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From Darwin to the Census of Marine Life: Marine Biology as Big Science  [PDF]
Niki Vermeulen
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0054284
Abstract: With the development of the Human Genome Project, a heated debate emerged on biology becoming ‘big science’. However, biology already has a long tradition of collaboration, as natural historians were part of the first collective scientific efforts: exploring the variety of life on earth. Such mappings of life still continue today, and if field biology is gradually becoming an important subject of studies into big science, research into life in the world's oceans is not taken into account yet. This paper therefore explores marine biology as big science, presenting the historical development of marine research towards the international ‘Census of Marine Life’ (CoML) making an inventory of life in the world's oceans. Discussing various aspects of collaboration – including size, internationalisation, research practice, technological developments, application, and public communication – I will ask if CoML still resembles traditional collaborations to collect life. While showing both continuity and change, I will argue that marine biology is a form of natural history: a specific way of working together in biology that has transformed substantially in interaction with recent developments in the life sciences and society. As a result, the paper does not only give an overview of transformations towards large scale research in marine biology, but also shines a new light on big biology, suggesting new ways to deepen the understanding of collaboration in the life sciences by distinguishing between different ‘collective ways of knowing’.
Synthetic Biology and Metabolic Engineering for Marine Carotenoids: New Opportunities and Future Prospects  [PDF]
Chonglong Wang,Jung-Hun Kim,Seon-Won Kim
Marine Drugs , 2014, DOI: 10.3390/md12094810
Abstract: Carotenoids are a class of diverse pigments with important biological roles such as light capture and antioxidative activities. Many novel carotenoids have been isolated from marine organisms to date and have shown various utilizations as nutraceuticals and pharmaceuticals. In this review, we summarize the pathways and enzymes of carotenoid synthesis and discuss various modifications of marine carotenoids. The advances in metabolic engineering and synthetic biology for carotenoid production are also reviewed, in hopes that this review will promote the exploration of marine carotenoid for their utilizations.
Metabolomics: Concept, methods and potential prospect in marine biology
Xuan Zhang,Hao Chen
Chinese Science Bulletin , 2012, DOI: 10.1007/s11434-012-5237-5
Abstract: The term “omics” refers to the comprehensive analysis of a specific biological system. With the development of omics, a number of omics subdisciplines have emerged, which play an important role in system biology. As a subdiscipline of omics, metabolomics provides a comprehensive analysis of the metabolome and has been widely applied to various fields of biology. In this paper, we introduce the concept, approaches, applications, and promising prospects of metabolomics.
Marine biology, biodiversity and conservation: foreword to the SIEBM 2010 Conference  [PDF]
Sánchez Lizaso, J. L.,Bayle Sempere, J.,Sánchez Jerez, P.
Animal Biodiversity and Conservation , 2011,
Abstract: The SIEBM (Iberian Symposium of Studies on Marine Biology) has a long tradition. The conference was first convened in 1979 and it has since been held approximately biannually. It was originally focused on marine benthos, but two editions ago it was decided to widen its objectives to include other related subjects. The XVIth edition was held at the University of Alicante from 6th to 10th September 2010. One of the strong points of SIEBM is that it provides the opportunity for interaction between well–known researchers and young marine scientists, mainly from Spain and Portugal. In the 2010 edition, however, it was attended by 268 participants from 15 countries.SIEBM 2010 focused on the human impact on marine ecosystems and the conservation of marine biodiversity to coincide with the United Nations declaring 2010 the International Year of Biodiversity. From a total number of 330 communications received, the Scientific Committee selected 70 for oral presentations and the rest were presented as posters. Each day a plenary conference covered what we considered as the fastest growing areas in marine biology: landscape ecology. The impact of global warming on marine ecosystems, approaches to fisheries management and the study and conservation of deep ecosystems. The oral presentations were divided into 15 sessions that included both basic research on biodiversity, phylogeny or marine ecology, and applied research in management, fisheries, conservation and the human impact on marine ecosystems. Abstracts, posters and presentations are available at http://www.siebm.org.The studies included in this volume show the variety of subjects and approaches addressed during the conference. These papers were selected and edited by a group of referees and we wish to thank them for their efforts and conscientious work. A list of their names is included. Of the 28 studies received, 13 were finally accepted for this volume.We also would like to thank all the people who helped in one way or another to make the XVIth SIEBM Conference and the proceedings such a success. We thank the Scientific Committee for revising the abstracts and selecting the oral presentations. Most members of this committee also chaired sessions and undertook this task with commitment and dedication. The planning, logistics and running of the conference were made possible thanks to the enthusiasm of the organising committee and a group of student helpers. We are profoundly indebted to Carlos Valle and Aitor Forcada for their invaluable contribution to the organisation. Finally, we thank all the sponsors wh
Biology of the Marine Heterotrophic Dinoflagellate Oxyrrhis marina: Current Status and Future Directions  [PDF]
Zhiling Guo,Huan Zhang,Sheng Liu,Senjie Lin
Microorganisms , 2013, DOI: 10.3390/microorganisms1010033
Abstract: Heterotrophic dinoflagellates are prevalent protists in marine environments, which play an important role in the carbon cycling and energy flow in the marine planktonic community. Oxyrrhis marina (Dinophyceae), a widespread heterotrophic dinoflagellate, is a model species used for a broad range of ecological, biogeographic, and evolutionary studies. Despite the increasing research effort on this species, there lacks a synthesis of the existing data and a coherent picture of this organism. Here we reviewed the literature to provide an overview of what is known regarding the biology of O. marina, and identify areas where further studies are needed. As an early branch of the dinoflagellate lineage, O. marina shares similarity with typical dinoflagellates in permanent condensed chromosomes, less abundant nucleosome proteins compared to other eukaryotes, multiple gene copies, the occurrence of trans-splicing in nucleus-encoded mRNAs, highly fragmented mitochondrial genome, and disuse of ATG as a start codon for mitochondrial genes. On the other hand, O. marina also exhibits some distinct cytological features (e.g., different flagellar structure, absence of girdle and sulcus or pustules, use of intranuclear spindle in mitosis, presence of nuclear plaque, and absence of birefringent periodic banded chromosomal structure) and genetic features (e.g., a single histone-like DNA-associated protein, cob- cox3 gene fusion, 5′ oligo-U cap in the mitochondrial transcripts of protein-coding genes, the absence of mRNA editing, the presence of stop codon in the fused cob- cox3 mRNA produced by post-transcriptional oligoadenylation, and vestigial plastid genes). The best-studied biology of this dinoflagellate is probably the prey and predators types, which include a wide range of organisms. On the other hand, the abundance of this species in the natural waters and its controlling factors, genome organization and gene expression regulation that underlie the unusual cytological and ecological characteristics are among the areas that urgently need study.
Reproductive biology of two marine catfishes (Siluriformes, Ariidae) in the Sepetiba Bay, Brazil
Gomes,Iracema David; Gerson Araújo,Francisco;
Revista de Biología Tropical , 2004,
Abstract: marine catfish are abundant in the sepetiba bay, a 305 km 2 area in southeast brazilian coast (lat. 22o 54?-23o 04?s; long. 43 o 44?-44 o 10?w), but the knowledge on their biology is still scanty. the reproductive biology of sciadeichthys luniscutis (valenciennes 1840) and genidens genidens (valenciennes 1839) was studied through monthly sampling, from october 1998 to september 1999. fishes were caught with a standardized otter trawl, in the interior of sepetiba bay, and near to the confluence with a major freshwater contributor. six gonadal stages were described, based on macroscopic observations of gonad form, size, weight, color and oocyte diameter, and microscopic observations of differences in size and staining in the nucleus and cytoplasm structures, as viewed through a light microscope. changes in the gonadosomatic index (gsi) and in stages of gonadal development showed what s. luniscutis spawned in spring, while g. genidens spawned in summer. total spawning was shown for both species as indicated by high concentration of post-ovulatory follicles in spent stages. fecundity was low (14-38 vitellogenic oocytes for s. luniscutis and 6-24 for g. genidens), when compared with other teleosts. low fecundity and separation in spawning period suggest that both species are k-strategist, able to avoid interspecific competition in early stages of life cycle to optimize the use of the available niche
Reproductive biology of two marine catfishes (Siluriformes, Ariidae) in the Sepetiba Bay, Brazil  [cached]
Iracema David Gomes,Francisco Gerson Araújo
Revista de Biología Tropical , 2004,
Abstract: Marine catfish are abundant in the Sepetiba Bay, a 305 km 2 area in Southeast Brazilian coast (Lat. 22o 54’-23o 04’S; Long. 43 o 44’-44 o 10’W), but the knowledge on their biology is still scanty. The reproductive biology of Sciadeichthys luniscutis (Valenciennes 1840) and Genidens genidens (Valenciennes 1839) was studied through monthly sampling, from October 1998 to September 1999. Fishes were caught with a standardized otter trawl, in the interior of Sepetiba Bay, and near to the confluence with a major freshwater contributor. Six gonadal stages were described, based on macroscopic observations of gonad form, size, weight, color and oocyte diameter, and microscopic observations of differences in size and staining in the nucleus and cytoplasm structures, as viewed through a light microscope. Changes in the gonadosomatic index (GSI) and in stages of gonadal development showed what S. luniscutis spawned in Spring, while G. genidens spawned in Summer. Total spawning was shown for both species as indicated by high concentration of post-ovulatory follicles in spent stages. Fecundity was low (14-38 vitellogenic oocytes for S. luniscutis and 6-24 for G. genidens), when compared with other teleosts. Low fecundity and separation in spawning period suggest that both species are k-strategist, able to avoid interspecific competition in early stages of life cycle to optimize the use of the available niche El pez-gato de mar es abundante el la Bahía Sepetiba, un área de 305 km2 en la costa del sureste brasile o, pero el conocimiento de su biología es aun escaso. La biología reproductiva de Sciadeichthys luniscutis y Genidens genidens fue estudiada a través de muestreos mensuales, desde octubre de 1998 a setiembre de 1999. Los peces fueron capturados con una red barredera estandarizada, en el interior de la Bahía Sepetiba, y cerca de la confluencia con un río tributario principal. Seis estadíos gonadales fueron descritos, basados en observaciones macroscópicas de diferencias en el tama o y tinción del núcleo y estructuras citoplasmáticas, observadas a través del microscopio de luz. Los cambio en el índice gonadosomático () y en los estadíos del desarrollo gonadal, mostraron que S. Luniscutis desova en primavera, mientras que G. genidens desova en verano. El desove fue evidenciado en ambas especies por una alta concentración de folículos post-ovulatorios en los estadios maduros. La fecundidad fue baja (14-38 oocitos vitelogénicos en S. luniscutis y 6-24 en G. genidens) cuando se la compara con otros teleósteos. La baja fecundidad y la separación en el período de desov
Marine Biodiversity in Japanese Waters  [PDF]
Katsunori Fujikura,Dhugal Lindsay,Hiroshi Kitazato,Shuhei Nishida,Yoshihisa Shirayama
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0011836
Abstract: To understand marine biodiversity in Japanese waters, we have compiled information on the marine biota in Japanese waters, including the number of described species (species richness), the history of marine biology research in Japan, the state of knowledge, the number of endemic species, the number of identified but undescribed species, the number of known introduced species, and the number of taxonomic experts and identification guides, with consideration of the general ocean environmental background, such as the physical and geological settings. A total of 33,629 species have been reported to occur in Japanese waters. The state of knowledge was extremely variable, with taxa containing many inconspicuous, smaller species tending to be less well known. The total number of identified but undescribed species was at least 121,913. The total number of described species combined with the number of identified but undescribed species reached 155,542. This is the best estimate of the total number of species in Japanese waters and indicates that more than 70% of Japan's marine biodiversity remains un-described. The number of species reported as introduced into Japanese waters was 39. This is the first attempt to estimate species richness for all marine species in Japanese waters. Although its marine biota can be considered relatively well known, at least within the Asian-Pacific region, considering the vast number of different marine environments such as coral reefs, ocean trenches, ice-bound waters, methane seeps, and hydrothermal vents, much work remains to be done. We expect global change to have a tremendous impact on marine biodiversity and ecosystems. Japan is in a particularly suitable geographic situation and has a lot of facilities for conducting marine science research. Japan has an important responsibility to contribute to our understanding of life in the oceans.
Bioactive Sesterterpenes and Triterpenes from Marine Sponges: Occurrence and Pharmacological Significance  [PDF]
Sherif S. Ebada,WenHan Lin,Peter Proksch
Marine Drugs , 2010, DOI: 10.3390/md8020313
Abstract: Marine ecosystems (>70% of the planet's surface) comprise a continuous resource of immeasurable biological activities and immense chemical entities. This diversity has provided a unique source of chemical compounds with potential bioactivities that could lead to potential new drug candidates. Many marine-living organisms are soft bodied and/or sessile. Consequently, they have developed toxic secondary metabolites or obtained them from microorganisms to defend themselves against predators [1]. For the last 30–40 years, marine invertebrates have been an attractive research topic for scientists all over the world. A relatively small number of marine plants, animals and microbes have yielded more than 15,000 natural products including numerous compounds with potential pharmaceutical potential. Some of these have already been launched on the pharmaceutical market such as Prialt ? (ziconotide; potent analgesic) and Yondelis ? (trabectedin or ET-743; antitumor) while others have entered clinical trials, e.g., alpidin and kahalalide F. Amongst the vast array of marine natural products, the terpenoids are one of the more commonly reported and discovered to date. Sesterterpenoids (C 25) and triterpenoids (C 30) are of frequent occurrence, particularly in marine sponges, and they show prominent bioactivities. In this review, we survey sesterterpenoids and triterpenoids obtained from marine sponges and highlight their bioactivities.
Impact of Marine Drugs on Animal Reproductive Processes  [PDF]
Francesco Silvestre,Elisabetta Tosti
Marine Drugs , 2009, DOI: 10.3390/md7040539
Abstract: The discovery and description of bioactive substances from natural sources has been a research topic for the last 50 years. In this respect, marine animals have been used to extract many new compounds exerting different actions. Reproduction is a complex process whose main steps are the production and maturation of gametes, their activation, the fertilisation and the beginning of development. In the literature it has been shown that many substances extracted from marine organisms may have profound influence on the reproductive behaviour, function and reproductive strategies and survival of species. However, despite the central importance of reproduction and thus the maintenance of species, there are still few studies on how reproductive mechanisms are impacted by marine bioactive drugs. At present, studies in either marine and terrestrial animals have been particularly important in identifying what specific fine reproductive mechanisms are affected by marine-derived substances. In this review we describe the main steps of the biology of reproduction and the impact of substances from marine environment and organisms on the reproductive processes.
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