American Journal of Biochemistry and Molecular Biology
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Open Access journal
ISSN (Print) 2150-4210 - ISSN (Online) 2150-4253
Published by Academic Journals Inc [4 journals]
- Characterization of ORF0 and ORF1 and their Roles in Recombination and
Replication of Sugarcane yellow leaf virus
Abstract: Background: Two open reading frames (ORF0 and ORF1) of Sugarcane yellow leaf virus (SCYLV) genome which play an important role in virus replication and accumulation in plants have been characterized. Materials and Methods: The RT-PCR and qRT-PCR have been used to evaluate the degree of infection with SCYLV using different genome locations (ORF0 and ORF1). Possible recombination events in two ORFs were identified using TOPALi (v2.5), RECCO and RDP softwares. Results: Transcript levels of two genes varied among infected plants but overall expression of ORF1 was higher than ORF0. Cultivar H73-6110 (susceptible) yielded the highest transcript levels of ORF1 whereas cultivar H78-4153 (resistant) exhibited the lowest levels. No significant differences were found between the sugarcane cultivars for the ORF0 transcripts in mature leaves and seedling tissues. Amino acid sequence similarity of ORF0 and ORF1 varied among SCYLV isolates and ranged from 69-99 and 73-99%, respectively. Possible recombination events located in the two ORFs were identified using TOPALi (v2.5), RECCO and RDP softwares. Conclusion: The results showed strong presence of recombination in aligned sequences of ORF0 and ORF1 when TOPALi and RECCO programs were used.
PubDate: 20 December, 2016
- Atrazine-induced Changes in some Biochemical Parameters of the Early
Developmental Stages of the African Catfish Clarias gariepinus (Burchell,
Abstract: Background and Objective: Atrazine is considered the most common aquatic herbicide used. So, the present study aimed at studying atrazine-induced changes in some biochemical characteristics during early embryonic stages of Clarias gariepinus . These characteristics include two metabolic enzymes, lactate hydrogenase (LDH) and glucose-6-phosphate dehydrogenase (G6PDH), two oxidative enzymes, glutathione reductase (GSH) and superoxide dismutase (SOD), two thyroid hormones, triiodothyronine (T3) and thyroxine (T4), lipid peroxidation (LPO), DNA damage and patterns of protein fractions of different early developmental stages. Material and Methods: Gametes were collected from mature specimens of the African catfish, C. gariepinus from the river Nile. The fertilized eggs were incubated in dechlorinized tap water (pH = 7.7, dissolved oxygen 88-94% saturation, temperature 27-29EC and photoperiod 12:12 (light:dark). Under atrazine influences, different measurements of enzyme activities, electrophoretic protein analysis, lipid peroxidation, DNA fragmentation, Total Protein (TP) and hormones were carried out. Results: The atrazine-induced significant fluctuation in the activity of G6PDH and LDH with a sharp decrease in 24 h-PFS after hatching. There is no significant variations in GSH activity under atrazine doses except in 24 and 96 h-PFS with a decrease in all developmental stages except at 72 h-PFS. Insignificant fluctuation in SOD activity in all developmental stages of C. gariepinus except 4, 20 and 24 h-PFS in comparison to control. Atrazine induced significant fluctuation in DNA damage and LPO/TP ratio in all developmental stages. Insignificant fluctuation in T3 activity but significant decrease in T4 activity in all developmental stages of C. gariepinus under exposure of sublethal doses of atrazine. Conclusion: One could conclude that atrazine significantly disturbe the metabolic parameters of embryonic and developmental stages of fishes and in turn most of these parameters could be used as indicators of environmental aquatic pollution.
PubDate: 20 December, 2016
- Evolutionary Lineages in Genus Lethrinus (Family: Lethrinidae) and the
Corresponding Trophic Evolution Based on DNA Barcoding
Abstract: Background: The present study aimed at studying the phylogenetic relationships of 18 Lethrinus species and their associated trophic evolution on the basis of their filtered and validated DNA barcoding (cytochrome oxidase subunite I (COI)-sequences) released by the BOLD system database. Materials and Methods: About 98 COI sequences of 18 Lethrinus species were retrieved from BOLD system released nucleotide database and analyzed using different phylogenetic softwares. Results: Intra and inter-specific variations in COI-sequences were recorded with emphasis on geographic variations. Some COI-sequences were postulated to be of misidentified specimens and others were questionable leading to paraphyla. The COI-based phylogenetics using different statistical methods established two lineages in genus Lethrinus with L. haematopterus as ancestor group. These two lineages were corresponding with two obvious trophic types: Low-bodied species with conical lateral teeth and high bodied species with molariform teeth with the sister group L. haematopterus of high-bodied species with conical teeth. Conclusion: These findings emphasizes on the higher validity of DNA barcoding in discovering phylogenetics of genus Lethrinus in comparison to those based on cytochrome b.
PubDate: 20 December, 2016