Molecular biodiversity. Case study: Porifera (sponges)

Biological diversity--or biodiversity--is the term given to the variety of life on Earth and the natural patterns it forms. The biodiversity we see today is the fruit of billions of years of evolution, shaped by natural processes and, increasingly, by the influence of humans. It forms the web of life of which we are an integral part and upon which we so fully depend. The research on molecular biodiversity tries to lay the scientific foundation of a rational conservation policy that has its roots in various disciplines including systematics/taxonomy (species richness), present day ecology (diversity of ecological systems), and functional genetics (genetic diversity). The results of ongoing genome analyses (genome projects and expressed sequence tag projects) and the achievements of molecular evolution may allow us not only to quantitate the diversity of the present biota but also to extrapolate to their diversification in the future. A link between biodiversity and genomics/molecular evolution will create a platform which we hope may facilitate a sustainable management of organismic life and ensure its exploitation for human benefit. In the present review we outline possible strategies, using the Porifera (sponges) as a prominent example. On the basis of solid taxonomy and ecological data, the high value of this phylum for human application becomes obvious, especially with regard to the field of chemical ecology and the desire to find novel potential drugs for clinical use. In addition, the benefit of trying to make sense of molecular biodiversity using sponges as an example can be seen in the fact that the study of these animals, which are "living fossils", gives us a good insight into the history of our planet, especially with respect to the evolution of Metazoa.     

A review on molecular topology: applying graph theory to drug discovery and design

Molecular topology is an application of graph theory and statistics in fields like chemistry, biology, and pharmacology, in which the molecular structure matters. Its scope is the topological characterization of molecules by means of numerical invariants, called topological indices, which are the main ingredients of the molecular topological models. These are statistical models that are instrumental in the discovery of new applications of naturally occurring molecules, as well as in the design of synthetic molecules with specific chemical, biological, or pharmacological properties. In this review, we focus on pharmacology, which is a novel field of application of molecular topology. Besides summarizing some recent developments, we also seek to bring closer this interesting biomedical application of mathematics to an interdisciplinary readership.

Enzymatic production of biosilica glass using enzymes from sponges: basic aspects and application in nanobiotechnology (material sciences and medicine)

Biomineralization, biosilicification in particular (i.e. the formation of biogenic silica, SiO₂), has become an exciting source of inspiration for the development of novel bionic approaches following “nature as model”. Siliceous sponges are unique among silica forming organisms in their ability to catalyze silica formation using a specific enzyme termed silicatein. In this study, we review the present state of knowledge on silicatein-mediated “biosilica” formation in marine sponges, the involvement of further molecules in silica metabolism and their potential application in nanobiotechnology and medicine. Werner E. G. Müller dedicated this study to Prof. Vera Gamulin (Rudjer Boskovic Institute, Zagreb, Croatia) in honour of her unique contributions in molecular evolution.     

生物除磷系统中聚磷菌检测常用技术

作为生物除磷系统中的主要功能菌,对聚磷菌菌群进行定性、定量分析是深入理解生物除磷系统、提高除磷效率的必然趋势。目前常用于检测聚磷菌的方法主要有生物化学法和分子生物学法,文章主要阐述了荧光原位杂交技术、聚合酶链反应技术、变性梯度凝胶电泳技术以及多技术结合使用的特点及应用情况,并在此基础上提出了改进措施以及聚磷菌检测技术的发展方向。     

Biosynthese und Struktur des Fettsäuresynthetase-Komplexes der Hefe

Genetic as well as biochemical data suggest that the yeast fatty-acid synthetase complex has an (AB)₆ protein structure where A and B represent multifunctional polypeptide chains with molecular weights of 185000 and 180000 daltons, respectively. Subunit A contains at least 3 and subunit B4 of the 8 known biochemical functions of the multienzyme complex. It is concluded that this complex structure has evolved from the corresponding prokaryotic system of monofunctional enzymes due to a selective advantage regarding the biosynthesis and assembly of the complex components.     

生物大分子加合物的检测及其在环境风险性评价中应用

环境中化学物质对人体致癌的风险性评价对于预防人类疾病和控制环境污染具有非常重要的意义。而反映暴露水平与生物效应的生物标记物研究不仅是导向预防研究的核心内容，也是环境致癌物风险评价的重要手段。传统的有毒化学物监测方法在研究人群暴露和危险度评价时得到的仅为近似接触量，而对个体在吸收、代谢、排泄，生物利用上的差异不能提供任何信息，分子生物标记物可用于检测生物暴露于环境致癌物的剂量和效应，生物体的遗传性或诱发性的敏感性差异，以及由环境致癌物引发的各种疾病的早期诊断，不仅提供个体有效接触量，还能提供许多化学物质结构与毒性之间关系及毒物代谢动力学方面的信息。与其他手段相比，分子生物标志物作为指示污染物危害效应的生物信号，其检测是从以往测定环境中化学物的含量估计生物体的接触水平，发展到直接检测化学物与生物受体结合产物的一种方法。文章对分子生物标志物一生物大分子加合物(如DNA，RNA，蛋白质加合物等)的形成机理以及在环境风险评价中的应用进行了综述：介绍了几种生物大分子加合物的检测方法，并对各种方法的特点进行评述，讨论了目前分子生物标志物研究存在的问题，并展望了该领域的应用前景。     

Physik der biologischen Gestaltbildung

In each generation cycle of a higher organism, a complex structure is formed under the instruction of the genes. In this process morphogenetic fields (probably spatial concentration patterns of substances) are involved which elicit cell responses giving rise to visible pattern and form. Autocatalytic short-range activation in conjunction with long-range (“lateral”) inhibition is capable of generating striking concentration patterns starting from near-uniform distributions. No features unusual in molecular biology are required, and self-regulatory properties observed experimentally in biological development can be accounted for. Cell responses to morphogenetic fields can include cell differentiation and the generation of bending moments, curvature and form in cell sheets giving rise to defined forms in organs and organisms. It appears that biological pattern formation is explicable on the basis of known physical laws and processes.     

Quantitative elimination of Flavokavines A and B from Kava Kava (<Emphasis Type="Italic">Piper methysticum</Emphasis> G. Forst) by isoelectric focused adsorptive bubble separation

Adsorptive bubble separation, though still rarely used, is a suitable method for enrichment of surface-active macromolecules such as enzymes and proteins. There is a lack of investigations with small molecules, which can also be separated from complex mixtures by this method. In this work, an aqueous extract of Kava Kava (Piper methysticum G. Forst) was used as a model system. Enrichment of undesirable Flavokavine A (7) and Flavokavine B (8) in the foam was influenced by the pH value, the amount of saponin as surface active substance, and the flow rate of the foam-forming gas. Efficiency was highest with diluted samples at pH 6.5. Under these conditions, transfer of Kavapyrone (1–6) to the foam was negligible.     

Biosensors as molecular tools for use in bioremediation

Biosensors are analytical tools, which use the biological specificity in sensing the target molecule. In this paper, the author reviews the design and application of molecular biosensors for use in bioremediation. The promoter selected from a genetic operon has been described as an interactive biological component for the target molecule to generate the signal. Different types of reporter systems have been described and as well as their application in tracking of levels of pollutants, nitrogen, phosphorus, dissolved oxygen in different habitats and toxic compounds. The paper emphasizes that in order to extend the applications of this scientific area, specialized research is needed in the aspects pertaining to bringing the biological recognition element into close proximity to the target molecules so that it can be integrated with the signal analysis system.     

Das Pinealorgan der Wirbeltiere: ein Modell für Untersuchungen von Rezeptor-und Effektormechanismen in neuronalen Systemen

Cell and molecular biological investigations have greatly contributed to our understanding of receptor and effector mechanisms in sensory, neuronal, and endocrine cells. A fascinating aspect of this line of research is how such mechanisms have evolved and how they interact with each other. As shown in this contribution, the vertebrate pineal organ is an interesting model to study these problems, because it undergoes a conspicuous transformation during phylogeny, comprises two well-chraracterized receptor mechanisms (photoreception and adrenoreception), and acts upon its targets via neuronal and neuroendocrine signals.

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Herrn Professor Dr. Drs. h. c. A. Oksche zum 65. Geburtstag gewidnet     

Soil organic matter and biological soil quality indicators after 21 years of organic and conventional farming

Organic farming systems often comprise crops and livestock, recycle farmyard manure for fertilization, and preventive or biocontrol measures are used for plant protection. We determined indicators for soil quality changes in the DOK long-term comparison trial that was initiated in 1978. This replicated field trial comprises organic and integrated (conventional) farming systems that are typical for Swiss agriculture. Livestock based bio-organic (BIOORG), bio-dynamic (BIODYN) and integrated farming systems (CONFYM) were compared at reduced and normal fertilization intensity (0.7 and 1.4 livestock units, LU) in a 7 year crop rotation. A stockless integrated system is fertilized with mineral fertilizers exclusively (CONMIN) and one control treatment remained unfertilized (NOFERT). The CONFYM system is amended with stacked manure, supplemental mineral fertilizers, as well as chemical pesticides. Manure of the BIOORG system is slightly rotted and in BIODYN it is composted aerobically with some herbal additives. In the third crop rotation period at normal fertiliser intensity soil organic carbon (C_org, w/w) in the plough layer (0–20 cm) of the BIODYN system remained constant and decreased by 7% in CONFYM and 9% in BIOORG as compared to the starting values. With no manure application C_org-loss was severest in NOFERT (22%), followed by CONMIN together with the systems at reduced fertiliser intensity (14–16%). Soil pH tended to increase in the organic systems, whereas the integrated systems had the lowest pH values. At the end of the third crop rotation period in 1998 biological soil quality indicators were determined. Compared to soil microbial biomass in the BIODYN systems the CONFYM soils showed 25% lower values and the systems without manure application were lower by 34%. Relative to the BIODYN soils at the same fertilization intensity dehydrogenase activity was 39–42% lower in CONFYM soils and even 62% lower in soils of CONMIN. Soil basal respiration did not differ between farming systems at the same intensity, but when related to microbial biomass (qCO₂) it was 20% higher in CONFYM soils and 52% higher in CONMIN as compared to BIODYN, suggesting a higher maintenance requirement of microbial biomass in soils of the integrated systems. The manure based farming systems of the DOK trial are likely to favour an active and fertile soil. Both, C_org and biological soil quality indicators were clearly depending on the quantity and quality of the applied manure types, but soil microbial biomass and activities were much more affected than C_org.     

胞外聚合物磷酸盐形态对生物除磷过程的影响研究

以不同DO条件下污泥龄(SRT)分别为10 d和30 d的两组实验室A/O-SBR反应器活性污泥为研究对象,探讨了胞外聚合物(EPS)磷酸盐形态对生物除磷过程的影响.结果表明,污泥絮体中的磷主要分布于EPS中,PO3-4-P和聚磷酸盐(Poly-P,包括低分子量聚磷酸盐LMW PolyP和高分子量聚磷酸盐HMW Poly-P)是EPS磷的主要形态;EPS对生物除磷的影响明显大于细菌细胞,EPS磷的厌氧降低量和好氧升高量为胞内磷变化量的2.8~6.4倍.EPS中的LMW Poly-P和HMW Poly-P含量均表现厌氧降低和好氧升高的变化规律;对于相同SRT的污泥,中DO(2.5~3.5 mg·L-1)条件较低DO(0.7~1.0 mg·L-1)条件下EPS的LMW Poly-P和HMW Poly-P有更大的厌氧降低量和好氧升高量,对应着更明显的生物除磷过程,说明EPS不仅是生物除磷过程的中转站,而且参与了生物聚磷过程.     

A new C12 alcohol identified as a sex pheromone and a trail-following pheromone in termites: the diene (<Emphasis Type="Italic">Z</Emphasis>,<Emphasis Type="Italic">Z</Emphasis>)-dodeca-3,6-dien-1-ol

The diunsaturated C12 alcohol (Z,Z)-dodeca-3,6-dien-1-ol (dodecadienol) has been characterized by GC-MS and FTIR as a novel releaser pheromone in termites. This alcohol identified in Ancistrotermes pakistanicus (Termitidae, Macrotermitinae) possesses a double pheromonal function which again illustrates the chemical parsimony of termites compared with other social insects. In workers, dodecadienol elicits trail-following at a very low concentration (activity threshold at 0.1 pg/cm of trail); in male alates it induces trail-following at a low concentration (1–10 pg/cm) and sexual attraction at a higher concentration (about 1 ng). Traces of the monounsaturated C12 alcohol (Z)-dodec-3-en-1-ol (dodecenol), known as a trail pheromone of several Macrotermitinae, were also found in the sternal gland extracts of A. pakistanicus, although only dodecadienol was present at the surface of the sternal gland. Workers of A. pakistanicus are not sensitive to dodecenol, but they are as sensitive to dodecatrienol as to dodecadienol. However, in the study area (Vietnam), A. pakistanicus is living in sympatry only with those Macrotermitinae using dodecenol as a trail pheromone, the foraging populations therefore being well isolated through their respective trail pheromones. The presence of three types of unsaturated C12 alcohols as releaser pheromones in the only Macrotermitinae subfamily is discussed, and a possible biosynthetic pathway from linoleic acid is proposed for dodecadienol.     

Contrasting factors controlling microbial respiratory activity in the sediment of two adjacent Mediterranean wetlands

Electron transport system (ETS) activity of sediments as an indication of microbial metabolic activity was examined in two adjacent Mediterranean wetlands (southern Spain). We determined the spatio-temporal variation in ETS, and we explored the potential biological [organic matter (OM), chlorophyll a (Chl a), aerobic and anaerobic bacteria] drivers of sediment ETS activity. ETS activity was notably higher in the eutrophic Lake Nueva (34.91 μl O₂ g⁻¹ D.W. h⁻¹) than in the hypertrophic Lake Honda (24.99 μl O₂ g⁻¹ D.W. h⁻¹). Strong spatial differences were observed in ETS in both study sites. Highest ETS values were achieved at the surface sediment at the deepest sampling station in each lake and a notable reduction in ETS with sediment depth was observed. By using linear regression and multiple regression analysis, OM was identified as the best predictor of ETS in Lake Honda while Chl a was the best predictor in Lake Nueva. The strong influence of OM supply on ETS activity in sediment from Lake Honda was the consequence of the labile nature of sedimentary OM, while a more refractory OM (with a higher contribution of vascular plants) comprised most of the sedimentary OM from Lake Nueva. By contrast, a large contribution of phytobenthos (supported by a higher lake water transparency) to ETS has been recognized in sediments from Lake Nueva. In summary, the results of this study revealed that the relative importance of planktonic primary producers (phytoplankton), benthic algae and vascular plants in the study sites could explain the differences observed in the intensity of sediment ETS as well as in their drivers.     

The Effect of Heat on the Physicochemical Properties of Bacteriophage MS2

The differences in physicochemical characteristics between infectious and non-infectious viral particles are poorly known. Even for heat, which is known as one of the most efficient treatments to inactivate enteric viruses, the global inactivation mechanisms have not been described yet. Such knowledge would help distinguish between both types of particles and therefore clarify the interpretation of the presence of viral genomes in food after heat treatment. In this study, we examined in particular the differences in electrostatic charge and hydrophobicity between the two particle types. MS2 phage, a common surrogate for enteric viruses, was used as a model virus. The heat-induced inactivation process of the infectious phages caused hydrophobic domains to be transiently exposed and their charge to become less negative. The particles also became progressively permeable to small molecules such as SYPRO Orange dye. The presence of non-infectious phage particles in which the genome was not accessible to RNases has been clearly demonstrated. These observations were done for MS2 phages exposed to a temperature of 60 °C. When exposed to a temperature higher than their critical temperature (72 °C), the particles were disrupted and the genome became available for RNases. At lower temperatures, 60 °C in this study, the transient expression of hydrophobic domains of remaining infectious phages appeared as an interesting parameter for improving their specific detection.     

水中细菌内毒素污染特性及检测方法研究进展

细菌内毒素是革兰氏阴性菌和某些蓝藻细胞壁的脂多糖复合物,主要由菌体死亡解体后释放,是常见的外源性致热原,具有强免疫刺激能力,与人类多种疾病密切相关.内毒素分子的耐受力好,耐热性强,不易被常规方法去除.饮用水和水环境中的内毒素可通过多种暴露途径导致机体潜在的健康风险,成为近年来研究的热点.本文概述了细菌内毒素的理化特性和生物活性,综述了细菌内毒素多种检测方法的研究进展,并对细菌内毒素的法定检测方法——鲎试验用于检测水体环境样品的干扰问题和排除方法进行分析.     

化学生物絮凝工艺的反应机理初探

考察了化学生物絮凝工艺中的Zeta电位、颗粒物粒度分布和溶解性有机物的分子质量分级,并分别与化学强化一级工艺和初沉池进行了对比.研究表明,相同药剂投加量下,化学生物絮凝工艺和化学强化一级工艺的出水Zeta电位值基本相等,化学生物絮凝工艺的回流污泥所携带的化学药剂几乎不影响反应池内颗粒物的稳定状态,其中的生物作用是该工艺对污染物的絮凝效果优于化学强化一级工艺的关键因素.在化学生物絮凝工艺中,投加药剂仅对粒径>10 μm颗粒物和分子质量>6 ku溶解性有机物有较好的去除效果,而生物絮凝作用不但可以促进对大粒径颗粒物和大分子质量溶解性有机物的去除,而且对小粒径颗粒物和小分子质量溶解性有机物也有较好的去除,其出水中粒径>3 μm的颗粒物被完全去除,分子质量为2～6 ku 的溶解性有机物的去除率也高达42.5%.     

Molecular Study of the Persistence of Infectious Human Norovirus on Food-Contact Surfaces

The aim of this study was to investigate the effect of relative humidity (RH) and temperature on norovirus (NoV) persistence as infectious particles on food-contact surfaces such as stainless steel and polyvinyl chloride (PVC). For this purpose, a new method combining enzymatic digestion with molecular beacon-based NASBA targeting the ORF1-ORF2 domain was developed to discriminate between infectious and noninfectious NoV. Stainless steel and PVC disks were contaminated with known amounts of human NoV and kept for 56 days at 7 and 20°C at high (86% ± 4%) and low (30% ± 10%) RH. NoV retained its putative infectivity for 56 days on PVC and for 49 days on stainless steel at 7°C and for 7 and 28 days, respectively, at low and high RH at 20°C on both tested surfaces. These results confirm that NoV persists in an infective state on inert surfaces for long periods of time and consequently may cause illness. The new molecular approach to detecting infectious NoV on inert surfaces may provide valuable information for evaluating environmental surface decontamination strategies.