Synthetic DNA probes for the identification of sibling species in the Anopheles gambiae complex

The cloned DNA sequences pAna1, pAnq1 and pAnm14, which may be used to distinguish between at least five of the six species in the Anopheles gambiae Giles complex of Afrotropical malaria vector mosquitoes, have been sequenced. Each clone was found to possess a series of repeated sequences of 41, 30 and 163 bases respectively. In pAnq1 and pAnm14 the repeats were in direct tandem array, whilst in pAna1 the repetitive sequence was found to be interspersed by 15-17 variable bases. A comparison of a number of copies of each of the repetitive sequences within the three clones enabled the definition of the consensus sequence for each repetitive element. Based on these consensus sequences, three oligonucleotides of 21, 23 and 26 bases were derived from pAna1, pAnq1 and pAnm14 respectively. When tested as probes against DNA dot-blots and squash-blots of mosquito specimens, each oligonucleotide retained the same species-specificity as the original clones from which they were derived. The radioactively labelled oligonucleotides were able to detect as little as 5 ng of target genomic DNA in an overnight autoradiographic exposure. The synthetic DNA probes will form the basis of a simplified system for the field identification of Anopheles gambiae sibling species specimens.     

Investigating structure and temporal scale in social organizations using identified individuals

Studies of individually identified animals can produce substantialdata sets containing information on the structure and temporalscale of social organizations. However, methods of analyzingsuch data are not well established. Important features of asocial organization are revealed by plotting the rate of persistenceof the associations between pairs of individuals over a rangeof time lags (lagged association rate). The consistency of long-termrelationships can be characterized using the rate of associationof pairs of individuals between their first and last observedassociations (intermediate association rate). A hierarchicalseries of models featuring exponentially decaying lagged associationrates may be fitted to these data. This technique retrievedthe essential parameters of five simulated social organizationsand, when used on real data, portrayed the essential featuresof the patterns of temporal change in relationships betweenanimals. The method should be especially useful for analyzingfissionfusion societies containing 10–10, 000 individuallyidentifiable animals.     

Role of autolysins in the EDTA-induced lysis of Pseudomonas aeruginosa

Abstract A DNA fragment containing the genes secE, nusG and rplK of Staphylococcus carnosus was cloned using the Escherichia coli rplK gene as a probe. The S. carnosus secE homologue encodes a protein of 65 amino acid residues which is homologous to the carboxyl-terminal region of the E. coli SecE protein. The S. carnosus SecE polypeptide which, in contrast to the E. coli SecE protein, contains only one putative transmembrane segment, could fully replace the E. coli SecE protein in two different secE mutants. These results strongly suggest that the identified secE gene encodes an important component of the S. carnosus protein export apparatus.     

Application of genetic markers to the discrimination of European Black Poplar (Populus nigra) from American Black Poplar (P. deltoides) and Hybrid Poplars (P. x canadensis) in Switzerland

European Black Poplar (Populus nigra) is considered a rare and endangered tree species because of severe reduction of its natural riverine habitat and potential hybridisation with the related non-indigenous taxa P. deltoides and P. x canadensis. As it is difficult to distinguish these taxa solely based on their morphology, we applied a PCR-based assay with an easy-to-use and robust molecular marker set (cpDNA trnL-trnF/RsaI RFLP, nDNA win3 and nDNA POPX/MspI RFLP) in order to identify pure P. nigra. Different plant tissues could be used for fast and standardised DNA extraction. The application of the three marker types was tested on a number of different Populus taxa, and they were also used for the verification of pure P. nigra in a sample of 304 putative P. nigra individuals from Switzerland. Cross-checking of the DNA data with those using a traditional allozyme approach resulted in complete agreement. The availability of molecular identification methods is an important prerequisite for the conservation of European Black Poplar, because pure, non-introgressed plant material can then be used in restoration projects of European floodplains.     

An experimental design and a statistical analysis separating interference from exploitation competition

Previous experimental studies of competition among foragers rarely distinguished between exploitation and interference competition. In many systems this separation is experimentally impossible without interfering with the natural behavior of the animals. Consequently, these studies can only demonstrate the combined effect of interference and exploitation on the forager’s feeding rate, namely, it usually decreases in a decelerating rate as a function of density. We suggest here a simple experimental and statistical procedure that facilitates the separation of the effects of interference from those of exploitation. This procedure includes manipulation of both predator density and the foraging experiment duration. The statistical analysis is based on multiple linear regression. The working assumption is that exploitation can be neglected at the beginning of the foraging experiment because, initially, predators do not experience diminishing returns in prey capture rates. Using both the results of an individual-based simulation and a field experiment dataset of gerbils foraging for seeds in an artificial food patch located in the field, we demonstrate that our procedure can successfully detect and separate the effect of interference from the combined overall effect of competition (i.e., interference plus exploitation). Inon Scharf and Ido Filin contributed equally to this paper.     

Propagation of soft tissue artifacts to the center of rotation: A model for the correction of functional calibration techniques

This paper presents a mathematical model for the propagation of errors in body segment kinematics to the location of the center of rotation. Three functional calibration techniques, usually employed for the gleno-humeral joint, are studied: the methods based on the pivot of the instantaneous helical axis (PIHA) or the finite helical axis (PFHA), and the “symmetrical center of rotation estimation” (SCoRE). A procedure for correcting the effect of soft tissue artifacts is also proposed, based on the equations of those techniques and a model of the artifact, like the one that can be obtained by double calibration. An experiment with a mechanical analog was performed to validate the procedure and compare the performance of each technique. The raw error (between 57 and 68 mm) was reduced by a proportion of between 1:6 and less than 1:15, depending on the artifact model and the mathematical method. The best corrections were obtained by the SCoRE method. Some recommendations about the experimental setup for functional calibration techniques and the choice of a mathematical method are derived from theoretical considerations about the formulas and the results of the experiment.     

Activity- and reactivity-based proteomics: Recent technological advances and applications in drug discovery

Activity-based protein profiling (ABPP) is recognized as a powerful and versatile chemoproteomic technology in drug discovery. Central to ABPP is the use of activity-based probes to report the activity of specific enzymes or reactivity of amino acid types in complex biological systems. Over the last two decades, ABPP has facilitated the identification of new drug targets and discovery of lead compounds in human and infectious disease. Furthermore, as part of a sustained global effort to illuminate the druggable proteome, the repertoire of target classes addressable with activity-based probes has vastly expanded in recent years. Here, we provide an overview of ABPP and summarise the major technological advances with an emphasis on probe development.     

The Production of Pyrethrins by Plant Cell and Tissue Cultures of Chrysanthemum cinerariaefolium and Tagetes Species

Pyrethrins, the most economically important natural insecticide, comprise a group of six closely related monoterpene esters. The industrial production is based on their extraction from Chrysanthemum cinerariaefolium (Pyrethrum) capitula. The world production of natural pyrethrins still falls short of global market demand stimulating the research in in vitro production as an alternative to conventional cultivation methods. The different biotechnological alternatives such as callus cultures, shoot and root cultures, plant cell suspension cultures, and bioconversion of precursors by means of enzymatic synthesis or genetically engineered microorganisms, as well as the progress achieved in methods for the identification and quantitation of insecticidal compounds have been reviewed. Although technology for plant cell culture exists, industrial applications have, to date, been limited due to both the low economical viability and technological feasibility at large scale. Bioconversion of readily available precursors looks more attractive, but more research is needed before this technology is used for the industrial production of pyrethrins.     

Auswirkungen des Anbaus einer Wirts- und einer Nichtwirtspflanze unter wechselnden ökologischen Bedingungen auf die Populationsdynamik von Rhizoctonia solani Kühn und Fusarium solani f. pisi (Jones) Snyd. et Hans

An isometric virus was isolated from Helianthus annuus L. plants showing a yellow leaf spot mosaic on affected leaves. Infected plants were found in different ecological regions of Ukraine. A procedure of virus purification is described. The diametres of the virus particles were nonuniform and ranged from 50 to 120 nm. The sedimentation coefficient of the virus was 518–540 S and the floating density in the CsCl gradient was 1.22 g/cm³. The MW of proteins separated by electrophoresis amounted to 78±0.9, 58±0.8, 52±0.2, and 27±0.8 kDa, respectively. The virus was assigned to the tospoviruses for which sunflower is a new previously undescribed natural host plant.     

Evaluation of knee functional calibration with and without the effect of soft tissue artefact

Functional calibration methods were devised to improve repeatability and accuracy of the knee flexion–extension axis, which is used to define the medio-lateral axis of the femur coordinate system in gait analysis. Repeatability of functional calibration methods has been studied extensively in healthy individuals, but not accuracy in the absence of a benchmark knee axis. We captured bi-plane fluoroscopy data of the knee joint in 17 subjects with unilateral total knee arthroplasty during treadmill walking. The prosthesis provided a benchmark knee axis to evaluate the functional calibration methods. Stereo-photogrammetry data of thigh and shank marker clusters were captured simultaneously to investigate the effect of soft tissue artefact (STA). Three methods were tested, the Axis Transformation Technique (ATT) finds the best single fixed axis of rotation, 2DofKnee finds the axis that minimises knee varus–valgus and trajAJC finds the axis perpendicular to the trajectory, in the transverse plane of the femur, of a point located on the longitudinal axis of the tibia. Using fluoroscopy data, functional axes formed an angle of less than 2° in the transverse plane with the benchmark axis. True internal–external range of movement was correlated with decreased accuracy for ATT, while varus–valgus range of movement was correlated with decreased accuracy for 2DofKnee and trajAJC. STA had negative impact on accuracy and variability. Using stereo-photogrammetry data, the accuracy of 2DofKnee was 1.7°(SD: 5.1°), smaller than ATT 2.9°(SD: 5.1°) but not to trajAJC 1.7°(SD: 5.2°). Our results confirm that of previous studies, which utilised the femur condylar axis as reference.