scholarly journals Integrin-mediated attachment of the blastoderm to the vitelline envelope impacts gastrulation of insects

2018 ◽  
Author(s):  
Stefan Münster ◽  
Akanksha Jain ◽  
Alexander Mietke ◽  
Anastasios Pavlopoulos ◽  
Stephan W. Grill ◽  
...  
Keyword(s):  
Large Scale ◽  
Fruit Fly ◽  
Complete Loss ◽  
Embryonic Tissue ◽  
Spatiotemporal Pattern ◽  
Protective Shell ◽  
Physical Forces ◽  
Vitelline Envelope ◽  
Contractile Forces ◽  
Multicellular Organisms

AbstractDuring gastrulation, physical forces reshape the simple embryonic tissue to form a complex body plan of multicellular organisms1. These forces often cause large-scale asymmetric movements of the embryonic tissue2,3. In many embryos, the tissue undergoing gastrulation movements is surrounded by a rigid protective shell4,5. While it is well recognized that gastrulation movements depend on forces generated by tissue-intrinsic contractility6,7, it is not known if interactions between the tissue and the protective shell provide additional forces that impact gastrulation. Here we show that a particular part of the blastoderm tissue of the red flour beetle Tribolium castaneum tightly adheres in a temporally coordinated manner to the vitelline envelope surrounding the embryo. This attachment generates an additional force that counteracts the tissue-intrinsic contractile forces to create asymmetric tissue movements. Furthermore, this localized attachment is mediated by a specific integrin, and its knock-down leads to a gastrulation phenotype consistent with complete loss of attachment. Moreover, analysis of another integrin in the fruit fly Drosophila melanogaster suggests that gastrulation in this organism also relies on adhesion between the blastoderm and the vitelline. Together, our findings reveal a conserved mechanism whereby the spatiotemporal pattern of tissue adhesion to the vitelline envelope provides controllable counter-forces that shape gastrulation movements in insects.

scholarly journals Genome-wide Analysis of Alternative Pre-mRNA Splicing

2007 ◽  
Vol 283 (3) ◽  
pp. 1229-1233 ◽  
Author(s):  
Claudia Ben-Dov ◽  
Britta Hartmann ◽  
Josefin Lundgren ◽  
Juan Valcárcel
Keyword(s):  
Alternative Splicing ◽  
Large Scale ◽  
Mrna Splicing ◽  
Diagnostic Tools ◽  
Primary Transcript ◽  
Genome Wide ◽  
Human Genes ◽  
Multicellular Organisms ◽  
Eukaryotic Genomes ◽  
Key Questions

Alternative splicing of mRNA precursors allows the synthesis of multiple mRNAs from a single primary transcript, significantly expanding the information content and regulatory possibilities of higher eukaryotic genomes. High-throughput enabling technologies, particularly large-scale sequencing and splicing-sensitive microarrays, are providing unprecedented opportunities to address key questions in this field. The picture emerging from these pioneering studies is that alternative splicing affects most human genes and a significant fraction of the genes in other multicellular organisms, with the potential to greatly influence the evolution of complex genomes. A combinatorial code of regulatory signals and factors can deploy physiologically coherent programs of alternative splicing that are distinct from those regulated at other steps of gene expression. Pre-mRNA splicing and its regulation play important roles in human pathologies, and genome-wide analyses in this area are paving the way for improved diagnostic tools and for the identification of novel and more specific pharmaceutical targets.

scholarly journals Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions

2019 ◽  
Vol 7 ◽  
Author(s):  
Brian Stucky ◽  
James Balhoff ◽  
Narayani Barve ◽  
Vijay Barve ◽  
Laura Brenskelle ◽  
...  
Keyword(s):  
Natural History ◽  
Large Scale ◽  
Use Cases ◽  
Data Systems ◽  
Multiple Sources ◽  
History Data ◽  
Insect Ecology ◽  
Many Sources ◽  
Multicellular Organisms ◽  
Initial Results

Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. These data are typically highly heterogeneous and widely scattered among many sources, which makes developing robust information systems to aggregate and disseminate them a significant challenge. As a step towards this goal, we report initial results of a new effort to develop a standardized vocabulary and ontology for insect natural history data. In particular, we describe a new database of representative insect natural history data derived from multiple sources (but focused on data from specimens in biological collections), an analysis of the abstract conceptual areas required for a comprehensive ontology of insect natural history data, and a database of use cases and competency questions to guide the development of data systems for insect natural history data. We also discuss data modeling and technology-related challenges that must be overcome to implement robust integration of insect natural history data.

scholarly journals A large-scale resource for tissue-specific CRISPR mutagenesis in Drosophila

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Fillip Port ◽  
Claudia Strein ◽  
Mona Stricker ◽  
Benedikt Rauscher ◽  
Florian Heigwer ◽  
...  
Keyword(s):  
Large Scale ◽  
Target Genes ◽  
High Efficiency ◽  
Direct Sequencing ◽  
Fine Tuning ◽  
Genetic Screens ◽  
Efficient Gene ◽  
Crispr Screen ◽  
High Gene ◽  
Multicellular Organisms

Genetic screens are powerful tools for the functional annotation of genomes. In the context of multicellular organisms, interrogation of gene function is greatly facilitated by methods that allow spatial and temporal control of gene abrogation. Here, we describe a large-scale transgenic short guide (sg) RNA library for efficient CRISPR-based disruption of specific target genes in a constitutive or conditional manner. The library consists currently of more than 2600 plasmids and 1700 fly lines with a focus on targeting kinases, phosphatases and transcription factors, each expressing two sgRNAs under control of the Gal4/UAS system. We show that conditional CRISPR mutagenesis is robust across many target genes and can be efficiently employed in various somatic tissues, as well as the germline. In order to prevent artefacts commonly associated with excessive amounts of Cas9 protein, we have developed a series of novel UAS-Cas9 transgenes, which allow fine tuning of Cas9 expression to achieve high gene editing activity without detectable toxicity. Functional assays, as well as direct sequencing of genomic sgRNA target sites, indicates that the vast majority of transgenic sgRNA lines mediate efficient gene disruption. Furthermore, we conducted the so far largest fully transgenic CRISPR screen in any metazoan organism, which further supported the high efficiency and accuracy of our library and revealed many so far uncharacterized genes essential for development.

scholarly journals Spatiotemporal Pattern and Aggregation Effects of Poplar Canker in Northeast China

Forests ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 454
Author(s):  
He Yan ◽  
Liyuan Chen ◽  
Quansheng Ge ◽  
Chengming Tian ◽  
Jixia Huang
Keyword(s):  
Incidence Rate ◽  
Northeast China ◽  
Large Scale ◽  
Predisposing Factors ◽  
Scan Statistics ◽  
Liaoning Province ◽  
Economic Losses ◽  
Spatiotemporal Pattern ◽  
Spatiotemporal Aggregation ◽  
Primary Cluster

Research Highlights: This study looks at poplar canker caused by Cytospora chrysosperma as a geographical phenomenon, and it applies spatial statistics to reveal the pattern and aggregation effects of the disease on a large scale in time and space. The incidence area of poplar canker in Northeast China has spatial (spatiotemporal) aggregation effects, which emphasize the importance of coordinated prevention. The results of spatial and spatiotemporal clusters can guide specific regional prevention and indicate the possible predisposing factors, respectively. Background and Objectives: Poplar canker, a harmful forest biological disease that is widespread throughout Northeast China, brings enormous ecological and economic losses. The limited cognition of its spatiotemporal pattern and aggregation effects restricts the decision-making for regional prevention and the identification of disease-inducing conditions. This study aims to explore the spatiotemporal pattern and to detect the aggregation effects of the disease, trying to provide references for prevention. Materials and Methods: According to the incidence data of poplar canker reported by each county in Northeast China from 2002 to 2015, we mapped the distribution of the incidence rate in ArcGIS and performed retrospective scan statistics in SaTScan to detect the spatial and spatiotemporal aggregation effects of the incidence area. Results: The spatiotemporal pattern of poplar canker’s incidence rate presents the characteristic of “outbreak-aggregation-spread-stability.” The incidence area of the disease when we performed spatial aggregation scan statistics showed the primary cluster covering Liaoning province (LLR = 86469.86, p < 0.001). The annual spatial scan statistics detected a total of 14 primary clusters and 37 secondary clusters, indicating three phases of aggregation. The incidence area of disease also shows spatiotemporal aggregation effects with the primary cluster located around Liaoning province, appearing from 2009 to 2015 (LLR = 64182.00, p < 0.001). Conclusions: The incidence area of poplar canker presents significant characteristics of spatial and spatiotemporal aggregation, and we suggest attaching importance to the clues provided by the aggregation effects in disease prevention and identification of predisposing factors.

scholarly journals Hedgehog Signaling in Organogenesis and the Tumor Microenvironment

2020 ◽  
Vol 21 (8) ◽  
pp. 2788
Author(s):  
Tsuyoshi Shimo
Keyword(s):  
Drosophila Melanogaster ◽  
Tumor Microenvironment ◽  
Signaling Pathway ◽  
Genetic Screening ◽  
Hedgehog Signaling ◽  
Large Scale ◽  
Fruit Fly ◽  
Hedgehog Signaling Pathway ◽  
Body Segment ◽  
Larval Body

The Hedgehog signaling pathway was first discovered in 1980 during a large-scale genetic screening seeking to find mutations that affect larval body segment development in the fruit fly, Drosophila melanogaster [...]

Connected through the force: mechanical signals in plant development

2019 ◽  
Vol 70 (14) ◽  
pp. 3507-3519 ◽  
Author(s):  
Benoit Landrein ◽  
Gwyneth Ingram
Keyword(s):  
Gene Expression ◽  
Plant Development ◽  
Growth And Development ◽  
Biological Processes ◽  
Plant Morphogenesis ◽  
Mechanical Signals ◽  
Physical Forces ◽  
Multicellular Organisms ◽  
Biochemical Signals

Abstract As multicellular organisms, plants acquire characteristic shapes through a complex set of biological processes known as morphogenesis. Biochemical signalling underlies much of development, as it allows cells to acquire specific identities based on their position within tissues and organs. However, as growing physical structures, plants, and their constituent cells, also experience internal and external physical forces that can be perceived and can influence key processes such as growth, polarity, and gene expression. This process, which adds another layer of control to growth and development, has important implications for plant morphogenesis. This review provides an overview of recent research into the role of mechanical signals in plant development and aims to show how mechanical signalling can be used, in concert with biochemical signals, as a cue allowing cells and tissues to coordinate their behaviour and to add robustness to developmental processes.

scholarly journals From trickle to flood: the large-scale, cryptic invasion of California by tropical fruit flies

2013 ◽  
Vol 280 (1768) ◽  
pp. 20131466 ◽  
Author(s):  
Nikos T. Papadopoulos ◽  
Richard E. Plant ◽  
James R. Carey
Keyword(s):  
Large Scale ◽  
Invasion Biology ◽  
Fruit Fly ◽  
Fruit Flies ◽  
Federal Agencies ◽  
Spatial Mapping ◽  
Tropical Fruit ◽  
Cryptic Invasion ◽  
Tephritid Species ◽  
Melon Fruit

Since 1954, when the first tropical tephritid fruit fly was detected in California, a total of 17 species in four genera and 11 386 individuals (adults/larvae) have been detected in the state at more than 3348 locations in 330 cities. We conclude from spatial mapping analyses of historical capture patterns and modelling that, despite the 250+ emergency eradication projects that have been directed against these pests by state and federal agencies, a minimum of five and as many as nine or more tephritid species are established and widespread, including the Mediterranean, Mexican and oriental fruit flies, and possibly the peach, guava and melon fruit flies. We outline and discuss the evidence for our conclusions, with particular attention to the incremental, chronic and insidious nature of the invasion, which involves ultra-small, barely detectable populations. We finish by considering the implications of our results for invasion biology and for science-based invasion policy.

scholarly journals Fully Interpretable Deep Learning Model of Transcriptional Control

2019 ◽  
Author(s):  
Yi Liu ◽  
Kenneth Barr ◽  
John Reinitz
Keyword(s):  
Systems Biology ◽  
Transcriptional Control ◽  
Fruit Fly ◽  
Early Embryo ◽  
Data Sets ◽  
Scientific Analysis ◽  
Genomic Scale ◽  
Biological Problem ◽  
Multicellular Organisms ◽  
Deep Learning Model

AbstractThe universal expressibility assumption of Deep Neural Networks (DNNs) is the key motivation behind recent work in the system biology community to employ DNNs to solve important problems in functional genomics and molecular genetics. Because of the black box nature of DNNs, such assumptions, while useful in practice, are unsatisfactory for scientific analysis. In this paper, we give an example of a DNN in which every layer is interpretable. Moreover, this DNN is biologically validated and predictive. We derive our DNN from a systems biology model that was not previously recognized as having a DNN structure. This DNN is concerned with a key unsolved biological problem, which is to understand the DNA regulatory code which controls how genes in multicellular organisms are turned on and off. Although we apply our DNN to data from the early embryo of the fruit fly Drosophila, this system serves as a testbed for analysis of much larger data sets obtained by systems biology studies on a genomic scale.

scholarly journals A large-scale resource for tissue-specific CRISPR mutagenesis in Drosophila

2019 ◽  
Author(s):  
Fillip Port ◽  
Claudia Strein ◽  
Mona Stricker ◽  
Benedikt Rauscher ◽  
Florian Heigwer ◽  
...  
Keyword(s):  
Large Scale ◽  
Target Genes ◽  
High Efficiency ◽  
Direct Sequencing ◽  
Fine Tuning ◽  
Genetic Screens ◽  
Efficient Gene ◽  
Crispr Screen ◽  
High Gene ◽  
Multicellular Organisms

SUMMARYGenetic screens are powerful tools for the functional annotation of genomes. In the context of multicellular organisms, interrogation of gene function is greatly facilitated by methods that allow spatial and temporal control of gene abrogation. Here, we describe a large-scale transgenic short guide (sg) RNA library for efficient CRISPR-based disruption of specific target genes in a constitutive or conditional manner. The library consists currently of more than 2600 plasmids and 1600 fly lines with a focus on targeting kinases, phosphatases and transcription factors, each expressing two sgRNAs under control of the Gal4/UAS system. We show that conditional CRISPR mutagenesis is robust across many target genes and can be efficiently employed in various somatic tissues, as well as the germline. In order to prevent artefacts commonly associated with excessive amounts of Cas9 protein, we have developed a series of novel UAS-Cas9 transgenes, which allow fine tuning of Cas9 expression to achieve high gene editing activity without detectable toxicity. Functional assays, as well as direct sequencing of genomic sgRNA target sites, indicates that the vast majority of transgenic sgRNA lines mediate efficient gene disruption. Furthermore, we conducted the so far largest fully transgenic CRISPR screen in any metazoan organism, which further supported the high efficiency and accuracy of our library and revealed many so far uncharacterized genes essential for development.

scholarly journals Advances in Postharvest Disinfestation of Fruits and Vegetables Using Hot Water Treatment Technology-Updates from Africa

2021 ◽  
Author(s):  
Shepard Ndlela ◽  
Nelson L. Mwando ◽  
Samira A. Mohamed
Keyword(s):  
Water Treatment ◽  
Large Scale ◽  
Fruits And Vegetables ◽  
Fruit Fly ◽  
Codling Moth ◽  
Hot Water ◽  
Hot Water Treatment ◽  
Treatment Technology ◽  
False Codling Moth ◽  
Water Treatment Technology

Hot Water Treatment (HWT) provides adequate phytosanitary assurance that treated fruits and vegetables exported abroad are free from devastating quarantine pests. Two systems for HWT are currently available for commercial use namely the batch/jacuzzi and the continuous flow system depending on user requirements. Several protocols have been developed the world over and a few in Africa, but adoption has been lagging because of various factors chief among them lack of large scale validations of experiments to guide application at the commercial level. Mango, Bell pepper, avocado, and French beans play an important role in the livelihoods of people in Africa. However, their export is constrained by pests such as the invasive Oriental fruit fly, the false codling moth, and thrips. To circumvent this issue, disinfestation HWT protocols have been developed which seek to provide quarantine assurance to lucrative export markets. Hot Water Treatment technology has several advantages over other conventional phytosanitary treatments. It provides a triple function of cleaning, disinfesting, and disinfecting and is friendly to users, consumers of the treated commodities, and the environment. We discuss HWT in the context of its future and applicability in Africa. It is the future of postharvest treatments.

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