DEEMY – the concept of a characterization and determination system for ectomycorrhizae

 A considerable amount of data has been published on morphological and anatomical characteristics of ectomycorrhizae but these are dispersed in several, sometimes not easily available, journals. The few keys that exist are mostly based upon host tree genera. No comprehensive determination tools for non-experts are available. An information system for specific characters of ectomycorrhizae and an interactive key are now provided by DEEMY on CD-ROM. Accepted: 6 May 1997     

Estimation of ecological exergy using weighing parameters determined from DNA contents of organisms – a case study

We studied the changes of exergy and specific exergy with data of benthic macrofauna communities, periodically sampled along an estuarine gradient of eutrophication in the Mondego estuary (Western Portugal). Exergy estimates were calculated from organism biomass, based on weighing factors for the relative content of exergy per unit of biomass determined from DNA contents of organisms. Results were discussed in terms of both the macrofauna biomass production and the structural organisation of the system. Estimates for the exergy indices provided useful indications for the evaluation of environmental impact due to the eutrophication process. Different average values for the indices of exergy and specific exergy were estimated relatively to areas with different levels of eutrophication, in the spatial gradient of eutrophication. Higher exergy levels and lower exergy content per unit of biomass (specific exergy) were associated to populations more stabilized or areas less perturbed. Additionally, the index of specific exergy seemed capable of providing indications for the qualitative alterations in the communities (in temporal and spatial terms) that go in the direction of the observations made in this ecosystem.     

SuperLigands – a database of ligand structures derived from the Protein Data Bank

Background  

Currently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds. Information about these PDB ligands can be very helpful in the field of molecular modelling and prediction, particularly for the prediction of protein binding sites and function.     

Have Chinese cities achieved the win–win between environmental protection and economic development? From the perspective of environmental efficiency

The development of a regional or national economy is always accompanied by a variety of environmental problems. Using meta-frontier and data envelopment analysis (DEA), this paper investigates the environmental protection mechanisms and economic development of 211 cities in China from the perspective of environmental efficiency. The major conclusions are: (1) the overall environmental efficiency of Chinese cities is low when the most advanced production technology is selected as the reference. Only 10% of cities have achieved a win–win, defined as an effective balance between environmental protection and economic growth. It is possible to increase economy and reduce pollutant emissions at the same time for most of cities. (2) The environmental efficiencies and production technologies of cities in five different groups (based on a widely accepted business index) present significant differences. First-tier cities possess more advanced technology, higher environmental efficiency and, therefore, a higher overall win–win balance between economic development and environmental protection; while the fourth-tier and fifth-tier cities have a relatively large gap between development and protection. (3) To achieve a win–win balance between environmental protection and economic development, the local government of different cities should develop appropriate policies that maximize the use of technology and management practices that enhance both growth and protection.     

On the kinematics and efficiency of advective mixing during gastric digestion – A numerical analysis

The mixing performance of gastric contents during digestion is expected to have a major role on the rate and final bioavailability of nutrients within the body. The aim of this study was to characterize the ability of the human stomach to advect gastric contents with different rheological properties. The flow behavior of two Newtonian fluids (10⁻³ Pa s, 1 Pa s) and a pseudoplastic solution (K=0.223 Pa s^0.59) during gastric digestion were numerically characterized within a simplified 3D model of the stomach geometry and motility during the process (ANSYS-FLUENT). The advective performances of each of these gastric flows were determined by analyzing the spatial distribution and temporal history of their stretching abilities (Lagrangian analysis). Results illustrate the limited influence that large retropulsive and vortex structures have on the overall dynamics of gastric flows. Even within the distal region, more than 50% of the flow experienced velocity and shear values lower than 10% of their respective maximums. While chaotic, gastric advection was always relatively poor (with Lyapunov exponents an order of magnitude lower than those of a laminar stirred tank). Contrary to expectations, gastric rheology had only a minor role on the advective properties of the flow (particularly within the distal region). As viscosity increased above 1 St, the role of fluid viscosity became largely negligible. By characterizing the fluid dynamic and mixing conditions that develop during digestion, this work will inform the design of novel in vitro systems of enhanced biomechanical performance and facilitate a more accurate diagnosis of gastric digestion processes.     

Genetic and epidemiologic analysis of hereditary diseases of the nervous system in the cities of Volgograd and Volzhskiĭ

A genetic epidemiological study of hereditary diseases of the nervous system (HDNS) was conducted in the cities of Volgograd and Volzhsky for the first time. In total, 1 323 500 individuals were examined including the populations of Volgograd and Volzhsky (1 012 800 and 310 700 persons, respectively). The prevalence of neurological diseases with autosomal dominant (AD), autosomal recessive (AR), and X-linked recessive inheritance was estimated. These data were compared with the estimates previously obtained for different population of the Russian Federation. A decrease was found in general HDNS load in Volgograd and Volzhsky. The compared populations were shown to differ in a contribution of AD, AR, and X-linked recessive diseases into the HDNS load formation. The possible effect of population dynamics factors on the HDNS load structure is discussed.     

A method for the production of D-tagatose using a recombinant Pichia pastoris strain secreting ß-D-galactosidase from Arthrobacter chlorophenolicus and a recombinant L-arabinose isomerase from

ABSTRACT: BACKGROUND: D-Tagatose is a natural monosaccharide which can be used as a low-calorie sugar substitute in food, beverages and pharmaceutical products. It is also currently being tested as an anti-diabetic and obesity control drug. D-Tagatose is a rare sugar, but it can be manufactured by the chemical or enzymatic isomerization of D-galactose obtained by a beta-D-galactosidase-catalyzed hydrolysis of milk sugar lactose and the separation of D-glucose and D-galactose. L-Arabinose isomerases catalyze in vitro the conversion of D-galactose to D-tagatose and are the most promising enzymes for the large-scale production of D-tagatose. RESULTS: In this study, the araA gene from psychrotolerant Antarctic bacterium Arthrobacter sp. 22c was isolated, cloned and expressed in Escherichia coli. The active form of recombinant Arthrobacter sp. 22c L-arabinose isomerase consists of six subunits with a combined molecular weight of approximately 335 kDa. The maximum activity of this enzyme towards D-galactose was determined as occurring at 52[DEGREE SIGN]C; however, it exhibited over 60% of maximum activity at 30[DEGREE SIGN]C. The recombinant Arthrobacter sp. 22c L-arabinose isomerase was optimally active at a broad pH range of 5 to 9. This enzyme is not dependent on divalent metal ions, since it was only marginally activated by Mg2+, Mn2+ or Ca2+ and slightly inhibited by Co2+ or Ni2+. The bioconversion yield of D-galactose to D-tagatose by the purified L-arabinose isomerase reached 30% after 36 h at 50[DEGREE SIGN]C. In this study, a recombinant Pichia pastoris yeast strain secreting beta-D-galactosidase Arthrobacter chlorophenolicus was also constructed. During cultivation of this strain in a whey permeate, lactose was hydrolyzed and D-glucose was metabolized, whereas D-galactose was accumulated in the medium. Moreover, cultivation of the P. pastoris strain secreting beta-D-galactosidase in a whey permeate supplemented with Arthrobacter sp. 22c L-arabinose isomerase resulted in a 90% yield of lactose hydrolysis, the complete utilization of D-glucose and a 30% conversion of D-galactose to D-tagatose. CONCLUSIONS: The method developed for the simultaneous hydrolysis of lactose, utilization of D-glucose and isomerization of D-galactose using a P. pastoris strain secreting beta-D-galactosidase and recombinant L-arabinose isomerase seems to offer an interesting alternative for the production of D-tagatose from lactose-containing feedstock.     

Mapping a forest mosaic – A comparison of vegetation and bird distributions using geographic boundary analysis

Many areas of ecological inquiry require the ability to detect and characterize change in ecological variables across both space and time. The purpose of this study was to investigate ways in which geographic boundary analysis techniques could be used to characterize the pattern of change over space in plant distributions in a forested wetland mosaic. With vegetation maps created using spatially constrained clustering and difference boundary delineation, we examined similarities between the identified boundaries in plant distributions and the occurrence of six species of songbirds. We found that vegetation boundaries were significantly cohesive, suggesting one or more crisp vegetation transition zones exist in the study site. Smaller, less cohesive boundary areas also provided important information about patterns of treefall gaps and dense patches of understory within the study area. Boundaries for songbird abundance were not cohesive, and bird and vegetation difference boundaries did not show significant overlap. However, bird boundaries did overlap significantly with vegetation cluster boundaries. Vegetation clusters delineated using constrained clustering techniques have the potential to be very useful for stratifying bird abundance data collected in different sections of the study site, which could be used to improve the efficiency of monitoring efforts for rare bird species.     

Production of Metarhizium anisopliae spores using nutrient‐impregnated membranes and its economic analysis

Metarhizium anisopliae spores were produced on nutrient‐impregnated membranes (NIMs). The NIM system involved wetting the membrane with a spore and nutrient suspension, followed by harvesting the spores produced after incubation. The cost efficiency of spore production was assessed for a range of nutrient sources and membrane types. Skim milk powder (20 g l^‐1) was found to be the most cost‐effective nutrient source of the nine nutrients examined. Yield was 5.7 × 10⁶ spores/cm² after 28 days incubation on a paper membrane. Supplementation of the skim milk with either sucrose (2 g l^‐1) or dextrose + KNO₃ maximized yield. Superwipe, an absorbent fibrous material, was the most efficient of 16 membranes tested which ranged from fibreglass mesh to paper and cloth. A series of small pilot plants were built, but the cost efficiency of spore production decreased as the size of the membrane increased from 24 × 24 cm to 270 × 15 cm and up to 100 × 80 cm. Yield on the two smaller pilot plants was over 10⁷spores/cm², but the cost (nutrient and membrane only) of producing 10¹³ spores (standard dose required per hectare) was around $A37 and was found not to be competitive with spore production on grain.     

Characterization of a novel steviol-producing β-glucosidase from Penicillium decumbens and optimal production of the steviol

This study aimed to develop an economically viable enzyme for the optimal production of steviol (S) from stevioside (ST). Of 9 commercially available glycosidases tested, S-producing β-glucosidase (SPGase) was selected and purified 74-fold from Penicillium decumbens naringinase by a three-step column chromatography procedure. The 121-kDa protein was stable at pH 2.3–6.0 and at 40–60 °C. Hydrolysis of ST by SPGase produced rubusoside (R), steviolbioside (SteB), steviol mono-glucoside (SMG), and S, as determined by HPLC, HPLC-MS, and ¹H- and ¹³C-nuclear magnetic resonance. SPGase showed higher activity toward steviol mono-glucosyl ester, ST, R, and SMG than other β-linked glucobioses. The optimal conditions for S production (30 mM, 64 % yield) were 47 mM ST and 43 μl of SPGase at pH 4.0 and 55 °C. This is the first report detailing the production of S from ST hydrolysis by a novel β-glucosidase, which may be useful for the pharmaceutical and agricultural areas.     

Investigation of the binding mode of (−)-meptazinol and bis-meptazinol derivatives on acetylcholinesterase using a molecular docking method

Molecular docking has been performed to investigate the binding mode of (-)-meptazinol (MEP) with acetylcholinesterase (AChE) and to screen bis-meptazinol (bis-MEP) derivatives for preferable synthetic candidates virtually. A reliable and practical docking method for investigation of AChE ligands was established by the comparison of two widely used docking programs, FlexX and GOLD. In our hands, we had more luck using GOLD than FlexX in reproducing the experimental poses of known ligands (RMSD<1.5 A). GOLD fitness values of known ligands were also in good agreement with their activities. In the present GOLD docking protocol, (-)-MEP seemed to bind with the enzyme catalytic site in an open-gate conformation through strong hydrophobic interactions and a hydrogen bond. Virtual screening of a potential candidate compound library suggested that the most promising 15 bis-MEP derivatives on the list were mainly derived from (-)-MEP with conformations of (S,S) and (SR,RS) and with a 2- to 7-carbon linkage. Although there are still no biological results to confirm the predictive power of this method, the current study could provide an alternate tool for structural optimization of (-)-MEP as new AChE inhibitors. [Figure: see text].     

Multidisciplinary approach to diagnosis and management of osteosarcoma – a review of the St Vincent's Hospital experience

Background

Osteosarcoma is the most common primary malignant bone tumour in children and young adults. Despite advances in the diagnosis and management of osteosarcoma, there have been few recent studies describing the experiences of tertiary referral centres. This paper aims to describe and discuss the clinical features, pre-operative work-up, management and outcomes of these patients at St Vincent's Hospital (Melbourne, Australia).

Methods

Retrospective study of fifty-nine consecutive patients managed for osteosarcoma at St Vincent's Hospital between 1995 and 2005.

Results

Median age at diagnosis was 21 (range, 11–84) years. Gender distribution was similar, with thirty-one male and twenty-eight female patients.Twenty-five patients had osteosarcoma in the femur, eleven each were located in the humerus and tibia, six were identified in the pelvis, and one each in the clavicle, maxilla, fibula, sacrum, ulna and radius.Pre-operative tissue diagnosis of osteosarcoma was obtained through computed tomography-guided percutaneous biopsy in over ninety percent of patients.Following initial therapy, over fifty percent of patients remained relapse-free during the follow-up period, with twelve percent and twenty-seven percent of patients documented as having local and distant disease recurrence, respectively. Of patients with recurrent disease, sixty-two percent remained disease-free following subsequent surgical intervention (most commonly, pulmonary metastatectomy).

Conclusion

Patient outcomes can be optimised through a multidisciplinary approach in a tertiary referral centre. At St Vincent's Hospital, survival and relapse rates of patients managed for osteosarcoma compare favourably with the published literature.

     

Application of traditional ecological knowledge in the management and sustainability of fisheries in East Africa: a long-neglected strategy?

Management and sustainability of fisheries has been guided by theories and models derived from modern ecological science. Traditional ecological knowledge (TEK) has been ignored in all spheres of decision-making for management and sustainability of fisheries in East Africa. TEK guided African communities in the way they associated and interacted with the natural environment around them. Spiritual rituals, religious practices, social taboos and sacred animal totems guided the peoples on how and when to utilize the available natural resources. In the advent of modern scientific knowledge, the African traditional knowledge quickly faded away and is generally seen as irrelevant. Today the potential of TEK in the management and sustainability of fisheries in East Africa has not been realized and its status and future is unknown. TEK should be complementary to modern scientific knowledge in the management and sustainability of fisheries. This paper therefore focuses on the potential application of TEK in the management and sustainability of fisheries in East Africa and the issues that impede its application.     

Cultural,economic, and ecological factors influencing management of wild plants and mushrooms interchanged in Purépecha markets of Mexico

Background

Traditional markets outstandingly contribute to conservation of biocultural diversity, social relations, and cultural values. These markets reflect life strategies and forms people of a region interact with their biodiversity and territories, as well as traditional ecological knowledge and management practices. To understand the factors motivating plant and mushroom management, we analyzed the resources cultural and economic values, their role in people’s subsistence, and the relation of these values with the resources spatial and temporal availability. Our study based on the supposition that traditional markets are settings of interchange of resources with the highest importance for people’s life in a region. Also, that the cultural, economic, and ecological factors influence values of the resources, and the demand on them determine pressures on the most valuable resources which, when scarce, motivate management innovation, otherwise become extinct.

Methods

We documented cultural, economic, and ecological aspects, as well as management techniques of wild and weedy plants and mushrooms interchanged in three traditional markets of the Pátzcuaro Lake region, in central-western Mexico. For doing that, from February 2015 to March 2018, we conducted 175 visits to markets and 89 semi-structured interviews to producers, gatherers, and sellers of wild and weedy plants and mushrooms. Based on participant observation and interviews, we identified variables related to culture, economic, and ecological aspects, as well as management regimes of resources and management systems, which were documented and used as indicators for quantitative analyses. Through principal components analyses (PCA), we determined the indexes of cultural and economic importance (ICEI), management intensity (IMI), and ecological risk (IR) of the resources studied. For conducting that, we classified plant and mushroom species according to their cultural, economic, ecological, and technological indicators, respectively. The score of the first principal component was considered as the index for each group of variables, respectively. To identify relations between cultural importance and risk, we performed linear regression analyses between ICEI and IR indexes.

Results

We recorded 57 species of wild and weedy plants used as food, medicine, and ornamental, and 17 species of edible mushrooms. The variables with the highest weight in the ICEI are related to the need of a resource according to people, its recognizing, the number of communities and markets offering it in markets, its explicit preference expressed by people, the effort invested in obtaining it, and the form it is interchanged. Gathering is practiced in all mushrooms and wild and weedy plants from forests and agricultural areas; 11 species in addition receive 1 or more forms of management (enhancing, selective let standing, propagation through seeds or vegetative parts, transplantation, and/or protection). The management intensity and complexity are explained by variables related to management practices and systems. Plants receiving selective management have the higher management intensity. Silvicultural management (in situ management in forests) was recorded in all species of mushrooms, as well as in more than 80% of medicinal, ceremonial and ornamental plants, and in more than 50% of the edible plants. In agricultural systems, people manage more than 90% of the edible plants recorded to be under a management regime, 25% of the managed medicinal plants, and 30.7% of the managed ceremonial and ornamental plants. In homegardens, people manage 41.6% of the medicinal plants recorded and 26.6% of the edible plants, to have them available near home. Nearly 63% of the species interchanged in the markets studied are gathered in forests without any other management form. In this group are included all mushroom species, 61.5% of ceremonial/ornamental plants, 50% of medicinal, and 33.3% of edible plants. The linear regression between ICEI an IER is significantly negative for edible species with high management intensity R²?=?0.505 (p?=?0.0316), because of their management. But in medicinal and ornamental plants, the risk is high if the cultural importance increases, even when management practices like transplanting and propagation in homegardens are carried out.

Conclusions

Traditional markets are settings of interchange of products, knowledge, and experiences, where the ongoing factors and processes motivating management innovation can be identified and documented. This approach allows documenting processes occurring at regional level but would be benefited from deeper studies at local level in communities.

     

Conservation management in the face of climatic uncertainty – the roles of flexibility and robustness

Climate change is uncertain and has uncertain effects on the suitabilities of species habitats. Conservation strategies have to take this uncertainty into account. Two concepts for addressing uncertainty are, to make strategies adaptive and robust. Using a stylized ecological-economic model in which a decision maker can allocate a conservation budget between two time periods and two regions, I explore how the cost-effective allocation of the budget depends on ecological and economic parameters, including parameters describing the uncertain dynamics of climate change; and under which circumstances adaptive allocation strategies significantly outperform fixed strategies. Even if an adaptive strategy is politically feasible, its optimisation requires some knowledge about the dynamics of the climate change in the form of statistics like mean and variance of climate parameters. If these statistics are estimated wrong then even an adaptive strategy may fail. To explore the risk of such failure I subject the cost-effective strategies derived in the first part of the analysis to a robustness analysis that, among others, identifies those strategies that are relatively prone to wrong expectations of the climate change. Amongst others, the analysis reveals that flexibility pays only if there is uncertainty in the relative performances of different strategies; and depending on whether substitution between the benefits of the two time periods is allowed or not, the most robust strategy is to concentrate conservation expenses to the first period or to allocate the budget evenly amongst the two time periods, respectively.     

Performance of a filter loop reactor using Zymomonas mobilis and validation of the ethanol production model — II

A special loop recycle reactor with capillary crossflow filters was designed to enhance ethanol productivity. The new set-up did not comprise a classical reaction vessel with a stirrer but the working volume consisted only of the void volumes of the filters and the peripheral equipment, however, it behaved as a well mixed CSTR. A circulating pump provided for both mixing and recirculation of the culture fluid. Degassing was accomplished with a cyclone type device. Even if the circulating pump destroyed cells and automated backflushing of the filters could not prevent membrane fouling, maximum biomass concentration reached 98 g l⁻¹ at a dilution rate of 4 h⁻¹ and the maximum ethanol productivity achieved was 224 g l⁻¹ h⁻¹. Using the loop recycle reactor, the ethanol production model proposed in Part I of this study (Nipkow et al. (1986) J. Biotechnol. 3, 35–47) extended with a variable rate accounting for mechanical destruction of cells was verified. It was demonstrated that the predicted productivity of 350 g l⁻¹ h⁻¹ — exploiting the biological potential of Zymomonas mobilis — should be attainable if improved mechanical equipment in a filter recycle system is employed.     

SNA – a toolbox for the stoichiometric analysis of metabolic networks

Background  

Despite recent algorithmic and conceptual progress, the stoichiometric network analysis of large metabolic models remains a computationally challenging problem.