Structure—chemical approach to organization of information on metabolic charts

A nontraditional approach to construction of metabolic charts is proposed. It is based on the discovery of symmetry in the structure of the network of metabolic reactions. So if compounds and reactions are located on the metabolic chart according to their chemical features, the chart structure will acquire a periodic pattern. The charts thus created have a natural two-dimensional coordinate system of the metabolic network. Points on the X-axis correspond to number of carbon atoms in the carbon skeleton of compounds in columns and points on the Y-axis correspond to number of -COOH groups in compounds filing in series of rows on the charts. As a result this coordinate system sections the field of the charts into rectangular blocks each of which containing compounds with the same numbers of carbon atoms and the same numbers of -COOH groups. The latter substantially improves the charts and makes them a more valid source of metabolic data possessing heuristic properties. The periodicity of the metabolic network structure enables us easily to remember information about biochemical reactions and their products. The charts can also be used as a universal key for any biological database information that is systematically connected with the metabolic information. The charts can be important for medicine and pharmacology because they can help to understand the metabolic processes involved in decomposition of a particular drug or to find the chain of reactions blocked or initiated by administering this drug into a living organism.Translated from Biokhimiya, Vol. 69, No. 12, 2004, pp. 1691–1699.Original Russian Text Copyright © 2004 by Malygin.     

Evolution of insect-plant relationships — a devil''s advocate approach

Most hypotheses concerning the evolution of insect-plant relationships are based on the assumptions that, (1) phytophagous insects reduce plant fitness, and that (2) insect-plant relationships are the result of unconstrained selection. It can be shown, however, that there is little evidence to support these assumptions. As an alternative, it is proposed that the evolution of insect-plant relationships results primarily from autonomous evolutionary events; namely from heritable functional changes within the insects' nervous system that determine plant recognition and ultimately host plant specificity. These changes cannot be evoked by selective ecological agents. They originate from intrinsic changes (mutationssensu lato) within the insect genome. Ecological factors play a secondary role: by either supporting or preventing the establishment of the new genotype with the novel food preference. This paper has been dedicated in warm friendship to Professor Louis M. Schoonhoven, the leading scientist in sensory physiology of phytophagous insects, on the occasion of his 60th birthday.     

Self-replicating micelles — A chemical version of a minimal autopoietic system

Reverse micelles hosting the internal production of the surfactant are proposed as experimentally feasible models of simple (or minimal) autopoietic systems. We describe the conditions under which these may be formed and their possible biological implications. The micellar systems considered here turn out also to exhibit a capacity for self-reproduction through fragmentation under plausible conditions, thus constituting also a minimal experimental model for prebiotic self-reproduction.     

Mutants of Burkholderia cenocepacia with a change in synthesis of N-acyl-homoserine lactones—Signal molecules of quorum sensing regulation

By means of plasposon mutagenesis, mutants of Burkholderia cenocepacia 370 with the change in production of N-acyl-homoserine lactones (AHL), signal molecules of the Quorum Sensing system of regulation, were obtained. To localize plasposon insertions in mutant strains, fragments of chromosomal DNA containing plasposons were cloned, adjacent DNA regions sequenced, and a search for homologous nucleotide sequences in the GeneBank was initiated. It has been shown that the insertion of plasposon into gene lon encoding Lon proteinase drastically decreases AHL synthesis. Upon insertion of plasposon into gene pps encoding phosphoenolpyruvate-synthase, enhancement of AHL production is observed. In mutant carrying inactivated gene lon, a strong decline of extracellular protease activity, hemolytic, and chitinolytic activities was observed in comparison with the original strain; lipase activity was not changed in this mutant. Mutation in gene pps did not affect these properties of B. cenocepacia 370. Mutations in genes lon and pps reduced the virulence of bacteria upon infection of mice.     

The heart—a different approach

The study of bryophytes forms an obvious part of school, college, and university courses which deal with cytology and developmental behaviour. They are readily obtained, conveniently cultured, and require fewer specialized skills than are necessary for similar work on other organisms. Information on preparing mitotic chromosomes for examination is provided, as are details of a technique by which Giemsa C-banding of chromosomes becomes for the first time a realistic proposition at all levels of education. Practical firsthand experience of the latter technique provides a useful way of coordinating the teaching of microscopic and molecular aspects of cell biology. Cytological behaviour can also be related to experiments on developmental aspects of the life cycle, a cycle which is noted for its well-marked alternation of generations. These include suggestions for monitoring the seasonal maturation of gametangia and sporophytes, as well as for examining photolropic responses made in liverworts by diploid setae and haploid archegoniophores.     

Bioremediation of multi-metal contaminated soil using biosurfactant — a novel approach

An unconventional nutrient medium, distillery spent wash (1:3) diluted) was used to produce di-rhamnolipid biosurfactant by Pseudomonas aeruginosa strain BS2. This research further assessed the potential of the biosurfactant as a washing agent for metal removal from multimetal contaminated soil (Cr-940 ppm; Pb-900 ppm; Cd-430 ppm; Ni-880 ppm; Cu-480 ppm). Out of the treatments of contaminated soil with tap water and rhamnolipid biosurfactant, the latter was found to be potent in mobilization of metal and decontamination of contaminated soil. Within 36 hours of leaching study, di-rhamnolipid as compared to tap water facilitated 13 folds higher removal of Cr from the heavy metal spiked soil whereas removal of Pb and Cu was 9–10 and 14 folds higher respectively. Leaching of Cd and Ni was 25 folds higher from the spiked soil. This shows that leaching behavior of biosurfactant was different for different metals. The use of wastewater for production of biosurfactant and its efficient use in metal removal make it a strong applicant for bioremediation.     

Identification of chilling and heat requirements of cherry trees—a statistical approach

Most trees from temperate climates require the accumulation of winter chill and subsequent heat during their dormant phase to resume growth and initiate flowering in the following spring. Global warming could reduce chill and hence hamper the cultivation of high-chill species such as cherries. Yet determining chilling and heat requirements requires large-scale controlled-forcing experiments, and estimates are thus often unavailable. Where long-term phenology datasets exist, partial least squares (PLS) regression can be used as an alternative, to determine climatic requirements statistically. Bloom dates of cherry cv. ‘Schneiders späte Knorpelkirsche’ trees in Klein-Altendorf, Germany, from 24 growing seasons were correlated with 11-day running means of daily mean temperature. Based on the output of the PLS regression, five candidate chilling periods ranging in length from 17 to 102 days, and one forcing phase of 66 days were delineated. Among three common chill models used to quantify chill, the Dynamic Model showed the lowest variation in chill, indicating that it may be more accurate than the Utah and Chilling Hours Models. Based on the longest candidate chilling phase with the earliest starting date, cv. ‘Schneiders späte Knorpelkirsche’ cherries at Bonn exhibited a chilling requirement of 68.6?±?5.7 chill portions (or 1,375?±?178 chilling hours or 1,410?±?238 Utah chill units) and a heat requirement of 3,473?±?1,236 growing degree hours. Closer investigation of the distinct chilling phases detected by PLS regression could contribute to our understanding of dormancy processes and thus help fruit and nut growers identify suitable tree cultivars for a future in which static climatic conditions can no longer be assumed. All procedures used in this study were bundled in an R package (‘chillR’) and are provided as Supplementary materials. The procedure was also applied to leaf emergence dates of walnut (cv. ‘Payne’) at Davis, California.     

Locoregional immunotherapy of head and neck cancers utilizing allogeneic spleen cells — a report of 2 cases

Frozen-stored human spleen cells (SC) cultured with streptococcus preparation OK-432 acquired direct cytotoxicity to autologous as well as allogeneic tumor cells. The activated cells started to produce cytocidal cytokine TGIF, which is distinct from previously known cytokines.We examined the possibility of allogeneic adoptive immunotherapy (AIT) using these OK-432-stimulated spleen cells (OK-SC) in two cancer patients. Rapid necrosis of cancer tissue and remarkable decreases of tumor markers in tumor effusion were observed. There were no severe side effects.     

Characterization of polychlorinated alkane mixtures—a Monte Carlo modeling approach

A Monte Carlo model was developed to characterize the molecular composition of polychlorinated alkane mixtures. The model is based upon a simulation of the free-radical chlorination process by which polychlorinated alkane mixtures are produced industrially from n-alkanes. In the model, the free-radical chlorination reaction was simulated by randomly selecting a position on a partially converted alkane molecule for target by chlorine free-radical attack. The relative reactivities of the hydrogen atoms on the alkane chain towards chlorine free-radical substitution were either determined experimentally or extrapolated from experimental results and incorporated into the model. The result of the simulation is the prediction of the detailed molecular composition of any PCA mixture. Good agreement was found when comparing the distribution of molecules predicted by the model to analytically determined distributions of real PCA mixtures. Results from the model were then coupled with rules describing the action of biological enzymes to estimate the upper limit possible for the aerobic biodegradation of PCA mixtures.     

Modification of chemical reactivity via a novel interaction of light and matter — A review

A new interaction of light, in the VIS region, and matter is presented. Theoretical preliminaries are introduced to support the experiments, in which different physical systems are irradiated with 546 nm; the experimental results show the time of irradiation to be an essential parameter. A tentative theory is presented and the prospect of using the effect in the field of molecular computers is briefly outlined.     

Microbial metabolism of quorum-sensing molecules acyl-homoserine lactones, γ-heptalactone and other lactones

The cell-to-cell communication of microorganisms is known to be via exertion of certain chemical compounds (signal molecules) and is referred to as quorum sensing (QS). QS phenomenon is widespread in microbial communities. Several Gram-positive and Gram-negative bacteria and fungi use lactone-containing compounds (e.g. acyl-homoserine lactones (AHLs), γ-heptalactone, butyrolactone-I) as signalling molecules. The ability of microorganisms to metabolise these compounds and the mechanisms they employ for this purpose are not clearly understood. Many studies, however, have focused on identifying AHL and other lactone-degrading enzymes produced by bacteria and fungi. Various strains that are able to utilise these signalling molecules as carbon and energy sources have also been isolated. In addition, several reports have provided evidence on the involvement of lactones and lactone-degrading enzymes in numerous biological functions. These studies, although focused on processes other than metabolism of lactone signalling molecules, still provide insights into further understanding of the mechanisms employed by various microorganisms to metabolise the QS compounds. In this review, we consider conceivable microbial strategies to metabolise AHL and other lactone-containing signalling molecules such as γ-heptalactones.     

Prodrugs for masking bitter taste of antibacterial drugs—a computational approach

DFT calculations for the acid-catalyzed hydrolysis of several maleamic acid amide derivatives revealed that the reaction rate-limiting step is determined on the nature of the amine leaving group. Further, it was established that when the amine leaving group was a secondary amine, acyclovir or cefuroxime moiety the tetrahedral intermediate formation was the rate-limiting step such as in the cases of acyclovir ProD 1- ProD 4 and cefuroxime ProD 1- ProD 4. In addition, the linear correlation between the calculated and experimental rates provided a credible basis for designing prodrugs for masking bitter taste of the corresponding parental drugs which have the potential to release the parent drug in a sustained release fashion. For example, based on the DFT calculated rates the predicted t_1/2 (a time needed for 50 % of the reactant to be hydrolyzed to products) for cefuroxime prodrugs, cefuroxime ProD 1- ProD 4, were 12 min, 18 min, 200 min and 123 min, respectively.

Is escaping deer browse just a matter of time in Picea sitchensis? A chemical and dendroecological approach

We combined chemical and dendroecological analyses to understand the mechanisms that are involved in escaping deer browse by young Sitka spruce (Picea sitchensis) exposed to browsing by Sitka black-tailed deer (Odocoileus hemionus sitchensis) on Haida Gwaii (British Columbia, Canada). We compared chemical defences (terpenes), nutritive compounds (nitrogen, non-structural constituents, cellulose, and lignin), as well as age and radial growth of two young spruce categories growing side by side: (1) stunted spruces that were heavily browsed, shorter than the browse line, and (2) escaped spruces that were taller than the browse line but still browsed below the browse line. Escaped and stunted spruces did not differ in terpene concentrations, or in nutritive compound contents, suggesting that they had similar palatability. Escaped spruces were older that stunted spruces. Stunted and escaped trees had similar slow growth when young, suggesting no difference in initial browsing between the two spruce categories. For escaped spruce, there was a dramatic increase in radial growth at about 12-13 years old, suggesting that the apex of the trees had escaped deer browse. Because the two categories of spruces were equally accessible and did not differ in chemical defences or in nutritive compounds, and because escaped spruces were older than stunted trees and had a similar slow radial growth in their first 12-13 years, we conclude that morphological differences between stunted and escaped browsed trees are due to age and that it is only a matter of time before spruce escape deer on Haida Gwaii.     

Biocatalytic ketone reduction—a powerful tool for the production of chiral alcohols—part II: whole-cell reductions

The tricarboxylic acid (TCA) cycle is an energy-producing pathway for aerobic organisms. However, it is widely accepted that the phylogenetic origin of the TCA cycle is the reductive TCA cycle, which is a non-Calvin-type carbon-dioxide-fixing pathway. Most of the enzymes responsible for the oxidative and reductive TCA cycles are common to the two pathways, the difference being the direction in which the reactions operate. Because the reductive TCA cycle operates in an energetically unfavorable direction, some specific mechanisms are required for the reductive TCA-cycle-utilizing organisms. Recently, the molecular mechanism for the “citrate cleavage reaction” and the “reductive carboxylating reaction from 2-oxoglutarate to isocitrate” in Hydrogenobacter thermophilus have been demonstrated. Both of these reactions comprise two distinct consecutive reactions, each catalyzed by two novel enzymes. Sequence analyses of the newly discovered enzymes revealed phylogenetic and functional relationships between other TCA-cycle-related enzymes. The occurrence of novel enzymes involved in the citrate-cleaving reaction seems to be limited to the family Aquificaceae. In contrast, the key enzyme in the reductive carboxylation of 2-oxoglutarate appears to be more widely distributed in extant organisms. The four newly discovered enzymes have a number of potential biotechnological applications.     

Recovery of Cognitive Performance from Sleep Debt: Do a Short Rest Pause and a Single Recovery Night Help?

We studied the recovery of multitask performance and sleepiness from acute partial sleep deprivation through rest pauses embedded in performance sessions and an 8 h recovery sleep opportunity the following night. Sixteen healthy men, aged 19–22 yrs, participated in normal sleep (two successive nights with 8 h sleep) and sleep debt (one 2 h night sleep followed by an 8 h sleep the following night) conditions. In both conditions, the participants performed four 70 min multitask sessions, with every other one containing a 10 min rest pause with light neck‐shoulder exercise. The multitask consisted of four simultaneously active subtasks, with the level of difficulty set in relation to each participant's ability. Physiological sleepiness was assessed with continuous electroencephalography/electro‐oculography recordings during the multitask sessions, and subjective sleepiness was self‐rated with the Karolinska Sleepiness Scale. Results showed that multitask performance and physiological and subjective sleepiness were impaired by the sleep debt (p>.001). The rest pause improved performance and subjective sleepiness for about 15 min, regardless of the amount of prior sleep (p>.01–.05). Following recovery sleep, all outcome measures showed marked improvement (p<.001), but they failed to reach the levels observed in the control condition (p<.001–.05). A correlation analysis showed the participants whose multitask performance deteriorated the most following the night of sleep loss tended to be the same persons whose performance was most impaired following the night of the recovery sleep (p<.001). Taken together, our results suggest that a short rest pause with light exercise is not an effective countermeasure in itself for sleep debt‐induced impairments when long‐term effects are sought. In addition, it seems that shift arrangements that lead to at least a moderate sleep debt should be followed by more than one recovery night to ensure full recovery. Persons whose cognitive performance is most affected by sleep debt are likely to require the most sleep to recover.     

LCA in architectural design—a parametric approach

Purpose

Life cycle assessment (LCA) has not been widely applied in the building design process because it is perceived to be complex and time-consuming. There is a high demand for simplified approaches that architects can use without detailed knowledge of LCA. This paper presents a parametric LCA approach, which allows architects to efficiently reduce the environmental impact of building designs.

Methods

First, the requirements for design-integrated LCA are analyzed. Then, assumptions to simplify the required data input are made and a parametric model is established. The model parametrizes all input, including building geometry, materials, and boundary conditions, and calculates the LCA in real time. The parametric approach possesses the advantage that input parameters can be adjusted easily and quickly. The architect has two options to improve the design: either through manually changing geometry, building materials, and building services, or through the use of an optimization solver. The parametric model was implemented in a parametric design software and applied using two cases: (a) the design of a new multi-residential building, and (b) retrofitting of a single-family house.

Results and discussion

We have successfully demonstrated the capability of the approach to find a solution with minimum environmental impact for both examples. In the first example, the parametric method is used to manually compare geometric design variants. The LCA is calculated based on assumptions for materials and building services. In the second example, evolutionary algorithms are employed to find the optimum combination of insulation material, heating system, and windows for retrofitting. We find that there is not one optimum insulation thickness, but many optima, depending on the individual boundary conditions and the chosen environmental indicator.

Conclusions

By incorporating a simplified LCA into the design process, the additional effort of performing LCA is minimized. The parametric approach allows the architect to focus on his main task of designing the building and finally makes LCA practically useful for design optimization. In the future, further performance analysis capabilities such as life cycle costing can also be integrated.