Supplementation of prebiotics in fish feed: a review

Aquaculture is one of the fastest growing industries in the world. There is a need for enhanced disease resistance, feed efficiency and growth performance of cultured fish species. The cost of production are likely to be reduced if growth performance and feed efficiency are increased in commercial aquaculture. Also if the survivility of the fishes increase, then their overall production cost would be remarkably reduced. Dietary supplementation of different feed additives e.g. immunostimulants, probiotics and prebiotics usually in small quantities for the purpose of fortifying it with certain nutrients have been found to be beneficial for improving immune status, feed efficiency and growth performance of crustaceans and finfishes. The present article was constructed to highlight the effect of dietary prebiotics on different body growth parameters of fish. However, the application of prebiotics and supplementary enzymes in fish feed is now gradually gaining importance in commercial aquaculture practices, the article stresses on the effect of prebiotics on live body weight gain, dressing percentage, weight of vital organs and muscles and mean villus lengths in digestive tract of fish along with their application as growth promoters in commercial aquafeed (Gatesoupe in Aqua Feeds Formul Beyond 2(3):3–5, 2005; Ganguly et al. in Israeli J Aquac Bamidgeh 62(3):130–138, 2010a, Fish Chimes 30(7):64, 2010b).     

Cooperative stabilization of Zn2+:DNA complexes through netropsin binding in the minor groove of FdU-substituted DNA

The simultaneous binding of netropsin in the minor groove and Zn²⁺ in the major groove of a DNA hairpin that includes 10 consecutive FdU nucleotides at the 3′-terminus (3′FdU) was demonstrated based upon NMR spectroscopy, circular dichroism (CD), and computational modeling studies. The resulting Zn²⁺/netropsin: 3′FdU complex had very high thermal stability with aspects of the complex intact at 85?°C, conditions that result in complete dissociation of Mg²⁺ complexes. CD and ¹⁹F NMR spectroscopy were consistent with Zn²⁺ binding in the major groove of the DNA duplex and utilizing F5 and O4 of consecutive FdU nucleotides as ligands with FdU nucleotides hemi-deprotonated in the complex. Netropsin is bound in the minor groove of the DNA duplex based upon 2D NOESY data demonstrating contacts between AH2 ¹H and netropsin ¹H resonances. The Zn²⁺/netropsin: 3′FdU complex displayed increased cytotoxicity towards PC3 prostate cancer (PCa) cells relative to the constituent components or separate complexes (e.g. Zn²⁺:3′FdU) indicating that this new structural motif may be therapeutically useful for PCa treatment.

An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:32     

Lesser known relatives of miRNA

Since the discovery of RNAi (RNA interference) major attention has focused on studying miRNA (microRNA) and siRNA (small interfering RNA). However, within the last few years, several other small ncRNAs (non-coding RNAs) have been discovered and thus various newer acronyms representing these ‘other’ classes of small ncRNAs have populated the literature. Of these, piRNA (Piwi-interacting RNA) has been gaining importance because of its role as the guardian of the germline genome. Some of the other newly discovered small ncRNAs have been mostly reported in plants, and they are yet to be studied more comprehensively. Nevertheless, piRNA and the ‘other’ small ncRNAs deserve some discussion because they are members of the increasingly large family of small ncRNAs.     

Differential antioxidative responses of indica rice cultivars to drought stress

The present study investigated the linkages between drought stress, oxidative damages and variations in antioxidants in the three rice varieties IR-29 (salt-sensitive), Pokkali (salt-tolerant) and aromatic Pusa Basmati (PB), to elucidate the antioxidative protective mechanism governing differential drought tolerance. Water deficit, induced by 20% (w/v) polyethylene glycol (PEG-6000), provoked severe damages in IR-29 and PB in the form of huge chlorophyll degradation and elevated H₂O₂, malondialdehyde and lipoxygenase (LOX, EC 1.13.11.12) levels as compared to Pokkali. The protein oxidation was more conspicuous in IR-29. Increment in antioxidants, particularly flavonoids and phenolics was several folds higher over control in Pokkali, while much lesser in IR-29 and PB. The activity of catalase (CAT, EC 1.11.1.6) and superoxide dismutase (SOD, EC 1.15.1.1) were decreased in IR-29 and PB, but unaltered in Pokkali. However, marked drought-induced increase in guaiacol peroxidase (GPX, EC 1.11.1.7) activity was noted in both IR-29 and PB. Induction in radical scavenging activity, being the maximum in IR-29, and increased reducing power ability in all the cultivars, accompanied with drought stress, were observed as a defense mechanism. The novelty of our work is that it showed the aromatic rice PB behaving more closely to IR-29 in greater susceptibility to dehydration stress, while the salt-tolerant Pokkali also showed effective drought tolerance properties.     

Microarrays in biology and medicine

The remarkable speed with which biotechnology has become critical to the practice of life sciences owes much to a series of technological revolutions. Microarray is the latest invention in this ongoing technological revolution. This technology holds the promise to revolutionize the future of biology and medicine unlike any other technology that preceded it. Development of microarray technology has significantly changed the way questions about diseases and/or biological phenomena are addressed. This is because microarrays facilitate monitoring the expression of thousands of genes or proteins in a single experiment. This enormous power of microarrays has enabled scientists to monitor thousands of genes and their products in a given living organism in one experiment, and to understand how these genes function in an orchestrated manner. Obtaining such a global view of life at the molecular level was impossible using conventional molecular biological techniques. However, despite all the progress made in developing this technology, microarray is yet to reach a point where all data are obtained, analyzed, and shared in a standardized fashion. The present article is a brief overview of microarray technologies and their applications with an emphasis on DNA microarray.     

Differential regulation of cytochrome P450 3A1 and P450 3A2 in rat liver following dexamethasone treatment

Induction of P450 3A1 and P450 3A2 was studied in adult rat liver following treatment with a single high dose of dexamethasone (DEX). The increase of both P450 3A1 and 3A2 occurred at the level of mRNA as well as protein. P450 3A isozymes thus induced were catalytically active. No constitutive expression of P450 3A1 mRNA or protein was observed in males or females. Constitutive expression of P450 3A2 mRNA and protein was observed in males but not in females. Additionally, in females, P450 3A2 was almost nondetectable compared to that in males, at any dose of DEX. A time course study following DEX treatment showed that P450 3A1 mRNA and protein were detectable in both sexes at 12 hours, increased until 48 hours, and then declined. The decline was more rapid in males. P450 3A2 mRNA and protein increased as early as 3 hours, increased further up to 48 hours, and slowly declined thereafter. A dose-response study indicated that P450 3A1 mRNA and protein progressively increased in both sexes from a dose of 30 mg/kg. In contrast, P450 3A2 mRNA and protein in males did not increase up to a dose of 30 mg/kg but increased at higher doses. Total P450 content and P450 3A catalytic activity were also found to increase with time and dose. © 1996 John Wiley & Sons, Inc.     

The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

Many cases of nonstandard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The "gain" represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The "loss" represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is codon disappearance (CD), where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the unassigned codon mechanism, the loss occurs first, whereas in the ambiguous intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. CD is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense-to-sense reassignments cannot be explained by CD. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the unassigned codon and the ambiguous intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.