Analysis of eigen's equations for selection of biological molecules with fluctuating mutation rates

1977 ◽  
Vol 39 (3) ◽  
pp. 311-316 ◽  
Author(s):  
B JONES
2005 ◽  
Vol 13 (01) ◽  
pp. 23-30
Author(s):  
JUKKA TIENARI

An attempt is made for pedagogical purposes to construct a model as simple as possible for analyzing biochemical control mechanisms that participate in the selection of molecules in biological systems. The analysis is simplified by an assumption that the system is in a steady state. The mechanisms result from the principle that in an open system the absolute rate constants determine the proportions of components. Reactions producing or consuming substances that influence the rates of other reactions in the system also influence the amounts of participating substances. Reciprocal effects result in internal control which selects some substances by increasing their relative amounts. Similar mechanisms also control processes other than chemical reactions. The selection contributes to the maintenance of the non-random distribution of molecules in the biosphere that allows certain biological molecules to be more abundant than other molecules consisting of the same elements and having comparable standard free energies of formation.


1994 ◽  
Vol 23 (487) ◽  
Author(s):  
Henrik Hautop Lund

We review different techniques for improving GA performance. By analysing the fitness landscape, a correlation measure between parents and offspring can be provided, and we can estimate effectively which genetic operator to use in the GA for a given fitness landscape. The response to selection equation further tells us how well the GA will do, and combining the two approaches gives us a powerful tool to automatically ensure the selection of the right parameter settings for a given problem. In dynamic environments the fitness landscape changes over time, and the evolved systems should be able to adapt to such changes. By introducing evolvable mutation rates and evolvable fitness formulae, we obtain such systems. The systems are shown to be able to adapt to both internal and external constraints and changes.


2000 ◽  
Vol 44 (10) ◽  
pp. 2740-2746 ◽  
Author(s):  
Kensuke Nagai ◽  
Todd A. Davies ◽  
Glenn A. Pankuch ◽  
Bonifacio E. Dewasse ◽  
Michael R. Jacobs ◽  
...  

ABSTRACT Ability of daily sequential subcultures in subinhibitory concentrations of clinafloxacin, ciprofloxacin, and trovafloxacin to select resistant mutants was studied in 10 pneumococci (ciprofloxacin MICs, 1 to 4 μg/ml, and clinafloxacin and trovafloxacin MICs, 0.06 to 0.125 μg/ml [n = 9]; ciprofloxacin, clinafloxacin, and trovafloxacin MICs, 32, 0.5, and 2 μg/ml, respectively [n = 1]). Subculturing was done 50 times, or until MICs increased fourfold or more. Mutants for which MICs were fourfold (or more) higher than those for parent strains were selected in five strains by clinafloxacin, in six strains by trovafloxacin, and nine strains by ciprofloxacin. Sequence analysis of type II topoisomerase showed that most mutants had mutations in ParC at Ser79 or Asp83 and in GyrA at Ser81, while a few mutants had mutations in ParE or GyrB. In the presence of reserpine, the MICs of ciprofloxacin and clinafloxacin for most mutants were lower (four to eight times lower), but for none of the mutants were trovafloxacin MICs lower, suggesting an efflux mechanism affecting the first two agents but not trovafloxacin. Single-step mutation rates were also determined for eight strains for which the MICs were as follows: 0.06 μg/ml (clinafloxacin), 0.06 to 0.125 μg/ml (trovafloxacin), and 1 μg/ml (ciprofloxacin). Single-step mutation rates with drugs at the MIC were 2.0×10−9 to <1.1×10−11, 5.0×10−4 to 3.6×10−9, and 4.8×10−4 to 6.7×10−9, respectively. For two strains with clinafloxacin MICs of 0.125 to 0.5 μg/ml trovafloxacin MICs of 0.125 to 2 μg/ml, ciprofloxacin MICs of 4 to 32 μg/ml mutation rates with drugs at the MIC were 1.1×10−8−9.6×10−8, 3.3×10−6−6.7×10−8, and 2.3×10−5−2.4×10−7, respectively. Clinafloxacin was bactericidal at four times the MIC after 24 h against three parent and nine mutant strains by time-kill study. This study showed that single and multistep clinafloxacin exposure selected for resistant mutants less frequently than similar exposures to other drugs studied.


2020 ◽  
Vol 74 (12) ◽  
pp. 939-945
Author(s):  
Cristina Müller ◽  
Martin Béhé ◽  
Susanne Geistlich ◽  
Nicholas P. van der Meulen ◽  
Roger Schibli

The concept of targeted radionuclide therapy (TRT) is the accurate and efficient delivery of radiation to disseminated cancer lesions while minimizing damage to healthy tissue and organs. Critical aspects for successful development of novel radiopharmaceuticals for TRT are: i) the identification and characterization of suitable targets expressed on cancer cells; ii) the selection of chemical or biological molecules which exhibit high affinity and selectivity for the cancer cell-associated target; iii) the selection of a radionuclide with decay properties that suit the properties of the targeting molecule and the clinical purpose. The Center for Radiopharmaceutical Sciences (CRS) at the Paul Scherrer Institute in Switzerland is privileged to be situated close to unique infrastructure for radionuclide production (high energy accelerators and a neutron source) and access to C/B-type laboratories including preclinical, nuclear imaging equipment and Swissmedic-certified laboratories for the preparation of drug samples for human use. These favorable circumstances allow production of non-standard radionuclides, exploring their biochemical and pharmacological features and effects for tumor therapy and diagnosis, while investigating and characterizing new targeting structures and optimizing these aspects for translational research on radiopharmaceuticals. In close collaboration with various clinical partners in Switzerland, the most promising candidates are translated to clinics for 'first-in-human' studies. This article gives an overview of the research activities at CRS in the field of TRT by the presentation of a few selected projects.


2002 ◽  
Vol 46 (3) ◽  
pp. 863-865 ◽  
Author(s):  
Antoine Giraud ◽  
Ivan Matic ◽  
Miroslav Radman ◽  
Michel Fons ◽  
François Taddei

ABSTRACT We show in a gnotobiotic mouse model that, in addition to direct selection of antibiotic-resistant bacteria, some antibiotic treatments also select for mutator alleles. Because of these mutator alleles' high mutation rates, the initial treatment failure increases the probability of failures in subsequent treatments with other drugs.


Author(s):  
K. Ramani Lata ◽  
P. Penczek ◽  
J. Frank

The present-day interactive manual selection of biological molecules from digitized micrographs for single particle averaging and reconstruction requires substantial effort and time. Thus a computer algorithm capable of recognition of structural content and selection of particles would be desirable.A few approaches have been proposed in the past. The method by Frank and Wagenknecht is based on the principle of correlation search. Van Heel's method is based on the computation of the local variance over a small area around each point of the image field. The method by Harauz and Fong-Lochovsky is based on edge-detection. The present work was focussed on the detection and classification of particlesby exploiting the standard statistical methods of discriminant analysis.The proposed technique is described in the block diagram (Fig.1). As illustrated in the figure, the program consists of three distinct segments devoted to, respectively, preparation of the data, training session and automatic selection based on a discriminant function set up in the training, hi the data preparation segment, the micrograph is (i) reduced four-fold in size, (ii) low-pass filtered and (iii) run through a peak search algorithm.


1995 ◽  
Vol 3 (3) ◽  
pp. 12-13
Author(s):  
K. Ramani Lata ◽  
P. Penczek ◽  
J. Frank

The present-day interactive manual selection of biological molecules from digitized micrographs for single particle averaging and reconstruction requires substantial effort and time. Thus a computer algorithm capable of recognition of structural content and selection of particles would be desirable. A few approaches have been proposed in the past. The method by Frank and Wagenknecht is based on the principle of correlation search. Van Heel's method is based on the computation of the local variance over a small area around each point of the image field. The method by Harauz and Fong- Lochovsky is based on edge-detection.


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