Diversity, abundance distribution and secondary production of intertidal and subtidal benthic macrofauna of Bushehr Province with emphasis on annelida groups

The present investigation was undertaken to establish a reference situation for future use, to identify temporal and spatial composition of macrofauna and estimate some ecological indices in the sub tidal waters along the Bushehr coastal waters in Persian Gulf. Six transects were selected including Genaveh, Farakeh, Shif, Bandargah, Rostami and Asalouyeh, at each transect 3 station were sampled in depths of zero, 5 and 10 metres. Sampling was seasonally carried out by a VAN VEEN grab 0.0225 m2, during summer 2008 until spring 2009. Samples were wet sieved immediately using 0.5 mm mesh size sieves and sediment retained in the sieve was preserved in 4% buffered formalin solution. Macrofauna specimen were separated from the sediments using decantation and elutriation methods, enumerated and identified up to the Genus level. Environmental factors such as temperature. pH, and salinity were recorded in field using sensitive probs and refractometer (for salinity) and also sediment samples were taken for TOM and grain size analysis in all the stations. 5611 specimens belonging to 66 genera were collected during the present study. Polychaetes were dominant both in terms of genus number (31) and relative abundance (74 % of total macrofaunal abundance). The other dominant groups were Artheropoda, (16.1%), Molusca (2.8%), Echinodermata (1.29%) and others including Nematoda, Nemertina, Echiura and Turbellaria (5.8%). Thirty one Genera belong of 27 families of polychaeta, one genus and family of Subphylum Chlicerata,19 genera belong to 14 families of Crustacea, 8 genera belong to 6 families of Molusca, were indentified in the studied region. 1 family (Polygordidae) and 3 genera (Flabeligera, Pilargis and Polygordius) of Polychaeta, 1 family (Nymphonidae) and genus (Nymphon) of Chelicerata, 1 Family (Nematoplanidae) and genus (Nematoplana) of Turbellaria, were identified for the first time in Persian Gulf area. The result indicated that macrofauna organism have strong relationship with the grain size characteristics of the sediments they inhabit. The most surface deposit feeder specimens such as Prionospio and Cossura were found in zero meters depth of Genaveh, Farakeh, Bandargah, Rostami and Asalouyeh stations with sandy substratum, however the most burrowing deposit feeder and scavenger specimens such as Capitella and Petaloproctus were collected in 5 and 10 meter depths of stations with silty–clay substratum. The annual mean abundance, Shanon- weiner diversity and evenness of macrofauna were estimated1152.73 N/ m² , 2.72 and 0.792 respectively .The annual average biomass and secondary production were computed 1.797 gDW m² and 3.594 gDW m² y-1 .The average of water temperature, salinity, pH and oxygen concentration were recorded between 16.37-36.05 °C, 38-42 g/l, 7.89-8.76 and 4.23-8.23 mg/l, respectively during this study in 6 studied region. Among of investigated stations Asalouyeh adjacent of effluent canal of Gas and petrochemical industry sewage and Farakeh regions adjacent the Helleh estuary had the lowets and the highest community indices. The average of diversity and density in 5 meters depth stations with moderate of sand, silt and clay were slightly more than 2 other depths stations, it seems that 5 meters stations are made a transition habitats between 2 sandy and clay habitats, that can be used by 2 groups of surface and borrowing deposit feeders. Based on the data provided in this survey, the temperature variation, sediment texture, TOM, type habitat and manmade factors of Gas and petrochemical industries have had the most effect on the macrofauna community structure in the studied region during sampling periods.

Assessment of pelagic primary and secondary production in Sefidrud River estuary

Sefid-Rood River Estuary (SRE) is the most important riverine ecosystem in the south Caspian Sea along the Iranian coast lines. The aim of this study was to examine spatial and temporal variability in Phytoplankton and Zooplankton abundance and diversity in SRE. Variability of Chlorophyll a and inorganic nutrient concentration were determined during a year (November 2004– October 2005) in five sampling stations. Primary and secondry production were determined during a year. Total chlorophyll a concentration during the investigation ranged between zero to 22.8 μgl-1 and the highest levels were consistently recorded during summer and the lowest during winter with a annual mean concentration 4.48 μgl-1. Nutrient concentration was seasonally related to river flow with annual mean concentration: NO2 0.05±0.2 mgl-1, NO3 1.13±0.57 mgl-1, NH4 0.51±0.66 mgl-1, total phosphate 0.13±0.1mgl-1 and SiO2 5.68±1.91 mgl-1. Bacillariophytes, Cyanophytes, Chlorophytes, Pyrophytes and Euglenophytes were the dominant phytoplankton groups in this shallow and turbid estuary. The diversity and abundance of phytoplankton had a seasonal pattern while Diatomas and Chrysophytes were dominant throughout the year but Cyanophytes observed only during the summer. Zooplankton community structure was dominated by copepods which 68% of the total zooplankton. In the winter and summer seasons two increased in the number of zooplankton community and usually toward the sea had occurred. Zooplankton also showed a significant spatial and temporal variation. The high turbidity and temperature prime characteristics of SRE seem to be determining factors acting directly on phytoplankton and zooplankton temporal variability and nutrient fluctuations. Everywhere in this estuary nutrients appeared to be in excess of algal requirement and did not influence a phytoplankton and zooplankton composition. Also there was a positive correlation between chlorophyll a and temperature and a negative one with DIN and TP. Primary production determined in this estuary by dark and light butter method and G.P.P. 38.27±34.12 mgcm-2h-1 and N,PP 201.6±289.9 mgcm-2d-1. secondry production determined 15/128 mgc/m3/year. Everywhere in this estuary nutrients appeared to be in excess to algal requirement and did not influence in Chl. a and primary production. The most important factor influence on Chl. a was water temperature.

Secondary structures of mRNAs and splicing of introns in eukaryotes.

After analyzing the secondary structures of 68 exon-intron-exon and the corresponding exon-exon sequence segments, it is found that about 90% of 5' and 3' terminal bases G (splicing sites) of introns are situated in the loops of secondary structures or at the ends of stems near the loops, and most of "G" s in loops are closed to the ends of loops. Approximately 92% of the connecting sites of the adjoining exons also show the similar features. About 82% of the branch point "A" s are situated in loops or at the ends of stems near the loops. Splicing sites and branch points approach each other in space because of the folding.

Secondary structure of yeast genomic downstream region and polyadenylation signals

Polyadenylation of 3 ' -forming in eukaryote concerns three elements located in precursor mRNA downstream region: efficiency element (EE), position element (PE) and the actual site for cleavage and polyadenylation. Several base sequences of EE and PE have

Phylogenetic analysis of the family Thermaceae with an emphasis on signature position and secondary structure of 16S rRNA

The sequences of the 16S rRNA genes from 38 strains of the family Thermaceae were compared by alignment analysis. The genus-specific and species-specific base substitutions or base deletions (signature positions) were found in three hypervariable regions (in the helices 6, 10 and 17). The differentiation of secondary structures of the high variable regions in the 5' end (38-497) containing several signature positions further supported the concept. Based on the comparisons of the secondary structures in the segments of 16S rRNAs, a key to the species of the family Thermaceae was proposed. (C) 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

The relation between translation speed and protein secondary structure

Based on the statistical analysis of 119 human and 92 E. coli proteins it was found that for both human and E. coli, the mRNA sequences consisting of tri-codon and tetra-codon with high translation speed preferably code for alpha helices more than for coils. For beta strand, the preference/ avoidance oscillates with the translation speed. Moreover, the non-homogeneous usages of tri-codon and tetra-codon with different translation speeds in a given secondary structure have also been found. These results cannot be simply explained by the effect of stochastic fluctuation.

Statistical correlation between protein secondary structure and messenger RNA stem-loop structure

Anew integrated sequence-structure database, called IADE (Integrated ASTRAL-DSSP-EMBL), incorporating matching mRNA sequence, amino acid sequence, and protein secondary structural data, is constructed. It includes 648 protein domains. Based on the IADE database, we studied the relation between RNA stem-loop frequencies and protein secondary structure. It was found that the alpha-helices and beta-strands on proteins tend to be preferably "coded" by mRNA stem region, while the coils on proteins tend to be preferably "coded" by mRNA loop region. These tendencies are more obvious if we observe the structural words (SWs). An SW is defined by a four-amino-acid-fragment that shows the pronounced secondary structural (alpha-helix or beta-strand) propensity. It is demonstrated that the deduced correlation between protein and mRNA structure can hardly be explained as the stochastic fluctuation effect. (C) 2003 Wiley Periodicals, Inc.