• Volume 28, Issue 4

      June 2003,   pages  359-528

    • Clipboard: Severe acute respiratory syndrome (SARS): an old virus jumping into a new host or a new creation?

      M S Shaila

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    • Clipboard: Blueprint of a red mould: Unusual and unexpected findings in the Neurospora genome sequence

      Durgadas P Kasbekar

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    • Clipboard: A branched chain fatty acid promotes cold adaptation in bacteria

      M K Chattopadhyay M V Jagannadham

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    • Commentary: HIV necessary though not sufficient for AIDS

      Harry W Haverkos

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    • Commentary: Can we obtain realistic HIV/AIDS estimates for India?

      Arni S R Srinivasa Rao

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    • Origin of the neutral and nearly neutral theories of evolution

      Tomoko Ohta

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    • Bioluminometric assay of ATP in mouse brain: Determinant factors for enhanced test sensitivity

      Haseeb Ahmad Khan

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      Firefly luciferase bioluminescence (FLB) is a highly sensitive and specific method for the analysis of adenosine-5-triphosphate (ATP) in biological samples. Earlier attempts to modify the FLB test for enhanced sensitivity have been typically based on in vitro cell systems. This study reports an optimized FLB procedure for the analysis of ATP in small tissue samples. The results showed that the sensitivity of the FLB test can be enhanced several fold by using ultraturax homogenizer, perchloric acid extraction, neutralization of acid extract and its optimal dilution, before performing the assay reaction.

    • The chemical bases of the various AIDS epidemics: recreational drugs, anti-viral chemotherapy and malnutrition

      Peter Duesberg Claus Koehnlein David Rasnick

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      In 1981 a new epidemic of about two-dozen heterogeneous diseases began to strike non-randomly growing numbers of male homosexuals and mostly male intravenous drug users in the US and Europe. Assuming immunodeficiency as the common denominator the US Centers for Disease Control (CDC) termed the epidemic, AIDS, for acquired immunodeficiency syndrome. From 1981–1984 leading researchers including those from the CDC proposed that recreational drug use was the cause of AIDS, because of exact correlations and of drug-specific diseases. However, in 1984 US government researchers proposed that a virus, now termed human immunodeficiency virus (HIV), is the cause of the non-random epidemics of the US and Europe but also of a new, sexually random epidemic in Africa. The virus-AIDS hypothesis was instantly accepted, but it is burdened with numerous paradoxes, none of which could be resolved by 2003: Why is there no HIV in most AIDS patients, only antibodies against it? Why would HIV take 10 years from infection to AIDS? Why is AIDS not self-limiting via antiviral immunity? Why is there no vaccine against AIDS? Why is AIDS in the US and Europe not random like other viral epidemics? Why did AIDS not rise and then decline exponentially owing to antiviral immunity like all other viral epidemics? Why is AIDS not contagious? Why would only HIV carriers get AIDS who use either recreational or anti-HIV drugs or are subject to malnutrition? Why is the mortality of HIV-antibody-positives treated with anti-HIV drugs 7–9%, but that of all (mostly untreated) HIV-positives globally is only 1.4%? Here we propose that AIDS is a collection of chemical epidemics, caused by recreational drugs, anti-HIV drugs, and malnutrition. According to this hypothesis AIDS is not contagious, not immunogenic, not treatable by vaccines or antiviral drugs, and HIV is just a passenger virus. The hypothesis explains why AIDS epidemics strike non-randomly if caused by drugs and randomly if caused by malnutrition, why they manifest in drug- and malnutrition-specific diseases, and why they are not self-limiting via anti-viral immunity. The hypothesis predicts AIDS prevention by adequate nutrition and abstaining from drugs, and even cures by treating AIDS diseases with proven medications.

    • Regulation of activity of the yeast TATA-binding protein through intra-molecular interactions

      Perumal Vanathi Anurag Kumar Mishra Purnima Bhargava

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      Dimerization is proposed to be a regulatory mechanism for TATA-binding protein (TBP) activity both in vitro and in vivo. The reversible dimer-monomer transition of TBP is influenced by the buffer conditions in vitro. Using in vitro chemical cross-linking, we found yeast TBP (yTBP) to be largely monomeric in the presence of the divalent cation Mg2+, even at high salt concentrations. Apparent molecular mass of yTBP at high salt with Mg2+, run through a gel filtration column, was close to that of monomeric yTBP. Lowering the monovalent ionic concentration in the absence of Mg2+, resulted in dimerization of TBP. Effect of Mg2+ was seen at two different levels: at higher TBP concentrations, it suppressed the TBP dimerization and at lower TBP levels, it helped keep TBP monomers in active conformation (competent for binding TATA box), resulting in enhanced TBP-TATA complex formation in the presence of increasing Mg2+. At both the levels, activity of the full-length TBP in the presence of Mg2+ was like that reported for the truncated C-terminal domain of TBP from which the N-terminus is removed. Therefore for full-length TBP, intra-molecular interactions can regulate its activity via a similar mechanism.

    • The transcriptional activator GAL4-VP16 regulates the intra-molecular interactions of the TATA-binding protein

      Anurag Kumar Mishra Perumal Vanathi Purnima Bhargava

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      Binding characteristics of yeast TATA-binding protein (yTBP) over five oligomers having different TATA variants and lacking a UASGAL, showed that TATA-binding protein (TBP)-TATA complex gets stabilized in the presence of the acidic activator GAL4-VP16. Activator also greatly suppressed the non-specific TBP-DNA complex formation. The effects were more pronounced over weaker TATA boxes. Activator also reduced the TBP dimer levels both in vitro and in vivo, suggesting the dimer may be a direct target of transcriptional activators. The transcriptional activator facilitated the dimer to monomer transition and activated monomers further to help TBP bind even the weaker TATA boxes stably. The overall stimulatory effect of the GAL4-VP16 on the TBP-TATA complex formation resembles the known effects of removal of the N-terminus of TBP on its activity, suggesting that the activator directly targets the N-terminus of TBP and facilitates its binding to the TATA box.

    • Hypervariable spacer regions are good sites for developing specific PCR-RFLP markers and PCR primers for screening actinorhizal symbionts

      Rajani Varghese Vineeta S Chauhan Arvind K Misra

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      While the ribosomal RNA like highly conserved genes are good molecular chronometers for establishing phylogenetic relationships, they can also be useful in securing the amplification of adjoining hyper-variable regions. These regions can then be used for developing specific PCR primers or PCR-RFL profiles to be used as molecular markers. We report here the use of ITS region of rrn operon of Frankia for developing PCR-RFL profiles capable of discriminating between closely related frankiae. We have also made use of the ITS1 region of the nuclear rrn operon of Alnus nepalensis (D Don) for designing a PCR primer for specific amplification of nuclear DNA of this tree.

    • A comparative phylogenetic analysis of full-length mariner elements isolated from the Indian tasar silkmoth, Antheraea mylitta (Lepidoptera: saturniidae)

      M Dharma Prasad J Nagaraju

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      Mariner like elements (MLEs) are widely distributed type II transposons with an open reading frame (ORF) for transposase. We studied comparative phylogenetic evolution and inverted terminal repeat (ITR) conservation of MLEs from Indian saturniid silkmoth, Antheraea mylitta with other full length MLEs submitted in the database. Full length elements from A. mylitta were inactive with multiple mutations. Many conserved amino acid blocks were identified after aligning transposase sequences. Mariner signature sequence, DD(34)D was almost invariable although a few new class of elements had different signatures. A. mylitta MLEs (Anmmar) get phylogenetically classified under cecropia subfamily and cluster closely with the elements from other Bombycoidea superfamily members implying vertical transmission from a common ancestor. ITR analysis showed a conserved sequence of AGGT(2-8N)ATAAGT for forward repeat and AGGT(2-8N)ATGAAAT for reverse repeat. These results and additional work may help us to understand the dynamics of MLE distribution in A. mylitta and construction of appropriate vectors for mariner mediated transgenics.

    • Structural and histochemical studies on grain-filling in the caryopsis of rice (Oryza sativa L.)

      S Krishnan P Dayanandan

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      The endosperm and embryo that constitute the filial tissues of rice caryopsis are isolated from the maternal tissues by the absence of any symplastic continuity. Nutrients are transported to the endosperm through a single ovular vascular trace present on the ventral side of the ovary. Initially solute enters through the chalaza into the nucellar projection and then into the endosperm. At later stages transport occurs through the nucellar epidermis, centripetally towards the endosperm. The cell walls of the nucellar epidermis are provided with rib-like thickenings. A comparison of grain-filling in C3 and C4 cereals suggests that rice has structural features allied to C3 cereals, such as wheat, but with significant differences.

    • Subcellular localization of Cd in the root cells of Allium sativum by electron energy loss spectroscopy

      Donghua Liu Ingrid Kottke

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      The ultrastructural investigation of the root cells of Allium sativum L. exposed to three different concentrations of Cd (100 𝜇M, 1 mM and 10 mM) for 9 days was carried out. The results showed that Cd induced several significant ultrastructural changes – high vacuolization in cytoplasm, deposition of electron-dense material in vacuoles and nucleoli and increment of disintegrated organelles. Data from electron energy loss spectroscopy (EELS) revealed that Cd was localized in the electron-dense precipitates in the root cells treated with 10 mM Cd. High amounts of Cd were mainly accumulated in the vacuoles and nucleoli of cortical cells in differentiating and mature root tissues. The mechanisms of detoxification and tolerance of Cd are briefly explained.

    • Sucrose mobilization in relation to essential oil biogenesis during palmarosa (Cymbopogon martinii Roxb. Wats. var. motia) inflorescence development

      Vinod Shanker Dubey Ritu Bhalla Rajesh Luthra

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      Palmarosa inflorescence with partially opened spikelets is biogenetically active to incorporate [U-14C]sucrose into essential oil. The percent distribution of 14C-radioactivity incorporated into geranyl acetate was relatively higher as compared to that in geraniol, the major essential oil constituent of palmarosa. At the partially opened spikelet stage, more of the geraniol synthesized was acetylated to form geranyl acetate, suggesting that majority of the newly synthesized geraniol undergoes acetylation, thus producing more geranyl acetate. In vitro development of palmarosa inflorescence, fed with [U-14C]sucrose, resulted in a substantial reduction in percent label from geranyl acetate with a corresponding increase in free geraniol, thereby suggesting the role of an esterase in the production of geraniol from geranyl acetate. At time course measurement of 14CO2 incorporation into geraniol and geranyl acetate substantiated this observation. Soluble acid invertase was the major enzyme involved in the sucrose breakdown throughout the inflorescence development. The activities of cell wall bound acid invertase, alkaline invertase and sucrose synthase were relatively lower as compared to the soluble acid invertase. Sucrose to reducing sugars ratio decreased till fully opened spikelets stage, concomitant with increased acid invertase activity and higher metabolic activity. The phenomenon of essential oil biosynthesis has been discussed in relation to changes in these physiological parameters.

    • Density-dependent growth and metamorphosis in the larval bronze frog Rana temporalis is influenced by genetic relatedness of the cohort

      S Girish S K Saidapur

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      Effects of density and kinship on growth and metamorphosis in tadpoles of Rana temporalis were studied in a 2 × 4 factorial experiment. Fifteen egg masses were collected from streams in the Western Ghat region of south India. The tadpoles were raised as siblings or in groups of non-siblings at increasing density levels, viz. 15, 30, 60 and 120/5 l water. With an increase in density level from 15 to 120 tadpoles/5 l water, duration of the larval stage increased and fewer individuals metamorphosed irrespective of whether they belonged to sibling or non-sibling groups by day 100 when the experiments were terminated. The size of individuals at metamorphosis declined significantly with increase in the density of rearing. However, at higher densities (60 and 120 tadpoles/5 l water) sibling group tadpoles performed better compared to mixed groups and took significantly less time to metamorphose. Also, more individuals of sibling groups metamorphosed compared to non-sibling groups at a given density. Mixed rearing retarded growth rates, prolonged larval duration resulting in a wider spectrum of size classes, and lowered the number of individuals recruited to terrestrial life. The study shows that interference competition occurred more strongly in cohorts of mixed relatedness than in sibling groups.

    • A technique for estimating maximum harvesting effort in a stochastic fishery model

      Ram Rup Sarkar J Chattopadhayay

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      Exploitation of biological resources and the harvest of population species are commonly practiced in fisheries, forestry and wild life management. Estimation of maximum harvesting effort has a great impact on the economics of fisheries and other bio-resources. The present paper deals with the problem of a bioeconomic fishery model under environmental variability. A technique for finding the maximum harvesting effort in fluctuating environment has been developed in a two-species competitive system, which shows that under realistic environmental variability the maximum harvesting effort is less than what is estimated in the deterministic model. This method also enables us to find out the safe regions in the parametric space for which the chance of extinction of the species is minimized. A real life fishery problem has been considered to obtain the inaccessible parameters of the system in a systematic way. Such studies may help resource managers to get an idea for controlling the system.

    • Status of Austro-Asiatic groups in the peopling of India: An exploratory study based on the available prehistoric, linguistic and biological evidences

      Vikrant Kumar B Mohan Reddy

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      Among the most contentious currently debated issues is about the people who had settled first in the Indian subcontinent. It has been suggested that the communities affiliated to the Austro-Asiatic linguistic family are perhaps the first to settle in India and the palaeoanthropological evidences suggest the earliest settlement probably around 60,000 years BP. Recent speculations, based on both traditional genetic markers and DNA markers, seem to corroborate the aforesaid view. However, these studies are inadequate both in terms of the representation of the constituent groups within this broad linguistic category as well as the number of samples that represent each of them. We strongly feel that, before making any formidable conclusions on the peopling of India and/or the history of settlement, it is necessary to ascertain that the Austro-Asiatic speakers, represented by over 30 different tribal groups, either genetically constitute a homogenous single entity or are a heterogeneous conglomeration, derived from different sources. As a first step towards this we tried to collate and analyse the existing information – geographic, ethno-historic, cultural and biological.

      The results of the analyses of anthropometric and genetic marker data indicate that the Austro-Asiatic groups, particularly the Mundari speakers, with certain exceptions, show greater homogeneity among them when compared to the other linguistic groups, although certain groups show as outliers. However, traditional genetic markers show lower within population heterozygosity compared to Dravidian and other Indian populations. This is contrary to what has been claimed in case of certain DNA markers. Given that relatively greater heterozygosity among the Austro-Asiatic populations has been taken as one of the important evidences supporting greater antiquity of these populations one should await results of detailed DNA studies being currently undertaken by us, involving a number of Austro-Asiatic and other ethnic populations of India to resolve the issue unequivocally.

    • On the origin of differentiation

      J T Bonner

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      Following the origin of multicellularity in many groups of primitive organisms there evolved more than one cell type. It has been assumed that this early differentiation is related to size – the larger the organism the more cell types. Here two very different kinds of organisms are considered: the volvocine algae that become multicellular by growth, and the cellular slime moulds that become multicellular by aggregation. In both cases there are species that have only one cell type and others that have two. It has been possible to show that there is a perfect correlation with size: the forms with two cell types are significantly larger than those with one. Also in both groups there are forms of intermediate size that will vary from one to two cell types depending on the size of the individuals, suggesting a form of quorum sensing. These observations reinforce the view that size plays a critical role in influencing the degree of differentiation.

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