Cardiac cell: a biological laser?

We present a new concept of cardiac cells based on an analogy with lasers, practical implementations of quantum resonators. In this concept, each cardiac cell comprises a network of independent nodes, characterised by a set of discrete energy levels and certain transition probabilities between them. Interaction between the nodes is given by threshold-limited energy transfer, leading to quantum-like behaviour of the whole network. We propose that in cardiomyocytes, during each excitation-contraction coupling cycle, stochastic calcium release and the unitary properties of ionic channels constitute an analogue to laser active medium prone to "population inversion" and "spontaneous emission" phenomena. This medium, when powered by an incoming threshold-reaching voltage discharge in the form of an action potential, responds to the calcium influx through L-type calcium channels by stimulated emission of Ca2+ ions in a coherent, synchronised and amplified release process known as calcium-induced calcium release. In parallel, phosphorylation-stimulated molecular amplification in protein cascades adds tuneable features to the cells. In this framework, the heart can be viewed as a coherent network of synchronously firing cardiomyocytes behaving as pulsed laser-like amplifiers, coupled to pulse-generating pacemaker master-oscillators. The concept brings a new viewpoint on cardiac diseases as possible alterations of "cell lasing" properties.     

Oxidative stress: a theoretical model or a biological reality?

Although oxidative stress has been extensively studied the last fifteen years, many physicians and biologists are still sceptical concerning its interest in biology and medicine. This is probably due, in part, to the fact that this subject is a matter of biophysics, and the first studies reported were written using a physical language that inspired these people used to a more concrete problematic very little. Another problem is the difficulty to detect the species mediating oxidative stress, and to determine their role in biological processes. This review is aimed at presenting oxidative stress, as well as reactive oxygen species and free radicals--the molecules that mediate it--in a clear form able to convince all researchers involved in life sciences that these short-lived intermediates are indissociable from any aerobic organism. Moreover, if reactive oxygen species and free radicals are undoubtedly involved in many pathologies, they have physiological functions too.     

Is information a proper observable for biological organization?

In the last century, jointly with the advent of computers, mathematical theories of information were developed. Shortly thereafter, during the ascent of molecular biology, the concept of information was rapidly transferred into biology at large. Several philosophers and biologists have argued against adopting this concept based on epistemological and ontological arguments, and also, because it encouraged genetic determinism. While the theories of elaboration and transmission of information are valid mathematical theories, their own logic and implicit causal structure make them inimical to biology, and because of it, their applications have and are hindering the development of a sound theory of organisms. Our analysis concentrates on the development of information theories in mathematics and on the differences between these theories regarding the relationship among complexity, information and entropy.     

Biosorption of heavy metals in a photo-rotating biological contactor—a batch process study

Metal removal potential of indigenous mining microorganisms from acid mine drainage (AMD) has been well recognised in situ at mine sites. However, their removal capacity requires to be investigated for AMD treatment. In the reported study, the capacity of an indigenous AMD microbial consortium dominated with Klebsormidium sp., immobilised in a photo-rotating biological contactor (PRBC), was investigated for removing various elements from a multi-ion synthetic AMD. The synthetic AMD was composed of major (Cu, Mn, Mg, Zn, Ca, Na, Ni) and trace elements (Fe, Al, Cr, Co, Se, Ag, Mo) at initial concentrations of 2 to 100 mg/L and 0.005 to 1 mg/L, respectively. The PRBC was operated for two 7-day batch periods under pH conditions of 3 and 5. The maximum removal was observed after 3 and 6 days at pH 3 and 5, respectively. Daily water analysis data demonstrated the ability of the algal–microbial biofilm to remove an overall average of 25–40 % of the major elements at pH 3 in the order of Na?>?Cu?>?Ca?>?Mg?>?Mn?>?Ni?>?Zn, whereas a higher removal (35–50 %) was observed at pH 5 in the order of Cu?>?Mn?>?Mg?>?Ca?>?Ni?>?Zn?>?Na. The removal efficiency of the system for trace elements varied extensively between 3 and 80 % at the both pH conditions. The batch data results demonstrated the ability for indigenous AMD algal–microbial biofilm for removing a variety of elements from AMD in a PRBC. The work presents the potential for further development and scale-up to use PBRC inoculated with AMD microorganisms at mine sites for first or secondary AMD treatment.     

“x” is not a bias,but a number with real biological significance

Recent literature criticized the use of the symbol “x” to denote basic chromosome number in cytotaxonomy. I show here that this criticism is superfluous and is based on historical confusion between the concepts of basic chromosome number (or monoploid chromosome number), which is objective, and ancestral basic chromosome number, which is always inferred, by means of several – more or less reliable – methods. The most relevant literature is discussed and, in the end, I propose the use of x for basic chromosome number and p for (hypothetical) ancestral basic chromosome number.     

Treatment of metal-contaminated wastes: why select a biological process?

Nature has demonstrated some subtle and intricate mechanisms for selectively controlling the mobility of metal pollutants in the environment. However, the application of this science to technology has been disappointing. A small number of pilot-plant studies have been carried out to investigate the potential of microorganisms (primarily bacteria) to remove metals from liquid wastes but only one system in the past 15 years has been commercialized. In order to explain this lack of application, it is important to understand the effectiveness, robustness and reliability of biological processes involving metals and their ability to compete with proven physicochemical technologies.     

Can an arbitrary sequence evolve towards acquiring a biological function?

Abstract To explore the possibility that an arbitrary sequence can evolve towards acquiring functional role when fused with other pre-existing protein modules, we replaced the D2 domain of the fd-tet phage genome with the soluble random polypeptide RP3-42. The replacement yielded an fd-RP defective phage that is six-order magnitude lower infectivity than the wild-type fd-tet phage. The evolvability of RP3-42 was investigated through iterative mutation and selection. Each generation consists of a maximum of ten arbitrarily chosen clones, whereby the clone with highest infectivity was selected to be the parent clone of the generation that followed. The experimental evolution attested that, from an initial single random sequence, there will be selectable variation in a property of interest and that the property in question was able to improve over several generations. fd-7, the clone with highest infectivity at the end of the experimental evolution, showed a 240-fold increase in infectivity as compared to its origin, fd-RP. Analysis by phage ELISA using anti-M13 antibody and anti-T7 antibody revealed that about 37-fold increase in the infectivity of fd-7 was attributed to the changes in the molecular property of the single polypeptide that replaced the D2 domain of the g3p protein. This study therefore exemplifies the process of a random polypeptide generating a functional role in rejuvenating the infectivity of a defective bacteriophage when fused to some preexisting protein modules, indicating that an arbitrary sequence can evolve toward acquiring a functional role. Overall, this study could herald the conception of new perspective regarding primordial polypeptides in the field of molecular evolution.     

What biological invasions ‘are’ is a matter of perspective

Invasion research today integrates active fields like biogeography, nature conservation, ecology, and evolutionary biology, and each of these fields contributes its own conceptual and terminological background. In this essay we advance the view that this is the reason why discussions on terminology keep flaring up time and time again. Our basic argument is that biological invasions cannot be perceived and defined independent of the specific research motivation. There are different, but equally valuable perspectives on biological invasions, each entailing a specific opinion about what the peculiarity of invasions is. We argue that a uniform usage of terms is not feasible, and even not desirable for invasion research, and suggest that the existing plurality of terms and concepts should be taken as an incentive to discuss the implications of different definitions. A stronger awareness and acknowledgement of the concepts underlying the terms used in interrelated research fields will enhance communication and promote progress in invasion research towards integrative, problem-oriented transdisciplinarity.     

Is a fluid-mosaic model of biological membranes fully relevant? Studies on lipid organization in model and biological membranes

The basic concept of the fluid-mosaic model of Singer and Nicolson, an essential point of which is that the membrane proteins are floating in a sea of excess lipid molecules organized in the lipid bilayer, may be misleading in understanding the movement of membrane components in biological membranes that show distinct domain structure. It seems that the lipid bilayer is an active factor in forming the membrane structure, and the lipid composition is responsible for the presence of domains in the membrane. The main role in the process of domain formation is played by cholesterol and sphingolipids. The results presented here show that in a binary mixture of cholesterol and unsaturated phospholipids, cholesterol is segregated out from the bulk unsaturated liquid-crystalline phase. This forms cholesterol-enriched domains or clustered cholesterol domains due to the lateral nonconformability between the rigid planar ring structure of cholesterol and the rigid bend of the unsaturated alkyl chain at double bond position. These cholesterol-enriched domains may be stabilized by the presence of saturated alkyl chains of sphingomyelin or glycosphingolipids, and also by specific proteins which selectively locate in these domains and stabilize them as a result of protein-protein interaction. Such lipid domains are called "rafts" and have been shown to be responsible both for signal transduction to and from the cell and for protein sorting. We also looked at whether polar carotenoids, compounds showing some similarities to cholesterol and affecting membrane properties in a similar way, would also promote domain formation and locate preferentially in one of the lipid phases. Our preliminary data show that in the presence of cholesterol, lutein (a polar carotenoid) may segregate out from saturated lipid regions (liquid-ordered phase) and accumulate in the regions rich in unsaturated phospholipids forming carotenoid-rich domains there. Conventional and pulse EPR (electron paramagnetic resonance) spin labeling techniques were employed to assess the molecular organization and dynamics of the raft-constituent molecules and of the raft itself in the membrane.     

Rehabilitating a biological notion of race? A response to Sesardic

The point Sesardic (Biol Philos 25: 143–162, 2010) makes about the possibility of distinguishing groups for which there is a lot of within-group variation is not sufficient to rehabilitate a biological concept of race. In this note, I sketch a number of issues that quickly arise once we delve more deeply into the relevant scientific knowledge, concepts, methods, and questions for inquiry.     

Does a biological clock reside in the eye of quail?

The site (intra- vs. extraocular) of the circadian clock driving an ocular melatonin rhythm in Japanese quail was investigated by alternately covering the left and right eyes of individual quail, otherwise held in constant light (LL), for 12-hr periods. This procedure exposed each eye to a light-dark (LD) 12:12 light cycle 180 degrees (12 hr) out of phase with the LD 12:12 light cycle experienced by the other eye. This protocol entrained the melatonin rhythm in the left eye of quail 180 degrees out of phase with the rhythm expressed in the right eye. These results are compatible with the hypothesis that an independent light-entrainable circadian pacemaker resides in each eye; they are incompatible with the hypothesis that a single (or functionally single) extraocular pacemaker drives the ocular melatonin rhythm in both eyes. However, the results are also compatible with a model in which two independent extraocular circadian pacemakers, each with an exclusive photic input from one eye, drive the ocular melatonin rhythm.     

Arabidopsis, a model to study biological functions of isoprene emission?

The volatile hemiterpene isoprene is emitted from plants and can affect atmospheric chemistry. Although recent studies indicate that isoprene can enhance thermotolerance or quench oxidative stress, the underlying physiological mechanisms are largely unknown. In this work, Arabidopsis (Arabidopsis thaliana), a natural nonemitter of isoprene and the model plant for functional plant analyses, has been constitutively transformed with the isoprene synthase gene (PcISPS) from Grey poplar (Populus x canescens). Overexpression of poplar ISPS in Arabidopsis resulted in isoprene-emitting rosettes that showed transiently enhanced growth rates compared to the wild type under moderate thermal stress. The findings that highest growth rates, higher dimethylallyl diphosphate levels, and enzyme activity were detected in young plants during their vegetative growth phase indicate that enhanced growth of transgenic plants under moderate thermal stress is due to introduced PcISPS. Dynamic gas-exchange studies applying transient cycles of heat stress to the wild type demonstrate clearly that the prime physiological role of isoprene formation in Arabidopsis is not to protect net assimilation from damage against thermal stress, but may instead be to retain the growth potential or coordinated vegetative development of the plant. Hence, this study demonstrates the enormous potential but also the pitfalls of transgenic Arabidopsis (or other nonnatural isoprenoid emitters) in studying isoprene biosynthesis and its biological function(s).     

Nitric oxide, a biological double-faced janus--is this good or bad?

Nitric oxide (NO) is a biological messenger molecule produced by one of the essential amino acids L-arginine by the catalytic action of the enzyme NO synthase (NOS). The dual role of NO as a protective or toxic molecule is due to several factors, such as; the isoform of NOS involved, concentration of NO and the type of cells in which it is synthesised, the availability of the substrate L-arginine, generation of guanosine 3,5'-cyclic monophosphate (cGMP) from soluble guanylate cyclase and the overall extra and intracellular environment in which NO is produced. NOS activation as a result of trauma (calcium influx) or infection leads to NO production, which activates its downstream receptor sGC to synthesise cGMP and/or leads to protein nitrosylation. This may lead to one or more systemic effects including altered neurotransmission which can be protective or toxic, vaso/bronchodilatation in the cardiovascular and respiratory systems and enhanced immune activity against invading pathogens. In addition to these major functions, NO plays important role in thermoregulation, renal function, gastrointestinal motility, endocrine function, and various functions of the urogenital system ranging from renin secretion to micturation; spermatogenesis to penile erection; and ovulation to implantation and parturition. A schematic summary of the functions of NO and the various isoforms of NOS expressed in body systems is shown in figure 1. In this review, the historical background, biochemistry and biosynthesis of NO and its enzymes together with the mechanism of NO actions in physiology and pathophysiology are discussed.     

Is Puccinia xanthii a suitable biological control agent of Ambrosia artemisiifolia?

Common ragweed, Ambrosia artemisiifolia, is a highly allergenic North American plant that has become invasive in some parts of Europe, Asia and Australia following its introduction to many places in the world. Some earlier works suggested that a microcyclic autoecious rust fungus, Puccinia xanthii, known to infect A. artemisiifolia in the USA only, can be considered as a potential classical biocontrol agent (BCA) of this noxious weed in Europe and elsewhere. However, an extensive field survey did not reveal the presence of either P. xanthii or any other rusts on common ragweed in 14 US states and two Canadian provinces in 2002 and 2003. Moreover, P. xanthii infecting A. artemisiifolia has never been recorded in Canada, although it is known to occur on A. trifida and Xanthium spp. there. Nevertheless, herbarium specimens collected between 1855 and 1963 in five states of the USA confirmed the presence of P. xanthii on A. artemisiifolia. It is concluded that currently P. xanthii cannot be regarded as a promising BCA of A. artemisiifolia, although it did occur on common ragweed at least a few decades ago in the USA and some forms of this rust species have already been evaluated as effective BCAs of Xanthium in Australia.     

The changing nature of plant–microbe interactions during a biological invasion

Invasive plant species can alter belowground microbial communities. Simultaneously, the composition of soil microbial communities and the abundance of key microbes can influence invasive plant success. Such reciprocal effects may cause plant–microbe interactions to change rapidly during the course of biological invasions in ways that either inhibit or promote invasive species growth. Here we use a space-for-time substitution to illustrate how effects of soil microbial communities on the exotic legume Vicia villosa vary across uninvaded sites, recently invaded sites, and sites invaded by V. villosa for over a decade. We find that soil microorganisms from invaded areas increase V. villosa growth compared to sterilized soil or live soils collected from uninvaded sites, likely because mutualistic nitrogen-fixing rhizobia are not abundant in uninvaded areas. Notably, the benefits resulting from inoculation with live soils were higher for soils from recently invaded sites compared to older invasions, potentially indicating that over longer time scales, soil microbial communities change in ways that may reduce the success of exotic species. These findings suggest that short-term changes to soil microbial communities following invasion may facilitate exotic legume growth likely because of increases in the abundance of mutualistic rhizobia, but also indicate that longer term changes to soil microbial communities may reduce the growth benefits belowground microbial communities provide to exotic species. Our results highlight the changing nature of plant–microbe interactions during biological invasions and illustrate how altered biotic interactions could contribute to both the initial success and subsequent naturalization of invasive legume species.     

Obestatin conformational features: a strategy to unveil obestatin's biological role?

Obestatin and its derivative Ob(11-23) are recently discovered peptides produced in the rat stomach. They have proven to be involved in the regulation of energy balance, inhibiting feeding, causing reductions in food intake, body weight and jejunal contraction in rodents. The G-protein coupled receptor, GPR39, was originally proposed as being an obestatin target receptor, but this remains controversial. As such, the molecular mechanism for obestatin's effects in vivo is still uncertain. Here we report the CD and NMR conformational analysis of obestatin and Ob(11-23). Both peptides assume a regular secondary structure in the C-terminal region of the molecule. In this region, structural elements similar to other GPCR binding neuropeptides support the identity of obestatin as a new and functionally autonomous GPCR ligand. Conversely sequence and conformational specificity point to a new farmacoforic structure, on which innovative derivatives with a potential role in the treatment of obesity can be designed and synthetized.     

The unified framework for biological invasions: a forest fungal pathogen perspective

Biological invasions in forests are growing in number and importance globally. The best studied examples are those caused by plants and animals, including insects. In contrast, forest invasions caused by microbes, including fungi, have received much lower levels of attention, particularly in the invasion biology literature. This can at least to some extent be due to the large number of these organisms involved and the fact that the majority of these have yet to be discovered and described. This is equally true for tree-infecting fungi, many of which are devastating pathogens responsible for dramatic invasions in natural and planted forests. This situation is changing through the application of molecular genetic tools that make it possible to accurately identify fungal tree pathogens, to determine their origins, pathways of movement, their modes of reproduction and change; all of which can influence invasions. The role and relevance of symbioses between tree pathogens and insects in forest invasions is also gaining increased attention. So too is our understanding that trees live in close association with large numbers of microbes that make up their holobiome. This has substantial relevance to invasion biology (Zenni et al. 2017). This commentary highlights four emerging issues that need to be considered regarding the invasions by fungal pathogens of trees and it emphasizes opportunities to better understand their relevance and impacts on natural and planted forests. A call is also made for plant pathologists to work more closely with ecologists such that fungal pathogens become more commonly integrated into invasion biology programmes.     

Plant cell culture technology–harnessing a biological approach for competitive cyclotides production

Cyclotides are naturally occurring mini-proteins that have a cyclic backbone and a knotted arrangement of three disulfide bonds. They are remarkably stable and have a diverse range of therapeutically useful biological activities, including antimicrobial and anti-HIV activity, although their natural function appears to be plant defence agents. Cyclotides are amenable to chemical synthesis; however currently most bioactivity studies have involved the use of peptides extracted from plants. Plant cell culture technology shows promise towards the goal of producing therapeutically active cyclotides in qualities and quantities required for drug development.     

Mechanism of PP2A-mediated IKKβ dephosphorylation: a systems biological approach

Background  

Biological effects of nuclear factor-κB (NFκB) can differ tremendously depending on the cellular context. For example, NFκB induced by interleukin-1 (IL-1) is converted from an inhibitor of death receptor induced apoptosis into a promoter of ultraviolet-B radiation (UVB)-induced apoptosis. This conversion requires prolonged NFκB activation and is facilitated by IL-1 + UVB-induced abrogation of the negative feedback loop for NFκB, involving a lack of inhibitor of κB (IκBα) protein reappearance. Permanent activation of the upstream kinase IKKβ results from UVB-induced inhibition of the catalytic subunit of Ser-Thr phosphatase PP2A (PP2Ac), leading to immediate phosphorylation and degradation of newly synthesized IκBα.