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Jia J, Dong C, Han M, Ma S, Chen W, Dou J, Feng C, Liu X. Multi-omics perspective on studying reproductive biology in Daphnia sinensis. Genomics 2022; 114:110309. [DOI: 10.1016/j.ygeno.2022.110309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/28/2021] [Accepted: 02/01/2022] [Indexed: 11/30/2022]
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2
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Perkin LC, Perez JL, Suh CPC. The Identification of Boll Weevil, Anthonomus grandis grandis (Coleoptera: Curculionidae), Genes Involved in Pheromone Production and Pheromone Biosynthesis. INSECTS 2021; 12:insects12100893. [PMID: 34680662 PMCID: PMC8540235 DOI: 10.3390/insects12100893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 12/01/2022]
Abstract
Simple Summary The boll weevil is a destructive pest of commercial cotton throughout the Americas. An eradication program in the United States has removed the boll weevil from most of its range. However, weevil populations in South Texas remain a threat to eradicated areas. Pheromone traps are used to monitor boll weevil activity, and when a weevil is captured, eradication programs rely on malathion for control. However, the effectiveness of pheromone traps in detecting incipient boll weevil populations is reduced during certain times of the year. Additionally, human safety and environmental concerns, as well as the potential development of malathion-resistant populations, have prompted program managers to seek alternative control methods. We sequenced and compared pheromone-producing and non-pheromone-producing weevils to identify genes involved in pheromone production, which, in turn, could be an environmentally friendly way to target gene-level pest control that is specific to the boll weevil. Our results revealed genes involved in pheromone production, as well as insect development and immunity, which may be targeted for boll weevil suppression. Abstract Eradication programs for the boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), rely almost exclusively on pheromone traps to indicate the need for insecticide applications. However, the effectiveness of traps in detecting weevil populations is reduced during certain times of the year, particularly when cotton is actively fruiting. Consequently, this could result in fields becoming heavily infested with weevils. It is widely speculated that the lack of weevil captures in traps during this period is largely due to the overwhelming amount of pheromone released by weevils in the field, which outcompete the pheromone released from traps. Thus, this work sought to identify genes involved in pheromone production so that new control methods that target these genes can be explored. We conducted an RNA-seq experiment that revealed 2479 differentially expressed genes between pheromone-producing and non-pheromone-producing boll weevils. Of those genes, 1234 were up-regulated, and 1515 were down-regulated, and most had gene annotations associated with pheromone production, development, or immunity. This work advances our understanding of boll weevil pheromone production and brings us one step closer to developing gene-level control strategies for this cotton pest.
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Deitz KC, Takken W, Slotman MA. The Genetic Architecture of Post-Zygotic Reproductive Isolation Between Anopheles coluzzii and An. quadriannulatus. Front Genet 2020; 11:925. [PMID: 33005168 PMCID: PMC7480394 DOI: 10.3389/fgene.2020.00925] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/24/2020] [Indexed: 11/15/2022] Open
Abstract
The Anopheles gambiae complex is comprised of eight morphologically indistinguishable species and has emerged as a model system for the study of speciation genetics due to the rapid radiation of its member species over the past two million years. Male hybrids between most An. gambiae complex species pairs are sterile, and some genotype combinations in hybrid males cause inviability. We investigated the genetic basis of hybrid male inviability and sterility between An. coluzzii and An. quadriannulatus by measuring segregation distortion and performing a QTL analysis of sterility in a backcross population. Hybrid males were inviable if they inherited the An. coluzzii X chromosome and were homozygous at one or more loci in 18.9 Mb region of chromosome 3. The An. coluzzii X chromosome has a disproportionately large effect on hybrid sterility when introgressed into an An. quadriannulatus genetic background. Additionally, an epistatic interaction between the An. coluzzii X and a 1.12 Mb, pericentric region of the An. quadriannulatus 3L chromosome arm has a statistically significant contribution to the hybrid sterility phenotype. This same epistatic interaction occurs when the An. coluzzii X is introgressed into the genetic background of An. arabiensis, the sister species of An. quadriannulatus, suggesting that this may represent one of the first Dobzhansky-Muller incompatibilities to evolve early in the radiation of the Anopheles gambiae species complex. We describe the additive effects of each sterility QTL, epistatic interactions between them, and genes within QTL with protein functions related to mating behavior, reproduction, spermatogenesis, and microtubule morphogenesis, whose divergence may contribute to post-zygotic reproductive isolation between An. coluzzii and An. quadriannulatus.
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Affiliation(s)
- Kevin C. Deitz
- Department of Entomology, Texas A&M University, College Station, TX, United States
| | - Willem Takken
- Laboratory of Entomology, Wageningen University and Research, Wageningen, Netherlands
| | - Michel A. Slotman
- Department of Entomology, Texas A&M University, College Station, TX, United States
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4
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Chen Y, Ou J, Liu Y, Wu Q, Wen L, Zheng S, Li S, Feng Q, Liu L. Transcriptomic analysis of the testicular fusion in Spodoptera litura. BMC Genomics 2020; 21:171. [PMID: 32075574 PMCID: PMC7029529 DOI: 10.1186/s12864-020-6494-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/14/2020] [Indexed: 01/28/2023] Open
Abstract
Background Lepidoptera is one group of the largest plant-feeding insects and Spodoptera litura (Lepidoptera: Noctuidae) is one of the most serious agricultural pests in Asia countries. An interesting and unique phenomenon for gonad development of Lepidoptera is the testicular fusion. Two separated testes fused into a single one during the larva-to-pupa metamorphosis, which is believed to contribute to sperm production and the prevalence in field. To study the molecular mechanism of the testicular fusion, RNA sequencing (RNA-seq) experiments of the testes from 4-day-old sixth instar larvae (L6D4) (before fusion), 6-day-old sixth instar larvae (L6D6, prepupae) (on fusing) and 4-day-old pupae (P4D) (after fusion) of S. litura were performed. Results RNA-seq data of the testes showed that totally 12,339 transcripts were expressed at L6D4, L6D6 and P4D stages. A large number of differentially expressed genes (DEGs) were up-regulated from L6D4 to L6D6, and then more genes were down-regulated from L6D6 to P4D. The DEGs mainly belongs to the genes related to the 20E signal transduction pathway, transcription factors, chitin metabolism related enzymes, the families of cytoskeleton proteins, extracellular matrix (ECM) components, ECM-related protein, its receptor integrins and ECM-remodeling enzymes. The expression levels of these genes that were up-regulated significantly during the testicular fusion were verified by qRT-PCR. The matrix metalloproteinases (MMPs) were found to be the main enzymes related to the ECM degradation and contribute to the testicular fusion. The testis was not able to fuse if MMPs inhibitor GM6001 was injected into the 5th abdomen region at L6D6 early stage. Conclusions The transcriptome and DEGs analysis of the testes at L6D4, L6D6 and P4D stages provided genes expression information related to the testicular fusion in S. litura. These results indicated that cytoskeleton proteins, ECM-integrin interaction genes and ECM-related proteins were involved in cell migration, adhesion and fusion during the testicular fusion. The ECM degradation enzymes MMPs probably play a critical role in the fusion of testis.
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Affiliation(s)
- Yaqing Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jun Ou
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yucheng Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Qiong Wu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Liang Wen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Sichun Zheng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China. .,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Lin Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China. .,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
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Wu S, Tong X, Li C, Lu K, Tan D, Hu H, Liu H, Dai F. Genome-wide identification and expression profiling of the C2H2-type zinc finger protein genes in the silkworm Bombyx mori. PeerJ 2019; 7:e7222. [PMID: 31316872 PMCID: PMC6613534 DOI: 10.7717/peerj.7222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/30/2019] [Indexed: 12/29/2022] Open
Abstract
Cys2-His2 zinc finger (C2H2-ZF) proteins comprise the largest class of putative eukaryotic transcription factors. The zinc finger motif array is highly divergent, indicating that most proteins will have distinctive binding sites and perform different functions. However, the binding sites and functions of the majority of C2H2-ZF proteins remain unknown. In this study, we identified 327 C2H2-ZF protein genes in the silkworm, 290 in the monarch butterfly, 243 in the fruit fly, 107 in elegans, 673 in mouse, and 1,082 in human. The C2H2-ZF protein genes of the silkworm were classified into three main grouping clades according to a phylogenetic classification, and 312 of these genes could be mapped onto 27 chromosomes. Most silkworm C2H2-ZF protein genes exhibited specific expression in larval tissues. Furthermore, several C2H2-ZF protein genes had sex-specific expression during metamorphosis. In addition, we found that some C2H2-ZF protein genes are involved in metamorphosis and female reproduction by using expression clustering and gene annotation analysis. Among them, five genes were selected, BGIBMGA002091 (CTCF), BGIBMGA006492 (fru), BGIBMGA006230 (wor), BGIBMGA004640 (lola), and BIGBMGA004569, for quantitative real-time PCR analysis from larvae to adult ovaries. The results showed that the five genes had different expression patterns in ovaries, among which BGIBMGA002091 (CTCF) gene expression level was the highest, and its expression level increased rapidly in late pupae and adult stages. These findings provide a basis for further investigation of the functions of C2H2-ZF protein genes in the silkworm, and the results offer clues for further research into the development of metamorphosis and female reproduction in the silkworm.
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Affiliation(s)
- SongYuan Wu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China.,College of Plant Protection, Southwest University, Chong Qing, China
| | - Xiaoling Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - ChunLin Li
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - KunPeng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - Duan Tan
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - Hai Hu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - Huai Liu
- College of Plant Protection, Southwest University, Chong Qing, China
| | - FangYin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
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Trivedi S, Starz-Gaiano M. Drosophila Jak/STAT Signaling: Regulation and Relevance in Human Cancer and Metastasis. Int J Mol Sci 2018; 19:ijms19124056. [PMID: 30558204 PMCID: PMC6320922 DOI: 10.3390/ijms19124056] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/08/2018] [Accepted: 12/11/2018] [Indexed: 12/26/2022] Open
Abstract
Over the past three-decades, Janus kinase (Jak) and signal transducer and activator of transcription (STAT) signaling has emerged as a paradigm to understand the involvement of signal transduction in development and disease pathology. At the molecular level, cytokines and interleukins steer Jak/STAT signaling to transcriptional regulation of target genes, which are involved in cell differentiation, migration, and proliferation. Jak/STAT signaling is involved in various types of blood cell disorders and cancers in humans, and its activation is associated with carcinomas that are more invasive or likely to become metastatic. Despite immense information regarding Jak/STAT regulation, the signaling network has numerous missing links, which is slowing the progress towards developing drug therapies. In mammals, many components act in this cascade, with substantial cross-talk with other signaling pathways. In Drosophila, there are fewer pathway components, which has enabled significant discoveries regarding well-conserved regulatory mechanisms. Work across species illustrates the relevance of these regulators in humans. In this review, we showcase fundamental Jak/STAT regulation mechanisms in blood cells, stem cells, and cell motility. We examine the functional relevance of key conserved regulators from Drosophila to human cancer stem cells and metastasis. Finally, we spotlight less characterized regulators of Drosophila Jak/STAT signaling, which stand as promising candidates to be investigated in cancer biology. These comparisons illustrate the value of using Drosophila as a model for uncovering the roles of Jak/STAT signaling and the molecular means by which the pathway is controlled.
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Affiliation(s)
- Sunny Trivedi
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
| | - Michelle Starz-Gaiano
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
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7
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Parker DJ, Wiberg RAW, Trivedi U, Tyukmaeva VI, Gharbi K, Butlin RK, Hoikkala A, Kankare M, Ritchie MG. Inter and Intraspecific Genomic Divergence in Drosophila montana Shows Evidence for Cold Adaptation. Genome Biol Evol 2018; 10:2086-2101. [PMID: 30010752 PMCID: PMC6107330 DOI: 10.1093/gbe/evy147] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 12/25/2022] Open
Abstract
The genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to ecological specialism from other sources of selection and more random changes is a challenge. Here, we describe the genome of Drosophila montana, which is the most extremely cold-adapted Drosophila species known. We use branch tests to identify genes showing accelerated divergence in contrasts between cold- and warm-adapted species and identify about 250 genes that show differences, possibly driven by a lower synonymous substitution rate in cold-adapted species. We also look for evidence of accelerated divergence between D. montana and D. virilis, a previously sequenced relative, but do not find strong evidence for divergent selection on coding sequence variation. Divergent genes are involved in a variety of functions, including cuticular and olfactory processes. Finally, we also resequenced three populations of D. montana from across its ecological and geographic range. Outlier loci were more likely to be found on the X chromosome and there was a greater than expected overlap between population outliers and those genes implicated in cold adaptation between Drosophila species, implying some continuity of selective process at these different evolutionary scales.
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Affiliation(s)
- Darren J Parker
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
- Center for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
- Department of Ecology and Evolution, University of Lausanne, Biophore, Switzerland
| | - R Axel W Wiberg
- Center for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
| | - Urmi Trivedi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Venera I Tyukmaeva
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Karim Gharbi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, United Kingdom
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Roger K Butlin
- Department of Animal and Plant Sciences, The University of Sheffield, UK
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | - Anneli Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Michael G Ritchie
- Center for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
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8
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Dove AE, Cook BL, Irgebay Z, Vecsey CG. Mechanisms of sleep plasticity due to sexual experience in Drosophila melanogaster. Physiol Behav 2017; 180:146-158. [PMID: 28851647 DOI: 10.1016/j.physbeh.2017.08.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/23/2017] [Accepted: 08/25/2017] [Indexed: 10/19/2022]
Abstract
Sleep can be altered by an organism's previous experience. For instance, female Drosophila melanogaster experience a post-mating reduction in daytime sleep that is purportedly mediated by sex peptide (SP), one of many seminal fluid proteins (SFPs) transferred from male to female during mating. In the present study, we first characterized this mating effect on sleep more fully, as it had previously only been tested in young flies under 12h light/12h dark conditions. We found that mating reduced sleep equivalently in 3-day-old or 14-day-old females, and could even occur in females who had been mated previously, suggesting that there is not a developmental critical period for the suppression of sleep by mating. In conditions of constant darkness, circadian rhythms were not affected by prior mating. In either constant darkness or constant light, the sleep reduction due to mating was no longer confined to the subjective day but could be observed throughout the 24-hour period. This suggests that the endogenous clock may dictate the timing of when the mating effect on sleep is expressed. We recently reported that genetic elimination of SP only partially blocked the post-mating female siesta sleep reduction, suggesting that the effect was unlikely to be governed solely by SP. We found here that the daytime sleep reduction was also reduced but not eliminated in females mated to mutant males lacking the vast majority of SFPs. This suggested that SFPs other than SP play a minimal role in the mating effect on sleep, and that additional non-SFP signals from the male might be involved. Males lacking sperm were able to induce a normal initial mating effect on female sleep, although the effect declined more rapidly in these females. This result indicated that neither the presence of sperm within the female reproductive tract nor female impregnation are required for the initial mating effect on sleep to occur, although sperm may serve to prolong the effect. Finally, we tested for contributions from other aspects of the mating experience. NorpA and eya2 mutants with disrupted vision showed normal mating effects on sleep. By separating males from females with a mesh, we found that visual and olfactory stimuli from male exposure, in the absence of physical contact, could not replicate the mating effect. Further, in ken/barbie male flies lacking external genitalia, courtship and physical contact without ejaculation were also unable to replicate the mating effect. These findings confirmed that the influence of mating on sleep does in fact require male/female contact including copulation, but may not be mediated exclusively by SP transfer.
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Affiliation(s)
- Abigail E Dove
- Biology Department, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, United States
| | - Brianne L Cook
- Neuroscience Program, Skidmore College, 815 N. Broadway, Saratoga Springs, NY 12866, United States
| | - Zhazira Irgebay
- Biology Department, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, United States
| | - Christopher G Vecsey
- Biology Department, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, United States; Neuroscience Program, Skidmore College, 815 N. Broadway, Saratoga Springs, NY 12866, United States.
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Field A, Xiang J, Anderson WR, Graham P, Pick L. Activation of Ftz-F1-Responsive Genes through Ftz/Ftz-F1 Dependent Enhancers. PLoS One 2016; 11:e0163128. [PMID: 27723822 PMCID: PMC5056698 DOI: 10.1371/journal.pone.0163128] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/03/2016] [Indexed: 12/11/2022] Open
Abstract
The orphan nuclear receptor Ftz-F1 is expressed in all somatic nuclei in Drosophila embryos, but mutations result in a pair-rule phenotype. This was explained by the interaction of Ftz-F1 with the homeodomain protein Ftz that is expressed in stripes in the primordia of segments missing in either ftz-f1 or ftz mutants. Ftz-F1 and Ftz were shown to physically interact and coordinately activate the expression of ftz itself and engrailed by synergistic binding to composite Ftz-F1/Ftz binding sites. However, attempts to identify additional target genes on the basis of Ftz-F1/ Ftz binding alone has met with only limited success. To discern rules for Ftz-F1 target site selection in vivo and to identify additional target genes, a microarray analysis was performed comparing wildtype and ftz-f1 mutant embryos. Ftz-F1-responsive genes most highly regulated included engrailed and nine additional genes expressed in patterns dependent on both ftz and ftz-f1. Candidate enhancers for these genes were identified by combining BDTNP Ftz ChIP-chip data with a computational search for Ftz-F1 binding sites. Of eight enhancer reporter genes tested in transgenic embryos, six generated expression patterns similar to the corresponding endogenous gene and expression was lost in ftz mutants. These studies identified a new set of Ftz-F1 targets, all of which are co-regulated by Ftz. Comparative analysis of enhancers containing Ftz/Ftz-F1 binding sites that were or were not bona fide targets in vivo suggested that GAF negatively regulates enhancers that contain Ftz/Ftz-F1 binding sites but are not actually utilized. These targets include other regulatory factors as well as genes involved directly in morphogenesis, providing insight into how pair-rule genes establish the body pattern.
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Affiliation(s)
- Amanda Field
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
| | - Jie Xiang
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
| | - W. Ray Anderson
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
| | - Patricia Graham
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
| | - Leslie Pick
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
- * E-mail:
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10
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Sap KA, Bezstarosti K, Dekkers DHW, van den Hout M, van Ijcken W, Rijkers E, Demmers JAA. Global quantitative proteomics reveals novel factors in the ecdysone signaling pathway in Drosophila melanogaster. Proteomics 2015; 15:725-38. [PMID: 25403936 DOI: 10.1002/pmic.201400308] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/19/2014] [Accepted: 11/12/2014] [Indexed: 01/06/2023]
Abstract
The ecdysone signaling pathway plays a major role in various developmental transitions in insects. Recent advances in the understanding of ecdysone action have relied to a large extent on the application of molecular genetic tools in Drosophila. Here, we used a comprehensive quantitative SILAC MS-based approach to study the global, dynamic proteome of a Drosophila cell line to investigate how hormonal signals are transduced into specific cellular responses. Global proteome data after ecdysone treatment after various time points were then integrated with transcriptome data. We observed a substantial overlap in terms of affected targets between the dynamic proteome and transcriptome, although there were some clear differences in timing effects. Also, downregulation of several specific mRNAs did not always correlate with downregulation of their corresponding protein counterparts, and in some cases there was no correlation between transcriptome and proteome dynamics whatsoever. In addition, we performed a comprehensive interactome analysis of EcR, the major target of ecdysone. Proteins copurified with EcR include factors involved in transcription, chromatin remodeling, ecdysone signaling, ecdysone biosynthesis, and other signaling pathways. Novel ecdysone-responsive proteins identified in this study might link previously unknown proteins to the ecdysone signaling pathway and might be novel targets for developmental studies. To our knowledge, this is the first time that ecdysone signaling is studied by global quantitative proteomics. All MS data have been deposited in the ProteomeXchange with identifier PXD001455 (http://proteomecentral.proteomexchange.org/dataset/PXD001455).
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Affiliation(s)
- Karen A Sap
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands; Netherlands Proteomics Center, Rotterdam, The Netherlands
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Abstract
The BTB-ZF (broad-complex, tramtrack and bric-à-brac--zinc finger) proteins are encoded by at least 49 genes in mouse and man and commonly serve as sequence-specific silencers of gene expression. This review will focus on the known physiological functions of mammalian BTB-ZF proteins, which include essential roles in the development of the immune system. We discuss their function in terminally differentiated lymphocytes and the progenitors that give rise to them, their action in hematopoietic malignancy and roles beyond the immune system.
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Affiliation(s)
- Owen M Siggs
- Department of Genetics, The Scripps Research Institute, La Jolla, CA, USA.
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12
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Zheng W, Peng T, He W, Zhang H. High-throughput sequencing to reveal genes involved in reproduction and development in Bactrocera dorsalis (Diptera: Tephritidae). PLoS One 2012; 7:e36463. [PMID: 22570719 PMCID: PMC3343016 DOI: 10.1371/journal.pone.0036463] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 04/06/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Tephritid fruit flies in the genus Bactrocera are of major economic significance in agriculture causing considerable loss to the fruit and vegetable industry. Currently, there is no ideal control program. Molecular means is an effective method for pest control at present, but genomic or transcriptomic data for members of this genus remains limited. To facilitate molecular research into reproduction and development mechanisms, and finally effective control on these pests, an extensive transcriptome for the oriental fruit fly Bactrocera dorsalis was produced using the Roche 454-FLX platform. RESULTS We obtained over 350 million bases of cDNA derived from the whole body of B. dorsalis at different developmental stages. In a single run, 747,206 sequencing reads with a mean read length of 382 bp were obtained. These reads were assembled into 28,782 contigs and 169,966 singletons. The mean contig size was 750 bp and many nearly full-length transcripts were assembled. Additionally, we identified a great number of genes that are involved in reproduction and development as well as genes that represent nearly all major conserved metazoan signal transduction pathways, such as insulin signal transduction. Furthermore, transcriptome changes during development were analyzed. A total of 2,977 differentially expressed genes (DEGs) were detected between larvae and pupae libraries, while there were 1,621 DEGs between adults and larvae, and 2,002 between adults and pupae. These DEGs were functionally annotated with KEGG pathway annotation and 9 genes were validated by qRT-PCR. CONCLUSION Our data represent the extensive sequence resources available for B. dorsalis and provide for the first time access to the genetic architecture of reproduction and development as well as major signal transduction pathways in the Tephritid fruit fly pests, allowing us to elucidate the molecular mechanisms underlying courtship, ovipositing, development and detailed analyses of the signal transduction pathways.
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Affiliation(s)
- Weiwei Zheng
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control and Institute of Urban and Horticultural Pests, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Tao Peng
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control and Institute of Urban and Horticultural Pests, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Wei He
- Shanghai Hanyu Bio-Lab, Shanghai, People's Republic of China
| | - Hongyu Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control and Institute of Urban and Horticultural Pests, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
- * E-mail:
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Aravind L, Anantharaman V, Venancio TM. Apprehending multicellularity: regulatory networks, genomics, and evolution. ACTA ACUST UNITED AC 2009; 87:143-64. [PMID: 19530132 DOI: 10.1002/bdrc.20153] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The genomic revolution has provided the first glimpses of the architecture of regulatory networks. Combined with evolutionary information, the "network view" of life processes leads to remarkable insights into how biological systems have been shaped by various forces. This understanding is critical because biological systems, including regulatory networks, are not products of engineering but of historical contingencies. In this light, we attempt a synthetic overview of the natural history of regulatory networks operating in the development and differentiation of multicellular organisms. We first introduce regulatory networks and their organizational principles as can be deduced using ideas from the graph theory. We then discuss findings from comparative genomics to illustrate the effects of lineage-specific expansions, gene-loss, and nonprotein-coding DNA on the architecture of networks. We consider the interaction between expansions of transcription factors, and cis regulatory and more general chromatin state stabilizing elements in the emergence of morphological complexity. Finally, we consider a case study of the Notch subnetwork, which is present throughout Metazoa, to examine how such a regulatory system has been pieced together in evolution from new innovations and pre-existing components that were originally functionally distinct.
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Affiliation(s)
- L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
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14
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Jordan KW, Carbone MA, Yamamoto A, Morgan TJ, Mackay TFC. Quantitative genomics of locomotor behavior in Drosophila melanogaster. Genome Biol 2008; 8:R172. [PMID: 17708775 PMCID: PMC2375002 DOI: 10.1186/gb-2007-8-8-r172] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 03/26/2007] [Accepted: 08/21/2007] [Indexed: 11/21/2022] Open
Abstract
The locomotor behavior of Drosophila melanogaster was quantified in a large population of inbred lines derived from a single natural population, showing that many pleiotropic genes show correlated transcriptional responses to multiple behaviors. Background Locomotion is an integral component of most animal behaviors, and many human health problems are associated with locomotor deficits. Locomotor behavior is a complex trait, with population variation attributable to many interacting loci with small effects that are sensitive to environmental conditions. However, the genetic basis of this complex behavior is largely uncharacterized. Results We quantified locomotor behavior of Drosophila melanogaster in a large population of inbred lines derived from a single natural population, and derived replicated selection lines with different levels of locomotion. Estimates of broad-sense and narrow-sense heritabilities were 0.52 and 0.16, respectively, indicating substantial non-additive genetic variance for locomotor behavior. We used whole genome expression analysis to identify 1,790 probe sets with different expression levels between the selection lines when pooled across replicates, at a false discovery rate of 0.001. The transcriptional responses to selection for locomotor, aggressive and mating behavior from the same base population were highly overlapping, but the magnitude of the expression differences between selection lines for increased and decreased levels of behavior was uncorrelated. We assessed the locomotor behavior of ten mutations in candidate genes with altered transcript abundance between selection lines, and identified seven novel genes affecting this trait. Conclusion Expression profiling of genetically divergent lines is an effective strategy for identifying genes affecting complex behaviors, and reveals that a large number of pleiotropic genes exhibit correlated transcriptional responses to multiple behaviors.
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Affiliation(s)
- Katherine W Jordan
- Department of Genetics and WM Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Mary Anna Carbone
- Department of Genetics and WM Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Akihiko Yamamoto
- Department of Genetics and WM Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Theodore J Morgan
- Division of Biology, Kansas State University, Ackert Hall, Manhattan, KS 66506, USA
| | - Trudy FC Mackay
- Department of Genetics and WM Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695-7614, USA
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15
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McClure KD, Schubiger G. A screen for genes that function in leg disc regeneration in Drosophila melanogaster. Mech Dev 2007; 125:67-80. [PMID: 18036784 DOI: 10.1016/j.mod.2007.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2007] [Revised: 09/26/2007] [Accepted: 10/08/2007] [Indexed: 11/16/2022]
Abstract
Many diverse animal species regenerate parts of an organ or tissue after injury. However, the molecules responsible for the regenerative growth remain largely unknown. The screen reported here aimed to identify genes that function in regeneration and the transdetermination events closely associated with imaginal disc regeneration using Drosophila melanogaster. We screened a collection of 97 recessive lethal P-lacZ enhancer trap lines for two primary criteria: first, the ability to dominantly modify wg-induced leg-to-wing transdetermination and second, for the activation or repression of the lacZ reporter gene in the blastema during disc regeneration. Of the 97 P-lacZ lines, we identified six genes (Krüppel-homolog-1, rpd3, jing, combgap, Aly and S6 kinase) that met both criteria. Five of these genes suppress, while one enhances, leg-to-wing transdetermination and therefore affects disc regeneration. Two of the genes, jing and rpd3, function in concert with chromatin remodeling proteins of the Polycomb Group (PcG) and trithorax Group (trxG) genes during Drosophila development, thus linking chromatin remodeling with the process of regeneration.
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Affiliation(s)
- Kimberly D McClure
- Department of Biology, University of Washington, Seattle, WA 98195, USA.
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16
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Allen MJ, Drummond JA, Sweetman DJ, Moffat KG. Analysis of two P-element enhancer-trap insertion lines that show expression in the giant fibre neuron of Drosophila melanogaster. GENES BRAIN AND BEHAVIOR 2006; 6:347-58. [PMID: 16879616 DOI: 10.1111/j.1601-183x.2006.00263.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The giant fibre system (GFS) of Drosophila is a simple neural circuit that mediates escape responses in adult flies. Here we report the initial characterization of two genes that are preferentially expressed in the GFS. Two P-element insertion lines, carrying the GAL4 transcriptional activator, were identified that exhibited pronounced expression in elements of the GFS and relatively low levels elsewhere within the adult central nervous system. Genomic DNA flanking the P-element insertion site was recovered from each of these lines, sequenced, and nearby transcripts identified and confirmed to exhibit GFS expression by in situ hybridization. This analysis revealed that these P-elements were in previously characterized genes. Line P[GAL4]-A307 has an insert in the gene short stop for which we have identified a novel transcript, while line P[GAL4]-141 has an insert in the transcription factor ken and barbie. Here we show that ken and barbie mutants have defects in escape behaviour, behavioural responses to visual stimuli and synaptic functions in the GFS. We have therefore revealed a neural role for a transcription factor that previously had no implicated neural function.
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Affiliation(s)
- M J Allen
- Department of Biological Sciences, University of Warwick, Coventry, and Department of Biosciences, University of Kent, Canterbury, United Kingdom
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Arbouzova NI, Bach EA, Zeidler MP. Ken & barbie selectively regulates the expression of a subset of Jak/STAT pathway target genes. Curr Biol 2006; 16:80-8. [PMID: 16401426 DOI: 10.1016/j.cub.2005.11.033] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Revised: 11/06/2005] [Accepted: 11/07/2005] [Indexed: 11/24/2022]
Abstract
A limited number of evolutionarily conserved signal transduction pathways are repeatedly reused during development to regulate a wide range of processes. Here we describe a new negative regulator of JAK/STAT signaling and identify a potential mechanism by which the pleiotropy of responses resulting from pathway activation is generated in vivo. As part of a genetic interaction screen, we have identified Ken & Barbie (Ken) , which is an ortholog of the mammalian proto-oncogene BCL6 , as a negative regulator of the JAK/STAT pathway. Ken genetically interacts with the pathway in vivo and recognizes a DNA consensus sequence overlapping that of STAT92E in vitro. Tissue culture-based assays demonstrate the existence of Ken-sensitive and Ken-insensitive STAT92E binding sites, while ectopically expressed Ken is sufficient to downregulate a subset of JAK/STAT pathway target genes in vivo. Finally, we show that endogenous Ken specifically represses JAK/STAT-dependent expression of ventral veins lacking (vvl) in the posterior spiracles. Ken therefore represents a novel regulator of JAK/STAT signaling whose dynamic spatial and temporal expression is capable of selectively modulating the transcriptional repertoire elicited by activated STAT92E in vivo.
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Affiliation(s)
- Natalia I Arbouzova
- Department of Molecular Developmental Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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Ren N, Zhu C, Lee H, Adler PN. Gene expression during Drosophila wing morphogenesis and differentiation. Genetics 2005; 171:625-38. [PMID: 15998724 PMCID: PMC1456776 DOI: 10.1534/genetics.105.043687] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The simple cellular composition and array of distally pointing hairs has made the Drosophila wing a favored system for studying planar polarity and the coordination of cellular and tissue level morphogenesis. We carried out a gene expression screen to identify candidate genes that functioned in wing and wing hair morphogenesis. Pupal wing RNA was isolated from tissue prior to, during, and after hair growth and used to probe Affymetrix Drosophila gene chips. We identified 435 genes whose expression changed at least fivefold during this period and 1335 whose expression changed at least twofold. As a functional validation we chose 10 genes where genetic reagents existed but where there was little or no evidence for a wing phenotype. New phenotypes were found for 9 of these genes, providing functional validation for the collection of identified genes. Among the phenotypes seen were a delay in hair initiation, defects in hair maturation, defects in cuticle formation and pigmentation, and abnormal wing hair polarity. The collection of identified genes should be a valuable data set for future studies on hair and bristle morphogenesis, cuticle synthesis, and planar polarity.
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Affiliation(s)
- Nan Ren
- Biology Department, Cancer Center and Morphogenesis and Regenerative Medicine Institute, University of Virginia, Charlottesville, 22903, USA
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