Digital elevation models and GIS for watershed modelling and flood prediction-A case study of Accra Ghana

Geographical Information Systems (GIS) and Digital Elevation Models (DEM) can be used to perform many geospatial and hydrological modelling including drainage and watershed delineation, flood prediction and physical development studies of urban and rural settlements. This paper explores the use of contour data and planimetric features extracted from topographic maps to derive digital elevation models (DEMs) for watershed delineation and flood impact analysis (for emergency preparedness) of part of Accra, Ghana in a GIS environment. In the study two categories of DEMs were developed with 5 m contour and planimetric topographic data; bare earth DEM and built environment DEM. These derived DEMs were used as terrain inputs for performing spatial analysis and obtaining derivative products. The generated DEMs were used to delineate drainage patterns and watershed of the study area using ArcGIS desktop and its ArcHydro extension tool from Environmental Systems Research Institute (ESRI). A vector-based approach was used to derive inundation areas at various flood levels. The DEM of built-up areas was used as inputs for determining properties which will be inundated in a flood event and subsequently generating flood inundation maps. The resulting inundation maps show that about 80% areas which have perennially experienced extensive flooding in the city falls within the predicted flood extent. This approach can therefore provide a simplified means of predicting the extent of inundation during flood events for emergency action especially in less developed economies where sophisticated technologies and expertise are hard to come by. © 2009 Springer Netherlands.

Enhanced expression of antifreeze protein genes drives the development of freeze tolerance in an Antarctica isolate of Chlorella vulgaris

In adaptation to new environments, organisms may accumulate mutations within encoding sequences to modify protein characteristics or acquire mutations within regulatory sequences to alter gene expression levels. With the development of antifreeze capability as the example, this study presents the evidence that change in gene expression level is probably the most important mechanism for adaptive evolution in a green alga Chlorella vulgaris. C. vulgaris NJ-7, an isolate from Antarctica, possesses an 18S rRNA sequence identical to that of a temperate isolate, SAG211-11b/UTEX259, but shows much higher freeze tolerance than the later isolate. The chromosomal DNA/cDNA of four antifreeze genes, namely hiC6, hiC12, rpl10a and hsp70, from the two isolates of C. vulgaris were cloned and sequenced, and very few variations of deduced amino acid sequences were found. In contrast, the transcription of hiC6, hiC12 and rpl10a was greatly intensified in NJ-7 compared to that in UTEX259, which is correlated to the significantly enhanced freeze tolerance of the Antarctica isolate. (C) 2009 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

Expression pattern, cellular localization and promoter activity analysis of ovarian aromatase (Cyp19a1a) in protogynous hermaphrodite red-spotted grouper

Aromatase plays a key role in sex differentiation of gonads. In this study, we cloned the full-length cDNA of ovarian aromatase from protogynous hermaphrodite red-spotted grouper (Epinephelus akaara), and prepared the corresponding anti-EaCyp19a1a antiserum. Western blot and immunofluorescence studies revealed ovary-specific expression pattern of EaCyp19a1a in adults and its dynamic expression change during artificial sex reversal. EaCyp19a1a was expressed by follicular cells of follicular layer around oocytes because strong EaCyp19a1a immunofluorescence was observed in the cells of ovaries. During artificial sex reversal, EaCyp19a1a expression dropped significantly from female to male, and almost no any positive EaCyp19a1a signal was observed in testicular tissues. Then, we cloned and sequenced a total of 1967 bp T-flanking sequence of EaCyp19a1a promoter, and showed a number of potential binding sites for some transcriptional factors, such as SOX5, GATA gene family, CREB, AP1, FOXL1, C/EBP, ARE and SF-1. Moreover, we prepared a series of 5' deletion promoter constructs and performed in vitro luciferase assays of EaCyp19a1a promoter activities. The data indicated that the CREB regulation region from -1010 to -898 might be a major cis-acting element to EaCyp19a1a promoter, whereas the elements GATA and SOX5 in the region from -1216 to -1010 might be suppression elements. Significantly, we found a common conserved sequence region in the fish ovary-type aromatase promoters with identities from 93% to 34%. And, the motifs of TATA box, SF-1, SOX5, and CREB existed in the region and were conserved among the most of fish species. (C) 2009 Elsevier Ireland Ltd. All rights reserved.

Analysis of genetic diversity in Glyptosternum maculatum (Sisoridae, Siluriformes) populations with AFLP markers

We determined the genetic diversity of geographic populations from three spawning grounds (Nyang River, Lhasa River, Shetongmon Reach of Yarlung Zangbo River) of Glyptosternum maculatum with amplified fragment length polymorphism (AFLP) markers. Five primer combinations detected 332 products, 51 of them (15.4%) were polymorphic in at least one population. The Shetongmon population was found to be the richest in genetic diversity as was indicated by the percentage of polymorphic loci and heterozygosity, followed by the Nyang population and the Lhasa population. The pair-wise genetic distance between populations were all very close, ranging from 0.0015 to 0.0042 with an average of 0.0024. The genetic distance was not proportional to the geographic distance. The analysis of molecular variance demonstrated that all variation occurred within populations. The average estimated fixation index (F (st)) of three populations across all polymorphic loci was -0.0184, indicating the absence of genetic differences among the three sampled populations. The differentiation among populations was not significant, and population structure was weak. Our observations will help identify the genetic relationship among populations as the first approach to understand the genetic diversity of Glyptosternum maculatum.

Depletion of Vipp1 in Synechocystis sp PCC 6803 affects photosynthetic activity before the loss of thylakoid membranes

A vipp1 mutant of Synechocystis sp. PCC 6803 could not be completely segregated under either mixotrophic or heterotrophic conditions. A vipp1 gene with a copper-regulated promoter (P-petE-vipp1) was integrated into a neutral platform in the genome of the merodiploid mutant. The copper-induced expression of P-petE-vipp1 allowed a complete segregation of the vipp1 mutant and observation of the phenotype of Synechocystis 6803 with different levels of vesicle-inducing protein in plastids 1 (Vipp1). When P-petE-vipp1 was turned off by copper deprivation, Synechocystis lost Vipp1 and photosynthetic activity almost simultaneously, and at a later stage, thylakoid membranes and cell viability. The photosystem II (PSII)-mediated electron transfer was much more rapidly reduced than the PSI-mediated electron transfer. By testing a series of concentrations, we found that P-petE-vipp1 cells grown in medium with 0.025 mu M Cu2+ showed no reduction of thylakoid membranes, but greatly reduced photosynthetic activity and viability. These results suggested that in contrast to a previous report, the loss of photosynthetic activity may not have been due to the loss of thylakoid membranes, but may have been caused more directly by the loss of Vipp1 in Synechocystis 6803.

Cloning and expression of medaka dazl during ernbryogenesis and gametogenesis

The Deleted in azoospermia family consists of RNA-binding proteins Bottle, Daz, and Daz-like (Dazl) that are expressed in the germline. Here, we report the cloning and expression of the medakafish (Oryzias latipes) dazl gene (odazl). Interestingly, although the predicted medaka Dazl protein (oDazl) contains a RRM motif and a DAZ repeat characteristic of its mammalian homologs, it lacks 80 aa at the C-terminus. By RT-PCR, RNA in situ hybridization, Western blotting and fluorescent immunohistochemistry using a rabbit anti-DazI antibody (alpha Oazl), we analyzed the expression patterns of odazl and its protein. The odazl transcript persists throughout embryogenesis and delineates with primordial germ cells. In adults, the expression of odazl RNA and its protein is restricted to germ cells of both the testis and ovary. We observed differential expression of RNA and protein at critical stages of gametogenesis. In the testis, the odazl RNA is low at premeiotic stages, abundant at meiotic stages, but absent in postmeiotic stages; whereas the oDazl protein is rich in premeiotic stages, reduced at meiotic stages, becomes barely detectable or absent in postmeiotic round spermatids or sperm, respectively. This is in sharp mature spermatozoa. In the ovary, the odazl RNA contrast to the human situation where the Dazl transcript and protein are present in and protein persist throughout oogenesis and also show differential expression at premeiotic, meiotic and postmeiotic stages. Thus, the odazl or its protein is a marker for germ cells during embryogenesis and at critical stages of gametogenesis in both sexes of medaka. (c) 2006 Elsevier B.V. All rights reserved.

Molecular cloning of growth hormone receptor (GHR) from common carp (Cyprinus carpio L.) and identification of its two forms of mRNA transcripts

The cDNA of growth hormone receptor (GHR) was cloned from the liver of 2-year common carp (Cyprinus carpio L.) by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA end (RACE). Its open reading frame (ORF) of 1806 nucleotides is translated into a putative peptide of 602 amino acids, including an extracellular ligand-binding domain of 244 amino acids (aa), a single transmembrane domain of 24 aa and an intracellular signal-transduction domain of 334 aa. Sequence analysis indicated that common carp GHR is highly homologous to goldfish (Carassius auratus) GHR at both gene and protein levels. Using a pair of gene-specific primers, a GHR fragment was amplified from the cDNA of 2-year common carp, a 224 bp product was identified in liver and a 321 bp product in other tissues. The sequencing of the products and the partial genomic DNA indicated that the difference in product size was the result of a 97 bp intron that alternatively spliced. In addition, the 321 bp fragment could be amplified from all the tissues of 4-month common carp including liver, demonstrating the occurrence of the alternative splicing of this intron during the development of common carp. Moreover, a semi-quantitative RT-PCR was performed to analyze the expression level of GHR in tissues of 2-year common carp and 4-month common carp. The result revealed that in the tissues of gill, thymus and brain, the expression level of GHR in 2-year common carp was significantly tower than that of 4-month common carp.

Digital Elevation Models and GIS for watershed modelling and flood prediction - A case study of Accra Ghana

Geographical Information Systems (GIS) and Digital Elevation Models (DEM) can be used to perform many geospatial and hydrological modelling including drainage and watershed delineation, flood prediction and physical development studies of urban and rural settlements. This paper explores the use of contour data and planimetric features extracted from topographic maps to derive digital elevation models (DEMs) for watershed delineation and flood impact analysis (for emergency preparedness) of part of Accra, Ghana in a GIS environment. In the study two categories of DEMs were developed with 5 m contour and planimetric topographic data; bare earth DEM and built environment DEM. These derived DEMs were used as terrain inputs for performing spatial analysis and obtaining derivative products. The generated DEMs were used to delineate drainage patterns and watershed of the study area using ArcGIS desktop and its ArcHydro extension tool from Environmental Systems Research Institute (ESRI). A vector-based approach was used to derive inundation areas at various flood levels. The DEM of built-up areas was used as inputs for determining properties which will be inundated in a flood event and subsequently generating flood inundation maps. The resulting inundation maps show that about 80% areas which have perennially experienced extensive flooding in the city falls within the predicted flood extent. This approach can therefore provide a simplified means of predicting the extent of inundation during flood events for emergency action especially in less developed economies where sophisticated technologies and expertise are hard to come by. © Springer Science + Business Media B.V. 2009.

Molecular identification and expression analysis of natural resistance associated macrophage protein (Nramp) cDNA from Japanese flounder (Paralichthys olivaceus)

Natural resistance associated macrophage protein (Nramp) controls partially innate resistance to intracellular parasites. Its function is to enhance the ability of macrophages to kill pathogens. However, little is known about the structure and function of Nramp in lower vertebrates such as teleosts. We have recently isolated a cDNA encoding Nramp from Japanese flounder (Paratichthys olivaceus). The full-length cDNA of the Nramp is 3066 bp in length, including 224 bp 5' terminal UTR, 1662 bp encoding region and 1180 bp 3' terminal UTR. The 1662-nt open reading frame was found to code for a protein with 554 amino acid residues. Comparison of amino acid sequence indicated that Japanese flounder Nramp consists of 12 transmembrane (TM) domains. A consensus transport motif (CTM) containing 20 residues was observed between transmembrane domains 8 and 9. The deduced amino acid sequence of Japanese flounder had 77.30%, 82.71%, 82.67%, 79.64%, 80.72%, 90.97%, 91.16%, 60.14%, 71.48%, 61.69%, 72.37% identity with that of rainbow trout Nramp alpha and beta, channel catfish Nramp, fathead minnow Nramp, common carp Nramp, striped sea bass Nramp, red sea bream Nramp, mouse Nramp 1 and 2, human Nramp 1 and 2, respectively. RT-PCR indicated that Nramp transcripts were highly abundant in spleen, head kidney, abundant in intestine, liver and gill, and less abundant in heart. The level of Nramp mRNA in embryos gradually increases during embryogenesis from 4 h (8 cell stage) to 80 h (hatched stage) after fertilization. (c) 2005 Elsevier Ltd. All rights reserved.

Methane and carbon dioxide fluxes from a shallow hypereutrophic subtropical Lake in China

Up to now, there have been few studies in the annual fluxes of greenhouse gases in lakes of subtropical regions. The fluxes of methane (CH4) and carbon dioxide (CO2) across air-water interface were measured in a shallow, hypereutrophic, subtropical Lake Donghu (China) over a year cycle, using a static chamber technique. During the year, Lake Donghu emitted CH4 and CO2; the average flux of CH4 and CO2 was 23.3 +/- 18.6 and 332.3 +/- 160.1 mg m(-2) d(-1), respectively. The fluxes of CH4 and CO2 showed strong seasonal dynamics: CH4 emission rate was highest in summer, remaining low in other seasons, whereas CO2 was adsorbed from the atmosphere in spring and summer, but exhibited a large emission in winter. Annual carbon (C) budget across air-water interface in Lake Donghu was estimated to be 7.52 +/- 4.07 x 10(8) g. CH4 emission was correlated positively with net primary production (NPP) and temperature, whereas CO2 flux correlated negatively with NPP and temperature; however, there were no significant relationships between the fluxes of CH4 and CO2 and dissolved organic carbon, a significant difference from boreal lakes, indicating that phytoplankton rather than allochthonous matter regulated C dynamics across air-water interface of subtropical lake enriched nutrient content. (c) 2005 Elsevier Ltd. All rights reserved.

Identification of immune genes in grass carp Ctenopharyngodon idella in response to infection of the parasitic copepod Sinergasilus major

The parasitic copepod Sinergasilus major is an important pathogen of grass carp Ctenopharyngodon idella. To understand the immune response of grass carp to the copepod infection, suppression subtractive hybridization method was employed to characterize genes up-regulation during the copepod infection in liver and gills of the fish. One hundred and twenty-two dot blot positive clones from infected subtracted library were sequenced. Searching available databases by using these nucleotide sequences revealed that 23 genes are immune-related, including known acute-phase reactants, and four novel genes encoding proteins such as source of immunodominant MHC-associated peptides (SIMP), TNF receptor-associated factor 2 binding protein (T2BP), poliovirus receptor-related protein 1 precursor, glycoprotein A repetitions predominant (GARP). The differential expression of seven immune genes, i.e. GARP, alpha-2-macroglobulin, MHC class I, C3, SIMP, T2BP, transferrin, as a result of infection was further confirmed by RT-PCR, with the up-regulation of alpha-2-macroglobulin, MHC class I, C3, SIMP and T2BP in the liver of infected fish, and down-regulation of SIMP in the gills of infected fish. The present study provides foundation for understanding grass carp immune response and candidate genes for further analysis.

Status of sturgeon aquaculture and sturgeon trade in China: a review based on two recent nationwide surveys

The authors reviewed the aquacultural history of Acipenseriformes in China, related the legal status and examined the current status of the cultured species or hybrids, origins of seedlings, quantities of production, geographic distribution in farming, and the sustainability for both restocking programmes and human consumption. The census shows that since 2000, the production of cultured sturgeons in China appears to have become the largest in the world. As of 2000, the rapid growth of sturgeon farming in China mainly for commercial purposes has shifted harvests in the Amur River from caviar production to the artificial culture of sturgeon seedlings. This dramatic development has also caused a series of extant and potential problems, including insufficient market availability and the impact of exotic sturgeons on indigenous sturgeon species. Annual preservation of sufficient higher-age sturgeons should be a national priority in order to establish a sustainable sturgeon-culture industry and to preserve a gene pool of critically endangered sturgeon species to prevent their extinction.

The reproductive strategies of an endemic Tibetan fish, Gymnocypris selincuoensis

The reproductive traits of Gymnocypris selincuoensis from Selincuo Lake and its tributaries were investigated in 1997 and 1998. The youngest mature male was age 7 with a standard length (SL) of 172.0 mm, and the youngest mature female was age 8 with a SL of 194.0 mm. The L(50)s Of SL and age at first maturity were respectively 250.32 mm and age 9 for males and 224.71 mm and age 8 for females. The gonadosomatic index (GSI) significantly changed with seasons for mature individuals but not for immature individuals. GSIs of mature females at stages IV and V of ovary development increased with SL and reached a maximum value at the SL range from 370 mm to 390 mm; the GSIs of mature males were negatively correlated with SL. The breeding season lasted from early April to early August. Egg size did not significantly change with SL but increased with the delay of spawning. The individual absolute fecundity varied from 1,341 to 28,002 eggs (mean 12,607+/-7,349), and the individual relative fecundity varied from 6.4 to 42.0 eggs.g(-1) (mean 25.5+/-9.7). The individual fecundity increased with total body weight; it also increased with SL for those of SL less than 370 mm. There was a rest of spawning for mature individuals.