和污染区域的划分,为反生物恐怖危害评估及应急响应提供决策依据。方法:以典型生物剂炭疽为例,利用计算流体力学中的离散相模型对小区环境中生物剂气溶胶的扩散规律进行研究;对扩散后生物剂气溶胶的数目分布进行量化分析,结合吸入式炭疽的剂量-反应模型进行污染区域的划分。结果:通过计算机模拟,得到了生物剂气溶胶在小区环境中的扩散规律及数目分布,并依据人员感染炭疽概率的不同划分出小区内的污染区域。结论:利用离散相模型和剂量-反应模型,可以对城市小区中生物剂气溶胶的扩散规律进行模拟并划分污染区域,为反生物恐怖危害评估及应急响应提供决策依据。     

A comparison of clinical and food Saccharomyces cerevisiae isolates on the basis of potential virulence factors

Saccharomyces cerevisiae is the most widely used yeast in industrial/commercial food and beverage production and is even consumed as a nutritional supplement. Various cases of fungemia caused by this yeast species in severely debilitated traumatized or immune-deficient patients have been reported in recent years, suggesting that this species could be an opportunistic pathogen in such patients. To determine whether the industrial S. cerevisiae strains can be included in this virulent group of strains, we carried out a comparative study between clinical and industrial yeasts based on the various phenotypic traits associated with pathogenicity in two other yeast species (Candida albicans and Cryptococcus neoformans). The majority of the clinical isolates were found to secrete higher levels of protease and phospholipase, grow better at 42°C and show strong pseudohyphal growth relative to industrial yeasts. However three industrial yeast strains, one commercial wine strain, baker’s yeast and one commercial strain of S. cerevisiae (var. boulardii), were exceptions and based on their physiological traits these yeasts would appear to be related to clinical strains.     

Identification of novel denitrifying bacteria Stenotrophomonas sp. ZZ15 and Oceanimonas sp. YC13 and application for removal of nitrate from industrial wastewater

Two novel denitrifying bacteria were successfully isolated from industrial wastewater and soil samples. Using morphological, biochemical/biophysical and 16S rRNA gene analyses, these two bacteria were identified as Stenotrophomonas sp. ZZ15 and Oceanimonas sp. YC13, respectively. Both of these two bacteria showed efficient NO₃ ⁻-N removing abilities under a semi-anaerobic condition without obvious accumulation of NO₂ ⁻-N, N₂O-N and NH₄ ⁺-N. NO₃ ⁻-N removal from paper mill wastewater was also successful by treatments with either a denitrifier or an immobilization method. Therefore, this study provides valuable denitrifying bacteria in biotreatment of industrial wastewater and other environmental pollution caused by NO₃ ⁻/NO₂ ⁻.     

Titration biosensors for the estimation of the biochemical nitrate demand of municipal and industrial wastes

An anoxic titrimetric test was investigated for measuring denitrification potential of different wastewaters, both municipal and industrial, and to quantify the denitrifying activity in an activated sludge system. The method measures the amount of acid that is required to maintain the pH set-point value in a batch denitrification experiment, and it was performed using a DENICON (denitrification controller) biosensor. The amount of acid is proportional to the nitrate used to oxidise the biodegradable chemical oxygen demand present in the wastewater, while the acid consumption rate is used to derive the denitrifying activity. The wastewaters tested were a municipal wastewater (MW), an industrial-municipal wastewater (MIW; 70% and 30%, respectively), and four industrial wastewaters drawn from an ice-cream factory (IW1), a beet-sugar factory (IW2), a brewery (IW3), and a tuna cannery industry (IW4). Good correlation between titration data and analyses was found.     

Comparison of Three Different LCIA Methods: EDIP97, CML2001 and Eco-indicator 99

Goal, Scope and Background

A number of impact assessment methodologies are available to the LCA practitioner. They differ, and often there is not one obvious choice among them. The question therefore naturally arises: ‘Does it make any difference to my conclusions which method I choose?’ To investigate this issue, a comparison is performed of three frequently applied life cycle impact assessment methods.

Methods

The three life cycle impact assessment methods EDIP97 [1], CML2001 [2] and Eco-indicator 99 [3] are compared on their performance through application to the same life cycle inventory from a study of a water-based UV-lacquer. EDIP97 and CML2001 are both midpoint approaches and hence quite similar in their scope and structure, and this allows a comparison during both characterisation and normalisation. The third impact assessment method Eco-indicator 99 is an endpoint method and different in scope and structure from the other two. A detailed comparison can not be done but a comparative analysis of the main contributors to the Eco-indicator 99 results and the weighted and aggregated EDIP97 results is performed.

Results and Discussion

Following a translation into common units of the EDIP97 and CML2001 output, differences up to two orders of magnitude are found for some of the indicator results for the impact categories describing toxicity to humans and ecosystems, and there is little similarity in the patterns of major contributors among the two methods. For human toxicity the CML2001 score is dominated by contribution from metals while the EDIP97 score is caused by a solvent and nitrogen oxides. For aquatic ecotoxicity, metals are the main contributors for both methods but while it is vanadium for CML2001, it is strontium for EDIP97. After normalisation, the differences are reduced but still considerable. For the other impact categories, the two methods show only minor differences. The comparison of the main contributors to the Eco-indicator 99 results and the weighted and aggregated EDIP97 results identifies nitrogen oxides as the main contributor for both methods. It is, however, much more dominant for Eco-indicator 99 while the EDIP97 score represents important contributions from a number of different substances, and furthermore, the analysis reveals that the aggregated scores for the two methods come from different impacts. It is thus difficult to extend the findings for these two methods to other inventories.

Conclusion

For EDIP97 and CML2001, it mainly matters which method is used if the chemical impacts on human health and ecosystem health are important for the study. For the other impact categories, the differences are minor for these two methodologies. For EDIP97 and Eco-indicator 99, the patterns of most important contributors to the weighted and aggregated impact scores are rather different, and considering the known differences in the underlying framework and models, the results of the two methods may well go in opposite directions for some inventories even if the conclusion is the same for the inventory studied in this paper.

Recommendations and Oudook

Particularly for the impact categories representing toxic impacts from chemicals, the study demonstrates the need for more a detailed analysis of the causes underlying the big differences revealed between the methods.

     

产业生态学的回顾与展望

对产业生态学的基本概念、研究方法和研究热点进行了总结与评述,认为产业生态学是研究人类产业活动与自然环境相互关系的一门综合性、垮学科的应用科学．它采用工业代谢、生命周期评价和区域生态建设的方法对产业活动全过程（包括原材料采掘、原材料生产、产品制造、产品使用、产品用后处理）进行定性描述和定量模拟．产业生态学着眼于人类和生态系统的长远利益,追求经济效益、生态效益和社会效益的统一．