• Volume 27, Issue 3

June 2002,   pages  187-298

• Clipboard: Amphibians as environmental sentinels

• Commentary: Dichotomies in the perception of speech

• Commentary: Analysing phenotypic variation: when old-fashioned means up-to-date

• Theoretical approaches to holistic biological features: Pattern formation, neural networks and the brain-mind relation

The topic of this article is the relation between bottom-up and top-down, reductionist and holistic” approaches to the solution of basic biological problems. While there is no doubt that the laws of physics apply to all events in space and time, including the domains of life, understanding biology depends not only on elucidating the role of the molecules involved, but, to an increasing extent, on systems theoretical approaches in diverse fields of the life sciences. Examples discussed in this article are the generation of spatial patterns in development by the interplay of autocatalysis and lateral inhibition; the evolution of integrating capabilities of the human brain, such as cognition-based empathy; and both neurobiological and epistemological aspects of scientific theories of consciousness and the mind.

• Carbon – the first frontier of information processing

Information is often encoded as an aperiodic chain of building blocks. Modern digital computers use bits as the building blocks, but in general the choice of building blocks depends on the nature of the information to be encoded. What are the optimal building blocks to encode structural information? This can be analysed by substituting the operations of addition and multiplication of conventional arithmetic with translation and rotation. It is argued that at the molecular level, the best component for encoding discretized structural information is carbon. Living organisms discovered this billions of years ago, and used carbon as the back-bone for constructing proteins that function according to their structure. Structural analysis of polypeptide chains shows that an efficient and versatile structural language of 20 building blocks is needed to implement all the tasks carried out by proteins. Properties of amino acids indicate that the present triplet genetic code was preceded by a more primitive one, coding for 10 amino acids using two nucleotide bases.

• An insight into the possible mechanism of working of two-cistronic gene expression systems and rational designing of newer systems

The initial attempts at hyper-expressing buffalo/goat growth hormone (GH)-ORFs in Escherichia coli directly under various strong promoters were not successful despite the presence of a functional gene. High level expression of GH was achieved as a fusion protein with glutathione-S-transferase (GST). To produce native GH in an unfused state, we adapted an established strategy of two-cistronic approach in our system. In this strategy, utilizing one of the highly efficient reported sequences as the first cistron led to a nearly 1000-fold enhancement in the level of expression under an E. coli promoter (trc). In search of a newer first-cistron sequence as well as to see the generality of the two-cistronic approach, we explored the ability of different lengths of a highly expressing natural gene to act as an efficient first cistron. Surprisingly, GST, which is naturally highly expressible in E. coli, could not be fitted into a successful two-cistronic construct. In addition, placement of the entire two-cistronic expression cassette (which had earlier given high-level GH expression under trc promoter) under the T7 promoter in E. coli failed to hyper-express GH. These results suggest that the successful exploitation of the two-cistron arrangement for hyper-expression of eukaryotic ORFs in bacteria is not as straightforward as was previously thought. It appears probable that factors such as the sequence context, together with the length and codons used in the first cistron are important as well.

• Overexpression and characterization of dimeric and tetrameric forms of recombinant serine hydroxymethyltransferase from Bacillus stearothermophilus

Serine hydroxymethyltransferase (SHMT), a pyridoxal-5′-phosphate (PLP) dependent enzyme catalyzes the interconversion of L-Ser and Gly using tetrahydrofolate as a substrate. The gene encoding for SHMT was amplified by PCR from genomic DNA of Bacillus stearothermophilus and the PCR product was cloned and overexpressed in Escherichia coli. The purified recombinant enzyme was isolated as a mixture of dimer (90%) and tetramer (10%). This is the first report demonstrating the existence of SHMT as a dimer and tetramer in the same organism. The specific activities at 37°C of the dimeric and tetrameric forms were 6.7 U/mg and 4.1 U/mg, respectively. The purified dimer was extremely thermostable with a 𝑇m of 85°C in the presence of PLP and L-Ser. The temperature optimum of the dimer was 80°C with a specific activity of 32.4 U/mg at this temperature. The enzyme catalyzed tetrahydrofolate-independent reactions at a slower rate compared to the tetrahydrofolate-dependent retro-aldol cleavage of L-Ser. The interaction with substrates and their analogues indicated that the orientation of PLP ring of B. stearothermophilus SHMT was probably different from sheep liver cytosolic recombinant SHMT (scSHMT).

• Human placental lipid induces mitogenesis and melanogenesis in B16F10 melanoma cells

A hydroalcoholic extract of fresh term human placenta was found to be mitogenic as well as melanogenic on B16F10 mouse melanoma in an in vitro culture. The extract, a reservoir of a large number of bioactive molecules, was resolved to get the lipid fraction. Its activity was evaluated on B16F10 mouse melanoma by assessing the change in cellular morphology, growth and melanin induction. The lipid fraction, placental total lipid fraction (PTLF) tested in the study employed doses of 0.01 to 200 𝜇g/ml; optimum growth and melanization accompanied by morphological changes were recorded at 10 and 100 𝜇g/ml respectively. At intermediate doses growth and melanization were found to show a pattern of change over between growth and melanization and finally reached at an inverse relation at the respective optimal dose of response. Compared with defined sphingolipids, C2 ceramide and sphingosine-1-phosphate, the results were mostly corroborative. The duality of biological response of sphingolipids as reported in numerous studies was comparable for the PTLF suggesting that its active component is a sphingolipid and showing its use for pigment recovery in vitiligo.

• Cloning and sequencing of complete 𝜏-crystallin cDNA from embryonic lens of Crocodylus palustris

𝜏-Crystallin is a taxon-specific structural protein found in eye lenses. We present here the cloning and sequencing of complete 𝜏-crystallin cDNA from the embryonic lens of Crocodylus palustris and establish it to be identical to the 𝛼-enolase gene from non-lenticular tissues. Quantitatively, the 𝜏-crystallin was found to be the least abundant crystallin of the crocodilian embryonic lenses. Crocodile 𝜏-crystallin cDNA was isolated by RT-PCR using primers designed from the only other reported sequence from duck and completed by 5′- and 3′-rapid amplification of cDNA ends (RACE) using crocodile gene specific primers designed in the study. The complete 𝜏-crystallin cDNA of crocodile comprises 1305 bp long ORF and 92 and 409 bp long untranslated 5′-and 3′-ends respectively. Further, it was found to be identical to its putative counterpart enzyme 𝛼-enolase, from brain, heart and gonad, suggesting both to be the product of the same gene. The study thus provides the first report on cDNA sequence of 𝜏-crystallin from a reptilian species and also re-confirms it to be an example of the phenomenon of gene sharing as was demonstrated earlier in the case of peking duck. Moreover, the gene lineage reconstruction analysis helps our understanding of the evolution of crocodilians and avian species.

• Molecular cloning of growth hormone encoding cDNA of Indian major carps by a modified rapid amplification of cDNA ends strategy

A modified rapid amplification of cDNA ends (RACE) strategy has been developed for cloning highly conserved cDNA sequences. Using this modified method, the growth hormone (GH) encoding cDNA sequences of Labeo rohita, Cirrhina mrigala and Catla catla have been cloned, characterized and overexpressed in Escherichia coli. These sequences show 96–98% homology to each other and are about 85% homologous to that of common carp. Besides, an attempt has been made for the first time to describe a 3-D model of the fish GH protein.

• Water temperature and pH influence olfactory sensitivity to pre-ovulatory and post-ovulatory ovarian pheromones in male Barilius bendelisis

The attractive response and sexual activity elicited by pre-ovulatory steroid sulphate and post-ovulatory 15K-PGF pheromones are greater in wild caught tubercular males and immature males which express breeding tubercles on the snout (at 12–13 days post androgen implant) than in non-tubercular and non-androgen implanted males of freshwater fish Barilius bendelisis. This shows that circulatory androgens exert an activational effect on olfactory receptors of male fish. Wild caught tubercular males and androgen implanted juvenile males exhibit a high responsiveness to steroid sulphate at the water temperature and pH which fish experience during the pre-spawning phase. The male’s sensitivity to 15K-PGF is almost equally high at the water temperature and pH which they experience in wild during the both pre-spawning and spawning periods. This suggests that the differential olfactory sensitivity to the two classes of pheromones in androgen implanted males is due to the varied temperature and pH of water, and that during the breeding season the male’s olfactory sensitivity to PGF pheromone is more widespread than to the steroidal pheromone. An increased and decreased olfactory sensitivity in mature males to sex pheromones and L-alanine respectively during the breeding phase is in agreement with the hypothesis that pheromonal stimuli dominate over feeding stimuli to promote spawning success.

• Cocoon production, morphology, hatching pattern and fecundity in seven tropical earthworm species – a laboratory-based investigation

Data on the reproductive biology of seven Indian species of earthworms, viz. Perionyx excavatus Perrier, Lampito mauritii Kinberg, Polypheretima elongata (Perrier), Pontoscolex corethrurus (Muller), Eutyphoeus gammiei (Beddard), Dichogaster modiglianii (Rosa) and Drawida nepalensis Michaelsen are presented. The peregrine earthworms such as Perionyx excavatus, Pontoscolex corethrurus, Dichogaster modiglianii, and Polypheretima elongata are considered to be continuous breeders with high fecundity. Native Lampito mauritii and Drawida nepalensis are semi-continuous and Eutyphoeus gammiei discrete breeders. There is a dramatic increase in cocoon production by most earthworm species of Tripura in the summer and monsoon with a corresponding peak during April and July. Cocoon production decreased or ceased during winter. Temperature affected the incubation period of cocoons. With increase in temperature, incubation period increased in the endogeic worms, Pontoscolex corethrurus, Polypheretima elongata and Drawida nepalensis and decreased in the epigeic worms, Perionyx excavatus and Dichogaster modiglianii, within a temperature range between 28–32°C under laboratory conditions. There was a significant (𝑃 < 0.05) positive correlation between number of hatchlings per cocoon and incubation period in Lampito mauritii. High rate of cocoon production, short development time with high hatching success, as well as continuous breeding strategies in the epigeic species Perionyx excavatus and Dichogaster modiglianii and the top soil endogeic species, Pontoscolex corethrurus, Drawida nepalensis and Lampito mauritii, indicate their possible usefulness in vermiculture. The giant anecic worm, Eutyphoeus gammiei, which has a very long cocoon development time, discrete breeding strategy and very low rate of cocoon production, is not a suitable species for vermiculture.

• A theropod tooth from the Late Triassic of southern Africa

An isolated, large recurved and finely serrated tooth found associated with the prosauropod Euskelosaurus from the Late Triassic part of the Elliot Formation is described here. It is compared to the Triassic thecodonts and carnivorous dinosaurs and its possible affinity is discussed. The tooth possibly belongs to a basal theropod and shows some features similar to the allosauroids. This tooth is of significance, as dinosaur remains except for some footprints and trackways, are poorly known in the Late Triassic horizons of southern Africa.

• # Journal of Biosciences

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