The urgency of building global capacity for biodiversity science

The biodiversity sciences represent the disciplines of whole-organism biology, including systematics, ecology, population biology, behaviour and the fields of comparative biology. The biodiversity sciences are critically important to society because it is knowledge of whole-organisms that is essential for managing and conserving the world's species. Because of an acceleration in environmental degradation and global biodiversity loss in recent decades, the need for the biodiversity sciences has never been more urgent. Yet, biodiversity science is not well supported relative to other fields of science, and thus the need for knowledge about organisms and their environment is far outstripping biologists' ability to provide it. National and international capacity for biodiversity science must therefore be increased substantially. Each nation should establish a national biodiversity research programme coordinated across all government agencies. An international biodiversity research programme should also be established, perhaps with an organizational structure that parallels the International Geosphere-Biosphere Programme. Biodiversity scientists must assume a leadership role in educating the public and bringing about policy changes that will enhance our understanding of the world's species and their ecosystems.     

Distribution of repeated DNA families in the human genome

By means of restriction enzymes analysis and molecular hybridization, the distribution of repeated DNA families has been studied in the different DNA components into which the human genome can be fractionated by density gradient techniques. Three classes of DNA molecules have been analyzed: i) an homogeneous DNA component (satellite-like sequences; Q = 1.696 g/cm3, 3% of total DNA, AT repeated), ii) AT rich (Q = 1.698 g/cm3, 30% of total DNA, AT main-band) and GC rich (Q = 1.708 g/cm3, 6% of total DNA, GC main-band) DNA components. By this approach we have observed that Sau3A digestion of GC main-band gives rise to two bands of 75bp and 150bp, absent or under-represented in both AT rich DNA components. A preliminary characterization of these DNA fragments suggests that they contain one or more families of repeated sequences which fail to hybridize to EcoRI, HindIII and AluI families of repeats. In addition, we have observed that EcoRI sequences (alpha-RI DNA) are under-represented in GC main-band and show the same clustered organization in both AT rich DNA components.     

Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae

Hemocyanins are multimeric copper-containing hemolymph proteins involved in oxygen binding and transport in all major arthropod lineages. Most arachnids have seven primary subunits (encoded by paralogous genes a–g), which combine to form a 24-mer (4 × 6) quaternary structure. Within some spider lineages, however, hemocyanin evolution has been a dynamic process with extensive paralog duplication and loss. We have obtained hemocyanin gene sequences from numerous representatives of the spider infraorders Mygalomorphae and Araneomorphae in order to infer the evolution of the hemocyanin gene family and estimate spider relationships using these conserved loci. Our hemocyanin gene tree is largely consistent with the previous hypotheses of paralog relationships based on immunological studies, but reveals some discrepancies in which paralog types have been lost or duplicated in specific spider lineages. Analyses of concatenated hemocyanin sequences resolved deep nodes in the spider phylogeny and recovered a number of clades that are supported by other molecular studies, particularly for mygalomorph taxa. The concatenated data set is also used to estimate dates of higher-level spider divergences and suggests that the diversification of extant mygalomorphs preceded that of extant araneomorphs. Spiders are diverse in behavior and respiratory morphology, and our results are beneficial for comparative analyses of spider respiration. Lastly, the conserved hemocyanin sequences allow for the inference of spider relationships and ancient divergence dates.     

Accounting for functional connectivity in cross-realm conservation planning in a data poor context: The Cyprus case

In the past years, efforts have been made to include connectivity metrics in conservation planning in order to promote and enhance well-connected systems of protected areas. Connectivity is particularly important for species that rely on more than one realm during their daily or life cycle (multi-realm species). However, conservation plans for the protection of multi-realm species usually involve a single realm, excluding other realms from the prioritization process. Here, we demonstrate an example of cross-realm conservation planning application for the island of Cyprus by taking into account the terrestrial and marine realms and their interface (i.e. coast). Operating within a data-poor context, we use functional connectivity metrics to identify priority areas for the conservation of six multi-realm species, by setting conservation targets simultaneously for the terrestrial and marine realms. MARXAN decision-support tool was used for the identification of the priority areas.Four scenarios were developed to evaluate the impacts of including connectivity in the prioritization process and the effectiveness of the existing coastal/marine protected areas in the achievement of the conservation targets set for the species. All scenarios considered land and sea anthropogenic uses as surrogate costs to influence the prioritization process.Our findings show an increase in the area of the reserve network and, therefore, the cost, when connectivity is included, whilst reducing the total boundary length. Furthermore, the current reserve network fails to achieve conservation targets, particularly for the marine part, which has a substantially smaller protection coverage than the terrestrial part.We conclude that focus should be given in the expansion of the current coastal/marine reserve network following a cross-realm conservation approach. This approach is not only relevant for the conservation of multi-realm species, but also for islandscapes, in particular, where the interdependence between the hinterland and the coast is larger and therefore the magnitude of the impacts generated in one realm and affects the other.     

The intra-annual variability of soft-bottom macrobenthos abundance patterns in the North Channel of the Seine estuary

Temporal and spatial variability of the Abra alba–Pectinaria koreni and Macoma balthica communities was examined in the northern part of the Seine estuary (North Channel) over different space and time scales in order to assess the role that the hydrologic regime and/or anthropogenic influences play in defining benthic communities over time. Sediment in the North Channel displayed strong spatial and temporal variability, sustained by intense sediment transport episodes. Total macrobenthic abundances ranged widely on the course of the year and there was no evidence of a seasonal signal for the density fluctuations, whatever the spatial scale considered. The bio-sedimentary dynamics can be divided into two periods: the first corresponds to the high flow rate period (January–May) during which fauna is influenced by fine silt/clay deposition, and the second to the low flow rate period (June–December) during which sandy deposits prevail. Despite the absence of significant correlations between sediment composition and abundance, episodes of sediment transport seem to be an important structuring mechanism in the Seine estuary. As a consequence, the faunal composition varied throughout the year. The winter and spring fauna, characterised by species living on muddy fine-sands or muds, were enriched during the summer and autumn by species living in clean fine sand, such as Donax vittatus, Nephtys cirrosa or Spio decoratus, mainly represented by adult individuals. Secondary settlement of drifters may explain the rapid structuration of assemblages a few days after the sandy deposits. Our results suggest the importance of the bentho-pelagic coupling, primarily induced by the sedimentary instability, on the macrobenthic fauna dynamics. The intra-annual variability of assemblages at the mouth of the Seine river and the silted situation of the North Channel might simply be the result of the silting up and alteration of the inner estuary, generated by several decades of man-made modifications and natural processes.     

Long-term effects of nitrogen deposition on vegetation in a deciduous forest near Munich,Germany

Question: What are the main reasons for changes in the spatial distribution of vegetation types during the last four decades? Location: Isolated small deciduous forest; surrounded by farmland in the northeast of Munich (Germany). Methods: Based on sequential vegetation mapping from the last four decades the spatial development of the vegetation was analysed. Additionally, environmental parameters (soil parameters, PAR, N-deposition) have been analysed to describe the different vegetation types. Results: By linking the vegetation types to environmental parameters, it was possible to identify N-deposition as the most important factor for the changes. In the 1960s to 1980s the replacement of vegetation types adapted to N-poor conditions by N-rich vegetation was very fast. A vegetation type containing species signifying soil impoverishment vanished totally, another vegetation type indicating nutrient poor conditions decreased dramatically. However, since 1985 up to now the decrease of N-poor vegetation types has slowed, but is still ongoing. As a reason for the decreased rate of replacement, we stressed changes in the vertical structure: From 1961 to 1985 both N-deposition as well as changes in vertical vegetation structure seem to be important. Since 1985 up to now only minor changes in vertical structure could be found; changes are mainly due to N-availability. Conclusion: In this paper, the limitations of different methods to detect vegetation changes are discussed. We focus on the potentials of historical vegetation data and vegetation maps. It is shown that valuable information on N-induced vegetation changes can be retrieved from historical vegetation data.     

Increase in CpG DNA-induced inflammatory responses by DNA oxidation in macrophages and mice

Unmethylated CpG dinucleotide (CpG motif) is involved in the exacerbation of DNA-associated autoimmune diseases. We investigated the effect of DNA containing 8-hydroxydeoxyguanosine (oxo-dG), a representative DNA biomarker for oxidative stress in the diseases, on CpG motif-dependent inflammatory responses. ODN1668 and ODN1720 were selected as CpG-DNA and non-CpG DNA, respectively. Deoxyguanosine in the CpG motif (G9) or outside the motif (G15) of ODN1668 was substituted with oxo-dG to obtain oxo(G9)-1668 and oxo(G15)-1668, respectively. Oxo(G15)-1668 induced a significantly higher amount of tumor necrosis factor (TNF)-α from RAW264.7 macrophage-like cells than ODN1668, whereas oxo(G9)-1668, oxo(G8)-1720, or oxo(G15)-1720 hardly did. CpG DNA-induced TNF-α production was significantly increased by addition of oxo(G8)-1720 or oxo(G15)-1720, but not of ODN1720. This oxo-dG-containing DNA-induced increase in TNF-α production was also observed in primary cultured macrophages isolated from wild-type mice, but not observed in those from Toll-like receptor (TLR)-9 knockout mice. In addition, TNF-α production by ligands for TLR3, TLR4, or TLR7 was not affected by oxo-dG-containing DNA. Then, the footpad swelling induced by subcutaneous injection of ODN1668 into mice was increased by coinjection with oxo(G8)-1720, but not with ODN1720. These results indicate that oxo-dG-containing DNA increases the CpG motif-dependent inflammatory responses, which would exacerbate DNA-related autoimmune diseases.     

Simulating the rice yield change in the middle and lower reaches of the Yangtze River under SRES B2 scenario

As one of the most important crops in China, rice accounts for 18% of the country’s total cultivated area. Increasing atmospheric CO₂ concentration and associated climate change may greatly affect the rice productivity. Therefore, understanding the impacts of climate change on rice production is of great significance. This paper aims to examine the potential impacts of future climate change on the rice yield in the middle and lower reaches of the Yangtze River, which is one of the most important food production regions in China. Climate data generated by the regional climate Model PRECIS for the baseline (1961–1990) and future (2021–2050) period under IPCC SRES B2 scenario were employed as the input of the rice crop model ORYZA2000. Four experimental schemes were carried out to evaluate the effects of future climate warming, CO₂ fertilization and water managements (i.e., irrigation and rain-fed) on rice production. The results indicated that the average rice growth duration would be shortened by 4 days and the average rice yield would be declined by more than 14% as mean temperature raised by 1.5 °C during the rice growing season in 2021–2050 period under B2 scenario. This negative effect of climate warming was more obvious on the middle and late rice than early rice, since both of them experience higher mean temperature and more extreme high temperature events in the growth period from July to September. The significance effect of the enhanced CO₂ fertilization to rice yield was found under elevated CO₂ concentrations in 2021–2050 period under B2 scenario, which would increase rice yield by more than 10%, but it was still not enough to offset the negative effect of increasing temperature. As an important limiting factor to rice yield, precipitation contributed less to the variation of rice yield than either increased temperature or CO₂ fertilization, while the spatial distribution of rice yield depended on the temporal and spatial patterns of precipitation and temperature. Compared to the rain-fed rice, the irrigated rice generally had higher rice yield over the study area, since the irrigated rice was less affected by climate change. Irrigation could increase the rice yield by more than 50% over the region north of the Yangtze River, with less contribution to the south, since irrigation can relieve the water stress for rice growing in the north region of the study area. The results above indicated that future climate change would significantly affect the rice production in the middle and lower reaches of the Yangtze River. Therefore, the adverse effect of future climate change on rice production will be reduced by taking adaptation measures to avoid disadvantages. However, there is uncertainty in the rice production response prediction due to the rice acclimation to climate change and bias in the simulation of rice yield with uncertainty of parameters accompanied with the uncertainty of future climate change scenario.     

A two-dimensional approach for lossless EEG compression

In this paper, we study various lossless compression techniques for electroencephalograph (EEG) signals. We discuss a computationally simple pre-processing technique, where EEG signal is arranged in the form of a matrix (2-D) before compression. We discuss a two-stage coder to compress the EEG matrix, with a lossy coding layer (SPIHT) and residual coding layer (arithmetic coding). This coder is optimally tuned to utilize the source memory and the i.i.d. nature of the residual. We also investigate and compare EEG compression with other schemes such as JPEG2000 image compression standard, predictive coding based shorten, and simple entropy coding. The compression algorithms are tested with University of Bonn database and Physiobank Motor/Mental Imagery database. 2-D based compression schemes yielded higher lossless compression compared to the standard vector-based compression, predictive and entropy coding schemes. The use of pre-processing technique resulted in 6% improvement, and the two-stage coder yielded a further improvement of 3% in compression performance.