Quorum Sensing and Biofilm Formation in Mycobacteria: Role of c-di-GMP and Methods to Study This Second Messenger

Bacteria have evolved to survive the ever-changing environment using intriguing mechanisms of quorum sensing (QS). Very often, QS facilitates formation of biofilm to help bacteria to persist longer and the formation of such biofilms is regulated by c-di-GMP. It is a well-known second messenger also found in mycobacteria. Several methods have been developed to study c-di-GMP signaling pathways in a variety of bacteria. In this review, we have attempted to highlight a connection between c-di-GMP and biofilm formation and QS in mycobacteria and several methods that have helped in better understanding of c-di-GMP signaling. (c) 2014 IUBMB Life, 66(12):823-834, 2014

Wave propagation of phonon and phason displacement modes in quasicrystals: Determination of wave parameters

The paper presents the study of wave propagation in quasicrystals. Our interest is in the computation of the wavenumber (k(n)) and group speed (c(g)) of the phonon and phason displacement modes of one, two, and three dimensional quasicrystals. These wave parameter expressions are derived and computed using the elasto-hydrodynamic equations for quasicrystals. For the computation of the wavenumber and group speeds, we use Fourier transform approximation of the phonon and the phason displacement modes. The characteristic equations obtained are a polynomial equation of the wavenumber (k(n)), with frequency as a parameter. The corresponding group speeds (c(g)) for different frequencies are then computed from the wavenumber k(n). The variation of wavenumber and group speeds with frequency is plotted for the 1-D quasicrystal, 2-D decagonal Al-Ni-Co quasicrystals, and 3-D icosahedral Al-Pd-Mn and Zn-Mg-Sc quasicrystals. From the wavenumber and group speeds plots, we obtain the cut-off frequencies for different spatial wavenumber eta(m). The results show that for 1-D, 2-D, and 3-D quasicrystals, the phonon displacement modes are non-dispersive for low values of eta(m) and becomes dispersive for increasing values of eta(m). The cut-off frequencies are not observed for very low values of eta(m), whereas the cut-off frequency starts to appear with increasing eta(m). The group speeds of the phason displacement modes are orders of magnitude lower than that of the phonon displacement modes, showing that the phason modes do not propagate, and they are essentially the diffusive modes. The group speeds of the phason modes are also not influenced by eta(m). The group speeds for the 2-D quasicrystal at 35 kHz is also simulated numerically using Galerkin spectral finite element methods in frequency domain and is compared with the results obtained using wave propagation analysis. The effect of the phonon and phason elastic constants on the group speeds is studied using 3-D icosahedral Al-Pd-Mn and Zn-Mg-Sc quasicrystals. It is also shown that the phason elastic constants and the coupling coefficient do not affect the group speeds of the phonon displacement modes. (C) 2015 AIP Publishing LLC.

Characterization of rice small heat shock proteins targeted to different cellular organelles

Small heat shock proteins (sHSPs) are a family of ATP-independent molecular chaperones which prevent cellular protein aggregation by binding to misfolded proteins. sHSPs form large oligomers that undergo drastic rearrangement/dissociation in order to execute their chaperone activity in protecting substrates from stress. Substrate-binding sites on sHSPs have been predominantly mapped on their intrinsically disordered N-terminal arms. This region is highly variable in sequence and length across species, and has been implicated in both oligomer formation and in mediating chaperone activity. Here, we present our results on the functional and structural characterization of five sHSPs in rice, each differing in their subcellular localisation, viz., cytoplasm, nucleus, chloroplast, mitochondria and peroxisome. We performed activity assays and dynamic light scattering studies to highlight differences in the chaperone activity and quaternary assembly of sHSPs targeted to various organelles. By cloning constructs that differ in the length and sequence of the tag in the N-terminal region, we have probed the sensitivity of sHSP oligomer assembly and chaperone activity to the length and amino acid composition of the N-terminus. In particular, we have shown that the incorporation of an N-terminal tag has significant consequences on sHSP quaternary structure.

Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond

In this discussion, we show that a static definition of a `bond' is not viable by looking at a few examples for both inter-and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan, Phys. Chem. Chem. Phys. 2009, 11, 8974) which showed a practical way to differentiate `hydrogen bonding' from `van der Waals interaction'. We report results from ab initio and atoms in molecules theoretical calculations for a series of Rg center dot center dot center dot HX complexes (Rg = He/Ne/Ar and X = F/Cl/Br) and ethane-1,2-diol. Results for the Rg center dot center dot center dot HX/DX complexes show that Rg center dot center dot center dot DX could have a `deuterium bond' even when Rg center dot center dot center dot HX is not `hydrogen bonded', according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an `intra-molecular hydrogen bond' can appear during a normal mode vibration which is dominated by the O center dot center dot center dot O stretching, though a `bond' is not found in the equilibrium structure. This dynamical `bond' formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration `breaks' an existing bond and in the later case, a vibration leads to `bond' formation. In both cases, the molecule/complex stays bound irrespective of what happens to this `hydrogen bond'. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunan et al. Pure. Appl. Chem. 2011, 83 1637) and justify the inclusive nature of the definition.

Do we see what we should see? Describing non-covalent interactions in protein structures including precision

The power of X-ray crystal structure analysis as a technique is to `see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this `seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and alpha-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.

Asymmetric cell division of granule neuron progenitors in the external granule layer of the mouse cerebellum

The plane of division of granule neuron progenitors (GNPs) was analysed with respect to the pial surface in P0 to P14 cerebellum and the results showed that there was a significant bias towards the plane of cell division being parallel to pial surface across this developmental window. In addition, the distribution of beta-Catenin in anaphase cells was analysed, which showed that there was a significant asymmetry in the distribution of beta-Catenin in dividing GNPs. Further, inhibition of Sonic Hedgehog (Shh) signalling had an effect on plane of cell division. Asymmetric distribution of beta-Catenin was shown to occur towards the source of a localized extracellular cue.

The X-C---Y (X = O/F, Y = O, S, F, Cl, Br, N, P,) Carbon bond and hydrophobic interactions

While the tetrahedral face of methane has an electron rich centre and can act as a hydrogen bond acceptor, substitution of one of its hydrogens with some electron withdrawing group (such as -F/OH) can make the opposite face electron deficient. Electrostatic potential calculations confirm this and high level quantum calculations show interactions between the positive face of methanol/methyl fluoride and electron rich centers of other molecules such as H2O. Analysis of the wave functions of atoms in molecules shows the presence of an unusual C···Y interaction, which could be called 'carbon bonding'. NBO analysis and vibrational frequency shifts confirm the presence of this interaction. Given the properties of alkyl groups bonded to electronegative elements in biological molecules, such interactions could play a significant role, which is yet to be recognized. This and similar interactions could give an enthalpic contribution to what is called the 'hydrophobic interactions'.

Exploring isospectral cantilever beams using electromagnetism inspired optimization technique

Isospectral beams have identical free vibration frequency spectrum for a specific boundary condition. The problem of finding non-uniform beams which are isospectral to a given uniform beam, with fixed-free boundary condition, leads to a multimodal optimization problem. The first Q natural frequencies of the given uniform Euler-Bernoulli beam are determined using analytical solution. The first Q natural frequencies of a non-uniform beam are obtained with the help of finite element modeling. In order to obtain the non-uniform beams isospectral to a given uniform beam, an error function is designed, which calculates the difference between the spectra of the given uniform beam and the non-uniform beam. In our study, this error function is minimized using electromagnetism inspired optimization technique, a population based iterative algorithm inspired by the attraction-repulsion physics of electromagnetism. Numerical results show the existence of the isospectral non-uniform beams for a given uniform beam, which occur as local minima. Non-uniform beams isospectral to a damaged beam, are also explored using the proposed methodology to illustrate the fact that accurate structural damage identification is difficult by just frequency measurements. (C) 2012 Elsevier B.V. All rights reserved.

Novel Alternative Splice Variants of Mouse Cdk5rap2

Autosomal recessive primary microcephaly (MCPH) is a rare neurodevelopmental disorder characterized by a pronounced reduction of brain volume and intellectual disability. A current model for the microcephaly phenotype invokes a stem cell proliferation and differentiation defect, which has moved the disease into the spotlight of stem cell biology and neurodevelopmental science. Homozygous mutations of the Cyclin-dependent kinase-5 regulatory subunit-associated protein 2 gene CDK5RAP2 are one genetic cause of MCPH. To further characterize the pathomechanism underlying MCPH, we generated a conditional Cdk5rap2 LoxP/hCMV Cre mutant mouse. Further analysis, initiated on account of a lack of a microcephaly phenotype in these mutant mice, revealed the presence of previously unknown splice variants of the Cdk5rap2 gene that are at least in part accountable for the lack of microcephaly in the mice.

Capability approach-based evaluation of a biomass cook-stove design

What is the scope and responsibilities of design? This work partially answers this by employing a normative approach to design of a biomass cook stove. This study debates on the sufficiency of existing design methodologies in the light of a capability approach. A case study of a biomass cook stove Astra Ole has elaborated the theoretical constructs of capability approach, which, in turn, has structured insights from field to evaluate the product. Capability approach based methodology is also prescriptively used to design the mould for rapid dissemination of the Astra Ole.

Understanding transitions in a rural Indian building typology in the context of well-being

Rural settlements in Karnataka in India predominantly use locally available resources to build their dwelling units. The houses are constructed either by the villagers themselves or by local masons skilled in traditional architecture. However, traditional houses and lifestyle are slowly giving way to modern concrete dwellings and a new lifestyle. To analyse this trend of transition to modern dwellings in rural settlements, a case study was conducted in three villages near the city of Bengaluru in Karnataka. The present article discusses this transition in the context of sustainable well-being of rural settlements.

Spectral solutions to the Korteweg-de-Vries and nonlinear Schrodinger equations

In this paper, we present the solutions of 1-D and 2-D non-linear partial differential equations with initial conditions. We approach the solutions in time domain using two methods. We first solve the equations using Fourier spectral approximation in the spatial domain and secondly we compare the results with the approximation in the spatial domain using orthogonal functions such as Legendre or Chebyshev polynomials as their basis functions. The advantages and the applicability of the two different methods for different types of problems are brought out by considering 1-D and 2-D nonlinear partial differential equations namely the Korteweg-de-Vries and nonlinear Schrodinger equation with different potential function. (C) 2015 Elsevier Ltd. All rights reserved.

A CAPABILITY APPROACH BASED STAKEHOLDER ANALYSIS FOR THE BASE OF THE PYRAMID: A CASE STUDY OF THE FIREWOOD BASED COOK-STOVES

People living under $2 income per day, referred as Base of the Pyramid (BoP), face undesired situations like lack of nutrition, health, education etc. Design as a process of changing current undesired situation to a desired situation has failed. A crucial reason behind these failures is lack of normative basis to identify and understand the absent or unsatisfied stakeholder. Currently stakeholder analysis in the design is heuristic. This paper uses a normative framework of Capability Approach (CA) for the stakeholder analysis. A brief discussion on stakeholder theory and analysis is used to identify gaps in the literature. The constructs of the CA are discussed for its suitability to the purpose. Along with methodological details, data generated from the stakeholder interviews, focus groups in a case study of dissemination of improved cook-stoves is used to interlink the theory with the practice. The scope of this work is in identifying and investigating the motives of the stakeholders in the involvement in the product. Though a lot of insights to discern and manage crucial stakeholders is inbuilt in the methodology, this work does not claim explicit coverage of these aspects.

Embodied and operational energy of urban residential buildings in India

Globally, buildings consume nearly half of the total energy produced, and consequently responsible for a large share of CO2 emissions. A building's life cycle energy (LCE) comprises its embodied energy (EE) and operational energy (OE). The building design, prevalent climatic conditions and occupant behaviour primarily determines its LCE. Thus, for the identification of appropriate emission-reduction strategies, studies into building LCE are crucial. While OE reflects the energy utilized in operating a, EE comprises the initial capital energy involved in its construction (material and burden associated with material consumption in buildings. Assessment of EE and OE in buildings is crucial towards identifying appropriate design and operational strategies for reduction of the building's life cycle energy. This paper discusses EE and OE assessment of a few residential buildings in different climatic locations in India. The study shows that share of OE and EE in LCE greatly depends upon the types of materials used in construction and extent of space conditioning adopted. In some cases EE can exceed life cycle OE. Buildings with reinforced concrete frame and monolithic reinforced concrete walls have very high EE. (C) 2015 Elsevier B.V. All rights reserved.

Multiple oligomeric structures of a bacterial small heat shock protein

Small heat shock proteins are ubiquitous molecular chaperones that form the first line of defence against the detrimental effects of cellular stress. Under conditions of stress they undergo drastic conformational rearrangements in order to bind to misfolded substrate proteins and prevent cellular protein aggregation. Owing to the dynamic nature of small heat shock protein oligomers, elucidating the structural basis of chaperone action and oligomerization still remains a challenge. In order to understand the organization of sHSP oligomers, we have determined crystal structures of a small heat shock protein from Salmonella typhimurium in a dimeric form and two higher oligomeric forms: an 18-mer and a 24-mer. Though the core dimer structure is conserved in all the forms, structural heterogeneity arises due to variation in the terminal regions.