WWW and the aerobiologist: operating instructions

For several years now, the World Wide Web (WWW) has left the realm of information technology and represents a fundamental everyday working tool for a wide variety of disciplines. Aerobiology, though a newcomer in this virtual space, is proceeding at a fast pace towards the creation of an easily accessible and effective information network. The web gives access to text, imagery, movie and sound with relatively low-cost and user-friendly interfaces conceived as graphical magazines. A practical way to start navigating and looking for information is to operate a ‘search engine’ which is a large database containing addresses on a wide spectrum of subjects. As an alternative, a few selected sites exist that can initialize your search by providing a thematic list of addresses. After leaving the entry ‘port’ you are directed from site to site and eventually end up with a lot more information than you initially thought. Excerpts: information on public and private institutions, access to databases and image catalogs, bibliographical information, overview of monitoring networks, directions on national and international research programs, news (calendar of meetings, courses, etc.). Information is provided for the non-expert user who asks himself the key questions: ‘Where do I start to browse the net?’ or ‘Can I become a provider of information on the net and, if so, is it terribly difficult?’ The idea is that everybody can in principle become a ‘surfer’ or a ‘provider’ dedicating a reasonable amount of time and effort to the task. What one ends up with is an easy-to-use and powerful tool that is already helping the whole aerobiological community to pursue its goals and reach out for necessary interdisciplinary approaches to unsolved scientific issues. The server AEROBIOLOGY INTERNATIONAL (http://www.fisbat.bo.cnr.it/AERO/) is presented as an example on how to proceed with the creation of a new server and its management.     

A universal approach for promoter strength evaluation supported by the web-based tool PromCal

In genetic engineering, gene expression is often modulated by replacements in promoter regions. Any deliberate intervention into the regulatory elements requires a subsequent evaluation based on analysis of reporter proteins. We have developed a new and rapid approach for characterization of promoter activity in which promoter strengths are determined by antibiotic resistance level. Values are expressed in comparison with those obtained from the reference promoter using the kanamycin resistance (aminoglycoside 3′-phosphotransferase) gene as a reporter. The new assay vector pSB1K0prom enables straightforward cloning of promoters or their subparts; therefore, mutations in different elements of the promoter region are easily introduced and analyzed. A series of promoters can be examined in parallel because no protein analysis is required other than determination of bacterial growth rates in the presence of increasing kanamycin concentrations. An internet application called PromCal for evaluation of experimental data has also been developed and is freely accessible at http://web.fkkt.uni-lj.si/biokemija/nskrlj/tools/PromCal.php.     

一种通用的、基于Agent的生物资源整合架构

众所周知,随着基因组测序工作的蓬勃发展和后基因组时代的到来,生物信息学数据呈指数级增长.生物界在享受着资源共享所带来便利的同时,也随着数据总量和复杂性的不断增加而变得异构化和分布化.目前,各种生物计算软件和数据库资源通常标准不一而且很难兼容.因此,如何在这些异构资源之间实现数据集成与软件共享是有效利用生物信息资源的关键.为解决以上问题,本文提出了一种新型的数据整合架构,该架构通过将web服务与并行计算相结合的方法,轻松地实现了对异地资源数据的访问、提取、转化以及整合.实验证明,本系统在处理异构、海量数据方面有着巨大的计算潜力.     

The Synthetic Gene Designer: a flexible web platform to explore sequence manipulation for heterologous expression

"Codon optimization" is a general approach to improving heterologous expression where genes are moved from their native genomes into alternatives that exhibit different patterns of codon usage. However, despite reports of successful manipulations and the existence of stand-alone codon optimization software packages or commercial services that offer to redesign genes, the scientific community lacks any systematic understanding of what exactly it means to optimize codon usage. Thus we present a bona fide web application, the "Synthetic Gene Designer," which contrasts with existing software by providing a centralized, free, and transparent platform for the broader scientific community to develop knowledge about synthetic gene design. Consistent with this goal, our software is associated with a moderated e-forum that promotes discussion of synthetic gene design and offers technical support. In addition, the Synthetic Gene Designer presents enhanced functionality over existing software options: for example, it enables users to work with non-standard genetic codes, with user-defined patterns of codon usage and an expanded range of methods for codon optimization. The Synthetic Gene Designer, together with on-line tutorials and the forum, is available at .     

The venomous secrets of the web droplets from the viscid spiral of the orb-weaver spider Nephila clavipes (Araneae, Tetragnatidae)

The capture web of N. clavipes presents viscous droplets, which play important roles in web mechanics and prey capture. By using scanning and transmission electron microscopy, it was demonstrated that the web droplets are constituted of different chemical environments, provided by the existence both of an aqueous and a lipid layer, which, in turn, present a suspension of tenths of vesicles containing polypeptides and/or lipids. GC/EI-MS Analysis of the contents of these vesicles led to the identification of some saturated fatty acids, such as decanoic acid, undecanoic acid, dodecanoic acid, tetradecanoic acid, octadecanoic acid, and icosanoic acid, while other components were unsaturated fatty acids, such as (Z)-tetradec-9-enoic acid, (Z)-octadec-9-enoic acid, and (Z)-icosa-11-enoic acid; and polyunsaturated fatty acids like (9Z,12Z)-octadeca-9,12-dienoic acid, (9Z,12Z,15Z)-octadeca-9,12,15-trienoic acid, and (11Z,14Z)-icosa-11,14-dienoic acid. Toxic proteins such as calcium-activated proteinase and metalloproteinase jararhagin-like precursor were also identified by using a proteomic approach, indicating the possible involvement of these enzymes in the pre-digestion of spiders' preys web-captured. Apparently, the mixture of fatty acids are relatively toxic to insects by topical application (LD50 64.3+/-7.6 ng mg(-1) honeybee), while the proteins alone present no topical effect; however, when injected into the prey-insects, these proteins presented a moderate toxicity (LD50 40.3+/-4.8 ng mg(-1) honeybee); the mixture of fatty acids and proteins is very toxic to the preys captured by the web droplets of the viscid spiral of Nephila clavipes when topically applied on them (LD50 14.3+/-1.8 ng mg(-1) honeybee).     

Chemical compound navigator: a web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds

A novel technique to annotate, query, and analyze chemical compounds has been developed and is illustrated by using the inhibitor data on HIV protease-inhibitor complexes. In this method, all chemical compounds are annotated in terms of standard chemical structural fragments. These standard fragments are defined by using criteria, such as chemical classification; structural, chemical, or functional groups; and commercial, scientific or common names or synonyms. These fragments are then organized into a data tree based on their chemical substructures. Search engines have been developed to use this data tree to enable query on inhibitors of HIV protease (http://xpdb.nist.gov/hivsdb/hivsdb.html). These search engines use a new novel technique, Chemical Block Layered Alignment of Substructure Technique (Chem-BLAST) to search on the fragments of an inhibitor to look for its chemical structural neighbors. This novel technique to annotate and query compounds lays the foundation for the use of the Semantic Web concept on chemical compounds to allow end users to group, sort, and search structural neighbors accurately and efficiently. During annotation, it enables the attachment of "meaning" (i.e., semantics) to data in a manner that far exceeds the current practice of associating "metadata" with data by creating a knowledge base (or ontology) associated with compounds. Intended users of the technique are the research community and pharmaceutical industry, for which it will provide a new tool to better identify novel chemical structural neighbors to aid drug discovery.     

蜘蛛位置对成功捕获猎物和球型网图案的影响

静坐在球型网的中心,蜘蛛可能遭受天敌的攻击并暴露在不利的天气条件下,如风和雨。然而,栖居于网的中心使蜘蛛比隐藏在隐蔽场所中的蜘蛛能更迅速地察觉并捕获猎物,这是因为猎物的位置仅能被位于网中心的蜘蛛所确定。对在隐蔽场所中的蜘蛛而言,提高对猎物捕获率的方式之一是尽量减少隐蔽所与网中心的距离。而且,网中心与隐蔽所之间较短的距离使蜘蛛能更迅速地逃离危险境况。我使用既在网中心、又在隐蔽场所的硬类肥蛛(Larinioides sclopetarius Clerck),来检验这两种行为如何影响对猎物的捕获成功率。隐藏在隐蔽场所中的蜘蛛更经常忽略猎物,使猎物也有比较多的逃离机会,这样,与在网中心的蜘蛛相比,猎物的损失率就更高。另外,研究了隐蔽场所的位置对球型网图案的影响。在大多数球型网中,网中心上方的区域比网下方小,丝也比较少,形成了结构不对称的网;隐蔽场所通常在网的上方。当隐蔽场所的位置在实验中被倒转时,就形成了非典型的球型网。最后,L．sclopetarius建造的网有很突出的边缘非对称性,与隐蔽场所相邻的区域面积较小,而远离隐蔽场所的区域面积较大,这也可解释为减少了隐蔽场所和网中心之间的距离[动物学报50(4)：559-565．2004]。     

Episodic-like memory: pigeons can report location pecked when unexpectedly asked

Pigeons were tested for their ability to report the location they recently pecked, without prior experience having to do so. They were first pretrained to report the location that they had just pecked. They were then trained on a conditional discrimination to associate yellow and blue samples with vertical and horizontal comparisons, respectively, independent of comparison location. On probe trials in testing, when after choosing a vertical or horizontal line following the yellow or blue sample, the pigeons were ‘asked’ which location they had just pecked, they showed a significant tendency to choose correctly in spite of the fact that location of the correct comparison was incidental to the task. Performing on probe trials is analogous to asking the pigeons an unexpected question about their recent behavior and it is similar to the episodic memory question asked of humans, “What did you have for breakfast this morning?”.     

A Service Approach for Architecting Application Independent Wireless Sensor Networks

The current sensor networks are assumed to be designed for specific applications, having data communication protocols strongly coupled to applications. The future sensor networks are envisioned as comprising heterogeneous devices assisting to a large range of applications. To achieve this goal, a new architecture approach is needed, having application specific features separated from the data communication protocol, while influencing its behavior. We propose a Web Services approach for the design of sensor network, in which sensor nodes are service providers and applications are clients of such services. Our main goal is to enable a flexible architecture in which sensor networks data can be accessed by users spread all over the world.