Visualization of endogenous gut bacteria in Drosophila melanogaster using fluorescence in situ hybridization

All metazoans are colonized by a complex and diverse set of microorganisms. The microbes colonize all parts of the body and are especially abundant in the gastrointestinal tract, where they constitute the gut microbiome. The fruit fly Drosophila melanogaster turned out to be an exquisite model organism to functionally test the importance of an intact gut microbiome. Still, however, fundamental questions remain unanswered. For example, it is unknown whether a fine-tuned regionalization of the gut microbiome exists and how such a spatial organization could be established. In order to pave the way for answering this question, we generated an optimized and adapted fluorescence in situ hybridization (FISH) protocol. We focused on the detection of the two major Drosophila gut microbiome constituting bacteria genera: Acetobacter and Lactobacillus. FISH allows to detect the bacteria in situ and thus to investigate their spatial localization in respect to the host as well as to other microbiome members. We demonstrate the applicability of the protocol using a diverse set of sample types.

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Quantitative investigation reveals distinct phases in Drosophila sleep

Communications Biology ◽

10.1038/s42003-021-01883-y ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Xiaochan Xu ◽

Wei Yang ◽

Binghui Tian ◽

Xiuwen Sui ◽

Weilai Chi ◽

...

Keyword(s):

Drosophila Melanogaster ◽

General Pattern ◽

Model Organism ◽

Infrared Camera ◽

Fruit Fly ◽

Genetic Dissection ◽

Power Law Distribution ◽

Quantitative Investigation ◽

Waking Up ◽

Set Up

AbstractThe fruit fly, Drosophila melanogaster, has been used as a model organism for the molecular and genetic dissection of sleeping behaviors. However, most previous studies were based on qualitative or semi-quantitative characterizations. Here we quantified sleep in flies. We set up an assay to continuously track the activity of flies using infrared camera, which monitored the movement of tens of flies simultaneously with high spatial and temporal resolution. We obtained accurate statistics regarding the rest and sleep patterns of single flies. Analysis of our data has revealed a general pattern of rest and sleep: the rest statistics obeyed a power law distribution and the sleep statistics obeyed an exponential distribution. Thus, a resting fly would start to move again with a probability that decreased with the time it has rested, whereas a sleeping fly would wake up with a probability independent of how long it had slept. Resting transits to sleeping at time scales of minutes. Our method allows quantitative investigations of resting and sleeping behaviors and our results provide insights for mechanisms of falling into and waking up from sleep.

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New Data on Organization and Spatial Localization of B-Chromosomes in Cell Nuclei of the Yellow-Necked Mouse Apodemus flavicollis

Cells ◽

10.3390/cells10071819 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1819

Author(s):

Tatyana Karamysheva ◽

Svetlana Romanenko ◽

Alexey Makunin ◽

Marija Rajičić ◽

Alexey Bogdanov ◽

...

Keyword(s):

In Situ Hybridization ◽

Sex Chromosomes ◽

Interphase Nucleus ◽

Spatial Organization ◽

Three Dimensional ◽

Dna Probes ◽

B Chromosomes ◽

Apodemus Flavicollis ◽

Yellow Necked Mouse

The gene composition, function and evolution of B-chromosomes (Bs) have been actively discussed in recent years. However, the additional genomic elements are still enigmatic. One of Bs mysteries is their spatial organization in the interphase nucleus. It is known that heterochromatic compartments are not randomly localized in a nucleus. The purpose of this work was to study the organization and three-dimensional spatial arrangement of Bs in the interphase nucleus. Using microdissection of Bs and autosome centromeric heterochromatic regions of the yellow-necked mouse (Apodemus flavicollis) we obtained DNA probes for further two-dimensional (2D)- and three-dimensional (3D)- fluorescence in situ hybridization (FISH) studies. Simultaneous in situ hybridization of obtained here B-specific DNA probes and autosomal C-positive pericentromeric region-specific probes further corroborated the previously stated hypothesis about the pseudoautosomal origin of the additional chromosomes of this species. Analysis of the spatial organization of the Bs demonstrated the peripheral location of B-specific chromatin within the interphase nucleus and feasible contact with the nuclear envelope (similarly to pericentromeric regions of autosomes and sex chromosomes). It is assumed that such interaction is essential for the regulation of nuclear architecture. It also points out that Bs may follow the same mechanism as sex chromosomes to avoid a meiotic checkpoint.

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Three-dimensional electron microscopy of ribosomal chromatin in two higher plants: a cytochemical, immunocytochemical, and in situ hybridization approach.

Journal of Histochemistry & Cytochemistry ◽

10.1177/39.11.1918926 ◽

1991 ◽

Vol 39 (11) ◽

pp. 1495-1506 ◽

Cited By ~ 22

Author(s):

P M Motte ◽

R Loppes ◽

M Menager ◽

R Deltour

Keyword(s):

Electron Microscopy ◽

In Situ Hybridization ◽

Spatial Organization ◽

Higher Plants ◽

Three Dimensional ◽

Spatial Arrangement ◽

Thin Sections ◽

Cytoplasmic Dna ◽

Immunocytochemical Techniques

We report the 3-D arrangement of DNA within the nucleolar subcomponents from two evolutionary distant higher plants, Zea mays and Sinapis alba. These species are particularly convenient to study the spatial organization of plant intranucleolar DNA, since their nucleoli have been previously reconstructed in 3-D from serial ultra-thin sections. We used the osmium ammine-B complex (a specific DNA stain) on thick sections of Lowicryl-embedded root fragments. Immunocytochemical techniques using anti-DNA antibodies and rDNA/rDNA in situ hybridization were also applied on ultra-thin sections. We showed on tilted images that the OA-B stains DNA throughout the whole thickness of the section. In addition, very low quantities of cytoplasmic DNA were stained by this complex, which is now the best DNA stain used in electron microscopy. Within the nucleoli the DNA was localized in the fibrillar centers, where large clumps of dense chromatin were also visible. In the two plant species intranucleolar chromatin forms a complex network with strands partially linked to chromosomal nucleolar-organizing regions identified by in situ hybridization. This study describes for the first time the spatial arrangement of the intranucleolar chromatin in nucleoli of higher plants using high-resolution techniques.

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Characterization of the genome of the mealybug Planococcus lilacinus, a model organism for studying whole-chromosome imprinting and inactivation

Genetics Research ◽

10.1017/s0016672302005566 ◽

2002 ◽

Vol 79 (2) ◽

pp. 111-118 ◽

Cited By ~ 6

Author(s):

K. NAGA MOHAN ◽

PARAMITA RAY ◽

H. SHARAT CHANDRA

Keyword(s):

Drosophila Melanogaster ◽

Repetitive Sequences ◽

Gc Content ◽

Model Organism ◽

Fruit Fly ◽

Single Copy ◽

Coding Sequences ◽

Repeat Sequences ◽

Chromosome Imprinting

The co-occurrence of three chromosome-wide phenomena – imprinting, facultative heterochromatization and diffuse centromere – in the mealybug Planococcus lilacinus makes investigation of the genomics of this species an attractive prospect. In order to estimate the complexity of the genome of this species, 300 random stretches of its DNA, constituting ∼0·1% of the genome, were sequenced. Coding sequences appear to constitute ∼53·5%, repeat sequences ∼44·5% and non-coding single-copy sequences ∼2% of the genome. The proportion of repetitive sequences in the mealybug is higher than that in the fruit fly Drosophila melanogaster (∼30%). The mealybug genome (∼220 Mb) is about 1·3 times the size of the fly genome (∼165 Mb) and its GC content (∼35%) less than that of the fly genome (∼40%). The relative abundance of various dinucleotides, as analysed by the method of Gentles and Karlin, shows that the dinucleotide signatures of the two species are moderately similar and that in the mealybug there is neither over-representation nor under-representation of any dinucleotide.

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The genome of the olive fruit fly Bactrocera oleae: localization of molecular markers by in situ hybridization to the salivary gland polytene chromosomes

Genome ◽

10.1139/gen-42-4-744 ◽

1999 ◽

Vol 42 (4) ◽

pp. 744-751 ◽

Cited By ~ 13

Author(s):

Anna Zambetaki ◽

Antigone Zacharopoulou ◽

Zacharias G. Scouras ◽

Penelope Mavragani-Tsipidou

Keyword(s):

Salivary Gland ◽

Molecular Markers ◽

In Situ Hybridization ◽

Polytene Chromosomes ◽

Fruit Fly ◽

Bactrocera Oleae ◽

Olive Fruit Fly ◽

Olive Fruit

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Cellular localization of mRNAs for prostaglandin E receptor subtypes in mouse gastrointestinal tract

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.1997.272.3.g681 ◽

1997 ◽

Vol 272 (3) ◽

pp. G681-G687 ◽

Cited By ~ 17

Author(s):

K. Morimoto ◽

Y. Sugimoto ◽

M. Katsuyama ◽

H. Oida ◽

K. Tsuboi ◽

...

Keyword(s):

Gastrointestinal Tract ◽

Epithelial Cells ◽

Cellular Localization ◽

The Body ◽

Prostaglandin E ◽

Receptor Subtypes ◽

Fundic Gland ◽

Intestinal Functions ◽

Myenteric Ganglia

Regional and cellular distribution of mRNAs for prostaglandin E (PGE) receptor subtypes was investigated in the mouse gastrointestinal tract by in situ hybridization. Strong signals for EP1 transcripts were detected in cells of the muscularis mucosae layer, especially in the body of the stomach. Intense signals for EP3 transcripts were detected in neurons of the myenteric ganglia throughout the tract. Moderate EP3 mRNA expression was also observed in fundic gland epithelial cells, except for surface mucous cells in the stomach. Expression of EP4 mRNA was moderate in surface epithelial cells of the corpus and in glands from the surface to the base of the antrum. Strong EP4 signals were observed in the epithelium in the duodenum, jejunum, and ileum. In the ileum, signals were only observed in the upper part of the villi. However, no or weak signals for EP2 transcripts were detected. These findings suggest that PGE2 modulates various gastric or intestinal functions via at least three different PGE receptors.

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Quantitative in situ hybridization of ribosomal RNA species to polytene chromosomes of Drosophila melanogaster

Journal of Molecular Biology ◽

10.1016/0022-2836(77)90170-x ◽

1977 ◽

Vol 115 (3) ◽

pp. 539-563 ◽

Cited By ~ 74

Author(s):

Paul Szabo ◽

Robert Elder ◽

Dale M. Steffensen ◽

Olke C. Uhlenbeck

Keyword(s):

Drosophila Melanogaster ◽

In Situ Hybridization ◽

Ribosomal Rna ◽

Polytene Chromosomes

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Location of PHM/VIP mRNA in human gastrointestinal tract detected by in situ hybridization

Cell and Tissue Research ◽

10.1007/s004410050085 ◽

1994 ◽

Vol 276 (2) ◽

pp. 229-238 ◽

Cited By ~ 1

Author(s):

Helle E. Bredkj'r ◽

Birgitte S. Wulff ◽

Piers C. Emson ◽

Jan Fahrenkrug

Keyword(s):

In Situ Hybridization ◽

Gastrointestinal Tract ◽

Human Gastrointestinal Tract

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Location of PHM/VIP mRNA in human gastrointestinal tract detected by in situ hybridization

Cell and Tissue Research ◽

10.1007/bf00306108 ◽

1994 ◽

Vol 276 (2) ◽

pp. 229-238 ◽

Cited By ~ 12

Author(s):

Helle E. Bredkj�r ◽

Birgitte S. Wulff ◽

Piers C. Emson ◽

Jan Fahrenkrug

Keyword(s):

In Situ Hybridization ◽

Gastrointestinal Tract ◽

Human Gastrointestinal Tract

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Transformation of Drosophila melanogaster with a suppressor tRNA gene from Schizosaccharomyces pombe

Genome ◽

10.1139/g88-036 ◽

1988 ◽

Vol 30 (2) ◽

pp. 211-217 ◽

Cited By ~ 3

Author(s):

Charles M. Molnar ◽

Tove Reece ◽

James A. Williams ◽

John B. Bell

Keyword(s):

Drosophila Melanogaster ◽

Salivary Gland ◽

In Situ Hybridization ◽

Schizosaccharomyces Pombe ◽

Southern Hybridization ◽

Trna Gene ◽

P Element ◽

Suppressor Trna ◽

Good Agreement

P-element mediated transformation was utilized to introduce a suppressor tRNA gene [Formula: see text] from Schizosaccharomyces pombe into Drosophila melanogaster. Thirteen independently transformed lines were characterized as to the number and cytological locations of the transposons. It was ascertained that the suppressor tRNA gene of interest was introduced into each transformed strain. The helper P element used (pπ25.1) allows further transposition to occur, and it was determined that from one to seven copies of the heterologous [Formula: see text] gene per strain were present among the respective transformed strains. The number of transposons per transformed line was established by in situ hybridization to salivary gland chromosomes as well as by Southern hybridization analyses and there was good agreement in the totals determined by these two techniques.Key words: Drosophila, Schizosaccharomyces, tRNA suppressor, transformation, transposon.

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