Construction of shuttle vectors useful for transforming Clostridium acetobutylicum

The symbiotic plasmid (pSym) DNA present in bacteroids of strain RCR1001 of Rhizobium leguminosarum biovar viceae has been compared qualitatively and quantitatively with that present in free living bacteria by hybridization experiments with appropriate probes. A decrease in the relative amount of pSym DNA was observed in bacteroids as compared to bacteria. No rearrangements of the symbiotically expressed pSym borne genes were detected in bacteroids.     

Mesoscale Modeling of Amphiphilic Fluid Dynamics

Abstract

So-called “vector models”, in which surfactant molecules retain only translational and orientational degrees of freedom, have been used to study the equilibrium properties of amphiphilic fluids for nearly a decade now. We demonstrate that hydrodynamic lattice-gas automata provide an effective means of coupling the Hamiltonian of such vector models to hydrodynamic flow with conserved momentum, thereby providing a self-consistent treatment of the hydrodynamics of amphiphilic fluids. In this “talk”, we describe these hydrodynamic lattice-gas models in two and three dimensions, and present their application to problems of amphiphilic-fluid hydrodynamics, including the dynamics of phase separation and the shear-induced sponge-to-lamellar phase transition.     

Animal xenodiversity in Italian inland waters: distribution, modes of arrival, and pathways

The paper provides a list of the non-indigenous animal species occurring today in Italian inland waters. Xenodiversity was found to amount to 112 species (64 invertebrates and 48 vertebrates), which contribute for about 2% to the inland-water fauna in Italy. Northern and central regions are most affected, and Asia, North America, and the rest of Europe are the main donor continents. The large majority of non-indigenous species entered Italy as a direct or indirect effect of human intervention. A difference between invertebrates and vertebrates was found for their mode of arrival (unintentional for invertebrates and intentional for vertebrates). Accidental transport, in association with both fish (for aquaculture or stock enhancement) and crops, has been the main vector of invertebrate introductions, whereas vertebrates were mostly released for stocking purposes. Overall stock enhancement (47.92%) and culture (37.5%) prevailed over the other pathways. Seventeen and 7 species of our list are included among the 100 worst invasive species of Europe (DAISIE) and of the world (IUCN), respectively. For some (but not all) non-indigenous species recorded in Italy the multilevel impact exerted on the recipient communities and ecosystems is known, even if rarely quantified, but knowledge on their chronic impact is still missing. Additional research is needed to provide criteria for prioritizing intervention against well established invaders and identify which new potential invader should be targeted as “unwanted”.     

Handling class imbalance problem in miRNA dataset associated with cancer

MiRNAs are small (~22nt long) non-coding RNA sequences; binds to the complementarity target sites in 3'' Untranslated Region (UTR) of mRNA sequences but not restricted to other mRNA regions viz., 5'' UTR and Coding sequences (CDS). Complementarity binding of miRNA to mRNA target sites either results in complete degradation of the mRNA itself or it may regulate the mRNA as an oncogene or as a tumor suppressor gene. However, the exact mechanism involved in identifying a miRNA to be associated with cancer is still unclear. Further, with the outburst in the number of miRNAs sequences recorded every year in miRBase, the gap is still widening mainly due to the laborious and economically unfavorable experimental procedures associated with the functional annotation. Motivated by the fact, we constructed a two-step support vector machine-based predictive model - miRSEQ and miRINT. However, the major pitfall during the construction of the model is the class imbalance problem. Hence, in order to overcome class imbalance problem, in the present study we empirically compare the effectiveness of two different methods viz., Synthetic Minority Oversampling Technique (SMOTE) and cost-senstive learning method. Performance measures were evaluated in terms of Precision and Recall. Based on our result, it was observed that for miRNA dataset with high class imbalance utilized for predicting association of cancer, cost-sensitive method outperformed the oversampling method.     

Mosquitoes and West Nile virus along a river corridor from prairie to montane habitats in eastern Colorado

We conducted studies on mosquitoes and West Nile virus (WNV) along a riparian corridor following the South Platte River and Big Thompson River in northeastern Colorado and extending from an elevation of 1,215 m in the prairie landscape of the eastern Colorado plains to 1,840 m in low montane areas at the eastern edge of the Rocky Mountains in the central part of the state. Mosquito collection during June‐September 2007 in 20 sites along this riparian corridor yielded a total of 199,833 identifiable mosquitoes of 17 species. The most commonly collected mosquitoes were, in descending order: Aedes vexans, Culex tarsalis, Ae. dorsalis, Ae. trivittatus, Ae. melanimon, Cx. pipiens, and Culiseta inornata. Species richness was higher in the plains than in foothills‐montane areas, and abundances of several individual species, including the WNV vectors Cx. tarsalis and Cx. pipiens and the nuisance‐biter and potential secondary WNV vector Ae. vexans, decreased dramatically from the plains (1,215‐1,487 m) to foothills‐montane areas (1,524‐1,840 m). Ae. vexans and Cx. tarsalis had a striking pattern of uniformly high abundances between 1,200‐1,450 m followed by a gradual decrease in abundance above 1,450 m to reach very low numbers above 1,550 m. Culex species were commonly infected with WNV in the plains portion of the riparian corridor in 2007, with 14 of 16 sites yielding WNV‐infected Cx. tarsalis and infection rates for Cx. tarsalis females exceeding 2.0 per 1,000 individuals in ten of the sites. The Vector Index for abundance of WNV‐infected Cx. tarsalis females during June‐September exceeded 0.5 in six plains sites along the South Platte River but was uniformly low (0–0.1) in plains, foothills and montane sites above 1,500 m along the Big Thompson River. A population genetic analysis of Cx. tarsalis revealed that all collections from the ≈190 km riparian transect in northeastern Colorado were genetically uniform but that these collections were genetically distinct from collections from Delta County on the western slope of the Continental Divide. This suggests that major waterways in the Great Plains serve as important dispersal corridors for Cx. tarsalis but that the Continental Divide is a formidable barrier to this WNV vector.     

Assessment of sustainable development: A case study of Wuhan as a pilot city in China

Building resource-conserving and environmental-friendly society (referred to as “two-oriented society”, TOS) is an important way proposed by the Chinese government to achieve sustainable development. In this paper, a pilot city of constructing TOS in China-Wuhan is taken as a case to evaluate the performance of TOS from 2005 to 2012. Treating the indicators of TOS as multi-dimensional vectors, this paper proposes a methodological framework by integrating the methods of vector angle and Euclidean distance to measure the angle and distance between the vector of annual status of TOS and the vector of planning target of TOS. Based on this, the paper employs coordination (the angle between the two vectors) and effectiveness (the distance between the two vectors) to describe the performance of TOS and its subsystems, including economic development (ED), social and people's well-being (SW), resource consumption (RC), resource recycling (RR), environmental quality (EQ) and pollution control (PC). Moreover, grey relational analysis approach is used to analyse the core factors influencing TOS construction. Results reveal that the performance of TOS in Wuhan is continually improved in the study period while the performance of its subsystems shows several differences: (1) both coordination and effectiveness of TOS, ED and SW keep on improving, while those of EQ fluctuate; (2) the effectiveness of both RR and PC shows a downward trend while the coordination of them fluctuates; (3) the actual value of RC indicators reaches the planning targets. Based on the analysis of determinants, we suggest that strengthening technological ability and adding investment are extremely important to improve the performance of RC and PC. For the sake of improving RR, it is critical to provide more government public expenditure and encourage financial institutions to provide more loans to stimulate and support the businesses. Moreover, increasing the amount of R&D funding and maintaining steady external economic environment are proved to be effective to improve all subsystems of TOS.     

Desert ants Cataglyphis fortis use self-induced optic flow to measure distances travelled

While foraging, desert ants of the genus Cataglyphis use a vector navigation (route integration) system for homing. Any vector navigation system requires that the animal is able to evaluate the angles steered and the distances travelled. Here we investigate whether the ants acquire the latter information by monitoring self-induced optic flow. To answer this question, the animals were trained and tested within perspex channels in which patterns were presented underneath a transparent walking platform. The patterns could be moved at different velocities (up to > 0.5 the ant's walking speed) in the same or in the opposite direction relative to the direction in which the animal walked. Experimental manipulations of the optic flow influenced the ant's homing distances (Figs. 2 and 4). Distance estimation depends on the speed of self-induced image motion rather than on the contrast frequency, indicating that the motion sensitive mechanism involved is different from mechanisms mediating the optomotor response. Experiments in which the ants walked on a featureless floor, or in which they wore eye covers (Fig. 6), show that they are able also to use additional (probably kinesthetic) cues for assessing their travel distance. Hence, even though optic flow cues are not the only ones used by the ants, the experiments show that ants are obviously able to exploit such cues for estimation of travel distance.     

毕赤酵母蛋白表达系统研究进展

选择合适的蛋白表达系统是外源基因能否成功表达的关键.毕赤酵母(Pichia pastoris)蛋白表达系统是近些年来发展起来的一种真核表达系统,与其他表达系统相比,该系统所具有的诸多优势使其研究价值和应用价值越来越广泛,已经成功表达了多种蛋白质.简要综述其特点、表达宿主菌、表达载体以及其元件、外源蛋白的表达及其影响因素等方面的基础研究和最新进展.     

CUP1为筛选标记的酿酒酵母整合型多基因表达载体的构建

为了赋予工业酿酒酵母对淀粉和纤维素的降解活性,提高酿酒酵母对粗木薯粉进行酒精发酵时的酒精产率;另一方面,为了解决工业酿酒酵母不适于使用营养缺陷型筛选标记对转化子进行筛选的问题,以及避免引入抗药性标记基因带来的安全性问题,构建了以抗铜蛋白基因CUP1为筛选标记的酿酒酵母整合型多基因表达载体.以载体pYES2-PMF-rDNA为基础,以新的筛选标记基因CUP1替换原有的尿嘧啶Ura-基因,得到载体pYES2M.再顺序插入葡聚糖内切酶基因eg3、葡萄糖淀糖酶基因gal和β-葡萄糖苷酶基因bgl1,构建得到以CUP1为筛选标记的酵母整合型三价表达载体pYES2M-eg3-ga1 -bgl1,其中每个基因都具有独立而完整的表达盒,包括启动子、信号肽和终止子,从而实现多基因单表达载体一次转化.     

Differential field response of two Mediterranean tree species to inputs of sewage sludge at the seedling stage

Land degradation and desertification is a common feature in Mediterranean landscapes due to extensive and intensive land use and natural or man induced disturbances. The ecosystem may need external inputs to recover its composition and function as soils are often impoverished and vegetal key stone species lost. We evaluated the effects of the application of fresh and air-dried biosolids in the establishment and morphological and physiological performance of seedlings of Pinus halepensis and Quercus ilex under dry Mediterranean field conditions. Seedling survival was not affected by biosolid treatments in any of the studied species both two and ten years after planting. During the first two years, growth was enhanced by the two biosolid treatments in relation to control, although the change in the biomass allocation pattern differed between species. Rooting depth was significantly enhanced by liquid biosolid in Q. ilex and marginally reduced in P. halepensis as well as the exploration of soil. As a consequence, root-to-shoot ratio reduced significantly with dry and liquid sludge due to promoted aboveground growth while maintaining and even reducing belowground fractions. An improvement of the nutritional status, of fertilized seedlings especially of phosphorus, is the explanation for the better field performance. Vector analysis revealed an important phosphorus limitation for both species that was overcome with the application of liquid (both species) and air-dried biosolid (pine). The higher growth of pine seedlings attained in the liquid biosolid treatment was coupled with a significant decrease in foliar δ¹³C, suggesting lower water use efficiency. The significant increase in foliar δ¹⁵N in the biosolid treatments in both species suggested that a large proportion of the total nitrogen uptake came from the applied biosolids. Instead, with regard to the low biosolid application rate used in the study, treatments had an overall positive effect as a restoration tool by improving nutritional status and promoting growth of planted seedlings.