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Organoboranes carrying electron-withdrawing substituents are commonly used as Lewis acidic catalysts or cocatalysts in a variety of organic processes. These Lewis acids also became popular through their application in `frustrated Lewis pairs', i.e. combinations of Lewis acids and bases that are unable to fully neutralize each other due to steric or electronic effects. We have determined the crystal and molecular structures of four heteroleptic arylboranes carrying 2-(trifluoromethyl)phenyl, 2,6-bis(trifluoromethyl)phenyl, 3,5-bis(trifluoromethyl)phenyl or mesityl substituents. [3,5-Bis(trifluoromethyl)phenyl]bis[2-(trifluoromethyl)phenyl]borane, C22H11BF12, (I), crystallizes with two molecules in the asymmetric unit which show very similar geometric parameters. In one of the two molecules, both trifluoromethyl groups of the 3,5-bis(trifluoromethyl)phenyl substituent are disordered over two positions. In [3,5-bis(trifluoromethyl)phenyl]bis[2,6-bis(trifluoromethyl)phenyl]borane, C24H9BF18, (II), only one of the two meta-trifluoromethyl groups is disordered. In [2,6-bis(trifluoromethyl)phenyl]bis[3,5-bis(trifluoromethyl)phenyl]borane, C24H9BF18, (III), both meta-trifluoromethyl groups of only one 3,5-bis(trifluoromethyl)phenyl ring are disordered. [3,5-Bis(trifluoromethyl)phenyl]dimesitylborane, C26H25BF6, (IV), carries only one meta-trifluoromethyl-substituted phenyl ring, with one of the two trifluoromethyl groups disordered over two positions. In addition to compounds (I)-(IV), the structure of bis[2,6-bis(trifluoromethyl)phenyl]fluoroborane, C16H6BF13, (V), is presented. None of the ortho-trifluoromethyl groups is disordered in any of the five compounds. In all the structures, the boron centre is in a trigonal planar coordination. Nevertheless, the bond angles around this atom vary according to the bulkiness and mutual repulsion of the substituents of the phenyl rings. Also, the ortho-trifluoromethyl-substituted phenyl rings usually show longer B-C bonds and tend to be tilted out of the BC3 plane by a higher degree than the phenyl rings carrying ortho H atoms. A comparison with related structures corroborates the conclusions regarding the geometric parameters of the boron centre drawn from the five structures in this paper. On the other hand, CF3 groups in meta positions do not seem to have a marked effect on the geometry involving the boron centre. Furthermore, it has been observed for the structures reported here and those reported previously that for CF3 groups in ortho positions of the aromatic ring, disorder of the F atoms is less probable than for CF3 groups in meta or para positions of the ring. [ABSTRACT FROM AUTHOR]

Stable mammalian production cell lines in suspension culture enable the reproducible expression of target genes in any desired scale using bioreactor technology. Targeted integration methods have been developed to cut down timelines for the generation of stable producer cell lines. The powerful Flp recombinase mediated cassette exchange (RMCE) technique allows fast integration of target genes in preselected and optimized high expression loci in so called master cell lines. Up to now, these cells only enable the expression from a single locus. Here, we describe the set-up required for the generation of multiple tagged master cell lines on the example of a binary RMCE expression system in the glycosylation mutant CHO Lec3.2.8.1 cell line. We show how this technology is used for the expression of proteins from multiple loci by generating a binary RMCE expression system. The tools and strategy for the construction of binary master cell lines with different combinations of expression level are described in detail. The binary production cell lines show independent expression of the individual exchange loci of the producer cell lines. The expression level for the model protein tdTomato is the cumulative expression for the chosen combination of the expression loci of the master cell line. This binary RMCE expression system can be further developed to a multi RMCE expression system for co-expression of protein complex subunits with predetermined expression ratio of each individual exchange locus. [ABSTRACT FROM AUTHOR]

Background: Clostridium acetobutylicum is a gram-positive, spore-forming, anaerobic bacterium capable of converting various sugars and polysaccharides into solvents (acetone, butanol, and ethanol). The sequencing of its genome has prompted new approaches to genetic analysis, functional genomics, and metabolic engineering to develop industrial strains for the production of biofuels and bulk chemicals. Results: The method used in this paper to knock-out or knock-in genes in C. acetobutylicum combines the use of an antibiotic-resistance gene for the deletion or replacement of the target gene, the subsequent elimination of the antibiotic-resistance gene with the flippase recombinase system from Saccharomyces cerevisiae, and a C. acetobutylicum strain that lacks upp, which encodes uracil phosphoribosyl-transferase, for subsequent use as a counter-selectable marker. A replicative vector containing (1) a pIMP13 origin of replication from Bacillus subtilis that is functional in Clostridia, (2) a replacement cassette consisting of an antibiotic resistance gene (MLSR) flanked by two FRT sequences, and (3) two sequences homologous to selected regions around target DNA sequence was first constructed. This vector was successfully used to consecutively delete the Cac824I restriction endonuclease encoding gene (CA_C1502) and the upp gene (CA-C2879) in the C. acetobutylicum ATCC824 chromosome. The resulting C. acetobutylicum Äcac1502Äupp strain is marker-less, readily transformable without any previous plasmid methylation and can serve as the host for the "marker-less" genetic exchange system. The third gene, CA-C3535, shown in this study to encode for a type II restriction enzyme (Cac824II) that recognizes the CTGAAG sequence, was deleted using an upp/5-FU counterselection strategy to improve the efficiency of the method. The restriction-less marker-less strain and the method was successfully used to delete two genes (ctfAB) on the pSOL1 megaplasmid and one gene (ldhA) on the chromosome to get strains no longer producing acetone or l-lactate. Conclusions: The restriction-less, marker-less strain described in this study, as well as the maker-less genetic exchange coupled with positive selection, will be useful for functional genomic studies and for the development of industrial strains for the production of biofuels and bulk chemicals. [ABSTRACT FROM AUTHOR]

Investigating the developmental, structural and functional complexity ofmammalian tissues and organs depends on identifying and gaining experimental access to diverse cell populations. Here, we describe a set of recombinase-responsive fluorescent indicator alleles in mice that significantly extends our ability to uncover cellular diversity by exploiting the intrinsic genetic signatures that uniquely define cell types. Using a recombinase-based intersectional strategy, these new alleles uniquely permit non-invasive labeling of cells defined by the overlap of up to three distinct gene expression domains. In response to different combinations of Cre, Flp and Dre recombinases, they express eGFP and/or tdTomato to allow the visualization of full cellular morphology. Here, we demonstrate the value of these features through a proof-of-principle analysis of the central noradrenergic system. We label previously inaccessible subpopulations of noradrenergic neurons to reveal details of their three-dimensional architecture and axon projection profiles. These new indicator alleles will provide experimental access to cell populations at unprecedented resolution, facilitating analysis of their developmental origin and anatomical, molecular and physiological properties. [ABSTRACT FROM AUTHOR]

A feature‐based log parsing method is presented for extracting log events from unstructured free‐text logs. It is a data‐driven log analytic solution with no training data needed and suitable for various types of log parsing tasks. Experiments show that the proposed method can achieve higher accuracy and lower time complexity in large‐scale log data than existing log parsing methods. [ABSTRACT FROM AUTHOR]

We designed a system to determine whether dicentric chromosomes in Drosophila melanogaster break at random or at preferred sites. Sister chromatid exchange in a Ring-X chromosome produced dicentric chromosomes with two bridging arms connecting segregating centromeres as cells divide. This double bridge can break in mitosis. A genetic screen recovered chromosomes that were linearized by breakage in the male germline. Because the screen required viability of males with this X chromosome, the breakpoints in each arm of the double bridge must be closely matched to produce a nearly euploid chromosome. We expected that most linear chromosomes would be broken in heterochromatin because there are no vital genes in heterochromatin, and breakpoint distribution would be relatively unconstrained. Surprisingly, approximately half the breakpoints are found in euchromatin, and the breakpoints are clustered in just a few regions of the chromosome that closely match regions identified as intercalary heterochromatin. The results support the Laird hypothesis that intercalary heterochromatin can explain fragile sites in mitotic chromosomes, including fragile X. Opened rings also were recovered after male larvae were exposed to X-rays. This method was much less efficient and produced chromosomes with a strikingly different array of breakpoints, with almost all located in heterochromatin. A series of circularly permuted linear X chromosomes was generated that may be useful for investigating aspects of chromosome behavior, such as crossover distribution and interference in meiosis, or questions of nuclear organization and function. [ABSTRACT FROM AUTHOR]

Genome engineering relies on DNA-modifying enzymes that are able to locate a DNA sequence of interest and initiate a desired genome rearrangement. Currently, the field predominantly utilizes site-specific DNA nucleases that depend on the host DNA repair machinery to complete a genome modification task. We show here that genome engineering approaches that employ target-specific variants of the self-sufficient, versatile site-specific DNA recombinase Flp can be developed into promising alternatives. We demonstrate that the Flp variant evolved to recombine an FRT-like sequence, FL- IL10A, which is located upstream of the human interleukin-10 gene, and can target this sequence in the model setting of Chinese hamster ovary and human embryonic kidney 293 cells. This target-specific Flp variant is able to perform the integration reaction and, when paired with another recombinase, the dual recombinase-mediated cassette exchange reaction. The efficiency of the integration reaction in human cells can be enhanced by 'humanizing' the Flp variant gene and by adding the nuclear localization sequence to the recombinase. [ABSTRACT FROM AUTHOR]

The isolable silylene 1 forms a frustrated Lewis pair with silylium ion 2 that is able to split hydrogen under ambient conditions. The protonated silylene 3 obtained in this reaction isomerizes to yield the hydrogen-bridged disilyl cation 4. Cation 4 is fully characterized by NMR spectroscopy and by XRD analysis. Its formation via the protonated silylene 3 is indicated by independent synthesis of cation 3 by hydride abstraction from the corresponding dihydridosilane 11 and is further supported by the results of density functional calculations. [ABSTRACT FROM AUTHOR]

Background Combination of fluoropyrimidines and a platinum derivative are currently standards for systemic chemotherapy in advanced adenocarcinoma of the stomach and gastroesophageal junction (GEJ). Nevertheless, individual likelihood for response to these therapeutic regimes remains uncertain. Even more, no predictive markers are available to determine which patients may benefit more from oxaliplatin versus cisplatin or vice versa. The new invasion and stem cell markers VEGFR-3 and CXCR4 have been linked prognostically with more aggressive esophagogastric cancer types. Thus, we aimed to assess correlations of VEGFR-3 and CXCR4 expression levels with clinical outcome in a randomized phase III study of patients with oxaliplatin/leucovorin/5-FU (FLO) versus cisplatin/leucovorin/5-FU (FLP). Methods The patients data examined in this study (n = 72) were from the collective of the FLO vs. FLP phase III AIO trial. Tumour tissues were stained via immunohistochemistry for VEGFR- 3 and CXCR4 expression and results were evaluated by two independent, blinded investigators. Outcome parameter: Survival analysis was calculated for patients receiving FLO vs. FLP in relation to VEGFR-3 and CXCR4 expression. Results 54% and 36% of the examined tumour tissues showed strong positive expression of VEGFR- 3 and CXCR4 respectively. No superiority of each regime was detected in terms of overall survival (OS) in the whole population. Patients with strong expression of CXCR4 on their tumour tissues profited more in terms of OS under the treatment of FLP (mOS: 28 vs 15 months, p = 0.05 respectively). Patients with negative VEGFR-3 and CXCR4 expression had a trend to live longer when FLO regime was applied (mOS: 22 vs. 9 months, p = 0.099 and 20 vs. 10 months, p = 0.073 respectively). In an exploratory analysis of patients older than 60 years at diagnosis, we observed a significant benefit in overall survival for VEGFR-3 and CXCR4-positive patients when treated with FLP (p = 0.002, p = 0.021 respectively). Conclusions CXCR4 positive patients profited in terms of OS from FLP, whereas FLO proved to be more effective in CXCR4 and VEGFR-3 negative patients. Our results suggest, despite the limited size of the study, a predictive value of these biomarkers concerning chemotherapy with FLP or FLO in advanced esophagogastric cancer. [ABSTRACT FROM AUTHOR]

Abstract: Profound neuropeptide diversity characterizes the nematode nervous system, but it has proven challenging to match neuropeptide G protein-coupled receptors (GPCR) with their cognate ligands in heterologous systems. We have expressed the Caenorhabditis elegans GPCR encoded in the locus T19F4.1, previously matched with FMRFamide-like peptides encoded on the flp-2 precursor gene, in mammalian cells and in the yeast Saccharomyces cerevisiae. Pharmacological characterization revealed that the receptor is potently activated by flp-2 peptides in CHO cells (∼10nM EC50) and in yeast (∼100nM EC50), signaling through a Gqα pathway in each system. The yeast GPCR expression system provides a robust assay for screening for agonists of the flp-2 receptor and is the target of an ongoing high-throughput screening exercise. [Copyright &y& Elsevier]

Článek je pohledem do problematiky lokací a alokací z hlediska optimalizačního kritéria, je polemikou nad využíváním optimalizačních kritérií v lokační analýze. Popisuje důvody, proč je vhodné hledat jiné možnosti řešení těchto úloh. Jako jedno z východisek navrhuje využít návratnosti investice jako optimalizačního kritéria a doplnit tak klasickou maximalizaci zisku či minimalizaci nákladů. V neposlední řadě jsou zde shrnuty některé experimentální výsledky porovnávající maximalizaci zisku a návratnost.

Highlights: [•] A strategy for recombineering of intact large plasmids with non-antibiotic markers is presented. [•] Designed for allowing biosafety requirements to be met for such plasmids. [•] Approach is demonstrated using the R995+SPI-1 and R995+SPI-2 plasmids. [•] The new constructs are functional, defective for conjugation, and transferred via electroporation. [•] The new constructs are stably maintained under conditions where original plasmids are not. [Copyright &y& Elsevier]

Diarylphosphino-substituted alkynes undergo a 1, 1-carboboration reaction with tris(pentafluorophenyl)borane to yield 2-diarylphosphino-substituted alkenylboranes. These unsaturated systems show a P/B interaction. Nevertheless, they feature a limited frustrated Lewis pair (FLP) reactivity. Four such unsaturated vicinal FLPs were shown to react with benzaldehyde to give the respective six-membered heterocyclic P/B FLP 1, 2-addition products, which were characterized by X-ray diffraction. [ABSTRACT FROM AUTHOR]

Abstract: Temporally precise inhibition of genetically defined cell populations in intact nervous systems has been enabled by the microbial halorhodopsin NpHR, a fast, light-activated chloride pump. Here, we report the generation of new mouse strains that express eNpHR2-EYFP fusion proteins after Cre- and/or Flp-mediated recombination to silence neural activity in vivo. In these mouse strains, Cre/Flp recombination induced a high-level of eNpHR2-EYFP expression. Slice whole-cell patch clamp experiments confirmed that eNpHR2-EYFP-expressing neurons could be optically hyperpolarized and inhibited from firing action potentials. Thus, these mouse strains offer powerful tools for light-induced silencing of neural activity in genetically defined cell populations. [Copyright &y& Elsevier]

Gamete formation is an important step in the life cycle of sexually reproducing organisms. In flowering plants, haploid spores are formed after the meiotic division of spore mother cells. These spores develop into male and female gametophytes containing gametes after undergoing mitotic divisions. In the female, the megaspore mother cell undergoes meiosis forming four megaspores, of which one is functional and three degenerate. The megaspore then undergoes three mitotic cycles thus generating an embryo sac with eight nuclei. The embryo sac undergoes cellularization to form the mature seven-celled female gametophyte. Entry into and progression through meiosis is essential for megasporogenesis and subsequent megagametogenesis, but control of this process is not well understood. FOUR LIPS (FLP) and its paralogue MYB88, encoding R2R3 MYB transcription factors, have been extensively studied for their role in limiting the terminal division in stomatal development by direct regulation of the expression of cell cycle genes. Here it is demonstrated that FLP and MYB88 also regulate female reproduction. Both FLP and MYB88 are expressed during ovule development and their loss significantly increases the number of ovules produced by the placenta. Despite the presence of excess ovules, single and double mutants exhibit reduced seed set due to reduced female fertility. The sterility results at least in part from defective meiotic entry and progression. Therefore, FLP and MYB88 are important regulators of entry into megasporogenesis, and probably act via the regulation of cell cycle genes. [ABSTRACT FROM AUTHOR]

Transgenic and conditional knockout mouse models play an important role in biomedical research and their use has grown exponentially in the last 5-10 years. Generating conditional knockouts often requires breeding multiple alleles onto the background of a single mouse or group of mice. Breeding these mice depends on parental genotype, litter size, transmission frequency, and the number of breeding rounds. Therefore, a well planned breeding strategy is critical for keeping costs to a minimum. However, designing a viable breeding strategy can be challenging. With so many different variables this would be an ideal task for a computer program. To facilitate this process, we created a Java-based program called Conditional Allele Mouse Planner (CAMP). CAMP is designed to provide an estimate of the number of breeders, amount of time, and costs associated with generating mice of a particular genotype. We provide a description of CAMP, how to use it, and offer it freely as an application. [ABSTRACT FROM AUTHOR]

Abstract: Reporters of Cre and/or Flp activity are important for defining the spatial and temporal extent of Cre/Flp-mediated recombination. Here, we describe R26-CAG-LF-mTFP1, a multifunctional fluorescent reporter mouse that strongly expresses mTFP1 (bright teal fluorescent protein) after Cre- and Flp-mediated recombination. To meet the need for single recombinase-mediated reporter expression, we generated derivatives of R26-CAG-LF-mTFP1. The germline excision of the Frt-flanked stop cassette in R26-CAG-LF-mTFP1 generated a Cre-dependent reporter (R26-CAG-LoxP-mTFP1). Similarly, R26-CAG-FRT-mTFP1, in which the loxP-flanked stop cassette was excised in the germline, requires only Flp to activate mTFP1 expression. [Copyright &y& Elsevier]

To assay the efficiency of the FLP/FRT site-specific recombination system in Danio rerio, a construct consisting of a muscle-specific promoter driving EGFP flanked by FRT sites was developed. FLPe capped RNA was microinjected into transgenic single cell stage zebrafish embryos obtained by crossing hemizygous transgenic males with wild-type females. By 48 h post fertilization (hpf), the proportion of embryos displaying green fluorescence following FLPe RNA microinjection was significantly lower (7.7%; P < 0.001) than would be expected from a cross in the absence of the recombinase (50%). Embryos that retained fluorescence displayed marked mosaicism. Inheritance of the excised transgene in non-fluorescent, transgenic embryos was verified by PCR analysis and FLPe-mediated recombination was confirmed by DNA sequencing. Sperm derived from confirmed transgenic males in these experiments was used to fertilize wild-type eggs to determine whether germline excision of the transgene had occurred. Clutches sired by FLPe-microinjected males contained 0-4% fluorescent embryos. Transgenic males that were phenotypically wild-type produced no fluorescent progeny, demonstrating complete excision of the transgene from their germline. FLPe microinjected males that retained some fluorescent muscle expression produced a small proportion of fluorescent offspring, suggesting that in mosaic males not all germline cells had undergone FLPe-mediated transgene excision. Our results show that FLPe, which is derived from Saccharomyces cerevisiae, is an efficient recombinase in zebrafish maintained at 28.5°C. [ABSTRACT FROM AUTHOR]

Abstract: FLP, like Cre, is a frequently employed site-specific recombinase. Because wild-type FLP (wtFLP) is thermolabile, a thermostable FLP mutant (FLPe) has been developed for efficient recombination of FLP in studies using mammalian cells and animals. FLPe and wtFLP have been compared in multiple assays in vitro and in vivo, and in mouse genetics, FLPe has been shown to be very effective like Cre. Here we show an adenovirus vector (AdV) system to be valuable for quantitative measurements of the enzyme activity in mammalian cells and, using this system, precisely compare activities of wtFLP and FLPe. Unexpectedly, we found that the recombination efficiency of FLPe enzyme was lower on a molar basis than that of wtFLP even at 37 °C and, consequently, that the higher recombination yield per transduced AdV genome expressing FLPe compared to wtFLP was due not to inherently higher enzyme activity, but rather to higher steady-state levels of FLPe by its thermostability. Therefore, trying to increase FLPe levels further, we generated a “humanized” FLPe (hFLPe) gene with codon usage optimized for mammals. hFLPe produced about 10-fold more FLPe enzyme in transfection experiments than FLPe, as expected. However, hFLPe-expressing AdV was unstable and could not be prepared without deletion, suggesting that a subtle deleterious effect of FLP on 293 cells may exist. With hFLPe-expressing AdV thus unavailable, of the AdV constructs tested, AdV-expressing FLPe yielded the most recombined targets, despite the lower recombination efficiency of FLPe per enzyme molecule compared with that of wtFLP. We found hFLPe to be valuable for plasmid transfection, and its properties are probably suitable for experiments involving cell lines and transgenic mice. [Copyright &y& Elsevier]

Abstract: To induce plant regeneration via somatic embryogenesis, a binary expression vector system was constructed containing a heat shock-inducible FRT/FLP system. In this system, the BABY BOOM (BBM) gene, which shows similarity to the AP2/ERF family, was under the control of cauliflower mosaic virus 35S (CaMV 35S) promoter and the gene coding for FLP site-specific recombinase was under the control of a heat shock-inducible promoter HSP18.2 from Arabidopsis thaliana. The promoters and genes were flanked by two FRT recombination sites in direct orientation. BBM overexpression induced formation of somatic embryos from calli of Chinese white poplar (Populus tomentosa Carr.). Six somatic embryos germinated to form transgenic plants with phenotypic alterations. The stem cuttings of the transgenic plants were treated with heat shock and they developed into phenotypically normal plants. Southern blot analysis further confirmed that the BBM gene was excised from the genomic DNA of the transgenic plants with normal phenotype. The system reported here can be used to obtain transgenic plants without the use of antibiotic or herbicide resistance genes and to provide a novel strategy for plant regeneration via somatic embryogenesis. [Copyright &y& Elsevier]

The catabolite gene activator protein (CAP) and the fumurate nitrate reductase (FNR) are two founder members of the growing CRP-FNR protein superfamily. The consensus FNR binding site (TTGAT-N4-ATCAA) closely resembles that of CRP to the extent that both contain a common core motif (NTGAN-N4-NTCAN). The transcription factor FNR plays a role in altering gene expression between aerobic and anaerobic conditions but CRP regulators control the response to glucose starvation. Protein DNA interactions occur between the regulatory protein and DNA at the corresponding promoter using the consensus either CRP or FNR binding sites. Successful transcriptional activation generally requires contact between a DNA-bound activator and RNA polymerase in order to generate on effective complex. CRP promoters are grouped into two classes depending on the location of DNA binding site. Class I promoters contains transcription activator binding sites centered near position -61.5, -71, -82 or -92. Class II promoters the regulator proteins bind to a site centered at or near - 41.5 so three possible contacts, αCTD-AR1, αNTD-AR2 and δ70-AR3, occur between regulator and RNA polymerase. FNR and FLP act as a class II activator. [ABSTRACT FROM AUTHOR]

Abstract: Neuropeptides are important signaling molecules that function in cell–cell communication as neurotransmitters or hormones to orchestrate a wide variety of physiological conditions and behaviors. These endogenous peptides can be monitored by high throughput peptidomics technologies from virtually any tissue or organism. The neuropeptide complement of the soil nematode Caenorhabditis elegans has been characterized by on-line two-dimensional liquid chromatography and quadrupole time-of-flight tandem mass spectrometry (2D-nanoLC Q-TOF MS/MS). Here, we use an alternative peptidomics approach combining liquid chromatography (LC) with matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry to map the peptide content of C. elegans and another Caenorhabditis species, Caenorhabditis briggsae. This study allows a better annotation of neuropeptide-encoding genes from the C. briggsae genome and provides a promising basis for further evolutionary comparisons. [Copyright &y& Elsevier]

The coding sequences of Cre (site-specific recombinase from bacteriophage P1) and FLP (yeast 2-µm plasmid site-specific recombinase) were fused in frame to produce a novel, dual-function, site-specific recombinase gene. Transgenic maize plants containing the Cre::FLP fusion expression vector were crossed to transgenic plants containing either the loxP or FRT excision substrate. Complete and precise excisions of chromosomal fragments flanked by the respective target sites were observed in the F1 and F2 progeny plants. The episomal DNA recombination products were frequently lost. Non-recombined FRT substrates found in the F1 plants were recovered in the F2 generation after the Cre::FLP gene segregated out. They produced the recombination products in the F3 generation when crossed back to the FLP-expressing plants. These observations may indicate that the efficiency of site-specific recombination is affected by the plant developmental stage, with site-specific recombination being more prevalent in developing embryos. The Cre::FLP fusion protein was also tested for excisions catalysed by Cre. Excisions were identified in the F1 plants and verified in the F2 plants by polymerase chain reaction and Southern blotting. Both components of the fusion protein (FLP and Cre) were functional and acted with similar efficiency. The crossing strategy proved to be suitable for the genetic engineering of maize using the FLP or Cre site-specific recombination system. [ABSTRACT FROM AUTHOR]

The aim of this paper is to develop a framework to aid in the evaluation and selection of Knowledge Management (KM) tools and technologies. In this paper, we propose a fuzzy linear programming technique (FLP) for multiple attribute group decision making (MAGDM) problems with preference information on alternatives. To reflect the decision maker's subjective preference information and to determine the weight vector of attributes, the linear programming technique for multidimensional analysis of preference (LINMAP) based on group consistency and inconsistency indices is used. This paper offers a methodology for analyzing individual and multidimensional preferences with linear programming technique under fuzzy environments and a systemic approach is proposed to evaluate an appropriate KM tool for the organization. In the proposed model both qualitative and quantitative criteria are evaluated according to the decision makers' preferences. Finally, the developed model is applied to a real case of assisting decision-makers in a leading logistics company in Turkey. [ABSTRACT FROM AUTHOR]

Abstract: Cellular synthesis of naturally occurring, bioactive peptides requires the proprotein convertase PC2/EGL-3 for cleavage from the larger peptide precursors. A neuroendocrine chaperone 7B2 is needed for the proteolytical activation of proPC2, as extensively studied in mouse models. To determine the role of its orthologue in Caenorhabditis elegans, we analyzed wild-type and 7B2-null strains by HPLC and matrix-assisted laser desorption ionization time-of-flight mass spectrometry, which allowed the identification of a novel neuropeptide gene, flp-33. The presence and/or absence of some neuropeptides in 7B2-null animals strongly differs form the peptide profile in wild-type, suggesting a specific and determined action of 7B2 in C. elegans. [Copyright &y& Elsevier]

Biologically active peptides are synthesized from inactive pre-proproteins or peptide precursors by the sequential actions of processing enzymes. Proprotein convertases cleave the precursor at pairs of basic amino acids, which are then removed from the carboxyl terminus of the generated fragments by a specific carboxypeptidase. Caenorhabditis elegans strains lacking proprotein convertase EGL-3 display a severely impaired neuropeptide profile ( Husson et al. 2006 , J. Neurochem. 98, 1999–2012). In the present study, we examined the role of the C. elegans carboxypeptidase E orthologue EGL-21 in the processing of peptide precursors. More than 100 carboxy-terminally extended neuropeptides were detected in egl-21 mutant strains. These findings suggest that EGL-21 is a major carboxypeptidase involved in the processing of FMRFamide-like peptide (FLP) precursors and neuropeptide-like protein (NLP) precursors . The impaired peptide profile of egl-3 and egl-21 mutants is reflected in some similar phenotypes. They both share a severe widening of the intestinal lumen, locomotion defects, and retention of embryos. In addition, egl-3 animals have decreased intestinal fat content. Taken together, these results suggest that EGL-3 and EGL-21 are key enzymes for the proper processing of neuropeptides that control egg-laying, locomotion, fat storage and the nutritional status. [ABSTRACT FROM AUTHOR]

Abstract: The nematode Caenorhabditis elegans joins the menagerie of behavioral model systems next to the fruit fly Drosophila melanogaster, the marine snail Aplysia californica and the mouse. In contrast to Aplysia, which contains 20,000 neurons having cell bodies of hundreds of microns in diameter, C. elegans harbors only 302 tiny neurons from which the cell lineage is completely described, as is the case for all the other somatic cells. As such, this nervous system appears at first sight incommensurable with those of higher organisms, although genome-wide comparison of predicted C. elegans genes with their counterparts in vertebrates revealed many parallels. Together with its short lifespan and ease of cultivation, suitability for high-throughput genetic screenings and genome-wide RNA interference approaches, access to an advanced genetic toolkit and cell-ablation techniques, it seems that this tiny transparent organism of only 1mm in length has nothing to hide. Recently, highly exciting developments have occurred within the field of neuropeptidergic signaling in C. elegans, not only because of the availability of a sequenced genome since 1998, but especially because of state of the art post genomic technologies, that allow for molecular characterization of the signaling molecules. Here, we will focus on endogenous, bioactive (neuro)peptides and mainly discuss biosynthesis, peptide sequence information, localization and G-protein coupled receptors of the three major peptide families in C. elegans. [Copyright &y& Elsevier]

Abstract: The catalytic pentad of tyrosine recombinases, that assists the tyrosine nucleophile, includes a conserved histidine/tryptophan (His/Trp-III). Flp and Cre harbor tryptophan at this position; most of their kin recombinases display histidine. Contrary to the conservation rule, Flp(W330F) is a much stronger recombinase than Flp(W330H). The hydrophobicity of Trp330 or Phe330 is utilized in correctly positioning Tyr343 during the strand cleavage step of recombination. Why then is phenylalanine almost never encountered in the recombinase family at this conserved position? Using exogenous nucleophiles and synthetic methylphosphonate or 5′-thiolate substrates, we decipher that Trp330 also assists in the activation of the scissile phosphate and the departure of the 5′-hydroxyl leaving group. These two functions are consistent with the hydrogen bonding property of Trp330 as well as its location in structures of the Flp recombination complexes. However, van der Waals contact between Trp330 and Arg308 may also be important for the phosphate activation step. A structure based suppression strategy permits the inactive variant Flp(W330A) to be rescued by a second site mutation A339M. Modeling alanine and methionine at positions 330 and 339, respectively, in the Flp crystal structure suggests a plausible mechanism for active site restoration. Successful suppression suggests the possibility of evolving, by design, new active site configurations for tyrosine recombination. [Copyright &y& Elsevier]

Abstract: The tyrosine family of recombinases produces two smaller DNA circles when acting on circular DNA harboring two recombination sites in head-to-tail orientation. If the substrate is supercoiled, these circles can be unlinked or form multiply linked catenanes. The topological complexity of the products varies strongly even for similar recombination systems. This dependence has been solved here. Our computer simulation of the synapsis showed that the bend angles, ϕ, created in isolated recombination sites by protein binding before assembly of the full complex, determine the product topology. To verify the validity of this theoretical finding we measured the values of ϕ for Cre/loxP and Flp/FRT systems. The measurement was based on cyclization of the protein-bound short DNA fragments in solution. Despite the striking similarity of the synapses for these recombinases, action of Cre on head-to-tail target sites produces mainly unlinked circles, while that of Flp yields multiply linked catenanes. In full agreement with theoretical expectations we found that the values of ϕ for these systems are very different, close to 35° and 80°, respectively. Our findings have general implications in how small protein machines acting locally on large DNA molecules exploit statistical properties of their substrates to bring about directed global changes in topology. [Copyright &y& Elsevier]

We describe fluorescent-labeled peptide (FLP) studies on living cells. The new technique is nonradioactive and it allows monitoring of the binding and internalization of Vasoactive Intestinal Peptide (VIP) in VIP receptor-expressing cells. The technique is easy to perform and the observed reaction is peptide sequence specific. [ABSTRACT FROM AUTHOR]

Abstract: Completion of the Caenorhabditis elegans genome sequencing project in 1998 has provided more insight into the complexity of nematode neuropeptide signaling. Several C. elegans neuropeptide precursor genes, coding for approximately 250 peptides, have been predicted from the genomic database. One can, however, not deduce whether all these peptides are actually expressed, nor is it possible to predict all post-translational modifications. Using two dimensional nanoscale liquid chromatography combined with tandem mass spectrometry and database mining, we analyzed a mixed stage C. elegans extract. This peptidomic setup yielded 21 peptides derived from formerly predicted neuropeptide-like protein (NLP) precursors and 28 predicted FMRFamide-related peptides. In addition, we were able to sequence 11 entirely novel peptides derived from nine peptide precursors that were not predicted or identified in any way previously. Some of the identified peptides display profound sequence similarities with neuropeptides from other invertebrates, indicating that these peptides have a long evolutionary history. [Copyright &y& Elsevier]

Strategies of directed evolution and combinatorial mutagenesis applied to the Flp site-specific recombinase have yielded recombination systems that utilize bi-specific hybrid target sites. A hybrid site is assembled from two half-sites, each harboring a distinct binding specificity. Satisfying the two specificities by a binary combination of Flp variants, while necessary, may not be sufficient to elicit recombination. We have identified amino acid substitutions that foster interprotomer collaboration between partner Flp variants to potentiate strand exchange in hybrid sites. One such substitution, A35T, acts specifically in cis with one of the two partners of a variant pair, Flp(K82M) and Flp(A35T, R281V). The same A35T mutation is also present within a group of mutations that rescue a Flp variant, Flp(Y60S), that is defective in establishing monomer–monomer interactions on the native Flp target site. Strikingly, these mutations are localized to peptide regions involved in interdomain and interprotomer interactions within the recombination complex. The same group of mutations, when transferred to the context of wild-type Flp, can relax its specificity to include non-native target sites. The hybrid Flp systems described here mimic the naturally occurring XerC/XerD recombination system that utilizes two recombinases with distinct DNA binding specificities. The ability to overcome the constraints of binding site symmetry in Flp recombination has important implications in the targeted manipulations of genomes. [Copyright &y& Elsevier]