Avenues of discovery in bioprospecting.
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Animals↗
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Ethnobotany/ethnopharmacology and mass bioprospecting: issues on intellectual property and benefit-sharing.
Ethnobotany/ethnopharmacology has contributed to the discovery of many important plant-derived drugs. Field explorations to seek and document indigenous/traditional medical knowledge (IMK/TMK), and/or the biodiversity with which the IMK/TMK is attached, and its conversion into a commercialized product is known as bioprospecting or biodiversity prospecting. When performed in a large-scale operation, the effort is referred to as mass bioprospecting. Experiences from the mass bioprospecting efforts undertaken by the United States National Cancer Institute, the National Cooperative Drug Discovery Groups (NCDDG) and the International Cooperative Biodiversity Groups (ICBG) programs demonstrate that mass bioprospecting is a complex process, involving expertise from diverse areas of human endeavors, but central to it is the Memorandum of Agreement (MOA) that recognizes issues on genetic access, prior informed consent, intellectual property and the sharing of benefits that may arise as a result of the effort. Future mass bioprospecting endeavors must take heed of the lessons learned from past and present experiences in the planning for a successful mass bioprospecting venture.
Conservation of Natural Resources↗
Venom evolution widespread in fishes: a phylogenetic road map for the bioprospecting of piscine venoms.
Knowledge of evolutionary relationships or phylogeny allows for effective predictions about the unstudied characteristics of species. These include the presence and biological activity of an organism's venoms. To date, most venom bioprospecting has focused on snakes, resulting in six stroke and cancer treatment drugs that are nearing U.S. Food and Drug Administration review. Fishes, however, with thousands of venoms, represent an untapped resource of natural products. The first step involved in the efficient bioprospecting of these compounds is a phylogeny of venomous fishes. Here, we show the results of such an analysis and provide the first explicit suborder-level phylogeny for spiny-rayed fishes. The results, based on approximately 1.1 million aligned base pairs, suggest that, in contrast to previous estimates of 200 venomous fishes, >1,200 fishes in 12 clades should be presumed venomous. This assertion was corroborated by a detailed anatomical study examining potentially venomous structures in >100 species. The results of these studies not only alter our view of the diversity of venomous fishes, now representing >50% of venomous vertebrates, but also provide the predictive phylogeny or "road map" for the efficient search for potential pharmacological agents or physiological tools from the unexplored fish venoms.
Animals↗
Scale and sustainability of marine bioprospecting for pharmaceuticals.
Collecting marine organisms for the discovery and development of pharmaceuticals has been perceived variously as sustaining and threatening conservation. Our initial expectations that marine bioprospecting might pose conservation challenges were largely not confirmed. Thousands of marine species have been collected for initial assessment, but usually only in very small amounts. Very few compounds are sufficiently promising to provoke re-collections, where volumes can be much larger. This is where conservation concerns may arise, particularly if the organism is rare, has a restricted distribution, or is targeted in one narrow area. However, industry generally seeks to avoid dependency on small populations, for economic as well as ecological reasons. Alternative supply strategies to wild capture include synthesis and culture. Mandatory collection protocols and environmental impact (stock) assessments are useful routes for management to achieve sustainable use where extraction is desirable. In general, the scanty information available suggests that marine bioprospecting for pharmaceuticals may have minimal impacts on the environment, particularly compared with those created by other pressures.
Animals↗
Brazil needs a national debate on bioprospecting.
An overview of current state-of-art methodologies and strategies applied in bioprospecting for drug discovery is presented. In view of the distance between these conditions and those being applied in Brazil a proposal is made concerning the urgent need for a national debate involving the society, scientific community and government agencies to build national policies, plans and goals for bioprospecting of Brazilian biodiversity. Some suggestions on how to implement such debate and questions that should be discussed are presented.
Biological Products↗
Bioprospecting microbial genomes to expand the biocatalytic toolbox of rubber oxygenases.
A set of rubber oxygenases was discovered through phylogenetic analysis and AI-based structural modeling of complexes of the putative enzymes with a substrate mimicking cis-1,4-polyisoprene. Sixteen candidate proteins were selected from thermophilic microorganisms, all sequence-related to the Latex clearing protein from Streptomyces sp. K30 (LcpK30). Sequence truncation and solubility tags were then evaluated to enhance protein expression, with the SUMO tag proving to be the most effective. Including LcpK30, nine heme-containing oxygenases were successfully expressed in E. coli NEB 10-beta cells, purified (35-157 mg L-1 yield) and characterized. Steady-state kinetics revealed significant rubber latex-degrading properties for six of them, with the truncated SUMO-fused LcpK30 (SUMO-LcpK30T) showing activity in agreement with literature. Notably, the catalytic efficiencies of all the expressed homologs lay within one order of magnitude and the oxygenase from Thermomonospora echinospora was found to be particularly promising in terms of activity, especially at high latex concentrations (more than 1% w/v). The analysis of reaction mixtures by both HPLC and HPLC-MS confirmed the oxidation of cis-1,4-polyisoprene to form the expected isoprenoid oligomers (n = 2-12), whose distribution was consistent with the usual endo-type cleavage pattern in all but one case. This bioprospecting effort afforded a platform of new rubber-degrading enzymes with diverse efficiencies and product profiles, capable of adapting to targeted applications.
Oxygenases↗
Bioprospecting in the developing world.
During the past ten years, species-rich nations in the developing world have sought to capitalize on their 'biological patrimony' through a variety of business relationships with multinational corporations as a means of underwriting their conservation efforts. Initially lauded, these relationships have generated more rhetoric than revenues to date. The ramifications of these results on bioprospecting are discussed along with the foreseeable changes in models of collaboration.
Animals↗
[Orthodontic concepts of bioprospective therapy in cases of collapsed vertical dimension].
Collapsed vertical dimension brings always a real problem in choosing therapeutic solutions. Among prosthodontics, surgical or orthodontics attempts, the author takes into account different options according to the Bioprospective Philosophy concepts.
Adult↗
Bioactive alkaloids of frog skin: combinatorial bioprospecting reveals that pumiliotoxins have an arthropod source.
Nearly 500 alkaloids have been detected in skin extracts from frogs of the family Dendrobatidae. All seem to have been sequestered unchanged into skin glands from alkaloid-containing arthropods. Ants, beetles, and millipedes seem to be the source of decahydroquinolines, certain izidines, coccinellines, and spiropyrrolizidine oximes. But the dietary source for a major group of frog-skin alkaloids, namely the pumiliotoxins (PTXs), alloPTXs, and homoPTXs, remained a mystery. In hopes of revealing an arthropod source for the PTX group, small arthropods were collected from eight different sites on a Panamanian island, where the dendrobatid frog (Dendrobates pumilio) was known to contain high levels of two PTXs. The mixed arthropod collections from several sites, each representing up to 20 arthropod taxa, contained PTX 307A and/or alloPTX 323B. In addition, the mixed arthropod collections from several sites contained a 5,8-disubstituted indolizidine (205A or 235B), representing another class of alkaloids previously unknown from an arthropod. An ant alkaloid, decahydroquinoline 195A, was detected in the mixed arthropod collections from several sites. Thus, "combinatorial bioprospecting" demonstrates that further collection and analysis of individual taxa of leaf-litter arthropods should reveal the taxa from which PTXs, alloPTXs, and 5,8-disubstituted indolizidines are derived.
Alkaloids↗
Bioprospecting the lat gene in soil samples.
Twenty soil communities from the northeastern forests (Assam) and the Western Ghats (Maharashtra) were screened for the presence of the lysine aminotransferase (lat) gene from Nocardia. Hybridization probes and primers were synthesized in accordance with the reported sequence of the Nocardia lat gene from GenBank (number: G1 49355). Seven positives were obtained from the 20 soils. Six of the seven positive were from the Western Ghats and one from the northeast Assam forests. Eighteen actinomycete isolates from the 7 positive soils showed the presence of the lat gene. Only 9 isolates actually produced an antibiotic. These results are discussed.
Bacterial Proteins↗
Identification of GFP-like proteins in nonbioluminescent, azooxanthellate anthozoa opens new perspectives for bioprospecting.
We screened nonbioluminescent, azooxanthellate cnidaria as potential sources for advanced marker proteins and succeeded in cloning a tetrameric green fluorescent protein (GFP) from the tentacles of Cerianthus membranaceus. The fluorescence of this protein (cmFP512) is characterized by excitation maximum at 503 nm, emission maximum at 512 nm, extinction coefficient of 58,800 M-1 cm-1, quantum yield of 0.66, and fluorescence lifetime of 2.4 ns. The chromophore is formed from the tripeptide Gln-Tyr-Gly. The amino acid sequence of this protein shares 17.8% identical residues with GFP from Aequorea victoria. Weak interactions between the subunits of the tetramer make cmFP512 a promising lead structure for the generation of monomeric variants of fluorescent proteins. Both red fluorescent proteins and nonfluorescent proteins of the GFP family were also purified from tissue homogenates of Adamsia palliata and Calliactis parasitica. The results presented here indicate that a photoprotective function of GFP-like proteins is unlikely in the examined anthozoa species.
Amino Acid Sequence↗
Bioprospecting Chromobacterium violaceum for bioremediation: an alternative to environmental lead pollution.
Lead pollution is a major environmental concern, but current decontamination technologies remain limited due to high costs. Therefore, alternative biotechnological processes have been successfully developed and applied due to their reduced cost and lower aggressiveness in the environment. The remarkable adaptive versatility of Chromobacterium violaceum in metal-contaminated environments makes this bacterium a promising candidate for Pb bioremediation. Therefore, the reference strain C. violaceum ATCC 12,472 and the environmental isolate C. violaceum SCV1, the first strain of this species isolated from a Brazilian area with natural Pb occurrence, were evaluated for Pb resistance under different Pb concentrations and exposure times. Pb biosorption was assessed by scanning electron microscopy, while strain-specific protein profiles were characterized using tandem mass spectrometry-based proteomic analysis. The results obtained revealed the potential of C. violaceum to perform lead bioremediation. Scanning electron microscopy analysis confirmed the biosorption of lead by C. violaceum strains. C. violaceum SCV1 was able to remove up to 40% more lead concentration when compared to ATCC 12,472 which suggested adaptation through natural selection process of C. violaceum SCV1. Proteome analysis revealed 1531 proteins, of which several are candidates for lead bioremediation. This is the first study on the resistance proteomics of C. violaceum against lead. The acclimatization of the bacteria linked to the identification of several proteins related to: biosorption; efflux and ionic uptake (bioaccumulation); biomolecule transport; and biomethylation, point out to this organism as a potential lead bioremediation agent.
Chromobacterium↗
Bioprospecting Rumphius's Ambonese Herbal: Volume I.
Collaborating with traditional healers remains a valid method for the identification of potential lead compounds for novel pharmaceuticals. However, the knowledge of these traditional healers is rapidly being lost. Historic herbal texts provide a unique window to identify plants whose specific uses are no longer known. We have identified nine plants in the 17th century Ambonese Herbal: Volume I which were documented as having medicinal properties but which have not been examined in the current literature. We demonstrate that by evaluating plant and herb efficacy reports from historic texts, in the context of comprehensive modern databases such as NAPRALERT, we can ultimately identify candidate specimens deserving further pharmacological study.
Ethnobotany↗
Bioprospecting in plants for engineered proteins.
For more than two decades, bioengineered plants have produced protein therapeutics for human and animal use. Almost all proteins produced by other existing systems, including antibodies, vaccines and plasma proteins, have now been manufactured in plants. Considering the limitations of microbial and mammalian reactor-based protein-production technologies and the impending bottleneck in manufacturing capacity, plants are now emerging as an attractive alternative system with which to supply the growing need for protein-based therapeutics. However, full realization of the promise of plant-derived engineered proteins requires that we confront the dual challenges of bioequivalence and product consistency, challenges that are largely related to post-translational protein modifications (PTMs) that are crucial to the structure and function of most eukaryotic proteins. Among the protein PTMs, the foremost challenge for bioactivity and acceptance by the pharmaceutical and biotechnology industries and regulatory agencies is glycosylation. Advances made in recent years that 'humanize' plant glycosylation pathways combined with the discovery of terminal sialic acids (SAs) in plants now make feasible the bioengineering in plants of glycoproteins that have mammalian-like glycosylation.
Animals↗
Techniques: Bioprospecting historical herbal texts by hunting for new leads in old tomes.
Ethnobotany has led to the identification of novel pharmacological agents but many challenges to using ethnobotany as a research tool remain. In particular, the loss of traditional knowledge together with the advent of high-throughput screening has made ethnobotanical techniques laborious and potentially unnecessary. However, historical herbal texts provide a preexisting resource that documents the traditional uses of various species as medicines. As generational losses of traditional knowledge accrue, these herbal texts become increasingly valuable. The methodology for extracting useful information contained within these resources had been cumbersome and consuming. However, the application of new bioinformatics data-mining systems to herbal texts holds great promise for identifying novel pharmacotherapeutic leads for bioactive compounds.
Ethnobotany↗
The Maasai ethnodiagnostic skill of livestock diseases: a lead to traditional bioprospecting.
A survey study was conducted on the ethnoveterinary knowledge of the Ilkisonko Maasai of Kenya. The data on the ethnodiagnostic skills of livestock diseases was gathered using a well-structured questionnaire. The result show that the Maasai rely not only on symptoms of diseases but also on vectors of disease, season effects and species affected by a particular malady. The Ilkisonko Maasai use 18 medicinal plant species to combat the diseases positively diagnosed. It is concluded that, the Maasai ethnodiagnostic skill is the bases of their traditional bioprosecting techniques.
Animal Husbandry↗
Bioprospecting for novel oxylipins in fungi: the presence of 3-hydroxy oxylipins in Pilobolus.
As previously found in various members of the Mucorales, 3-hydroxy oxylipins in Mucor genevensis are associated with the sporangia, i.e. mainly the columella structure and between aggregating sporangiospores. To determine if this phenomenon is also true in distantly related members, the mucoralean fungus Pilobolus was examined. This fungus is characterized by relatively large sub sporangial-columella structures which actively eject sporangia in a sticky liquid for attachment onto herbage surrounding its growth medium--in this case horse dung. Strikingly, this fungus produced a novel oxylipin i.e. a 3-hydroxy monounsaturated fatty acid, possibly a nonenoic acid, which is mainly associated with the sub sporangial-columella structure and aggregating sporangiospores. The specificity of the antibody against 3-hydroxy oxylipins used in immunofluorescence mapping of the mucoralean fungi, was further confirmed in the yeast, Saccharomycopsis malanga which produces 3-hydroxy palmitate in crystal form. These crystals occur between aggregating yeast cells. On the basis of the available data, we hypothesize that 3-hydroxy oxylipins probably function as adhesives, attaching fungal cells to each other or to other surfaces through entropic based hydrophobic forces and/or hydrogen bonds.
Fatty Acids, Unsaturated↗
Bioprospecting for novel hydroxyoxylipins in fungi: presence of 3-hydroxy palmitic acid in Saccharomycopsis malanga.
Electron microscopy studies indicated that the major oxylipin 3-hydroxy palmitic acid (16:0) was associated with aggregating vegetative cells and formed a web-like structure around these cells. Cross sections through this structure showed a hydrophilic outer layer and a more hydrophobic inner layer suggesting that the web-like structure is in fact tube-like micelles. This information sheds more light on the role of these hydroxyoxylipins in fungi.
Cell Wall↗