Yeast transformation process studied by fluorescence labeling technique

A new method based on fluorescence imaging and flow cytometry was developed to investigate the transformation process of Saccharomyces cerevisiae AY. Yeast and fluorescent-labeled plasmid pUC18 were used as models of cells and DNA molecules, respectively. Binding of DNA molecules to yeast cell surfaces was observed. Factors influencing DNA binding to cell surfaces were investigated. It has been found that poly(ethylene glycol) (PEG) could induce DNA binding to yeast surfaces, while Li(+) showed a weak effect on the binding. When both Li(+) and PEG were used, synergetic effect occurred, resulting in the binding of pUC18 to the surface of more yeast cells compared with that in the presence of PEG or Li(+) only. It was also confirmed that heat shock, Li(+), and PEG all can increase the permeability of yeast cells. This simple method is helpful for understanding the process of yeast transformation and can be used to investigate the interaction of DNA with cell surfaces.     

Flybow: genetic multicolor cell labeling for neural circuit analysis in Drosophila melanogaster

To facilitate studies of neural network architecture and formation, we generated three Drosophila melanogaster variants of the mouse Brainbow-2 system, called Flybow. Sequences encoding different membrane-tethered fluorescent proteins were arranged in pairs within cassettes flanked by recombination sites. Flybow combines the Gal4-upstream activating sequence binary system to regulate transgene expression and an inducible modified Flp-FRT system to drive inversions and excisions of cassettes. This provides spatial and temporal control over the stochastic expression of one of two or four reporters within one sample. Using the visual system, the embryonic nervous system and the wing imaginal disc, we show that Flybow in conjunction with specific Gal4 drivers can be used to visualize cell morphology with high resolution. Finally, we demonstrate that this labeling approach is compatible with available Flp-FRT-based techniques, such as mosaic analysis with a repressible cell marker; this could further support the genetic analysis of neural circuit assembly and function.     

Temporal classification of Drosophila segmentation gene expression patterns by the multi-valued neural recognition method

In order to reconstruct the establishment of the body pattern over time in Drosophila embryos, we have developed automated methods for detecting the age of an embryo on the basis of knowledge about its gene expression patterns. In this paper we perform temporal classification of confocal images of expression patterns of genes controlling segmentation by means of a neural network based on multi-valued neurons (MVN). MVN are artificial neural processing elements with complex-valued weights and high functionality, which proved to be efficient for solving the image recognition problems. The results obtained by this method confirm its efficiency for image recognition and indicate that the method can detect characteristic features of expression patterns which mark their development over time.     

Automated annotation of Drosophila gene expression patterns using a controlled vocabulary

MOTIVATION: Regulation of gene expression in space and time directs its localization to a specific subset of cells during development. Systematic determination of the spatiotemporal dynamics of gene expression plays an important role in understanding the regulatory networks driving development. An atlas for the gene expression patterns of fruit fly Drosophila melanogaster has been created by whole-mount in situ hybridization, and it documents the dynamic changes of gene expression pattern during Drosophila embryogenesis. The spatial and temporal patterns of gene expression are integrated by anatomical terms from a controlled vocabulary linking together intermediate tissues developed from one another. Currently, the terms are assigned to patterns manually. However, the number of patterns generated by high-throughput in situ hybridization is rapidly increasing. It is, therefore, tempting to approach this problem by employing computational methods. RESULTS: In this article, we present a novel computational framework for annotating gene expression patterns using a controlled vocabulary. In the currently available high-throughput data, annotation terms are assigned to groups of patterns rather than to individual images. We propose to extract invariant features from images, and construct pyramid match kernels to measure the similarity between sets of patterns. To exploit the complementary information conveyed by different features and incorporate the correlation among patterns sharing common structures, we propose efficient convex formulations to integrate the kernels derived from various features. The proposed framework is evaluated by comparing its annotation with that of human curators, and promising performance in terms of F1 score has been reported.     

Intertidal exposure zones: A way to subdivide the shore

A new way of subdividing the shore is described and Doty's concept of critical tide levels (CTLs), on which the scheme is based, is revised. The various cycles of the tide (e.g., daily, monthly, and annual cycles) define several different orders of CTL at which the duration of continuous exposure or submergence increases abruptly by a discrete interval, the magnitude of which is determined by cycle period. Contrary to popular belief, most CTLs are common to all tidal types (i.e., mixed, semi-diurnal, and diurnal) and thus they can be used as reference levels for cross-comparing different intertidal regions, regardless of tidal type. CTLs naturally subdivide the intertidal region into discrete exposure zones, here called the atmozone, amphizone, and aquazone, which have upper and lower subzones. The amphizone, the intertidal core, experiences exposure and submergence extremes in terms of hours (? 1 lunar day). The overlying lower atmozone and underlying upper aquazone experience exposure and submergence extremes, respectively, of the order of days (?2 to ≈10 days), while in the upper atmozone and lower aquazone extremes are measured in months or years (> ≈20 days).In most intertidal environments (tidal flats, saltmarshes, brackish marshes, and sheltered rocky shores) CTLs (including exposure zone boundaries) probably limit some biological zones. For tidal flats experiencing large tidal ranges it is possible that biological zones in the fringes of the intertidal region shift in response to long-term fluctuations in the levels of CTLs, due to the effects of the 18.6 year soli-lunar cycle.     

Activity labeling patterns in the medulla of Drosophila melanogaster caused by motion stimuli

Summary We quantitatively describe 2-deoxyglucose (2-DG) neuronal activity labeling patterns in the first and second visual neuropil regions of the Drosophila brain, the lamina and the medulla. Careful evaluation of activity patterns resulting from large-field motion stimulation shows that the stimulus-specific bands in the medulla correspond well to the layers found in a quantitative analysis of Golgi-impregnated columnar neurons. A systematic analysis of autoradiograms of different intensities reveals a hierarchy of labeling in the medulla. Under certain conditions, only neurons of the lamina are labeled. Their characteristic terminals in the medulla are used to differentiate among the involved lamina monopolar cell types. The 2-DG banding pattern in the medulla marks layers M1 and M5, the input layers of pathway p1 (the L1 pathway). Therefore, activity labeling of L1 by motion stimuli is very likely. More heavily labeled autoradiograms display activated cells also in layers M2, M9, and M10. The circuitry involved in the processing of motion information thus concentrates on pathways p1 and p2. Layers M4 and M6 of the distal medulla hardly display any label under the stimulus conditions used. The functional significance of selective activity in the medulla is discussed.     

Road to precision: recombinase-based targeting technologies for genome engineering

In the past years, recombinase-based approaches for integrating transgenes into defined chromosomal loci of mammalian cells have gained increasing attention. This method is attractive since it enables to precisely integrate transgenes of interest into pre-defined integration sites, thereby allowing to predict the expression properties of a genetically manipulated cell. This review focuses on the current state of targeting strategies including RMCE employing site-specific recombinases such as Cre, Flp and PhiC31. In particular, applications for protein expression, virus production, transgenic animals and chromosome engineering are described.     

Application of 2-aminopyridine fluorescence labeling to glycosaminoglycans

A pyridylamination method was applied to glycosaminoglycans and the characteristics of the resulting pyridylamino glycosaminoglycans were examined. First, glycosaminoglycan chains, which uniformly possess a xylose residue at their reducing termini, were liberated from proteoglycan by successive digestion with protease and endo-beta-xylosidase. Then the glycosaminoglycan chains were coupled with 2-aminopyridine by reductive amination with sodium cyanoborohydride for 15 h according to the method of Hase, S. et al. [J. Biochem. 95, 197-203 (1984)]. The pyridylamination reaction caused neither depolymerization, de-N-acetylation, nor de-N- or de-O-sulfation. The pyridylamino glycosaminoglycan chains had an intact linkage region (GlcA-Gal-Gal-Xyl) between the carbohydrate chain and the peptide core of the proteoglycan. These pyridylamino glycosaminoglycans should be useful as substrates for endo-type glycosidases that act on glycosaminoglycan chains and as markers for studies of glycosaminoglycan metabolism.     

Analysis of biofilm structure and gene expression using fluorescence dual labeling.

The use of biofilms for the degradation of recalcitrant environmental contaminants or for the production of secondary metabolites necessitates understanding and controlling gene expression. In this work, dual labeling with green fluorescent protein (GFP) variants was used to investigate inducible gene expression in a biofilm. Colocalization of GFP emissions was used to determine regions of attached cells and to correlate structure and activity within the biofilm. The labeling strategy reported here is unique in that the two GFP signals were distinguished by differential excitation rather than differential emission.     

Correspondence of banding patterns to 3H-thymidine labeling patterns in polytene chromosomes

³H-thymidine labeling frequencies over X chromosomal region 1A-4E of Drosophila melanogaster, were analysed with reference to chromosome sections with and without prominent bands. A correspondence was found between band sections and late start of silver grain labeling at the initial stage in combination with late labeling at the end stage of replication. A complementary situation is always to be found over puff/interband sections, where an early start of labeling at the initial stage is generally combined with early labeling completion at the end stage of replication.     

Drosophila olfactory memory: single genes to complex neural circuits

A central goal of neuroscience is to understand how neural circuits encode memory and guide behaviour. Studying simple, genetically tractable organisms, such as Drosophila melanogaster, can illuminate principles of neural circuit organization and function. Early genetic dissection of D. melanogaster olfactory memory focused on individual genes and molecules. These molecular tags subsequently revealed key neural circuits for memory. Recent advances in genetic technology have allowed us to manipulate and observe activity in these circuits, and even individual neurons, in live animals. The studies have transformed D. melanogaster from a useful organism for gene discovery to an ideal model to understand neural circuit function in memory.     

Modulation of neural carbohydrate epitope expression in Drosophila melanogaster cells

Neural pathways in invertebrates are often tracked using anti-horseradish peroxidase, a cross-reaction due to the presence of core alpha1,3-fucosylated N-glycans. In order to investigate the molecular basis of this epitope in a cellular context, we compared two Drosophila melanogaster cell lines: the S2 and the neuronal-like BG2-c6 cell lines. As shown by mass spectrometric and chromatographic analyses, only the BG2-c6 cell line expresses alpha1,3/alpha1,6-difucosylated N-glycans, a result that correlates with anti-horseradish peroxidase binding. Of all four alpha1,3-fucosyltransferase homologues previously identified, the core alpha1,3-fucosyltransferase (FucTA; EC 2.4.1.214) is expressed in the neuronal cell line as well as throughout fly development and in heads and bodies of flies of both sexes. This pattern is distinctive in comparison with the expression of the other three alpha1,3-fucosyltransferase homologues (FucTB, FucTC, and FucTD). Furthermore, only transfection of FucTA cDNA into S2 cells resulted in expression of the anti-horseradish peroxidase epitope, a result compatible with its substrate specificity in vitro. Finally, silencing of FucTA by RNAi in the neuronal cell line led to a significant reduction of anti-horseradish peroxidase binding. The present study, in conjunction with our previous in vitro data, thereby shows that FucTA is indispensable for expression of the neural carbohydrate epitope in Drosophila cells.     

Changes in the fluorescence patterns of translocated Y chromosome segments in Drosophila melanogaster

Fluorescence analysis after quinacrine staining in squashes of Varese wild stock male larval ganglia confirmed that the Y chromosome has four characteristic sections of bright fluorescence. In one Y/X and in one Y/III translocation the section of bright fluorescence on the short arm of the Y is no longer bright when translocated onto the terminal portion of the X and on the right arm of the III chromosome, respectively. Fluorescence analysis has also permitted the identification of a structurally abnormal Y chromosome in a cell line of Drosophila melanogaster established in vitro. The findings in the two translocations call for caution in the interpretation of structural rearrangements by fluorescence analysis.     

Embryonic expression patterns of the Drosophila dystrophin-associated glycoprotein complex orthologs

Mutations in genes encoding proteins of the human dystrophin-associated glycoprotein complex (DGC) cause the Duchenne, Becker and limb-girdle muscular dystrophies. Subsets of the DGC proteins form tissue-specific complexes which are thought to play structural and signaling roles in the muscle and at the neuromuscular junction. Furthermore, mutations in the dystrophin gene that lead to Duchenne muscular dystrophy are frequently associated with cognitive and behavioral deficits, suggesting a role for dystrophin in the nervous system. Despite significant progress over the past decade, many fundamental questions about the roles played by dystrophin and the other DGC proteins in the muscle and peripheral and central nervous systems remain to be answered. Mammalian models of DGC gene function are complicated by the existence of fully or partially redundant genes whose functions can mask effects of the inactivation of a given DGC gene. The genome of the fruitfly Drosophila melanogaster encodes a single ortholog of the majority of the mammalian DGC protein subclasses, thus potentially simplifying their functional analysis. We report here the embryonic mRNA expression patterns of the individual DGC orthologs. We find that they are predominantly expressed in the nervous system and in muscle. Dystrophin, dystrobrevin-like, dystroglycan-like, syntrophin-like 1, and all three sarcoglycan orthologs are found in the brain and the ventral nerve cord, while dystrophin, dystrobrevin-like, dystroglycan-like, syntrophin-like 2, sarcoglycan alpha and sarcoglycan delta are expressed in distinct and sometimes overlapping domains of mesoderm-derived tissues, i.e. muscles of the body wall and around the gut.     

The Drosophila neural lineages: a model system to study brain development and circuitry

In Drosophila, neurons of the central nervous system are grouped into units called lineages. Each lineage contains cells derived from a single neuroblast. Due to its clonal nature, the Drosophila brain is a valuable model system to study neuron development and circuit formation. To better understand the mechanisms underlying brain development, genetic manipulation tools can be utilized within lineages to visualize, knock down, or over-express proteins. Here, we will introduce the formation and development of lineages, discuss how one can utilize this model system, offer a comprehensive list of known lineages and their respective markers, and then briefly review studies that have utilized Drosophila neural lineages with a look at how this model system can benefit future endeavors.     

Embryonic expression patterns of Drosophila ACS family genes related to the human sialin gene

The anion/cation symporter (ACS) family is a large subfamily of the major facilitator superfamily (MFS) of transporters. ACS family permeases are widely distributed in nature and transport either organic or inorganic anions in response to chemiosmotic cation gradients. The only protein in the ACS family to which a human disease has been linked, is sialin, the proton-driven lysosomal carrier for sialic acid. Genetic defects in sialin cause a lysosomal storage disease in humans. Here we have identified a group of conserved Drosophila ACS family genes related to sialin and studied their expression patterns throughout embryogenesis. Drosophila sialin-related genes are expressed in a wide variety of tissues. Expression is frequently observed throughout various parts of the intestinal tract, including Malpighian tubules and salivary glands. Additionally, some genes are expressed in vitellophages (yolk nuclei), nervous system, respiratory tract and a number of other embryonic tissues. These data will aid the establishment of a fruitfly model of human lysosomal storage disorders, the most common cause of neurodegeneration in childhood.     

Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization

We present an efficient method of introducing fluorophore labels at selected locations in a large RNA. The method is based on specific and highly efficient hybridization between a fluorophore-containing DNA oligonucleotide and a modular hairpin loop replacing a functionally unimportant hairpin loop in the RNA. We demonstrate its feasibility using a 255-nucleotide RNA derived from the catalytic domain of RNase P from Bacillus subtilis. Hybridization of the DNA oligonucleotide to the modular hairpin loop minimally perturbs the structure and function of this RNA. This labeling scheme should be applicable in studies of RNA conformational dynamics by ensemble and single molecule fluorescence methods.