Phototropism: mechanisms and ecological implications

Abstract. Phototropism in seed plants, either etiolated or de-etiolated, is mediated by unidentified photoreceptor(s) sensitive to blue and near-UV regions of the light spectrum. Green plants may have an additional phototropic system sensitive to red light. Fluence-response studies of the blue light-sensitive phototropism, initially made on oat coleoptiles, have indicated the occurrence of multiple response types. Of those, two are found to be general: the first pulse-induced positive phototropism (fPIPP), or the so-called first positive curvature, and the time-dependent phototropism (TDP) or the second positive curvature. The fPIPP, elicited by a pulse stimulus shorter than a few minutes, is characterized by a bell-shaped fluence-response curve and the validity of reciprocity. The TDP, elicited by prolonged irradiation, is characterized by its dependence on the exposure time and the invalidity of reciprocity. Studies made on these two response types have revealed the following: (1) plants acquire directional light information for phototropism by sensing internal light gradients created by light scattering and absorption; (2) phototropism results from redistribution of growth, i.e. inhibition on the irradiated side and compensating stimulation on the shaded side; (3) lateral movement of growth regulators, the principle of the Cholodny-Went theory, can account for the growth redistribution, and auxin is clearly the mediating regulator in maize coleoptiles. This review further describes some mechanistic implications of fPIPP. Experimental results indicate that (1) fPIPP is mediated by a single step of photoreaction, (2) the responsiveness, reflected in the height of the fluenceresponse curve, is reduced by pre-irradiation with blue light and recovers gradually afterward, and (3) the light sensitivity, reflected in the position of the fluence-response curve along the log fluence axis, is also reduced by the pre-irradiation and recovers gradually. Analyses of these results, based on kinetic models, suggest that the bell-shaped fluence-response curve is caused by the difference in the amounts of a photoproduct between irradiated and shaded sides, and that fPIPP represents a mechanism of TDP. It is also indicated that phytochrome in the red-absorbing form exerts two separate effects on phototropism: reduction of the light sensitivity and enhancement of the responsiveness. Along with the discussion of the mechanisms of phototropism, their ecological implications are considered.     

Cardiomyocyte death: mechanisms and translational implications

Cardiovascular disease (CVD) is the leading cause of morbidity and mortality worldwide. Although treatments have improved, development of novel therapies for patients with CVD remains a major research goal. Apoptosis, necrosis, and autophagy occur in cardiac myocytes, and both gradual and acute cell death are hallmarks of cardiac pathology, including heart failure, myocardial infarction, and ischemia/reperfusion. Pharmacological and genetic inhibition of autophagy, apoptosis, or necrosis diminishes infarct size and improves cardiac function in these disorders. Here, we review recent progress in the fields of autophagy, apoptosis, and necrosis. In addition, we highlight the involvement of these mechanisms in cardiac pathology and discuss potential translational implications.     

Damage induced arrhythmias: mechanisms and implications

Little is known about the role played by non-uniform myocardial stress and strain distributions and by non-uniform excitation contraction coupling in mechanisms underlying the premature beats that initiate an arrhythmia. We will review the evidence in support of a mechanism in which both non-uniform contraction and increased Ca2+ load of cells adjacent to acutely damaged cells are essential in the "spontaneous" generation of Ca2+ transients during the relaxation phase of the electrically driven twitch. The putative mechanism of initiation of the propagating Ca2+ waves involves feedback of rapid length (or force) changes to dissociation of Ca2+ from the contractile filaments. A novel aspect of this concept is that these mechanically elicited Ca2+ transients induce propagating Ca2+ waves that travel into the adjacent normal myocardium and cause after-depolarizations, which, in turn, may cause premature action potentials. These premature action potentials will further load the cells with Ca2+, which promotes the subsequent generation of propagating Ca2+ transients and leads to triggered arrhythmias. The damage-induced premature beats may also initiate re-entry arrhythmias in non-uniform myocardium. These observations strongly support the concept that abnormal cellular Ca2+ transport plays a crucial role in the initiation of arrhythmias in damaged and non-uniform myocardium.     

Virus-induced neurobehavioral disorders: mechanisms and implications

One hypothesis for the etiology of neuropsychiatric disorders proposes that viral infection contributes to the induction of neuronal system dysfunction, resulting in a wide range of behavioral abnormalities. Recent research in molecular biology supports this hypothesis and refocuses on the role of viral infection in the development of psychiatric disorders. Viral infection can induce deleterious effects in the central nervous system by direct and/or indirect pathways. Understanding the mechanisms of glial cell dysfunction caused by persistent viral infection should lead to novel insights into the development of neurobehavioral disorders, including human mental illnesses, and to the possible development of treatments.     

Quorum-quenching microbial infections: mechanisms and implications

The discovery of antibiotics early in the past century marked the beginning of active control and prevention of infectious microbial diseases. However, extensive use of antibiotics has also unavoidably resulted in the emergence of ‘superbugs’ that resist conventional antibiotics. The finding that many pathogens rely on cell-to-cell communication mechanisms, known as quorum sensing, to synchronize microbial activities essential for infection and survival in the host suggests a promising disease control strategy, i.e. quenching microbial quorum sensing or in short, quorum quenching. Work over the past few years has demonstrated that quorum-quenching mechanisms are widely conserved in many prokaryotic and eukaryotic organisms. These naturally occurring quorum-quenching mechanisms appear to play important roles in microbe–microbe and pathogen–host interactions and have been used, or served as lead compounds, in developing and formulating a new generation of antimicrobials. Characterization of the crystal structures of several types of quorum-quenching enzymes has provided valuable information to elucidate the catalytic mechanisms, as well as clues for future protein tailoring and molecular improvement. The discovery of quorum-sensing signal degradation enzymes in mammalian species represents a new milestone in quorum sensing and quorum quenching research. The finding highlights the importance of investigating their roles in host innate defence against infectious diseases and to determine the factors influencing their in vivo concentrations and catalytic activities.     

Murine alveolar macrophage-mediated lymphocyte cytostasis: Kinetics and mechanisms

Recent reports have demonstrated that alveolar macrophages (AM) from several species regulate antigen- and mitogen-induced blastogenesis. In this study, we confirm that murine AM also mediate lymphocyte cytostasis and define, in part, the mechanism involved. AM were found to inhibit homologous splenocyte responses to concanavalin A in a dose-dependent manner. The inclusion of 1 AM:10 lymphocytes abrogated mitogenesis. Kinetic studies revealed that maximal inhibition of the splenocyte response required the inclusion of AM at culture initiation, stimulation of splenocytes with an optimal Con A dose, and an optimal incubation period of 72 hr. In addition, suppression of Con A-induced blastogenesis by AM was not genetically restricted, as Balb/c AM suppressed allogeneic CBA/J spleen cells comparably to homologous control cells. The addition of either catalase or indomethacin to partially suppressed cultures (containing 3% AM) totally reversed the inhibition. In contrast, catalase did not protect lymphocytes from absolute suppression mediated by higher AM numbers (10% AM), while indomethacin offered partial protection. A synergistic effect was noted upon the addition of both substances. Thus, prostaglandin and hydrogen peroxide released by AM contribute to the suppressive effects of these cells.     

DNA multiplex hybridization on microarrays and thermodynamic stability in solution: a direct comparison

Hybridization intensities of 30 distinct short duplex DNAs measured on spotted microarrays, were directly compared with thermodynamic stabilities measured in solution. DNA sequences were designed to promote formation of perfect match, or hybrid duplexes containing tandem mismatches. Thermodynamic parameters ΔH°, ΔS° and ΔG° of melting transitions in solution were evaluated directly using differential scanning calorimetry. Quantitative comparison with results from 63 multiplex microarray hybridization experiments provided a linear relationship for perfect match and most mismatch duplexes. Examination of outliers suggests that both duplex length and relative position of tandem mismatches could be important factors contributing to observed deviations from linearity. A detailed comparison of measured thermodynamic parameters with those calculated using the nearest-neighbor model was performed. Analysis revealed the nearest-neighbor model generally predicts mismatch duplexes to be less stable than experimentally observed. Results also show the relative stability of a tandem mismatch is highly dependent on the identity of the flanking Watson–Crick (w/c) base pairs. Thus, specifying the stability contribution of a tandem mismatch requires consideration of the sequence identity of at least four base pair units (tandem mismatch and flanking w/c base pairs). These observations underscore the need for rigorous evaluation of thermodynamic parameters describing tandem mismatch stability.     

Species-range-size distributions: patterns, mechanisms and implications

Species-range-size distributions have received remarkably little attention in contrast to species-abundance distributions. However, recognition of the importance of regional scale phenomena for local assemblage structure, and the emergence of 'macroecology', have begun to change this situation. A growing number of studies suggests that these distributions are, in general, approximately lognormal, although interpretation is complicated by a variety of factors. Assuming the distribution pattern to be real, it can be viewed in terms of evolutionary and ecological determinants of species occurrences, although their relative significance remains unclear. The form of the distribution has a variety of important consequences, particularly for inventories of faunas and floras and for conservation.     

Lithium neuroprotection: molecular mechanisms and clinical implications

Lithium has emerged as a neuroprotective agent efficacious in preventing apoptosis-dependent cellular death. Lithium neuroprotection is provided through multiple, intersecting mechanisms, although how lithium interacts with these mechanisms is still under investigation. Lithium increases cell survival by inducing brain-derived neurotrophic factor and thereby stimulating activity in anti-apoptotic pathways, including the phosphatidylinositol 3-kinase/Akt and the mitogen-activated protein kinase pathways. In addition, lithium reduces pro-apoptotic function by directly and indirectly inhibiting glycogen synthase kinase-3beta activity and indirectly inhibiting N-methyl-D-aspartate (NMDA)-receptor-mediated calcium influx. Lithium-induced regulation of anti- and pro-apoptotic pathways alters a wide variety of downstream effectors, including beta-catenin, heat shock factor 1, activator protein 1, cAMP-response-element-binding protein, and the Bcl-2 protein family. Lithium neuroprotection has a wide variety of clinical implications. Beyond its present use in bipolar mood disorder, lithium's neuroprotective abilities imply that it could be used to treat or prevent brain damage following traumatic injury, such as stroke, and neurodegenerative diseases such as Huntington's and Alzheimer's diseases.     

Differential allocation: tests, mechanisms and implications

Differential allocation occurs when reproductive investment is influenced by mate attractiveness. Recently, wide-ranging empirical support for differential allocation has been obtained. These data suggest that mates can affect the payoffs from reproduction, thus making sacrifices of reproductive value worthwhile when breeding with an attractive mate. As an example of an adaptive parental effect, the existence of differential allocation has some interesting implications for empirical studies of sexual selection and for predicting evolutionary responses to selection.     

Post-translational modifications of adiponectin: mechanisms and functional implications

Adiponectin is an insulin-sensitizing adipokine with anti-diabetic, anti-atherogenic, anti-inflammatory and cardioprotective properties. This adipokine is secreted from adipocytes into the circulation as three oligomeric isoforms, including trimeric, hexameric and the HMW (high-molecular-mass) oligomeric complex consisting of at least 18 protomers. Each oligomeric isoform of adiponectin exerts distinct biological properties in its various target tissues. The HMW oligomer is the major active form mediating the insulin-sensitizing effects of adiponectin, whereas the central actions of this adipokine are attributed primarily to the hexameric and trimeric oligomers. In patients with Type 2 diabetes and coronary heart disease, circulating levels of HMW adiponectin are selectively decreased due to an impaired secretion of this oligomer from adipocytes. The biosynthesis of the adiponectin oligomers is a complex process involving extensive post-translational modifications. Hydroxylation and glycosylation of several conserved lysine residues in the collagenous domain of adiponectin are necessary for the intracellular assembly and stabilization of its high-order oligomeric structures. Secretion of the adiponectin oligomers is tightly controlled by a pair of molecular chaperones in the ER (endoplasmic reticulum), including ERp44 (ER protein of 44 kDa) and Ero1-Lalpha (ER oxidoreductase 1-Lalpha). ERp44 inhibits the secretion of adiponectin oligomers through a thiol-mediated retention. In contrast, Ero1-Lalpha releases HMW adiponectin trapped by ERp44. The PPARgamma (peroxisome-proliferator-activated receptor gamma) agonists thiazolidinediones selectively enhance the secretion of HMW adiponectin through up-regulation of Ero1-Lalpha. In the present review, we discuss the recent advances in our understanding of the structural and biological properties of the adiponectin oligomeric isoforms and highlight the role of post-translational modifications in regulating the biosynthesis of HMW adiponectin.     

Kinetics and thermodynamics of DNA hybridization on gold nanoparticles

Hybridization of single-stranded DNA immobilized on the surface of gold nanoparticles (GNPs) into double stranded DNA and its subsequent dissociation into ssDNA were investigated. Melting curves and rates of dissociation and hybridization were measured using fluorescence detection based on hybridization-induced fluorescence change. Two distribution functions, namely the state distribution and the rate distribution, were proposed in order to take interfacial heterogeneity into account and to quantitatively analyze the data. Reaction and activation enthalpies and entropies of DNA hybridization and dissociation on GNPs were derived and compared with the same quantities in solution. Our results show that the interaction between GNPs and DNA reduces the energetic barrier and accelerates the dissociation of adhered DNA. At low surface densities of ssDNA adhered to GNP surface, the primary reaction pathway is that ssDNA in solution first adsorbs onto the GNP, and then diffuses along the surface until hybridizing with an immobilized DNA. We also found that the secondary structure of a DNA hairpin inhibits the interaction between GNPs and DNA and enhances the stability of the DNA hairpin adhered to GNPs.     

Kinetics of hybridization on surface oligonucleotide microchips: theory, experiment, and comparison with hybridization on gel-based microchips

The optimal design of oligonucleotide microchips and efficient discrimination between perfect and mismatch duplexes strongly depend on the external transport of target DNA to the cells with immobilized probes as well as on respective association and dissociation rates at the duplex formation. In this paper we present the relevant theory for hybridization of DNA fragments with oligonucleotide probes immobilized in the cells on flat substrate. With minor modifications, our theory also is applicable to reaction-diffusion hybridization kinetics for the probes immobilized on the surface of microbeads immersed in hybridization solution. The main theoretical predictions are verified with control experiments. Besides that, we compared the characteristics of the surface and gel-based oligonucleotide microchips. The comparison was performed for the chips printed with the same pin robot, for the signals measured with the same devices and processed by the same technique, and for the same hybridization conditions. The sets of probe oligonucleotides and the concentrations of probes in respective solutions used for immobilization on each platform were identical as well. We found that, despite the slower hybridization kinetics, the fluorescence signals and mutation discrimination efficiency appeared to be higher for the gel-based microchips with respect to their surface counterparts even for the relatively short hybridization time about 0.5-1 hour. Both the divergence between signals for perfects and the difference in mutation discrimination efficiency for the counterpart platforms rapidly grow with incubation time. In particular, for hybridization during 3 h the signals for gel-based microchips surpassed their surface counterparts in 5-20 times, while the ratios of signals for perfect-mismatch pairs for gel microchips exceeded the corresponding ratios for surface microchips in 2-4 times. These effects may be attributed to the better immobilization efficiency and to the higher thermodynamic association constants for duplex formation within gel pads.