Recombination Research Papers - Academia.edu (original) (raw)

The coat protein (CP) gene of 75 South African Potato virus Y (PVY) isolates was amplified using reversetranscriptase polymerase chain reaction (RT-PCR). The resulting cDNA products were cloned and sequenced. These sequences were used to identify the strains to which the isolates belonged. Some, when compared to reference sequences, belonged to the PVY N and PVY O strains. A number of isolates were found to demonstrate significant homology to PVY N strains from China. A large number of South African isolates possessed CP sequences showing evidence of recombination between PVY N and PVY O strains, similar to those of PVY NTN isolates. Multiplex RT-PCR analysis allowed further differentiation of PVY O isolates and revealed that the majority were of the PVY N -Wilga strain. It was deduced that the most likely way in which these isolates reached South Africa was via the importation of infected material.

- by
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- Biological Sciences, Phylogeny, South Africa, Plant diseases

Spodoptera frugiperda (Lepidoptera: Noctuidae) is a major pest in maize crops in Colombia, and affects several regions in America. A granulovirus isolated from S. frugiperda (SfGV VG008) has potential as an enhancer of insecticidal activity of previously described nucleopolyhedrovirus from the same insect species (SfMNPV). The SfGV VG008 genome was sequenced and analyzed showing circular double stranded DNA of 140,913 bp encoding 146 putative ORFs that include 37 Baculoviridae core genes, 88 shared with betabaculoviruses, two shared only with betabaculoviruses from Noctuide insects, two shared with alphabaculoviruses, three copies of own genes (paralogs) and the other 14 corresponding to unique genes without representation in the other baculovirus species. Particularly, the genome encodes for important virulence factors such as 4 chitinases and 2 enhancins.

- by Gloria Barrera
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- Colombia, Horizontal Gene Transfer, DNA, Viruses

To evaluate the possibility of improving glucoamylase (

- by Anne Van Diepeningen
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- Engineering, Genetics, Technology, Production

The deletion events that have plagued attempts to maintain molecular clones with long palindromic DNA sequences in Escherichia coli have been shown to be less frequent in mcBCsbcB hosts [Collins et al., Gene 19 (1982) 139-1461. This study sought to determine if such hosts would permit the stable propagation of plasmid clones carrying the deletion-generating, 206 nucleotide (nt) long, imperfect palindrome derived from the 5' terminus of the genome of minute virus of mice (MVM), an autonomous parvovirus [Astell et al., Nucleic Acids Res. 11(1983) 999-10181. To this end these hybrid plasmids were used to transform several different mutant recBCsbcB hosts, followed by the isolation and restriction mapping of plasmid DNA from selected transformants. Characterization of plasmid DNA isolated from a recBCsbcBrecF host indicated deletion-resistant propagation of the intact species. Sequence analysis of unamplified and chloramphenicol (Cm)-amplified plasmid DNA obtained from these clones confirmed the integrity of the palindromic region of the viral DNA insert.

- by Robert Boissy
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- Genetics, Mutation, Escherichia coli, Genetic transformation

Monocotyledonous and dicotyledonous plant infecting mastreviruses threaten various agricultural systems throughout Africa, Eurasia and Australasia. In Australia three distinct mastrevirus species are known to infect dicotyledonous hosts such as chickpea, bean and tobacco. Amongst 34 new "dicot-infecting" mastrevirus full genome sequences obtained from these hosts we discovered one new species, four new strains, and various variants of previously described mastrevirus species. Besides providing additional support for the hypothesis that evolutionary processes operating during dicot-infecting mastrevirus evolution (such as patterns of pervasive homologous and non-homologous recombination, and strong purifying selection acting on all genes) have mostly mirrored those found in their monocot-infecting counterparts, we find that the Australian dicot-infecting viruses display patterns of phylogeographic clustering reminiscent of those displayed by monocot infecting mastrevirus species such as Panicum streak virus and Maize streak virus.

- by Simona Kraberger and +1
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- Molecular Evolution, Australia, Taxonomy, Evolution
- by Erika Hagelberg
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- Molecular Evolution, Kinetics, Mitochondria, Heterogeneity

Reporter genes have proved to be an excellent tool for studying disease progression. Recently, the green fluorescent protein (GFP) ability to quantitatively monitor gene expression has been demonstrated in different organisms. This report describes the use of Leishmania tarentolae (L. tarentolae) expression system (LEXSY) for high and stable levels of GFP production in different Leishmania species including L. tarentolae, L. major and L. infantum. The DNA expression cassette (pLEXSY-EGFP) was integrated into the chromosomal ssu locus of Leishmania strains through homologous recombination. Fluorescent microscopic image showed that GFP transgenes can be abundantly and stably expressed in promastigote and amastigote stages of parasites. Furthermore, flow cytometry analysis indicated a clear quantitative distinction between wild type and transgenic Leishmania strains at both promastigote and amastigote forms. Our data showed that the footpad lesions with GFP-transfected L. major are progressive over time by using fluorescence small-animal imaging system. Consequently, the utilization of stable GFP-transfected Leishmania species will be appropriate for in vitro and in vivo screening of anti-leishmanial drugs and vaccine development as well as understanding the biology of the host-parasite interactions at the cellular level.

- by farnaz zahedifard
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- Microbiology, Flow Cytometry, Macrophages, Leishmania

fragment length polymorphisms (RFLPs) within the spacer regions of the riboso-ma1 RNA (rRNA) gene complex have proven useful for species identification and the detection and analysis of interspecific hybrids in Schistosoma [1,. DNA sequences of the first internal transcribed spacer (ITSl) of ribosomal DNA (rDNA) from S. haematobium, S. intercalatum and S. mattheei revealed that RFLPs affecting this location were due to large (72280 mer), repeat elements arranged as one or more, tandemly-repeated copies starting close to the 5' end of ITS 1, These were followed by a region of non-repetitive Abbreoiations: ITS, internal transcribed spacer; ITSl, first internal transcribed spacer; rRNA, ribosomal RNA; rDNA, ribosomal DNA; PCR, polymerase chain reaction; RFLP, restriction fragment length polymorphism

- by David Rollinson
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- Polymorphism, Molecular Evolution, Biological Sciences, PCR

Meiosis halves diploid genomes to haploid and is essential for sexual reproduction in eukaryotes. Meiotic recombination ensures physical association of homologs and their subsequent accurate segregation and results in the redistribution of genetic variations among progeny. Most organisms have two classes of cross-overs (COs): interference-sensitive (type I) and -insensitive (type II) COs. DNA synthesis is essential for meiotic recombination, but whether DNA synthesis has a role in differentiating meiotic CO pathways is unknown. Here, we show that Arabidopsis POL2A, the homolog of the yeast DNA polymerase-ε (a leading-strand DNA polymerase), is required for plant fertility and meiosis. Mutations in POL2A cause reduced fertility and meiotic defects, including abnormal chromosome association, improper chromosome segregation, and fragmentation. Observation of prophase I cell distribution suggests that pol2a mutants likely delay progression of meiotic recombination. In addition, the residual COs in pol2a have reduced CO interference, and the double mutant of pol2a with mus81, which affects type II COs, displayed more severe defects than either single mutant, indicating that POL2A functions in the type I pathway. We hypothesize that sufficient leading-strand DNA elongation promotes formation of some type I COs. Given that meiotic recombination and DNA synthesis are conserved in divergent eukaryotes, this study and our previous study suggest a novel role for DNA synthesis in the differentiation of meiotic recombination pathways.

- by Ming-huang Hong and +1
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- Arabidopsis thaliana, Meiosis, Crossover Interference, Recombination

The term “genetically modified organisms (GMO)” is becoming a contentious issue as its advantages both Potential biomedical impacts and side impact on the economy are bolstered for food suppliers and users. GM animal feed is an emergent method that may affect livestock as well as the pharmaceutical industry. Whilst two pharmaceuticals have yet to join the industry, food materials derived from GE animals. In order to revisit the progress in identifying the main causes, the study was carried out. Affecting GM applications adoption and their possible risks and advantages, GM-derived food products have still not entered the market. However, the active conversation on GM crops and the current conversations on a basis with socio-economic concerns involving the incorporation with GM animals through food and pharmaceutical chains lay the protection and values of food and medicinal products derived from the cloned animals. The same key influences driving the introduction of genetically modified animal products in agriculture including pharmaceutical chains were its endorsement by the population and farmers, government decisions, human wellbeing, animal welfare, impact on environment and conservation. Throughout this paper we explored the financial and leadership benefits and drawbacks of genetically modified animal or pharmaceutical products, and their effect on their introduction.

For many astronomers, the progressive development of life has been seen as a natural occurrence given proper environmental conditions on a planet: even though such beings would not be identical to humans, there would be significant parallels. A striking contrast is seen in writings of nonphysical scientists, who have held more widely differing views. But within this diversity, reasons for differences become more apparent when we see how views about extraterrestrials can be related to the differential emphasis placed on modern evolutionary theory by scientists of various disciplines. One clue to understanding the differences between the biologists, paleontologists, and anthropologists who speculated on extraterrestrials is suggested by noting who wrote on the subject. Given the relatively small number of commentators on the topic, it seems more than coincidental that four of the major contributors to the evolutionary synthesis in the 1930s and 1940s are among them. Upon closer examination it is evident that the exobiological arguments of Theodosius Dobzhansky and George Gaylord Simpson and, less directly, of H. J. Muller and Ernst Mayr are all related to their earlier work in formulating synthetic evolution. By examining the variety of views held by nonphysical scientists, we can see that there were significant disagreements between them about evolution into the 1960s. By the mid-1980s, many believed that “higher” life, particularly intelligent life, probably occurs quite infrequently in the universe; nevertheless, some held out the possibility that convergence of intelligence could occur across worlds. Regardless of the final conclusions these scientists reached about the likely prevalence of extraterrestrial intelligence, the use of evolutionary arguments to support their positions became increasingly common.

- by Douglas Vakoch
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- Evolutionary Biology, Paleontology, Human Evolution, Philosophy of Biology
- by Christophe Merlin
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- Bacteria, Transposition, Recombination, Transposon

A thin compact layer of TiO 2 deposited on the conductive transparent substrate of a dye-sensitized solar cell photoanode, (blocking layer, BL) can enhance the performances of the entire device. In this paper, an optimized spin coating process using an alcoholic TiCl 4 solution was developed and correlated to the final properties of the layer. The physicochemical characteristics of the precursor solution and the spin coating parameters were optimised to obtain a uniform layer. XRD, FE-SEM, UV-Vis spectroscopy, AFM, cyclic voltammetry and electrochemical impedance spectroscopy were used to evaluate the influence of the number of deposition cycles on the TiO 2 layer. The results were compared with those obtained using a conventional dip coating technique, showing that the newly developed spin coating process produces blocking layers with superior properties. Finally, analyses of the photovoltaic performances of the complete cell confirmed that an optimized blocking layer can lead to an improvement of the solar conversion efficiency of about 84%.

- by Alessandra Sanson
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- Engineering, Dye Sensitized Solar Cells, Ceramics, CHEMICAL SCIENCES

Background: The present study is aimed at investigating the degradation of azo dye solution of AR 274 by wet air oxidation conditions. The central composite design matrix and response surface methodology were applied in designing the experiments to evaluate the interactive effects of the three most important operating variables. Thus, the interactive effects of oxygen pressure (3.0 to 5.0 MPa), temperature (100°C to 250°C), and time (30 to 90 min) on the degradation of dye were investigated. Results: The predicted values were found to be in good agreement with the experimental values (R 2 = 0.9981 and Adj-R 2 = 0.9965), which define the propriety of the model and the achievement of CCD in the optimization of WAO process. Conclusions: Intermediates of dye degradation were detected by GC-MS, the possible degradation mechanism for the WAO of dye was discussed, and the probable degradation pathway was deduced.

- by Shouliang yi
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- Engineering, Chemical Engineering, Artificial Intelligence, Chemistry

John Maynard Smith was one of the most original thinkers in evolutionary biology of the post neo-Darwinian synthesis age. He was able to define new problems with clarity and by doing so open up new research directions. He did this in a number of areas including game theory and evolution, the evolution of sex, animal behavior, evolutionary transitions and molecular evolution. Although he is best known for his research and his ideas, he was a great expositor and wrote many books, including introductory texts in the areas of evolution and genetics, ecology and mathematical modeling, as well as advanced expositions of research problems. 1 Annu. Rev. Genet. 2005.39:1-8. Downloaded from arjournals.annualreviews.org by STEWARD OBSERVATORY on 11/22/05. For personal use only. Annu. Rev. Genet. 2005.39:1-8. Downloaded from arjournals.annualreviews.org by STEWARD OBSERVATORY on 11/22/05. For personal use only.

- by Richard E Michod
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- Genetics, Game Theory, Biology, Fitness

ABSTRACT We explore the double-edged sword of recombination in generating breakthrough innovation: recombination of distant or diverse knowledge is needed because knowledge in a narrow domain might trigger myopia; but, recombination can be counterproductive when local search is needed to identify anomalies. We take into account how creativity shapes both the cognitive novelty of the idea and the subsequent realization of economic value. We develop a text-based measure of novel ideas in patents using topic modeling to identify those patents that originate new topics in a body of knowledge. We find that, counter to theories of recombination, patents that originate new topics are more likely to be associated with local search, while economic value is the product of broader recombinations as well as novelty.

- by Sarah Kaplan
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- Marketing, Creativity, Cognition, Strategic Management

Nineteen arabica coffee introgression lines (BC1F4) and two accessions derived from a spontaneous interspecific cross (i.e. Timor Hybrid) between Coffea arabica (2n=4x=44) and C. canephora (2n=2x=22) were analysed for the introgression of C. canephora genetic material. The Timor Hybrid-derived genotypes were evaluated by AFLP, using 42 different primer combinations, and compared to 23 accessions of C. arabica and 8 accessions

- by Francois Anthony
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- Genetics, Technology, Polymorphism, Biotechnology

The part of the gene encoding the mature Staphylococcus aureus lipase (SAL3) was cloned using PCR technique. The sequence corresponding to the mature lipase was subcloned into pET-14b or pOP-T expression vector and expressed in E. coli BL21 (DE3). The tagged (His 6 -SAL3) and untagged (r-SAL3) Staphylococcus aureus lipases were purified to homogeneity using Ni-NTA resin and classical chromatographic techniques, respectively. We performed a comparative study on the biochemical properties of two recombinant Staphylococcus aureus lipases and the wild type form. The major differences among these lipases are mainly reflected in their stability at high and low temperature, measured in aqueous media as well as in various organic solvents. Furthermore, our results indicate that the presence of the His-tag in the N-terminus of the SAL3 as well as the recombination process significantly affect the adsorption of these proteins onto CaCO 3 used as support and their capacity to synthesise diesel additive by esterification of butanol with oleic acid.

- by Selmene Ouertani
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- Comparative Study, Stability, Molecular, PCR

In this paper, we examine photoluminescence spectra (PL) of Cu 2 ZnSnSe 4 /CdS/ZnO solar cells, based on an absorber layer fabricated by selenization of sputtered Cu, Zn, Sn multilayers, via temperaturedependent and illumination power-dependent measurements. We observe anomalous emission behavior: the PL peak initially decreases with increasing temperature (red shift) in the temperature range 10-60 K, followed by a blue shift at higher temperature in the range 60-180 K. A recombination model is proposed that is able to explain both temperature dependent PL as well as power-dependent PL. The important aspect of the proposed model is taking into account the presence of strong potential fluctuations in the absorber layer, which can also contribute to the low V oc values generally observed in Cu 2 ZnSnSe 4 , based solar cells.

- by Jef POORTMANS
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- Engineering, Physical sciences, CHEMICAL SCIENCES, Recombination

Photoconductance measurements are frequently used to determine the minority-carrier effective lifetime (t eff ), from which the bulk lifetime (t b ) and surface recombination velocity (S) must be extracted. The exact solution to the continuity equation is used to determine the conditions of validity for three approximate equations relating t eff to t b and S: the steady-state approximation, the transient approximation, and the widely used simple equation (1=t eff ¼ 1=t b þ 2S=W ). We show that only the steady-state approximation matches the exact solution over the entire range of t eff ; when the lamp time constant is 2.3 ms. When t eff > 20 ms; all the equations give approximately the same result. However, when t eff o10 ms, only the steady-state equation is valid, while the error in the transient and simple equations may exceed 100%. r (J. Brody). 0927-0248/02/$ -see front matter r 2002 Elsevier Science B.V. All rights reserved. PII: S 0 9 2 7 -0 2 4 8 ( 0 2 ) 0 0 3 5 0 -1

- by Alan Ristow
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- Engineering, Physical sciences, Steady state, CHEMICAL SCIENCES

Nuclear integrations of mitochondrial DNA (Numts) are widespread in many taxa and if left undetected can confound phylogeny interpretation and bias estimates of mitochondrial DNA (mtDNA) diversity. This is particularly true in gorillas, where recent studies suggest multiple integrations of the Wrst hypervariable (HV1) domain of the mitochondrial control region. Problems can also arise through the inadvertent incorporation of artifacts produced by in vitro recombination between sequence types during polymerase chain reaction ampliWcation. This issue has attracted little attention yet could potentially exacerbate errors in databases already contaminated by Numts. Using a set of existing diagnostic tools, this study set out to systematically inventory Numts and PCR recombinants in a gorilla HV1 sequence database and address the degree to which existing public databases are contaminated. Phylogenetic analysis revealed three distinct gorilla HV1 Numt groups (I, II, and III) that could be readily diVerentiated from mtDNA sequences by Numt-speciWc diagnostic sites and sequence-based motifs. Several instances of genuine recombination were also identiWed by a suite of detection methods. The location of putative breakpoints was identiWed by eye and by likelihood analysis. Findings from this study reveal widespread nuclear contamination of gorilla HV1 GenBank databases and underline the importance of recognizing not only Numts but also PCR recombinant artifacts as potential sources of data contamination. Guidelines for the routine identiWcation of Numts and in vitro recombinants are presented and should prove useful in the detection of similar artifacts in other species mtDNA databases.

- by Michael W. Bruford
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- Evolutionary Biology, Genetics, Zoology, Phylogeography
- by Peter Gill
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- Biological Sciences, Simulation, Computer Simulation, Mathematical Sciences

U tilizing the concept of synthetic lethality has provided new opportunities for the development of targeted therapies, by allowing the targeting of loss of function genetic aberrations. In cancer cells with BRCA1 or BRCA2 loss of function, which harbor deficiency of DNA repair by homologous recombination, inhibition of PARP1 enzymatic activity leads to an accumulation of single strand breaks that are converted to double strand breaks but cannot be repaired by homologous recombination. Inhibition of PARP has therefore been advanced as a novel targeted therapy for cancers harboring BRCA1/2 mutations. Preclinical and preliminary clinical evidence, however, suggests a potentially broader scope for PARP inhibitors. Loss of function of various proteins involved in double strand break repair other than BRCA1/2 has been suggested to be synthetically lethal with PARP inhibition. Inactivation of these genes has been reported in a subset of human cancers and might therefore constitute predictive biomarkers for PARP inhibition. Here we discuss the evidence that the clinical use of PARP inhibition may be broader than targeting of cancers in BRCA1/2 germ-line mutation carriers.

- by Konstantin Dedes
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- Cell Cycle, Enzyme Inhibitors, DNA repair, Gene expression

Living cells suffer numerous and varied alterations of their genetic material. Of these, the DNA double-strand break (DSB) is both particularly threatening and common. Double-strand breaks arise from exposure to DNA damaging agents, but also from cell metabolism-in a fortuitous manner during DNA replication or repair of other kinds of lesions and in a programmed manner, for example during meiosis or V(D)J gene rearrangement. Cells possess several overlapping repair pathways to deal with these breaks, generally designated as genetic recombination. Genetic and biochemical studies have provided considerable amounts of data about the proteins involved in recombination processes and their functions within these processes. Although they have long played a key role in building understanding of genetics, relatively little is known at the molecular level of the genetic recombination processes in plants. The use of reverse genetic approaches and the public availability of sequence tagged mutants in Arabidopsis thaliana have led to increasingly rapid progress in this field over recent years. The rapid progress of studies of recombination in plants is obviously not limited to the DSB repair machinery as such and we ask readers to understand that in order to maintain the focus and to rest within a reasonable length, we present only limited discussion of the exciting advances in the of plant meiosis field, which require a full review in their own right [1,2]. We thus present here an update on recent advances in understanding of the DSB repair machinery of plants, focussing on Arabidopsis and making a particular effort to place these in the context of more general of understanding of these processes.

- by Jean-Yves Bleuyard
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- Genetics, Biology, DNA replication, DNA damage

Conjugation allows bacteria to acquire genes for antibiotic resistance, novel virulence attributes, and alternative metabolic pathways. Using a fluorescent protein fusion, SeqA-YFP, we have visualized this process in real time and in single cells of Escherichia coli. We found that the F pilus mediates DNA transfer at considerable cell-to-cell distances. Integration of transferred DNA by recombination occurred in up to 96% of recipients; in the remaining cells, the transferred DNA was fully degraded by the RecBCD helicase/nuclease. The acquired integrated DNA was tracked through successive replication rounds and was found to occasionally split and segregate with different chromosomes, leading to the inheritance of different gene clusters within the cell lineage. The incidence of DNA splitting corresponds to about one crossover per cell generation.

- by Marin Vulic
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- Science, Fluorescence Microscopy, Horizontal Gene Transfer, Multidisciplinary

The ability to repair DNA damage is crucial to all organisms. Much of what we learned about these processes was gained from studies carried out in Bacteria, especially in Escherichia coli, or Eucarya, particularly in the yeast Saccharomyces cerevisiae. The repair of DNA damage occurs by at least four different pathways: direct reversal of DNA damage, excision of damaged nucleotides (nucleotide excision repair or NER) or bases (base excision repair or BER), excision of misincorporated nucleotides (mismatch repair or MMR), and recombinational repair. Proteins involved in these processes have recently been identified in the third domain of life, the Archaea. Here we present a summary of DNA repair proteins in both the Bacteria and Eucarya, and discuss similarities and differences between these two domains and what is currently known in the Archaea. 1999).

- by Sampada Lotlikar
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- Microbiology, Medical Microbiology, Applied microbiology, DNA repair

Yellow rust, caused by Puccinia striiformis f.sp. tritici (PST), is an important disease that threatens wheat production in Pakistan. This study was designed to explore the virulence and simple sequence repeat (SSR) diversity of the Pakistani PST population and the ongoing selective pressures of widely grown wheat cultivars. Analyses of 49 isolates sampled from the North-West Frontier Province of Pakistan led to the identification of 12 distinct pathotypes. The virulence frequencies of v2 (virulent against Yr2), v6, v7, v9, vSU and v27 ranged from 63% to 100%. Virulences v3, v4, v17 and vSD were uncommon, whilst v5, v10, v15, v24, v32 and vSp were not detected. The pathotypes thus described were then classified into 27 distinct genotypes. Bayesian STRUCTURE analysis clustered these genotypes into five groups (in addition to one hybrid isolate) which represent three distinct lineages of the SSR-based phylogenetic tree. Of the studied isolates, 80%, represented by three predominant pathotypes (P1-P3), belonged to the same characteristic Pakistani lineage, whilst the other isolates were close to either a Mediterranean lineage or a Northern European lineage. Genetic recombination was detected within P2 isolates. Resistance genes postulated in 40 Pakistani wheat cultivars indicated the high frequency of Yr2, Yr6, Yr7, Yr9, Yr27 and YrSU. Only 11 cultivars were found to be resistant to P1-P3. Migration and varietal diversity factors might contribute to maintaining the currently high genetic diversity in Pakistani PST, and have serious regional implications for wheat improvement programmes.

- by syed Shah
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- Ecology, Virulence, Triticum Aestivum, Wheat Rust Resistance

Explaining the adaptive value of sex is one of the great outstanding problems in biology. The challenge comes from the difficulty in identifying the benefits provided by sex, which must outweigh the substantial costs of sex. Here, we consider the adaptive value of sex in viruses, bacteria and fungi, and particularly the information available on the adaptive role of sex in pathogenic microorganisms. Our general theme is that the varied aspects of sex in pathogens illustrate the varied issues surrounding the evolution of sex generally. These include, the benefits of sex (in the shortand long-term), as well as the costs of sex (both to the host and to the pathogen). For the benefits of sex (that is, its adaptive value), we consider three hypotheses: (i) sex provides for effective and efficient recombinational repair of DNA damages, (ii) sex provides DNA for food, and (iii) sex produces variation and reduces genetic associations among alleles under selection. Although the evolution of sex in microbial pathogens illustrates these general issues, our paper is not a general review of theories for the evolution of sex in all organisms. Rather, we focus on the adaptive value of sex in microbial pathogens and conclude that in terms of short-term benefits, the DNA repair hypothesis has the most support and is the most generally applicable hypothesis in this group. In particular, recombinational repair of DNA damages may substantially benefit pathogens when challenged by the oxidative defenses of the host. However, in the long-term, sex may help get rid of mutations, increase the rate of adaptation of the population, and, in pathogens, may infrequently create new infective strains. An additional general issue about sex illustrated by pathogens is that some of the most interesting consequences of sex are not necessarily the reasons for which sex evolved. For example, antibiotic resistance may be transferred by bacterial sex, but this transfer is probably not the reason sex evolved in bacteria. #

- by Richard E Michod and +1
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- Genetics, Fungi, DNA damage, DNA repair

Leptysma argentina is polymorphic for a centric fusion between pairs 3 and 6 of the basic complement, for interstitial (S1) and proximal (Sn) supernumerary segments in the smallest member of the complement, and for a B-chromosome. Fusion 3/6 is associated with several effects that would lead to a drastic reduction of recombination (Colombo 1987(Colombo , 1988. Nine populations from the Argentine provinces of Buenos Aires, Entre RIos and Santa Fe were analysed for total (T), proximal (P), interstitial (I) and distal (D) chiasma frequencies, and for the morphometrical characters tegmina length, total length, femur length, tibia length, thorax length and thorax height. There was a strong negative correlation of T, P and I frequencies, and a significant positive correlation of D, with fusion 3/6 frequency. Fusion carriers were significantly bigger than basic homozygotes, leading to highly significant correlations of all morphometrical variables with fusion frequency.

- by Pablo Colombo
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- Evolutionary Biology, Genetics, Polymorphism, Population Genetics

Biodegradation of chicken feathers waste directed by Bacillus subtilis DB 100 (p5.2) cells was successfully carried out in 14 L Bio Flo 110 laboratory scale fermentor. Seven liters of feathers-based modified basal medium II, feathers-based tap water and feathers-based distilled water separately in the fermentor were inoculated with activated bacterial cells. The fermentation processes were conducted at 37°C, 700 rpm agitation speed and 0.7 vvm air flow rate in the absence of kanamycin. Highest net levels of released feathers hydrolysis end products [soluble proteins and NH 2 -free amino groups] and keratinolytic alkaline protease activity in the fermentor were greatly comparable to those of shake flasks. Interestingly, the plasmid (p5.2) inside the recombinant B. subtilis cells growing in the fermentor displayed 100% stability till the fifth day of incubation and this presents a great challenge. Data certainly would encourage the transfer to larger scale fermentors to carry out feathers biodegradation process.

- by Taha Zaghloul
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- Agriculture, Multidisciplinary, Biodegradation, Air flow

A memetic algorithm for tackling multiobjective optimization problems is presented. The algorithm employs the proven local search strategy used in the Pareto archived evolution strategy (PAES) and combines it with the use of a population and recombination. Verification of the new M-PAES (memetic PAES) algorithm is carried out by testing it on a set of multiobjective 0/1 knapsack problems. On each problem instance, a comparison is made between the new memetic algorithm, the (1+ 1)-PAES local searcher, and the strength ...

- by David W. Corne
- •
- Computer Science, Operations Research, Evolutionary Computation, Cybernetics
- by Caue Ribeiro
- •
- Environmental Engineering, Chemical Engineering, Film, Heterogeneous Catalysis

Genetic colour polymorphisms are widespread across animals and often subjected to complex selection regimes. Traditionally, colour morphs were used as simple visual markers to measure allele frequency changes in nature, selection, population divergence and speciation. With advances in sequencing technology and analysis methods, several model systems are emerging where the molecular targets of selection are being described. Here, we discuss recent studies on the genetics of sexually selected colour polymorphisms, aiming at (i) reviewing the evidence of sexual selection on colour polymorphisms, (ii) highlighting the genetic architecture, molecular and developmental basis underlying phenotypic colour diversification and (iii) discuss how the maintenance of such polymorphisms might be facilitated or constrained by these. Studies of the genetic architecture of colour polymorphism point towards the importance of tight clustering of colour loci with other trait loci, such as in the case of...

- by Erik Svensson
- •
- Pigmentation, Mate Choice, Sexual Selection, Molecular Ecology

. Dye regeneration and charge recombination in dye-sensitized solar cells with ferrocene derivatives as redox mediators. Energy and Environmental Science, 5 (5), 7090-7099. Dye regeneration and charge recombination in dye-sensitized solar cells with ferrocene derivatives as redox mediators Abstract Ferrocene compounds are promising redox shuttles for application in dye-sensitized solar cells (DSCs). Chemical modification of the cyclopentadienyl rings is easily achievable affording almost unlimited variation of the redox properties. This allows fine-tuning of the driving force for dye-regeneration and optimization of the energy conversion efficiency of DSCs. Herein, six ferrocene derivatives have been chosen for investigation which cover the large redox potential range of 0.85 V, by virtue of simple alkylation and halogenation of the cyclopentadienyl ring, and enable improved matching of the energy levels of the sensitizer and the electrolyte. Although the focus of this work was to examine the effect of the redox potential on charge transfer processes, DSCs were fabricated which achieved high energy conversion efficiencies of over 5%. Charge transfer reactions were studied to reveal the dependence of the dye regeneration rate, recombination losses and recombination pathways on the reaction driving force. An increase in redox potential led to a higher efficiency due to higher open circuit potentials until a threshold is reached. At this threshold, the driving force for dye regeneration (18 kJ DE ¼ 0.19 V) becomes too small for efficient device operation, leading to rapid recombination between the oxidized dye and electrons in the TiO2 conduction band. As a result of this work guidelines can be formulated to aid the selection of redox couples for a particular sensitizer in order to maximize the utilization of incident solar energy.

- by Leone Spiccia
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- Regeneration, Multidisciplinary, Derivatives, Charge

Success in plant genetic transformation depends on the efficiency of explant regeneration and transgene integration. Whereas the former one depends on explant totipotency, the latter depends on the activity of host DNA repair and chromatin organisation factors. We analyzed whether factors that result in an increase in recombination frequency can also increase transformation efficiency. Here, we report that a threefold increase in the concentration of NH 4 NO 3 in the growth medium results in more than a threefold increase in the Agrobacterium tumefaciens-mediated transformation frequency of Nicotiana tabacum plants. Regeneration of calli without selection showed that the increase in transformation frequency was primarily due to the increase in transgene integration efficiency rather than in tissue regeneration efficiency. PCR analysis of insertion sites showed a decrease in the frequency of truncations of the T-DNA right border and an increase on the left border. We hypothesize that exposure to ammonium nitrate modifies the activity of host factors leading to higher frequency of transgene integrations and possibly to the shift in the mechanism of transgene integrations.

- by Igor Kovalchuk
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- Regeneration, Transformation, Plant Biology, Tobacco

The role of 4-tert butyl pyridine (4TBP) adsorption on TiO 2 surface band bending has been studied using photoelectron spectroscopy. Surface oxygen vacancies pin the Fermi level near the conduction band edge on rutile (110). 4TBP preferentially adsorbs in those vacancies and shift the Fermi level to lower binding energy in the band gap. This is done by transferring vacancy excess charge into the empty π * orbital in the pyridine ring. The anatase (100) surface contains much less oxygen vacancies although the surface is much rougher than the rutile (110). 4TBP adsorption does not have any significant effect on the surface band bending. Thus the positive role associated with 4TBP addition to solar cell electrolytes is suggested to protection against adsorption of other electrolyte components such as Li and I.

- by Marcelo Zuleta and +1
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- Adsorption, CHEMICAL SCIENCES, Electrolytes, Recombination
- by Joaquim Faria
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- Engineering, Transmission Electron Microscopy, Doping, Heterogeneous Catalysis

Human artificial chromosomes (HACs), which carry a fully functional centromere and are maintained as a single-copy episome, are not associated with random mutagenesis and offer greater control over expression of ectopic genes on the HAC. Recently, we generated a HAC with a conditional centromere, which includes the tetracycline operator (tet-O) sequence embedded in the alphoid DNA array. This conditional centromere can be inactivated, loss of the alphoid tet-O (tet-O HAC) by expression of tet-repressor fusion proteins. In this report, we describe adaptation of the tet-O HAC vector for gene delivery and gene expression in human cells. A loxP cassette was inserted into the tet-O HAC by homologous recombination in chicken DT40 cells following a microcell-mediated chromosome transfer (MMCT). The tet-O HAC with the loxP cassette was then transferred into Chinese hamster ovary cells, and EGFP transgene was efficiently and accurately incorporated into the tet-O HAC vector. The EGFP transgene was stably expressed in human cells after transfer via MMCT. Because the transgenes inserted on the tet-O HAC can be eliminated from cells by HAC loss due to centromere inactivation, this HAC vector system provides important novel features and has potential applications for gene expression studies and gene therapy.

- by V. Larionov
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- Genetics, Fluorescence, Gene expression, In Situ Hybridization

Perovskite-based solar cells have attracted much recent research interest with efficiency approaching 20%. While various combinations of material parameters and processing conditions are attempted for improved performance, there is still a lack of understanding in terms of the basic device physics and functional parameters that control the efficiency. Here we show that perovskite-based solar cells have two universal features: an ideality factor close to two and a space-charge-limited current regime. Through detailed numerical modeling, we identify the mechanisms that lead to these universal features. Our model predictions are supported by experimental results on solar cells fabricated at five different laboratories using different materials and processing conditions. Indeed, this work unravels the fundamental operation principle of perovskite-based solar cells, suggests ways to improve the eventual performance, and serves as a benchmark to which experimental results from various laboratories can be compared. SECTION: Energy Conversion and Storage; Energy and Charge Transport

- by Naresh K Kumawat
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- Photovoltaics, Solar Cell, Dye Sensitized Solar Cells, Perovskites
- by Retno Danarti
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- Dermatology, Adolescent, Growth, Child

Microsatellites, or tandem simple sequence repeats (SSR), are abundant across genomes and show high levels of polymorphism. SSR genetic and evolutionary mechanisms remain controversial. Here we attempt to summarize the available data related to SSR distribution in coding and noncoding regions of genomes and SSR functional importance. Numerous lines of evidence demonstrate that SSR genomic distribution is nonrandom. Random expansions or contractions appear to be selected against for at least part of SSR loci, presumably because of their effect on chromatin organization, regulation of gene activity, recombination, DNA replication, cell cycle, mismatch repair system, etc. This review also discusses the role of two putative mutational mechanisms, replication slippage and recombination, and their interaction in SSR variation.

- by Abraham Korol
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- Molecular Evolution, Molecular Ecology, Biological Sciences, Genetic variation

recombination comes largely from studies in Saccharomyces cerevisiae. A particularly interesting set of genes involved in meiotic and mitotic recombination, the RAD50-RAD57 series, was originally identified in screens for mutations... more

- by J. Schimenti
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- Genetics, Infertility, Biological Sciences, Meiosis
- by matthew tobin
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- Genetics, Structural Biology, Molecular Evolution, Biotechnology

Sequence data from a portion of the external transcribed spacer (ETS) and from the internal transcribed spacers (ITS1 and ITS2) of 18S-26S nuclear ribosomal DNA were used together with chloroplast DNA PCR-RFLP data to unravel patterns of allotetraploid speciation within the Western European Dactylorhiza polyploid complex. A maximum likelihood tree based on combined ETS and ITS sequences suggests that the Western European Dactylorhiza allotetraploids have evolved by hybridization between four main diploid lineages. Cloned sequences and the topology of the ITS plus ETS tree indicate that the allotetraploid species D. elata, D. brennensis, and D. sphagnicola have originated from the autotetraploid D. maculata together with the diploid D. incarnata, while D. majalis, D. traunsteineri, and D. angustata seem to have evolved by hybridization between the D. fuchsii s.str and D. incarnata lineages. Finally, the diploid D. saccifera lineage seems to have been involved together with the D. incarnata lineage in the formation of the allotetraploid D. praetermissa. The observed congruence between the chloroplast tree and the ITS/ETS tree suggests a directional evolution of the nrDNA after polyploidization in favor of the maternal genome. Considered together with morphological, biogeographical, and ecological evidence, the molecular analysis leads us to recognize four species within the investigated allotetraploid complex, namely D. majalis, D. praetermissa, D. elata, and D. sphagnicola.

- by Sang-Hun Oh
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- Evolutionary Biology, Genetics, Zoology, Hybridization

The exact nature of the sequence differences between the medically important family of gonococcal penicillinase-producing plasmids has been ascertained. The entire DNA sequence of the Asia-type plasmid, pJD4, demonstrated that it is 7426 bp and contains two direct repeats (DR30) that are implicated in the formation of deletion variant plasmids, such as the Africa-type plasmid. We have identified putative DnaA and IHF binding sites, various open reading frames that are thought to specify functional proteins, and some important DNA sequences involved with conjugative transfer of gonococcal ␤-lactamase plasmids. The deletion in the Africa-type plasmid is 1827 bp and one of the DR30 repeats is also missing. The deletion in the Rio-type plasmid and several Toronto-type plasmids was determined to be 2273 bp and the sequence spanning the deletion was identical irrespective of geographic or temporal origin. The Nîmes-type plasmid is an Africa-type plasmid and also contains an IS5 insertion sequence. Since IS5 has not been identified in gonococcal isolates, we suggest that this sequence may have been inserted after the original gonococcal plasmid was transformed into Escherichia coli. The New Zealand plasmid is an Asia-type plasmid that contains an endogenous tandem duplication of 1883 bp and the direct DR2 is implicated in this duplication. The nature of the defined truncation of Tn2 present in the various plasmids is also discussed.

- by abu tholib
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- Genetics, Sequence Analysis, Escherichia coli, New Zealand

For the first time, the charge state distribution inside the MEsskammer für FlugzeitInStrumente und Time-Of-Flight (MEFISTO) electron cyclotron resonance (ECR) plasma and in the extracted ion beam was successfully simulated. A self-consistent ECR plasma ionization model (Hohl M 2002 MEFISTO II: Design, setup, characterization and operation of an improved calibration facility for solar plasma instrumentation PhD Thesis University of Bern) was further developed, recomputing the ion confinement time for every ion species and in every time step based on the actual plasma potential rather than using a prescribed constant ion confinement time. The simulation starts with a user defined set of initial conditions and develops the problem in time space by an adaptive step length fourth order Runge-Kutta (RK4) solver, considering particle densities based on ionization rates, recombination rates, ion confinement times and plasma potential. At the simulation end, a steady-state ion charge state distribution is reached, which is in excellent agreement with the measured ion beam charge state distribution of the MEFISTO ion source for Ar 1+ to Ar 5+ and in good agreement for Ar 6+ .

- by Markus Hohl and +1
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- Design, Instrumentation, Conception, Calibration

Telomeres play critical roles in protecting genome stability, and their dysfunction contributes to cancer and age-related degenerative diseases. The precise architecture of telomeres, including their single-stranded 3′ overhangs, bound proteins, and ability to form unusual secondary structures such as t-loops, is central to their function and thus requires careful processing by diverse factors. Furthermore, telomeres provide unique challenges to the DNA replication and recombination machinery, and are particularly suited for extension by the telomerase reverse transcriptase. Helicases use the energy from NTP hydrolysis to track along DNA and disrupt base pairing. Here we review current findings concerning how helicases modulate several aspects of telomere form and function.

- by Alejandro Chavez
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- Aging, DNA replication, Telomerase, Biological Sciences

Reactive Ion Etching (RIE) is used in the fabrication of some types of solar cells to achieve a highly directional etch. However, cells fabricated using RIE have lower than expected efficiency, possibly caused by increased carrier recombination. Characterisation of the carrier lifetime in solar cells was conducted using the quasi steady state photoconductance (QSSPC) measurement technique. Substantial effective lifetime degradation was observed for silicon samples processed by RIE. Lifetime degradation for samples where RIE etches into silicon is found to be permanent, while for samples where RIE etches only on dielectric layers of SiO 2 grown on the wafer, the lifetime degradation is found to be reversible. The reversible degradation in RIE-processed samples is associated with radiation damage. By reducing the proportion of a wafer exposed to RIE, the degradation of the effective lifetime of RIE-etched silicon samples can be minimised, and the performance of silicon solar cells can be improved significantly.

- by Ngwe Zin
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- Crystalline silicon solar cells, Reactive ion etching, Silicon Solar Cell, Recombination

Photocatalytic activities were found to be enhanced when noble metals were deposited on the semiconductors because the metal nanoparticles store electrons within them and in turn are recognized to act as a sink for photoinduced charge carriers, promoting interfacial charge transfer processes. This motivates us to modify the bare ZnO powder by doping with nano sized silver to yield metal-semiconductor nanocomposites by simple material syntheses route to suppress detrimental recombination of the photogenerated charge carriers. The materials were characterized by different analytical techniques and it is potentially utilized for the photocatalytic degradation of an azo dye (Acid Red 88; AR88) in the visible region (l . 400 nm). A possible mechanism for the photocatalytic degradation of AR88 by Ag-ZnO in the absence and presence of other oxidizing agents (peroxomonosulfate (PMS), peroxodisulfate (PDS) & hydrogen peroxide (H 2 O 2 )) has been proposed. The extent of mineralization of the target pollutant was also evaluated using Total Organic Carbon (TOC) analysis.

- by Sambandam Anandan
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- Water, Catalysis, Photochemistry, Carbon