• Volume 31, Issue 1

March 2006,   pages  1-176e

• Clipboard: Ancient Indian roots?

• Commentary: Magic with moulds: Meiotic and mitotic crossing over in Neurospora inversions and duplications

• Erwin Bünning (1906–1990): A centennial homage

• Living in a physical world VI. Gravity and life in the air

• What history tells us IV. Ciliates as models... of what?

• Allele-specific suppression of the temperature sensitivity of fitA/fitB mutants of Escherichia coli by a new mutation (fitC4): isolation, characterization and its implications in transcription control

The temperature sensitive transcription defective mutant of Escherichia coli originally called fitA76 has been shown to harbour two missense mutations namely pheS5 and fit95. In order to obtain a suppressor of fitA76, possibly mapping in rpoD locus, a Ts+ derivative (JV4) was isolated from a fitA76 mutant. It was found that JV4 neither harbours the lesions present in the original fitA76 nor a suppressor that maps in or near rpoD. We show that JV4 harbours a modified form of fitA76 (designated fitA76*) together with its suppressor. The results presented here indicate that the fit95 lesion is intact in the fitA76* mutant and the modification should be at the position of pheS5. Based on the cotransduction of the suppressor mutation and/or its wild type allele with pps, aroD and zdj-3124::Tn10 kan we have mapped its location to 39⋅01 min on the E. coli chromosome. We tentatively designate the locus defined by this new extragenic suppressor as fitC and the suppressor allele as fitC4. While fitC4 could suppress the Ts phenotype of fitA76* present in JV4, it fails to suppress the Ts phenotype of the original fitA76 mutant (harbouring pheS5 and fit95). Also fitC4 could suppress the Ts phenotype of a strain harbouring only pheS5. Interestingly, the fitC4 Ts phenotype could also be suppressed by fit95. The pattern of decay of pulse labelled RNA in the strains harbouring fitC4 and the fitA76* resembles that of the original fitA76 mutant implying a transcription defect similar to that of fitA76 in both these mutants. The implications of these findings with special reference to transcription control by Fit factors in vivo are discussed.

• Coat protein sequence shows that Cucumber mosaic virus isolate from geraniums (Pelargonium spp.) belongs to subgroup II

A viral disease was identified on geraniums (Pelargonium spp.) grown in a greenhouse at the Institute of Himalayan Bioresource Technology (IHBT), Palampur, exhibiting mild mottling and stunting. The causal virus (Cucumber mosaic virus, CMV) was identified and characterized on the basis of host range, aphid transmission, enzyme linked immunosorbent assay (ELISA), DNA-RNA hybridization and reverse transcription polymerase chain reaction (RTPCR). A complete coat protein (CP) gene was amplified using degenerate primers and sequenced. The CP gene showed nucleotide and amino acid homology up to 97%–98% and 96%–99%, respectively with the sequences of CMV subgroup II. The CP gene also showed homologies of 75%–97% in nucleotide and 77%–96% in amino acid with the CMV Indian isolates infecting various crops. On the basis of sequence homology, it was concluded that CMV-infecting geraniums in India belong to subgroup II.

• Age-related changes of structures in cerebellar cortex of cat

We studied the structures of the cerebellar cortex of young adult and old cats for age-related changes, which were statistically analysed. Nissl staining was used to visualize the cortical neurons. The immunohistochemical method was used to display glial fibrillary acidic protein (GFAP)-immunoreactive (IR) astrocytes and neurofilament-immunoreactive (NF-IR) neurons. Under the microscope, the thickness of the cerebellar cortex was measured; and the density of neurons in all the layers as well as that of GFAP-IR cells in the granular layer was analysed. Compared with young adult cats, the thickness of the molecular layer and total cerebellar cortex was significantly decreased in old cats, and that of the granular layer increased. The density of neurons in each layer was significantly lower in old cats than in young adult ones. Astrocytes in old cats were significantly denser than in young adult ones, and accompanied by evident hypertrophy of the cell bodies and enhanced immunoreaction of GFAP substance. Purkinje cells (PCs) in old cats showed much fewer NF-IR dendrites than those in young adults. The above findings indicate a loss of neurons and decrease in the number of dendrites of the PCs in the aged cerebellar cortex, which might underlie the functional decline of afferent efficacy and information integration in the senescent cerebellum. An age-dependent enhancement of activity of the astrocytes may exert a protective effect on neurons in the aged cerebellum.

• Ni2+ -uptake in Pseudomonas putida strain S4: a possible role of Mg2+ -uptake pump

Essential metal ion homeostasis is based on regulated uptake of metal ions, both during its scarcity and abundance. Pseudomonas putida strain S4, a multimetal resistant bacterium, was employed to investigate Ni2+ entry into cells. It was observed that Mg2+ regulates the entry of Ni2+ and by this plays a protective role to minimize Ni2+ toxicity in this strain. This protection was evident in both growth as well as viability. Intracellular accumulation of Ni2+ varied in accordance with Mg2+ concentrations in the medium. It was hypothesized that Ni2+ enters the cell using a broad Mg2+ pump, i.e. the CorA system, as the CorA inhibitor, i.e. Co(III) Hex, also inhibits Ni2+ uptake. This led to the inference that Mg2+-based protection was basically due to competitive inhibition of Ni2+ uptake. We also show that Zn2+ can further regulate the entry of Ni2+.

• Candidate genes for drought tolerance and improved productivity in rice (Oryza sativa L.)

Candidate genes are sequenced genes of known biological action involved in the development or physiology of a trait. Twenty-one putative candidate genes were designed after an exhaustive search in the public databases along with an elaborate literature survey for candidate gene products and/or regulatory sequences associated with enhanced drought resistance. The downloaded sequences were then used to design primers considering the flanking sequences as well. Polymerase chain reaction (PCR) performed on 10 diverse cultivars that involved Japonica, Indica and local accessions, revealed 12 polymorphic candidate genes. Seven polymorphic candidate genes were then utilized to genotype 148 individuals of CT9993 × IR62266 doubled haploid (DH) mapping population. The segregation data were tested for deviation from the expected Mendelian ratio (1:1) using a Chi-square test (<1%). Based on this, four candidate genes were assessed to be significant and the remaining three, as non-significant. All the significant candidate genes were biased towards CT9993, the female parent in the DH mapping population. Single-marker analysis strongly associated ( < 1%) them to different traits under both well-watered and low-moisture stress conditions. Two candidate genes, EXP15 and EXP13, were found to be associated with root number and silicon content in the stem respectively, under both well-watered and low-moisture stress conditions.

• Lyriform slit sense organs on the pedipalps and spinnerets of spiders

Lyriform slits sense organs (LSSO) are a precise assembly of stress detecting cuticular slit sensilla found on the appendages of arachnids. While these structures on the legs of the wandering spider Cupennius salei are well studied in terms of morphology, function and contribution to behaviour, their distribution on pedipalps and spinnerets of spiders is not well explored. A study was therefore carried out to observe the distribution of LSSO on pedipalps and spinnerets of some spider species. Haplogyne spiders belonging to family Pholcidae have a simple complement of LSSOs represented by one or two LSSOs on their femur. The entelegyne spiders possess a complex assembly of LSSOs on the distal segments of their pedipalps. Various types of LSSOs are found on the pedipalps indicating a capacity for analysis of complex cuticular stress. It is suggested that the complexity of LSSOs on pedipalps of entelegyne spiders relates to courtship and spermatophore transfer and may help in reproductive isolation. Lack of LSSOs on the distal segments of pedipalps leads us to infer that unlike legs, pedipalps are less likely to receive vibratory input through their distal segments.

Spinnerets have a relatively simple complement of LSSOs. One LSSO is found only on anterior spinnerets and it is a common feature observed among spiders, irrespective of the variations in web building behaviour. The orb-weaving araneid Argiope pulchella, however, has two LSSOs on the anterior spinneret. As non-web builders and orb weavers do not differ markedly in terms of LSSOs on the spinnerets and LSSOs are simple in nature (type A), it is likely that spinning and weaving are not largely regulated by sensory input from LSSOs on the spinnerets.

• Natural recovery of steppe vegetation on vehicle tracks in central Mongolia

Steppe desertification due to vehicle travel is a severe environmental issue in Mongolia. We studied natural vegetation recovery on abandoned vehicle tracks in the central Mongolia steppe through vegetation surveys and stable isotopic techniques. The following issues were addressed:

1. invasion of pioneering plant species,
2. alteration of soil surface features, and
3. contribution of revegetated plants to soil organic matter (SOM).

The pioneering plant species that firstly invaded the abandoned tracks are those that could germinate, root and survive in the compacted track surface. Salsola collina is one of these candidate plants. Due to revegetation, soil surface hardness was reduced. With the improvement of surface microenvironmental conditions, other plants began to colonize and establish; concomitantly species richness and species diversity increased. Carbon isotope ratios of SOM at the top surface layer indicated that C4-derived carbon contributed more to SOM in the early phase of recovery and decreased with further recovery.

• Phylogenetic tests of distribution patterns in South Asia: towards an integrative approach

The last four decades have seen an increasing integration of phylogenetics and biogeography. However, a dearth of phylogenetic studies has precluded such biogeographic analyses in South Asia until recently. Noting the increase in phylogenetic research and interest in phylogenetic biogeography in the region, we outline an integrative framework for studying taxon distribution patterns. While doing so, we pay particular attention to challenges posed by the complex geological and ecological history of the region, and the differences in distribution across taxonomic groups. We outline and compare three widely used phylogenetic biogeographic approaches: topology-based methods (TBMs), pattern-based methods (PBMs) and event-based methods (EBMs). TBMs lack a quantitative framework and utilize only part of the available phylogenetic information. Hence, they are mainly suited for preliminary enquiries. Both PBMs and EBMs have a quantitative framework, but we consider the latter to be particularly suited to the South Asian context since they consider multiple biogeographic processes explicitly, and can accommodate a reticulated history of areas. As an illustration, we present a biogeographic analysis of endemic Sri Lankan agamid lizards. The results provide insights into the relative importance of multiple processes and specific zones in the radiation of two speciose lizard clades.

• Record of Lower Gondwana megafloral assemblage from Lower Kamthi Formation of Ib River Coalfield, Orissa, India

Recent investigations carried out in the Ib River Coalfield, Mahanadi Master Basin, Orissa, identified some fossiliferous beds in the Lower Gondwana deposits. Two exposures of the Lower Kamthi Formation yielded diverse and abundant plant remains, which include Neomariopteris, Vertebraria, and a scale leaf along with 14 Glossopteris species otherwise mapped as Barren Measures and Upper Kamthi formations. Glossopteris indica dominates the flora (22.78%) followed by G. communis (17.72%) and G. browniana (13.92%). Based on megafloral assemblages, different beds exposed at Gopalpur and Laxamanpur Pahar are assigned here to the Lower Kamthi Formation (Late Permian). The floristic composition suggests that a warm and humid climate prevailed during the Late Permian. The status of the Kamthi Formation in the Ib River Coalfield has been redefined in the present study.

• A model for the dynamics of human weight cycling

The resolution to lose weight by cognitive restraint of nutritional intake often leads to repeated bouts of weight loss and regain, a phenomenon known as weight cycling or yo-yo dieting”. A simple mathematical model for weight cycling is presented. The model is based on a feedback of psychological nature by which a subject decides to reduce dietary intake once a threshold weight is exceeded. The analysis of the model indicates that sustained oscillations in body weight occur in a parameter range bounded by critical values. Only outside this range can body weight reach a stable steady state. The model provides a theoretical framework that captures key facets of weight cycling and suggests ways to control the phenomenon. The view that weight cycling represents self-sustained oscillations has indeed specific implications. In dynamical terms, to bring weight cycling to an end, parameter values should change in such a way as to induce the transition of body weight from sustained oscillations around an unstable steady state to a stable steady state. Maintaining weight under a critical value should prevent weight cycling and allow body weight to stabilize below the oscillatory range.

• The ubiquitin-proteasome system

The 2004 Nobel Prize in chemistry for the discovery of protein ubiquitination has led to the recognition of cellular proteolysis as a central area of research in biology. Eukaryotic proteins targeted for degradation by this pathway are first ‘tagged’ by multimers of a protein known as ubiquitin and are later proteolyzed by a giant enzyme known as the proteasome. This article recounts the key observations that led to the discovery of ubiquitin-proteasome system (UPS). In addition, different aspects of proteasome biology are highlighted. Finally, some key roles of the UPS in different areas of biology and the use of inhibitors of this pathway as possible drug targets are discussed.

• Mechanism of bacterial adaptation to low temperature

Survival of bacteria at low temperatures provokes scientific interest because of several reasons. Investigations in this area promise insight into one of the mysteries of life science – namely, how the machinery of life operates at extreme environments. Knowledge obtained from these studies is likely to be useful in controlling pathogenic bacteria, which survive and thrive in cold-stored food materials. The outcome of these studies may also help us to explore the possibilities of existence of life in distant frozen planets and their satellites.

• Looking back, looking beyond: revisiting the ethics of genome generation

This paper will explore some of the ethical imperatives that have shaped strategic and policy frameworks for the use of new genetic technologies and how these play a role in shaping the nature of research and changing attitudes; with an attempt to conceptualize some theories of genetic determinism. I analyse why there is a need to put bioethical principles within a theoretical framework in the context of new technologies, and how, by doing so, their practical applications for agriculture, environment medicine and health care can be legitimized.

There are several theories in favour of and against the use of genetic technologies that focus on genes and their role in our existence. In particular the theory of geneticisation is commonly debated. It highlights the conflicting interests of science, society and industry in harnessing genetic knowledge when the use of such knowledge could challenge ethical principles. Critics call it a reductionist’ approach, based on arguments that are narrowed down to genes, often ignoring other factors including biological, social and moral ones. A parallel theory is that there is something special about genes, and it is this `genetic exceptionalism” that creates hopes and myths. Either way, the challenging task is to develop a common ground for understanding the importance of ethical sensitivities.

As research agendas become more complex, ethical paradigms will need to be more influential. New principles are needed to answer the complexities of ethical issues as complex technologies develop. This paper reflects on global ethical principles and the tensions between ethical principles in legitimizing genetic technologies at the social and governance level.

• Journal of Biosciences Editorial Board

• Erwin Bünning (1906–1990): A centennial homage