Autonomous and non-autonomous traits mediate social cooperation in Dictyostelium discoideum

In the trishanku (triA(-)) mutant of the social amoeba Dictyostelium discoideum, aggregates are smaller than usual and the spore mass is located mid-way up the stalk, not at the apex. We have monitored aggregate territory size, spore allocation and fruiting body morphology in chimaeric groups of (quasi-wild-type) Ax2 and triA(-) cells. Developmental canalisation breaks down in chimaeras and leads to an increase in phenotypic variation. A minority of triA(-) cells causes largely Ax2 aggregation streams to break up; the effect is not due to the counting factor. Most chimaeric fruiting bodies resemble those of Ax2 or triA(-). Others are double-deckers with a single stalk and two spore masses, one each at the terminus and midway along the stalk. The relative number of spores belonging to the two genotypes depends both on the mixing ratio and on the fruiting body morphology. In double-deckers formed from 1:1 chimaeras, the upper spore mass has more Ax2 spores, and the lower spore mass more triA(-) spores, than expected. Thus, the traits under study depend partly on the cells' own genotype and partly on the phenotypes, and so genotypes, of other cells: they are both autonomous and non-autonomous. These findings strengthen the parallels between multicellular development and behaviour in social groups. Besides that, they reinforce the point that a trait can be associated with a genotype only in a specified context.

Nature's Swiss Army Knives: Ovipositor Structure Mirrors Ecology in a Multitrophic Fig Wasp Community

Background: Resource partitioning is facilitated by adaptations along niche dimensions that range from morphology to behaviour. The exploitation of hidden resources may require specially adapted morphological or sensory tools for resource location and utilisation. Differences in tool diversity and complexity can determine not only how many species can utilize these hidden resources but also how they do so. Methodology and Principal Findings: The sclerotisation, gross morphology and ultrastructure of the ovipositors of a seven-member community of parasitic wasps comprising of gallers and parasitoids developing within the globular syconia (closed inflorescences) of Ficus racemosa (Moraceae) was investigated. These wasps also differ in their parasitism mode (external versus internal oviposition) and their timing of oviposition into the expanding syconium during its development. The number and diversity of sensilla, as well as ovipositor teeth, increased from internally ovipositing to externally ovipositing species and from gallers to parasitoids. The extent of sclerotisation of the ovipositor tip matched the force required to penetrate the syconium at the time of oviposition of each species. The internally ovipositing pollinator had only one type of sensillum and a single notch on the ovipositor tip. Externally ovipositing species had multiple sensilla types and teeth on their ovipositors. Chemosensilla were most concentrated at ovipositor tips while mechanoreceptors were more widely distributed, facilitating the precise location of hidden hosts in these wasps which lack larval host-seeking behaviour. Ovipositor traits of one parasitoid differed from those of its syntopic galler congeners and clustered with those of parasitoids within a different wasp subfamily. Thus ovipositor tools can show lability based on adaptive necessity, and are not constrained by phylogeny. Conclusions/Significance: Ovipositor structure mirrored the increasingly complex trophic ecology and requirements for host accessibility in this parasite community. Ovipositor structure could be a useful surrogate for predicting the biology of parasites in other communities.

Structural biology of Mycobacterium tuberculosis proteins: The Indian efforts

Among the many different objectives of large scale structural genomics projects are expanding the protein fold space, enhancing understanding of a model or disease-related organism, and providing foundations for structure-based drug discovery. Systematic analysis of protein structures of Mycobacterium tuberculosis has been ongoing towards meeting some of these objectives. Indian participation in these efforts has been enthusiastic and substantial. The proteins of M. tuberculosis chosen for structural analysis by the Indian groups span almost all the functional categories. The structures determined by the Indian groups have led to significant improvement in the biochemical knowledge on these proteins and consequently have started providing useful insights into the biology of M. tuberculosis. Moreover, these structures form starting points for inhibitor design studies, early results of which are encouraging. The progress made by Indian structural biologists in determining structures of M. tuberculosis proteins is highlighted in this review. (C) 2011 Elsevier Ltd. All rights reserved.

Systems biology of tuberculosis

Systems biology seeks to study biological systems as a whole, by adopting an integrated approach to study and understand the function of biological systems, particularly, the response of such systems to various perturbations. In this article, we focus on the Indian efforts towards systems-level studies of Mycobacterium tuberculosis and its interaction with the host. Availability of a variety of genome-scale experimental data, providing first level `omics' descriptions of the pathogen, render it feasible to study it at a systems level. Various aspects of the pathogen, from metabolic pathways to protein-protein interaction networks have been modelled and simulated, while host-pathogen interactions have been studied experimentally using siRNA-based techniques. These studies have been useful in obtaining a global perspective of the pathogen and its interactions with the host in many ways. For example, significant insights have been gained about different aspects such as proteins essential for bacterial survival, proteins that are highly influential in the network, pathways that are highly connected, host factors responsible for maintaining the TB infection and key factors involved in autophagy and pathogenesis. A rational pipeline developed for drug target identification incorporating analyses of the interactome, reactome, genome, pocketome and the transcriptome is discussed. Finally, exploring host factors as drug targets and insights about the emergence of drug resistance are also discussed. (C) 2011 Elsevier Ltd. All rights reserved.

A meta-analysis of the traits affecting dispersal ability in butterflies: can wingspan be used as a proxy?

1. Dispersal ability of a species is a key ecological characteristic, affecting a range of processes from adaptation, community dynamics and genetic structure, to distribution and range size. It is determined by both intrinsic species traits and extrinsic landscape-related properties. 2. Using butterflies as a model system, the following questions were addressed: (i) given similar extrinsic factors, which intrinsic species trait(s) explain dispersal ability? (ii) can one of these traits be used as a proxy for dispersal ability? (iii) the effect of interactions between the traits, and phylogenetic relatedness, on dispersal ability. 3. Four data sets, using different measures of dispersal, were compiled from published literature. The first data set uses mean dispersal distances from capture-mark-recapture studies, and the other three use mobility indices. Data for six traits that can potentially affect dispersal ability were collected: wingspan, larval host plant specificity, adult habitat specificity, mate location strategy, voltinism and flight period duration. Each data set was subjected to both unifactorial, and multifactorial, phylogenetically controlled analyses. 4. Among the factors considered, wingspan was the most important determinant of dispersal ability, although the predictive powers of regression models were low. Voltinism and flight period duration also affect dispersal ability, especially in case of temperate species. Interactions between the factors did not affect dispersal ability, and phylogenetic relatedness was significant in one data set. 5. While using wingspan as the only proxy for dispersal ability maybe problematic, it is usually the only easily accessible species-specific trait for a large number of species. It can thus be a satisfactory proxy when carefully interpreted, especially for analyses involving many species from all across the world.

Chemistry and biology of DNA-binding small molecules

Regulation of the transcription machinery is one of the many ways to achieve control of gene expression. This has been done either at the transcription initiation stage or at the elongation stage. Different methodologies are known to inhibit transcription initiation via targeting of double-stranded (ds) DNA by: (i) synthetic oligonucleotides, (ii) ds-DNA-specific, sequenceselective minor-groove binders (distamycin A), intercalators (daunomycin) combilexins and (iii) small molecule (peptide or intercalator)-oligonucleotide conjugates. In some cases, instead of ds-DNA, higher order G-quadruplex structures are formed at the start site of transcription. In this regard G-quadruplex DNA-specific small molecules play a significant role towards inhibition of the transcription machinery. Different types of designer DNA-binding agents act as powerful sequence-specific gene modulators, by exerting their effect from transcription regulation to gene modification. But most of these chemotherapeutic agents have serious side effects. Accordingly, there is always a challenge to design such DNA-binding molecules that should not only achieve maximum specific DNA-binding affinity, and cellular and nuclear transport activity, but also would not interfere with the functions of normal cells.

Application of vibrational microspectroscopy to biology and medicine

Vibrational microspectroscopic (Raman and infrared (IR)) techniques are rapidly emerging as effective tools to probe the basic processes of life. This review mainly focuses on the applications of Raman and IR microspectroscopy to biology and biomedicine, ranging from studies on cellular components in single cells to advancement in techniques for in vitro to in vivo applications. These techniques have proved to be instrumental in studying the biological specimen with minimum perturbation, i.e. without the use of dyes and contrast-inducing agents. These techniques probe the vibrational modes of the molecules and provide spectra that are specific to the molecular properties and chemical nature of the species.

Computational Biology and Language

Current scientific research is characterized by increasing specialization, accumulating knowledge at a high speed due to parallel advances in a multitude of sub-disciplines. Recent estimates suggest that human knowledge doubles every two to three years – and with the advances in information and communication technologies, this wide body of scientific knowledge is available to anyone, anywhere, anytime. This may also be referred to as ambient intelligence – an environment characterized by plentiful and available knowledge. The bottleneck in utilizing this knowledge for specific applications is not accessing but assimilating the information and transforming it to suit the needs for a specific application. The increasingly specialized areas of scientific research often have the common goal of converting data into insight allowing the identification of solutions to scientific problems. Due to this common goal, there are strong parallels between different areas of applications that can be exploited and used to cross-fertilize different disciplines. For example, the same fundamental statistical methods are used extensively in speech and language processing, in materials science applications, in visual processing and in biomedicine. Each sub-discipline has found its own specialized methodologies making these statistical methods successful to the given application. The unification of specialized areas is possible because many different problems can share strong analogies, making the theories developed for one problem applicable to other areas of research. It is the goal of this paper to demonstrate the utility of merging two disparate areas of applications to advance scientific research. The merging process requires cross-disciplinary collaboration to allow maximal exploitation of advances in one sub-discipline for that of another. We will demonstrate this general concept with the specific example of merging language technologies and computational biology.

Recent Developments in the Chemistry and Biology of G-Quadruplexes with Reference to the DNA Groove Binders

DNA is the chemotherapeutic target for treating diseases of genetic origin. Besides well-known double-helical structures (A, B, Z, parallel stranded-DNA etc.), DNA is capable of forming several multi-stranded structures (triplex, tetraplex, i-motif etc.) which have unique biological significance. The G-rich 3'-ends of chromosomes, called telomeres, are synthesized by telomerase, a ribonucleoprotein, and over-expression of telomerase is associated with cancer. The activity of telomerase is suppressed if the G-rich region is folded into the four stranded structures, called G-quadruplexes (G4-DNAs) using small synthetic ligands. Thus design and synthesis of new G4-DNA ligands is an attractive strategy to combat cancer. G4-DNA forming sequences are also prevalent in other genomic regions of biological significance including promoter regions of several oncogenes. Effective gene regulation may be achieved by inducing a G4-DNA structure within the G-rich promoter sequences. To date, several G4-DNA stabilizing ligands are known. DNA groove binders interact with the duplex B-DNA through the grooves (major and minor groove) in a sequence-specific manner. Some of the groove binders are known to stabilize the G4-DNA. However, this is a relatively under explored field of research. In this review, we focus on the recent advances in the understanding of the G4-DNA structures, particularly made from the human telomeric DNA stretches. We summarize the results of various investigations of the interaction of various organic ligands with the G4-DNA while highlighting the importance of groove binder-G4-DNA interactions.

Micro-shock wave assisted bacterial transformation

A gene is a unit of heredity in a living organism. It normally resides on a stretch of DNA that codes for a type of protein or for an RNA chain that has a function in the organism. All living things depend on genes, as they specify all proteins and functional RNA chains. Genes hold the information to build and maintain an organism’s cells and pass genetic traits to offspring. The gene has to be transferred to bacteria or eukaryotic cells for basic and applied molecular biology studies. Bacteria can uptake exogenous genetic material by three ways: conjugation, transduction and transformation. Genetic material is naturally transferred to bacteria in case of conjugation and transferred through bacteriophage in transduction. Transformation is the acquisition of exogenous genetic material through cell wall. The ability of bacteria of being transformed is called competency and those bacteria which have competency are competent cells. Divalent Calcium ions can make the bacteria competent and a heat shock can cause the bacteria to uptake DNA. But the heat shock method cannot be used for all the bacteria. In electroporation, a brief electric shock with an electric field of 10-20kV/cmmakes pores in the cell wall, facilitates the DNA to enter into the bacteria. Microprecipitates, microinjection, liposomes, and biological vectors are also used to transfer polar molecules like DNA into host cells.

Interspecies and intraspecies interactions in social amoebae

The stable co-existence of individuals of different genotypes and reproductive division of labour within heterogeneous groups are issues of fundamental interest from the viewpoint of evolution. Cellular slime moulds are convenient organisms in which to address both issues. Strains of a species co-occur, as do different species; social groups are often genetically heterogeneous. Intra- and interspecies 1:1 mixes of wild isolates of Dictyostelium giganteum and D.purpureum form chimaeric aggregates, following which they segregate to varying extents. Intraspecies aggregates develop in concert and give rise to chimaeric fruiting bodies that usually contain more spores (reproductives) of one component than the other. Reproductive skew and variance in the proportion of reproductives are positively correlated. Interspecies aggregates exhibit almost complete sorting; most spores in a fruiting body come from a single species. Between strains, somatic compatibility correlates weakly with sexual compatibility. It is highest within clones, lower between strains of a species and lowest between strains of different species. Trade-offs among fitness-related traits (between compatible strains), sorting out (between incompatible strains) and avoidance (between species) appear to lie behind coexistence.

THE LEGACY OF GN RAMACHANDRAN AND THE DEVELOPMENT OF STRUCTURAL BIOLOGY IN INDIA

G.N. Ramachandran is among the founding fathers of structural molecular biology. He made pioneering contributions in computational biology, modelling and what we now call bioinformatics. The triple helical coiled coil structure of collagen proposed by him forms the basis of much of collagen research at the molecular level. The Ramachandran map remains the simplest descriptor and tool for validation of protein structures. He has left his imprint on almost all aspects of biomolecular conformation. His contributions in the area of theoretical crystallography have been outstanding. His legacy has provided inspiration for the further development of structural biology in India. After a pause, computational biology and bioinformatics are in a resurgent phase. One of the two schools established by Ramachandran pioneered the development of macromolecular crystallography, which has now grown into an important component of modern biological research in India. Macromolecular NMR studies in the country are presently gathering momentum. Structural biology in India is now poised to again approach heights of the kind that Ramachandran conquered more than a generation ago.

Interplay of male traits, male mating strategies and female mate choice in the Asian elephant, Elephas maximus

Elaborate male traits with no apparent adaptive value may have evolved through female mate discrimination. Tusks are an elaborate male-only trait in the Asian elephant that could potentially influence female mate choice. We examined the effect of male body size, tusk possession and musth status on female mate choice in an Asian elephant population. Large/musth males received positive responses from oestrous females towards courtship significantly more often than did small/non-musth males. Young, tusked non-musth males attempted courtship significantly more often than their tuskless peers, and received more positive responses (though statistically insignificant) than did tuskless males. A positive response did not necessarily translate into mating because of mate-guarding by a dominant male. Female elephants appear to choose mates based primarily on traits such as musth that signal direct fertility benefits through increased sperm received than for traits such as tusks that may signal only indirect fitness benefits.