Identification of triosephosphate isomerase (TIM) genes from Microcystis (Cyanobacteria : Chroococcales) and theoretical analyses of the potential of cyanobacterial TIM as a target for designing specific inhibitors

The genes encoding triosephosphate isomerase (TIM) in three species of Microcystis (M. aeruginosa, M. viridis and M. wesenbergii) were investigated. Reverse transcriptase-polymerase chain reaction indicated that they were transcribed in the cells. Analyses showed that their DNA and deduced amino acid sequences were highly conserved between all the three species, only a single nonsynonymous substitution was seen at position 31, from an Asp in M. aeruginosa and M. viridis to Glu in M. wesenbergii. Sequence alignment of these with 12 other known cyanobacterial TIM sequences showed that all the cyanobacterial TIMs had a very high level of amino acid identity (over 50% between each two). Comparison of the cyanobacterial TIMs with other reported TIMs (from diverse lineages of the three Domains) showed that they possessed common active-site residues and sequence motifs. All cyanobacterial TIMs have two common cysteine residues (Cys127 and Cys176), and the Cys176 is almost cyanobacteria-specific with only one exception in Streptomyces coelicolor. Both secondary structure alignment and comparative modelling of Synechocystis sp. TIM showed that Cys176 was located at the hinge region of the flexible loop-6 and might therefore be critical to the movement of TIM's loop-6, which is important to the function of the enzyme. Thus, the cyanobacterial TIM-specific Cys176 may be a potential site for the discovery of suitable drugs against cyanobacteria, and such drugs may have utility in controlling water blooms due to cyanobacteria.

Identification, characteristic and phylogenetic analysis of type II DNA topoisomerase gene in Giardia lamblia

The genes encoding type II DNA topoisomerases were investigated in Giardia lamblia genome, and a type IIA gene, GlTop 2 was identified. It is a single copy gene with a 4476 by long ORF without intron. The deduced amino acid sequence shows strong homology to eukaryotic DNA Top 2. However, some distortions were found, such as six insertions in the ATPase domain and the central domain, a similar to 100 as longer central domain; a similar to 200 as shorter C-terminal domain containing rich charged residues. These features revealed by comparing with Top 2 of the host, human, might be helpful in exploiting drug selectivity for antigiardial therapy. Phylogenetic analysis of eukaryotic enzymes showed that kinetoplastids, plants, fungi, and animals were monophyletic groups, and the animal and fungi lineages shared a more recent common ancestor than either did with the plant lineage; microsporidia grouped with fungi. However, unlike many previous phylogenetic analyses, the "amitochondriate" G. lamblia was not the earliest branch but diverged after mitochondriate kinetoplastids in our trees. Both the finding of typical eukaryotic type IIA topoisomerase and the phylogenetic analysis suggest G. lamblia is not possibly as primitive as was regarded before and might diverge after the acquisition of mitochondria. This is consistent with the recent discovery of mitochondrial remnant organelles in G. lamblia.

Identification of a Giardia krr1 homolog gene and the secondarily anucleolate condition of Giaridia lamblia

Giaridia lamblia was long considered to be one of the most primitive eukaryotes and to lie close to the transition between prokaryotes and eukaryotes, but several supporting features, such as lack of mitochondrion and Golgi, have been challenged recently. It was also reported previously that G. lamblia lacked nucleolus, which is the site of pre-rRNA processing and ribosomal assembling in the other eukaryotic cells. Here, we report the identification of the yeast homolog gene, krr1, in the anucleolate eukaryote, G. lamblia. The krr1 gene, encoding one of the pre-rRNA processing proteins in yeast, is actively transcribed in G. lamblia. The deduced protein sequence of G. lamblia krr1 is highly similar to yeast KRR1p that contains a single-KH domain. Our database searches indicated that krr1 genes actually present in diverse eukaryotes and also seem to present in Archaea. However, only the eukaryotic homologs, including that of G. lamblia, have the single-KH domain, which contains the conserved motif KR(K)R. Fibrillarin, another important pre-rRNA processing protein has also been identified previously in G. lamblia. Moreover, our database search shows that nearly half of the other nucleolus-localized protein genes of eukaryotic cells also have their homologs in Giardia. Therefore, we suggest that a common mechanism of pre-RNA processing may operate in the anucleolate eukaryote G. lamblia and in the other eukaryotes and that like the case of "lack of mitochondrion," "lack of nucleolus" may not be a primitive feature, but a secondarily evolutionary condition of the parasite.

Genome-wide computational identification of microRNAs and their targets in the deep-branching eukaryote Giardia lamblia

Using a combined computational program. we identified 50 potential microRNAs (miRNAs) in Giardia lamblia. one of the most primitive unicellular eukaryotes. These miRNAs are unique to G. lamblia and no homologues have been found in other organisms; miRNAs.

Identification and association of the single nucleotide polymorphisms in calpain3 (CAPN3) gene with carcass traits in chickens

Background: The aim of this study is to screen single nucleotide polymorphisms (SNP) of chicken Calpain3 (CAPN3) gene and to analyze the potential association between CAPN3 gene polymorphisms and carcass traits in chickens. We screened CAPN3 single nucleo

Identification and distribution of cartilaginous fishes of the Persian Gulf (Bushehr Province waters)

Class Condrichthyes consist of two sub-classes: Holocehali and. Elasmobranchii, the second one are more divers and has more importance. Selachimorpha (sharkes) and Batidoidimorpha (rays and skates) are two super-order of Elasmobranchii, which they have crucial role in ecological balance in marine ecosystmes. Except few cases, most of sharks and rays (rays and skates) are not well identified, so a lot of works need to be done in this regards. The area of study is located between 49°, 35' and 52°, 33' E and between 27°, 21' and 30°, 02' N in depth of 7 to 78 in. Study were conducted diuring August 1998, September 1999. Samples were taken during 3 sea cruises from 70 bottom trawl net. All sharks and batoid fishes were identified based on biometric specifications (weight, total, length and sexuality for both group and extra biometric specifications, disc width, disc length, and tail length only for, batoid fishes). The 1140 specimens of batoid fishes identified belonged to 6 families, and 18 species. 3 new species were identified, they are Himantura sp.1 and Himantura sp.2 belonged to Dasyatidae family and Rhinobatos sp. belonged to Rhinobatidae Familiy. It needs more works and more adaquate ducuments for cl.earfing scientific names of these species. The 275 specimens of sharks identified belonged to 6 families and 10 species. Chiloscyllium sp. belonged to Hemiscylliidae, family as a new species was identified.

Market opportunity identification for minor crops for food security through value chain studies

The brochure is to contribute to the overall goal of stimulating the adaptation of pro-poor agri-food systems innovations to improve food security and sustainable natural resource management among rural poor farmers. The paper seeks to identify and exploit opportunities for expanding market access for minor crops and NRM products. The minor crops studied included cow pea, sorghum, groundnut, sweet potato and yam.

Key for the identification of the East African marine fishes to family level

The paper provides key for the identification of the East African marine fishes. Just like in most determination keys this one is based on the "either-or" principle, i.e. there is a single alternatIve at each point. A specimen either fits all the characters recorded, or fails to conform to one or more characters and you should then proceed to the next number, keeping this up until the fish to be identified does fit all the characters.

MCMC-based tracking and identification of leaders in groups

We present a novel framework for identifying and tracking dominant agents in groups. Our proposed approach relies on a causality detection scheme that is capable of ranking agents with respect to their contribution in shaping the system's collective behaviour based exclusively on the agents' observed trajectories. Further, the reasoning paradigm is made robust to multiple emissions and clutter by employing a class of recently introduced Markov chain Monte Carlo-based group tracking methods. Examples are provided that demonstrate the strong potential of the proposed scheme in identifying actual leaders in swarms of interacting agents and moving crowds. © 2011 IEEE.

Parameters identification by a single point free response measurement

When a thin rectangular plate is restrained on the two long edges and free on the remaining edges, the equivalent stiffness of the restraining joints can be identified by the order of the natural frequencies obtained using the free response of the plate at a single location. This work presents a method to identify the equivalent stiffness of the restraining joints, being represented as simply supporting the plate but elastically restraining it in rotation. An integral transform is used to map the autospectrum of the free response from the frequency domain to the stiffness domain in order to identify the equivalent torsional stiffness of the restrained edges of the plate and also the order of natural frequencies. The kernel of the integral transform is built interpolating data from a finite element model of the plate. The method introduced in this paper can also be applied to plates or shells with different shapes and boundary conditions. © 2011 Elsevier Ltd. All rights reserved.