Effect of water velocity on the early development of manganese-depositing biofilm in a drinking-water distribution system

Abstract A study of the development of biofilm colonizing the surfaces of pipes in a drinking-water distribution system has shown that water velocity significantly influenced the nature and physiological activity of the biofilm. Biofilm developed at a velocity of 0.5 m s⁻¹ actively oxidized and deposited manganese, but at 0.01 m s⁻¹ no manganese was deposited. Budding bacteria were the dominant microorganisms depositing manganese but a variety of other organisms were also present in the biofilms. The budding bacteria oxidizing manganese were Pedomicrobium manganicum and Metallogenium .     

Corrosion of metals in natural waters influenced by manganese oxidizing microorganisms

Case histories and proposed mechanisms formicrobiologically influenced corrosion of metals andalloys by metal depositing microorganisms arereviewed. Mechanisms with indirect participation ofthese microorganisms, usually iron- and manganeseoxidizing species, are distinguished from anothermechanism which accounts specifically for theelectrochemical properties of deposits containingoxides and hydroxides of Mn in higher oxidationstates. The possible influence of such deposits whichwere formed microbiologically is evaluated. Theevaluation is based on the principles ofelectrochemical corrosion of metals and on theelectrochemical properties of Mn^3+/4+- compounds.After briefly reviewing the microbiologicalMn-oxidation, experimental evidence for the predictedcorrosion by such deposits is provided and a model formicrobiologically influenced corrosion by manganeseoxidizing microorganisms is proposed for stainlesssteel. Possible consequences of the model andpractical aspects of such a corrosion are discussed.     

Plasmon-waveguide resonance studies of ligand binding to integral proteins in membrane fragments derived from bacterial and mammalian cells

A procedure has been developed for directly depositing membrane fragments derived from bacterial cells (chromatophores from Rhodopseudomonas sphaeroides) and mammalian cells (μ-opioid receptor- and MC4 receptor-transfected human embryonic kidney (HEK) cells and rat trigeminal ganglion cells) on the silica surface of a plasmon-waveguide resonance (PWR) spectrometer. Binding of ligands (cytochrome c₂ for the chromatophores, the peptide agonists DAMGO and melanotan-II that are specific for the μ-opioid and MC4 receptors, and two nonpeptide agonists that are specific for the CB1 receptor) to these membrane fragments has been observed and characterized with high sensitivity using PWR spectral shifts. The K_D values obtained are in excellent agreement with conventional pharmacological assays and with prior PWR studies using purified receptors inserted into deposited lipid bilayer membranes. These studies provide a new tool for obtaining useful biological information about receptor-mediated processes in real biological membranes.     

Sharing Research Data and Intellectual Property Law: A Primer

Sharing research data by depositing it in connection with a published article or otherwise making data publicly available sometimes raises intellectual property questions in the minds of depositing researchers, their employers, their funders, and other researchers who seek to reuse research data. In this context or in the drafting of data management plans, common questions are (1) what are the legal rights in data; (2) who has these rights; and (3) how does one with these rights use them to share data in a way that permits or encourages productive downstream uses? Leaving to the side privacy and national security laws that regulate sharing certain types of data, this Perspective explains how to work through the general intellectual property and contractual issues for all research data.For the researcher seeking to use another’s data, this Perspective offers some good news and some not as good news. The good news is that if a source of data—the researcher or repository—gives permission to reuse the data and one’s intended use fits within the scope of the permission, one need not be overly concerned with the details of the discussion that follows because the permission provides the legal basis for data reuse. For example, if one seeks data from the European Bioinformatics Institute, one will find that the terms of use state that “[t]he public databases of EMBL-EBI [The European Molecular Biology Laboratory-The European Bioinformatics Institute] are freely available by any individual and for any purpose” [1]. This would appear to give any individual academic researcher permission to copy and reuse the data at will. It leaves open a question about whether an employee acting on behalf of his or her employer (is s/he acting as “an individual”?) is equally granted this permission.There is, however, a catch. The EBI’s terms also warn the user that some third parties may claim intellectual property or other legal rights on the original data, and it is up to the researcher not to infringe these rights. This kind of legal uncertainty interferes with the productive reuse of research data. It can be avoided if the repository requires depositors to grant permission to downstream users or to give up any intellectual property rights they may have in the data. Alternatively, the final section of this Perspective describes means by which repositories can make it easy for depositors to signal the scope of the permission they grant to downstream users.In the absence of clear permission, mapping how intellectual property law does—and does not—apply to research data may be of use. In my view, the law makes all of this far more complicated than it need be. For those seeking to pick and choose which reuses of another’s data may be permitted by law, regrettably, the answers to the above questions are more context dependent than many would like.This is so for two reasons. First, the source of all intellectual property rights is national law. Certain international treaties harmonize intellectual property owners’ rights but leave the users’ rights to vary by country. Second, certain countries have added protection beyond what the treaties require. Specifically, the members of the European Union, candidate countries in Eastern Europe, Mexico [2], and South Korea have created a specialized database right that applies to certain databases created or maintained within their borders. These laws regulate uses of these databases only within their borders.     

Man-made microbes and man-made law

The Supreme Court of the US in 1980 granted a patent for a strain of Pseudomonas containing two plasmides after genetic manipulation. This is the first case of patenting a living organism. Whereas the patent law of US and of many other countries further more on supports the principle that natural products are not patentable man-made microorganisms on the other hand fullfil very important crucials of patentability as far as they are new, unobvious, reproducible and useful. The situation arising as the result of this decision is described and the implications and consequenses for the patent law, the taxonomy and the general biological thought are discussed.     

Problems related to the deposition of microorganisms in the patent procedure

Some practical aspects concerning deposition of microbial strains in connection with patenting are discussed. In particular, situations requiring deposition of individual strains, mixed cultures or associants are analysed. Problems of patent legislation pertinent to deposition of microorganisms are discussed.     

Rapid identification and quantitation of small numbers of microorganisms by a chemiluminescent immunoreaction.

A method (patent pending) for rapidly identifying and quantitating small numbers of microorganisms was developed based on the specific immunoreaction of microorganisms with homologous antibodies linked by conjugation to peroxidase. The high sensitivity of the method is due to the use of a chemiluminescent reaction for the determination of the enzyme. The reaction was performed on Alcar supports with low nonspecific adsorption. The very low noise achieved permitted the detection of as few as 30 to 300 bacterial cells.     

专利微生物菌种的保藏与发放统计分析

对WIPO公开的"国际保藏机构2001～2010年专利微生物保藏与发放"数据进行了统计分析。结果表明:全世界的专利菌种保藏量与发放量处于快速增长中;美国是专利菌种保藏与发放量最多的国家;近年中国的专利菌种年保藏量实现三连冠,但专利菌种的发放率处于极低水平。     

Rapid identification and quantitation of small numbers of microorganisms by a chemiluminescent immunoreaction.

A method (patent pending) for rapidly identifying and quantitating small numbers of microorganisms was developed based on the specific immunoreaction of microorganisms with homologous antibodies linked by conjugation to peroxidase. The high sensitivity of the method is due to the use of a chemiluminescent reaction for the determination of the enzyme. The reaction was performed on Alcar supports with low nonspecific adsorption. The very low noise achieved permitted the detection of as few as 30 to 300 bacterial cells.     

Use of the method of enriching of soil samples with calcium carbonate for isolation of Actinomyces

Possible application of a modified procedure for treatment of soil samples with calcium carbonate under humid conditions to isolation of actinomycetes was studied. The procedure proved to be rather efficient in regard to increasing the number of the isolates including representatives of rare genera as compared with the routine methods. The number of microorganisms isolated from the soil samples treated with calcium carbonate under humid conditions was 2 orders higher than that from untreated soil samples. 1033 actinomycete cultures were isolated from the soil samples treated in accordance with the above procedure and only 597 cultures were isolated from the untreated soil samples. The antibiotic activity of the isolates was studied and their taxonomic position at the genus level was determined. The preliminary treatment of soil samples equally stimulated development of actinomycetes belonging to different genera. It is advisable that the described procedure for isolation of actinomycetes from soil samples in screening of cultures producing new antibiotics be used in combination with other selective methods of isolation.     

Antibody-drug conjugates: Intellectual property considerations

Antibody-drug conjugates are highly complex entities that combine an antibody, a linker and a toxin. This complexity makes them demanding both technically and from a regulatory point of view, and difficult to deal with in their patent aspects. This article discusses different issues of patent protection and freedom to operate with regard to this promising new class of drugs.     

Antibody-drug conjugates: Intellectual property considerations

Antibody-drug conjugates are highly complex entities that combine an antibody, a linker and a toxin. This complexity makes them demanding both technically and from a regulatory point of view, and difficult to deal with in their patent aspects. This article discusses different issues of patent protection and freedom to operate with regard to this promising new class of drugs.     

Molecular Threading: Mechanical Extraction,Stretching and Placement of DNA Molecules from a Liquid-Air Interface

We present “molecular threading”, a surface independent tip-based method for stretching and depositing single and double-stranded DNA molecules. DNA is stretched into air at a liquid-air interface, and can be subsequently deposited onto a dry substrate isolated from solution. The design of an apparatus used for molecular threading is presented, and fluorescence and electron microscopies are used to characterize the angular distribution, straightness, and reproducibility of stretched DNA deposited in arrays onto elastomeric surfaces and thin membranes. Molecular threading demonstrates high straightness and uniformity over length scales from nanometers to micrometers, and represents an alternative to existing DNA deposition and linearization methods. These results point towards scalable and high-throughput precision manipulation of single-molecule polymers.     

Biology of budding bacteria

Summary Budding bacteria from aquatic or terrestrial habitats were found to accumulate ferric oxide hydrate (ferric hydroxide) on their cell surfaces. Metal paper clips served as the source of oxidizable iron. Pure cultures deposited ferric hydroxide during growth on sea water medium at a pH of 7.8, but not in a mineral salts medium of normal ionic strength, of pH 7.2, and without NaCl, although some active strains came from fresh water or soil.Ferric iron deposition was found to be initiated at primary active sites on the cell surface; the hyphae and rods eventually become completely encased by the heavy coat.The presence of iron depositing, budding bacteria in fresh water, brackish water or sea water indicates an ubiquitous distribution of these microorganisms.Actively depositing isolates from marine environments are more closely related to Pedomicrobium than to Hyphomicrobium spp. because of their multiple formation of hyphae from rod-shaped swarmer cells. A taxonomic and cultural study of these new forms is in progress.     

A new technique of depositing phospholipid bilayers on quartz surfaces: its use in membrane spin-label studies

We have developed a new improved technique termed the parallel-beam spattering (PBS) method for depositing phospholipid bilayers on quartz surfaces. This technique involves atomizing the phospholipid mixture with a stream of nitrogen gas and passing this atomized mixture through two orifices separated by a distance to achieve a parallel beam of atomized particles before deposition on the quartz plate. A static electric field can easily be applied to the quartz surface. Also a goniometer of new design has been constructed to allow precise positioning of the deposited phospholipid bilayers with reference to the magnetic field. We have utilized the PBS method to deposit phosphatidylcholine/nitroxyl labeled cholestane mixtures on quartz plates and have found that hydrated bilayers of these mixtures yield ESR spectra with essentially the same characteristics as those obtained using more conventional techniques. The distinct advantage of the new technique for depositing bilayers is that there is no spectral anomaly present which usually is present when the more conventional method of depositing bilayers is used. The spectral anomaly is apparently caused by a portion of the bilayers aligned in directions not directly parallel to the quartz surface. For precision work the spectral anomaly is unacceptable. It is not observed with the new PBS method which has yielded highly reproducible results.     

United States patents and fungal cultures

Summary Fungal biotechnology has generated a voluminous amount of technical literature and scientific data. Patents probably contain the most complete and detailed information about the use of fungal cultures in biotechnology. This article contains a brief review of the United States patent system where microorganisms form an integral part of the disclosure and explains the role of the American Type Culture Collection (ATCC) as a patent culture depository. A list based on the application of the ATCC fungal strains which have been cited or used in US patents and the names of the inventors, the titles of the inventions, and their patent numbers are included. This provides resource material particularly for developing countries as they begin to establish their own biotechnology.     

Transposon tools: worldwide landscape of intellectual property and technological developments

DNA transposons are considered to be good candidates for developing tools for genome engineering, insertional mutagenesis and gene delivery for therapeutic purposes, as illustrated by the recent first clinical trial of a transposon. In this article we set out to highlight the interest of patent information, and to develop a strategy for the technological development of transposon tools, similar to what has been done in many other fields. We propose a patent landscape for transposon tools, including the changes in international patent applications, and review the leading inventors and applicants. We also provide an overview of the potential patent portfolio for the prokaryotic and eukaryotic transposons that are exploited by spin-off companies. Finally, we discuss the difficulties involved in tracing relevant state-of-the-art of articles and patent documents, based on the example of one of the most promising transposon systems, including all the impacts on the technological development of transposon tools.     

Stress: a Factor to be Considered in Heterotrophic Microorganism Enumeration from Aquatic Environments

Heterotrophic microorganisms in water samples are susceptible to the transient stress of warmed agar used in the standard methods pour plate procedure, causing significantly decreased recoveries in comparison with a spread plate technique. Microbial starvation can increase susceptibility to a transient warming stress. The standard plate count procedure, as presently described, should not be considered for quantitation of microorganisms from aquatic environments.     

Patenting in biotechnology: a review of the 20th Symposium of ECB8

The patenting of biotechnological inventions is practically in harmony with the general requirements of patent protection. It stands still in the foreground of interests since this is the only technical field where the living material itself may be the subject matter of patents. In consequence ethical problems have arisen first of all in the patenting of human cells and genes in which there is no agreement between R&D firms, patent offices and green movements. This has called for the elaboration of special Directives. On the other hand, patent systems are instrumental in safeguarding biodiversity. This review gives a picture of the patenting situation in biotechnology in the European Patent Office and in Hungary, the host country of the Congress. It also gives practical advice to biotechnological researchers on how to draft the applications and to observe the time limits, as well as on the necessity and possibilities of the deposit of microorganisms.