Milestones in the Biochemistry of Silicon: From Basic Research to Biotechnological Applications

6.7 Gigatonnes of silicon are processed each year by marine organisms. Since it was known that silicon is an essential element for many biological systems, significant advances in the biochemistry of this element have been achieved from the classical viewpoint of silicon being a purely inorganic element. This article describes the proteins, genes, and molecular mechanisms of silicon metabolism in diatoms and sponges. These studies may help to reveal the role of silicon for optimal development and growth in many plants and animals as well as initiate the development of new technological methods for the shape-controlled production of new patterned silicone-based materials.     

A novel fluorescent silica tracer for biological silicification studies.

BACKGROUND: Biological silica production has drawn intense attention and several molecules involved in biosilicification have been identified. Cellular mechanisms, however, remain unknown mainly due to the lack of probes required for obtaining information on live specimens. RESULTS: The fluorescence spectra of the compound 2-(4-pyridyl)-5-((4-(2-dimethylaminoethylaminocarbamoyl)methoxy)phenyl)oxazole (PDMPO) are affected by the presence of >3.2 mM silicic acid. Increase in intensity and shift in the fluorescence coincide with the polymerization of Si. The unique PDMPO-silica fluorescence is explored here to visualize Si deposition in living diatoms. The fluorophore is selectively incorporated and co-deposited with Si into the newly synthesized frustules (the outer silica shells) showing an intense green fluorescence. CONCLUSIONS: We suggest that a fluorescence shift is due to an interaction between PDMPO and polymeric silicic acid. PDMPO is an excellent probe for imaging newly deposited silica in living cells and has also a potential for a wide range of applications in various Si-related disciplines, including biology of living organisms as diatoms, sponges, and higher plants, clinical research (e.g. lung fibrosis and cancer, bone development, artificial bone implantation), and chemistry and physics of materials research.     

Multidimensional approaches in biochemical speciation analysis

An understanding of the mechanisms controlling the essentiality and toxicity of trace elements in biological systems at the molecular level depends critically on the possibility of the identification, characterization, and quantification of chemical forms of these elements involved in life processes.Hyphenated techniques based on the combination of (electro)chromatography with ICP MS have become a routine tool for the analysis for metallospecies present in biological tissues. Finer analytical information on the true (down to individual species) speciation of trace elements in living organisms can be obtained by adding additional dimensions to the separation and detection steps, consisting of a sequential use of different HPLC separation mechanisms and capillary electrophoresis at the separation level, and of the use of electrospray MS, including collision induced dissociation MS, on the detection level. The value of the instrumental analytical data is decisively enhanced by the complementary use of molecular biology approaches involving gene identification, cloning and in vitro reproduction of the metal-controlled processes. A brief summary of the recent progress in biochemical speciation analysis is presented in the context of the latest research carried out in the authors' laboratory.     

Marine natural products

This review covers the marine natural products literature for the year 2000 and is organized phylogenetically, with sections on marine microorganisms and phytoplankton, green algae, brown algae, red algae, sponges, coelenterates, bryozoans, molluscs, tunicates. echinoderms and miscellaneous marine organisms. There is an emphasis on new structures, stressing their biological activities, source organisms and countries of origin, and also syntheses that confirm the structures of known compounds. The review contains 869 structures and 592 references, of which 434 appeared between January and December 2000.     

式根岛海绵宏基因组文库的抗菌吲哚三聚体

构建了式根岛海绵的宏基因组文库,对其进行双层琼脂抗菌活性功能筛选,得到1株抗菌活性克隆pDC111. 以抗菌活性为指导,对pDC111的化学成分进行分析和分离,得到化合物1,并通过1D NMR（¹H NMR和 ¹³C NMR）及2D NMR（¹H-¹H COSY,HMQC和HMBC）结合HR-TOFMS数据,确定其结构为吲哚三聚体. 抗菌活性实验结果表明,化合物1在10 μg/paper（id=6 mm）时,对蜡状芽孢杆菌的抑菌圈达到12 mm. 本文利用功能宏基因组方法,从蕴藏大量不可培养微生物的海绵中寻找到活性物,并具有通过分子生物学技术获得其功能基因的潜能.     

An Approach toward 17-Arylsubstituted Marginatafuran-Type Isospongian Diterpenoids via a Palladium-Catalyzed Heck–Suzuki Cascade Reaction of 16-Bromolambertianic Acid

Isospongian diterpenes are a small but growing family of natural tetracyclic secondary metabolites isolated from marine organisms, primarily sponges and nudibranchs. A palladium-catalyzed domino Heck–Suzuki reaction sequence for the synthesis of the tetracyclic skeleton of marginatafuran-type isospongian diterpenoids with a wide variety of substituents in the C-17 position is reported. The proposed approach was based on selective transformations of the accessible plant diterpenoid lambertianic acid and includes an intramolecular Heck reaction of 16-bromolambertianic and arylation of the palladium intermediate with arylboronic acid. The influence of the nature of the substituent both in arylboronic acids and in the furan ring of 16-bromolambertianic acid on the direction and chemoselectivity of the reaction has been studied. The described derivatization of natural furanolabdanoid lambertianic acid produced new functionalized molecules for biological study and gave novel insights into the reactivity of complex molecular structures.     

八十年代海洋天然有机化学的进展

八十年代以来,海洋天然有机化学仍然继续发展,大量新的化合物,尤其是具有生理活性的化合物不断出现,海洋天然物的生物合成和人工合成研究也有新的进展。在海洋生物中,研究得最多的是海藻和海绵,其次便是珊瑚。     

Cold-water marine natural products

Marine natural products isolated from organisms collected from cold-water habitats are described. Emphasis is on bioactive compounds from tunicates, sponges, microbes, bryozoans, corals, algae, molluscs and echinoderms. Synthetic studies of several important classes of cold-water compounds are highlighted.     

DNA Methylation: Site-Specific Methylations Cause Gene Inactivation

In the molecular biology of eukaryotic organisms, the elucidation of mechanisms involved in the regulation of gene expression has assumed an important role. All cells of an organism carry the same genes, but differ in the patterns of genes they express. There is an increasing amount of evidence that cancer cells exhibit a pattern of gene expression which can be very different from that of normal cells. One of the molecular signals that has been recognized in the regulation of gene expression in eukaryotes is the modified nucleotide 5-methylcytosine (5-mC). Through experiments in well-characterized eukaryotic systems, evidence has been adduced that the introduction of 5-mC into highly specific sequences, particularly into the 5′ and promoter regions of a gene, can cause gene inactivation. Viral and other eukaryotic systems have helped in the recognition of this cause-and-effect relationship. Inactive genes are frequently hypermethylated in the promoter region; active genes are hypomethylated. However, these correlations are not always as simple and straightforward. The biochemical mechanisms by which site-specific DNA methylations cause gene inactivation have not yet been determined. It is plausible to postulate that promoter methylations could somehow affect the binding of cellular enzymes involved in recognizing the promoter of a gene. Structural alterations of DNA promoter sequences arising from DNA methylations could also be important. DNA methylation is likely to represent a long-term inactivation signal, since it is presently thought that patterns of DNA methylation can be changed only by DNA replication and specific inhibition of post-replicative maintenance methylation.     

Gelatine thin films as biomimetic surfaces for silica particles formation

The formation of silica nanostructures by several living organisms, such as diatoms or sponges, involves specific macromolecules that control the growth and the organization of silica nanoparticles. In order to investigate if a single molecular system could perform both particle size control and morphological template, gelatine thin films of various concentration and strength were prepared as biomimetic models and their reactivity towards sodium silicate aqueous solutions was studied. Simultaneous formation of silica particles in the nanometric and micrometric size range was observed. The former corresponds to colloids grown at the surface of the gelatine films and the latter to particles induced by gelatine chain brushes formed at the film/water interface. These results are in good agreement with well-known principles of biomineralization and suggest that multi-molecular systems, rather than single components, are responsible for biogenic silica nanostructure formation.     

Biologically Active Metabolites from Marine Organisms

The authors' chemical studies on the secondary metabolites from marine organisms are summarized. From marine sponges, algae and soft corals grown in the South China Sea, thirty five compounds were isolated. Their structures were elucidated mainly on the basis of spectral evidence. The biological activities of dysamides, 1–6 , stelletin 21 and lactone 23 are reported.     

Modeling in biological chemistry. From biochemical kinetics to systems biology

A brief review on biochemical kinetics in the twentieth century mainly concerned with enzyme kinetics and cooperative processes is presented. Molecular biology and, in particular, structural biology provided the basis for modeling biological phenomena at the molecular level. Structure was recognized as the ultimate and only level at which biological processes find an explanation that is satisfactory for chemists and physicists. A new epoch in biology was initiated by successful extensions of the molecular approach from individual molecules and reactions to the cellular and organismic level. Starting with sequencing of whole genomes in the 1980s more and more techniques became available that are suitable for upscaling from molecules to cells. A series of research programs was initiated: genomics dealing with sequencing the DNA of whole organisms, proteomics considering all proteins of a cell and their interactions, metabolomics studying all metabolic reactions of a cell or an organism, and functional genomics or systems biology aiming at an exploration of the dynamics of complete biological entities. At the same time computational facilities have experienced an unexpected development in speed of calculations and storing devices. At present computer simulations of whole cells at molecular resolution are within reach. The challenge for the theorist in biology is to develop methods for handling the enormously complex networks of gene regulation and metabolism in such a way that biological questions can be addressed. This goal cannot be achieved by dynamical systems theory alone. What is needed is a joint effort from different mathematical disciplines supported by empirical knowledge and tools from discrete mathematics to informatics. Two sections with selected examples from our own laboratory dealing with structural bioinformatics of RNA and with a dynamical systems approach to gene regulation are added.     

At a glance: cellular biology for engineers

Engineering contributions have played an important role in the rise and evolution of cellular biology. Engineering technologies have helped biologists to explore the living organisms at cellular and molecular levels, and have created new opportunities to tackle the unsolved biological problems. There is now a growing demand to further expand the role of engineering in cellular biology research. For an engineer to play an effective role in cellular biology, the first essential step is to understand the cells and their components. However, the stumbling block of this step is to comprehend the information given in the cellular biology literature because it best suits the readers with a biological background. This paper aims to overcome this bottleneck by describing the human cell components as micro-plants that form cells as micro-bio-factories. This concept can accelerate the engineers' comprehension of the subject. In this paper, first the structure and function of different cell components are described. In addition, the engineering attempts to mimic various cell components through numerical modelling or physical implementation are highlighted. Next, the interaction of different cell components that facilitate complicated chemical processes, such as energy generation and protein synthesis, are described. These complex interactions are translated into simple flow diagrams, generally used by engineers to represent multi-component processes.     

A comparative survey of proteins from recalcitrant tissues of a non-model gymnosperm, Douglas-fir

Most research in plants and other organisms has, for the sake of convenience, focused on the use of model species to identify mechanisms that are conserved throughout the whole kingdom. Nevertheless, unique features and processes such as those related to plant cell wall and fiber formation, and to wood quality, sometimes need to be studied directly in the non-model organism of interest. Such organisms, like the economically and ecologically important gymnosperm Douglas-fir (Pseudotsuga menziesii), which is one of the crucial softwood timber species in Northern America, are often difficult to investigate. High phenolic, resin, and tannin contents in the woody tissues, as well as an incompletely sequenced genome, have contributed greatly to the species' recalcitrance for molecular biology investigations. In this study, we present a complete procedure detailing protein sample preparation, separation, and proteomic analysis based on cross-species identification of Douglas-fir. Proteins from the cambial zone, mature needles, and in vitro callus were extracted, purified, and separated via 1D and 2D SDS-PAGE. One-dimensional electrophoresis coupled with ESI-MS/MS was used for cross-species protein identification in order to evaluate the potential of this approach and reveal major differences in protein profiles among tested tissues. Identified proteins were functionally and developmentally compared. The likely contribution of these proteins to the properties of the cell wall and wood is indicated and discussed.     

A journey under the sea: the quest for marine anti-cancer alkaloids

The alarming increase in the global cancer death toll has fueled the quest for new effective anti-tumor drugs thorough biological screening of both terrestrial and marine organisms. Several plant-derived alkaloids are leading drugs in the treatment of different types of cancer and many are now being tested in various phases of clinical trials. Recently, marine-derived alkaloids, isolated from aquatic fungi, cyanobacteria, sponges, algae, and tunicates, have been found to also exhibit various anti-cancer activities including anti-angiogenic, anti-proliferative, inhibition of topoisomerase activities and tubulin polymerization, and induction of apoptosis and cytotoxicity. Two tunicate-derived alkaloids, aplidin and trabectedin, offer promising drug profiles, and are currently in phase II clinical trials against several solid and hematologic tumors. This review sheds light on the rich array of anti-cancer alkaloids in the marine ecosystem and introduces the most investigated compounds and their mechanisms of action.     

Biomineralization of unicellular organisms: an unusual membrane biochemistry for the production of inorganic nano- and microstructures

With evolution, Nature has ingeniously succeeded in giving rise to an impressive variety of inorganic structures. Every organism that synthesizes biogenic minerals does so in a form that is unique to that species. This biomineralization is apparently biologically controlled. It is thus expected that both the synthesis and the form of every specific biogenic mineral is genetically determined and controlled. An investigation of the mechanism of biomineralization has only become possible with the development of modern methods in molecular biology. Unicellular organisms such as magnetic bacteria, calcareous algae, and diatoms, all of which are amongst the simplest forms of life, are particularly suited to be investigated by these methods. Crystals and composites of proteins and amorphous inorganic polymers are formed as complex structures within these organisms; these structures are not known in conventional inorganic chemistry.     

Bioactive Peptides and Proteins from Centipede Venoms

Venoms are a complex cocktail of biologically active molecules, including peptides, proteins, polyamide, and enzymes widely produced by venomous organisms. Through long-term evolution, venomous animals have evolved highly specific and diversified peptides and proteins targeting key physiological elements, including the nervous, blood, and muscular systems. Centipedes are typical venomous arthropods that rely on their toxins primarily for predation and defense. Although centipede bites are frequently reported, the composition and effect of centipede venoms are far from known. With the development of molecular biology and structural biology, the research on centipede venoms, especially peptides and proteins, has been deepened. Therefore, we summarize partial progress on the exploration of the bioactive peptides and proteins in centipede venoms and their potential value in pharmacological research and new drug development.     

分子信标的构建及其应用研究进展

分子信标（molecular beacon,MB）是一种寡聚核苷酸荧光探针,其具有灵敏度高、特异性强、操作简单以及不必与未反应的探针分离即可实时检测等优点,在分子生物学和基因组学及分子医学等领域具有十分重要的应用价值。 本文介绍了近年来出现的各种新型分子信标的结构及工作原理,概述了分子信标技术在生命科学领域中的应用,展望了分子信标技术的发展趋势。     

Accreditation of GMO detection laboratories: Improving the reliability of GMO detection

Reliable and efficient methods for detecting genetically modified organisms (GMOs) are essential for establishing an effective system for traceability all along the supply chain from seed producers to final consumers. The latter is especially meaningful in European Union and other countries where strict legislations on GMOs were set up. Performance of the methods used in laboratories around the world should be uniform, in order to obtain reliable and comparable results. Accreditation is a suitable system for harmonising procedures in each testing laboratory. In this paper, key elements for the accreditation of molecular biology methods for GMO detection according to ISO/IEC 17025 are described. The procedures described are also valuable for the accreditation of molecular methods for all laboratory diagnostics where qualitative and quantitative characterisation of nucleic acids is needed.     

Natural Products from Tongan Marine Organisms

The islands of the South Pacific Ocean have been in the limelight for natural product biodiscovery, due to their unique and pristine tropical waters and environment. The Kingdom of Tonga is an archipelago in the central Indo-Pacific Ocean, consisting of 176 islands, 36 of which are inhabited, flourishing with a rich diversity of flora and fauna. Many unique natural products with interesting bioactivities have been reported from Indo-Pacific marine sponges and other invertebrate phyla; however, there have not been any reviews published to date specifically regarding natural products from Tongan marine organisms. This review covers both known and new/novel Marine Natural Products (MNPs) and their biological activities reported from organisms collected within Tongan territorial waters up to December 2020, and includes 109 MNPs in total, the majority from the phylum Porifera. The significant biological activity of these metabolites was dominated by cytotoxicity and, by reviewing these natural products, it is apparent that the bulk of the new and interesting biologically active compounds were from organisms collected from one particular island, emphasizing the geographic variability in the chemistry between these organisms collected at different locations.