Automatic annotation techniques for gene expression images of the fruit fly embryo

Circadian clocks are cell-autonomous endogenous oscillators, generated and maintained by self-sustained 24-h rhythms of clock gene expression. In the fruit fly Drosophila melanogaster, these daily rhythms of gene expression regulate the activity of approximately 150 clock neurons in the fly brain, which are responsible for driving the daily rest/activity cycles of these insects. Despite their endogenous character, circadian clocks communicate with the environment in order to synchronize their self-sustained molecular oscillations and neuronal activity rhythms (internal time) with the daily changes of light and temperature dictated by the Earth’s rotation around its axis (external time). Light and temperature changes are reliable time cues (Zeitgeber) used by many organisms to synchronize their circadian clock to the external time. In Drosophila, both light and temperature fluctuations robustly synchronize the circadian clock in the absence of the other Zeitgeber. The complex mechanisms for synchronization to the daily light–dark cycles are understood with impressive detail. In contrast, our knowledge about how the daily temperature fluctuations synchronize the fly clock is rather limited. Whereas light synchronization relies on peripheral and clock-cell autonomous photoreceptors, temperature input to the clock appears to rely mainly on sensory cells located in the peripheral nervous system of the fly. Recent studies suggest that sensory structures located in body and head appendages are able to detect temperature fluctuations and to signal this information to the brain clock. This review will summarize these studies and their implications about the mechanisms underlying temperature synchronization.

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Temporal patterns of gene expression in the antenna of the adult Drosophila melanogaster.

Genetics ◽

10.1093/genetics/140.2.549 ◽

1995 ◽

Vol 140 (2) ◽

pp. 549-555 ◽

Cited By ~ 1

Author(s):

S L Helfand ◽

K J Blake ◽

B Rogina ◽

M D Stracks ◽

A Centurion ◽

...

Keyword(s):

Gene Expression ◽

Life Span ◽

Time Course ◽

Adult Life ◽

Temporal Patterns ◽

Fruit Fly ◽

Reporter Protein ◽

Adult Age ◽

Biological Time ◽

Adult Drosophila

Abstract The time course of gene expression in the adult fruit fly has been partially characterized by using enhancer trap and reporter gene constructs that mark 49 different genes. The relative intensity of the reporter protein in individual cells of the antennae was measured as a function of adult age. Most genes showed a graduated expression, and the intensity of expression had a reproducible and characteristic time course. Different genes displayed different temporal patterns of expression and more often than not the pattern of expression was complex. We found a number of genes having patterns that scaled with life span. In these cases the intensity of gene expression was found to be invariant with respect to biological time, when expressed as a fraction of the life span of the line. The scaling was observed even when life span was varied as much as threefold. Such scaling serves to (1) further demonstrate that deterministic mechanisms such as gene regulation act to generate the temporal patterns of expression seen during adult life, (2) indicate that control of these regulatory mechanisms is linked to life span, and (3) suggest mechanisms by which this control is accomplished. We have concluded that gene expression in the adult fly is often regulated in a fashion that allows for graduated expression over time, and that the regulation itself is changing throughout adult life according to some prescribed program or algorithm.

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Dietary wheat germ oil influences gene expression in larvae and eggs of the oriental fruit fly

Archives of Insect Biochemistry and Physiology ◽

10.1002/arch.20398 ◽

2010 ◽

Vol 76 (2) ◽

pp. 67-82 ◽

Cited By ~ 9

Author(s):

Thomas A. Coudron ◽

Chiou Ling Chang ◽

Cynthia L. Goodman ◽

David Stanley

Keyword(s):

Gene Expression ◽

Wheat Germ ◽

Fruit Fly ◽

Oriental Fruit Fly ◽

Wheat Germ Oil

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Evaluation of endogenous references for gene expression profiling in different tissues of the oriental fruit fly Bactrocera dorsalis (Diptera: Tephritidae)

BMC Molecular Biology ◽

10.1186/1471-2199-11-76 ◽

2010 ◽

Vol 11 (1) ◽

Cited By ~ 117

Author(s):

Guang-Mao Shen ◽

Hong-Bo Jiang ◽

Xiao-Na Wang ◽

Jin-Jun Wang

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Fruit Fly ◽

Bactrocera Dorsalis ◽

Oriental Fruit Fly ◽

Different Tissues

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GA-repeats on mammalian X chromosomes support Ohno’s hypothesis of dosage compensation by transcriptional upregulation

10.1101/485300 ◽

2018 ◽

Author(s):

Edridge D’Souza ◽

Elizaveta Hosage ◽

Kathryn Weinand ◽

Steve Gisselbrecht ◽

Vicky Markstein ◽

...

Keyword(s):

Gene Expression ◽

Transposable Elements ◽

X Chromosome ◽

Dosage Compensation ◽

Binding Sites ◽

Convergent Evolution ◽

Fruit Fly ◽

Dosage Compensation Complex ◽

X Chromosomes ◽

Repeat Sequences

ABSTRACTOver 50 years ago, Susumo Ohno proposed that dosage compensation in mammals would require upregulation of gene expression on the single active X chromosome, a mechanism which to date is best understood in the fruit fly Drosophila melanogaster. Here, we report that the GA-repeat sequences that recruit the conserved MSL dosage compensation complex to the Drosophila X chromosome are also enriched across mammalian X chromosomes, providing genomic support for the Ohno hypothesis. We show that mammalian GA-repeats derive in part from transposable elements, suggesting a mechanism whereby unrelated X chromosomes from dipterans to mammals accumulate binding sites for the MSL dosage compensation complex through convergent evolution, driven by their propensity to accumulate transposable elements.

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From Egg to Organism

10.1093/oso/9780197604540.003.0010 ◽

2021 ◽

pp. 131-150

Author(s):

Franklin M. Harold

Keyword(s):

Gene Expression ◽

Cell Migration ◽

Single Cell ◽

Sea Urchin ◽

Spatial Organization ◽

Fruit Fly ◽

Chemical Gradients ◽

Developmental Fate ◽

Multiple Cycles ◽

Fertilized Egg

How an egg turns into an organism continues to baffle the imagination. We can describe how it happens and many of the particulars, but still struggle to comprehend how events at the levels of genes and cells produce a fruit fly, a sea urchin, or a baby. The fertilized egg, at bottom a single cell, undergoes multiple cycles of division with concurrent differentiation and transformations of shape, resulting in a multicellular embryo whose several regions are committed to develop into distinct organs. Differentiation relies on elaborate networks of control on gene expression that promote certain genes and silence others. Spatial organization of the embryo commonly involves diffusible “morphogens,” hormone-like substances that instruct cells as to their developmental fate. Chemical gradients are supplemented by diverse processes that draw on active transport, mechanical forces, and cell migration. Genes do not hold a comprehensive blueprint for development. They operate in the context of cells that are directed by both genes and self-organization, and there is no plan separable from its execution. How an egg turns into an organism may no longer be mysterious or miraculous, but it remains as wondrous as ever that an assemblage of lifeless molecules can build a butterfly.

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AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model

Bioinformatics ◽

10.1093/bioinformatics/bty1064 ◽

2019 ◽

Vol 35 (16) ◽

pp. 2834-2842 ◽

Cited By ~ 2

Author(s):

Yang Yang ◽

Mingyu Zhou ◽

Qingwei Fang ◽

Hong-Bin Shen

Keyword(s):

Gene Expression ◽

Large Scale ◽

Image Annotation ◽

Fruit Fly ◽

Genome Project ◽

Supplementary Information ◽

Berkeley Drosophila Genome Project ◽

Drosophila Genome ◽

Single Instance ◽

Temporal Expression Pattern

Abstract Motivation In the post-genomic era, image-based transcriptomics have received huge attention, because the visualization of gene expression distribution is able to reveal spatial and temporal expression pattern, which is significantly important for understanding biological mechanisms. The Berkeley Drosophila Genome Project has collected a large-scale spatial gene expression database for studying Drosophila embryogenesis. Given the expression images, how to annotate them for the study of Drosophila embryonic development is the next urgent task. In order to speed up the labor-intensive labeling work, automatic tools are highly desired. However, conventional image annotation tools are not applicable here, because the labeling is at the gene-level rather than the image-level, where each gene is represented by a bag of multiple related images, showing a multi-instance phenomenon, and the image quality varies by image orientations and experiment batches. Moreover, different local regions of an image correspond to different CV annotation terms, i.e. an image has multiple labels. Designing an accurate annotation tool in such a multi-instance multi-label scenario is a very challenging task. Results To address these challenges, we develop a new annotator for the fruit fly embryonic images, called AnnoFly. Driven by an attention-enhanced RNN model, it can weight images of different qualities, so as to focus on the most informative image patterns. We assess the new model on three standard datasets. The experimental results reveal that the attention-based model provides a transparent approach for identifying the important images for labeling, and it substantially enhances the accuracy compared with the existing annotation methods, including both single-instance and multi-instance learning methods. Availability and implementation http://www.csbio.sjtu.edu.cn/bioinf/annofly/ Supplementary information Supplementary data are available at Bioinformatics online.

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