A Modified Valley Restrained Monte Carlo Method to Efficiently Search the Low Energy Structures of Peptides

Abstract

A new Monte Carlo sampling scheme, namely the Modified Valley Restrained Monte Carlo procedure, is used to obtain the global energy minimum conformations for polypeptides, such as Met-enkephalin and Melittin. For each peptide, we found close agreement with previous results from both theoretical and experimental studies. The simple idea for controlling the step size according to the Valley Function, provides useful suggestions in searching the global energy minimum structures, and furthermore helps solve the multiple minima problem.     

Legume diversity patterns in west central Africa: influence of species biology on distribution models

Objectives

Species Distribution Models (SDMs) are used to produce predictions of potential Leguminosae diversity in West Central Africa. Those predictions are evaluated subsequently using expert opinion. The established methodology of combining all SDMs is refined to assess species diversity within five defined vegetation types. Potential species diversity is thus predicted for each vegetation type respectively. The primary aim of the new methodology is to define, in more detail, areas of species richness for conservation planning.

Methodology

Using Maxent, SDMs based on a suite of 14 environmental predictors were generated for 185 West Central African Leguminosae species, each categorised according to one of five vegetation types: Afromontane, coastal, non-flooded forest, open formations, or riverine forest. The relative contribution of each environmental variable was compared between different vegetation types using a nonparametric Kruskal-Wallis analysis followed by a post-hoc Kruskal-Wallis Paired Comparison contrast. Legume species diversity patterns were explored initially using the typical method of stacking all SDMs. Subsequently, five different ensemble models were generated by partitioning SDMs according to vegetation category. Ecological modelers worked with legume specialists to improve data integrity and integrate expert opinion in the interpretation of individual species models and potential species richness predictions for different vegetation types.

Results/Conclusions

Of the 14 environmental predictors used, five showed no difference in their relative contribution to the different vegetation models. Of the nine discriminating variables, the majority were related to temperature variation. The set of variables that played a major role in the Afromontane species diversity model differed significantly from the sets of variables of greatest relative important in other vegetation categories. The traditional approach of stacking all SDMs indicated overall centers of diversity in the region but the maps indicating potential species richness by vegetation type offered more detailed information on which conservation efforts can be focused.     

The Relation Between Growth of Gastrodia elata Protocorms and Fungi

Armillaria mellea penetrated protocorms from seed germination and vegetative multiplication corms of Gastrodia elata with rhizomorph. At beginning, they formed a hypha passing road and a hypha flow in the inner cells of cortex, and then, they both penetrated inside of large cells and penetrated outside of cortical cells. Gastrodia elata seeds depended on digesting Mycenct osmundicola etc gain nutrition to germinate at the stage of sexual reproduction, but its corms of vegetative multiplication must be penetrated by Armillaria mellea obtaining nutrition for normal growth at the stage of vegetative propagation.     

Spermatozoa production in male <Emphasis Type="Italic">Varroa destructor</Emphasis> and its impact on reproduction in worker brood of <Emphasis Type="Italic">Apis mellifera</Emphasis>

Reproduction in Varroa destructor exclusively takes place within the sealed honey bee brood cell and is, therefore, limited by the duration of the postcapping period. Oogenesis, ontogenetic development and mating must be optimized to ensure the production of as many mated daughter mites as possible. One adult male mite has to mate with up to five sister mites and transfer 30–40 spermatozoa to each female. We analyzed the production and transfer of male spermatozoa during a reproductive cycle by counting all spermatozoa in the genital tracts of the male and daughter mites in 80 worker brood cells at defined times after cell capping. We could show that spermatozoa production in male mites is an ongoing process throughout their adult lifetime starting after the adult molt. The spermatozoa are transferred to the females in an early non-capacitated stage and require further maturation within the female’s genital tract. Our study points out that a Varroa male has at any time in the brood cell enough spermatozoa to inseminate all daughter mites but does not waste energy in producing a big surplus. In total one male produced, on average, 125 spermatozoa during a reproductive cycle in worker brood which is sufficient for successful matings with at least three daughter mites. Spermiogenesis in Varroa males represents therefore a further adaptation to the limited time available for reproduction.     

Life cycle assessment of chitosan production in India and Europe

Purpose

The aim of this article is to present the first life cycle assessment of chitosan production based on data from two real producers located in India and Europe. The goal of the life cycle assessment (LCA) was to understand the main hot spots in the two supply chains, which are substantially different in terms of raw materials and production locations.

Methods

The LCA is based on consequential modelling principles, whereby allocation is avoided by means of substitution, and market mixes include only flexible, i.e. non-constrained suppliers. The product system is cradle to gate and includes the production of raw materials, namely waste shells from snow crab and shrimp in Canada and India, respectively, the processing of these in China and India and the manufacture of chitosan in Europe and India. Primary data for chitin and chitosan production were obtained from the actual producers, whereas raw material acquisition as well as waste management activities were based on literature sources. The effects of indirect land use change (iLUC) were also included. Impact assessment was carried out at midpoint level by means of the recommended methods in the International Life Cycle Data (ILCD) handbook.

Results and discussion

In the Indian supply chain, the production of chemicals (HCl and NaOH) appears as an important hot spot. The use of shrimp shells as raw material affects the market for animal feed, resulting in a credit in many impact indicators, especially in water use. The use of protein waste as fertilizer is also an important source of greenhouse-gas and ammonia emissions. In the European supply chain, energy use is the key driver for environmental impacts, namely heat production based on coal in China and electricity production in China and Europe. The use of crab shells as raw material avoids the composting process they would be otherwise subject to, leading to a saving in composting emissions, especially ammonia. In the Indian supply chain, the effect of iLUC is relevant, whereas in the European one, it is negligible.

Conclusions

Even though we assessed two products from the same family, the results show that they have very different environmental profiles, reflecting their substantially different supply chains in terms of raw material (shrimp shells vs. crab shells), production locations (locally produced vs. a global supply chain involving three continents) and the different applications (general-purpose chitosan vs. chitosan for the medical sector).

     

Antibody binding capacity of different peptide chains isolated from digested and purified horse diphtheria antitoxin

In commercial digested and purified horse diphtheria antitoxin, which is formed largely of the gamma globulin fragment with the sedimentation coefficient 5.3 S, the reactive disulphide bonds were destroyed by S-sulphonation. Gel filtration on Sephadex G-100 in 0.05 M formic acid with 6 M urea showed that the molecule of the S-sulphonated preparation dissociated into chains similar in character to the peptide chains of native horse antitoxins. Antibody activity was still partly maintained even after treatment with 6 M urea. On mixing the two types of chains isolated by gel filtration, antibody activity was recovered, the amount of antibody protein determined in the mixed fractions being greater than the sum of the amounts in the separate fractions. The neutralizing activity of the mixed fractions tested against toxinin vivo was also greater than the sum of the activity of the separate fractions.     

QTL detection on porcine chromosome 12 for fatty-acid composition and association analyses of the fatty acid synthase, gastric inhibitory polypeptide and acetyl-coenzyme A carboxylase alpha genes

Refinement of previous QTL on porcine chromosome 12 for fatty-acid composition and a candidate gene association analysis were conducted using an Iberian × Landrace cross. The concentrations of ten fatty acids were assayed in backfat tissue from which four metabolic ratios were calculated for 403 F₂ animals. Linkage analysis identified two significant QTL. The first QTL was associated with the average chain length ratio and the percentages of myristic, palmitic and gadoleic acids. The second QTL was associated with percentages of palmitoleic, stearic and vaccenic acids. Based upon its position on SSC12, fatty acid synthase was tested as a candidate gene for the first QTL and no significant effects were found. Similarly, gastric inhibitory polypeptide ( GIP ) and acetyl-coenzyme A carboxylase alpha ( ACACA ) were tested as candidate genes for the second QTL using three SNPs in GIP and 15 synonymous SNPs in ACACA cDNA sequences. Two missense SNPs in GIP showed significant effects with palmitoleic and stearic fatty-acid concentration. Highly significant associations were found for two SNPs in ACACA with stearic, palmitoleic and vaccenic fatty-acid concentrations. These associations could be due to linkage disequilibrium with the causal mutations.