Models of Darwinian processes and evolutionary principles

Evolutionary processes are described as stochastic motions in a genotype space (set of sequences with a Hamming distance) and a phenotype space (vector space of phenotypic properties). Real value functions are introduced which form a landscape over these spaces; smoothness postulates are formulated. Evolution is considered as a kind of hill climbing on these adaptive landscapes. A rather simple diffusion approximation for the phenotypic processes is proposed which leads to similar mathematical problems as the Schrödinger equation for disordered potential distributions.     

The fairytale of the GSSG/GSH redox potential

Background

The term GSSG/GSH redox potential is frequently used to explain redox regulation and other biological processes.

Scope of review

The relevance of the GSSG/GSH redox potential as driving force of biological processes is critically discussed. It is recalled that the concentration ratio of GSSG and GSH reflects little else than a steady state, which overwhelmingly results from fast enzymatic processes utilizing, degrading or regenerating GSH.

Major conclusions

A biological GSSG/GSH redox potential, as calculated by the Nernst equation, is a deduced electrochemical parameter based on direct measurements of GSH and GSSG that are often complicated by poorly substantiated assumptions. It is considered irrelevant to the steering of any biological process. GSH-utilizing enzymes depend on the concentration of GSH, not on [GSH]², as is predicted by the Nernst equation, and are typically not affected by GSSG. Regulatory processes involving oxidants and GSH are considered to make use of mechanistic principles known for thiol peroxidases which catalyze the oxidation of hydroperoxides by GSH by means of an enzyme substitution mechanism involving only bimolecular reaction steps.

General significance

The negligibly small rate constants of related spontaneous reactions as compared with enzyme-catalyzed ones underscore the superiority of kinetic parameters over electrochemical or thermodynamic ones for an in-depth understanding of GSH-dependent biological phenomena. At best, the GSSG/GSH potential might be useful as an analytical tool to disclose disturbances in redox metabolism. This article is part of a Special Issue entitled Cellular Functions of Glutathione.     

<Emphasis Type="Italic">In vitro</Emphasis> study of HAX1 gene therapy by retro viral transduction as a therapeutic target in severe congenital neutropenia

Severe congenital neutropenia (SCN) is a primary immunodeficiency disease in which a number of underlying gene defects are responsible for abnormalities in neutrophil development. The HCLS1-associated protein X1 (HAX1) mutation is associated with an autosomal-recessive form of SCN. Considering the potential of gene therapy approaches for the treatment of monogenic disorders, in this study we aimed to develop retroviral vectors expressing coding sequences (CDS) to be used for the removal of the genetic blockade in deficient hematopoietic cells. Following amplification of CDS with primers containing appropriate restriction sites, HAX1 CDS was cloned into an intermediate vector using TA-cloning. The sequence was transferred into a retroviral vector, followed by retroviral packaging in Plat-A cells. To show HAX1 protein expression, HEK293T cells were exposed to 10 multiplicity of infection (MOI) of retroviral particles and HAX1 expression was confirmed in these cells, using indirect intracellular flow cytometry. This vector was applied for in vitro transduction of hematopoietic stem cell with HAX1 mutation; after 11 days, cultured cells were analyzed for CD66acde and CD177 (neutrophil surface markers) expression. Increased neutrophil production in HAX1 viral vector-expressing hematopoietic cells was observed as compared to control vector transduced cells. Hence, according to the results, this type of therapy could be considered a potential treatment protocol for the disease.     

The economic value of an improved malaria treatment programme in Zambia: results from a contingent valuation survey

Background

Pools of salt water and puddles created by giant waves from the sea due to the tsunami that occurred on 26^th December 2004 would facilitate increased breeding of brackish water malaria vector, Anopheles sundaicus. Land uplifts in North Andaman and subsidence in South Andaman have been reported and subsidence may lead to environmental disturbances and vector proliferation. This warrants a situation analysis and vector surveillance in the tsunami hit areas endemic for malaria transmitted by brackish water mosquito, An. sundaicus to predict the risk of outbreak.

Methods

An extensive survey was carried out in the tsunami-affected areas in Andaman district of the Andaman and Nicobar Islands, India to assess the extent of breeding of malaria vectors in the habitats created by seawater flooding. Types of habitats in relation to source of seawater inundation and frequency were identified. The salinity of the water samples and the mosquito species present in the larval samples collected from these habitats were recorded. The malaria situation in the area was also analysed.

Results

South Andaman, covering Port Blair and Ferrargunj sub districts, is still under the recurring phenomenon of seawater intrusion either directly from the sea or through a network of creeks. Both daily cycles of high tides and periodical spring tides continue to cause flooding. Low-lying paddy fields and fallow land, with a salinity ranging from 3,000 to 42,505 ppm, were found to support profuse breeding of An. sundaicus, the local malaria vector, and Anopheles subpictus, a vector implicated elsewhere. This area is endemic for both vivax and falciparum malaria. Malaria slide positivity rate has started increasing during post-tsunami period, which can be considered as an indication of risk of malaria outbreak.

Conclusion

Paddy fields and fallow land with freshwater, hitherto not considered as potential sites for An. sundaicus, are now major breeding sites due to saline water. Consequently, there is a risk of vector abundance with enhanced malaria transmission potential, due to the vastness of these tsunami-created breeding grounds and likelihood of them becoming permanent due to continued flooding in view of land subsidence. The close proximity of the houses and paucity of cattle may lead to a higher degree of man/vector contact causing a threat of malaria outbreak in this densely populated area. Measures to prevent the possible outbreak of malaria in this tsunami-affected area are discussed.     

Characteristics of the motor potentials in disorders of the subcortical motor structures of the human brain

Properties of motor potentials (MPs) were studied in patients with disturbance of function of subcortical motor structures--disturbance causing parkinsonism manifestations. MPs components are singled out preceding movement--"readiness potential" (N1), "motor potential" (N2) and MP components which are electrophysiological correlates of realization processes (component P2) and movement completion (component N3). It is revealed that MPs in patients with parkinsonism are changed in comparison with the norm; the most significant differences are observed in components N1, P2, N3, what is expressed in prolongation and a certain amplitude decrease of these components. Amplitude-temporal parameters most similar to the norm belong to the component N2, which is considered as an electrophysiological correlate of movement triggering. A hypothesis is suggested on its cortical origin.     

Liquefied natural gas for the UK: a life cycle assessment

Purpose

Liquefied natural gas (LNG) is expected to become an important component of the UK’s energy supply because the national hydrocarbon reserves on the continental shelf have started diminishing. However, use of any carbon-based fuel runs counter to mitigation of greenhouse gas emissions (GHGs). Hence, a broad environmental assessment to analyse the import of LNG to the UK is required.

Methods

A cradle to gate life cycle assessment has been carried out of a specific but representative case: LNG imported to the UK from Qatar. The analysis covers the supply chain, from gas extraction through to distribution to the end-user, assuming state-of-the-art facilities and ships. A sensitivity analysis was also conducted on key parameters including the energy requirements of the liquefaction and vaporisation processes, fuel for propulsion, shipping distance, tanker volume and composition of raw gas.

Results and discussion

All environmental indicators of the CML methodology were analysed. The processes of liquefaction, LNG transport and evaporation determine more than 50% of the cradle to gate global warming potential (GWP). When 1% of the total gas delivered is vented as methane emissions leakage throughout the supply chain, the GWP increases by 15% compared to the GWP of the base scenario. The variation of the GWP increases to 78% compared to the base scenario when 5% of the delivered gas is considered to be lost as vented emissions. For all the scenarios analysed, more than 75% of the total acidification potential (AP) is due to the sweetening of the natural gas before liquefaction. Direct emissions from transport always determine between 25 and 49% of the total eutrophication potential (EP) whereas the operation and maintenance of the sending ports strongly influences the fresh water aquatic ecotoxicity potential (FAETP).

Conclusions

The study highlights long-distance transport of LNG and natural gas processing, including sweetening, liquefaction and vaporisation, as the key operations that strongly affect the life cycle impacts. Those cannot be considered negligible when the environmental burdens of the LNG supply chain are considered. Furthermore, the effect of possible fugitive methane emissions along the supply chain are critical for the impact of operations such as extraction, liquefaction, storage before transport, transport itself and evaporation.

     

Minimal mixture principle as a method of choosing the form of a dynamic model]

The extremality principle for molecular processes in biological systems is considered. The principle is based on an assumption that the main function of biological processes is the separation of the "product" from the "scheme". The form of the dynamical model of the process is determined from the requirement of the "minimum mixture". As an example Selkov's model of glycolysis is considered.     

On the physical origin of biological handedness

In the racemic conglomerate crystallization of over 1000 samples of D, L-sodium-ammonium tartrate the effect of³²P beta irradiation on the weight, optical activity, and crystallite size was measured. Both weight and optical activity showed a statistical dependence on the intensity of beta irradiation. The crystallite size is also affected by the presence of³²P. Asymmetric crystals are suggested to have been potential mediators between asymmetric parity violating forces and molecular asymmetry so that stereo-selective prebiotic chemical reactions involving crystals need not be considered chance processes.No measurable difference in the energy content of optical isomers was found. An upper limit for the direct contribution of weak interactions to electromagnetic ones has been calculated. The mechanism of stereoselective crystal seeding by beta particles is discussed.     

Source-sink landscape theory and its ecological significance

Exploring the relatiouships between landscape pattern and ecological processes is the key topic of landscape ecology,for which,a large number of indices as well as landscape pattern analysis model were developed.However,one problem faced by landscape ecologists is that it is hard to link the landscape indices with a specific ecological process.Linking landscape pattern and ecological processes has become a challenge for landscape ecologists."Source" and "sink" are common concepts used in air pollution research,by which the movement direction and pattern of different pollutants in air can be clearly identified.In fact,for any ecological process,the research can be considered as a balance between the source and the sink in space.Thus,the concepts of "source" and "sink" could be implemented to the research of landscape pattern and ecological processes.In this paper,a theory of sourcesink landscape was proposed,which include:(1) In the research of landscape pattern and ecological process,all landscape types can be divided into two groups,"source"landscape and "sink" landscape."Source" landscape contributes positively to the ecological process,while "sink" landscape is unhelpful to the ecological process.(2) Both landscapes are recognized with regard to the specific ecological process."Source" landscape in a target ecological process may change into a "sink"landscape as in another ecological process.Therefore,the ecological process should be determined before "source"or "sink" landscape were defined.(3) The key point to distinguish "source" landscape from "sink" landscape is to quantify the effect of landscape on ecological process.The positive effect is made by "source" landscape,and the negative effect by "sink" landscape.(4) For the same ecological process,the contribution of "source" landscapes may vary,and it is the same to the "sink"landscapes.It is required to determine the weight of each landscape type on ecological processes.(5) The sourcesink principle can be applied to non-point source pollution control,biologic diversity protection,urban heat island effect mitigation,etc.However,the landscape evaluation models need to be calibrated respectively,because different ecological processes correspond with different source-sink landscapes and evaluation models for the different study areas.This theory is helpful to further study landscape pattern and ecological process,and offers a basis for new landscape index design.     

Uncoupling Effect of Fatty Acids in Halo- and Alkalotolerant Bacterium Bacillus pseudofirmus FTU

Natural uncouplers of oxidative phosphorylation, long-chain non-esterified fatty acids, cause uncoupling in the alkalo- and halotolerant bacterium Bacillus pseudofirmus FTU. The uncoupling effect in the bacterial cells was manifested as decrease of membrane potential and increase of respiratory activity. The membrane potential decrease was detected only in bacterial cells exhausted by their endogenous substrates. In proteoliposomes containing reconstituted bacterial cytochrome c oxidase, fatty acids caused a "mild" uncoupling effect by reducing membrane potential only at low rate of membrane potential generation. "Free respiration" induced by the "mild" uncouplers, the fatty acids, can be considered as possible mechanism responsible for adaptation of the bacteria to a constantly changed environment.     

Behavioural and Electrophysiological Responses of Mosquito Vectors <Emphasis Type="Italic">Aedes aegypti,Anopheles stephensi</Emphasis> and <Emphasis Type="Italic">Culex quinquefasciatus</Emphasis> to an Ethyl Ester: Ethyl 2-aminobenzoate

Mosquito control using different methods remains an integral component of intervention programmes which aim to protect humans from various mosquito-borne diseases. The host seeking behaviour of mosquitoes is essentially guided by odorant receptor neurons housed in the antenna, maxillary palps and proboscis. The odorant receptor neurons are responsible for detecting chemical cues from hosts and also useful for developing sustainable mosquito-control strategies that exploit host-seeking behaviours. The present investigation evaluates host seeking behavioural responses of a novel, non-toxic and environment friendly repellent, ethyl 2-aminobenzoate against three known vector species of mosquitoes viz. Aedes aegypti, Anopheles stephensi and Culex quinquefasciatus maintained in laboratory. The flight orientation of the test mosquitoes was studied using Y-tube olfactometer, whereas the antennae of adult female mosquitoes were used to investigate the effect of ethyl 2-aminobenzoate on the peripheral olfactory system using electroantennogram (EAG). The findings demonstrate that ethyl 2-aminobenzoate exhibited significant response in Y-tube olfactometer against all the three known vector species of mosquitoes. However, only Anopheles stephensi significantly elicited responses in EAG experiments, while the responses obtained for Aedes aegypti and Culex quinquefasciatus were not statistically significant. The results conclude that currently evaluated chemical ethyl 2-aminobenzoate has potential against some well established mosquito vector species and could be exploited to develop new and comparatively more effective anti-mosquito formulations.     

Measuring frequency domain granger causality for multiple blocks of interacting time series

In the past years, several frequency-domain causality measures based on vector autoregressive time series modeling have been suggested to assess directional connectivity in neural systems. The most followed approaches are based on representing the considered set of multiple time series as a realization of two or three vector-valued processes, yielding the so-called Geweke linear feedback measures, or as a realization of multiple scalar-valued processes, yielding popular measures like the directed coherence (DC) and the partial DC (PDC). In the present study, these two approaches are unified and generalized by proposing novel frequency-domain causality measures which extend the existing measures to the analysis of multiple blocks of time series. Specifically, the block DC (bDC) and block PDC (bPDC) extend DC and PDC to vector-valued processes, while their logarithmic counterparts, denoted as multivariate total feedback $f^\mathrm{m}$ and direct feedback $g^\mathrm{m}$ , represent into a full multivariate framework the Geweke’s measures. Theoretical analysis of the proposed measures shows that they: (i) possess desirable properties of causality measures; (ii) are able to reflect either direct causality (bPDC, $g^\mathrm{m})$ or total (direct + indirect) causality (bDC, $f^\mathrm{m})$ between time series blocks; (iii) reduce to the DC and PDC measures for scalar-valued processes, and to the Geweke’s measures for pairs of processes; (iv) are able to capture internal dependencies between the scalar constituents of the analyzed vector processes. Numerical analysis showed that the proposed measures can be efficiently estimated from short time series, allow to represent in an objective, compact way the information derived from the causal analysis of several pairs of time series, and may detect frequency domain causality more accurately than existing measures. The proposed measures find their natural application in the evaluation of directional interactions in neurophysiological settings where several brain activity signals are simultaneously recorded from multiple regions of interest.     

Next Generation Sequencing Reveals Regulation of Distinct Aedes microRNAs during Chikungunya Virus Development

Background

Application of genomics and Next Generation sequencing has led to the identification of new class of cellular functional molecules, namely, small RNAs. Of the several classes of ncRNAs (non-coding RNA), microRNAs have been demonstrated to exert determinative influence on various cellular processes. It is becoming abundantly clear that host/vector/pathogen encoded microRNAs impact eventual pathogenesis. In this context, the participation of vector based microRNAs in disease transmission and pathogen development is being investigated intensively. A few studies have highlighted the role of vector encoded microRNAs in pathogen infection. We conducted this study to evaluate the role of host miRNAs upon CHIKV (Chikungunya Virus) infection in an important vector, Aedes albopictus.

Findings

We identified 88 and 79 known miRNAs in uninfected and CHIKV infected Ae. albopictus Singh''s cell line respectively. We further identified nine novel miRNAs in Ae. albopictus. Comparison of the two libraries revealed differential expression of 77 common miRNAs between them. CHIKV infection specifically altered the miRNA profile of a specific set of eight miRNAs. Putative targets of these regulated miRNAs were identified and classified into their pathways.

Conclusions

In our study we have identified and described the profiles of various miRNAs upon CHIKV infection in Ae. albopictus. This investigation provides an insight about cellular modification by miRNAs during CHIKV infection and the results provide leads for identifying potential candidates for vector based antiviral strategies.     

Taphonomic features of Arctic pollen

The composition of the primary pollen changes during pollen transfer and redistribution over the Earths surface and fossilization. These processes are particularly pronounced in the tundra zone. Patterns of pollen spectra formation in the subaerial and subaqueous deposits of the tundra zone were considered and the differences in the content of palynomorphs with exine rupture were revealed. The changes in the effect of regional and local taphonomic factors on Arctic tundra slopes were traced. Pollen conservation in the deposits of the tundra zone, snowfields, and wedge ice was considered.Translated from Izvestiya Akademii Nauk, Seriya Biologicheskaya, No. 2, 2005, pp. 240–252.Original Russian Text Copyright © 2005 by Vasilchuk.     

Application of Structural Equation Models for Elucidating the Ecological Drivers of Anopheles sinensis in the Three Gorges Reservoir

Objective

To identify the major ecological drivers for malaria vector density using the structural equation model (SEM) in the Three Gorges Reservoir.

Method

An 11-year longitudinal surveillance of malaria vector as well as its related ecological factors was carried out in the Three Gorges Reservoir. The Delphi method was used to identify associated ecological factors. The structural equation model was repeatedly corrected and improved by the corrected index, combined with the actual situation. The final model was defined by relative simplicity, best fitting as well as the practicality.

Result

The final model indicated that the direct effects of temperature, livestock, humidity, and breeding on the vector were 0.015, −0.228, 0.450, 0.516 respectively, their total effects on the vector were 0.359, −0.112, 0.850, and 0.043 through different pathways.

Conclusion

SEM was effective and convenient in elucidating the mechanism by which malaria vector dynamics operated in this study. It identified that the breeding had the highest direct effect on vector and played a key role for mediating effect of temperature and humidity.     

Biotechnological production and applications of the ω-3 polyunsaturated fatty acid docosahexaenoic acid

Docosahexaenoic acid (DHA) is a polyunsaturated fatty acid composed of 22 carbon atoms and six double bonds. Because the first double bond, as counted from the methyl terminus, is at position three, DHA belongs to the so-called -3 group. In recent years, DHA has attracted much attention because of its beneficial effect on human health. At present, fish oil is the major source of DHA, but alternatively it may be produced by use of microorganisms. Marine microorganisms may contain large quantities of DHA and are considered a potential source of this important fatty acid. Some of these organisms can be grown heterotrophically on organic substrates without light. These processes can be well controlled and DHA with constant quality can be produced all year round. This paper reviews recent advances in the biotechnological production of DHA by marine microorganisms.     

Leishmania parasites: could we consider them as living organisms per se?

Over the last 10 years - in Microbes and Infection - the publications dealing with protozoan parasites were mainly providing insights on the pathogenic processes leading to the local or systemic damages in the mammals, these parasitic organisms exploit/subvert as hosts. As a result, many investigators introduced the objectives of their analysis by referring to "host-pathogen" interactions. Though we, as investigators, are all determined to decipher the pathogenic processes which can indeed be coupled to the parasite uncontrolled development, I think that the parasites - alike the living organisms they subvert as hosts - need to be considered as living organisms per se, instead of being considered as "pathogens". Such a conceptual frame will promote research on the processes on which relies their perpetuation whatever the level under investigations - individual and/or population level. Only the unicellular protozoan parasites of the genus Leishmania known to be hosted by blood-feeding insects and mammals will be further considered in this brief contribution.     

Extracellular potentials of a single myelinated nerve fiber in an unbounded volume conductor

The extracellular potentials of a single myelinated nerve fiber in an unbounded volume conductor were studied. The spatial distribution of the transmembrane potential was obtained by integrating the system of partial differential equations characterizing the electric processes in the active myelinated nerve fiber. The spatial distribution of the extracellular potentials at various radial distances in the volume conductor were calculated using the line source model. Up to a certain radial distance (500 m) the discontinuity of the action potential propagation is reflected in the extracellular potentials, while further in the volume conductor the potentials are smooth. The effect of the fiber diameter and the internodal distance on the volume conductor potentials as well as the changes in the magnitude of the extracellular potential (in the time domain) between two adjacent nodes at various radial distances were studied. The radial decline of the peak-to-peak amplitude of the extracellular potential depends on the radial coordinater of the field point and increases with the increase ofr.     

Adenovirus gene transfer to amelogenesis imperfecta ameloblast-like cells

To explore gene therapy strategies for amelogenesis imperfecta (AI), a human ameloblast-like cell population was established from third molars of an AI-affected patient. These cells were characterized by expression of cytokeratin 14, major enamel proteins and alkaline phosphatase staining. Suboptimal transduction of the ameloblast-like cells by an adenovirus type 5 (Ad5) vector was consistent with lower levels of the coxsackie-and-adenovirus receptor (CAR) on those cells relative to CAR-positive A549 cells. To overcome CAR -deficiency, we evaluated capsid-modified Ad5 vectors with various genetic capsid modifications including "pK7" and/or "RGD" motif-containing short peptides incorporated in the capsid protein fiber as well as fiber chimera with the Ad serotype 3 (Ad3) fiber "knob" domain. All fiber modifications provided an augmented transduction of AI-ameloblasts, revealed following vector dose normalization in A549 cells with a superior effect (up to 404-fold) of pK7/RGD double modification. This robust infectivity enhancement occurred through vector binding to both α(v)β3/α(v)β5 integrins and heparan sulfate proteoglycans (HSPGs) highly expressed by AI-ameloblasts as revealed by gene transfer blocking experiments. This work thus not only pioneers establishment of human AI ameloblast-like cell population as a model for in vitro studies but also reveals an optimal infectivity-enhancement strategy for a potential Ad5 vector-mediated gene therapy for AI.     

The Effect of Electrotonus on the Olfactory Epithelium

The effect of electrotonus on the slow potential of the olfactory epithelium of the frog was studied. The "on"-slow potential induced by a general odor like amyl acetate increased its magnitude in accordance with increase of anodal current, while it decreased its magnitude with increase of cathodal current. Similar relations were also found in the case of the vapors of organic solvents like ethyl ether of low concentrations. Conversely, the on-slow potential induced by the vapors of organic solvents of high concentration decreased its magnitude in accordance with the increase of anodal current, while it increased its magnitude with the increase of cathodal current. The "off"-slow potential induced by the vapors of organic solvents of high concentration showed a potential change under the action of electrotonic currents which is similar to the change of the on-slow potential induced by general odors. It was concluded that there are two receptive processes in the olfactory cell. One is an ordinary excitatory process which produces an electronegative slow potential in response to general odors. The other is a process of a different kind which is activated only by the vapor of an organic solvent of high concentration and which shows an entirely opposite reaction from that generally found in excitable tissues when an electrotonic current is applied.