How Many Initiator tRNA Genes Does Escherichia coli Need?

Multiple copies of a gene require enhanced investment on the part of the cell and, as such, call for an explanation. The observation that Escherichia coli has four copies of initiator tRNA (tRNA(i)) genes, encoding a special tRNA (tRNA(fMet)) required to start protein synthesis, is puzzling particularly because the cell appears to be unaffected by the removal of one copy. However, the fitness of an organism has both absolute and relative connotations. Thus, we carried out growth competition experiments between E. coli strains that differ in the number of tRNA(i) genes they contain. This has enabled us to uncover an unexpected link between the number of tRNA(i) genes and protein synthesis, nutritional status, and fitness. Wild-type strains with the canonical four tRNA(i) genes are favored in nutrient-rich environments, and those carrying fewer are favored in nutrient-poor environments. Auxotrophs behave as if they have a nutritionally poor internal environment. A heuristic model that links tRNA(i) gene copy number, genetic stress, and growth rate accounts for the findings. Our observations provide strong evidence that natural selection can work through seemingly minor quantitative variations in gene copy number and thereby impact organismal fitness.

Optimal maintenance policy for equipment subject to random deterioration and random failure A modern control theory approach.

The stochastic version of Pontryagin's maximum principle is applied to determine an optimal maintenance policy of equipment subject to random deterioration. The deterioration of the equipment with age is modelled as a random process. Next the model is generalized to include random catastrophic failure of the equipment. The optimal maintenance policy is derived for two special probability distributions of time to failure of the equipment, namely, exponential and Weibull distributions Both the salvage value and deterioration rate of the equipment are treated as state variables and the maintenance as a control variable. The result is illustrated by an example

Natural history and behaviour of the primitively eusocial wasp Ropalidia marginata (Hymenoptera: Vespidae): a comparison of the two sexes

We report the natural history and behaviour of the primitively eusocial wasp Ropalidia marginata with a special reference to the males. We found that just as nests of this species are found throughout the year, so are the males. Females spend all their life in their nests but males stay in their natal nests only for 1-12 days and leave to lead a nomadic life. Males maintained in the laboratory can live for up to 140 days. Like all eusocial hymenopteran males, R. marginata males also do not perform any colony maintenance activities. We found that males did not forage or feed larvae. Compared with females, males showed fewer dominance and subordinate behaviours and being solicited behaviour and more feeding self and soliciting behaviours. By comparing males with young females, we found similar differences, except that the males showed similar rates of feeding self and higher rates of subordinate behaviour.

A rain forest dusk chorus: cacophony or sounds of silence?

A rain forest dusk chorus consists of a large number of individuals of acoustically communicating species signaling at the same time. How different species achieve effective intra-specific communication in this complex and noisy acoustic environment is not well understood. In this study we examined acoustic masking interference in an assemblage of rain forest crickets and katydids. We used signal structures and spacing of signalers to estimate temporal, spectral and active space overlap between species. We then examined these overlaps for evidence of strategies of masking avoidance in the assemblage: we asked whether species whose signals have high temporal or spectral overlap avoid calling together. Whereas we found evidence that species with high temporal overlap may avoid calling together, there was no relation between spectral overlap and calling activity. There was also no correlation between the spectral and temporal overlaps of the signals of different species. In addition, we found little evidence that species calling in the understorey actively use spacing to minimize acoustic overlap. Increasing call intensity and tuning receivers however emerged as powerful strategies to minimize acoustic overlap. Effective acoustic overlaps were on average close to zero for most individuals in natural, multispecies choruses, even in the absence of behavioral avoidance mechanisms such as inhibition of calling or active spacing. Thus, call temporal structure, intensity and frequency together provide sufficient parameter space for several species to call together yet communicate effectively with little interference in the apparent cacophony of a rain forest dusk chorus.

How to be a fig wasp parasite on the fig-fig wasp mutualism

The nursery pollination mutualism between figs and pollinating fig wasps is based on adaptations that allow wasps to enter the enclosed inflorescences of figs, to facilitate seed set, and to have offspring that develop within the nursery and that leave to enter other inflorescences for pollination. This closed mutualistic system is not immune to parasitic fig wasps. Although the life histories and basic biology of the mutualists have been investigated, the biology of the fig wasp parasites has been severely neglected. This review brings together current knowledge of the many different ways in which parasites can enter the system, and also points to the serious lacunae in our understanding of the intricate interactions between gallers, kleptoparasites, seed eaters and parasitoids within this mutualism.

Microstructure related influence on the electrical properties of pulsed laser ablated (Ba, Sr)TiO3 thin films

The microstructural dependence of electrical properties of (Ba, Sr)TiO3(BST) thin films were studied from the viewpoint of dc and ac electrical properties. The films were grown using a pulsed laser deposition technique in a temperature range of 300 to 600 degrees C, inducing changes in grain size, structure, and morphology. Consequently, two different types of films were realized, of which type I, was polycrystalline, multigrained, while type II was [100] oriented possessing a densely packed fibrous microstructure. Leakage current measurements were done at elevated temperatures to provide evidence of the conduction mechanism present in these films. The results revealed a contribution from both electronic and ionic conduction. In the case of type I films, two trapping levels were identified with energies around 0.5 and 2.73 eV, which possibly originate from oxygen vacancies V-O and Ti3+ centers, respectively. These levels act as shallow and deep traps and are reflected in the current-voltage characteristics of the BST thin films. The activation energy associated with oxygen vacancy motion in this case was obtained as 1.28 eV. On the contrary, type II films showed no evidence of deep trap energy levels, while the identified activation energy associated with shallow traps was obtained as 0.38 eV. The activation energy obtained for oxygen vacancy motion in type II films was around 1.02 eV. The dc measurement results were further elucidated through ac impedance analysis, which revealed a grain boundary dominated response in type I in comparison to type II films where grain response is highlighted. A comparison of the mean relaxation time of the two films revealed three orders of magnitude higher relaxation time in the case of type I films. Due to smaller grain size in type I films the grains were considered to be completely depleted giving rise to only grain boundary response for the bulk of the film. The activation energy obtained from conductivity plots agree very well with that of dc measurements giving values 1.3 and 1.07 eV for type I and type II films, respectively. Since oxygen vacancy transport have been identified as the origin of resistance degradation in BST thin films, type I films with their higher value of activation energy for oxygen ion mobility explains the improvement in breakdown characteristics under constant high dc field stress. The role of microstructure in controlling the rate of degradation is found useful in this instance to enhance the film properties under high electric field stresses. (C) 2000 American Institute of Physics. [S0021-8979(00)00418-7].

Studies on follicular growth in the immature rat and hamster: Effect of a single injection of gonadotropin or estrogen on the rate of3H-thymidine incorporation into ovarian DNAin vitro

Initiation of follicular growth by specific hormonal stimuli in ovaries of immature rats and hamsters was studied by determining the rate of incorporation of3H-thymidine into ovarian DNAin vitro. Incorporation was considered as an index of DNA synthesis and cell multiplication. A single injection of pregnant mare serum gonadotropin could thus maximally stimulate by 18 hr3H-thymidine incorporation into DNA of the ovary of immature hamsters. Neutralization of pregnant mare serum gonadotropin by an antiserum to ovine follicle stimulating hormone only during the initial 8–10 hr and not later could inhibit the increase in3H-thymidine incorporationin vitro observed at 18 hr, suggesting that the continued presence of gonadotropin stimulus was not necessary for this response. The other indices of follicular growth monitored such as ovarian weight, serum estradiol and uterine weight showed discernible increase at periods only after the above initial event. A single injection of estrogen (diethyl stilbesterol or estradiol-l7β) could similarly cause 18 hr later, a stimulation in the rate of incorporation of3H-thymidine into DNAin vitro in ovaries of immature rats. The presence of endogenous gonadotropins, however, was obligatory for observing this response to estrogen. Evidence in support of the above was two-fold: (i) administration of antiserum to follicle stimulating hormone or luteinizing hormone along with estrogen completely inhibited the increase in3H-thymidine incorporation into ovarian DNAin vitro; (ii) a radioimmunological measurement revealed following estrogen treatment, the presence of a higher concentration of endogenous follicle stimulating hormone in the ovary. Finally, administration of varying doses of ovine follicle stimulating hormone along with a constant dose of estrogen to immature rats produced a dose-dependent increment in the incorporation of3H-thymidine into ovarian DNAin vitro. These observations suggested the potentiality of this system for developing a sensitive bioassay for follicle stimulating hormone.

A structural study of Li2S---B2S3 glasses by neutron diffraction

The radial distribution functions (RDFs) of five xLi2S.(1 - x)B2S3 glasses (x = 0.55, 0.60, 0.67, 0.71 and 0.75) have been determined from neutron diffraction experiments performed at the Institut Laue-Langevin, Grenoble. These glasses are prepared by casting a molten mixture of boron, sulphur and Li2S inside a controlled atmosphere glovebox. Addition of the Li2S Modifier is found gradually to suppress all peaks corresponding to interatomic distances > 3.5 angstrom, which implies that the structural entities present in these glasses become segmented, and therefore more ionic, as x increases. The assumption of the existence of four main structural entities based on four- and three-coordinated borons (the latter carrying bridging and/or non-bridging sulphurs) accounts for all the peaks present in the RDFs as a function of composition. Furthermore, in the most modified glass (x = 0.75), that which contains only 'isolated' BS33- triangles, there seems to be evidence for either octahedral or tetrahedral coordination of Li+ by S- ions

Crucible Steel in South India-Preliminary Investigations on Crucibles from Some Newly Identified Sites

European accounts from the 17th century onwards have referred to the repute and manufacture of “wootz’, a traditional crucible steel made especially in parts of southern India in the former provinces of Golconda, Mysore and Salem. Pliny's Natural History mentions the import of iron and steel from the Seres which have been thought to refer to the ancient southern Indian kingdom of the Cheras. As yet the scale of excavations and surface surveys is too limited to link the literary accounts to archaeometallurgical evidence, although pioneering exploratory investigations have been made by scholars, especially on the pre-industrial production sites of Konasamudram and Gatihosahalli discussed in 18th-19th century European accounts. In 1991–2 during preliminary surveys of ancient base metal mining sites, Srinivasan came across unreported dumps with crucible fragments at Mel-Siruvalur in Tamil Nadu, and Tintini and Machnur in Karnataka and she collected surface specimens from these sites as well as from the known site of Gatihosahalli. She was also given crucible fragments by the Tamil University, Tanjavur, from an excavated megalithic site at Kodumanal, dated to ca 2nd c. Bc, mentioned in Tamil Sangam literature (ca 3rd c. BC-3rd c. AD), and very near Karur, the ancient capital of the Sangam Cheras. Analyses of crucible fragments from the surface collection at Mel-Siruvalur showed several iron prills with a uniform pearlitic structure of high-carbon hypereutectoid steel (∼1–1.5% C) suggesting that the end product was uniformly a high-carbon steel of a structure consistent with those of high-carbon steels used successfully to experimentally replicate the watered steel patterns on ‘Damascus’ swords. Investigations indicate that the process was of carburisation of molten low carbon iron (m.p. 1400° C) in crucibles packed with carbonaceous matter. The fabric of crucibles from all the above mentioned sites appears similar. Preliminary investigations on these crucibles are thus reported to establish their relationship to crucible production of carbon steel and to thereby extend the known horizons of this technology further.

Study of the dynamics of protein folding through minimalistic models

Starting with the Levinthal paradox, a brief introduction to the protein folding problem is presented. The existing theories of protein folding, including the folding funnel scenario, are discussed. After briefly discussing different simulation studies of model proteins, we discuss our recent work on the dynamics of folding of the model HP-36 (the chicken villin headpiece) protein by using a simplified hydropathy scale. Special attention has been paid to the statics and dynamics of contact formation among the hydrophobic residues. The results obtained from this simple model appear to be surprisingly similar to several features observed in the folding of real proteins. The account concludes with a discussion of future problems.

Structure-function relationship in serine hydroxymethyltransferase

Serine hydroxymethyltransferase (SHMT), a pyridoxal-5V-phosphate (PLP)-dependent enzyme catalyzes thetetrahydrofolate (H4-folate)- dependent retro-aldol cleavage of serine to form 5,10-methylene H4-folate and glycine. The structure–function relationship of SHMT wasstudied in our laboratory initially by mutation of residues that are conserved in all SHMTs and later by structure-based mutagenesis of residues located in the active site. The analysis of mutants showed that K71, Y72, R80, D89, W110, S202, C203, H304, H306 and H356 residues are involved in maintenance of the oligomeric structure. The mutation of D227, a residue involved in charge relay system, led to the formation of inactive dimers, indicating that this residue has a role in maintaining the tetrameric structure and catalysis. E74, a residue appropriately positioned in the structure of the enzyme to carry out proton abstraction, was shown by characterization of E74Q and E74K mutants to be involved in conversion of the enzyme from an ‘open’ to ‘closed’ conformation rather than proton abstraction from the hydroxylgroup of serine. K256, the residue involved in the formation of Schiffs base with PLP, also plays a crucial role in the maintenance of the tetrameric structure. Mutation of R262 residue established the importance of distal interactions in facilitating catalysis and Y82 is not involved in the formaldehyde transfer via the postulated hemiacetal intermediate but plays a role in stabilizing the quinonoid intermediate.The mutational analysis of scSHMT along with the structure of recombinant Bacillus stearothermophilus SHMT and its substrate(s)complexes was used to provide evidence for a direct transfer mechanism rather than retro-aldol cleavage for the reaction catalyzed by SHMT.

Experimental Investigation on the Effect of Advanced Bus-Clamping Pulsewidth Modulation on Motor Acoustic Noise

Voltage source inverters (VSIs) supply nonsinusoidal voltages to induction motor drives, leading to line current distortion and torque pulsation. Conventional space vector pulsewidth modulation (PWM) techniques are widely used in VSIs on the account of good waveform quality and high dc bus utilization. In a conventional space vector PWM technique, the switching sequence begins with one zero state and ends with the other zero state in a subcycle. Some novel switching sequences have been proposed, which employ only one zero state but apply one of the two active states twice in a subcycle. One pair of such special switching sequences has recently been shown to reduce the pulsating torque considerably. In this paper, the conventional and special switching sequences are compared experimentally in terms of acoustic noise. In the low-and medium-speed ranges, the special switching sequence is seen to reduce the amplitude of the tonal component of noise at the switching frequency considerably and is also found to result in spread spectrum.

A Study of Early Afterdepolarizations in a Model for Human Ventricular Tissue

Sudden cardiac death is often caused by cardiac arrhythmias. Recently, special attention has been given to a certain arrhythmogenic condition, the long-QT syndrome, which occurs as a result of genetic mutations or drug toxicity. The underlying mechanisms of arrhythmias, caused by the long-QT syndrome, are not fully understood. However, arrhythmias are often connected to special excitations of cardiac cells, called early afterdepolarizations (EADs), which are depolarizations during the repolarizing phase of the action potential. So far, EADs have been studied mainly in isolated cardiac cells. However, the question on how EADs at the single-cell level can result in fibrillation at the tissue level, especially in human cell models, has not been widely studied yet. In this paper, we study wave patterns that result from single-cell EAD dynamics in a mathematical model for human ventricular cardiac tissue. We induce EADs by modeling experimental conditions which have been shown to evoke EADs at a single-cell level: by an increase of L-type Ca currents and a decrease of the delayed rectifier potassium currents. We show that, at the tissue level and depending on these parameters, three types of abnormal wave patterns emerge. We classify them into two types of spiral fibrillation and one type of oscillatory dynamics. Moreover, we find that the emergent wave patterns can be driven by calcium or sodium currents and we find phase waves in the oscillatory excitation regime. From our simulations we predict that arrhythmias caused by EADs can occur during normal wave propagation and do not require tissue heterogeneities. Experimental verification of our results is possible for experiments at the cell-culture level, where EADs can be induced by an increase of the L-type calcium conductance and by the application of I-Kr blockers, and the properties of the emergent patterns can be studied by optical mapping of the voltage and calcium.

An extended Shine-Dalgarno sequence in mRNA functionally bypasses a vital defect in initiator tRNA

Initiator tRNAs are special in their direct binding to the ribosomal P-site due to the hallmark occurrence of the three consecutive G-C base pairs (3GC pairs) in their anticodon stems. How the 3GC pairs function in this role, has remained unsolved. We show that mutations in either the mRNA or 16S rRNA leading to extended interaction between the Shine-Dalgarno (SD) and anti-SD sequences compensate for the vital need of the 3GC pairs in tRNA(fMet) for its function in Escherichia coli. In vivo, the 3GC mutant tRNA(fMet) occurred less abundantly in 70S ribosomes but normally on 30S subunits. However, the extended SD:anti-SD interaction increased its occurrence in 70S ribosomes. We propose that the 3GC pairs play a critical role in tRNA(fMet) retention in ribosome during the conformational changes that mark the transition of 30S preinitiation complex into elongation competent 70S complex. Furthermore, treating cells with kasugamycin, decreasing ribosome recycling factor (RRF) activity or increasing initiation factor 2 (IF2) levels enhanced initiation with the 3GC mutant tRNA(fMet), suggesting that the 70S mode of initiation is less dependent on the 3GC pairs in tRNA(fMet).

Organic photovoltaics: key photophysical, device and design aspects

Key aspects of Organic Photovoltaics (OPVs) have been reviewed in this tutorial. Issues pertaining to the choice of materials, fabrication processes, photophysical mechanisms, device characterization, morphology of active layers and manufacturing are discussed. Special emphasis has been given to recent developments in large-area modules. Current strategies in enhancing the performance using external optical engineering approaches have also been highlighted. OPVs as a technology combine low weight, flexibility, low cost, good form factor and high-throughput processing; making them a promising PV technology for the future.