Production of shotgun libraries using random amplification

In the following report, thermal cycling coupled with random 10-mers as primers was used to construct randomly amplified shotgun libraries (RASLs). This approach allowed shotgun libraries to be constructed from nanogram quantities of input DNA. RASLs contained inserts from throughout a target genome in an unbiased fashion and did not appear to contain chimeric sequences. This protocol should be useful for shotgun sequencing the genomes of unculturable organisms and rapidly producing shotgun libraries from cosmids, fosmids, yeast artificial chromosomes (YACs), and bacterial artificial chromosomes (BACs).     

Can Scat Analysis Describe the Feeding Habits of Big Cats? A Case Study with Jaguars (Panthera onca) in Southern Pantanal,Brazil

Large cats feeding habits have been studied through two main methods: scat analysis and the carcasses of prey killed by monitored animals. From November 2001 to April 2004, we studied jaguar predation patterns using GPS telemetry location clusters on a cattle ranch in southern Pantanal. During this period, we recorded 431 carcasses of animals preyed upon by monitored jaguars. Concurrently, we collected 125 jaguar scats opportunistically. We compared the frequencies of prey found through each method. We also compared the prey communities using Bray-Curtis similarity coefficient. These comparisons allowed us to evaluate the use of scat analysis as a means to describe jaguar feeding habits. Both approaches identified prey communities with high similarity (Bray-Curtis coefficient > 70). According to either method, jaguars consume three main prey: cattle (Bos taurus), caiman (Caiman yacare) and peccaries (Tayassu pecari and Pecari tajacu). The two methods did not differ in the frequency of the three main prey over dry and wet seasons or years sampled. Our results show that scat analysis is effective and capable of describing jaguar feeding habits.     

Geomagnetic effects on a circadian difference in reaction times in earthworms

Summary The effect of geomagnetic force on the light-withdrawal reflex of earthworms, Lumbricus terrestris, L., was investigated during the autumn of 1968. The reactions of worms kept in the earth's magnetic field were timed beginning at 12:00 and at 20:00, E.S.T. on each of 63 days; the same was done for worms maintained in a field whose intensity was essentially zero. The worms in the earth's field withdrew from light significantly faster at night then at midday. No significant difference between the mean reaction times at 12:00 and those of the evening were found for the animals which lived and were tested in the greatly reduced magnetic field. Therefore, geomagnetism does have some effect on the circadian difference in reaction rates in this species.

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Zusammenfassung Die Wirkung des erdmagnetisohen Feldes auf die Lichtreaktion von Lumbricus terrestris wurde untersucht (Herbst 1968). Als Test wurde die Reaktion auf einen Lichtreiz verwendet. Ein Teil der Würmer wurde im natürlichen erdmagnetisehen Feld, ein anderer Teil in einem auf Null kompensierten Feld gehalten. Die Reaktionszeiten auf den Lichtreiz wurden bei beiden Gruppen um 12.00 und um 20.00 Uhr gemessen. Die Reaktionszeiten im natürlichen erdmagnetischen Feld waren abends signifikant (p=0,005) kürzer (7,2 sec) als mittags (8,9 sec). Im Feld, das nahezu auf Null kompensiert war, waren die Reaktionszeiten abends und mittags gleich (8,8 bzw. 8,7 sec). Der Erdmagnetismus hat also einen Einfluß auf die circadiane Differenz der Reaktionszeiten bei Lumbricus.

     

Rational Design of Antibiotic Treatment Plans: A Treatment Strategy for Managing Evolution and Reversing Resistance

The development of reliable methods for restoring susceptibility after antibiotic resistance arises has proven elusive. A greater understanding of the relationship between antibiotic administration and the evolution of resistance is key to overcoming this challenge. Here we present a data-driven mathematical approach for developing antibiotic treatment plans that can reverse the evolution of antibiotic resistance determinants. We have generated adaptive landscapes for 16 genotypes of the TEM β-lactamase that vary from the wild type genotype “TEM-1” through all combinations of four amino acid substitutions. We determined the growth rate of each genotype when treated with each of 15 β-lactam antibiotics. By using growth rates as a measure of fitness, we computed the probability of each amino acid substitution in each β-lactam treatment using two different models named the Correlated Probability Model (CPM) and the Equal Probability Model (EPM). We then performed an exhaustive search through the 15 treatments for substitution paths leading from each of the 16 genotypes back to the wild type TEM-1. We identified optimized treatment paths that returned the highest probabilities of selecting for reversions of amino acid substitutions and returning TEM to the wild type state. For the CPM model, the optimized probabilities ranged between 0.6 and 1.0. For the EPM model, the optimized probabilities ranged between 0.38 and 1.0. For cyclical CPM treatment plans in which the starting and ending genotype was the wild type, the probabilities were between 0.62 and 0.7. Overall this study shows that there is promise for reversing the evolution of resistance through antibiotic treatment plans.     

An integrated approach to better define the concept and functions of Urban Biosphere Reserves

Abstract

The UNESCO-MAB Programme, and in particular the Biosphere Reserve Network, is described within the context of international strategies aimed at ecological sustainability in cities. An innovative acceptation of Biosphere Reserves for urban areas, based on the landscape ecology principle of the integration of natural, social, economic and cultural knowledge, is proposed. The interdisciplinary definition of structure and functions for Urban Biosphere Reserves envisages: (i) the inclusion of the whole metropolitan territory within the Reserve's boundaries; (ii) specific criteria for the delimitation of core areas and buffer zones in urban and periurban contexts; (iii) special focus on transition area requirements; (iv) the improvement in living conditions and a solution to the conflict between humans and the environment by enhancing and harmonizing the overall natural, economic, social and cultural qualities of cities; and (v) support for sustainable planning strategies on a local scale rather than the imposition of new conservation ties.     

An ELISA-based procedure for assaying proteins in digests of human leukocytes and cell lines, using specifically selected peptides and appropriate antibodies

Background  

We describe the application of an ELISA-based assay (the Peptidomatrix) that can be used to simultaneously identify and quantitate a number of proteins in biological samples. The biological sample (blood component, biopsy, culture or other) is first lysed to release all the proteins, without any additional separation. The denatured proteins in the sample are then digested in bulk with the desired proteolytic enzyme(s). The peptides in the digest are then assayed by appropriate antibodies, using a competition ELISA protocol.     

Role of Thiobacillus thioparus in the biodegradation of carbon disulfide in a biofilter packed with a recycled organic pelletized material

This study reports the biodegradation of carbon disulfide (CS₂) in air biofilters packed with a pelletized mixture of composted manure and sawdust. Experiments were carried out in two lab-scale (1.2 L) biofiltration units. Biofilter B was seeded with activated sludge enriched previously on CS₂-degrading biomass under batch conditions, while biofilter A was left as a negative inoculation control. This inoculum was characterized by an acidic pH and sulfate accumulation, and contained Achromobacter xylosoxidans as the main putative CS₂ biodegrading bacterium. Biofilter operation start-up was unsuccessfully attempted under xerophilic conditions and significant CS₂ elimination was only achieved in biofilter A upon the implementation of an intermittent irrigation regime. Sustained removal efficiencies of 90–100 % at an inlet load of up to 12 g CS₂ m^?3 h^?1 were reached. The CS₂ removal in this biofilter was linked to the presence of the chemolithoautotrophic bacterium Thiobacillus thioparus, known among the relatively small number of species with a reported capacity of growing on CS₂ as the sole energy source. DGGE molecular profiles confirmed that this microbe had become dominant in biofilter A while it was not detected in samples from biofilter B. Conventional biofilters packed with inexpensive organic materials are suited for the treatment of low-strength CS₂ polluted gases (IL <12 g CS₂ m^?3 h^?1), provided that the development of the adequate microorganisms is favored, either upon enrichment or by inoculation. The importance of applying culture-independent techniques for microbial community analysis as a diagnostic tool in the biofiltration of recalcitrant compounds has been highlighted.