Digital library

  • Next generation sequencing (NGS) technologies have revolutionized many areas of biological research due to the sharp reduction in costs that has led to the generation of massive amounts of sequence information. Analysis of large genome data sets is however still a challenging task because it often requires significant computer resources and knowledge of bioinformatics. Here, we provide a guide for an uninitiated who wish to analyze high-throughput NGS data. We focus specifically on the analysis of organelle genome and metagenome data and describe the current bioinformatic pipelines suited for this purpose.

    Author(s):
  • Different propagation techniques for cultivationof vegetativeGigartina skottsbergiifronds were testedusing a system of suspended ropes, to which inoculantswere attached. Our results showed that triangular fragmentsobtained from the circularG. skottsbergiithalli producedharvestable frond of 800 cm2after 8 months. In contrast,inoculants of intact juvenile fronds of comparable sizeneeded at least 10 months to reach the same size. A controlexperiment with spores developing on an artificial substrateshowed that 20 months were needed to reach a surface of500 cm2, confirming the superiority of our fragment culturesystem. A pilot study demonstrated that with a density ofsix fronds m−1of farming line, the proposed system can beeconomically interesting for local fishermen.

    Author(s): Renato Westermeier, David J. Patiño, Pedro Murúa, Juan C. Quintanilla, Juan Correa, Alejandro H. Buschmann, Ismael Barros
  • A polysaccharide (Sarg) extracted from the brown marine alga Sargassum stenophyllum was studied for its antivasculogenic effects in both in vivo and in vitro assays, as well as for its capacity to modify embryonic morphogenetic processes endogenously regulated by bFGF, a well-known angiogenic stimulator. The antivasculogenic activity of Sarg (6–1500 μg/implant) was evaluated in a chick yolk sac membrane assay and the embryonic morphogenesis was measured as the percentage cephalic length. Sarg alone (96–1500 μg/implant) and co-administered with hydrocortisone (HC; 156 μg/implant) decreased the vitelline vessel number by 23–100% and 54–100% respectively. The polysaccharide potentiated the antivasculogenic effect of HC (42% inhibition). Basic fibroblast growth factor-stimulated vasculogenesis (141% of vessels as compared to control) was partially reversed by Sarg. The treatment with Sarg also decreased the percentage cephalic length of 3.5- and 4-day chick embryos (as cultured in vivo and in vitro, respectively), uncoupled from any impairment in the body shape or embryotoxic effect. Due to polyanionic characteristics of Sarg, which are similar to those seen in the heparin molecule, we suggest that this polysaccharide should modulate the activity of heparin-binding vascular growth factors (such as bFGF, which also acts as a morphogen) mimetically interfering with heparan sulfate proteoglycans during microvessel formation.

    Author(s): Paulo Fernando Dias, Jarbas Mota Siqueira Jr., Marcelo Maraschin, Antônio Gilberto Ferreira, Antônio Ricardo Gagliardi, Rosa Maria Ribeiro-do-Valle
  • We examined three species of diminutive Porphyra, Porphyra suborbiculata Kjellman from the North Pacific, Porphyra lilliputiana W. A. Nelson, G. A. Knight et M. W. Hawkes from the South Pacific, and Porphyra carolinensis Coll et J. Cox from the western North Atlantic. These taxa were compared in terms of morphology, habitat data and sequence haplotypes of nuclear small subunit rDNA (SSU) and internal transcribed spacers of the nuclear rDNA cistron (ITS). These three species have similar morphologies and growth habits, and share very similar type descriptions and habitat records. Haplotype variation was found within the 11 samples of P. lilliputiana we examined and within P. suborbiculata samples from two locations, but the single P. carolinensis haplotype (from collections from two separate locations) was identical to one found in several widespread P. lilliputiana samples. Unrooted phylogenetic trees based on sequence data do not support any of the three species as being a monophyletic group. We conclude that these three taxa represent a single species with the oldest name P. suborbiculata having nomenclatural priority. It is likely that P. suborbiculata has recently been introduced to the western Atlantic from the Pacific region.

    Author(s): L. E. AGUILAR ROSAS, R. AGUILAR ROSAS, W. A. JONES, C. YARISH, W. A. NELSON, J. E. BROOM
  • Summary of the seaweed Furcellaria lumbricalis

    Author(s): Will Rayment
  • The fundamental aim in fisheries management is to determine an optimal fishing effort for sustainably harvesting from a replenishable resource. The current management objective of Australia's Northern Prawn Fishery is to maximize the long-term net economic return following Australian government policy, resulting in an average recent catch of tiger prawn species of about 1,250 tons only. However, the maximum sustainable catch stated from different studies is around 3,000-4,700 tons. We also evaluated the net profit assuming that there was no buyback scheme in 2005 and the fishing fleet was kept at 89 vessels since 2005 and concluded that 40% more catch on average (2006-2009) and an additional total profit of A$17 million (excluding crew cost) could have been gained in addition to the many millions of dollars of savings in the buyback scheme. These findings have great implications for future management in Australia and elsewhere because there is a grave concern of overfishing worldwide.

    Author(s): Na Wang, You-Gan Wang
  • Natural polysaccharides from different sources have long been studied and widely used in different areas, such as food and feed, medicine and pharmaceutics, and in papermaking. In recent decades, there has been an increased interest in the utilization of polysaccharides, particularly bioactive ones, for various novel applications owing to their biocompatibility, biodegradability, non-toxicity, and some specific therapeutic activities. The main goal of this paper was to review the sources, natively biological activities, isolation, characterization, and the structural features of natively bioactive polysaccharides. Moreover, the article has also been forcused on the chemical/chemo-enzymatic functionalizations that may create novel opportunities to maximally exploit the various valuable properties of polysaccharides, particularly from wood species, in previously unperceived applications especially for biomedical applications, such as tissue engineering, wound healing, and drug delivery. This article was to review novel strategies to tailor functional materials with above mentioned application potentials for the polysaccharides from wood species.

    Author(s): Jun Liu, Stefan Willfor, Chunlin Xu
  • Being a heat source or sink, aquifers have been used to store large quantities of thermal energy to match cooling and heating supply and demand on both a short-term and long-term basis. The current technical, economic, and environmental status of aquifer thermal energy storage (ATES) is promising. General information on the basic operation principles, design, and construction of ATES systems is discussed in this paper. Numerous projects in operation around the world are summarized to illustrate the present status of ATES. Hydrogeological-thermal simulation has become an integral part of predicting ATES system performance. Numerical models which are available to simulate an ATES system by modeling mass and heat transport in the aquifer have been summarized. This paper also presents an example of numerical simulation and thermohydraulic evaluation of a two-well, ATES system operating under a continuous flow regime.

    Author(s): Kun Sang Lee
  • The success of commerical cultivation of Kappaphycus seaweed in several countries is directly related to the easy vegetative reproduction of this species, high growth rate, simple cultivation techniques and their uses in different segments of the food, pharmaceutical, cosmetic and agricultural industries.

    Author(s): Miguel Sepulveda
  • This paper reviews the status, investment and market considerations, and technical constraints to the development of offshore aquaculture in temperate regions of the world. It explores trends in production and discusses the importance of farming seafood products that are “affordable” if they are going to meet mass-market demand. In this respect, it notes that there are relatively few dominant (i.e. one million metric tonne/year) species and speculates on why this might be so. It reviews technical constraints to the future development of offshore aquaculture, among them engineering and operational challenges, questions of species selection, juvenile supply, aquatic animal health issues and the availability of suitable feed ingredients. It also considers issues of predator control, environmental impact and the critical importance of adequately trained people. It concludes by suggesting that offshore marine aquaculture will only develop to its full potential if enthusiasm for the idea is backed by an equal measure of political will. By presenting a long-range vision for this, the Food and Agriculture Organization of the United Nations (FAO) can help society to understand its benefits and make a case for it that cannot be denied.

    Author(s): John Forster

Pages