Adaptive significance of circadian rhythms biological clocks and darwinian fitness in cyanobacteria

This article does not have an abstract

Gene prioritization in Type 2 Diabetes using domain interactions and network analysis

<p>Abstract</p> <p>Background</p> <p>Identification of disease genes for Type 2 Diabetes (T2D) by traditional methods has yielded limited success. Based on our previous observation that T2D may result from disturbed protein-protein interactions affected through disrupting modular domain interactions, here we have designed an approach to rank the candidates in the T2D linked genomic regions as plausible disease genes.</p> <p>Results</p> <p>Our approach integrates Weight value (Wv) method followed by prioritization using clustering coefficients derived from domain interaction network. Wv for each candidate is calculated based on the assumption that disease genes might be functionally related, mainly facilitated by interactions among domains of the interacting proteins. The benchmarking using a test dataset comprising of both known T2D genes and non-T2D genes revealed that Wv method had a sensitivity and specificity of 0.74 and 0.96 respectively with 9 fold enrichment. The candidate genes having a Wv > 0.5 were called High Weight Elements (HWEs). Further, we ranked HWEs by using the network property-the clustering coefficient (C_i). Each HWE with a C_i< 0.015 was prioritized as plausible disease candidates (HWEc) as previous studies indicate that disease genes tend to avoid dense clustering (with an average C_iof 0.015). This method further prioritized the identified disease genes with a sensitivity of 0.32 and a specificity of 0.98 and enriched the candidate list by 6.8 fold. Thus, from the dataset of 4052 positional candidates the method ranked 435 to be most likely disease candidates. The gene ontology sharing for the candidates showed higher representation of metabolic and signaling processes. The approach also captured genes with unknown functions which were characterized by network motif analysis.</p> <p>Conclusions</p> <p>Prioritization of positional candidates is essential for cost-effective and an expedited discovery of disease genes. Here, we demonstrate a novel approach for disease candidate prioritization from numerous loci linked to T2D.</p

Network Medicine in the Age of Biomedical Big Data

Network medicine is an emerging area of research dealing with molecular and genetic interactions, network biomarkers of disease, and therapeutic target discovery. Large-scale biomedical data generation offers a unique opportunity to assess the effect and impact of cellular heterogeneity and environmental perturbations on the observed phenotype. Marrying the two, network medicine with biomedical data provides a framework to build meaningful models and extract impactful results at a network level. In this review, we survey existing network types and biomedical data sources. More importantly, we delve into ways in which the network medicine approach, aided by phenotype-specific biomedical data, can be gainfully applied. We provide three paradigms, mainly dealing with three major biological network archetypes: protein-protein interaction, expression-based, and gene regulatory networks. For each of these paradigms, we discuss a broad overview of philosophies under which various network methods work. We also provide a few examples in each paradigm as a test case of its successful application. Finally, we delineate several opportunities and challenges in the field of network medicine. We hope this review provides a lexicon for researchers from biological sciences and network theory to come on the same page to work on research areas that require interdisciplinary expertise. Taken together, the understanding gained from combining biomedical data with networks can be useful for characterizing disease etiologies and identifying therapeutic targets, which, in turn, will lead to better preventive medicine with translational impact on personalized healthcare

Multi-oscillatory control of eclosion and oviposition rhythms in Drosophila melanogaster: evidence from limits of entrainment studies

The eclosion and oviposition rhythms of flies from a population of Drosophila melanogaster maintained under constant conditions of the laboratory were assayed under constant light (LL), constant darkness (DD), and light/dark (LD) cycles of 10:10 h (T20), 12:12 h (T24), and 14:14 h (T28). The mean (±95% confidence interval; CI) free-running period (t) of the oviposition rhythm was 26.34 ± 1.04 h and 24.50 ± 1.77 h in DD and LL, respectively. The eclosion rhythm showed a t of 23.33 ± 0.63 h (mean ± 95% CI) in DD, and eclosion was not rhythmic in LL. The t of the oviposition rhythm in DD was significantly greater than that of the eclosion rhythm. The eclosion rhythm of all 10 replicate vials entrained to the three periodic light regimes, T20, T24, and T28, whereas the oviposition rhythm of only about 24 and 41% of the individuals entrained to T20 and T24 regimes, respectively, while about 74% of the individuals assayed in T28 regimes showed entrainment. Our results thus clearly indicate that the t and the limits of entrainment of eclosion rhythm are different from those of the oviposition rhythm, and hence this reinforces the view that separate oscillators may regulate these two rhythms in D. melanogaster

Circadian clocks and life-history related traits: is pupation height affected by circadian organization in Drosophila melanogaster?

In D. melanogaster, the observation of greater pupation height under constant darkness than under constant light has been explained by the hypothesis that light has an inhibitory effect on larval wandering behaviour, preventing larvae from crawling higher up the walls of culture vials prior to pupation. If this is the only role of light in affecting pupation height, then various light : dark regimes would be predicted to yield pupation heights intermediate between those seen in constant light and constant darkness. We tested this hypothesis by measuring pupation height under various light : dark regimes in four laboratory populations ofDrosophila melanogaster. Pupation height was the greatest in constant darkness, intermediate in constant light, and the least in a light/dark regime of LD 14:14 h. The results clearly suggest that there is more to light regime effects on pupation height than mere behavioural inhibition of wandering larvae, and that circadian organization may play some role in determining pupation height, although the details of this role are not yet clear. We briefly discuss these results in the context of the possible involvement of circadian clocks in life-history evolution

Structural and mechanistic basis of anti-termination of Rho-dependent transcription termination by bacteriophage P4 capsid protein Psu

The conserved bacterial transcription terminator, Rho, is a potent target for bactericidal agents. Psu, a bacteriophage P4 capsid protein, is capable of inducing anti-termination to the Rho-dependent transcription termination. Knowledge of structural and mechanistic basis of this anti-termination is required to design peptide-inhibitor(s) of Rho from Psu. Using suppressor genetics, cross-linking, protein foot-printing and FRET analyses, we describe a conserved disordered structure, encompassing 139–153 amino acids of Rho, as the primary docking site for Psu. Also a neighbouring helical structure, comprising 347–354 amino acids, lining its central channel, plays a supportive role in the Rho–Psu complex formation. Based on the crystal structure of Psu, its conformation in the capsid of the P4 phage, and its interacting regions on Rho, we build an energy-minimized structural model of the Rho:Psu complex. In this model, a V-shaped dimer of Psu interacts with the two diagonally opposite subunits of a hexameric Rho, enabling Psu to form a ‘lid’ on the central channel of the latter. We show that this configuration of Psu makes the central channel of Rho inaccessible, and it causes a mechanical impediment to its translocase activity

A case for multiple oscillators controlling different circadian rhythms in Drosophila melanogaster

A population of the fruit fly Drosophila melanogaster was raised in periodic light/dark (LD) cycles of 12:12 h for about 35 generations. Eclosion, locomotor activity, and oviposition were found to be rhythmic in these flies, when assayed in constant laboratory conditions where the light intensity, temperature, humidity and other factors which could possibly act as time cue for these flies, were kept constant. These rhythms also entrained to a LD cycle of 12:12 h in the laboratory with each of them adopting a different temporal niche. The free-running periods (t) of the eclosion, locomotor activity and oviposition rhythms were significantly different from each other. The peak of eclosion and the onset of locomotor activity occurred during the light phase of the LD cycle, whereas the peak of oviposition was found to occur during the dark phase of the LD cycle. Based on these results, we conclude that different circadian oscillators control the eclosion, locomotor activity and oviposition rhythms in the fruit fly D. melanogaster

Possible role of eclosion rhythm in mediating the effects of light-dark environments on pre-adult development in Drosophila melanogaster

BACKGROUND: In insects, circadian clocks have been implicated in affecting life history traits such as pre-adult development time and adult lifespan. Studies on the period (per) mutants of Drosophila melanogaster, and laboratory-selected lines of Bactrocera cucurbitae suggested a close link between circadian clocks and development time. There is a possibility of clock genes having pleiotropic effects on clock period and pre-adult development time. In order to avoid such pleiotropic effects we have used wild type flies of same genotype under environments of different periodicities, which phenotypically either speeded up or slowed down the eclosion clock of D. melanogaster. RESULTS: We assayed pre-adult development time and pre-adult survivorship of four laboratory populations of D. melanogaster, under five different light regimes, continuous light (LL), continuous darkness (DD), and light-dark (LD) cycles of 10:10 h (T20), 12:12 h (T24), and 14:14 h (T28). Although the development time was significantly different in most light regimes, except for females under T24 &T28, pre-adult survivorship remained largely unaffected. The development time was shortest under LL, followed by T20, DD, T24 and T28 regimes, in that order. Interestingly the development time showed a positive correlation with the period of eclosion rhythm, i.e., faster oscillations were associated with faster development, and slower oscillations with slower development. CONCLUSION: Based on these results we conclude that periodicity of imposed LD cycles, and/or of eclosion rhythm plays a key role in regulating the duration of pre-adult development in D. melanogaster in a manner that does not involve direct pleiotropic effects of clock genes on both clock period and development time

Advances in Electromagnetic Therapy for Wound Healing

Understanding the molecular basis of wound healing and tissue regeneration continues to remain as one of the major challenges in modern medicine. There is absolute necessity to unveil the rather elusive mechanism with a special emphasis on the approaches to accelerate wound healing. Low frequency low intensity Pulsed electromagnetic therapy is evidenced to have a significant impact on wound repair and regeneration. It provides a non-invasive reparative technique to treat an injury. In vitro studies reported a significant effect of electromagnetic field on neovascularisation and angiogenesis. There are also many pieces of evidence which support its efficiency in reducing the duration of wound healing and improving the tensile strength of scars. Here, we compared the traditional stigma associated with pulsed electromagnetic fields and weighed them with its potential therapeutic effect on wound healing. Furthermore, we emphasized the need for more focused research to determine the therapeutic strategies and optimised parameters of pulsed electromagnetic field that can assure efficient wound healing and regeneration.