The Bacterial Microbiome of the Tomato Fruit Is Highly Dependent on the Cultivation Approach and Correlates With Flavor Chemistry

The modes of interactions between plants and plant-associated microbiota are manifold, and secondary metabolites often play a central role in plant-microbe interactions. Abiotic and biotic (including both plant pathogens and endophytes) stress can affect the composition and concentration of secondary plant metabolites, and thus have an influence on chemical compounds that make up for the taste and aroma of fruit. While the role of microbiota in growth and health of plants is widely acknowledged, relatively little is known about the possible effect of microorganisms on the quality of fruit of plants they are colonizing. In this work, tomato (Solanum lycopersicum L.) plants of five different cultivars were grown in soil and in hydroponics to investigate the impact of the cultivation method on the flavor of fruit, and to assess whether variations in their chemical composition are attributable to shifts in bacterial microbiota. Ripe fruit were harvested and used for bacterial community analysis and for the analysis of tomato volatiles, sugars and acids, all contributing to flavor. Fruit grown in soil showed significantly higher sugar content, whereas tomatoes from plants under hydroponic conditions had significantly higher levels of organic acids. In contrast, aroma profiles of fruit were shaped by the tomato cultivars, rather than the cultivation method. In terms of bacterial communities, the cultivation method significantly defined the community composition in all cultivars, with the bacterial communities in hydroponic tomatoes being more variable that those in tomatoes grown in soil. Bacterial indicator species in soil-grown tomatoes correlated with higher concentrations of volatiles described to be perceived as "green" or "pungent." A soil-grown specific reproducibly occurring ASV (amplicon sequence variants) classified as Bacillus detected solely in "Solarino" tomatoes, which were the sweetest among all cultivars, correlated with the amount of aroma-relevant volatiles as well as of fructose and glucose in the fruit. In contrast, indicator bacterial species in hydroponic-derived tomatoes correlated with aroma compounds with "sweet" and "floral" notes and showed negative correlations with glucose concentrations in fruit. Overall, our results point toward a microbiota-related accumulation of flavor and aroma compounds in tomato fruit, which is strongly dependent on the cultivation substrate and approach.

16S rRNA gene-based microbiome analysis identifies candidate bacterial strains that increase the storage time of potato tubers

In the past, the potato plant microbiota and rhizosphere have been studied in detail to improve plant growth and fitness. However, less is known about the postharvest potato tuber microbiome and its role in storage stability. The storage stability of potatoes depends on genotype and storage conditions, but the soil in which tubers were grown could also play a role. To understand the ecology and functional role of the postharvest potato microbiota, we planted four potato varieties in five soil types and monitored them until the tubers started sprouting. During storage, the bacterial community of tubers was analysed by next-generation sequencing of the 16S rRNA gene amplicons. The potato tubers exhibited soil-dependent differences in sprouting behaviour. The statistical analysis revealed a strong shift of the tuber-associated bacterial community from harvest to dormancy break. By combining indicator species analysis and a correlation matrix, we predicted associations between members of the bacterial community and tuber sprouting behaviour. Based on this, we identified Flavobacterium sp. isolates, which were able to influence sprouting behaviour by inhibiting potato bud outgrowth.

The bacterial community in potato is recruited from soil and partly inherited across generations

Strong efforts have been made to understand the bacterial communities in potato plants and the rhizosphere. Research has focused on the effect of the environment and plant genotype on bacterial community structures and dynamics, while little is known about the origin and assembly of the bacterial community, especially in potato tubers. The tuber microbiota, however, may be of special interest as it could play an important role in crop quality, such as storage stability. Here, we used 16S rRNA gene amplicon sequencing to study the bacterial communities that colonize tubers of different potato cultivars commonly used in Austrian potato production over three generations and grown in different soils. Statistical analysis of sequencing data showed that the bacterial community of potato tubers has changed over generations and has become more similar to the soil bacterial community, while the impact of the potato cultivar on the bacterial assemblage has lost significance over time. The communities in different tuber parts did not differ significantly, while the soil bacterial community showed significant differences to the tuber microbiota composition. Additionally, the presence of OTUs in subsequent tuber generation points to vertical transmission of a subset of the tuber microbiota. Four OTUs were common to all tuber generations and all potato varieties. In summary, we conclude that the microbiota of potato tubers is recruited from the soil largely independent from the plant variety. Furthermore, the bacterial assemblage in potato tubers consists of bacteria transmitted from one tuber generation to the next and bacteria recruited from the soil.

The potential of plant microbiota in reducing postharvest food loss

The role of the plant microbiota in plant establishment, growth and health is well studied, but the dynamics of postharvest crop microbiota and its role in postharvest crop quality are largely unexplored, although food loss is an enormous issue worldwide. The microbiota might be especially important during crop storage by either preventing or favouring rots, or quality loss due to, for example, sprouting, saccharification, water loss or spoilage. We need more research on plant-microbe interactions in postharvest crops to be in future able to provide microbial solutions for plant production along the whole food chain from field to fork.

A genome-wide RNAi screen identifies proteins modulating aberrant FLT3-ITD signaling

Fms-like tyrosine kinase-3 is a commonly mutated gene in acute myeloid leukemia, with about one-third of patients carrying an internal-tandem duplication of the juxtamembrane domain in the receptor (FLT3-ITD). FLT3-ITD exhibits altered signaling quality, including aberrant activation of STAT5. To identify genes affecting FLT3-ITD-mediated STAT5 signaling, we performed an esiRNA-based RNAi screen utilizing a STAT5-driven reporter assay. Knockdowns that caused reduced FLT3-ITD-mediated STAT5 signaling were enriched for genes encoding proteins involved in protein secretion and intracellular protein transport, indicating that modulation of protein transport processes could potentially be used to reduce constitutive STAT5 signaling in FLT3-ITD-positive cells. The relevance of KDELR1, a component involved in the Golgi-ER retrograde transport, was further analyzed. In FLT3-ITD-expressing leukemic MV4-11 cells, downregulation of KDELR1 resulted in reduced STAT5 activation, proliferation and colony-forming capacity. Stable shRNA-mediated depletion of KDELR1 in FLT3-ITD-expressing 32D cells likewise resulted in reduced STAT5 signaling and cell proliferation. Importantly, these cells also showed a reduced capacity to generate a leukemia-like disease in syngeneic C3H/HeJ mice. Together our data suggest intracellular protein transport as a potential target for FLT3-ITD driven leukemias, with KDELR1 emerging as a positive modulator of oncogenic FLT3-ITD activity.

Chip-calorimetry provides real time insights into the inactivation of biofilms by predatory bacteria

Control or removal of undesired biofilms has frequently been found to be quite difficult. In addition to biocidal or antibiotic chemicals or materials designed to prevent biofouling, biological control agents appear to be promising. Reports of bacterial predators eradicating biofilms or eliminating pathogens motivate a more systematic screening of biofilm-eliminating bacterial predators. Unfortunately, the analysis of the eradication process is demanding. In the present study, chip-calorimetry was applied to monitor the elimination of Pseudomonas sp. biofilms by Bdellovibrio bacteriovorus. The method uses metabolic heat as a real-time parameter for biofilm activity. The method is non-invasive, fast and convenient due to real-time data acquisition. In addition, heat-production data can reveal information about the energetics of the predator-prey interaction. The calorimetric results were validated by confocal laser scanning microscopy. The approach described may be useful for the screening of biofilm susceptibility to different predators.

Isothermal titration calorimetry - a new method for the quantification of microbial degradation of trace pollutants

The environmental fate and, in particular, biodegradation rates of hydrophobic organic compounds (HOC) are of high interest due to the ubiquity, persistence, and potential health effects of these compounds. HOC tend to interact with bioreactor materials and sampling devices and are frequently volatile, so that conventionally derived degradation parameters are often biased. We report on the development and validation of a novel calorimetric approach that serves to gain real time information on the kinetics and the physiology of HOC bioconversion in aqueous systems while overcoming weaknesses of conventional biodegradation experiments. Soil bacteria Mycobacterium frederiksbergense LB501T, Rhodococcus erythropolis K2-3 and Pseudomonas putida G7 were exposed to pulsed titrations of dissolved anthracene, 4-(2,4-dichlorophenoxy)butyric acid or naphthalene, respectively, and the thermal responses were monitored. The combinations of strains and pollutants were selected as examples for complete and partial biodegradation and complete degradation with storage product formation, respectively. Heat production signals were interpreted thermodynamically and in terms of Michaelis-Menten kinetics. The half-saturation constant k(D) and the degradation rate r(D)(Max) were derived. Comparison with conventional methods shows the suitability to extract kinetic degradation parameters of organic trace pollutants from simple ITC experiments, while thermodynamic interpretation provided further information about the metabolic fate of HOC compounds.

AML1 deletion in adult mice causes splenomegaly and lymphomas

AML1 (RUNX1) encodes a DNA-binding subunit of the CBF transcription factor family and is required for the establishment of definitive hematopoiesis. AML1 is one of the most frequently mutated genes associated with human acute leukemia, suggesting that genetic alterations of the gene contribute to leukemogenesis. Here, we report the analysis of mice carrying conditional AML1 knockout alleles that were inactivated using the Cre/loxP system. AML1 was deleted in adult mice by inducing Cre activity to replicate AML1 deletions found in human MDS, familial platelet disorder and rare de novo human AML. At a latency of 2 months after induction, the thymus was reduced in size and frequently populated by immature double negative thymocytes, indicating defective T-lymphocyte maturation, resulting in lymphatic diseases with 50% penetrance, including atypical hyperplasia and thymic lymphoma. Metastatic lymphomas to the liver and the meninges were observed. Mice also developed splenomegaly with an expansion of the myeloid compartment. Increased Howell-Jolly body counts indicated splenic hypofunction. Thrombocytopenia occurred due to immaturity of mini-megakaryocytes in the bone marrow. Together with mild lymphocytopenia in the peripheral blood and increased fractions of immature cells in the bone marrow, AML1 deficient mice display features of a myelodysplastic syndrome, suggesting a preleukemic state.

Downregulation of Apaf-1 and caspase-3 by RNA interference in human glioma cells: Consequences for erucylphosphocholine-induced apoptosis

Erucylphosphocholine (ErPC) exerts strong anticancer activity in vivo and in vitroand induces apoptosis even in chemoresistant glioma cell lines. We investigated the contribution of Apaf-1 and caspase-3 to the apoptotic response to ErPC using RNA interference (RNAi) in human glioblastoma cells. We could demonstrate that human glioma cell lines are susceptible to RNAi. Apaf-1 and caspase-3 are amenable to specific small interfering RNA (siRNA)-induced degradation resulting in a reduction of protein levels to 8-33% (Apaf-1) and to 30-50% (caspase-3). Transfection of siRNA directed to Apaf-1 and caspase-3 specifically reduced caspase-3 processing induced by ErPC treatment and yielded a reduction in cells that undergo ErPC-induced apoptosis to 17-33% (Apaf-1) and to 38-50% (caspase-3). The caspase-3 siRNA experiments were corroborated in caspase-3-deficient and -reconstituted MCF-7 breast cancer cells. Survival assays and morphological observations revealed that caspase-3 reconstitution significantly sensitized MCF-7 cells to ErPC. Exploring the caspase cascade responsible for ErPC-induced apoptosis MCF-7 cells provided evidence that caspase-3 is required for the activation of caspases-2, -6 and -8 and also participates in a feedback amplification loop. Our results provide evidence that Apaf-1 and caspase-3 are major determinants of ErPC-induced apoptosis and the possible use of ErPC in a clinical setting is discussed.

Citrate synthase and pyruvate kinase activities during early life stages of the shrimp Farfantepenaeus paulensis (Crustacea, Decapoda, Penaeidae): effects of development and temperature

Energy metabolism in early life stages of the shrimp Farfantepenaeus paulensis subjected to temperature reduction (26 and 20 degrees C) was determined using the activities of citrate synthase (CS) and pyruvate kinase (PK). At both temperatures, weight-specific activity of CS decreased throughout the ontogenetic development from protozoea II (PZ II) to postlarva XII-XIV (PL XII-XIV). PK activity reached a pronounced peak in PL V-VI, followed by a further decrease in PL XII-XIV. Temperature reduction produced variation in oxygen consumption rates (QO(2)), ammonia-N excretion and in enzyme activities. Ammonia-N excretion was higher at 20 degrees C in mysis III (M III), PL V-VI and PL XII-XIV, resulting in substantially lower O:N ratios in these stages. QO(2) was increased in protozoea II (PZ II) and mysis I (M I) at 26 degrees C, while no difference in QO(2) was detected in the subsequent stages at either temperature. This fact coincided with higher CS and PK activities in M III, PL V-VI and PL XII-XIV at 20 degrees C compared with 26 degrees C. Regressions between individual enzyme activities and dry weight exhibited slope values of 0.85-0.92 for CS and 1.1-1.2 for PK and temperature reduction was reflected by higher slope values at 20 than at 26 degrees C for both enzymes. Weight-specific CS activity was positively correlated with QO(2) at 20 and 26 degrees C, and may thus be used as an indicator of aerobic metabolic rate throughout the early stages of F. paulensis. The variation in enzyme activities is discussed in relation to possible metabolic adaptations during specific ontogenetic events of the F. paulensis life cycle. Here, the catalytic efficiency of energy-metabolism enzymes was reflected in ontogenetic shifts in behaviour such as larval settlement and the adoption of a benthic existence in early postlarvae. In most cases, enhanced enzyme activities appeared to counteract negative effects of reduced temperature.

Codon-improved Cre recombinase (iCre) expression in the mouse

By applying the mammalian codon usage to Cre recombinase, we improved Cre expression, as determined by immunoblot and functional analysis, in three different mammalian cell lines. The improved Cre (iCre) gene was also designed to reduce the high CpG content of the prokaryotic coding sequence, thereby reducing the chances of epigenetic silencing in mammals. Transgenic iCre expressing mice were obtained with good frequency, and in these mice loxP-mediated DNA recombination was observed in all cells expressing iCre. Moreover, iCre fused to two estrogen receptor hormone binding domains for temporal control of Cre activity could also be expressed in transgenic mice. However, Cre induction after administration of tamoxifen yielded only low Cre activity. Thus, whereas efficient activation of Cre fusion proteins in the brain needs further improvements, our studies indicate that iCre should facilitate genetic experiments in the mouse.

Alteration of Cre recombinase site specificity by substrate-linked protein evolution

Directed molecular evolution was applied to generate Cre recombinase variants that recognize a new DNA target sequence. Cre was adapted in a three-stage strategy to evolve recombinases to specifically recombine the new site. This complex multicycle task was made feasible by an improved directed-evolution procedure that relies on placing the recombination substrate next to the recombinase coding region. Consequently, those DNA molecules carrying the coding region for a successful recombinase are physically marked by the action of that recombinase on the linked substrate and are easily retrieved from a large background of unsuccessful candidates by PCR amplification. We term this procedure substrate-linked protein evolution (SLiPE). The method should facilitate the development of new recombinases and other DNA-modifying enzymes for applications in genetic engineering, functional genomics, and gene therapy.

LoxP-directed cloning: use of Cre recombinase as a universal restriction enzyme

We have developed a novel way to use the Cre/loxP system for in vitro manipulation of DNA and a technique to clone DNA into circular episomes. The method is fast, reliable, and allowsflexible cloning of DNA fragments into episomes containing a loxP site. We show that a loxP site can serve as a universal target site to clone a DNA fragment digested with any restriction enzyme(s). This technique abolishes the need for compatible restriction sites in cloning vectors and targets by generating custom-designed 5' 3', or blunt ends in the desired orientation and reading frame in the vector Therefore, this method eliminates the limitations encountered when DNA fragments are cloned into vectors with a confined number of cloning sites. The 34-bp loxP sequence assures uniqueness, even when large episomes are manipulated. We present three examples, including the manipulation of a bacterial artificial chromosome. Because DNA manipulation takes place at a loxP site, we refer to this technique as loxP-directed cloning.

Studies on metabolic properties in the Northern Krill, Meganyctiphanes norvegica (Crustacea, euphausiacea): influence of nutrition and season on pyruvate kinase

The specific activity and the kinetic properties of partly purified pyruvate kinase (PK) (EC 2.7.1.40) from the Northern Krill, Meganyctiphanes norvegica, were investigated in relation to varying food resources. In order to evaluate the effect of starvation on the total energy metabolism, the respiration rates of fed and unfed krill were determined. The FPLC-elution profile of PK displayed two distinct peaks - PK I and II. The first isoform represented 80% of the total PK activity in the organism, and 20% was contributed by the second isoform. PK I was inhibited by ATP but was not influenced by fructose-1,6-bisphosphate (FBP). In contrast, PK II showed ATP inhibition and up to 2.5-fold increased activity by addition of 17 micromol.l(-1) FBP. The Michaelis-Menten constants of both isoforms were 2-10-fold higher for ADP than for phosphoenolpyruvate (PEP). Alanine showed no regulatory effect on PK I and II. In specimens starved for 7 days oxygen consumption decreased by 20%. Neither the feeding experiments nor the animals captured in the field during low and high productive seasons indicate that PK properties of M. norvegica are modified in relation to food supply. Accordingly, alternative mechanisms are involved in the depression of the metabolic rate in terms of oxygen consumption.

Inducible chromosomal translocation of AML1 and ETO genes through Cre/loxP-mediated recombination in the mouse

Transgenic mice have been used to explore the role of chromosomal translocations in the genesis of tumors. But none of these efforts has actually involved induction of a translocation in vivo. Here we report the use of Cre recombinase to replicate in vivo the t(8;21) translocation found in human acute myeloid leukemia (AML). As in the human tumors, the murine translocation fuses the genes AML1 and ETO. We used homologous recombination to place loxP sites at loci that were syntenic with the break points for the human translocation. Cre activity was provided in mice by a transgene under the control of the Nestin promoter, or in cultured B cells by infecting with a retroviral vector encoding Cre. In both instances, Cre activity mediated interchromosomal translocations that fused the AML1 and ETO genes. Thus, reciprocal chromosomal translocations that closely resemble rearrangements found in human cancers can be achieved in mice.

RecE/RecT and Redalpha/Redbeta initiate double-stranded break repair by specifically interacting with their respective partners

The initial steps of double-stranded break (DSB) repair by homologous recombination mediated by the 5'-3' exonuclease/annealing protein pairs, RecE/RecT and Redalpha/Redbeta, were analyzed. Recombination was RecA-independent and required the expression of both components of an orthologous pair, even when the need for exonuclease activity was removed by use of preresected substrates. The required orthologous function correlated with a specific protein-protein interaction, and recombination was favored by overexpression of the annealing protein with respect to the exonuclease. The need for both components of an orthologous pair was observed regardless of whether recombination proceeded via a single-strand annealing or a putative strand invasion mechanism. The DSB repair reactions studied here are reminiscent of the RecBCD/RecA reaction and suggest a general mechanism that is likely to be relevant to other systems, including RAD52 mediated recombination.

Effects of temperature on the respiration rates and the kinetics of citrate synthase in two species of Idotea (Isopoda, Crustacea)

The two species of isopods, Idotea baltica (Pallas) and Idotea emarginata (Fabricius), co-occur frequently near Helgoland, North Sea, occupying different ecological niches. Respiration rates and kinetic properties of citrate synthase (CS) were compared in these species in order to identify possible mechanisms of temperature adaptation. Specimens were acclimated to 5 and 15 degrees C prior to further investigations. Respiration rates were measured under normoxic conditions at 5, 10 and 15 degrees C. CS was partly purified chromatographically and influences of temperature, pH, substrate saturation and ATP-concentration on enzyme activity were examined. In both species, rising temperatures led to linearly increasing oxygen consumption, with estimated Q10 values between 3.2 and 4.2. Only I. baltica showed an effect of short term acclimation: warm adapted animals had always higher respiration rates than cold adapted ones. In I. emarginata, the acclimation temperature had no effect on oxygen consumption. Furthermore, its CS slightly indicates higher affinity to oxaloacetic acid when specimens were adapted to 15 degrees C compared to those maintained at 5 degrees C. Any effect of the experimental temperature on CS in I. baltica was negligible. The results are discussed in view of the different habitats occupied by the species compared.

Comparative kinetic analysis of FLP and cre recombinases: mathematical models for DNA binding and recombination

The integrase class site specific recombinases FLP from Saccharomyces cerevisiae, and Cre from bacteriophage P1, have been extensively used to direct DNA rearrangements in heterologous organisms. Although their reaction mechanisms have been relatively well characterised, little comparative analysis of the two enzymes has been published. We present a comparative kinetic analysis of FLP and Cre, which identifies important differences. Gel mobility shift assays show that Cre has a higher affinity for its target, loxP (7. 4x10(10) M-1), than FLP for its target, FRT (8.92x10(8) M-1). We show that both recombinases bind the two halves of their target sites cooperatively, and that Cre shows approximately threefold higher cooperativity than FLP. Using a mathematical model describing the sequential binding of recombinase monomers to DNA, we have determined values for the association and dissociation rate constants for FLP and Cre.FLP and Cre also showed different characteristics in in vitro recombination assays. In particular, approximately tenfold more active FLP was required than Cre to optimally recombine a given quantity of excision substrate. FLP was able to reach maximum excision levels approaching 100%, whilst Cre-mediated excision did not exceed 75%. To investigate possible reasons for these differences a mathematical model describing the excision recombination reaction was established. Using measured DNA binding parameters for FLP and Cre in the model, and comparing simulated and experimental recombination data, the values of the remaining unknown parameters were determined. This analysis indicates that the synaptic complex is more stable for Cre than for FLP.

A new logic for DNA engineering using recombination in Escherichia coli

A straightforward way to engineer DNA in E. coli using homologous recombination is described. The homologous recombination reaction uses RecE and RecT and is transferable between E. coli strains. Several target molecules were manipulated, including high copy plasmids, a large episome and the E. coli chromosome. Sequential steps of homologous or site-specific recombination were used to demonstrate a new logic for engineering DNA, unlimited by the disposition of restriction endonuclease cleavage sites or the size of the target DNA.

Isoforms of an N-acetyl-beta-D-glucosaminidase from the Antarctic krill, Euphausia superba: purification and antibody production

Two forms of the chitinolytic enzyme N-acetyl-beta-D-glucosaminidase (NAGase, EC 3.2.1.52) have been isolated from the Antarctic krill, Euphausia superba, in order to study their potential role in temperature adaptation processes. A chromatographic protocol was developed that allowed complete separation of the two enzyme forms, named NAGase B and NAGase C. The latter was purified to homogeneity with 600-fold enrichment and a yield of 17%. The molecular mass was 150 kDa. NAGase B showed characteristics of a glycoprotein due to affinity towards concanavalin A sepharose, while NAGase C did not. Highly specific polyclonal antibodies to NAGase C [anti-(E. superba-NAGase C)-IgG] showed only negligible cross-reactivity with NAGase B isoforms. A comparison with the Northern krill, Meganyctiphanes norvegica, revealed a corresponding chromatographic pattern with two main activity peaks, for differentiation named NAGase II and NAGase III. Application of the antibody on M. norvegica revealed a high specificity toward NAGase III and a low cross-reactivity with NAGase II. First indication is given that the two forms are no isoenzymes in a strict sense but instead may have different functions in the metabolism of krill.

Rhodamine 123 efflux modulation in the presence of low or high serum from CD56+ hematopoietic cells or CD34+ leukemic blasts by B9309-068, a newly designed pyridine derivative

The newly designed pyridine derivative B9309-068 and a series of structurally different compounds were tested for their ability to modulate rhodamine 123 (RHO) efflux from CD56+ hematopoietic cells in the presence of either 10% fetal calf serum or undiluted human AB serum. Furthermore, efflux modulation was investigated on CD34+ blast populations obtained from four patients with relapsed state AML. Target cells were specified throughout by labeling with peridinine chlorophyll protein (PerCP)-conjugated monoclonal antibodies, allowing clear differentiation from RHO emission spectrum by flow cytometry. In the presence of low serum each compound efficiently modulated RHO efflux without significant differences in the range of final concentrations (1.0-3.0 microM). At 0.1 microM, however, RHO efflux was differentially modulated following the series GF120918 approximately B9309-068 > PSC 833 > DNIG approximately DVER. With CD56+ cells in the presence of undiluted human AB serum at a final modulator concentration of 0.1 microM, all chemosensitizers tested were found to be inefficient. At final concentrations of 0.3 microM or higher, distinct RHO efflux modulation was found with the following efficacies: B9309-068 approximately GF120918 > PSC 833 >> DVER approximately DNIG. The efficacies seen in undiluted human AB serum at 3.0 microM were comparable to those seen on CD56+ cells at final modulator concentrations of 0.1 microM in low serum. Our results identify the pyridine derivative B9309-068 as a promising compound for modulating P-glycoprotein-mediated drug resistance under conditions resembling the clinical setting. Nonetheless, modulation potencies of a series of structurally very different chemosensitizers was revealed to be substantially diminished at high serum concentrations in vitro.

Improved properties of FLP recombinase evolved by cycling mutagenesis

The site-specific recombinases FLP and Cre are useful for genomic engineering in many living systems. Manipulation of their enzymatic properties offers a means to improve their applicability in different host organisms. We chose to manipulate the thermolability of FLP recombinase. A lacZ-based recombination assay in Escherichia coli was used for selection in a protein evolution strategy that relied on error-prone PCR and DNA shuffling. Improved FLP recombinases were identified through cycles of increasing stringency imposed by both raising temperature and reducing protein expression, combined with repetitive cycles of screening at the same stringency to enrich for clones with improved fitness. An eighth generation clone (termed FLPe) showed improved properties in E. coli, in vitro, in human 293- and mouse ES-cells.

Inducible expression based on regulated recombination: a single vector strategy for stable expression in cultured cells

When fused to the ligand binding domain (LBD) of steroid hormone nuclear receptors, site-specific recombinases (SSRs) acquire a ligand-dependent activity. Here, we describe the use of SSR-LBD fusion proteins in an inducible expression system, introduced into cells in a single step. A single transgene contains a constitutively active, bi-directional enhancer/promoter, which directs expression, on one side, of an SSR-LBD fusion protein gene and, on the other, a selectable marker/inducible gene cassette. The selectable marker, the puromycin acetyltransferase (pac) gene, is used for stable genomic integration of the transgene and is flanked by recombination target sites. The inducible gene is not expressed because the pac gene lies between it and the promoter. Activation of the SSR-LBD by a ligand induces recombination and the pac gene is excised. The inducible gene is thus positioned next to the promoter and so is expressed. This describes a ligand-inducible expression strategy that relies on regulated recombination rather than regulated transcription. By inducible expression of diptheria toxin, evidence that this system permits inducible expression of very toxic proteins is presented. The combination of the complete regulatory circuit and inducible gene in one transgene relates expression of the selectable marker gene to expression from the bi-directional enhancer/promoter. We exploit this relationship to show that graded increases in selection pressure can be used to select for clones with different induction properties.

Positive selection of CD56+ lymphocytes by magnetic cell sorting

A new method for the isolation of CD56+ lymphocytes from peripheral mononuclear blood cells is described. Magnetic microbeads conjugated to goat antimouse antiserum in combination with a murine monoclonal anti-CD56 antibody were coated to the CD56+ target cells. CD56+ cells were then isolated with the use of a magnetic cell sorter. The purity of the CD56+ cells was 98.4 +/- 1% (n = 12) with a recovery of the CD56+ lymphocytes of 57.2 +/- 9% (range 48-77%). The natural killer, activity of the CD56+ lymphocytes as well as the interleukin-2-induced proliferative response were not affected by the isolation procedure or the presence of the magnetic microbeads on the CD56+ cells. The described method might be a useful tool for the further characterization of CD56+ cells and their subsets and can easily be upgraded for clinical use in adoptive immunotherapy with CD56+ lymphocytes.

Interleukin-12- and interleukin-2-stimulated release of interferon-gamma by uterine CD56++ large granular lymphocytes is amplified by decidual macrophages

Numerous studies have suggested that interferon-gamma (IFN-gamma) exhibits an inhibitory effect on conceptus development during pregnancy, and recent investigations have shown that decidual CD56++, CD16- large granular lymphocytes (LGL) contain mRNA for IFN-gamma. We have investigated the influence of exogenous interleukin-12 (IL-12) and interleukin-2 (IL-2) on IFN-gamma secretion by cultivated LGL and macrophages isolated from first trimester human decidua. The effect of decidual macrophages on IFN-gamma secretion by LGL was also assessed using co-incubation experiments. Neither IL-12 nor IL-2 stimulated the secretion of IFN-gamma by decidual macrophages. IL-12 alone, but not IL-2 alone, stimulated the release of IFN-gamma by LGL. However, IL-2 acted synergistically with IL-12 to enhance the release of IFN-gamma by LGL. Unstimulated and IL-12- and IL-2-stimulated LGL incubated with macrophages exhibited a marked increase in secretion of IFN-gamma compared to those in monoculture. This effect was also seen when the LGL and macrophages were separated by a semi-permeable membrane. The results suggest that interactions between decidual LGL and macrophages, possibly mediated by soluble factors, could play a role in regulating IFN-gamma secretion at the materno-fetal interface and thus contribute to the control of invasion by the trophoblast.

Different thermostabilities of FLP and Cre recombinases: implications for applied site-specific recombination

Genomic manipulations using site-specific recombinases rely on their applied characteristics in living systems. To understand their applied properties so that they can be optimally deployed, we compared the recombinases FLP and Cre in two assays. In both Escherichia coli and in vitro, FLP shows a different temperature optimum than Cre. FLP is more thermolabile, having an optimum near 30 degrees C and little detectable activity above 39 degrees C. Cre is optimally efficient at 37 degrees C and above. Consistent with FLP thermolability, recombination in a mammalian cell line mediated by a ligand- regulated FLP-androgen receptor fusion protein is more efficient at 35 degrees C than at higher temperatures. We also document a mutation in a commercially available FLP plasmid (FLP-F70L) which renders this recombinase even more thermolabile. The different temperature optima of FLP, FLP-F70L and Cre influence their strategies of usage. Our results recommend the use of Cre for applications in mice that require efficient recombination. The thermolabilities of FLP and FLP-F70L can be usefully exploited for gain of function and cell culture applications.

A simple assay to determine the functionality of Cre or FLP recombination targets in genomic manipulation constructs

We report the construction of two Escherichia coli strains (294-Cre and 294-FLP) which express either Cre- or FLP-recombinase. Plasmids containing authentic recognition targets for either recombinase (loxPs or FRTs) are recombined when propagated in the appropriate strain. 294-Cre and 294-FLP thus provide a simple test for the recombination competence of constructs that are designed for use in Cre- or FLP-mediated genomic manipulations.

A novel family of Cys-Cys, His-Cys zinc finger transcription factors expressed in developing nervous system and pituitary gland

A screen designed to identify proteins that specifically bind to retinoic acid response elements resulted in the identification of a rat cDNA encoding a novel protein containing six Cys-Cys, His-Cys zinc fingers. This gene is expressed in a restricted fashion exhibiting distinct temporal and spatial patterns in the developing nervous system, primarily brain, spinal cord, sensory ganglia, retina, and nasal epithelia, as well as in the pituitary, and is referred to as neural zinc finger factor 1 (NZF-1). NZF-1 binds specifically to a cis-regulatory element of the beta-retinoic acid receptor (RAR beta) gene, as well as to other related DNA elements, including two in the upstream enhancer region of the mouse Pit-1 gene. In heterologous cells, NZF-1 activates transcription from promoters containing specific binding sequences and can synergize with other factors, such as Pit-1, to regulate gene expression. These results suggest that NZF-1 may exert regulatory roles in the developing and mature nervous system and in the pituitary gland. Identification of a second mouse gene highly homologous to NZF-1, encoded by a distinct genomic locus, reveals a dispersed gene family encoding proteins containing Cys-Cys, His-Cys motifs.

Brain death: practicability of evoked potentials

Multimodally evoked potentials were registered in 85 patients who fulfilled the criteria for brain death. While somatosensory and visual evoked potentials have been found to be of limited value for the diagnosis of brain death, the stepwise abolition of brain stem auditory evoked potentials (BAEP) confirmed brain death in 26 out of 85 patients, i.e. 31%. Registration of the abolition of BAEP is concluded to be a safe and acceptable confirmatory test. It is, however, more feasible for institutions, in which BAEP are analysed routinely. In spite of all efforts sequential BAEP could not be used for the diagnosis of brain death in the majority of cases either because of absence of reproducible responses at the initial registration or because the patient was already apnoic at the time of the initial BAEP. Assuming that bilateral preservation of wave I has the same significance as the stepwise abolition of BAEP, since it also proves the integrity of the peripheral receptor, BAEP are relevant for the declaration of brain death in approximately 30% of patients.

Macrophage- and lymphocyte-subtypes in the endometrium during different phases of the ovarian cycle

The presence of immunocompetetive cells in the endometrium during the proliferative and secretory phase of the ovarian cycle is demonstrated on the light and electron microscopic level using monoclonal antibodies (MoAb). Subtypes of monocytes, macrophages and T-lymphocytes appear during the different phases in variable extent and different localization. Some subpopulations of the monocyte/macrophage system and T-helper lymphocytes increase in number on day 21/22. Our observations indicate that cells with bone marrow origin take part in functional events of the endometrium during the ovarian cycle.

Lymphoreticular cells in invasive carcinoma of the uterine cervix: an immunohistological study

In the present study the immunohistology of the cellular stromal reaction of invasive squamous cell carcinoma of the cervix is investigated. Tumor tissue from 10 patients with invasive squamous cell carcinoma of the uterine cervix (stages Ib-IIb, according to FIGO) was immunostained by the alkaline phosphatase-anti-alkaline phosphatase (APAAP) method. The monoclonal antibodies OKT3, OKT4, OKT8, TO15, Ki-M1, and Ki-M6 were applied. The cells in the stroma and the tumor foci were evaluated separately. In all cases, the overwhelming majority of lymphoreticular cells were found in the stroma and the tumor-cell complexes contained relatively low numbers of these cells. While B-lymphocytes were present only in low numbers or were virtually absent from the lymphoreticular infiltrates, cells of the mononuclear-phagocyte system were found to be another prominent constituent of the tumor's cellular stromal reaction.

Recombinant human interferon (IFN) alpha-2b in chronic myelogenous leukaemia: dose dependency of response and frequency of neutralizing anti-interferon antibodies

Twenty-seven patients with Philadelphia chromosome positive chronic myelogenous leukaemia in the chronic phase were treated with low doses of recombinant interferon (IFN) alpha-2b. Ten patients entered a complete and six a partial haematologic remission with a median duration of 5.8 and 9.1 months respectively. Five minor cytogenetic responses were observed. These results are inferior compared to other studies with higher interferon-doses. Fever was an acute side effect after injection of IFN, limb pains and fatigue occurred protractedly. Haematologic side effects, nonspecific EEG changes, weight loss, and development of pulmonary infiltrates were observed in later periods of the treatment. Eight patients developed neutralizing anti-IFN antibodies after 4.2-20.4 months (median 12.8 months). Anti-IFN antibodies were associated with relapse or refractoriness to IFN treatment: five out of nine patients with rising WBC after initial fall had antibodies, while four did not. Two out of four patients with primary non-response had IFN-antibodies. These results may indicate a serious problem in the long-term treatment of CML with recombinant interferon.

[Immunophenotyping of lymphoreticular cells in the human decidua]

The endometrial stroma is transformed into decidua by an adequate hormonal stimulus or by pregnancy, the endometrial stroma is transformed into decidua. There is increasing evidence, that the decidua has a central functional relevance for the survival of the mammalian embryo in an immunological competent host. In this study, the decidua of 10 patients were examined after therapeutic abortion in the 8th-10th week of pregnancy. Various monoclonal antibodies were used for immunophenotyping of lymphoreticular cells. Most intradecidual lymphoreticular cells could be identified as Ki-M6+ and Ki-M8+ macrophages, which also expressed HLA-DR (class-II) antigens. This finding is underlined by the fact, that Tü-35+ cells occurred in comparable numbers as macrophages and B-lymphocytes were virtually absent from the decidua. Next in frequency were OKT3-positive T-lymphocytes. Most of the lymphoid cells were detected by monoclonal antibody OKT8 (suppressor/cytotoxic lymphocytes) while OKT4+ helper/inducer cells occurred only in low numbers. Though definite conclusions in the cells' functional properties cannot be drawn from an immunohistological study, our findings might be regarded as a basis to explain the tolerance of the embryo in this apparently privileged immunological site.

Histopathology of tubal pregnancy

The histopathological examination of several sections of tubal ectopic pregnancies shows that the growth of the trophoblast usually takes place in an extraluminal subperitoneal site and dilation of the tube is caused by coagulated blood and not by the trophoblast. For conservative surgery of the tube it is necessary to keep in mind the histopathological findings of tubal pregnancies.

[Lymphoreticular cells in the human endometrial stroma]

The endometrium of 12 patients with a normal spontaneous uterine cycle was examined immunohistochemically with the indirect PAP-method using various monoclonal antibodies. Lymphoreticular cells, which are responsible for non-specific defense mechanisms and for the cell-mediated immune reactions were identified. In all phases of the normal cycle, high numbers of cells belonging to the mononuclear phagocyte system (MPS) and T-lymphocytes were detected in the endometrial stroma. The overwhelming majority of T-lymphocytes were found to be of the suppressor/cytotoxic cell type, while helper/inducer cells were seen only in comparably low numbers. B-lymphocytes were virtually absent from the endometrial stroma.

[Immuno-oncologic aspects in invasive squamous cell carcinoma of the uterine cervix]

Five patients with an invasive squamous cell carcinoma of the cervix uteri were investigated histologically and immunohistologically to assess localization and composition of the lymphoreticular infiltrates. The relevant cell populations of local immunomechanisms (T-lymphocytes, monocytes/macrophages and plasma cells) were often found numerous in all neoplasms. It must be emphasized that an in situ histomorphological analysis of the cellular part of the stromal reaction of invasive squamous cell carcinoma of the cervix allows only limited conclusions concerning the functional properties of the tumor-infiltrating lymphoreticular cells.

Surface morphology of the perfused rabbit ovary

Using transmission electron microscopy we examined the morphology of the surface epithelium of the isolated and perfused rabbit ovary after an ovulatory dose of HCG. Rupture of follicles occurred in vitro approximately 13 h after HCG-injection and 6 h after the start of perfusion. The ultrastructural changes during the perfusion were similar to those occurring in vivo. The perfused ovarian epithelium had villous processes of varied architectural complexity with squamoid and cuboid epithelial cells. The superficial cells contained pinocytotic vesicles, coated and noncoated endocytotic caveolae, and occasional vacuoles. Dense bodies were more commonly found in vitro than in vivo. Occasionally structures similar to "Call-Exner-bodies" were found on the surface epithelium near to preovulatory follicles. Intercellular spaces of various sizes were also numerous. Disappearance of surface epithelium in the apex of follicles was often observed and the matrix of the tunica albuginea consisted of dissociated fibers and degenerating cells. This study showed that the isolated perfused rabbit ovary can serve as a model for studying the biology and pathology of ovarian surface epithelium.

[Extramammary Paget's disease: clinical and histologic documentation of 2 forms]

There are two forms of extramammary Paget's disease in respect of clinic, therapy and prognosis. In most cases (about 95%) extramammary Paget's disease is an intraepidermal manifestation of a cutaneous adenocarcinoma. After horizontal spreading within the epidermis, malignant growth continues along the adjacent adnexal structures with dermal spreading and subsequent metastases. In rare cases (approx. 5%), extramammary Paget's disease is an epidermal manifestation of an adenocarcinoma primarily located in the intestinal or urogenital tract. Further diagnostic and therapeutical procedures depend upon the type of extramammary Paget's disease.

[Histopathology of tubal pregnancy]

The histopathological examination of several sections of tubal ectopic pregnancies shows that the growth of the trophoblast mostly takes place in an extraluminal site subperitoneally and that the dilated tube is caused by coagulated blood and not by the trophoblast.

[Ovarian surface epithelium and its histogenic relation to ovarian cancer]

Approximately 80 to 90 per cent of adult ovarian cancers are assumed to originate from ovarian surface cells. A series of morphological and biochemical studies has been recently conducted to test this. The ovarian surface epithelium shows permanent morphological changes such as crypts, inclusion cysts, villous processes and different forms of müllerian epithelium. The unique nature of ovarian surface changes and their abrupt disappearance in immediately adjacent mesothelia suggest that local factors may play an important part in modifying the growth and morphogenesis of the epithelium of the ovarian surface. Whether these endogenous and/or exogenous factors may also induce surface neoplasia is a moot point.

[Extraoral manifestation of a white sponge nevus of the mucosa]

The nevus spongiosus albus mucosae (resp. white sponge nevus in the angloamerican literature) is a hereditary leukokeratosis localised preferably in the oral mucosa, but may simultaneously manifest itself in other regions, e.g. perianally. We report the case of a 18-year old patient with a primarily and exclusively extraorally located nevus spongiosus albus mucosae of the vulva. The differential diagnosis and clinical as well as therapeutical problems of this extremely rare disease are discussed.