• Volume 32, Issue 4

June 2007,   pages  629-805

• Commentary: Keratins: Markers of cell differentiation or regulators of cell differentiation?

• Sources for Imanishi Kinji’s views of sociality and evolutionary outcomes

Prior to the contribution of genetics or the modern evolutionary synthesis (MES) to natural selection theory, social ecologists searched for factors in addition to natural selection that could influence species change. The idea that sociality, not just biology, was important in determining evolutionary outcomes was prevalent in research in social ecology in the 1920s and 1930s. The influence of ‘tradition’ (or the transmission of learned behaviours between generations) and the view that animals are active in selecting their own environments, rather than passive organisms acted upon by chance, were given as much attention as natural selection theory in European ecology, while animal aggregation and cooperation studies were pursued in America. Imanishi Kinji’s personal library and his scientific notes and papers reveal that he was well aware of this literature and had been profoundly influenced by these earlier viewpoints prior to writing his view of nature in his first book, Seibutsu no Sekai (The World of Living Things, 1941). Evidence is presented to show that he developed his theories based partly on early western debates in social ecology while finding inspiration and a way to express his views in the writings of philosopher Nishida Kitarō and, perhaps, General J C Smuts. One of Imanishi’s lasting contributions is in the demonstrated results of over 40 years of subsequent ecological and ethological research by Imanishi and those trained by him that maintained the broader viewpoints on evolution that had been dropped from the western corpus of research by the 1950s. The current attempt to again get beyond natural selection theory is reflected in debates surrounding genetic and cultural evolution of cooperation, the biology of ‘traditions’ and the idea of ‘culture’ in animal societies.

• Living in a physical world XI. To twist or bend when stressed

• What history tells us IX. Z-DNA: when nature is not opportunistic

• Complete nucleotide sequence analysis of Cymbidium mosaic virus Indian isolate: further evidence for natural recombination among potexviruses

The complete nucleotide sequence of an Indian strain of Cymbidium mosaic virus (CymMV) was determined and compared with other potexviruses. Phylogenetic analyses on the basis of RNA-dependent RNA polymerase (RdRp), triple gene block protein and coat protein (CP) amino acid sequences revealed that CymMV is closely related to the Narcissus mosaic virus (NMV), Scallion virus X (SVX), Pepino mosaic virus (PepMV) and Potato aucuba mosaic virus (PAMV). Different sets of primers were used for the amplification of different regions of the genome through RT-PCR and the amplified genes were cloned in a suitable vector. The full genome of the Indian isolate of CymMV from Phaius tankervilliae shares 96–97% similarity with isolates reported from other countries. It was found that the CP gene of CymMV shares a high similarity with each other and other potexviruses. One of the Indian isolates seems to be a recombinant formed by the intermolecular recombination of two other CymMV isolates. The phylogenetic analyses, Recombination Detection Program (RDP2) analyses and sequence alignment survey provided evidence for the occurrence of a recombination between an Indian isolate (AM055720) as the major parent, and a Korean type-2 isolate (AF016914) as the minor parent. Recombination was also observed between a Singapore isolate (U62963) as the major parent, and a Taiwan CymMV (AY571289) as the minor parent.

• Frequency of infection with A and B supergroup Wolbachia in insects and pests associated with mulberry and silkworm

Wolbachia is a ubiquitous, Gram-negative, vertically transmitted, alpha-proteobacterium that causes an array of reproductive abnormalities including cytoplasmic incompatibility, feminization of genetic males, parthenogenesis in a number of insect species, among others. Wolbachia is now being exploited as an agent for pest and vector control. Previous surveys indicated that it is commonly seen in 16–76% of arthropods. In this paper, using polymerase chain reaction assay based on specific amplification of the ftsZ-A and -B supergroup Wolbachia gene fragments, we found that 30% of insects and pests screened were positive for Wolbachia. Among them 66.7% harbour double Wolbachia infection, while 33.3% harbour single Wolbachia infection. These results indicate widespread infection with both double and single Wolbachia, and provide a wealth of information to exploit this endobacterium for the management of pests and vectors.

• Strong and weak hydrogen bonds in drug–DNA complexes: A statistical analysis

A statistical analysis of strong and weak hydrogen bonds in the minor groove of DNA was carried out for a set of 70 drug–DNA complexes. The terms strong’ and weak’ pertain to the inherent strengths and weakness of the donor and acceptor fragments rather than to any energy considerations. The dataset was extracted from the protein data bank (PDB). The analysis was performed with an in-house software, hydrogen bond analysis tool (HBAT). In addition to strong hydrogen bonds such as O−H···O and N−H···O, the ubiquitous presence of weak hydrogen bonds such as C−H···O is implicated in molecular recognition. On an average, there are 1.4 weak hydrogen bonds for every strong hydrogen bond. For both categories of interaction, the N(3) of purine and the O(2) of pyrimidine are favoured acceptors. Donor multifurcation is common with the donors generally present in the drug molecules, and shared by hydrogen bond acceptors in the minor groove. Bifurcation and trifurcation are most commonly observed. The metrics for strong hydrogen bonds are consistent with established trends. The geometries are variable for weak hydrogen bonds. A database of recognition geometries for 26 literature amidinium-based inhibitors of Human African Trypanosomes (HAT) was generated with a docking study using seven inhibitors which occur in published crystal structures included in the list of 70 complexes mentioned above, and 19 inhibitors for which the drug–DNA complex crystal structures are unknown. The virtual geometries so generated correlate well with published activities for these 26 inhibitors, justifying our assumption that strong and weak hydrogen bonds are optimized in the active site.

• Ion pairs in non-redundant protein structures

Ion pairs contribute to several functions including the activity of catalytic triads, fusion of viral membranes, stability in thermophilic proteins and solvent–protein interactions. Furthermore, they have the ability to affect the stability of protein structures and are also a part of the forces that act to hold monomers together. This paper deals with the possible ion pair combinations and networks in 25% and 90% non-redundant protein chains. Different types of ion pairs present in various secondary structural elements are analysed. The ion pairs existing between different subunits of multisubunit protein structures are also computed and the results of various analyses are presented in detail. The protein structures used in the analysis are solved using X-ray crystallography, whose resolution is better than or equal to 1.5 Å and R-factor better than or equal to 20%. This study can, therefore, be useful for analyses of many protein functions. It also provides insights into the better understanding of the architecture of protein structure.

• Molecular cloning and expression of the C-terminus of spider flagelliform silk protein from Araneus ventricosus

A cDNA coding for the C-terminus of spider flagelliform silk protein (AvFlag) was cloned from Araneus ventricosus. Analysis of the cDNA sequence shows that the C-terminus of AvFlag consists of 167 amino acids of a repetitive region and 87 amino acids of a C-terminal non-repetitive region. The peptide motifs found in spider flagelliform silk proteins, GPGGX and GGX, were conserved in the repetitive region of AvFlag. Phylogenetic analysis further confirmed that AvFlag belongs to the spider flagelliform silk proteins. The AvFlag cDNA was expressed as a 28 kDa polypeptide in baculovirus-infected insect cells. As a new expression approach for spider silk protein, the combination of polyhedrin and AvFlag creates a polyhedrin AvFlag fusion protein (61 kDa) that is produced as recombinant polyhedra; this provides a basis for the source of spider silk proteins for various applications.

• Diversity and evolutionary relationship of nucleotide binding site-encoding disease-resistance gene analogues in sweet potato (Ipomoea batatas Lam.)

Most plant disease-resistance genes (𝑅-genes) isolated so far encode proteins with a nucleotide binding site (NBS) domain and belong to a superfamily. NBS domains related to 𝑅-genes show a highly conserved backbone of an amino acid motif, which makes it possible to isolate resistance gene analogues (RGAs) by degenerate primers. Degenerate primers based on the conserved motif (P-loop and GLPL) of the NBS domain from 𝑅-genes were used to isolate RGAs from the genomic DNA of sweet potato cultivar Qingnong no. 2. Five distinct clusters of RGAs (22 sequences) with the characteristic NBS representing a highly diverse sample were identified in sweet potato genomic DNA. Sequence identity among the 22 RGA nucleotide sequences ranged from 41.2% to 99.4%, while the deduced amino acid sequence identity from the 22 RGAs ranged from 20.6% to 100%. The analysis of sweet potato RGA sequences suggested mutation as the primary source of diversity. The phylogenetic analyses for RGA nucleotide sequences and deduced amino acids showed that RGAs from sweet potato were classified into two distinct groups—toll and interleukin receptor-1 (TIR)-NBS-LRR and non-TIR-NBS-LRR. The high degree of similarity between sweet potato RGAs and NBS sequences derived from 𝑅-genes cloned from tomato, tobacco, flax and potato suggest an ancestral relationship. Further studies showed that the ratio of non-synonymous to synonymous substitution within families was low. These data obtained from sweet potato suggest that the evolution of NBS-encoding sequences in sweet potato occur by the gradual accumulation of mutations leading to purifying selection and slow rates of divergence within distinct 𝑅-gene families.

• Selenium acts as an insulin-like molecule for the down-regulation of diabetic symptoms via endoplasmic reticulum stress and insulin signalling proteins in diabetes-induced non-obese diabetic mice

To investigate whether selenium (Sel) treatment would impact on the onset of diabetes, we examined serum biochemical components including glucose and insulin, endoplasmic reticulum (ER) stress and insulin signalling proteins, hepatic C/EBP-homologous protein (CHOP) expression and DNA fragmentation in diabetic and non-diabetic conditions of non-obese diabetic (NOD) mice. We conclude that

1. Sel treatment induced insulin-like effects in lowering serum glucose level in Sel-treated NOD mice,

2. Sel-treated mice had significantly decreased serum biochemical components associated with liver damage and lipid metabolism,

3. Sel treatment led to the activation of the ER stress signal through the phosphorylation of JNK and eIF2 protein and insulin signal mechanisms through the phosphorylation of Akt and PI3 kinase, and

4. Sel-treated mice were significantly relieved apoptosis of liver tissues indicated by DNA fragmentation assay in the diabetic NOD group.

These results suggest that Sel compounds not only serve as insulin-like molecules for the downregulation of glucose level and the incidence of liver damage, but may also have the potential for the development of new drugs for the relief of diabetes by activating the ER stress and insulin signalling pathways.

• Synergy between verapamil and other multidrug -resistance modulators in model membranes

Various cationic lipophilic compounds can reverse the multidrug resistance of cancer cells. Possible interaction between these compounds, which are known as modulators, has been assessed by measuring leakage of Sulphan blue from anionic liposomes, induced both by verapamil alone and by verapamil in combination with diltiazem, quinine, thioridazine or clomipramine. An equation was derived to quantify the permeation doses and Hill coefficients of the drugs and mixtures between them by simultaneous fitting of the experimental data. The interaction was tested by two methods, the competition plot and the isobole method; both showed synergy between verapamil and each of diltiazem, quinine and thioridazine. The dose factor of potentiation for verapamil determined within membranes was 4.0 ± 0.4 with diltiazem, 3.2 ± 0.4 with quinine and 2.4 ± 0.3 with thioridazine. The results suggest that the effectiveness of reversing multidrug resistance may be increased with modulators such as verapamil and diltiazem that have a much greater effect in combination than what would be expected from their effects when considered separately.

• Diet-dependent depletion of queuosine in tRNAs in Caenorhabditis elegans does not lead to a developmental block

Queuosine (Q), a hypermodified nucleoside, occurs at the wobble position of transfer RNAs (tRNAs) with GUN anticodons. In eubacteria, absence of Q affects messenger RNA (mRNA) translation and reduces the virulence of certain pathogenic strains. In animal cells, changes in the abundance of Q have been shown to correlate with diverse phenomena including stress tolerance, cell proliferation and tumour growth but the function of Q in animals is poorly understood. Animals are thought to obtain Q (or its analogues) as a micronutrient from dietary sources such as gut microflora. However, the difficulty of maintaining animals under bacteria-free conditions on Q-deficient diets has severely hampered the study of Q metabolism and function in animals. In this study, we show that as in higher animals, tRNAs in the nematode Caenorhabditis elegans are modified by Q and its sugar derivatives. When the worms were fed on Q-deficient Escherichia coli, Q modification was absent from the worm tRNAs suggesting that C. elegans lacks a de novo pathway of Q biosynthesis. The inherent advantages of C. elegans as a model organism, and the simplicity of conferring a Q-deficient phenotype on it make it an ideal system to investigate the function of Q modification in tRNA.

• Hyaluronidase and collagenase inhibitory activities of the herbal formulation Triphala guggulu

Myrrh (guggulu) oleoresin from the Commiphora mukul tree is an important component of antiarthritic drugs in Ayurvedic medicine. Clinical data suggest that elevated levels of hyaluronidase and collagenase type 2 enzymes contribute significantly to cartilage degradation. Triphala guggulu (TG) is a guggulu-based formulation used for the treatment of arthritis. We assessed the chondroprotective potential of TG by examining its effects on the activities of pure hyaluronidase and collagenase type 2 enzymes. Triphala shodith guggulu (TSG), an intermediate in the production of TG, was also examined. A spectrophotometric method was used to assay Hyaluronidase activity, and to detect potential Hyaluronidase inhibitors. Aqueous and hydro-alcoholic extracts of TSG showed weak but dose-dependent inhibition of hyaluronidase activity. In contrast, the TG formulation was 50 times more potent than the TSG extract with respect to hyaluronidase inhibitory activity. A validated X-ray film-based assay was used to measure the gelatinase activity of pure collagenase type 2. Hydro-alcoholic extracts of the TG formulation were 4 times more potent than TSG with respect to collagenase inhibitory activity. Components of Triphala were also evaluated for their inhibitory activities on hyaluronidase and collagenase. This is the first report to show that the T2 component of Triphala (T. chebula) is a highly potent hyaluronidase and collagenase inhibitor. Thus, the TG formulation inhibits two major enzymes that can degrade cartilage matrix. Our study provides the first in vitro preclinical evidence of the chondroprotective properties of TG.

• Cytological evidence for population-specific sex chromosome heteromorphism in Palaearctic green toads (Amphibia, Anura)

A chromosome study was carried out on a number of European and Central Asiatic diploid green toad populations by means of standard and various other chromosome banding and staining methods (Ag-NOR-, Q-, CMA3-, late replicating [LR] banding pattern, C- and sequential C-banding + CMA3 + DAPI). This study revealed the remarkable karyological uniformity of specimens from all populations, with the only exception being specimens from a Moldavian population, where one chromosome pair was heteromorphic. Though similar in shape, size and with an identical heterochromatin distribution, the difference in the heteromorphic pair was due to a large inverted segment on its long arms. This heteromorphism was restricted to females, suggesting a female heterogametic sex chromosome system of ZZ/ZW type at a very early step of differentiation.

• Presence of two types of flowers with respect to nectar sugar in two gregariously flowering species

Many species of animal-pollinated flowers are known to vary widely in the nectar content of flowers. Some proportion of flowers in many species is apparently nectarless, and such flowers are believed to be ‘cheaters’. Cheating may explain a part of the variability in nectar content. If cheating exists as a qualitatively different strategy then we expect bimodality in the distribution of nectar content of flowers. It has been shown in a multispecies study that gregarious species have a higher proportion of cheater flowers. We studied the frequency distribution of total nectar sugar in two gregariously flowering species Lantana camara and Utricularia purpurascens, which differed in other floral and ecological characters. At the population level, both the species showed significant bimodality in the total sugar content of flowers. The obvious sources of heterogeneity in the data did not explain bimodality. In Lantana camara, bimodality was observed within flowers of some of the individual plants sampled. In Utricularia purpurascens the proportion of nectarless flowers was more in high-density patches, suggesting that the gregariousness hypothesis may work within a species as well. The results support the hypothesis of cheating as a distinct strategy since two distinct types of flowers were observed in both the species. The effect of density in Utricularia purpurascens also supports the gregariousness hypothesis.

• Sociobiology of biodegradation and the role of predatory protozoa in biodegrading communities

• Patterns of species discovery in the Western Ghats, a megadiversity hot spot in India

Even since Linnaeus, naturalists and taxonomists have been systematically describing species new to science. Besides indicating gaps in taxonomic effort, understanding the temporal patterns of species discovery could help in identifying drivers that determine discovery. In this study we report the patterns of discovery of eight taxa – birds, butterflies, frogs, tiger beetles, grasses, asters, ferns and orchids – in the Western Ghats, a megadiversity centre in India. Our results indicate that the discovery curves for birds and butterflies have been saturated while those for frogs and grasses continue to increase. Within each taxon, the major drivers of discovery were commonness of the species and their size. The average years taken for discovery across taxa were directly related to the per cent endemicity and species richness of the taxa. We discuss the trajectories of discovery with respect to rarity or endemicity of the species and life history features, and the implications these might have for strategizing the discovery process in India.

• Do we live in a largely top-down regulated world ?

Based on a review of mostly recent literature for a public lecture, the question is discussed whether we live in a largely top-down” regulated world rather than one formed bottom-up” by the resources for plant and animal growth. Of course, the top-down mechanism is predicated by bottom-up production, especially by the plants. Examples for the effects of grazing and predation for the land and the open sea, but including coral reefs, are discussed. The answer to the question posed by the title is affirmative. Ecosystems altered by man and urgent needs for marine conservation are briefly treated.

• Singing of Neoconocephalus robustus as an example of deterministic chaos in insects

We use nonlinear time series analysis methods to analyse the dynamics of the sound-producing apparatus of the katydid Neoconocephalus robustus. We capture the dynamics by analysing a recording of the singing activity. First, we reconstruct the phase space from the sound recording and test it against determinism and stationarity. After confirming determinism and stationarity, we show that the maximal Lyapunov exponent of the series is positive, which is a strong indicator for the chaotic behaviour of the system. We discuss that methods of nonlinear time series analysis can yield instructive insights and foster the understanding of acoustic communication among insects.

• Special issue Journal of Biosciences Volume 32, Number 1, Janurary 2007 Computational Biology

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