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Drosophila embryo

Toshiyuki Harumoto, Takema Fukatsu, Bruno Lemaitre
Male killing is a selfish reproductive manipulation caused by symbiotic bacteria, where male offspring of infected hosts are selectively killed. The underlying mechanisms and the process of their evolution are of great interest not only in terms of fundamental biology, but also their potential applications. The two bacterial Drosophila symbionts, Wolbachia and Spiroplasma , have independently evolved male-killing ability. This raises the question whether the underlying mechanisms share some similarities or are specific to each bacterial species...
March 28, 2018: Proceedings. Biological Sciences
Xiaoping Su, Kuiqing Cui, Shanshan Du, Hongli Li, Fenghua Lu, Deshun Shi, Qingyou Liu
Myostatin (MSTN), a protein encoded by growth differentiation factor 8 (GDF8), is primarily expressed in skeletal muscle and negatively regulates the development and regeneration of muscle. Accordingly, myostatin-deficient animals exhibit a double-muscling phenotype. The CRISPR/Cas9 system has proven to be an efficient genome-editing tool and has been applied to gene modification in cells from many model organisms such as Drosophila melanogaster, zebrafish, mouse, rat, sheep, and human. Here, we edited the GDF8 gene in fibroblasts and embryos of Debao pig and swamp buffalo using the CRISPR/Cas9 system...
March 19, 2018: In Vitro Cellular & Developmental Biology. Animal
Olga Y Rybina, Yakov M Rozovsky, Ekaterina R Veselkina, Elena G Pasyukova
Molecular mechanisms governing gene expression and defining complex phenotypes are central to understanding the basics of development and aging. Here, we demonstrate that naturally occurring polymorphisms of the Lim3 regulatory region that are associated with variation in gene expression and Drosophila lifespan control are located exclusively in the Polycomb response element (PRE). We find that the Polycomb group (PcG) protein Polycomb (PC) is bound to the PRE only in embryos where Lim3 is present in both repressed and active states...
March 16, 2018: Biochimica et Biophysica Acta
Natsuki Hemmi, Yasuko Akiyama-Oda, Koichi Fujimoto, Hiroki Oda
One of the conserved traits of arthropod embryonic development is striped expression of homologs of Drosophila segment polarity genes, including hedgehog (hh). Although a diversity of stripe-forming processes is recognized among arthropod embryos, such varied stripe-forming processes have not been well characterized from cellular and quantitative perspectives. The spider Parasteatoda tepidariorum embryo, which has a hh-dependent mechanism of axis formation, offers a cell-based field where the stripes of Pt-hh (a hh homolog) expression dynamically develop in accordance with axis formation and growth, with the patterning processes varying among the regions of the field...
March 15, 2018: Developmental Biology
Darren A Cusanovich, James P Reddington, David A Garfield, Riza M Daza, Delasa Aghamirzaie, Raquel Marco-Ferreres, Hannah A Pliner, Lena Christiansen, Xiaojie Qiu, Frank J Steemers, Cole Trapnell, Jay Shendure, Eileen E M Furlong
Understanding how gene regulatory networks control the progressive restriction of cell fates is a long-standing challenge. Recent advances in measuring gene expression in single cells are providing new insights into lineage commitment. However, the regulatory events underlying these changes remain unclear. Here we investigate the dynamics of chromatin regulatory landscapes during embryogenesis at single-cell resolution. Using single-cell combinatorial indexing assay for transposase accessible chromatin with sequencing (sci-ATAC-seq), we profiled chromatin accessibility in over 20,000 single nuclei from fixed Drosophila melanogaster embryos spanning three landmark embryonic stages: 2-4 h after egg laying (predominantly stage 5 blastoderm nuclei), when each embryo comprises around 6,000 multipotent cells; 6-8 h after egg laying (predominantly stage 10-11), to capture a midpoint in embryonic development when major lineages in the mesoderm and ectoderm are specified; and 10-12 h after egg laying (predominantly stage 13), when each of the embryo's more than 20,000 cells are undergoing terminal differentiation...
March 14, 2018: Nature
Lars Kullmann, Michael P Krahn
Apical-basal polarity is an important characteristic of epithelia and Drosophila neural stem cells. The conserved Par complex, which consists of the atypical protein kinase C and the scaffold proteins Baz and Par6, is a key player in the establishment of apical-basal cell polarity. Membrane recruitment of Baz has been reported to be accomplished by several mechanisms, which might function in redundancy, to ensure the correct localization of the complex. However, none of the described interactions was sufficient to displace the protein from the apical junctions...
March 10, 2018: Cellular and Molecular Life Sciences: CMLS
Terrence Hanscom, Varandt Y Khodaverdian, Mitch McVey
In this chapter, we describe a method for the recovery and analysis of alternative end-joining (alt-EJ) DNA double-strand break repair junctions following I-SceI cutting in Drosophila melanogaster embryos. Alt-EJ can be defined as a set of Ku70/80 and DNA ligase 4-independent end-joining processes that are typically mutagenic, producing deletions, insertions, and chromosomal rearrangements more frequently than higher-fidelity repair pathways such as classical nonhomologous end joining or homologous recombination...
2018: Methods in Enzymology
Yiwen Wang, Jürgen Berger, Bernard Moussian
Terminal differentiation of an organ is the last step in development that enables the organism to survive in the outside world after birth. Terminal differentiation of the insect tracheae that ends with filling the tubular network with gas is not fully understood at the tissue level. Here, we demonstrate that yet unidentified valves at the end of the tracheal system of the fruit fly Drosophila melanogaster embryo are important elements allowing terminal differentiation of this organ. Formation of these valves depends on the function of the zona pellucida protein Trynity (Tyn)...
March 5, 2018: Developmental Biology
Beatriz Hernández de Madrid, Jordi Casanova
The Drosophila GATA factor gene serpent (srp) is required for the early differentiation of the anterior and posterior midgut primordia. In particular, srp is sufficient and necessary for the primordial gut cells to undertake an epithelial-to-mesenchimal transition (EMT). Two other GATA factor genes, dGATAe and grain (grn), are also specifically expressed in the midgut. On the one hand, dGATAe expression is activated by srp. Embryos homozygous for a deficiency uncovering dGATAe were shown to lack the expression of some differentiated midgut genes...
2018: PloS One
Mustafa G Aydogan, Alan Wainman, Saroj Saurya, Thomas L Steinacker, Anna Caballe, Zsofia A Novak, Janina Baumbach, Nadine Muschalik, Jordan W Raff
Centrioles are highly structured organelles whose size is remarkably consistent within any given cell type. New centrioles are born when Polo-like kinase 4 (Plk4) recruits Ana2/STIL and Sas-6 to the side of an existing "mother" centriole. These two proteins then assemble into a cartwheel, which grows outwards to form the structural core of a new daughter. Here, we show that in early Drosophila melanogaster embryos, daughter centrioles grow at a linear rate during early S-phase and abruptly stop growing when they reach their correct size in mid- to late S-phase...
March 2, 2018: Journal of Cell Biology
Ekaterina Myasnikova, Alexander Spirov
Commonly among the model parameters characterizing complex biological systems are those that do not significantly influence the quality of the fit to experimental data, so-called "sloppy" parameters. The sloppiness can be mathematically expressed through saturating response functions (Hill's, sigmoid) thereby embodying biological mechanisms responsible for the system robustness to external perturbations. However, if a sloppy model is used for the prediction of the system behavior at the altered input (e...
January 25, 2018: Journal of Bioinformatics and Computational Biology
Alexander L Auld, Sacha A Roberts, Ciaran B Murphy, Jaclyn M Camuglia, Eric S Folker
During muscle development myonuclei undergo a complex set of movements that result in evenly spaced nuclei throughout the muscle cell. In Drosophila two separate pools of Kinesin and Dynein work in synchrony to drive this process. However, how these two pools are specified is not known. Here, we investigate the role of Aplip1 ( Drosophila JIP1), a known regulator of both Kinesin and Dynein, in myonuclear positioning. Aplip1 localizes to myotendinous junction and has genetically separable roles in myonuclear positioning and muscle stability...
February 27, 2018: Journal of Cell Science
Masatoshi Hara, Sebastian Lourido, Boryana Petrova, Hua Jane Lou, Jessica R Von Stetina, Helena Kashevsky, Benjamin E Turk, Terry L Orr-Weaver
The Drosophila Pan Gu (PNG) kinase complex regulates hundreds of maternal mRNAs that become translationally repressed or activated as the oocyte transitions to an embryo. In a previous paper (Hara et al., 2017), we demonstrated PNG activity is under tight developmental control and restricted to this transition. Here, examination of PNG specificity showed it to be a Thr-kinase yet lacking a clear phosphorylation site consensus sequence. An unbiased biochemical screen for PNG substrates identified the conserved translational repressor Trailer Hitch (TRAL)...
February 26, 2018: ELife
Michael P Meers, Karen Adelman, Robert J Duronio, Brian D Strahl, Daniel J McKay, A Gregory Matera
BACKGROUND: High-resolution transcription start site (TSS) mapping in D. melanogaster embryos and cell lines has revealed a rich and detailed landscape of both cis- and trans-regulatory elements and factors. However, TSS profiling has not been investigated in an orthogonal in vivo setting. Here, we present a comprehensive dataset that links TSS dynamics with nucleosome occupancy and gene expression in the wandering third instar larva, a developmental stage characterized by large-scale shifts in transcriptional programs in preparation for metamorphosis...
February 21, 2018: BMC Genomics
Pavel V Mazin, Elena Shagimardanova, Olga Kozlova, Alexander Cherkasov, Roman Sutormin, Vita V Stepanova, Alexey Stupnikov, Maria Logacheva, Aleksey Penin, Yoichiro Sogame, Richard Cornette, Shoko Tokumoto, Yugo Miyata, Takahiro Kikawada, Mikhail S Gelfand, Oleg Gusev
Polypedilum vanderplanki is a striking and unique example of an insect that can survive almost complete desiccation. Its genome and a set of dehydration-rehydration transcriptomes, together with the genome of Polypedilum nubifer (a congeneric desiccation-sensitive midge), were recently released. Here, using published and newly generated datasets reflecting detailed transcriptome changes during anhydrobiosis, as well as a developmental series, we show that the TCTAGAA DNA motif, which closely resembles the binding motif of the Drosophila melanogaster heat shock transcription activator (Hsf), is significantly enriched in the promoter regions of desiccation-induced genes in P...
February 20, 2018: Proceedings of the National Academy of Sciences of the United States of America
Berta Verd, Erik Clark, Karl R Wotton, Hilde Janssens, Eva Jiménez-Guri, Anton Crombach, Johannes Jaeger
Insects determine their body segments in two different ways. Short-germband insects, such as the flour beetle Tribolium castaneum, use a molecular clock to establish segments sequentially. In contrast, long-germband insects, such as the vinegar fly Drosophila melanogaster, determine all segments simultaneously through a hierarchical cascade of gene regulation. Gap genes constitute the first layer of the Drosophila segmentation gene hierarchy, downstream of maternal gradients such as that of Caudal (Cad). We use data-driven mathematical modelling and phase space analysis to show that shifting gap domains in the posterior half of the Drosophila embryo are an emergent property of a robust damped oscillator mechanism, suggesting that the regulatory dynamics underlying long- and short-germband segmentation are much more similar than previously thought...
February 16, 2018: PLoS Biology
Massimo Vergassola, Victoria E Deneke, Stefano Di Talia
Early embryogenesis of most metazoans is characterized by rapid and synchronous cleavage divisions. Chemical waves of Cdk1 activity were previously shown to spread across Drosophila embryos, and the underlying molecular processes were dissected. Here, we present the theory of the physical mechanisms that control Cdk1 waves in Drosophila The in vivo dynamics of Cdk1 are captured by a transiently bistable reaction-diffusion model, where time-dependent reaction terms account for the growing level of cyclins and Cdk1 activation across the cell cycle...
February 15, 2018: Proceedings of the National Academy of Sciences of the United States of America
Emir E Avilés-Pagán, Terry L Orr-Weaver
The transition from oocyte to embryo marks the onset of development. This process requires complex regulation to link developmental signals with profound changes in mRNA translation, cell cycle control, and metabolism. This control is beginning to be understood for most organisms, and research in the fruit fly Drosophila melanogaster has generated new insights. Recent findings have increased our understanding of the roles played by hormone and Ca 2+ signaling events as well as metabolic remodeling crucial for this transition...
February 12, 2018: Seminars in Cell & Developmental Biology
Deborah A Hursh, Brian G Stultz
Zinc finger in the cerebellum (Zic) proteins are a family of transcription factors with multiple roles during development, particularly in neural tissues. The founding member of the Zic family is the Drosophila odd-paired (opa) gene. The Opa protein has a DNA binding domain containing five Cys2His2-type zinc fingers and has been shown to act as a sequence-specific DNA binding protein. Opa has significant homology to mammalian Zic1, Zic2, and Zic3 within the zinc finger domain and in two other conserved regions outside that domain...
2018: Advances in Experimental Medicine and Biology
Mehmet Ilyas Cosacak, Hatice Yiğit, Caghan Kizil, Bünyamin Akgül
Small ribonucleic acids (RNAs) are known to regulate gene expression during early development. However, the dynamics of interaction between small RNAs and polysomes during this process is largely unknown. To investigate this phenomenon, 0-1 h and 7-8 h Drosophila melanogaster embryos were fractionated on sucrose density gradients into four fractions based on A 254 reading (1) translationally inactive messenger ribonucleoprotein (mRNP), (2) 60S, (3) monosome, and (4) polysome. Comparative analysis of deep-sequencing reads from fractionated and un-fractionated 0-1 h and 7-8 h embryos revealed development-specific co-sedimentation pattern of small RNAs with the cellular translation machinery...
February 10, 2018: Genes
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